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pasteseq |
pasteseq inserts one sequence into another at a specified position and writes the new, combined sequence to an output file.
To insert the sequence 'tsw:flav_nossm' after position 67 in sequence 'tsw:amir_pseae' and write the results to the file 'amir_pseae.fasta':
% pasteseq tsw:amir_pseae tsw:flav_nossm -pos=67 Insert one sequence into another output sequence [amir_pseae.fasta]: |
Go to the input files for this example
Go to the output files for this example
Example 2
This does the same thing, but the output qualifier is explicitly used:
% pasteseq tsw:amir_pseae tsw:flav_nossm -out=amirplus.seq -pos=67 Insert one sequence into another |
Go to the output files for this example
Example 3
To insert the sequence 'tsw:flav_nossm' before the start of sequence 'tsw:amir_pseae' use -pos=0:
% pasteseq tsw:amir_pseae tsw:flav_nossm -out=amirplus.seq -pos=0 Insert one sequence into another |
Go to the output files for this example
Standard (Mandatory) qualifiers:
[-asequence] sequence (Gapped) sequence filename and optional
format, or reference (input USA)
[-bsequence] sequence Sequence to insert
-pos integer [$(asequence.end)] The position in the main
input sequence to insert after.
To insert before the start use the position
0. (Integer 0 or more)
[-outseq] seqout [
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-asequence] (Parameter 1) |
(Gapped) sequence filename and optional format, or reference (input USA) | Readable sequence | Required |
| [-bsequence] (Parameter 2) |
Sequence to insert | Readable sequence | Required |
| -pos | The position in the main input sequence to insert after. To insert before the start use the position 0. | Integer 0 or more | $(asequence.end) |
| [-outseq] (Parameter 3) |
Sequence filename and optional format (output USA) | Writeable sequence | <*>.format |
| Additional (Optional) qualifiers | Allowed values | Default | |
| (none) | |||
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| (none) | |||
ID AMIR_PSEAE Reviewed; 196 AA.
AC P10932;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 08-DEC-2000, sequence version 2.
DT 20-MAR-2007, entry version 55.
DE Aliphatic amidase regulator.
GN Name=amiR; OrderedLocusNames=PA3363;
OS Pseudomonas aeruginosa.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=287;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=PAC433;
RX MEDLINE=89211409; PubMed=2495988; DOI=10.1016/0014-5793(89)80249-2;
RA Lowe N., Rice P.M., Drew R.E.;
RT "Nucleotide sequence of the aliphatic amidase regulator gene (amiR) of
RT Pseudomonas aeruginosa.";
RL FEBS Lett. 246:39-43(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228;
RX MEDLINE=20437337; PubMed=10984043; DOI=10.1038/35023079;
RA Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T.,
RA Reizer J., Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT "Complete genome sequence of Pseudomonas aeruginosa PAO1, an
RT opportunistic pathogen.";
RL Nature 406:959-964(2000).
RN [3]
RP CHARACTERIZATION.
RX MEDLINE=95286483; PubMed=7539417;
RA Wilson S.A., Drew R.E.;
RT "Transcriptional analysis of the amidase operon from Pseudomonas
RT aeruginosa.";
RL J. Bacteriol. 177:3052-3057(1995).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF COMPLEX WITH AMIC.
RC STRAIN=PAC1;
RX MEDLINE=99437995; PubMed=10508151; DOI=10.1093/emboj/18.19.5175;
RA O'Hara B.P., Norman R.A., Wan P.T., Roe S.M., Barrett T.E., Drew R.E.,
RA Pearl L.H.;
RT "Crystal structure and induction mechanism of AmiC-AmiR: a ligand-
RT regulated transcription antitermination complex.";
RL EMBO J. 18:5175-5186(1999).
CC -!- FUNCTION: Positive controlling element of amiE, the gene for
CC aliphatic amidase. Acts as a transcriptional antitermination
[Part of this file has been deleted for brevity]
CC -!- SIMILARITY: Contains 1 ANTAR domain.
