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hmoment |
hmoment plots or writes out the hydrophobic moment calculated for overlapping windows over one or more input protein sequences. The hydrophic moment reflects the periodicity of hydrophobicity of a peptide, as measured per residue for a specified angle of rotation. The window size, alpha helix angle, and beta sheet angle are user-specified. The alpha helix moment and beta sheet moment may be plotted or output.
The hydrophobic moment is measured within a moving window using the method of Eisenberg et al. The default angle of 100 degrees is used for the alpha-helix results and the default of 160 degrees is used for the beta-sheet results. These angles can be changed if required using the appropriate options.
% hmoment tsw:hbb_human Calculate and plot hydrophobic moment for protein sequence(s) Output file [hbb_human.hmoment]: |
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers (* if not always prompted):
[-seqall] seqall Protein sequence(s) filename and optional
format, or reference (input USA)
* -graph xygraph [$EMBOSS_GRAPHICS value, or x11] Graph type
(ps, hpgl, hp7470, hp7580, meta, cps, x11,
tekt, tek, none, data, xterm, png, gif)
* -outfile outfile [*.hmoment] Output file name
Additional (Optional) qualifiers:
-window integer [10] Window (Any integer value)
-aangle integer [100] Alpha helix angle (degrees) (Any
integer value)
-bangle integer [160] Beta sheet angle (degrees) (Any
integer value)
Advanced (Unprompted) qualifiers:
-baseline float [0.35] Graph marker line (Any numeric value)
-plot toggle [N] Produce graphic
-double boolean [N] Plot two graphs
Associated qualifiers:
"-seqall" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-graph" associated qualifiers
-gprompt boolean Graph prompting
-gdesc string Graph description
-gtitle string Graph title
-gsubtitle string Graph subtitle
-gxtitle string Graph x axis title
-gytitle string Graph y axis title
-goutfile string Output file for non interactive displays
-gdirectory string Output directory
"-outfile" associated qualifiers
-odirectory string Output directory
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. 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
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-seqall] (Parameter 1) |
Protein sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| -graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11 |
| -outfile | Output file name | Output file | <*>.hmoment |
| Additional (Optional) qualifiers | Allowed values | Default | |
| -window | Window | Any integer value | 10 |
| -aangle | Alpha helix angle (degrees) | Any integer value | 100 |
| -bangle | Beta sheet angle (degrees) | Any integer value | 160 |
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -baseline | Graph marker line | Any numeric value | 0.35 |
| -plot | Produce graphic | Toggle value Yes/No | No |
| -double | Plot two graphs | Boolean value Yes/No | No |
ID HBB_HUMAN Reviewed; 147 AA.
AC P68871; P02023; Q13852; Q14481; Q14510; Q45KT0; Q6FI08; Q8IZI1;
AC Q9BX96; Q9UCP8; Q9UCP9;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 20-MAR-2007, entry version 43.
DE Hemoglobin subunit beta (Hemoglobin beta chain) (Beta-globin).
GN Name=HBB;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE.
RX MEDLINE=81064667; PubMed=6254664; DOI=10.1016/0092-8674(80)90428-6;
RA Lawn R.M., Efstratiadis A., O'Connell C., Maniatis T.;
RT "The nucleotide sequence of the human beta-globin gene.";
RL Cell 21:647-651(1980).
RN [2]
RP NUCLEOTIDE SEQUENCE.
RX MEDLINE=77126403; PubMed=1019344;
RA Marotta C., Forget B., Cohen-Solal M., Weissman S.M.;
RT "Nucleotide sequence analysis of coding and noncoding regions of human
RT beta-globin mRNA.";
RL Prog. Nucleic Acid Res. Mol. Biol. 19:165-175(1976).
RN [3]
RP NUCLEOTIDE SEQUENCE.
RA Lu L., Hu Z.H., Du C.S., Fu Y.S.;
RT "DNA sequence of the human beta-globin gene isolated from a healthy
RT Chinese.";
RL Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE, AND VARIANT DURHAM-N.C. PRO-115.
RC TISSUE=Blood;
RA Kutlar F., Abboud M., Leithner C., Holley L., Brisco J., Kutlar A.;
RT "Electrophoretically silent, very unstable, thalassemic mutation at
RT codon 114 of beta globin (hemoglobin Durham-N.C.) detected by cDNA
RT sequencing of mRNA, from a Russian women.";
RL Submitted (AUG-1999) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE, AND VARIANT LOUISVILLE LEU-43.
RC TISSUE=Blood;
RA Kutlar F., Harbin J., Brisco J., Kutlar A.;
RT "Rapid detection of electrophoretically silent, unstable human
RT hemoglobin 'Louisville', (Beta; Phe 42 Leu/TTT to CTT) by cDNA
RT sequencing of mRNA.";
RL Submitted (JAN-1999) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE, AND VARIANT TY GARD GLN-125.
[Part of this file has been deleted for brevity]
FT VARIANT 141 141 A -> T (in St Jacques: O(2) affinity up).
FT /FTId=VAR_003081.
FT VARIANT 141 141 A -> V (in Puttelange; polycythemia; O(2)
FT affinity up).
FT /FTId=VAR_003082.
FT VARIANT 142 142 L -> R (in Olmsted; unstable).
FT /FTId=VAR_003083.
FT VARIANT 143 143 A -> D (in Ohio; O(2) affinity up).
