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)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
HMM file: /usr1/pfam-23.0/Pfam_fs
Sequence file: 91781420.fa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query sequence: gi|91781420|ref|YP_556626.1|
Accession: [none]
Description: Rhs family protein [Burkholderia xenovorans LB400]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
RHS_repeat RHS Repeat 269.3 8.8e-78 17
RHS RHS protein 47.6 1.9e-14 2
PTH2 Peptidyl-tRNA hydrolase PTH2 3.0 0.26 1
DUF2394 Domain of unknown function (DUF2394) 6.9 0.27 3
TrfA TrfA protein 3.9 0.72 1
DUF1456 Protein of unknown function (DUF1456) 6.3 0.77 1
Glyco_hydro_45 Glycosyl hydrolase family 45 4.1 0.82 1
PSK_trans_fac Rv0623-like transcription factor 4.8 0.82 1
DUF2332 Uncharacterized protein conserved in 2.0 0.85 1
Ribosomal_S4e Ribosomal family S4e 5.1 0.94 2
DUF2365 Uncharacterized conserved protein (DU 3.6 1.4 1
UTRA UTRA domain 3.1 2 1
Transposase_7 Transposase 1.1 2.7 1
DUF2152 Uncharacterized conserved protein (DU -0.0 4.7 1
PRC PRC-barrel domain 3.0 4.7 1
NDUF_C2 NADH-ubiquinone oxidoreductase subuni 0.3 4.8 1
Tom7 TOM7 family 3.1 5.3 1
CBM_6 Carbohydrate binding module (family 6 1.3 5.5 1
DUF1041 Domain of Unknown Function (DUF1041) 1.4 6 1
BiPBP_C Penicillin-Binding Protein C-terminus 1.9 6.1 1
Herpes_LMP1 Herpesvirus latent membrane protein 1 -0.5 6.1 1
CC CC domain 4.0 6.9 1
UnbV_ASPIC ASPIC and UnbV 1.8 7.2 1
DUF1821 Domain of unknown function (DUF1821) 1.1 7.4 1
Ank Ankyrin repeat 3.3 7.5 1
Fumerase Fumarate hydratase (Fumerase) 0.5 7.7 1
Birna_RdRp Birnavirus RNA dependent RNA polymera -2.0 8.7 1
Mo-co_dimer Mo-co oxidoreductase dimerisation dom 0.5 9.1 1
AIRS AIR synthase related protein, N-termi 0.8 9.2 1
B-block_TFIIIC B-block binding subunit of TFIIIC -0.6 9.6 1
RDV-p3 Rice dwarf virus p3 -3.3 9.8 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
Transposase_7 1/1 1 15 [. 1 15 [. 1.1 2.7
Fumerase 1/1 69 87 .. 74 93 .. 0.5 7.7
Birna_RdRp 1/1 156 168 .. 978 990 .] -2.0 8.7
CC 1/1 178 195 .. 1 18 [. 4.0 6.9
RHS_repeat 1/17 320 357 .. 1 44 [] 6.1 0.71
Ribosomal_S4e 1/2 332 345 .. 1 14 [. 0.5 19
PSK_trans_fac 1/1 336 348 .. 78 90 .] 4.8 0.82
RHS_repeat 2/17 391 428 .. 1 44 [] 17.1 0.00054
RHS_repeat 3/17 436 457 .. 1 23 [. 0.8 23
DUF1821 1/1 439 457 .. 12 30 .. 1.1 7.4
BiPBP_C 1/1 486 497 .. 82 94 .] 1.9 6.1
RHS_repeat 4/17 497 534 .. 1 44 [] 33.4 1.3e-08
