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ohmmpfam |
Please help by correcting and extending the Wiki pages.
% ohmmpfam 7LES_DROME ../ohmm-own-keep4/myhmms
Align single sequence with an HMM
HMMER hmmpfam program output file [7les_drome.ohmmpfam]:
CS PSPPRNFSVRVLSPRELEVSWLPPE LRSESVYYTLHWQQELDGEN
RF PSPPRNFSVRVLSPRELEVSWLPPE LRSESVYYTLHWQQELDGEN
*->PsaPtnltvtdvtstsltlsWsppt.gngpitgYevtyqpknggee.
Ps+P+n++v+ +++ +l +sW pp++ +++ +Y++++q++ +ge
7LES_DROME 1799 PSPPRNFSVRVLSPRELEVSWLPPEqLRSESVYYTLHWQQELDGENv 1845
CS EAHERRLETAGTHRLTGIKPGSGYSLWVQAHATPTKSNSS
RF EAHERRLETAGTHRLTGIKPGSGYSLWVQAHATPTKSNSS
......wneltvpgtttsytltgLkPgteYtvrVqAvnggGnGpeS<-*
+++++ + +++ t+ ++ ltg kPg+ Y+++VqA+ + + + S
7LES_DROME 1846 qdrrewEAHERRLETAGTHRLTGIKPGSGYSLWVQAHATPTKSNSS 1891
CS LKLLRFLGSGAFGEVYEGQLK EEPQRVAIKSLR ASEFAELL
RF LKLLRFLGSGAFGEVYEGQLK EEPQRVAIKSLR ASEFAELL
*->yelleklGeGsfGkVykakhk....ktgkivAvKilk..keslsefl
++ll+ lG+G+fG+Vy++++k+++++ ++vA+K l+++++++ e+l
7LES_DROME 2209 LKLLRFLGSGAFGEVYEGQLKtedsEEPQRVAIKSLRkgASEFAELL 2255
CS QEAQLMSNFKHENIVRLVGICFDTESISLIMEHMEAGDLLSYLRAAR
RF QEAQLMSNFKHENIVRLVGICFDTESISLIMEHMEAGDLLSYLRAAR
rEiqilkrlsHpNIvrllgvfeeddhlylvmEymegGdLfdylrrng...
E+q++ +++H+NIvrl g++ + +++ l+mE+me GdL++ylr+ + ++
7LES_DROME 2256 QEAQLMSNFKHENIVRLVGICFDTESISLIMEHMEAGDLLSYLRAARats 2305
CS GLSLSELLAMCIDVANGCSYLEDMHFVHRDLACRNCLVTES
RF GLSLSELLAMCIDVANGCSYLEDMHFVHRDLACRNCLVTES
........plsekeakkialQilrGleYLHsngivHRDLKpeNILlden.
+++++++ ls e++ ++ ++++G +YL+++++vHRDL+ +N+L++e +
7LES_DROME 2306 tqepqptaGLSLSELLAMCIDVANGCSYLEDMHFVHRDLACRNCLVTESt 2355
CS RTVKIGDFGLARDIYK DYYRKEGEGLLPVRW SPESLVDGLFT
RF RTVKIGDFGLARDIYK DYYRKEGEGLLPVRW SPESLVDGLFT
......gtvKiaDFGLArlles.sseklttfvGTpwYm.APEvlegrgys
++++++ tvKi+DFGLAr+++ ++++++ + + p+++ +PE l + ++
7LES_DROME 2356 gstdrrRTVKIGDFGLARDIYKsDYYRKEGEGLLPVRWmSPESLVDGLFT 2405
CS TQSDVWAFGVLCWEILTL QQPYAA-NNFEVLAHVKEG--GRLQQPPMCT
RF TQSDVWAFGVLCWEILTL QQPYAA-NNFEVLAHVKEG--GRLQQPPMCT
skvDvWSlGviLyElltg.klPfsdidpleelfrikkrpplrlplpsncS
+++DvW++Gv+++E+lt +++P+ ++++e l k++ rl +p+ c
7LES_DROME 2406 TQSDVWAFGVLCWEILTLgQQPYAARNNFEVLAHVKEG--GRLQQPPMCT 2453
CS EKLYSLLLLCWRTDPWERPSFRRCYNTL
RF EKLYSLLLLCWRTDPWERPSFRRCYNTL
eelkdLlkkcLnkDPskRptakeilnhp<-*
e l++Ll c++ DP++Rp+++ + n +
7LES_DROME 2454 EKLYSLLLLCWRTDPWERPSFRRCYNTL 2481
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Go to the input files for this example
Go to the output files for this example
Align single sequence with an HMM
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-seqall] seqall Sequence(s) filename and optional format, or
reference (input USA)
[-hmmfile] infile HMMER hidden markov model file
[-outfile] outfile [*.ohmmpfam] HMMER hmmpfam program output
file
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-nucleic boolean [N] Force nucleic comparison
-nalign integer [100] Number of alignments (Any integer
value)
-evalue float [10.] E-value cutoff (Any numeric value)
-hitcut float [-1000000.] Hit score cutoff (Any numeric
value)
-dbsize integer [59021] Calc E-value for DB size n (Any
integer value)
-cpu integer [0] Number of CPUs (Any integer value)
-dome float [1000000.] E-value domain cutoff (Any
numeric value)