FT /FTId=VAR_003084.
FT VARIANT 144 144 H -> D (in Rancho Mirage).
FT /FTId=VAR_003085.
FT VARIANT 144 144 H -> P (in Syracuse; O(2) affinity up).
FT /FTId=VAR_003087.
FT VARIANT 144 144 H -> Q (in Little Rock; O(2) affinity
FT up).
FT /FTId=VAR_003086.
FT VARIANT 144 144 H -> R (in Abruzzo; O(2) affinity up).
FT /FTId=VAR_003088.
FT VARIANT 145 145 K -> E (in Mito; O(2) affinity up).
FT /FTId=VAR_003089.
FT VARIANT 146 146 Y -> C (in Rainier; O(2) affinity up).
FT /FTId=VAR_003090.
FT VARIANT 146 146 Y -> H (in Bethesda; O(2) affinity up).
FT /FTId=VAR_003091.
FT VARIANT 147 147 H -> D (in Hiroshima; O(2) affinity up).
FT /FTId=VAR_003092.
FT VARIANT 147 147 H -> L (in Cowtown; O(2) affinity up).
FT /FTId=VAR_003093.
FT VARIANT 147 147 H -> P (in York; O(2) affinity up).
FT /FTId=VAR_003094.
FT VARIANT 147 147 H -> Q (in Kodaira; O(2) affinity up).
FT /FTId=VAR_003095.
FT HELIX 5 15
FT TURN 20 22
FT HELIX 23 34
FT HELIX 36 41
FT HELIX 43 45
FT HELIX 51 56
FT HELIX 58 76
FT TURN 77 79
FT HELIX 81 93
FT TURN 94 96
FT HELIX 101 118
FT HELIX 119 121
FT HELIX 124 141
FT HELIX 143 145
SQ SEQUENCE 147 AA; 15998 MW; A31F6D621C6556A1 CRC64;
MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK
VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG
KEFTPPVQAA YQKVVAGVAN ALAHKYH
//
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Otherwise it writes out a files containing the two columns separated by space or TAB characters. The first column is the position of the start of the window that the hydrophobic moment was calculated in. The second is the hydrophobic moment ('uH'). (If the option '-double' is given then the beta-sheet angle hydrophobicity is given as a third column.)
HMOMENT of HBB_HUMAN from 1 to 147 Window: 10 Angle: 100 Max uH: 0.714 Position uH 1 0.086 2 0.091 3 0.216 4 0.208 5 0.123 6 0.211 7 0.194 8 0.185 9 0.169 10 0.312 11 0.292 12 0.185 13 0.092 14 0.050 15 0.164 16 0.245 17 0.187 18 0.130 19 0.262 20 0.396 21 0.317 22 0.342 23 0.492 24 0.508 25 0.517 26 0.418 27 0.416 28 0.350 29 0.292 30 0.196 31 0.102 32 0.288 33 0.314 34 0.442 35 0.560 36 0.464 37 0.577 38 0.584 39 0.676 40 0.714 41 0.670 42 0.462 43 0.369 44 0.221 45 0.176 46 0.073 [Part of this file has been deleted for brevity] 88 0.179 89 0.201 90 0.065 91 0.041 92 0.110 93 0.181 94 0.261 95 0.312 96 0.200 97 0.263 98 0.369 99 0.310 100 0.362 101 0.495 102 0.585 103 0.450 104 0.488 105 0.547 106 0.315 107 0.311 108 0.252 109 0.187 110 0.215 111 0.295 112 0.425 113 0.303 114 0.421 115 0.528 116 0.487 117 0.436 118 0.501 119 0.532 120 0.409 121 0.447 122 0.308 123 0.383 124 0.252 125 0.361 126 0.374 127 0.314 128 0.219 129 0.310 130 0.361 131 0.439 132 0.433 133 0.507 134 0.336 135 0.344 136 0.207 137 0.234 138 0.299 |
When proteins of known three-dimensional structure are examined, it is found that sequences that form alpha helices tend to have, on average, a strong periodicity in the hydrophobicity of af 3.6 residues, the period of the alpha helix. The angle of rotation per residue in alpha helices is 100 degrees. Similarly, many sequences that form strands of beta sheets tend to have a periodicity in their hydrophobicity of about 2.3 residues, the period typical of beta structure. The angle of rotation per residue in beta sheets is 160 degrees. This means that many protein sequences tend to form the periodic structure that maximizes their amphiphilicity.
Periodicities in the polar/apolar character of the amino acid sequence of a protein can be examined by assigning to each residue a numerical hydrophobicity and searching for periodicity in the resulting one-dimensional function. The strength of each periodic component is the quantity that has been termed the hydrophobic moment.
The -plot option must be specified to produce a plot. hmoment can plot two graphs when the option -double is given, one for the alpha helix moment and one for the beta sheet moment. Otherwise it just plots the alpha helix moment.
| Program name | Description |
|---|---|
| garnier | Predicts protein secondary structure using GOR method |
| helixturnhelix | Identify nucleic acid-binding motifs in protein sequences |
| pepcoil | Predicts coiled coil regions in protein sequences |
| pepnet | Draw a helical net for a protein sequence |
| pepwheel | Draw a helical wheel diagram for a protein sequence |
| tmap | Predict and plot transmembrane segments in protein sequences |