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: /usr1/pfam-23.0/Pfam_fs
Sequence file: 82545955.fa
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Query sequence: gi|82545955|ref|YP_409902.1|
Accession: [none]
Description: hypothetical protein SBO_3593 [Shigella boydii Sb227]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
RHS_repeat RHS Repeat 252.7 8.7e-73 13
RHS RHS protein 94.8 1.7e-29 3
PAAR_motif PAAR motif 9.0 0.17 1
PSCyt3 Protein of unknown function (DUF1588) 6.5 0.28 1
FerB FerB (NUC096) domain 4.5 0.63 1
SpvB Salmonella virulence plasmid 65kDa B 0.7 0.97 1
CHD5 CHD5-like protein 2.8 1.2 1
Pox_L5 Poxvirus L5 protein family 4.6 1.5 1
PDE8 PDE8 phosphodiesterase 4.0 1.6 1
DUF2147 Uncharacterized protein conserved in 4.9 1.7 1
HXXSHH Protein of unknown function (DUF1552) 1.7 1.9 1
MerR MerR family regulatory protein 5.2 2.2 1
DBI_PRT Phosphoribosyltransferase 0.6 2.6 1
DUF480 Protein of unknown function, DUF480 3.0 3.2 1
DUF924 Bacterial protein of unknown function 0.8 3.3 1
PemK PemK-like protein 3.1 3.6 1
DASH_Dam1 DASH complex subunit Dam1 3.1 3.9 1
Spermine_synth Spermine/spermidine synthase 0.8 4 1
Raffinose_syn Raffinose synthase or seed inhibition -0.3 4.1 1
Sucrose_synth Sucrose synthase -1.2 5.3 1
Glyco_hydro_65N Glycosyl hydrolase family 65, N-termi 1.0 5.4 1
PilO Pilus assembly protein, PilO 1.3 5.5 1
CmcI Cephalosporin hydroxylase 0.2 5.6 1
DUF1615 Protein of unknown function (DUF1615) 0.7 5.9 1
DUF2460 Conserved hypothetical protein 2217 ( 1.4 6 1
CysG_dimeriser Sirohaem synthase dimerisation region 2.7 6.1 1
Vitellogenin_N Lipoprotein amino terminal region -1.2 6.5 1
IRF-3 Interferon-regulatory factor 3 0.8 6.6 1
eIF_4EBP Eukaryotic translation initiation fac -0.8 7.7 1
Replicase Replicase family 1.4 7.7 1
APC10 Anaphase-promoting complex, subunit 1 1.1 8 1
His_biosynth Histidine biosynthesis protein 0.0 8.7 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
eIF_4EBP 1/1 1 9 [. 1 9 [. -0.8 7.7
PAAR_motif 1/1 2 16 .. 11 25 .] 9.0 0.17
FerB 1/1 93 106 .. 60 74 .. 4.5 0.63
DUF2147 1/1 216 224 .. 120 128 .] 4.9 1.7
DUF2460 1/1 235 248 .. 103 116 .. 1.4 6
CysG_dimeriser 1/1 246 269 .. 41 64 .] 2.7 6.1
RHS_repeat 1/13 316 356 .. 1 44 [] 7.6 0.27
IRF-3 1/1 341 375 .. 9 48 .. 0.8 6.6
Raffinose_syn 1/1 356 371 .. 831 847 .] -0.3 4.1
RHS_repeat 2/13 361 397 .. 1 44 [] 18.3 0.00024
PilO 1/1 367 384 .. 132 151 .] 1.3 5.5