RHS 1/2 501 531 .. 10 41 .] 0.4 22
Herpes_LMP1 1/1 508 519 .. 371 382 .] -0.5 6.1
DUF1041 1/1 546 562 .. 1 17 [. 1.4 6
RHS_repeat 5/17 561 598 .. 1 44 [] 29.9 1.3e-07
UTRA 1/1 568 602 .. 107 141 .] 3.1 2
Mo-co_dimer 1/1 577 591 .. 35 50 .. 0.5 9.1
AIRS 1/1 583 636 .. 1 49 [. 0.8 9.2
B-block_TFIIIC 1/1 587 603 .. 532 548 .] -0.6 9.6
RHS_repeat 6/17 603 640 .. 1 44 [] 39.9 1.8e-10
Tom7 1/1 608 624 .. 1 19 [. 3.1 5.3
Glyco_hydro_45 1/1 637 644 .. 1 8 [. 4.1 0.82
RHS_repeat 7/17 645 682 .. 1 44 [] 19.9 8.3e-05
DUF2332 1/1 669 686 .. 347 366 .] 2.0 0.85
RHS_repeat 8/17 689 724 .. 3 44 .] 13.7 0.0048
Ribosomal_S4e 2/2 720 736 .. 1 17 [. 4.5 1.3
RHS_repeat 9/17 729 770 .. 1 44 [] 23.1 1.1e-05
DUF2394 1/3 744 759 .. 27 44 .] 1.9 9.5
RHS_repeat 10/17 776 804 .. 13 44 .] 6.2 0.69
DUF2394 2/3 807 820 .. 29 44 .] 3.7 2.6
RHS_repeat 11/17 811 824 .. 1 14 [. 6.6 0.5
RHS_repeat 12/17 831 871 .. 1 44 [] 23.6 7.4e-06
UnbV_ASPIC 1/1 856 882 .. 1 28 [. 1.8 7.2
DUF2365 1/1 881 899 .. 72 88 .. 3.6 1.4
RHS_repeat 13/17 897 922 .. 1 28 [. 5.9 0.81
RHS_repeat 14/17 948 982 .. 1 44 [] 17.9 0.00033
RDV-p3 1/1 961 971 .. 957 967 .] -3.3 9.8
DUF2394 3/3 964 978 .. 28 44 .] 1.3 15
RHS_repeat 15/17 1015 1052 .. 1 44 [] 15.3 0.0018
RHS_repeat 16/17 1058 1076 .. 21 44 .] 6.4 0.58
TrfA 1/1 1076 1101 .. 201 226 .. 3.9 0.72
RHS 2/2 1126 1160 .. 1 35 [. 47.2 2.6e-14
PTH2 1/1 1135 1148 .. 75 88 .. 3.0 0.26
RHS_repeat 17/17 1139 1167 .. 9 44 .] 3.6 3.7
NDUF_C2 1/1 1173 1182 .. 1 10 [. 0.3 4.8
DUF1456 1/1 1272 1294 .. 22 44 .. 6.3 0.77
CBM_6 1/1 1291 1315 .. 1 25 [. 1.3 5.5
DUF2152 1/1 1296 1306 .. 554 564 .. -0.0 4.7
Ank 1/1 1325 1333 .. 25 33 .] 3.3 7.5
PRC 1/1 1338 1355 .. 31 48 .. 3.0 4.7
Alignments of top-scoring domains:
Transposase_7: domain 1 of 1, from 1 to 15: score 1.1, E = 2.7
*->Mpvrfllteqereyl<-*
Mp+ +l+++q +++l
gi|9178142 1 MPRGKLTPTQVQNFL 15
Fumerase: domain 1 of 1, from 69 to 87: score 0.5, E = 7.7
*->evplegggieeaineGVreA<-*
++p++ g++++ain+GV+ A
gi|9178142 69 NIPVI-GSLFNAINAGVYLA 87
Birna_RdRp: domain 1 of 1, from 156 to 168: score -2.0, E = 8.7
*->rKmaKRrekqkre<-*
+ + KR+ekq++e
gi|9178142 156 KRAEKRAEKQAGE 168
CC: domain 1 of 1, from 178 to 195: score 4.0, E = 6.9
*->ydsstltCksatgvgpPa<-*
+++++C+ +gvg+P+
gi|9178142 178 EKEKQEACRNNKGVGHPV 195
RHS_repeat: domain 1 of 17, from 320 to 357: score 6.1, E = 0.71
*->YDanGrLtavtdpsgpvgq.t.YrYDaagrltaltlttstdasGtt<
