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: 160899155.fa
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Query sequence: gi|160899155|ref|YP_001564737.1|
Accession: [none]
Description: YD repeat-containing protein [Delftia acidovorans SPH-1]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
RHS_repeat RHS Repeat 159.7 8.9e-45 15
RHS RHS protein 16.1 0.00022 1
Chlorovi_GP_rpt Chlorovirus glycoprotein repeat 6.5 0.45 1
Connexin50 Gap junction alpha-8 protein (Cx50) 3.5 0.73 2
Ribonuclease_BN Ribonuclease BN-like family 2.4 1.6 1
FlgN FlgN protein 3.6 1.8 1
ATE_C Arginine-tRNA-protein transferase, C 3.1 2 1
Lipase Lipase 2.7 2 1
Transposase_9 Transposase 3.8 2.8 1
Flg_new Listeria-Bacteroides repeat domain (L 4.9 3.4 1
Peptidase_S49_N Peptidase family S49 N-terminal -0.2 3.7 1
SNO SNO glutamine amidotransferase family 0.5 3.9 1
HGD-D 2-hydroxyglutaryl-CoA dehydratase, D- 0.8 4.2 1
TonB Gram-negative bacterial tonB protein 4.0 4.2 2
SelP_C Selenoprotein P, C terminal region 1.9 4.4 1
Parvo_coat_N Parvovirus coat protein VP1 2.0 4.5 1
PhdYeFM Phd_YefM 2.8 4.9 1
eIF-4B Plant specific eukaryotic initiation -2.8 5.1 1
QH-AmDH_gamma Quinohemoprotein amine dehydrogenase, 2.6 5.2 1
GSPII_N Bacterial type II secretion system pr 0.4 5.5 1
Av_adeno_fibre Avian adenovirus fibre 2.4 5.6 1
Sulfatase Sulfatase 0.2 6.1 1
DUF2083 Predicted transcriptional regulator ( 2.5 6.5 1
FTHFS Formate--tetrahydrofolate ligase -1.0 7.8 1
DUF2325 Uncharacterized protein conserved in 1.0 8 1
He_PIG Putative Ig domain 2.1 8.1 1
ACP_syn_III 3-Oxoacyl-[acyl-carrier-protein (ACP) 2.2 8.2 1
Plug TonB-dependent Receptor Plug Domain 1.5 8.7 1
FAD_binding_1 FAD binding domain 0.2 8.7 1
MFS_1 Major Facilitator Superfamily 0.1 9.5 1
Antirestrict Antirestriction protein 0.5 9.6 1
DUF287 Drosophila protein of unknown functio 2.3 9.8 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
TonB 1/2 7 16 .. 26 35 .] 0.4 46
DUF287 1/1 12 28 .. 1 17 [. 2.3 9.8
Antirestrict 1/1 49 59 .. 7 17 .. 0.5 9.6
RHS_repeat 1/15 65 79 .. 1 15 [. 3.6 3.6
RHS_repeat 2/15 88 122 .. 4 44 .] 4.5 2.1
SNO 1/1 96 103 .. 114 121 .. 0.5 3.9
TonB 2/2 122 139 .. 18 35 .] 3.6 5.4
RHS_repeat 3/15 127 167 .. 1 44 [] 13.3 0.0065
ACP_syn_III 1/1 161 177 .. 69 86 .] 2.2 8.2
MFS_1 1/1 184 203 .. 371 390 .] 0.1 9.5
GSPII_N 1/1 203 240 .. 218 257 .] 0.4 5.5
Lipase 1/1 229 262 .. 134 167 .. 2.7 2
RHS_repeat 4/15 317 348 .. 7 44 .] 4.2 2.4
ATE_C 1/1 329 342 .. 70 83 .. 3.1 2