Vitellogenin_N 1/1 372 383 .. 1 12 [. -1.2 6.5
PSCyt3 1/1 424 438 .. 90 104 .] 6.5 0.28
RHS_repeat 3/13 425 463 .. 1 44 [] 23.5 8.2e-06
DBI_PRT 1/1 452 475 .. 1 24 [. 0.6 2.6
His_biosynth 1/1 463 472 .. 242 251 .] 0.0 8.7
RHS_repeat 4/13 468 505 .. 1 44 [] 26.4 1.2e-06
SpvB 1/1 476 483 .. 1 8 [. 0.7 0.97
RHS 1/3 488 502 .. 27 41 .] 11.0 0.009
DUF1615 1/1 500 524 .. 229 253 .. 0.7 5.9
RHS_repeat 5/13 533 570 .. 1 44 [] 17.5 0.00041
MerR 1/1 573 594 .. 17 39 .] 5.2 2.2
RHS_repeat 6/13 575 595 .. 1 22 [. 11.2 0.025
PemK 1/1 577 591 .. 1 17 [. 3.1 3.6
RHS_repeat 7/13 596 631 .. 1 44 [] 22.6 1.5e-05
RHS 2/3 616 630 .. 27 41 .] 2.5 4.6
Glyco_hydro_65N 1/1 629 649 .. 158 180 .. 1.0 5.4
RHS_repeat 8/13 637 674 .. 1 44 [] 30.7 7.2e-08
Pox_L5 1/1 646 663 .. 64 82 .] 4.6 1.5
DUF480 1/1 663 681 .. 62 81 .. 3.0 3.2
RHS_repeat 9/13 679 715 .. 1 44 [] 24.2 5.2e-06
RHS_repeat 10/13 720 757 .. 1 44 [] 20.2 6.9e-05
Sucrose_synth 1/1 733 768 .. 519 550 .] -1.2 5.3
HXXSHH 1/1 758 782 .. 314 338 .] 1.7 1.9
Spermine_synth 1/1 796 817 .. 292 316 .] 0.8 4
DUF924 1/1 819 831 .. 153 165 .. 0.8 3.3
CmcI 1/1 858 869 .. 253 264 .] 0.2 5.6
RHS_repeat 11/13 859 893 .. 1 44 [] 22.8 1.3e-05
PDE8 1/1 869 895 .. 24 52 .] 4.0 1.6
RHS_repeat 12/13 939 985 .. 1 44 [] 24.6 3.9e-06
RHS_repeat 13/13 994 1044 .. 1 44 [] 3.0 5.5
Replicase 1/1 1067 1079 .. 1 13 [. 1.4 7.7
RHS 3/3 1143 1183 .. 1 41 [] 81.3 3.4e-25
DASH_Dam1 1/1 1164 1174 .. 48 58 .] 3.1 3.9
APC10 1/1 1274 1291 .. 204 222 .] 1.1 8
CHD5 1/1 1309 1319 .. 180 190 .] 2.8 1.2
Alignments of top-scoring domains:
eIF_4EBP: domain 1 of 1, from 1 to 9: score -0.8, E = 7.7
*->MSaspiarQ<-*
MS+ p+arQ
gi|8254595 1 MSGKPAARQ 9
PAAR_motif: domain 1 of 1, from 2 to 16: score 9.0, E = 0.17
*->nGkPAARlGDsvvCp<-*
+GkPAAR+GD+++ +
gi|8254595 2 SGKPAARQGDMTQYG 16
FerB: domain 1 of 1, from 93 to 106: score 4.5, E = 0.63
*->GpaGWkvpvkirvnl<-*
Gp GWk+p+ ir++l
gi|8254595 93 GP-GWKMPADIRLQL 106
DUF2147: domain 1 of 1, from 216 to 224: score 4.9, E = 1.7
*->lcrtQtWtR<-*
++rtQt +R
gi|8254595 216 FGRTQTFHR 224
DUF2460: domain 1 of 1, from 235 to 248: score 1.4, E = 6
*->iGiGDGatttFQLv<-*
+G++DGa ++FQLv
gi|8254595 235 TGVTDGAGRHFQLV 248
CysG_dimeriser: domain 1 of 1, from 246 to 269: score 2.7, E = 6.1
*->elvlaGdeeeAealleqaLagaaa<-*
+lvl + ++Ae++ +qa++g+++
gi|8254595 246 QLVLTTQAQRAEEARQQAISGGTE 269
RHS_repeat: domain 1 of 13, from 316 to 356: score 7.6, E = 0.27