-domt float [-1000000.] Hit score domain cutoff (Any
numeric value)
-forward boolean [N] Use forward algorithm
-nulltwo boolean [N] Turn off second null model
-pvm boolean [N] Use parallel virtual machine
-xnu boolean [N] Use XNU filtering
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
"-outfile" associated qualifiers
-odirectory3 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 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
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| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-seqall] (Parameter 1) |
seqall | Sequence(s) filename and optional format, or reference (input USA) | Readable sequence(s) | Required |
| [-hmmfile] (Parameter 2) |
infile | HMMER hidden markov model file | Input file | Required |
| [-outfile] (Parameter 3) |
outfile | HMMER hmmpfam program output file | Output file | <*>.ohmmpfam |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| -nucleic | boolean | Force nucleic comparison | Boolean value Yes/No | No |
| -nalign | integer | Number of alignments | Any integer value | 100 |
| -evalue | float | E-value cutoff | Any numeric value | 10. |
| -hitcut | float | Hit score cutoff | Any numeric value | -1000000. |
| -dbsize | integer | Calc E-value for DB size n | Any integer value | 59021 |
| -cpu | integer | Number of CPUs | Any integer value | 0 |
| -dome | float | E-value domain cutoff | Any numeric value | 1000000. |
| -domt | float | Hit score domain cutoff | Any numeric value | -1000000. |
| -forward | boolean | Use forward algorithm | Boolean value Yes/No | No |
| -nulltwo | boolean | Turn off second null model | Boolean value Yes/No | No |
| -pvm | boolean | Use parallel virtual machine | Boolean value Yes/No | No |
| -xnu | boolean | Use XNU filtering | Boolean value Yes/No | No |
| Associated qualifiers | ||||
| "-seqall" associated seqall qualifiers | ||||
| -sbegin1 -sbegin_seqall |
integer | Start of each sequence to be used | Any integer value | 0 |
| -send1 -send_seqall |
integer | End of each sequence to be used | Any integer value | 0 |
| -sreverse1 -sreverse_seqall |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask1 -sask_seqall |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide1 -snucleotide_seqall |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein1 -sprotein_seqall |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower1 -slower_seqall |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper1 -supper_seqall |
boolean | Make upper case | Boolean value Yes/No | N |
| -sformat1 -sformat_seqall |
string | Input sequence format | Any string | |
| -sdbname1 -sdbname_seqall |
string | Database name | Any string | |
| -sid1 -sid_seqall |
string | Entryname | Any string | |
| -ufo1 -ufo_seqall |
string | UFO features | Any string | |
| -fformat1 -fformat_seqall |
string | Features format | Any string | |
| -fopenfile1 -fopenfile_seqall |
string | Features file name | Any string | |
| "-outfile" associated outfile qualifiers | ||||
| -odirectory3 -odirectory_outfile |
string | Output directory | 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 |
ID 7LES_DROME STANDARD; PRT; 2554 AA.