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DR EMBL; X13776; CAA32023.1; -; Genomic_DNA.
DR EMBL; AE004091; AAG06751.1; -; Genomic_DNA.
DR PIR; B83226; B83226.
DR PIR; S03884; S03884.
DR PDB; 1QO0; X-ray; D/E=1-196.
DR IntAct; P10932; -.
DR GenomeReviews; AE004091_GR; PA3363.
DR KEGG; pae:PA3363; -.
DR BioCyc; PAER287:PA3363-MONOMER; -.
DR InterPro; IPR005561; AmiR_NasR_reg.
DR InterPro; IPR011006; CheY_like.
DR InterPro; IPR008327; Res_reg_antiterm.
DR Pfam; PF03861; ANTAR; 1.
DR PIRSF; PIRSF036382; RR_antiterm; 1.
DR PROSITE; PS50921; ANTAR; 1.
KW 3D-structure; Complete proteome; Transcription;
KW Transcription antitermination; Transcription regulation.
FT CHAIN 1 196 Aliphatic amidase regulator.
FT /FTId=PRO_0000064582.
FT DOMAIN 129 190 ANTAR.
FT CONFLICT 48 48 S -> A (in Ref. 1).
FT CONFLICT 64 64 R -> G (in Ref. 1).
FT CONFLICT 141 141 E -> D (in Ref. 1).
FT CONFLICT 154 154 A -> V (in Ref. 1).
FT CONFLICT 170 170 Y -> H (in Ref. 1).
FT HELIX 3 8
FT HELIX 9 12
FT STRAND 14 19
FT HELIX 23 35
FT STRAND 38 42
FT STRAND 54 59
FT HELIX 65 75
FT STRAND 81 86
FT HELIX 91 100
FT STRAND 103 109
FT HELIX 112 114
FT HELIX 115 160
FT HELIX 164 175
FT TURN 176 179
FT HELIX 182 189
SQ SEQUENCE 196 AA; 21903 MW; 306A4F30E8E4C6C0 CRC64;
MSANSLLGSL RELQVLVLNP PGEVSDALVL QLIRIGCSVR QCWPPPESFD VPVDVVFTSI
FQNRHHDEIA ALLAAGTPRT TLVALVEYES PAVLSQIIEL ECHGVITQPL DAHRVLPVLV
SARRISEEMA KLKQKTEQLQ ERIAGQARIN QAKALLMQRH GWDEREAHQY LSREAMKRRE
PILKIAQELL GNEPSA
//
|
ID FLAV_NOSSM Reviewed; 35 AA.
AC P35707;
DT 01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1994, sequence version 1.
DT 31-OCT-2006, entry version 30.
DE Flavodoxin (Fragment).
OS Nostoc sp. (strain MAC).
OC Bacteria; Cyanobacteria; Nostocales; Nostocaceae; Nostoc.
OX NCBI_TaxID=35822;
RN [1]
RP PROTEIN SEQUENCE.
RA Takruri I.A.H., Boulter D., Fitzgerald M.P., Hutber G.N., Rogers L.J.;
RT "N-terminal amino acid sequences of flavodoxins from Chondrus crispus
RT and Nostoc strain MAC.";
RL Phytochemistry 25:2113-2115(1986).
CC -!- FUNCTION: Low-potential electron donor to a number of redox
CC enzymes.
CC -!- COFACTOR: FMN.
CC -!- SIMILARITY: Belongs to the flavodoxin family.
CC -!- SIMILARITY: Contains 1 flavodoxin-like domain.
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CC Distributed under the Creative Commons Attribution-NoDerivs License
CC -----------------------------------------------------------------------
DR HSSP; P11241; 1RCF.
DR InterPro; IPR001226; Flavodoxin.
DR InterPro; IPR008254; Flavodoxin_1.
DR Pfam; PF00258; Flavodoxin_1; 1.