D + L+a +++ g + ++ YD+ag+ + +da+G++
gi|9178142 320 NDGTLPLVA---IGDRYGNhQrLLYDEAGMPALI-----HDAGGRV 357
-*
gi|9178142 - -
Ribosomal_S4e: domain 1 of 2, from 332 to 345: score 0.5, E = 19
*->ktnenYRvlyDekG<-*
+ + + R+lyDe+G
gi|9178142 332 RYGNHQRLLYDEAG 345
PSK_trans_fac: domain 1 of 1, from 336 to 348: score 4.8, E = 0.82
*->dakllyDEmGlpa<-*
+ +llyDE G pa
gi|9178142 336 HQRLLYDEAGMPA 348
RHS_repeat: domain 2 of 17, from 391 to 428: score 17.1, E = 0.00054
*->YDanGrLtavtdpsgpvgqt.YrYDaagrltaltlttstdasGtt<-
Y+ G+L+ v+d++g+++ ++YrY++ + l+ + ++ +
gi|9178142 391 YSPEGDLVRVRDADGQAT-ReYRYNN-HILIEH-----SQPGALI 428
*
gi|9178142 - -
RHS_repeat: domain 3 of 17, from 436 to 457: score 0.8, E = 23
*->YDanGrLtavtdpsgpvgqtYrY<-*
Y +G+++ ++ g+++ +rY
gi|9178142 436 YTLDGKVLRLENNLGQTW-QFRY 457
DUF1821: domain 1 of 1, from 439 to 457: score 1.1, E = 7.4
*->edsAmvshtdaGhlWkFkY<-*
++++ + +++ G +W+F+Y
gi|9178142 439 DGKVLRLENNLGQTWQFRY 457
BiPBP_C: domain 1 of 1, from 486 to 497: score 1.9, E = 6.1
*->vDadGrsdrvVrf<-*
+Da+G++ r+ +
gi|9178142 486 IDAAGNATRI-DV 497
RHS_repeat: domain 4 of 17, from 497 to 534: score 33.4, E = 1.3e-08
*->YDanGrLtavtdpsgpvgq.tYrYDaagrltaltlttstdasGtt<-
D +G+ + vtdp+g+v++ t YDa+g++t+l tda+G++
gi|9178142 497 VDGQGNPLRVTDPAGGVRLaT--YDARGNMTSL-----TDAAGRR 534
*
gi|9178142 - -
RHS: domain 1 of 2, from 501 to 531: score 0.4, E = 22
*->GtPLeLtdseGeivWqArYdaWGnvleEevsq<-*
G PL +td+ G ++ A+Yda Gn +++ +
gi|9178142 501 GNPLRVTDPAGGVRL-ATYDARGNMTSLTDAA 531
Herpes_LMP1: domain 1 of 1, from 508 to 519: score -0.5, E = 6.1
*->DPHGPvqLsYYD<-*
DP G v L+ YD
gi|9178142 508 DPAGGVRLATYD 519
DUF1041: domain 1 of 1, from 546 to 562: score 1.4, E = 6
*->ktvvkdclkaaarvwyd<-*
+t++ d++ aa+rv yd
gi|9178142 546 PTLIVDAMGAATRVAYD 562
RHS_repeat: domain 5 of 17, from 561 to 598: score 29.9, E = 1.3e-07
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
YDa+G+L+ t++ g v+ Y YD+ gr++++ tda G+
gi|9178142 561 YDAAGNLIRRTNALGHVT-GYAYDDDGRVIRI-----TDAHGKH 598
UTRA: domain 1 of 1, from 568 to 602: score 3.1, E = 2
*->ippgaPvLviervtydadGrpvEysrsyyrgDryr<-*
i + ++ +++ ++yd+dGr++ + + + ++
gi|9178142 568 IRRTNALGHVTGYAYDDDGRVIRITDAHGKHRHFA 602
Mo-co_dimer: domain 1 of 1, from 577 to 591: score 0.5, E = 9.1
CS EEEEEE-STT--EEEE
*->ikGYAYsGGGRrItRV<-*
+ GYAY+ +G r++R+
gi|9178142 577 VTGYAYDDDG-RVIRI 591
AIRS: domain 1 of 1, from 583 to 636: score 0.8, E = 9.2
CS ---B------ --EEEEEEEEEETTTS--.TTS..