*->YDanGrLtavtdpsgpvgqt.YrYDa..agrltaltlttstdasGtt
+ +G L av+d s++++ ++++YD++ +gr++a+ + ++ +
gi|8254595 316 WTPRGELAAVYDRSNTQV-RsFTYDDkyRGRMVAH-----RHTGRPE 356
<-*
gi|8254595 - -
IRF-3: domain 1 of 1, from 341 to 375: score 0.8, E = 6.6
CS EETTEEEEEEEEE-TT-EEE...ES-STTS.TTSSSEEEE
*->yYrGrlVlqvtvsspeGcRLfyslglPtpplqeglfgpas<-*
+YrGr+V +++++ pe +R + ++ + + + + pa+
gi|8254595 341 KYRGRMVAHRHTGRPE-IRY---RYDSDGR-VTEQLNPAG 375
Raffinose_syn: domain 1 of 1, from 356 to 371: score -0.3, E = 4.1
*->eveFkYdedtglVtvqv<-*
e+ + Yd+d g Vt q+
gi|8254595 356 EIRYRYDSD-GRVTEQL 371
RHS_repeat: domain 2 of 13, from 361 to 397: score 18.3, E = 0.00024
*->YDanGrLtavtdpsgpvgq.t.YrYD.aagrltaltlttstdasGtt
YD++Gr+t+ + +p+g++++Y+Y +++ +t++ +++ +
gi|8254595 361 YDSDGRVTE---QLNPAGLsYtYQYEkDRITITDS-----LNRR--E 397
<-*
gi|8254595 - -
PilO: domain 1 of 1, from 367 to 384: score 1.3, E = 5.5
*->vsekslLrlsvrakTYrYkd<-*
v+e+ L ++ +TY+Y
gi|8254595 367 VTEQ--LNPAGLSYTYQYEK 384
Vitellogenin_N: domain 1 of 1, from 372 to 383: score -1.2, E = 6.5
CS --BTEEEEEEEE
*->fqpgkeYvYkye<-*
+g Y+Y+ye
gi|8254595 372 NPAGLSYTYQYE 383
PSCyt3: domain 1 of 1, from 424 to 438: score 6.5, E = 0.28
*->nFDaiGrWRdqedgg<-*
+FDa+Gr R+q d
gi|8254595 424 QFDAVGRLRTQTDAA 438
RHS_repeat: domain 3 of 13, from 425 to 463: score 23.5, E = 8.2e-06
*->YDanGrLtavtdpsgpvgqtYrYD.aagrltaltlttstdasGtt<-
+Da GrL ++td++g+++ +Y+ D +g +t++ t+++G++
gi|8254595 425 FDAVGRLRTQTDAAGRTT-EYSPDvVTGLITRI-----TTPDGRA 463
*
gi|8254595 - -
DBI_PRT: domain 1 of 1, from 452 to 475: score 0.6, E = 2.6
CS HHHT-----HHHHHHHHHHHHTBS
*->liarippaDaaalaaararqdtLT<-*
li ri +D+ a+a + +++ +LT
gi|8254595 452 LITRITTPDGRASAFYYNHHSQLT 475
His_biosynth: domain 1 of 1, from 463 to 472: score 0.0, E = 8.7
CS SHHHHTTSS-
*->GsAlyeGeit<-*
+sA+y+++++
gi|8254595 463 ASAFYYNHHS 472
RHS_repeat: domain 4 of 13, from 468 to 505: score 26.4, E = 1.2e-06
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
Y+ + +Lt+ t p+g + + +YD++grl++ t ++G +
gi|8254595 468 YNHHSQLTSATGPDGLEI-RREYDEWGRLIQE-----TAPDGDI 505
SpvB: domain 1 of 1, from 476 to 483: score 0.7, E = 0.97
*->aaAGPDGl<-*
+a GPDGl
gi|8254595 476 SATGPDGL 483
RHS: domain 1 of 3, from 488 to 502: score 11.0, E = 0.009
*->rYdaWGnvleEevsq<-*
+Yd+WG++++E ++
gi|8254595 488 EYDEWGRLIQETAPD 502
DUF1615: domain 1 of 1, from 500 to 524: score 0.7, E = 5.9
*->aLDGDLlrYgsggqpraepSsTelA<-*
a+DGD++rY + ++ p +Te A
