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SIGSCANLIG documentation |
Generates LHF files (ligand hits file) of hits from scanning sequences against a library of ligand-binding signatures.
> Q9WVI4^.^516^664^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^PSIBLAST^84.40^0.000e+00^2.000e-16 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASG LHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLF GNNVTLASKFESGSHPRRINISPTTYQLL > Q9ERL9^.^480^631^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^PSIBLAST^72.10^0.000e+00^1.000e-12 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLH RESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGN NVTLANKFESCSVPRKINVSPTTYRLLKDCPG > Q9DGG6^.^380^560^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^PSIBLAST^142.00^0.000e+00^8.000e-34 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAG CPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVW SNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL I > Q99396^.^262^473^.^55074^Alpha and beta proteins (a+b)^.^.^Ferredoxin-like^Adenylyl and guanylyl cyclase catalytic domain^Adenylyl and guanylyl cyclase catalytic domain^PSIBLAST^192.00^0.000e+00^0.000e+00 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMI ACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVY RQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN |
LIGID PATCHES SITES SCORE 101 0 1 0.48 |
This directory contains output files, for example Q99396^.^262^473^.lhf Q9DGG6^.^380^560^.lhf Q9ERL9^.^480^631^.lhf and Q9WVI4^.^516^664^.lhf.
> Q99396^.^262^473^.^55074^Alpha^.^99^138^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^7.00^0.000e+00^0.000e+00 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN > Q99396^.^262^473^.^55074^Alpha^.^97^138^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^5.33^0.000e+00^0.000e+00 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN > Q99396^.^262^473^.^55074^Alpha^.^130^210^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^4.00^0.000e+00^0.000e+00 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN > Q99396^.^262^473^.^55074^Alpha^.^12^17^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^3.00^0.000e+00^0.000e+00 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN > Q99396^.^262^473^.^55074^Alpha^.^12^56^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^2.00^0.000e+00^0.000e+00 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN > Q99396^.^262^473^.^55074^Alpha^.^11^55^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^1.83^0.000e+00^0.000e+00 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN > Q99396^.^262^473^.^55074^Alpha^.^16^126^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^1.00^0.000e+00^0.000e+00 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN > Q99396^.^262^473^.^55074^Alpha^.^32^126^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.94^0.000e+00^0.000e+00 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN > Q99396^.^262^473^.^55074^Alpha^.^22^126^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.74^0.000e+00^0.000e+00 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN > Q99396^.^262^473^.^55074^Alpha^.^16^126^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.59^0.000e+00^0.000e+00 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN > Q99396^.^262^473^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-1000000.00^0.000e+00^0.000e+00 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIENYDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFDEFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHTGLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHSLSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN |
> Q9DGG6^.^380^560^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.50^0.000e+00^0.000e+00 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI > Q9DGG6^.^380^560^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.50^0.000e+00^0.000e+00 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI > Q9DGG6^.^380^560^.^55074^Alpha^.^8^13^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.17^0.000e+00^0.000e+00 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI > Q9DGG6^.^380^560^.^55074^Alpha^.^99^179^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^4.00^0.000e+00^0.000e+00 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI > Q9DGG6^.^380^560^.^55074^Alpha^.^100^139^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^3.50^0.000e+00^0.000e+00 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI > Q9DGG6^.^380^560^.^55074^Alpha^.^20^61^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^2.33^0.000e+00^0.000e+00 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI > Q9DGG6^.^380^560^.^55074^Alpha^.^74^178^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^1.00^0.000e+00^0.000e+00 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI > Q9DGG6^.^380^560^.^55074^Alpha^.^84^178^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.82^0.000e+00^0.000e+00 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI > Q9DGG6^.^380^560^.^55074^Alpha^.^68^178^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.65^0.000e+00^0.000e+00 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI > Q9DGG6^.^380^560^.^55074^Alpha^.^68^178^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.47^0.000e+00^0.000e+00 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI > Q9DGG6^.^380^560^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-1000000.00^0.000e+00^0.000e+00 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKCEKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEKKEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGVAGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYLI |
> Q9ERL9^.^480^631^.^55074^Alpha^.^6^50^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.50^0.000e+00^0.000e+00 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG > Q9ERL9^.^480^631^.^55074^Alpha^.^6^50^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.17^0.000e+00^0.000e+00 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG > Q9ERL9^.^480^631^.^55074^Alpha^.^98^137^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^4.50^0.000e+00^0.000e+00 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG > Q9ERL9^.^480^631^.^55074^Alpha^.^6^11^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.17^0.000e+00^0.000e+00 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG > Q9ERL9^.^480^631^.^55074^Alpha^.^63^104^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^4.00^0.000e+00^0.000e+00 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG > Q9ERL9^.^480^631^.^55074^Alpha^.^22^102^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^2.50^0.000e+00^0.000e+00 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG > Q9ERL9^.^480^631^.^55074^Alpha^.^4^114^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.60^0.000e+00^0.000e+00 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG > Q9ERL9^.^480^631^.^55074^Alpha^.^25^119^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.29^0.000e+00^0.000e+00 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG > Q9ERL9^.^480^631^.^55074^Alpha^.^12^122^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.24^0.000e+00^0.000e+00 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG > Q9ERL9^.^480^631^.^55074^Alpha^.^15^119^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.21^0.000e+00^0.000e+00 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG > Q9ERL9^.^480^631^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-1000000.00^0.000e+00^0.000e+00 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYKVETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGEPIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPRKINVSPTTYRLLKDCPG |
> Q9WVI4^.^516^664^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.50^0.000e+00^0.000e+00 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL > Q9WVI4^.^516^664^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.17^0.000e+00^0.000e+00 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL > Q9WVI4^.^516^664^.^55074^Alpha^.^100^139^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^4.50^0.000e+00^0.000e+00 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL > Q9WVI4^.^516^664^.^55074^Alpha^.^8^13^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.17^0.000e+00^0.000e+00 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL > Q9WVI4^.^516^664^.^55074^Alpha^.^25^105^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^3.50^0.000e+00^0.000e+00 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL > Q9WVI4^.^516^664^.^55074^Alpha^.^43^84^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^3.33^0.000e+00^0.000e+00 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL > Q9WVI4^.^516^664^.^55074^Alpha^.^27^121^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.53^0.000e+00^0.000e+00 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL > Q9WVI4^.^516^664^.^55074^Alpha^.^17^121^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.42^0.000e+00^0.000e+00 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL > Q9WVI4^.^516^664^.^55074^Alpha^.^6^116^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.33^0.000e+00^0.000e+00 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL > Q9WVI4^.^516^664^.^55074^Alpha^.^14^124^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.18^0.000e+00^0.000e+00 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL > Q9WVI4^.^516^664^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-1000000.00^0.000e+00^0.000e+00 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDIYKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPDGRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSHPRRINISPTTYQLL |
This directory contains output files, for example Q99396^.^262^473^.aln Q9DGG6^.^380^560^.aln Q9ERL9^.^480^631^.aln and Q9WVI4^.^516^664^.aln.