RHS_repeat 5/15 355 391 .. 1 44 [] 24.4 4.5e-06
Sulfatase 1/1 364 386 .. 475 500 .] 0.2 6.1
RHS_repeat 6/15 396 433 .. 1 44 [] 20.1 7.7e-05
RHS_repeat 7/15 437 464 .. 1 29 [. 6.7 0.5
RHS_repeat 8/15 468 498 .. 11 44 .] 5.7 0.94
SelP_C 1/1 472 506 .. 1 35 [. 1.9 4.4
PhdYeFM 1/1 477 514 .. 39 76 .] 2.8 4.9
FlgN 1/1 509 534 .. 124 150 .] 3.6 1.8
RHS_repeat 9/15 526 563 .. 1 44 [] 14.9 0.0022
RHS_repeat 10/15 568 603 .. 1 44 [] 12.0 0.015
FAD_binding_1 1/1 579 587 .. 230 238 .] 0.2 8.7
RHS_repeat 11/15 610 647 .. 1 44 [] 17.7 0.00035
Plug 1/1 618 663 .. 1 42 [. 1.5 8.7
Parvo_coat_N 1/1 654 663 .. 1 10 [. 2.0 4.5
RHS_repeat 12/15 668 704 .. 3 44 .] 5.1 1.3
RHS_repeat 13/15 720 746 .. 5 32 .. 9.3 0.087
FTHFS 1/1 738 747 .. 602 611 .] -1.0 7.8
Peptidase_S49_N 1/1 795 800 .. 159 164 .] -0.2 3.7
RHS_repeat 14/15 837 891 .. 1 44 [] 11.3 0.024
He_PIG 1/1 847 860 .. 1 36 [. 2.1 8.1
Av_adeno_fibre 1/1 889 898 .. 1 10 [. 2.4 5.6
HGD-D 1/1 899 917 .. 396 414 .] 0.8 4.2
Connexin50 1/2 909 916 .. 62 69 .] 1.3 4.4
DUF2083 1/1 916 921 .. 1 6 [. 2.5 6.5
RHS_repeat 15/15 933 990 .. 1 44 [] 6.8 0.44
DUF2325 1/1 968 980 .. 81 96 .] 1.0 8
Transposase_9 1/1 1051 1077 .. 50 76 .. 3.8 2.8
RHS 1/1 1056 1076 .. 5 25 .. 16.1 0.00022
Connexin50 2/2 1101 1106 .. 64 69 .] 2.2 2.2
Flg_new 1/1 1177 1185 .. 1 9 [. 4.9 3.4
Ribonuclease_BN 1/1 1177 1190 .. 1 14 [. 2.4 1.6
eIF-4B 1/1 1178 1182 .. 617 621 .] -2.8 5.1
QH-AmDH_gamma 1/1 1213 1233 .. 43 63 .. 2.6 5.2
Chlorovi_GP_rpt 1/1 1254 1271 .. 7 24 .. 6.5 0.45
Alignments of top-scoring domains:
TonB: domain 1 of 2, from 7 to 16: score 0.4, E = 46
*->dGrVsnvrVl<-*
+G++s++++l
gi|1608991 7 SGHPSSISIL 16
DUF287: domain 1 of 1, from 12 to 28: score 2.3, E = 9.8
*->ieSILtPtadEKlLLer<-*
++SIL P+a+ +l L++
gi|1608991 12 SISILLPDASSVLFLKE 28
Antirestrict: domain 1 of 1, from 49 to 59: score 0.5, E = 9.6
*->GGyWhFytLSN<-*
GG W +y+ S+
gi|1608991 49 GGSWKYYRASD 59
RHS_repeat: domain 1 of 15, from 65 to 79: score 3.6, E = 3.6
*->YDanGrLtavtdpsg<-*
+D++G+Lt vt +g
gi|1608991 65 FDSQGWLTNVTLRNG 79
RHS_repeat: domain 2 of 15, from 88 to 122: score 4.5, E = 2.1
*->nGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
nG++++vt++ g+++ +++Y a g l ++ ++G t
gi|1608991 88 NGKVLSVTNSFGRQV-DFGYRADGKLNSV-----ALPDGNT 122
SNO: domain 1 of 1, from 96 to 103: score 0.5, E = 3.9
CS --S-TTTS
*->NAFGRQvd<-*
N+FGRQvd
gi|1608991 96 NSFGRQVD 103
TonB: domain 2 of 2, from 122 to 139: score 3.6, E = 5.4
*->vVqFtvdadGrVsnvrVl<-*
+V+++ da G++s+v+V