DR PROSITE; PS00201; FLAVODOXIN; 1.
DR PROSITE; PS50902; FLAVODOXIN_LIKE; 1.
KW Direct protein sequencing; Electron transport; Flavoprotein; FMN;
KW Transport.
FT CHAIN 1 >35 Flavodoxin.
FT /FTId=PRO_0000171640.
FT DOMAIN 4 >35 Flavodoxin-like.
FT NON_TER 35 35
SQ SEQUENCE 35 AA; 3820 MW; B6EEB5CA7A45DDA6 CRC64;
SKKIGLFYGT ZTGKTESVAE IIDEFGDEVV TLDID
//
|
>AMIR_PSEAE Aliphatic amidase regulator. MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSI FQNRHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQERIAG QARINQAKALLMQRHGWDEREAHQYLSREAMKRREPILKIAQELLGNEPSA |
>AMIR_PSEAE Aliphatic amidase regulator. MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSI FQNRHHDSKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDEIAALLAAGTPRTTLVAL VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQERIAG QARINQAKALLMQRHGWDEREAHQYLSREAMKRREPILKIAQELLGNEPSA |
>AMIR_PSEAE Aliphatic amidase regulator. SKKIGLFYGTZTGKTESVAEIIDEFGDEVVTLDIDMSANSLLGSLRELQVLVLNPPGEVS DALVLQLIRIGCSVRQCWPPPESFDVPVDVVFTSIFQNRHHDEIAALLAAGTPRTTLVAL VEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQERIAG QARINQAKALLMQRHGWDEREAHQYLSREAMKRREPILKIAQELLGNEPSA |
| Program name | Description |
|---|---|
| aligncopy | Reads and writes alignments |
| aligncopypair | Reads and writes pairs from alignments |
| biosed | Replace or delete sequence sections |
| codcopy | Copy and reformat a codon usage table |
| cutseq | Removes a section from a sequence |
| degapseq | Removes non-alphabetic (e.g. gap) characters from sequences |
| descseq | Alter the name or description of a sequence |
| entret | Retrieves sequence entries from flatfile databases and files |
| extractalign | Extract regions from a sequence alignment |
| extractfeat | Extract features from sequence(s) |
| extractseq | Extract regions from a sequence |
| featcopy | Reads and writes a feature table |
| featreport | Reads and writes a feature table |
| listor | Write a list file of the logical OR of two sets of sequences |
| makenucseq | Create random nucleotide sequences |
| makeprotseq | Create random protein sequences |
| maskambignuc | Masks all ambiguity characters in nucleotide sequences with N |
| maskambigprot | Masks all ambiguity characters in protein sequences with X |
| maskfeat | Write a sequence with masked features |
| maskseq | Write a sequence with masked regions |
| newseq | Create a sequence file from a typed-in sequence |
| nohtml | Remove mark-up (e.g. HTML tags) from an ASCII text file |
| noreturn | Remove carriage return from ASCII files |
| nospace | Remove all whitespace from an ASCII text file |
| notab | Replace tabs with spaces in an ASCII text file |
| notseq | Write to file a subset of an input stream of sequences |
| nthseq | Write to file a single sequence from an input stream of sequences |
| revseq | Reverse and complement a nucleotide sequence |
| seqret | Reads and writes (returns) sequences |
| seqretsplit | Reads sequences and writes them to individual files |
| sizeseq | Sort sequences by size |
| skipredundant | Remove redundant sequences from an input set |
| skipseq | Reads and writes (returns) sequences, skipping first few |
| splitter | Split sequence(s) into smaller sequences |
| trimest | Remove poly-A tails from nucleotide sequences |
| trimseq | Remove unwanted characters from start and end of sequence(s) |
| trimspace | Remove extra whitespace from an ASCII text file |
| union | Concatenate multiple sequences into a single sequence |
| vectorstrip | Removes vectors from the ends of nucleotide sequence(s) |
| yank | Add a sequence reference (a full USA) to a list file |