*->GDDAAvirlp.............gpvlvvttDgvvtkvhfakldfea
DD+ vir+ + ++++++ + +++l + +D+ ++ +h +
gi|9178142 583 DDDGRVIRITdahgkhrhfaydvHGRLTSHIDCSGRATH-------Y 622
CS .-HHHHHHHHHHHHH
ldPydiGakavagnv<-*
++d G++a+ n+
gi|9178142 623 -GWDDWGHLALVTNA 636
B-block_TFIIIC: domain 1 of 1, from 587 to 603: score -0.6, E = 9.6
*->aivrdtedeGrirfyRy<-*
+++r+t+ +G+ r++ y
gi|9178142 587 RVIRITDAHGKHRHFAY 603
RHS_repeat: domain 6 of 17, from 603 to 640: score 39.9, E = 1.8e-10
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
YD +GrLt+ d sg+++ +Y++D++g+l + t+a+G+t
gi|9178142 603 YDVHGRLTSHIDCSGRAT-HYGWDDWGHLALV-----TNAAGET 640
Tom7: domain 1 of 1, from 608 to 624: score 3.1, E = 5.3
*->KErigktlkiskvVaHYGF<-*
r++ ++ s +++HYG+
gi|9178142 608 --RLTSHIDCSGRATHYGW 624
Glyco_hydro_45: domain 1 of 1, from 637 to 644: score 4.1, E = 0.82
CS EEEEEEE-
*->sGttTRYW<-*
+G tTRYW
gi|9178142 637 AGETTRYW 644
RHS_repeat: domain 7 of 17, from 645 to 682: score 19.9, E = 8.3e-05
*->YDanGrLtavtdpsgpvgq.t.YrYDaagrltaltlttstdasGtt<
+++GrL+ ++++ g++++++YD grl+a+ tda G+
gi|9178142 645 RNRRGRLLR---TRHADGTgEeFTYDIHGRLIAH-----TDAHGAS 682
-*
gi|9178142 - -
DUF2332: domain 1 of 1, from 669 to 686: score 2.0, E = 0.85
*->depeetLgradpHGrwveWl<-*
+ + ++++d+HG+ +W
gi|9178142 669 HGRL--IAHTDAHGASTQWE 686
RHS_repeat: domain 8 of 17, from 689 to 724: score 13.7, E = 0.0048
*->anGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
a+G ++ d+ g + +Y+YDaa+rl +l t+ +G+
gi|9178142 689 ADGLPVTRIDALGHCL-RYEYDAARRLQTL-----TNENGAP 724
Ribosomal_S4e: domain 2 of 2, from 720 to 736: score 4.5, E = 1.3
*->ktnenYRvlyDekGRlv<-*
+++ YR yD++GRlv
gi|9178142 720 ENGAPYRFTYDTAGRLV 736
RHS_repeat: domain 9 of 17, from 729 to 770: score 23.1, E = 1.1e-05
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltltts..tdasGtt<
YD +GrL+++ +g+ +YrYDaag+lt ++ + + ++++
gi|9178142 729 YDTAGRLVEQQGFDGRLI-RYRYDAAGWLTEQ---IElgAYEDHAA 770
-*
gi|9178142 - -
DUF2394: domain 1 of 3, from 744 to 759: score 1.9, E = 9.5
*->rvrvYrldaaadGkLtpa<-*
r++ Yr+d a+G Lt+
gi|9178142 744 RLIRYRYD--AAGWLTEQ 759
RHS_repeat: domain 10 of 17, from 776 to 804: score 6.2, E = 0.69
*->psgpvgqtYrYDaagrltaltltts.tdasGtt<-*
p++ ++ tY+ D agr+ta+ t ++ ++ +t
gi|9178142 776 PDTLRT-TYERDKAGRITAT---TIsRAGDERT 804
DUF2394: domain 2 of 3, from 807 to 820: score 3.7, E = 2.6
*->rvYrldaaadGkLtpa<-*
+++r+d a+G+L++a
gi|9178142 807 ITWRYD--AAGRLIEA 820
RHS_repeat: domain 11 of 17, from 811 to 824: score 6.6, E = 0.5
*->YDanGrLtavtdps<-*
YDa+GrL++ ++++
gi|9178142 811 YDAAGRLIEASNDC 824
RHS_repeat: domain 12 of 17, from 831 to 871: score 23.6, E = 7.4e-06
*->YDanGrLtavt.dpsgpvgq.tYrYDaagrltaltlttstdasGtt<
YDa GrL + t+ +g++++ Y++Da+g+ +++ t ++G+
gi|9178142 831 YDAVGRLSSETsHVAGRSLTvSYEHDALGNHIRT-----TLPDGRH 871
-*
gi|9178142 - -
UnbV_ASPIC: domain 1 of 1, from 856 to 882: score 1.8, E = 7.2
*->dAiGAtVtvttPgdrvltrqVtgGgGYl<-*
dA G +++ t d++ ++ ++ G+G+l