gi|1608991 122 TVSYDYDAKGNLSSVKVN 139
RHS_repeat: domain 3 of 15, from 127 to 167: score 13.3, E = 0.0065
*->YDanGrLtavtdpsgpvgq.t.YrYD.aagrltaltlttstdasGtt
YDa G+L +v+ +g ++++++Y+ + g lta+ d +G
gi|1608991 127 YDAKGNLSSVK-VNGFQTRtYsYESSvSPGLLTAI-----GDSQGNQ 167
<-*
gi|1608991 - -
ACP_syn_III: domain 1 of 1, from 161 to 177: score 2.2, E = 8.2
CS ...SS--.B---EEEE-G
*->gdeeepgailssvlgsDG<-*
gd+ ++ +l++v sDG
gi|1608991 161 GDSQGNQ-VLGFVYNSDG 177
MFS_1: domain 1 of 1, from 184 to 203: score 0.1, E = 9.5
*->rGtvsGlyntagslggalgp<-*
r+ vsG+y++++s ++++g+
gi|1608991 184 RAGVSGVYSVSYSGAASVGT 203
GSPII_N: domain 1 of 1, from 203 to 240: score 0.4, E = 5.5
*->qfqgtlkpgaelPdllkkllAtlgqpDeQGrrPlrfQGrL<-*
++ + +pga++P k+ + t+ pD+ G+ + +QG
gi|1608991 203 TAGMLVAPGADDPNWYKASVTTTA-PDGNGAT-RHYQGSA 240
Lipase: domain 1 of 1, from 229 to 262: score 2.7, E = 2
CS HHHHSS-HHHHHHHHHHHHHHHHHHHHHHHHHH-
*->gsgsttfyrqAtlNvrvVGaevakllveLeeeln<-*
g+g+t +y+ ++ vr+VG+ a ++++ +eeln
gi|1608991 229 GNGATRHYQGSAAGVRLVGQSKATFWAKFKEELN 262
RHS_repeat: domain 4 of 15, from 317 to 348: score 4.2, E = 2.4
*->LtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
L++ +g+++ ++Y++ grl+ + lt ++as tt
gi|1608991 317 LIT---ETGRTT-KLSYGGGGRLVGAALT--DNASNTT 348
ATE_C: domain 1 of 1, from 329 to 342: score 3.1, E = 2
*->yrldgkLiaVavtD<-*
y+++g+L+++a+tD
gi|1608991 329 YGGGGRLVGAALTD 342
RHS_repeat: domain 5 of 15, from 355 to 391: score 24.4, E = 4.5e-06
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
Y+a+G + td++g+++ ++YD +g++ + t+a G +
gi|1608991 355 YNAQGLPETYTDAAGQTL--FGYDTRGNRNKV-----TNALGHV 391
Sulfatase: domain 1 of 1, from 364 to 386: score 0.2, E = 6.1
CS CCCS TSEEEEEEEEECTTTTTT-S--
*->pada.tttltkppllYdltgdpgelen<-*
++da ++tl++ Yd++g+++++ n
gi|1608991 364 YTDAaGQTLFG----YDTRGNRNKVTN 386
RHS_repeat: domain 6 of 15, from 396 to 433: score 20.1, E = 7.7e-05
*->YDanGrLtavtdpsgpvgq.t.YrYDaagrltaltlttstdasGtt<
+D +Gr+++ + p+g++++Y+Y+++g+lt++ ++ t
gi|1608991 396 HDGAGRILT---AMAPSGLeRsYSYNPRGQLTRV-----SVGGQQT 433
-*
gi|1608991 - -
RHS_repeat: domain 7 of 15, from 437 to 464: score 6.7, E = 0.5
*->YDanGrLtavt.dpsgpvgqtYrYDaagrl<-*
Y n+rL ++t ++++ + Y+YD+a+r+
gi|1608991 437 YLPNDRLGTITfANGHAIT--YQYDDARRI 464
RHS_repeat: domain 8 of 15, from 468 to 498: score 5.7, E = 0.94
*->tdpsgpvgqtYrYDaagrltaltltts.tdasGtt<-*
+d++g++g Y D ++++t+ +++a+ t+
gi|1608991 468 SDNRGNSG-QYVLDQWDNRTSE---LIkDSAAQTA 498
SelP_C: domain 1 of 1, from 472 to 506: score 1.9, E = 4.4