# DE Alignment of query sequence against library of signatures # XX # > Q99396^.^262^473^.^55074^Alpha^.^99^138^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^7.00^0.000e+00^0.000e+00 # XX Q99396^.^262^473^.^55074^Alpha1 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIEN 45 101_2_0 - --------------------------------------------- Q99396^.^262^473^.^55074^Alpha46 YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFD 90 101_2_0 - --------------------------------------------- Q99396^.^262^473^.^55074^Alpha91 EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHT 135 101_2_0 - ---------*----------------------------------- Q99396^.^262^473^.^55074^Alpha136 GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS 180 101_2_0 - ---*----------------------------------------- Q99396^.^262^473^.^55074^Alpha181 LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN 225 101_2_0 - -------------------------------- # XX # > Q99396^.^262^473^.^55074^Alpha^.^97^138^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^5.33^0.000e+00^0.000e+00 # XX Q99396^.^262^473^.^55074^Alpha1 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIEN 45 MN_1_0 - --------------------------------------------- Q99396^.^262^473^.^55074^Alpha46 YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFD 90 MN_1_0 - --------------------------------------------- Q99396^.^262^473^.^55074^Alpha91 EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHT 135 MN_1_0 - -------*-*----------------------------------- Q99396^.^262^473^.^55074^Alpha136 GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS 180 MN_1_0 - ---*----------------------------------------- Q99396^.^262^473^.^55074^Alpha181 LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN 225 MN_1_0 - -------------------------------- # XX # > Q99396^.^262^473^.^55074^Alpha^.^130^210^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^4.00^0.000e+00^0.000e+00 # XX Q99396^.^262^473^.^55074^Alpha1 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIEN 45 PO4_1_0 - --------------------------------------------- Q99396^.^262^473^.^55074^Alpha46 YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFD 90 PO4_1_0 - --------------------------------------------- Q99396^.^262^473^.^55074^Alpha91 EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHT 135 PO4_1_0 - ----------------------------------------*---- Q99396^.^262^473^.^55074^Alpha136 GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS 180 PO4_1_0 - --------------------------------------------- Q99396^.^262^473^.^55074^Alpha181 LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN 225 PO4_1_0 - ------------------------------*- # XX # > Q99396^.^262^473^.^55074^Alpha^.^12^17^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^3.00^0.000e+00^0.000e+00 # XX Q99396^.^262^473^.^55074^Alpha1 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIEN 45 POP_1_0 - ------------******--------------------------- Q99396^.^262^473^.^55074^Alpha46 YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFD 90 POP_1_0 - --------------------------------------------- Q99396^.^262^473^.^55074^Alpha91 EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHT 135 POP_1_0 - --------------------------------------------- Q99396^.^262^473^.^55074^Alpha136 GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS 180 [Part of this file has been deleted for brevity] # > Q99396^.^262^473^.^55074^Alpha^.^32^126^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.94^0.000e+00^0.000e+00 # XX Q99396^.^262^473^.^55074^Alpha1 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIEN 45 HEM_1_0 - --------------------------------**-**-------- Q99396^.^262^473^.^55074^Alpha46 YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFD 90 HEM_1_0 - ---*--**--*-----------------*--**---*-*---**- Q99396^.^262^473^.^55074^Alpha91 EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHT 135 HEM_1_0 - -*----------------------------------*-------- Q99396^.^262^473^.^55074^Alpha136 GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS 180 HEM_1_0 - --------------------------------------------- Q99396^.^262^473^.^55074^Alpha181 LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN 225 HEM_1_0 - -------------------------------- # XX # > Q99396^.^262^473^.^55074^Alpha^.^22^126^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.74^0.000e+00^0.000e+00 # XX Q99396^.^262^473^.^55074^Alpha1 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIEN 45 HEM_3_0 - ----------------------*------*--**-**-------- Q99396^.^262^473^.^55074^Alpha46 YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFD 90 HEM_3_0 - ---*--**--*-----------------*--**---*-*---**- Q99396^.^262^473^.^55074^Alpha91 EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHT 135 HEM_3_0 - -*----------------------------------*-------- Q99396^.^262^473^.^55074^Alpha136 GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS 180 HEM_3_0 - --------------------------------------------- Q99396^.^262^473^.^55074^Alpha181 LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN 225 HEM_3_0 - -------------------------------- # XX # > Q99396^.^262^473^.^55074^Alpha^.^16^126^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.59^0.000e+00^0.000e+00 # XX Q99396^.^262^473^.