gi|9178142 856 DALGNHIRTTL-PDGRHIDYLYYGSGHL 882
DUF2365: domain 1 of 1, from 881 to 899: score 3.6, E = 1.4
*->hmhq..IDPsVLvDLErea<-*
h+hq +ID+ V +D+Er a
gi|9178142 881 HLHQisIDGEVISDIERDA 899
RHS_repeat: domain 13 of 17, from 897 to 922: score 5.9, E = 0.81
*->YDanGrLtavtdpsgpvgqtYrYDaagr<-*
Da++r ++ t ++ v +Y+YD gr
gi|9178142 897 RDALHREVSRT-QGELVS-HYQYDLQGR 922
RHS_repeat: domain 14 of 17, from 948 to 982: score 17.9, E = 0.00033
*->YDanGrLtavt.dpsgpvgqtYrYDaagrltaltlttstdasGtt<-
YD+ G++ ++t+ +sg + YrYD++g+ l + +++t
gi|9178142 948 YDEVGNVREMTdRQSGVHR--YRYDPLGQ---L-----IESEHET 982
*
gi|9178142 - -
RDV-p3: domain 1 of 1, from 961 to 971: score -3.3, E = 9.8
*->qiGvHeVllDP<-*
q GvH + DP
gi|9178142 961 QSGVHRYRYDP 971
DUF2394: domain 3 of 3, from 964 to 978: score 1.3, E = 15
*->vrvYrldaaadGkLtpa<-*
v+ Yr+d G+L++
gi|9178142 964 VHRYRYD--PLGQLIES 978
RHS_repeat: domain 15 of 17, from 1015 to 1052: score 15.3, E = 0.0018
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltlttstdasGtt<-*
YD +G+++++ ++++ ++ Y +a+r++++ + a+ t
gi|9178142 1015 YDMHGNVVEKISGAHTRI-RLDYSPAHRIERA-----RVARNGT 1052
RHS_repeat: domain 16 of 17, from 1058 to 1076: score 6.4, E = 0.58
*->YrYDaagrltaltlttstdasGtt<-*
Y+YDa+gr++ + +asG t
gi|9178142 1058 YGYDALGRRVFR-----KNASGIT 1076
TrfA: domain 1 of 1, from 1076 to 1101: score 3.9, E = 0.72
*->tKFvWEKYRKLsPtrdrRmFDYFasH<-*
t FvWE R Ls rd R F Y +H
gi|9178142 1076 TLFVWEGNRLLSEVRDDRTFVYVYAH 1101
RHS: domain 2 of 2, from 1126 to 1160: score 47.2, E = 2.6e-14
*->vyYYHtDqiGtPLeLtdseGeivWqArYdaWGnvl<-*
++YYHtDqiG+P e td+ G + W+ArY aWG++l
gi|9178142 1126 IRYYHTDQIGLPYESTDDAGRTQWRARYAAWGRLL 1160
PTH2: domain 1 of 1, from 1135 to 1148: score 3.0, E = 0.26
CS T--EEEEEETTSSS
*->GLptalIrDAGRTQ<-*
GLp++ DAGRTQ
gi|9178142 1135 GLPYESTDDAGRTQ 1148
RHS_repeat: domain 17 of 17, from 1139 to 1167: score 3.6, E = 3.7
*->avtdpsgpvgqtYr.YDaagrltaltlttstdasGtt<-*
+ td++g++ + +Y a+grl l +G +
gi|9178142 1139 ESTDDAGRTQ-WRArYAAWGRL--L-----GANGGHE 1167
NDUF_C2: domain 1 of 1, from 1173 to 1182: score 0.3, E = 4.8
*->gRrgreplkF<-*
gR+ ++pl+F
gi|9178142 1173 GRQAHQPLRF 1182
DUF1456: domain 1 of 1, from 1272 to 1294: score 6.3, E = 0.77
*->IlalagveVskeelaAyLrKede<-*
I++l g +++++el++y+r +++
gi|9178142 1272 IADLSGETLTPSELGDYMREASN 1294
CBM_6: domain 1 of 1, from 1291 to 1315: score 1.3, E = 5.5
CS ETTG-SEEESTEEEEEES.TT.SSE
*->eAEtydkqsGvstektttgygGgGy<-*
eA +y+++ v+++ ++ g+gG ++
gi|9178142 1291 EASNYRQGQPVTLYACHLGAGGKNS 1315
DUF2152: domain 1 of 1, from 1296 to 1306: score -0.0, E = 4.7
*->rqdqpVklYAC<-*
rq+qpV lYAC
gi|9178142 1296 RQGQPVTLYAC 1306
Ank: domain 1 of 1, from 1325 to 1333: score 3.3, E = 7.5
CS TSTTTTBTT
*->GAdlnaqdd<-*
GAd+na +d
gi|9178142 1325 GADVNAPTD 1333
PRC: domain 1 of 1, from 1338 to 1355: score 3.0, E = 4.7
CS EETTTTEEEEEEEEETTT
*->idegegdvlglvvsvggf<-*
id g+gdv++lv +gg+
gi|9178142 1338 IDLGDGDVMALVANGGGW 1355
//