*->GqhRqGHlencDtpasEgLqlslaqkKLCRkrCin<-*
G+ q l++ D +sE +++s aq L +r in
gi|1608991 472 GNSGQYVLDQWDNRTSELIKDSAAQTALQMQRSIN 506
PhdYeFM: domain 1 of 1, from 477 to 514: score 2.8, E = 4.9
CS EEEEHHHHHHHHH.HHCCHHSHHHHHHHHHHHHHHHTT
*->Vlisaedyeslqeltlyllrslanaerlresiaqveag<-*
++++++d + + +++ ++ ++++r +++i +++++
gi|1608991 477 YVLDQWDNRTSELIKDSAAQTALQMQRSINGINRISSE 514
FlgN: domain 1 of 1, from 509 to 534: score 3.6, E = 1.8
*->nqrlLniLqgsrgassttYgadGqtst<-*
n+ + + ++g + +tY+a+G +t
gi|1608991 509 NRISSETIRG-NQSTALTYDANGDLAT 534
RHS_repeat: domain 9 of 15, from 526 to 563: score 14.9, E = 0.0022
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
YDanG+L + ++ g+++ t+ D+++rlt + td+ +
gi|1608991 526 YDANGDLATASNGLGQTT-TLDVDGLRRLTKI-----TDPLNAS 563
RHS_repeat: domain 10 of 15, from 568 to 603: score 12.0, E = 0.015
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
Y+a++ +ta d g ++ tY+ Da+g+ a t+++ +
gi|1608991 568 YNALDAVTAAQDFKGVTT-TYTRDALGNAKAE-----TTPD--A 603
FAD_binding_1: domain 1 of 1, from 579 to 587: score 0.2, E = 8.7
CS EE-HHHHHH
*->irkGvaSny<-*
++kGv+++y
gi|1608991 579 DFKGVTTTY 587
RHS_repeat: domain 11 of 15, from 610 to 647: score 17.7, E = 0.00035
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
YDa+G + + +d++g+++ + Da+gr ++l ++s +t
gi|1608991 610 YDALGLIATAKDAAGRTL-AVQRDALGRPIQL-----QYGSTAT 647
Plug: domain 1 of 1, from 618 to 663: score 1.5, E = 8.7
CS HHTTSSSCEEEEEHHHHHHT T SSBHHHHHTT STTEEECCEEE
*->dledtpgsvsvvtaedlekr...p.asslsdaLrr.vPGvavvrggg
+++d++g + v++++l++ + + +s+++ Lr+++PG++ +g+g
gi|1608991 618 TAKDAAGRTLAVQRDALGRPiqlQyGSTATSTLRYdLPGTT-YNGPG 663
CS
<-*
gi|1608991 - -
Parvo_coat_N: domain 1 of 1, from 654 to 663: score 2.0, E = 4.5
*->LPGYkYLGPG<-*
LPG+ Y GPG
gi|1608991 654 LPGTTYNGPG 663
RHS_repeat: domain 12 of 15, from 668 to 704: score 5.1, E = 1.3
*->anGrLtavtdpsgpvgqtYrYDaagrltaltltts.tdasGtt<-*
++G+L ++ dp+ ++ Y+ D +gr+ + s+ a+G t
gi|1608991 668 STGHLSEIQDPGVTTQ--YQRDILGRVLRK----SqILANGDT 704
RHS_repeat: domain 13 of 15, from 720 to 746: score 9.3, E = 0.087
*->GrLtavtdpsgpvgqtYrYDaagrltal<-*
G L ++t+psg + tY YD++g++t l
gi|1608991 720 GELQSITYPSGKQA-TYLYDSTGQITGL 746
FTHFS: domain 1 of 1, from 738 to 747: score -1.0, E = 7.8
*->dedGeIvGLF<-*
d +G+I+GL
gi|1608991 738 DSTGQITGLQ 747
Peptidase_S49_N: domain 1 of 1, from 795 to 800: score -0.2, E = 3.7
*->LAASQL<-*
LA+SQL
gi|1608991 795 LASSQL 800
RHS_repeat: domain 14 of 15, from 837 to 891: score 11.3, E = 0.024