^55074^Alpha1 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIEN 45 HEM_2_0 - ----------------*---------**----------------- Q99396^.^262^473^.^55074^Alpha46 YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFD 90 HEM_2_0 - ---*--**--**----------------*--**---*-*---**- Q99396^.^262^473^.^55074^Alpha91 EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHT 135 HEM_2_0 - -*----------------------------------*-------- Q99396^.^262^473^.^55074^Alpha136 GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS 180 HEM_2_0 - --------------------------------------------- Q99396^.^262^473^.^55074^Alpha181 LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN 225 HEM_2_0 - -------------------------------- # XX # > Q99396^.^262^473^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-1000000.00^0.000e+00^0.000e+00 # XX Q99396^.^262^473^.^55074^Alpha1 KELADPVTLIFTDIESSTAQWATQPELMPDAVATHHSMVRSLIEN 45 FOK_1_0 - *-------------------------------------------- Q99396^.^262^473^.^55074^Alpha46 YDCYEVKTVGDSFMIACKSPFAAVQLAQELQLRFLRLDWGTTVFD 90 FOK_1_0 - --------------------------------------------- Q99396^.^262^473^.^55074^Alpha91 EFYREFEERHAEEGDGKYKPPTARLDPEVYRQLWNGLRVRVGIHT 135 FOK_1_0 - --------------------------------------------- Q99396^.^262^473^.^55074^Alpha136 GLCDIRYDEVTKGYDYYGQTANTAARTESVGNGGQVLMTCETYHS 180 FOK_1_0 - --------------------------------------------- Q99396^.^262^473^.^55074^Alpha181 LSTAERSQFDVTPLGGVPLRGVSEPVEVYQLN 225 FOK_1_0 - -------------------------------- |
# DE Alignment of query sequence against library of signatures # XX # > Q9DGG6^.^380^560^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.50^0.000e+00^0.000e+00 # XX Q9DGG6^.^380^560^.^55074^Alpha1 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKC 45 101_1_0 - --------*---**------------------------------- Q9DGG6^.^380^560^.^55074^Alpha46 EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEK 90 101_1_0 - -----***------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha91 KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGV 135 101_1_0 - --------------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha136 AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL 180 101_1_0 - --------------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha181 I 225 101_1_0 - - # XX # > Q9DGG6^.^380^560^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.50^0.000e+00^0.000e+00 # XX Q9DGG6^.^380^560^.^55074^Alpha1 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKC 45 MG_1_0 - --------**--*-------------------------------- Q9DGG6^.^380^560^.^55074^Alpha46 EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEK 90 MG_1_0 - -------*------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha91 KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGV 135 MG_1_0 - --------------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha136 AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL 180 MG_1_0 - --------------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha181 I 225 MG_1_0 - - # XX # > Q9DGG6^.^380^560^.^55074^Alpha^.^8^13^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.17^0.000e+00^0.000e+00 # XX Q9DGG6^.^380^560^.^55074^Alpha1 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKC 45 POP_1_0 - --------******------------------------------- Q9DGG6^.^380^560^.^55074^Alpha46 EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEK 90 POP_1_0 - --------------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha91 KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGV 135 POP_1_0 - --------------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha136 AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL 180 POP_1_0 - --------------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha181 I 225 POP_1_0 - - # XX # > Q9DGG6^.^380^560^.^55074^Alpha^.^99^179^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^4.00^0.000e+00^0.000e+00 # XX Q9DGG6^.^380^560^.^55074^Alpha1 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKC 45 PO4_1_0 - --------------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha46 EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEK 90 PO4_1_0 - --------------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha91 KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGV 135 PO4_1_0 - ---------*----------------------------------- Q9DGG6^.^380^560^.^55074^Alpha136 AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL 180 [Part of this file has been deleted for brevity] # > Q9DGG6^.^380^560^.^55074^Alpha^.^84^178^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.82^0.000e+00^0.000e+00 # XX Q9DGG6^.^380^560^.^55074^Alpha1 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKC 45 HEM_1_0 - --------------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha46 EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEK 90 HEM_1_0 - ---------------------------------------**-**- Q9DGG6^.^380^560^.^55074^Alpha91 KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGV 135 HEM_1_0 - ----------*--**--*-----------------*--**---*- Q9DGG6^.^380^560^.^55074^Alpha136 AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL 180 HEM_1_0 - *---**--*----------------------------------*- Q9DGG6^.^380^560^.^55074^Alpha181 I 225 HEM_1_0 - - # XX # > Q9DGG6^.^380^560^.^55074^Alpha^.