AC P13368;
DT 01-JAN-1990 (REL. 13, CREATED)
DT 01-JAN-1990 (REL. 13, LAST SEQUENCE UPDATE)
DT 01-NOV-1995 (REL. 32, LAST ANNOTATION UPDATE)
DE SEVENLESS PROTEIN (EC 2.7.1.112).
GN SEV.
OS DROSOPHILA MELANOGASTER (FRUIT FLY).
OC EUKARYOTA; METAZOA; ARTHROPODA; INSECTA; DIPTERA.
RN [1]
RP SEQUENCE FROM N.A.
RC STRAIN=CANTON-S;
RX MEDLINE; 88282538.
RA BASLER K., HAFEN E.;
RL CELL 54:299-311(1988).
RN [2]
RP SEQUENCE FROM N.A.
RC STRAIN=OREGON-R;
RX MEDLINE; 88329706.
RA BOWTELL D.L.L., SIMON M.A., RUBIN G.M.;
RL GENES DEV. 2:620-634(1988).
RN [3]
RP IDENTIFICATION OF FN-III REPEATS.
RX MEDLINE; 90199889.
RA NORTON P.A., HYNES R.O., RESS D.J.G.;
RL CELL 61:15-16(1990).
CC -!- FUNCTION: RECEPTOR FOR AN EXTRACELLULAR SIGNAL REQUIRED TO
CC INSTRUCT A CELL TO DIFFERENTIATE INTO A R7 PHOTORECEPTOR. THE
CC LIGAND FOR SEV IS THE BOSS (BRIDE OF SEVENLESS) PROTEIN ON THE
CC SURFACE OF THE NEIGHBORING R8 CELL.
CC -!- CATALYTIC ACTIVITY: ATP + A PROTEIN TYROSINE = ADP +
CC PROTEIN TYROSINE PHOSPHATE.
CC -!- SUBUNIT: MAY FORM A COMPLEX WITH DRK AND SOS.
CC -!- SIMILARITY: BELONGS TO THE INSULIN RECEPTOR FAMILY OF TYROSINE-
CC PROTEIN KINASES.
CC -!- SIMILARITY: CONTAINS SEVEN FIBRONECTIN TYPE III-LIKE DOMAINS.
CC -!- CAUTION: UNCLEAR WHETHER THE POTENTIAL MEMBRANE SPANNING REGION
CC NEAR THE N-TERMINUS IS PRESENT AS A TRANSMEMBRANE DOMAIN IN THE
CC NATIVE PROTEIN OR SERVES AS A CLEAVED SIGNAL SEQUENCE.
DR EMBL; X13666; G8579; ALT_INIT.
DR EMBL; J03158; G158419; -.
DR PIR; A28912; TVFF7L.
DR FLYBASE; FBGN0003366; SEV.
DR PROSITE; PS00107; PROTEIN_KINASE_ATP.
DR PROSITE; PS00109; PROTEIN_KINASE_TYR.
DR PROSITE; PS00239; RECEPTOR_TYR_KIN_II.
DR PROSITE; PS50011; PROTEIN_KINASE_DOM.
KW TRANSFERASE; TYROSINE-PROTEIN KINASE; TRANSMEMBRANE; ATP-BINDING;
KW PHOSPHORYLATION; RECEPTOR; VISION; REPEAT.
FT DOMAIN 1 2123 EXTRACELLULAR (POTENTIAL).
[Part of this file has been deleted for brevity]
FT VARIANT 1703 1703 N -> H.
FT VARIANT 1730 1730 R -> K.
FT VARIANT 1731 1731 G -> E.
FT VARIANT 1741 1741 V -> M.
FT VARIANT 2271 2271 R -> C.
FT CONFLICT 1823 1823 E -> Q (IN REF. 2).