gi|8254595 500 APDGDIIRYRYDNPHSDLPCATEDA 524
RHS_repeat: domain 5 of 13, from 533 to 570: score 17.5, E = 0.00041
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
+++ G+L++ td sg v+ +Y +D +g++ta+ + +G
gi|8254595 533 WSRYGQLLSFTDCSGYVT-RYDHDRFGQMTAV-----HREEGLS 570
MerR: domain 1 of 1, from 573 to 594: score 5.2, E = 2.2
CS HHHHHTTSSS-SCEETTTS-EEE
*->RyYereGLllppprrtegGyRrY<-*
R+Y+++G +l + ++t+g rY
gi|8254595 573 RAYDSRG-QLIAVKDTQGHETRY 594
RHS_repeat: domain 6 of 13, from 575 to 595: score 11.2, E = 0.025
*->YDanGrLtavtdpsgpvgqtYr<-*
YD++G+L+av+d+ g ++ +Y+
gi|8254595 575 YDSRGQLIAVKDTQGHET-RYE 595
PemK: domain 1 of 1, from 577 to 591: score 3.1, E = 3.6
CS -TTEEEEEE--S--TTS
*->rRGeiwlvdldPasGSE<-*
+RG++++v + ++G+E
gi|8254595 577 SRGQLIAVKD--TQGHE 591
RHS_repeat: domain 7 of 13, from 596 to 631: score 22.6, E = 1.5e-05
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
Y+a+G+Ltav p+g++ +YDa+g a+ ++++G+
gi|8254595 596 YNAAGDLTAVIAPDGSRN-GTQYDAWGK--AI-----RTTQGEL 631
RHS: domain 2 of 3, from 616 to 630: score 2.5, E = 4.6
*->rYdaWGnvleEevsq<-*
+YdaWG++++ + +
gi|8254595 616 QYDAWGKAIRTTQGE 630
Glyco_hydro_65N: domain 1 of 1, from 629 to 649: score 1.0, E = 5.4
*->GvLtRslrwrskgGkgsvrvtse<-*
G+LtRs ++ +++G++ +r+tse
gi|8254595 629 GELTRSMEY-DAAGRV-IRLTSE 649
RHS_repeat: domain 8 of 13, from 637 to 674: score 30.7, E = 7.2e-08
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
YDa+Gr++ t +g+ + t+rYD ++rl++ t +G+t
gi|8254595 637 YDAAGRVIRLTSENGSHT-TFRYDVLDRLIQE-----TGFDGRT 674
Pox_L5: domain 1 of 1, from 646 to 663: score 4.6, E = 1.5
*->LrSINGrSskvSlndilrR<-*
L S NG S+++ +d+l R
gi|8254595 646 LTSENG-SHTTFRYDVLDR 663
DUF480: domain 1 of 1, from 663 to 681: score 3.0, E = 3.2
*->gLvreqsgfgsRVpKYeHrf<-*
+L+ e +gf +R+ +Y+H +
gi|8254595 663 RLIQE-TGFDGRTQRYHHDL 681
RHS_repeat: domain 9 of 13, from 679 to 715: score 24.2, E = 5.2e-06
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
+D +G+L+ + g v+ +++YD+a+rlt++ t + t+
gi|8254595 679 HDLTGKLIRSE-DEGLVT-HWHYDEADRLTHR-----TVNGETA 715
RHS_repeat: domain 10 of 13, from 720 to 757: score 20.2, E = 6.9e-05
*->YDanGrLtavt.dpsgpvgq.tYrYDaagrltaltlttstdasGtt<
YD +G+Lt +++ + g +++ +YrYD+ gr l t + t+
gi|8254595 720 YDKRGWLTDIShLSEGHRVTvHYRYDEKGR---L-----TGERQTV 757
-*
gi|8254595 - -
Sucrose_synth: domain 1 of 1, from 733 to 768: score -1.2, E = 5.3
*->sPGADmsiYFpytekek....RLtalHpeiEeLLYs<-*