^68^178^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.65^0.000e+00^0.000e+00 # XX Q9DGG6^.^380^560^.^55074^Alpha1 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKC 45 HEM_2_0 - --------------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha46 EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEK 90 HEM_2_0 - -----------------------*---------**---------- Q9DGG6^.^380^560^.^55074^Alpha91 KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGV 135 HEM_2_0 - ----------*--**--**----------------*--**---*- Q9DGG6^.^380^560^.^55074^Alpha136 AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL 180 HEM_2_0 - *---**--*----------------------------------*- Q9DGG6^.^380^560^.^55074^Alpha181 I 225 HEM_2_0 - - # XX # > Q9DGG6^.^380^560^.^55074^Alpha^.^68^178^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.47^0.000e+00^0.000e+00 # XX Q9DGG6^.^380^560^.^55074^Alpha1 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKC 45 HEM_4_0 - --------------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha46 EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEK 90 HEM_4_0 - -----------------------*---------**---------- Q9DGG6^.^380^560^.^55074^Alpha91 KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGV 135 HEM_4_0 - ----------*--**--*--------------------**---*- Q9DGG6^.^380^560^.^55074^Alpha136 AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL 180 HEM_4_0 - *---**--*----------------------------------*- Q9DGG6^.^380^560^.^55074^Alpha181 I 225 HEM_4_0 - - # XX # > Q9DGG6^.^380^560^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-1000000.00^0.000e+00^0.000e+00 # XX Q9DGG6^.^380^560^.^55074^Alpha1 EQVSILFADIVGFTKMSANKSAHALVGLLNDLFGRFDRLCEDTKC 45 FOK_1_0 - *-------------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha46 EKISTLGDCYYCVAGCPEPRADHAYCCIEMGLGMIKAIEQFCQEK 90 FOK_1_0 - --------------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha91 KEMVNMRVGVHTGTVLCGILGMRRFKFDVWSNDVNLANLMEQLGV 135 FOK_1_0 - --------------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha136 AGKVHISEATAKYLDDRYEMEDGKVTERVGQSAVADQLKGLKTYL 180 FOK_1_0 - --------------------------------------------- Q9DGG6^.^380^560^.^55074^Alpha181 I 225 FOK_1_0 - - |
# DE Alignment of query sequence against library of signatures # XX # > Q9ERL9^.^480^631^.^55074^Alpha^.^6^50^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.50^0.000e+00^0.000e+00 # XX Q9ERL9^.^480^631^.^55074^Alpha1 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45 MG_1_0 - ------**--*---------------------------------- Q9ERL9^.^480^631^.^55074^Alpha46 VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90 MG_1_0 - -----*--------------------------------------- Q9ERL9^.^480^631^.^55074^Alpha91 PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135 MG_1_0 - --------------------------------------------- Q9ERL9^.^480^631^.^55074^Alpha136 KINVSPTTYRLLKDCPG 180 MG_1_0 - ----------------- # XX # > Q9ERL9^.^480^631^.^55074^Alpha^.^6^50^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.17^0.000e+00^0.000e+00 # XX Q9ERL9^.^480^631^.^55074^Alpha1 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45 101_1_0 - ------*---**--------------------------------- Q9ERL9^.^480^631^.^55074^Alpha46 VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90 101_1_0 - ---***--------------------------------------- Q9ERL9^.^480^631^.^55074^Alpha91 PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135 101_1_0 - --------------------------------------------- Q9ERL9^.^480^631^.^55074^Alpha136 KINVSPTTYRLLKDCPG 180 101_1_0 - ----------------- # XX # > Q9ERL9^.^480^631^.^55074^Alpha^.^98^137^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^4.50^0.000e+00^0.000e+00 # XX Q9ERL9^.^480^631^.^55074^Alpha1 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45 101_2_0 - --------------------------------------------- Q9ERL9^.^480^631^.^55074^Alpha46 VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90 101_2_0 - --------------------------------------------- Q9ERL9^.^480^631^.^55074^Alpha91 PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135 101_2_0 - --------*------------------------------------ Q9ERL9^.^480^631^.^55074^Alpha136 KINVSPTTYRLLKDCPG 180 101_2_0 - --*-------------- # XX # > Q9ERL9^.^480^631^.^55074^Alpha^.^6^11^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.17^0.000e+00^0.000e+00 # XX Q9ERL9^.^480^631^.^55074^Alpha1 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45 POP_1_0 - ------******--------------------------------- Q9ERL9^.^480^631^.^55074^Alpha46 VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90 POP_1_0 - --------------------------------------------- Q9ERL9^.^480^631^.^55074^Alpha91 PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135 POP_1_0 - --------------------------------------------- Q9ERL9^.^480^631^.^55074^Alpha136 KINVSPTTYRLLKDCPG 180 POP_1_0 - ----------------- # XX # > Q9ERL9^.^480^631^.^55074^Alpha^.^63^104^LIGAND^1ii7;^d1ii7a_^MN^1^1^0^0^1DF^4.00^0.000e+00^0.000e+00 # XX Q9ERL9^.^480^631^.^55074^Alpha1 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45 MN_1_0 - --------------------------------------------- [Part of this file has been deleted for brevity] HEM_4_0 - ----*---------**--------------------*--**--*- Q9ERL9^.^480^631^.