SQ SEQUENCE 2554 AA; 287107 MW; 1143D891 CRC32;
MTMFWQQNVD HQSDEQDKQA KGAAPTKRLN ISFNVKIAVN VNTKMTTTHI NQQAPGTSSS
SSNSQNASPS KIVVRQQSSS FDLRQQLARL GRQLASGQDG HGGISTILII NLLLLILLSI
CCDVCRSHNY TVHQSPEPVS KDQMRLLRPK LDSDVVEKVA IWHKHAAAAP PSIVEGIAIS
SRPQSTMAHH PDDRDRDRDP SEEQHGVDER MVLERVTRDC VQRCIVEEDL FLDEFGIQCE
KADNGEKCYK TRCTKGCAQW YRALKELESC QEACLSLQFY PYDMPCIGAC EMAQRDYWHL
QRLAISHLVE RTQPQLERAP RADGQSTPLT IRWAMHFPEH YLASRPFNIQ YQFVDHHGEE
LDLEQEDQDA SGETGSSAWF NLADYDCDEY YMCEILEALI PYTQYRFRFE LPFGENRDEV
LYSPATPAYQ TPPEGAPISA PVIEHLMGLD DSHLAVHWHP GRFTNGPIEG YRLRLSSSEG
NATSEQLVPA GRGSYIFSQL QAGTNYTLAL SMINKQGEGP VAKGFVQTHS ARNEKPAKDL
TESVLLVGRR AVMWQSLEPA GENSMIYQSQ EELADIAWSK REQQLWLLNV HGELRSLKFE
SGQMVSPAQQ LKLDLGNISS GRWVPRRLSF DWLHHRLYFA MESPERNQSS FQIISTDLLG
ESAQKVGESF DLPVEQLEVD ALNGWIFWRN EESLWRQDLH GRMIHRLLRI RQPGWFLVQP
QHFIIHLMLP QEGKFLEISY DGGFKHPLPL PPPSNGAGNG PASSHWQSFA LLGRSLLLPD
SGQLILVEQQ GQAASPSASW PLKNLPDCWA VILLVPESQP LTSAGGKPHS LKALLGAQAA
KISWKEPERN PYQSADAARS WSYELEVLDV ASQSAFSIRN IRGPIFGLQR LQPDNLYQLR
VRAINVDGEP GEWTEPLAAR TWPLGPHRLR WASRQGSVIH TNELGEGLEV QQEQLERLPG
PMTMVNESVG YYVTGDGLLH CINLVHSQWG CPISEPLQHV GSVTYDWRGG RVYWTDLARN
CVVRMDPWSG SRELLPVFEA NFLALDPRQG HLYYATSSQL SRHGSTPDEA VTYYRVNGLE
GSIASFVLDT QQDQLFWLVK GSGALRLYRA PLTAGGDSLQ MIQQIKGVFQ AVPDSLQLLR
PLGALLWLER SGRRARLVRL AAPLDVMELP TPDQASPASA LQLLDPQPLP PRDEGVIPMT
VLPDSVRLDD GHWDDFHVRW QPSTSGGNHS VSYRLLLEFG QRLQTLDLST PFARLTQLPQ
AQLQLKISIT PRTAWRSGDT TRVQLTTPPV APSQPRRLRV FVERLATALQ EANVSAVLRW
DAPEQGQEAP MQALEYHISC WVGSELHEEL RLNQSALEAR VEHLQPDQTY HFQVEARVAA
TGAAAGAASH ALHVAPEVQA VPRVLYANAE FIGELDLDTR NRRRLVHTAS PVEHLVGIEG
EQRLLWVNEH VELLTHVPGS APAKLARMRA EVLALAVDWI QRIVYWAELD ATAPQAAIIY
RLDLCNFEGK ILQGERVWST PRGRLLKDLV ALPQAQSLIW LEYEQGSPRN GSLRGRNLTD
GSELEWATVQ PLIRLHAGSL EPGSETLNLV DNQGKLCVYD VARQLCTASA LRAQLNLLGE
DSIAGQLAQD SGYLYAVKNW SIRAYGRRRQ QLEYTVELEP EEVRLLQAHN YQAYPPKNCL
LLPSSGGSLL KATDCEEQRC LLNLPMITAS EDCPLPIPGV RYQLNLTLAR GPGSEEHDHG
VEPLGQWLLG AGESLNLTDL LPFTRYRVSG ILSSFYQKKL ALPTLVLAPL ELLTASATPS
PPRNFSVRVL SPRELEVSWL PPEQLRSESV YYTLHWQQEL DGENVQDRRE WEAHERRLET
AGTHRLTGIK PGSGYSLWVQ AHATPTKSNS SERLHVRSFA ELPELQLLEL GPYSLSLTWA
GTPDPLGSLQ LECRSSAEQL RRNVAGNHTK MVVEPLQPRT RYQCRLLLGY AATPGAPLYH
GTAEVYETLG DAPSQPGKPQ LEHIAEEVFR VTWTAARGNG APIALYNLEA LQARSDIRRR
RRRRRRNSGG SLEQLPWAEE PVVVEDQWLD FCNTTELSCI VKSLHSSRLL LFRVRARSLE
HGWGPYSEES ERVAEPFVSP EKRGSLVLAI IAPAAIVSSC VLALVLVRKV QKRRLRAKKL
LQQSRPSIWS NLSTLQTQQQ LMAVRNRAFS TTLSDADIAL LPQINWSQLK LLRFLGSGAF
GEVYEGQLKT EDSEEPQRVA IKSLRKGASE FAELLQEAQL MSNFKHENIV RLVGICFDTE
SISLIMEHME AGDLLSYLRA ARATSTQEPQ PTAGLSLSEL LAMCIDVANG CSYLEDMHFV
HRDLACRNCL VTESTGSTDR RRTVKIGDFG LARDIYKSDY YRKEGEGLLP VRWMSPESLV
DGLFTTQSDV WAFGVLCWEI LTLGQQPYAA RNNFEVLAHV KEGGRLQQPP MCTEKLYSLL
