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: 42527068.fa
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Query sequence: gi|42527068|ref|NP_972166.1|
Accession: [none]
Description: YD repeat-containing protein [Treponema denticola ATCC 35405]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
RHS_repeat RHS Repeat 39.8 1.9e-10 7
GSH-S_N Prokaryotic glutathione synthetase, N 4.9 0.77 1
DUF2089 Uncharacterized protein conserved in 3.4 0.79 1
FliJ Flagellar FliJ protein 4.4 1.2 1
Ribophorin_II Ribophorin II (RPN2) 0.1 2.1 1
Varsurf_PPLC Variant-surface-glycoprotein phosphol 3.6 2.4 1
CBM_3 Cellulose binding domain 3.5 2.8 1
Peptidase_S13 D-Ala-D-Ala carboxypeptidase 3 (S13) 0.8 3.8 1
PD40 WD40-like Beta Propeller Repeat 2.8 4 1
NOT2_3_5 NOT2 / NOT3 / NOT5 family 2.0 4.1 1
PPC Bacterial pre-peptidase C-terminal do 2.8 4.4 1
DAP3 Mitochondrial ribosomal death-associa 0.5 5.2 1
DUF965 Bacterial protein of unknown function 1.3 5.7 1
DUF888 Protein of unknown function (DUF888) 3.2 5.7 1
RHS RHS protein 2.1 6.3 1
Transket_pyr Transketolase, pyrimidine binding dom 0.4 9.6 1
Trp_leader2 Tryptophan operon leader peptide 0.5 9.9 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
RHS_repeat 1/7 220 259 .. 1 44 [] 2.4 8.1
DUF965 1/1 262 275 .. 53 66 .. 1.3 5.7
DUF2089 1/1 266 275 .. 48 57 .. 3.4 0.79
DAP3 1/1 268 276 .. 370 378 .] 0.5 5.2
RHS_repeat 2/7 290 329 .. 1 44 [] 2.6 6.9
RHS_repeat 3/7 332 369 .. 1 40 [. 11.2 0.025
RHS_repeat 4/7 436 475 .. 1 44 [] 9.6 0.071
PD40 1/1 446 464 .. 16 41 .] 2.8 4
Ribophorin_II 1/1 476 505 .. 396 428 .. 0.1 2.1
FliJ 1/1 486 495 .. 135 144 .] 4.4 1.2
RHS_repeat 5/7 534 561 .. 1 26 [. 0.1 36
RHS_repeat 6/7 636 671 .. 1 44 [] 7.7 0.25
NOT2_3_5 1/1 669 678 .. 187 196 .] 2.0 4.1
Varsurf_PPLC 1/1 689 694 .. 46 51 .] 3.6 2.4
RHS_repeat 7/7 714 750 .. 1 44 [] 6.1 0.7
GSH-S_N 1/1 769 775 .. 122 128 .] 4.9 0.77
CBM_3 1/1 807 824 .. 39 56 .. 3.5 2.8
RHS 1/1 808 816 .. 1 10 [. 2.1 6.3
Peptidase_S13 1/1 941 955 .. 385 399 .] 0.8 3.8
PPC 1/1 972 986 .. 70 85 .] 2.8 4.4
Trp_leader2 1/1 992 1001 .. 33 41 .] 0.5 9.9
DUF888 1/1 1022 1029 .. 27 34 .] 3.2 5.7
Transket_pyr 1/1 1117 1125 .. 180 189 .] 0.4 9.6
Alignments of top-scoring domains:
RHS_repeat: domain 1 of 7, from 220 to 259: score 2.4, E = 8.1
*->YDanGrLtavtdpsgpvgq.tYrYDaagrltaltlttstdasGtt<-
YD+ +r + +t p+g + +++Y+ D+ ++t + td++ +
gi|4252706 220 YDDIDRNILTTLPDGHTQKtEYSIDSSLQITKA-----TDPKENI 259
*
gi|4252706 - -
DUF965: domain 1 of 1, from 262 to 275: score 1.3, E = 5.7
*->rhkdARnlIRkiER<-*
+ kdAR IR +ER
gi|4252706 262 SKKDARGNIREVER 275
DUF2089: domain 1 of 1, from 266 to 275: score 3.4, E = 0.79
*->cRGNIKEvEK<-*
+RGNI+EvE+
gi|4252706 266 ARGNIREVER 275
DAP3: domain 1 of 1, from 268 to 276: score 0.5, E = 5.2
*->GNprelekl<-*
GN+re+e+l
gi|4252706 268 GNIREVERL 276
RHS_repeat: domain 2 of 7, from 290 to 329: score 2.6, E = 6.9
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltltts.tdasGtt<-
Y+ +G + +d+ ++ + YD +gr+++l ++ d+++++