^55074^Alpha46 VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90 HEM_4_0 - -------------------**---*-*---**--*---------- Q9ERL9^.^480^631^.^55074^Alpha91 PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135 HEM_4_0 - ------------------------*-------------------- Q9ERL9^.^480^631^.^55074^Alpha136 KINVSPTTYRLLKDCPG 180 HEM_4_0 - ----------------- # XX # > Q9ERL9^.^480^631^.^55074^Alpha^.^25^119^LIGAND^2hhb;^.^HEM^1^4^0^0^1DF^0.29^0.000e+00^0.000e+00 # XX Q9ERL9^.^480^631^.^55074^Alpha1 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45 HEM_1_0 - -------------------------**-**-----------*--* Q9ERL9^.^480^631^.^55074^Alpha46 VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90 HEM_1_0 - *--*-----------------*--**---*-*---**--*----- Q9ERL9^.^480^631^.^55074^Alpha91 PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135 HEM_1_0 - -----------------------------*--------------- Q9ERL9^.^480^631^.^55074^Alpha136 KINVSPTTYRLLKDCPG 180 HEM_1_0 - ----------------- # XX # > Q9ERL9^.^480^631^.^55074^Alpha^.^12^122^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.24^0.000e+00^0.000e+00 # XX Q9ERL9^.^480^631^.^55074^Alpha1 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45 HEM_2_0 - ------------*---------**--------------------* Q9ERL9^.^480^631^.^55074^Alpha46 VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90 HEM_2_0 - --**--**----------------*--**---*-*---**--*-- Q9ERL9^.^480^631^.^55074^Alpha91 PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135 HEM_2_0 - --------------------------------*------------ Q9ERL9^.^480^631^.^55074^Alpha136 KINVSPTTYRLLKDCPG 180 HEM_2_0 - ----------------- # XX # > Q9ERL9^.^480^631^.^55074^Alpha^.^15^119^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.21^0.000e+00^0.000e+00 # XX Q9ERL9^.^480^631^.^55074^Alpha1 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45 HEM_3_0 - ---------------*------*--**-**-----------*--* Q9ERL9^.^480^631^.^55074^Alpha46 VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90 HEM_3_0 - *--*-----------------*--**---*-*---**--*----- Q9ERL9^.^480^631^.^55074^Alpha91 PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135 HEM_3_0 - -----------------------------*--------------- Q9ERL9^.^480^631^.^55074^Alpha136 KINVSPTTYRLLKDCPG 180 HEM_3_0 - ----------------- # XX # > Q9ERL9^.^480^631^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-1000000.00^0.000e+00^0.000e+00 # XX Q9ERL9^.^480^631^.^55074^Alpha1 VTMLFSDIVGFTAICSQCSPLQVITMLNALYTRFDQQCGELDVYK 45 FOK_1_0 - *-------------------------------------------- Q9ERL9^.^480^631^.^55074^Alpha46 VETIGDAYCVAGGLHRESDTHAVQIALMALKMMELSNEVMSPHGE 90 FOK_1_0 - --------------------------------------------- Q9ERL9^.^480^631^.^55074^Alpha91 PIKMRIGLHSGSVFAGVVGVKMPRYCLFGNNVTLANKFESCSVPR 135 FOK_1_0 - --------------------------------------------- Q9ERL9^.^480^631^.^55074^Alpha136 KINVSPTTYRLLKDCPG 180 FOK_1_0 - ----------------- |
# DE Alignment of query sequence against library of signatures # XX # > Q9WVI4^.^516^664^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^MG^1^1^0^0^1DF^5.50^0.000e+00^0.000e+00 # XX Q9WVI4^.^516^664^.^55074^Alpha1 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45 MG_1_0 - --------**--*-------------------------------- Q9WVI4^.^516^664^.^55074^Alpha46 YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90 MG_1_0 - -------*------------------------------------- Q9WVI4^.^516^664^.^55074^Alpha91 GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135 MG_1_0 - --------------------------------------------- Q9WVI4^.^516^664^.^55074^Alpha136 PRRINISPTTYQLL 180 MG_1_0 - -------------- # XX # > Q9WVI4^.^516^664^.^55074^Alpha^.^8^52^LIGAND^1cs4;^d1cs4a_^101^1^2^0^0^1DF^5.17^0.000e+00^0.000e+00 # XX Q9WVI4^.^516^664^.^55074^Alpha1 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45 101_1_0 - --------*---**------------------------------- Q9WVI4^.^516^664^.^55074^Alpha46 YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90 101_1_0 - -----***------------------------------------- Q9WVI4^.^516^664^.^55074^Alpha91 GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135 101_1_0 - --------------------------------------------- Q9WVI4^.^516^664^.^55074^Alpha136 PRRINISPTTYQLL 180 101_1_0 - -------------- # XX # > Q9WVI4^.^516^664^.^55074^Alpha^.^100^139^LIGAND^1ii7;^d1ii7a_^101^2^2^0^0^1DF^4.50^0.000e+00^0.000e+00 # XX Q9WVI4^.^516^664^.^55074^Alpha1 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45 101_2_0 - --------------------------------------------- Q9WVI4^.^516^664^.^55074^Alpha46 YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90 101_2_0 - --------------------------------------------- Q9WVI4^.^516^664^.^55074^Alpha91 GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135 101_2_0 - ----------*---------------------------------- Q9WVI4^.^516^664^.^55074^Alpha136 PRRINISPTTYQLL 180 101_2_0 - ----*--------- # XX # > Q9WVI4^.^516^664^.^55074^Alpha^.^8^13^LIGAND^1cs4;^d1cs4a_^POP^1^1^0^0^1DF^4.17^0.000e+00^0.000e+00 # XX Q9WVI4^.^516^664^.^55074^Alpha1 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45 POP_1_0 - --------******------------------------------- Q9WVI4^.^516^664^.^55074^Alpha46 YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90 POP_1_0 - --------------------------------------------- Q9WVI4^.^516^664^.