LLCWRTDPWE RPSFRRCYNT LHAISTDLRR TQMASATADT VVSCSRPEFK VRFDGQPLEE
HREHNERPED ENLTLREVPL KDKQLYANEG VSRL
//
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HMMER2.0
NAME 7LES_DROME/1799-1891
ACC
DESC
LENG 85
ALPH Amino
RF yes
CS yes
MAP yes
COM ohmmbuild ../../data/hmm/fn3.slx -sf selex fn3.hmm
COM ohmmcalibrate myhmms -seed 1079460101
NSEQ 109
DATE Fri Jul 15 12:00:00 2011
CKSUM 8440
XT -8455 -4 0 * -8455 -4 0 *
NULT -4 -8455
NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644
EVD -7.722639 0.628102
HMM A C D E F G H I K L M N P Q R S T V W Y
m->m m->i m->d i->m i->i d->m d->d b->m m->e
-13 * -6769
1 -1712 -4227 -5498 -865 -4208 -2901 -1274 -566 -2467 395 -3420 -4836 3619 -1858 -4835 -1203 -1345 -131 -4660 -1520 1
P -150 -501 232 46 -382 399 104 -628 211 -461 -722 274 395 44 95 358 118 -368 -296 -251
P -151 -3421 -12973 -19 -6286 -701 -1378 -1013 -7392
2 -626 -5402 1665 -881 -5720 541 -3570 -5469 -3152 -906 -4492 -539 1858 -1555 -2021 1928 -595 -1313 -5587 -1487 3
S -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
S -9 -11931 -12973 -894 -1115 -701 -1378 -7406 -7384
3 1982 -5408 -2052 103 -5729 -1682 -3568 -5480 246 -3106 -4497 -1099 2207 785 -341 -15 -969 -591 -5592 -1728 4
P -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
P -9 -11931 -12973 -894 -1115 -701 -1378 -7406 -7375
4 -1926 -4682 -2749 -6731 -4830 -6496 -5599 -144 -6364 -1674 -3977 -6224 3833 -6035 -1363 -5637 -2263 1172 -5463 -5108 5
P -148 -501 232 42 -382 397 104 -620 209 -460 -713 274 394 44 98 358 116 -371 -296 -251
P -133 -3608 -12999 -21 -6130 -701 -1378 -7406 -7366
5 -1312 -699 -1390 365 -156 656 -278 -5500 196 -1273 -1315 -1810 -383 1165 1059 988 1349 -1727 -330 -1786 7
R -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
R -23 -11957 -6753 -894 -1115 -701 -1378 -7406 -7358
6 -952 -5420 1492 -589 -2060 995 -241 -588 -1239 -1246 -4509 2702 -765 546 117 -1666 -1058 -5042 -5603 -1781 8
N -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
N -9 -11943 -12986 -894 -1115 -373 -2136 -7406 -7349
7 -1910 -4186 -1403 -683 554 -5930 -4807 398 -5685 2189 658 -5576 664 -5305 -5486 -5017 -4309 1814 -4661 -4323 9
F -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
F -31 -11957 -6051 -894 -1115 -701 -1378 -7406 -7340
8 -1843 -858 -1320 -329 -1890 -1639 2015 -1004 837 -3190 -4500 -528 -5007 1351 1283 933 1453 118 -5594 -4912 10
S -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
S -9 -11935 -12977 -894 -1115 -288 -2468 -7406 -7331
9 1390 190 -6595 -5959 1799 -625 -4670 917 -2544 -64 -175 -5444 -2246 -521 -2424 -1906 -2445 2071 -270 -4193 11
V -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
V -10 -11957 -12999 -894 -1115 -701 -1378 -7406 -7322
