hmmpfam - search one or more sequences against HMM database
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
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HMM file: testInput.hmm
Sequence file: testInput.fasta
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Query sequence: Test
Accession: [none]
Description: [none]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
TEST 184.7 2.5e-56 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
TEST 1/1 8 97 .] 1 95 [] 184.7 2.5e-56
Alignments of top-scoring domains:
TEST: domain 1 of 1, from 8 to 97: score 184.7, E = 2.5e-56
*->svfqqqqssksttgstvtAiAiAigYRYRYRAvtWnsGsLssGvnDn
sv+qqqq+ + +vtAiAiAigYRYRYRAv Wn GsLs G nDn
Test 8 SVYQQQQGGSA----MVTAIAIAIGYRYRYRAVVWNKGSLSTGTNDN 50
DnDqqsdgLYtiYYsvtvpssslpsqtviHHHaHkasstkiiikiePr<-
DnDq +d LYtiYYsvtv +ss+p q+v+HHHaH+asstkiiiki P
Test 51 DNDQAAD-LYTIYYSVTVSASSWPGQSVTHHHAHPASSTKIIIKIAPS 97
*
Test - -
//
Sequence 0
Query sequence: lcl|gi|340783625|Plus1
Accession: [none]
Description: megaplasmid, complete sequence [UNKNOWN]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
IS66_ORF3.uniq -30.0 1.7e-15 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
IS66_ORF3.uniq 1/1 60792 61184 .. 1 558 [] -30.0 1.7e-15
Alignments of top-scoring domains:
IS66_ORF3.uniq: domain 1 of 1, from 60792 to 61184: score -30.0, E = 1.7e-15
*->mSSPLDLSLFPNLmtevvkmnaalpddlslLkAalqkqQavvea..l
L S FP + + aa+p+ l + l + v + +
lcl|gi|340 60792 SCTGLWDSEFPPVFPVNGSQRAATPF-LPVGPDELSSPPSSVLXscY 60837
dakianleelIEkLka.qldkLRRmkFGkrSEKkRhkLeldiaQiekale
d + l +L ++q LR ++r
lcl|gi|340 60838 DFPLCQSLSLCFRLGFpQALALRVRQRAPRGCH----------------- 60870
dLEddLnetqaeiaeaekkieaPAssppkeaPiaskPesPRqerkRkPLP
+ +a+ + A+ +p++ + + LP
lcl|gi|340 60871 ------AHRRARGLFFTDTPHPVAVPRPQR----------DLTGSLVTLP 60904
eeLPReerRlePestvCPcggGqLkriGEDvsEqLDlvpaaFeVIqTvRp
+ +P e P + + P + + D vp+ +
lcl|gi|340 60905 APMPCSET---PVESQHPGH-----------TGRSDAVPTPNTMKTS--- 60937
KyACrqCdtiVQAPaPakpIErGiptaGLLArvlVSKyaEHlPLYRQsEI
lcl|gi|340 - -------------------------------------------------- -
yaRqGVeiaRstLadWVgrtgarLaPLvdALaeyVLkeGklHADeTPVqV
+i s L V++ + r
lcl|gi|340 60938 ------AIMISGLIHGVSARCLRF-------------------------- 60955
LaPGnkKTKTGyLWAYvRDDRnagsSlppaVvfayspdRkGEHaqvhLae
k TG R D Slp+ + + R G e
lcl|gi|340 60956 -----KRSVTG-----PRQD-----SLPADGL---RLCREG-------VE 60980
ysGkLqaDAyaGYnalyesgRVGGDpikEAgCwAHaRRKifDlhvrnpSe
sG + + + ++ wAH RR ++D+ pS+
lcl|gi|340 60981 PSGSQXKVSVTSILLSRTXP---------VASWAHVRRHFYDVNQGAPSP 61021
lteEALerIaaLYeIEaeIRGspaEdRlavRqelSvPlvkslseWLtaqr
++ AL rI +LYeIEaeI p+E+ Rq+++ Pl+ s+ WL r
lcl|gi|340 61022 VAQTALLRIHELYEIEAEIKDDPPEQKMLARQQRAAPLLESFWTWLNDTR 61071
KtlsrgseLAKALaYlLnrWdALtryldDGqVpIDNNivENAiRrvAlGR
+ +s+ AKA Y+L+rW ALt+yl+ G+ IDNN vE A+R vA+GR
lcl|gi|340 61072 AQVAPKSAIAKAIGYALKRWKALTLYLQEGHLGIDNNPVERALRGVAIGR 61121
kNyLFaGSDrGGeraAliySLIgTCKmNgVePyaYLrdVltrLadwplnk
kN+LFaG D GGeraA++y LI TCK+NgVeP aYL+dVl++L++wp +
lcl|gi|340 61122 KNFLFAGNDAGGERAAAFYTLIETCKLNGVEPFAYLCDVLEKLPTWPNKR 61171
DideLLPWayasai<-*
+eLLPW++
lcl|gi|340 61172 -LHELLPWNWKNLT 61184
//
Sequence 1