^55074^Alpha91 GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135 POP_1_0 - --------------------------------------------- Q9WVI4^.^516^664^.^55074^Alpha136 PRRINISPTTYQLL 180 POP_1_0 - -------------- # XX # > Q9WVI4^.^516^664^.^55074^Alpha^.^25^105^LIGAND^2hhb;^.^PO4^1^1^0^0^1DF^3.50^0.000e+00^0.000e+00 # XX Q9WVI4^.^516^664^.^55074^Alpha1 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45 PO4_1_0 - -------------------------*------------------- [Part of this file has been deleted for brevity] HEM_1_0 - ---------------------------**-**-----------*- Q9WVI4^.^516^664^.^55074^Alpha46 YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90 HEM_1_0 - -**--*-----------------*--**---*-*---**--*--- Q9WVI4^.^516^664^.^55074^Alpha91 GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135 HEM_1_0 - -------------------------------*------------- Q9WVI4^.^516^664^.^55074^Alpha136 PRRINISPTTYQLL 180 HEM_1_0 - -------------- # XX # > Q9WVI4^.^516^664^.^55074^Alpha^.^17^121^LIGAND^2hhb;^.^HEM^3^4^0^0^1DF^0.42^0.000e+00^0.000e+00 # XX Q9WVI4^.^516^664^.^55074^Alpha1 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45 HEM_3_0 - -----------------*------*--**-**-----------*- Q9WVI4^.^516^664^.^55074^Alpha46 YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90 HEM_3_0 - -**--*-----------------*--**---*-*---**--*--- Q9WVI4^.^516^664^.^55074^Alpha91 GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135 HEM_3_0 - -------------------------------*------------- Q9WVI4^.^516^664^.^55074^Alpha136 PRRINISPTTYQLL 180 HEM_3_0 - -------------- # XX # > Q9WVI4^.^516^664^.^55074^Alpha^.^6^116^LIGAND^2hhb;^.^HEM^4^4^0^0^1DF^0.33^0.000e+00^0.000e+00 # XX Q9WVI4^.^516^664^.^55074^Alpha1 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45 HEM_4_0 - ------*---------**--------------------*--**-- Q9WVI4^.^516^664^.^55074^Alpha46 YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90 HEM_4_0 - *--------------------**---*-*---**--*-------- Q9WVI4^.^516^664^.^55074^Alpha91 GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135 HEM_4_0 - --------------------------*------------------ Q9WVI4^.^516^664^.^55074^Alpha136 PRRINISPTTYQLL 180 HEM_4_0 - -------------- # XX # > Q9WVI4^.^516^664^.^55074^Alpha^.^14^124^LIGAND^2hhb;^.^HEM^2^4^0^0^1DF^0.18^0.000e+00^0.000e+00 # XX Q9WVI4^.^516^664^.^55074^Alpha1 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45 HEM_2_0 - --------------*---------**------------------- Q9WVI4^.^516^664^.^55074^Alpha46 YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90 HEM_2_0 - -*--**--**----------------*--**---*-*---**--* Q9WVI4^.^516^664^.^55074^Alpha91 GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135 HEM_2_0 - ----------------------------------*---------- Q9WVI4^.^516^664^.^55074^Alpha136 PRRINISPTTYQLL 180 HEM_2_0 - -------------- # XX # > Q9WVI4^.^516^664^.^55074^Alpha^.^0^0^LIGAND^1cs4;^d1cs4a_^FOK^1^1^0^0^1DF^-1000000.00^0.000e+00^0.000e+00 # XX Q9WVI4^.^516^664^.^55074^Alpha1 DDVTMLFSDIVGFTAICAQCTPMQVISMLNELYTRFDHQCGFLDI 45 FOK_1_0 - *-------------------------------------------- Q9WVI4^.^516^664^.^55074^Alpha46 YKVETIGDAYCVASGLHRKSLCHAKPIALMALKMMELSEEVLTPD 90 FOK_1_0 - --------------------------------------------- Q9WVI4^.^516^664^.^55074^Alpha91 GRPIQMRIGIHSGSVLAGVVGVRMPRYCLFGNNVTLASKFESGSH 135 FOK_1_0 - --------------------------------------------- Q9WVI4^.^516^664^.^55074^Alpha136 PRRINISPTTYQLL 180 FOK_1_0 - -------------- |
This directory contains output files, for example Q99396^.^262^473^.results Q9DGG6^.^380^560^.results Q9ERL9^.^480^631^.results and Q9WVI4^.^516^664^.results.
LIGID PATCHES SITES SCORE MN 1 1 5.33 101 2 2 4.42 PO4 1 1 4.00 POP 1 1 3.00 MG 1 1 2.00 HEM 4 4 0.82 FOK 1 1 -1000000.00 |
LIGID PATCHES SITES SCORE MG 1 1 5.50 101 2 2 4.50 POP 1 1 4.17 PO4 1 1 4.00 MN 1 1 2.33 HEM 4 4 0.73 FOK 1 1 -1000000.00 |
LIGID PATCHES SITES SCORE MG 1 1 5.50 101 2 2 4.83 POP 1 1 4.17 MN 1 1 4.00 PO4 1 1 2.50 HEM 4 4 0.33 FOK 1 1 -1000000.00 |
LIGID PATCHES SITES SCORE MG 1 1 5.50 101 2 2 4.83 POP 1 1 4.17 PO4 1 1 3.50 MN 1 1 3.33 HEM 4 4 0.37 FOK 1 1 -1000000.00 |
Searches ligand-signature library & writes hits (LHF file)
Version: EMBOSS:6.2.0
Standard (Mandatory) qualifiers:
[-siginfilesdir] dirlist [./] This option specifies the directory of
signature files (input). A 'signature file'
contains a sparse sequence signature
suitable for use with the SIGSCAN and
SIGSCANLIG programs. The files are generated
by using SIGGEN and SIGGENLIG.
[-dbseqall] seqall This option specifies the name of the
database of query sequences.
-sub matrixf [EBLOSUM62] This option specifies the
scoring matrix to use, e.g. residue
substitution matrix (1D signatures) or
matrix of 3D:1D (environment:residue) scores
(3D).
-mode menu [1] This option specifies the mode of
scoring ligands. In 'Patch Score Mode' (mode
1) the score for a ligand is the mean of
its patch scores. In 'Site Score Mode' the
score for a ligand is the mean of its site
scores. A site score is the mean of patch
score for all patches for a given site.
(Values: 1 (Patch score mode); 2 (Site score
mode))
-gapo float [10.0 for any sequence] This option
specifies the gap insertion penalty. The gap
insertion penalty is the score taken away
when a gap is created. The best value
depends on the choice of comparison matrix.