10 -1212 -976 -129 110 -5720 -2845 -164 383 351 -777 230 -1215 -2266 -366 198 1223 1864 -91 -385 -1640 12
R -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
[Part of this file has been deleted for brevity]
V -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
V -17 -11290 -12332 -894 -1115 -701 -1378 -7171 -6443
57 -2038 -3436 -5943 -5308 -1145 -5154 -4025 2255 423 1498 1203 -4797 -1707 -478 -1267 -2117 -3548 1450 -3893 -931 75
L -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
L -18 -11291 -12333 -894 -1115 -701 -1378 -7171 -6426
58 622 -4802 1764 1486 -5123 -4302 -2961 -1060 334 -4818 -3891 -420 -4396 1293 1148 487 -3268 -1087 -4985 -429 76
D -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
D -102 -11291 -4156 -894 -1115 -701 -1378 -7171 -6409
59 1265 -231 -1498 1351 -5045 -262 -355 -4796 922 -1073 -3813 778 -4318 877 -34 53 386 -2030 289 -4225 77
Q -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
Q -18 -11207 -12249 -894 -1115 -160 -3250 -7171 -6392
60 -684 813 -5723 -473 532 -2124 -3981 -2958 -121 2114 2840 -1421 -5174 -4409 -926 -4196 -1685 -376 -3915 497 78
K -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
K -18 -11291 -12333 -894 -1115 -701 -1378 -7171 -6375
61 -1812 -4803 1626 -749 -515 -1133 -415 -4875 -1294 -4819 -3892 3181 -793 1470 -1377 -246 -3268 -4425 -4986 -193 79
E -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
E -18 -11291 -12333 -894 -1115 -701 -1378 -7171 -6358
62 -1812 -4808 -1465 33 -1509 2998 1583 -4879 122 -4823 -3897 972 -4400 -1078 -3055 -1613 -682 -4429 -4991 -1114 80
H -149 -500 232 43 -378 398 105 -627 212 -466 -721 275 393 45 98 359 117 -367 -295 -250
H -98 -4229 -12334 -49 -4901 -701 -1378 -7171 -6340
63 -676 -4701 -742 -1422 825 -589 -545 255 1702 -2571 812 -2986 -4424 796 418 -221 1302 -1179 -4912 1028 82
R -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
R -19 -11292 -12334 -894 -1115 -701 -1378 -7171 -6322
64 -3341 -4695 350 1378 -1551 -1973 -2998 477 1265 78 273 -1163 21 504 -1507 -1108 282 114 -19 473 83
L -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
L -19 -11292 -12334 -894 -1115 -701 -1378 -7171 -6304
65 -3605 -3444 -949 -2090 2356 -1177 -4010 1410 -1703 1341 -404 -1673 -747 -4487 -4679 -2139 -1048 1197 -3900 411 84
D -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
D -19 -11292 -12334 -894 -1115 -701 -1378 -7171 -6285
66 -655 -539 1179 279 -1324 1202 -2962 -1895 147 -682 1298 1427 -2056 608 756 -1119 -1893 -4419 -4982 140 85
G -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
G -19 -11292 -12335 -894 -1115 -701 -1378 -7171 -6267
67 -1814 -4814 166 -2636 -5135 2921 -568 -4885 -1333 -2415 -3903 1495 -4406 -312 -619 602 -1672 -4436 -4997 -4314 86
R -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