*->YDanGrLta..............vtdpsgpvgq.t.YrYDaagrlta
YDa GrLta+ ++ +++ + +++ + +++ ++ +Y +Da g++t+
gi|1608991 837 YDAVGRLTAsahsapsgltlptgWSLADTIELSaSgYAWDANGNRTQ 883
ltlttstdasGtt<-*
+ ++ + +
gi|1608991 884 V-----HYSNALA 891
He_PIG: domain 1 of 1, from 847 to 860: score 2.1, E = 8.1
*->tytlTkpsdgslasysttpggggLPsGLtLdsstGr<-*
++++ PsGLtL +tG+
gi|1608991 847 AHSA--------------------PSGLTL--PTGW 860
Av_adeno_fibre: domain 1 of 1, from 889 to 898: score 2.4, E = 5.6
*->yltSGtstLq<-*
+l SGtstLq
gi|1608991 889 ALASGTSTLQ 898
HGD-D: domain 1 of 1, from 899 to 917: score 0.8, E = 4.2
*->RnFdeaQlkTRleAFlEmL<-*
Rn++ a +Rl++++++L
gi|1608991 899 RNYQTAAGTNRLQSYAQTL 917
Connexin50: domain 1 of 2, from 909 to 916: score 1.3, E = 4.4
*->tLPSYAQv<-*
+L SYAQ+
gi|1608991 909 RLQSYAQT 916
DUF2083: domain 1 of 1, from 916 to 921: score 2.5, E = 6.5
*->TLQRpG<-*
TLQRpG
gi|1608991 916 TLQRPG 921
RHS_repeat: domain 15 of 15, from 933 to 990: score 6.8, E = 0.44
*->YDanGrLta..................vt.dpsgpvgqt.YrYDaag
YDa+G L+ +++++ + + +++ + + + d+++++ +Y Y+a+g
gi|1608991 933 YDAAGALVKkgdnhlhygadgriakagEYaDAADARA-VsYVYNALG 978
rltaltlttstdasGtt<-*
+++ da+G+
gi|1608991 979 QRVLK-----SDARGAG 990
DUF2325: domain 1 of 1, from 968 to 980: score 1.0, E = 8
*->RSwsslyqeLRkdeqc<-*
R++s++y++L +q
gi|1608991 968 RAVSYVYNAL---GQR 980
Transposase_9: domain 1 of 1, from 1051 to 1077: score 3.8, E = 2.8
*->rpllpdddivaeLreLtrrredLvadr<-*
r++++++d ++++r+Lt +++++++++
gi|1608991 1051 RLYAIHTDHLNTPRRLTNQQGQVAWQW 1077
RHS: domain 1 of 1, from 1056 to 1076: score 16.1, E = 0.00022
*->HtDqiGtPLeLtdseGeivWq<-*
HtD++ tP Lt+++G+++Wq
gi|1608991 1056 HTDHLNTPRRLTNQQGQVAWQ 1076
Connexin50: domain 2 of 2, from 1101 to 1106: score 2.2, E = 2.2
*->PSYAQv<-*
PSYAQ+
gi|1608991 1101 PSYAQA 1106
Flg_new: domain 1 of 1, from 1177 to 1185: score 4.9, E = 3.4
*->PTkeGYtFa<-*
PT+eG tFa
gi|1608991 1177 PTREGWTFA 1185
Ribonuclease_BN: domain 1 of 1, from 1177 to 1190: score 2.4, E = 1.6
*->neddvsllAAaLaY<-*
+++++++AAaL+Y
gi|1608991 1177 PTREGWTFAAALTY 1190
eIF-4B: domain 1 of 1, from 1178 to 1182: score -2.8, E = 5.1
*->tReGW<-*
tReGW
gi|1608991 1178 TREGW 1182
QH-AmDH_gamma: domain 1 of 1, from 1213 to 1233: score 2.6, E = 5.2
CS TTTS-TTTTTTTTTTTTSSCH
*->PAQVPDtmstYpdWskdaads<-*
PAQ +D + t p W ++ + +
gi|1608991 1213 PAQLADLIKTLPSWKAGDHRP 1233
Chlorovi_GP_rpt: domain 1 of 1, from 1254 to 1271: score 6.5, E = 0.45
*->sfLtGvtatiPgtqniDI<-*
s L Gv++t P+tq+ +I
gi|1608991 1254 SKLLGVPVTAPTTQTWNI 1271
//