The default value assumes you are using the
EBLOSUM62 matrix for protein sequences, and
the EDNAMAT matrix for nucleotide sequences.
(Floating point number from 1.0 to 100.0)
-gape float [0.5 for any sequence] This option specifies
the gap extension penalty. The gap
extension penalty is added to the standard
gap penalty for each base or residue in the
gap. This is how long gaps are penalized.
Usually you will expect a few long gaps
rather than many short gaps, so the gap
extension penalty should be lower than the
gap penalty. (Floating point number from 0.0
to 10.0)
-nterm menu [1] This option specifies the N-terminal
matching option. This determines how the
first signature position is aligned to a
sequence from the database. (Values: 1
(Align anywhere and allow only complete
signature-sequence fit); 2 (Align anywhere
and allow partial signature-sequence fit); 3
(Use empirical gaps only))
[-hitsoutdir] outdir [./] This option specifies the directory of
the LHF files (ligand hits files) (output).
A 'ligand hits file' contains database hits
(sequences) with ligand classification
information, in the LHF format (FASTA-like).
The hits are putative ligand-binding
sequences and are found from a search of a
sequence database, in this case, by using
SIGSCANLIG.
[-alignoutdir] outdir [./] This option specifies the name of the
SAF (signature alignment file) (output).A
'signature alignment file' contains one or
more signnature-sequence alignments. The
file is in DAF format (CLUSTAL-like) and is
annotated with bibliographic information,
either the domain family classification (for
SIGSCAN output) or ligand classification
(for SIGSCANLIG output). The files generated
by SIGSCAN will contain a
signature-sequence alignment for a single
signature against a library of one or more
sequences. The files generated by using
SIGSCANLIG will contain a signature-sequence
alignment for a single query sequence
against a library of one or more signatures.
[-resultsoutdir] outdir [./] This option specifies the directory for
the results files. A results file is
generated for each query sequence and
contains a list of hits (ligands),
rank-ordered on the basis of score.
Additional (Optional) qualifiers (* if not always prompted):
-nhits integer [100] This option specifies the maximum
number of hits to output. (Any integer
value)
-domax toggle [N] This option specifies whether to
consider a max. number of top-scoring hits
only for each ligand.
* -maxhits integer [0] This option specifies the maximum number
of top-scoring hits to consider for each
ligand. (Any integer value)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-dbseqall" associated qualifiers
-sbegin2 integer Start of each sequence to be used
-send2 integer End of each sequence to be used
-sreverse2 boolean Reverse (if DNA)
-sask2 boolean Ask for begin/end/reverse
-snucleotide2 boolean Sequence is nucleotide
-sprotein2 boolean Sequence is protein
-slower2 boolean Make lower case
-supper2 boolean Make upper case
-sformat2 string Input sequence format
-sdbname2 string Database name
-sid2 string Entryname
-ufo2 string UFO features
-fformat2 string Features format
-fopenfile2 string Features file name
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit
|
| Qualifier | Type | Description | Allowed values | Default | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||||||||
| [-siginfilesdir] (Parameter 1) |
dirlist | This option specifies the directory of signature files (input). A 'signature file' contains a sparse sequence signature suitable for use with the SIGSCAN and SIGSCANLIG programs. The files are generated by using SIGGEN and SIGGENLIG. | Directory with files | ./ | ||||||
| [-dbseqall] (Parameter 2) |
seqall | This option specifies the name of the database of query sequences. | Readable sequence(s) | Required | ||||||
| -sub | matrixf | This option specifies the scoring matrix to use, e.g. residue substitution matrix (1D signatures) or matrix of 3D:1D (environment:residue) scores (3D). | Comparison matrix file in EMBOSS data path | EBLOSUM62 | ||||||
| -mode | list | This option specifies the mode of scoring ligands. In 'Patch Score Mode' (mode 1) the score for a ligand is the mean of its patch scores. In 'Site Score Mode' the score for a ligand is the mean of its site scores. A site score is the mean of patch score for all patches for a given site. |
|
1 | ||||||
| -gapo | float | This option specifies the gap insertion penalty. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAMAT matrix for nucleotide sequences. | Floating point number from 1.0 to 100.0 | 10.0 for any sequence | ||||||
| -gape | float | This option specifies the gap extension penalty. The gap extension penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. | Floating point number from 0.0 to 10.0 | 0.5 for any sequence | ||||||
| -nterm | list | This option specifies the N-terminal matching option. This determines how the first signature position is aligned to a sequence from the database. |
|
1 | ||||||
| [-hitsoutdir] (Parameter 3) |
outdir | This option specifies the directory of the LHF files (ligand hits files) (output). A 'ligand hits file' contains database hits (sequences) with ligand classification information, in the LHF format (FASTA-like). The hits are putative ligand-binding sequences and are found from a search of a sequence database, in this case, by using SIGSCANLIG. | Output directory | ./ | ||||||
| [-alignoutdir] (Parameter 4) |
outdir | This option specifies the name of the SAF (signature alignment file) (output).A 'signature alignment file' contains one or more signnature-sequence alignments. The file is in DAF format (CLUSTAL-like) and is annotated with bibliographic information, either the domain family classification (for SIGSCAN output) or ligand classification (for SIGSCANLIG output). The files generated by SIGSCAN will contain a signature-sequence alignment for a single signature against a library of one or more sequences. The files generated by using SIGSCANLIG will contain a signature-sequence alignment for a single query sequence against a library of one or more signatures. | Output directory | ./ | ||||||