s G ++ + y ek + +++R t Hp+ E LL+
gi|8254595 733 SEGHRVTVHYRYDEKGRltgeRQTVHHPQPEALLWQ 768
HXXSHH: domain 1 of 1, from 758 to 782: score 1.7, E = 1.9
*->HhgndeeklaklakidrwhveqfAy<-*
Hh + e l++ +++ +++++ +A
gi|8254595 758 HHPQPEALLWQHETRHAYNAQGLAN 782
Spermine_synth: domain 1 of 1, from 796 to 817: score 0.8, E = 4
CS TSGGGEEEEEEEESS...TT..SSS
*->TYpsggwgfavaskkislpevdlkn<-*
TY+sg+ + ++ + p+vd++
gi|8254595 796 TYGSGWLAGMKLGDT---PLVDFTR 817
DUF924: domain 1 of 1, from 819 to 831: score 0.8, E = 3.3
*->rrHrdIIaRFGRF<-*
r Hr+ +RFGR+
gi|8254595 819 RLHRETLRRFGRY 831
CmcI: domain 1 of 1, from 858 to 869: score 0.2, E = 5.6
*->AWnpnGYLkRlr<-*
+Wn nG L+R+
gi|8254595 858 TWNDNGELIRIS 869
RHS_repeat: domain 11 of 13, from 859 to 893: score 22.8, E = 1.3e-05
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
+++nG L+ ++ p+ ++ Y+Y +grlt + ++++ +
gi|8254595 859 WNDNGELIRISSPRQTRS--YSYSTTGRLTGV-----HTTA--A 893
PDE8: domain 1 of 1, from 869 to 895: score 4.0, E = 1.6
*->ssPrqttsvsqGtAAaLhGLFvktDAAea<-*
ssPrqt s s t L G v+t AA+
gi|8254595 869 SSPRQTRSYSYSTTGRLTG--VHTTAANL 895
RHS_repeat: domain 12 of 13, from 939 to 985: score 24.6, E = 3.9e-06
*->YDanGrLtavtd........psgpvgqt.YrYDaagrltaltlttst
YD++GrLt++td ++++ ++++ ++ ++Y+YD+ +rl++ t
gi|8254595 939 YDRHGRLTEKTDlipeggirTDDERT-HrYHYDSQHRLVHY-----T 979
dasGtt<-*
++ ++
gi|8254595 980 RTQYAE 985
RHS_repeat: domain 13 of 13, from 994 to 1044: score 3.0, E = 5.5
*->YDanGrLta.............vtdpsgpvgqt.YrYDaagrltalt
YD +Gr +a++ +++++ ++ ++ ++ p++ t Y++D+ +rlt++
gi|8254595 994 YDPLGRRVAkrvwrrerdltgwMSLSRKPEV-TwYGWDG-DRLTTI- 1037
lttstdasGtt<-*
+ + ++
gi|8254595 1038 ----QNDRTRI 1044
Replicase: domain 1 of 1, from 1067 to 1079: score 1.4, E = 7.7
*->pglyrrsraaALr<-*
++++rrs a+AL+
gi|8254595 1067 AKTQRRSLADALQ 1079
RHS: domain 3 of 3, from 1143 to 1183: score 81.3, E = 3.4e-25
*->vyYYHtDqiGtPLeLtdseGeivWqArYdaWGnvleEevsq<-*
+++YH+D++G+PL+L++ eG ++W+A+Yd+W n+l++e+++
gi|8254595 1143 IHLYHCDHRGLPLALISTEGATAWCAEYDEWSNLLSDENPH 1183
DASH_Dam1: domain 1 of 1, from 1164 to 1174: score 3.1, E = 3.9
*->NawCVdFPnaP<-*
+awC+++ +
gi|8254595 1164 TAWCAEYDEWS 1174
APC10: domain 1 of 1, from 1274 to 1291: score 1.1, E = 8
CS ---....XXXXXXXXXXXX
*->fhgNHATptsvdfqtyatl<-*
++g H Tpts++ +t++ +
gi|8254595 1274 IGG-HGTPTSIESATRSIM 1291
CHD5: domain 1 of 1, from 1309 to 1319: score 2.8, E = 1.2
*->SltiWlwAcnk<-*
+ t+Wl+ cn+
gi|8254595 1309 GMTVWLFSCNT 1319
//