gi|4252706 290 YSVLGEMLKAYDAKDNLL-AVNYDMLGRRISL----EsKDTGKKE 329
*
gi|4252706 - -
RHS_repeat: domain 3 of 7, from 332 to 369: score 11.2, E = 0.025
*->YDanGrLtavtd....psgpvgqtYrYDaagrltaltlttstda<-*
YD+ GrL a td+ ++ ++ +Y+YD+++r++ + +++
gi|4252706 332 YDDKGRLYAETDsvlkNKAAEI-RYEYDGFDRIIKT-----DYP 369
RHS_repeat: domain 4 of 7, from 436 to 475: score 9.6, E = 0.071
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltltts...tdasGtt
Y +Gr ++++p+g + tY+YD g+l + s+ +t+ +G +
gi|4252706 436 Y--LGRMQSMKYPDGETI-TYTYDKGGQLKGV----SgakTTNKGSI 475
<-*
gi|4252706 - -
PD40: domain 1 of 1, from 446 to 464: score 2.8, E = 4
*->PDGktivFssnrgdgddgsGsfdiyv<-*
PDG ti++++++g G+ v
gi|4252706 446 PDGETITYTYDKG------GQL-KGV 464
Ribophorin_II: domain 1 of 1, from 476 to 505: score 0.1, E = 2.1
*->kYdFlvkvvLDEsdnrKvYiteiAnTKVelavk<-*
kY ++ k+ DE + r vYi + n Ve + k
gi|4252706 476 KYSYVDKILYDEHAQR-VYIKY-GNG-VETRYK 505
FliJ: domain 1 of 1, from 486 to 495: score 4.4, E = 1.2
*->DEfAarlfrr<-*
DE+A+r +++
gi|4252706 486 DEHAQRVYIK 495
RHS_repeat: domain 5 of 7, from 534 to 561: score 0.1, E = 36
*->YDanGrLtavt.dpsgpvgq.tYrYDaa<-*
+D G++ + +d+++ ++q+tY+YD++
gi|4252706 534 FDPVGNVRGYNnDATTYETQqTYSYDNL 561
RHS_repeat: domain 6 of 7, from 636 to 671: score 7.7, E = 0.25
*->YDanGrLtavtdpsgpvgqtYrYDaagrltaltltts....tdasGt
Y ++rL+ +g++ YrYDa g++ta ++++ td +
gi|4252706 636 Y--AHRLIH----AGTRY--YRYDANGNITAE----KdgpfTDEEEF 670
t<-*
t
gi|4252706 671 T 671
NOT2_3_5: domain 1 of 1, from 669 to 678: score 2.0, E = 4.1
*->dFrleYsyLe<-*
+F+++Ysy+e
gi|4252706 669 EFTFTYSYFE 678
Varsurf_PPLC: domain 1 of 1, from 689 to 694: score 3.6, E = 2.4
*->FGlDAP<-*
FGlDAP
gi|4252706 689 FGLDAP 694
RHS_repeat: domain 7 of 7, from 714 to 750: score 6.1, E = 0.7
*->YDanGrLtavtdpsgpvgq.tYrYDaagrltaltlttstdasGtt<-
+++++ Lt +s++ + +YrY++ g++ + +G+
gi|4252706 714 WNERNLLTK---SSDRNFTvHYRYGDDGQRALK-----YTDEGRS 750
*
gi|4252706 - -
GSH-S_N: domain 1 of 1, from 769 to 775: score 4.9, E = 0.77
CS S-HHHHH
*->NnPqgLR<-*
NnPqgLR
gi|4252706 769 NNPQGLR 775
CBM_3: domain 1 of 1, from 807 to 824: score 3.5, E = 2.8
CS EEEEE-SSHHHECEECCC
*->RYYyTldgnkaqgfwcdw<-*
RYYy+ d+ +++f dw
gi|4252706 807 RYYYHSDHLGSAQFVTDW 824
RHS: domain 1 of 1, from 808 to 816: score 2.1, E = 6.3
*->vyYYHtDqiG<-*
yYYH D++G
gi|4252706 808 -YYYHSDHLG 816
Peptidase_S13: domain 1 of 1, from 941 to 955: score 0.8, E = 3.8
CS ECTTC-EEEEEEEEE
*->ttdsGrklaFsfisN<-*
tt +G +++++++ N
gi|4252706 941 TTEDGAEVTVIIYYN 955
PPC: domain 1 of 1, from 972 to 986: score 2.8, E = 4.4
CS EECC.-SEEEEEEEEE
*->sftapeaGtYyirVyg<-*
s+++ +++tY i+Vy+
gi|4252706 972 SYSN-QDNTYLIEVYT 986
Trp_leader2: domain 1 of 1, from 992 to 1001: score 0.5, E = 9.9
*->ssW.WAnvYF<-*
s W+W nvYF
gi|4252706 992 SQWsWLNVYF 1001
DUF888: domain 1 of 1, from 1022 to 1029: score 3.2, E = 5.7
*->LalRkGNL<-*
L++++GNL
gi|4252706 1022 LYFKGGNL 1029
Transket_pyr: domain 1 of 1, from 1117 to 1125: score 0.4, E = 9.6
CS E-SSEE--.-
*->rlprqllrhk<-*
rlpr+++r k
gi|4252706 1117 RLPRRNYR-K 1125
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