| [-resultsoutdir] (Parameter 5) |
outdir | This option specifies the directory for the results files. A results file is generated for each query sequence and contains a list of hits (ligands), rank-ordered on the basis of score. | Output directory | ./ | ||||||
| Additional (Optional) qualifiers | ||||||||||
| -nhits | integer | This option specifies the maximum number of hits to output. | Any integer value | 100 | ||||||
| -domax | toggle | This option specifies whether to consider a max. number of top-scoring hits only for each ligand. | Toggle value Yes/No | No | ||||||
| -maxhits | integer | This option specifies the maximum number of top-scoring hits to consider for each ligand. | Any integer value | 0 | ||||||
| Advanced (Unprompted) qualifiers | ||||||||||
| (none) | ||||||||||
| Associated qualifiers | ||||||||||
| "-dbseqall" associated seqall qualifiers | ||||||||||
| -sbegin2 -sbegin_dbseqall |
integer | Start of each sequence to be used | Any integer value | 0 | ||||||
| -send2 -send_dbseqall |
integer | End of each sequence to be used | Any integer value | 0 | ||||||
| -sreverse2 -sreverse_dbseqall |
boolean | Reverse (if DNA) | Boolean value Yes/No | N | ||||||
| -sask2 -sask_dbseqall |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N | ||||||
| -snucleotide2 -snucleotide_dbseqall |
boolean | Sequence is nucleotide | Boolean value Yes/No | N | ||||||
| -sprotein2 -sprotein_dbseqall |
boolean | Sequence is protein | Boolean value Yes/No | N | ||||||
| -slower2 -slower_dbseqall |
boolean | Make lower case | Boolean value Yes/No | N | ||||||
| -supper2 -supper_dbseqall |
boolean | Make upper case | Boolean value Yes/No | N | ||||||
| -sformat2 -sformat_dbseqall |
string | Input sequence format | Any string | |||||||
| -sdbname2 -sdbname_dbseqall |
string | Database name | Any string | |||||||
| -sid2 -sid_dbseqall |
string | Entryname | Any string | |||||||
| -ufo2 -ufo_dbseqall |
string | UFO features | Any string | |||||||
| -fformat2 -fformat_dbseqall |
string | Features format | Any string | |||||||
| -fopenfile2 -fopenfile_dbseqall |
string | Features file name | Any string | |||||||
| General qualifiers | ||||||||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | ||||||
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | ||||||
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | ||||||
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | ||||||
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | ||||||
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | ||||||
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | ||||||
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | ||||||
| -error | boolean | Report errors | Boolean value Yes/No | Y | ||||||
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | ||||||
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | ||||||
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | ||||||
% sigscanlig
Searches ligand-signature library & writes hits (LHF file)
Domainatrix signature directories [./]: ../siggenlig-keep
Database of query sequences.: swtiny
Scoring matrix [EBLOSUM62]:
Available modes
1 : Patch score mode
2 : Site score mode
Select mode of scoring ligands. [1]: 1
Gap insertion penalty [10]:
Gap extension penalty [0.5]:
N-terminal matching options
1 : Align anywhere and allow only complete signature-sequence fit
2 : Align anywhere and allow partial signature-sequence fit
3 : Use empirical gaps only
Select number [1]:
Domainatrix LHF ligand hits file output directory [./]: lhf
Domainatrix signature alignment file output directory [./]: aln
Domainatrix sigscanlig program output file output directory [./]: results
|
Go to the input files for this example
Go to the output files for this example
| FILE TYPE | FORMAT | DESCRIPTION | CREATED BY | SEE ALSO |
| Ligand hits file | LHF format (FASTA-like). | Database hits (sequences) with ligand classification information. The hits are putative ligand-binding sequences and are found from a search of a discriminating element (e.g. a protein signature) against a sequence database. | SIGSCANLIG (hits retrieved by 1D and 3D signatures). | N.A. |
| Signature alignment file | SAF format (CLUSTAL-like). | One or more signnature-sequence alignments, annotated with bibliographic information, either the domain family classification (for SIGSCAN output) or ligand classification (for SIGSCANLIG output). | SIGSCAN (signature-sequence alignments for a single signature against a database of one or more sequences) or SIGSCANLIG (signature-sequence alignment for a single query sequence against a library of one or more signatures). | N.A. |
| Signature file | SIG format | Contains a sparse sequence signature suitable for use with the SIGSCANLIG program. Contains a sparse sequence signature. | SIGGEN, SIGGENLIG, LIBGEN | The files are generated by using SIGGEN. |
| Program name | Description |
|---|---|
| contacts | Generate intra-chain CON files from CCF files |
| domainalign | Generate alignments (DAF file) for nodes in a DCF file |
| domainrep | Reorder DCF file to identify representative structures |
| domainreso | Remove low resolution domains from a DCF file |
| interface | Generate inter-chain CON files from CCF files |
| libgen | Generate discriminating elements from alignments |
| matgen3d | Generate a 3D-1D scoring matrix from CCF files |
| psiphi | Calculates phi and psi torsion angles from protein coordinates |
| rocon | Generates a hits file from comparing two DHF files |
| rocplot | Performs ROC analysis on hits files |
| seqalign | Extend alignments (DAF file) with sequences (DHF file) |
| seqfraggle | Removes fragment sequences from DHF files |
| seqsearch | Generate PSI-BLAST hits (DHF file) from a DAF file |
| seqsort | Remove ambiguous classified sequences from DHF files |
| seqwords | Generates DHF files from keyword search of UniProt |
| siggen | Generates a sparse protein signature from an alignment |
| siggenlig | Generates ligand-binding signatures from a CON file |
| sigscan | Generates hits (DHF file) from a signature search |
See also http://emboss.sourceforge.net/