R -20 -11293 -12335 -894 -1115 -701 -1378 -7171 -6248
68 -3329 1217 -624 -797 -1594 -4303 1580 -4872 2069 -2414 -3890 617 -4396 283 2449 -560 -267 -2067 -4984 -1334 87
V -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
V -20 -11293 -12335 -894 -1115 -701 -1378 -7171 -6229
69 108 566 -1460 747 -1608 -4306 -2965 -30 1407 -2607 -3878 346 1033 -336 863 -1038 745 617 -4975 -4296 88
I -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
I -20 -11293 -12335 -894 -1115 -701 -1378 -7171 -6209
70 -1318 -3465 -283 -172 -3423 -2053 -3974 1957 -4721 1761 1425 -4678 -1762 -4391 -1578 -1974 -1561 1341 -3918 -3570 89
D -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
D -20 -11293 -12336 -894 -1115 -701 -1378 -7171 -6190
71 -1165 -4790 -240 -275 -5105 -4306 1035 -2009 1665 -395 707 -1334 -218 -188 1891 -1077 -383 404 110 348 90
P -149 -500 233 43 -381 398 106 -626 210 -464 -720 275 394 45 96 359 117 -369 -294 -249
P -43 -6001 -12336 -150 -3342 -701 -1378 -7171 -6170
72 -1929 1218 -1535 -1647 -3990 -4677 -3410 1725 207 -1481 -3117 -3608 -810 -1118 -743 -1942 428 2687 -4324 -3869 92
K * * * * * * * * * * * * * * * * * * * *
K * * * * * * * -7171 0
//
|
Query: 7LES_DROME SEVENLESS PROTEIN (EC 2.7.1.112). Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- 7LES_DROME/2209-2481 303.5 2.5e-87 1 7LES_DROME/1799-1891 62.6 3.9e-15 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- 7LES_DROME/1799-1891 1/1 1799 1891 .. 1 85 [] 62.6 3.9e-15 7LES_DROME/2209-2481 1/1 2209 2481 .. 1 248 [. 303.5 2.5e-87 Alignments of top-scoring domains: 7LES_DROME/1799-1891: domain 1 of 1, from 1799 to 1891: score 62.6, E = 3.9e-15 7LES_DROME/2209-2481: domain 1 of 1, from 2209 to 2481: score 303.5, E = 2.5e-87 // |
| Program name | Description |
|---|---|
| ehmmalign | Align sequences to an HMM profile |
| ehmmbuild | Build a profile HMM from an alignment |
| ehmmcalibrate | Calibrate HMM search statistics |
| ehmmconvert | Convert between profile HMM file formats |
| ehmmemit | Generate sequences from a profile HMM |
| ehmmfetch | Retrieve an HMM from an HMM database |
| ehmmindex | Create a binary SSI index for an HMM database |
| ehmmpfam | Search one or more sequences against an HMM database |
| ehmmsearch | Search a sequence database with a profile HMM |
| libgen | Generate discriminating elements from alignments |
| ohmmalign | Align sequences with an HMM |
| ohmmbuild | Build HMM |
| ohmmcalibrate | Calibrate a hidden Markov model |
| ohmmconvert | Convert between HMM formats |
| ohmmemit | Extract HMM sequences |
| ohmmfetch | Extract HMM from a database |
| ohmmindex | Index an HMM database |
| ohmmsearch | Search sequence database with an HMM |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.