hmmsearch - search a sequence database with a profile HMM 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: pr11.hmm [domains_only] Sequence database: ./protein-matching-PF00196.fasta per-sequence score cutoff: >= 20.0 per-domain score cutoff: [none] per-sequence Eval cutoff: <= 10 per-domain Eval cutoff: [none] - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query HMM: domains_only Accession: [none] Description: [none] [HMM has been calibrated; E-values are empirical estimates] Scores for complete sequences (score includes all domains): Sequence Description Score E-value N -------- ----------- ----- ------- --- P11470|reviewed|Spore germination protein G 38.3 1.9e-13 1 P0AGA6|reviewed|Transcriptional regulatory protein Uh 33.1 8.4e-12 1 P0AGA8|reviewed|Transcriptional regulatory protein Uh 33.1 8.4e-12 1 P0AGA9|reviewed|Transcriptional regulatory protein Uh 33.1 8.4e-12 1 P0AGA7|reviewed|Transcriptional regulatory protein Uh 33.1 8.4e-12 1 P27667|reviewed|Transcriptional regulatory protein Uh 32.0 1.8e-11 1 P26319|reviewed|Fimbriae Z protein|taxID:99287 31.5 2.7e-11 1 P55184|reviewed|Uncharacterized transcriptional regul 30.5 5.2e-11 1 P56644|reviewed|Probable transcriptional regul 25.2 2.4e-09 1 O07528|reviewed|Uncharacterized transcriptional regul 23.7 7.1e-09 1 P0AEL8|reviewed|Fimbriae Z protein|taxID:83333 21.7 3.1e-08 1 P0AEL9|reviewed|Fimbriae Z protein|taxID:83334 21.7 3.1e-08 1 P31802|reviewed|Nitrate/nitrite response regulator pr 21.2 4.3e-08 1 P0A4H3|reviewed|Virulence factors putative posi 20.9 5.4e-08 1 P0A4H2|reviewed|Virulence factors putative posi 20.9 5.4e-08 1 P0A4H4|reviewed|Virulence factors putative posi 20.9 5.4e-08 1 Parsed for domains: Sequence Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- P11470|reviewed|Spore 1/1 12 68 .. 191 245 .] 38.3 1.9e-13 P0AGA6|reviewed|Transcriptional 1/1 137 182 .. 190 235 .. 33.1 8.4e-12 P0AGA8|reviewed|Transcriptional 1/1 137 182 .. 190 235 .. 33.1 8.4e-12 P0AGA9|reviewed|Transcriptional 1/1 137 182 .. 190 235 .. 33.1 8.4e-12 P0AGA7|reviewed|Transcriptional 1/1 137 182 .. 190 235 .. 33.1 8.4e-12 P27667|reviewed|Transcriptional 1/1 137 182 .. 190 235 .. 32.0 1.8e-11 P26319|reviewed|Fimbriae 1/1 146 193 .. 187 234 .. 31.5 2.7e-11 P55184|reviewed|Uncharacterized 1/1 158 211 .. 192 245 .] 30.5 5.2e-11 P56644|reviewed|Probable 1/1 148 202 .. 191 245 .] 25.2 2.4e-09 O07528|reviewed|Uncharacterized 1/1 149 203 .. 191 245 .] 23.7 7.1e-09 P0AEL8|reviewed|Fimbriae 1/1 150 193 .. 191 234 .. 21.7 3.1e-08 P0AEL9|reviewed|Fimbriae 1/1 150 193 .. 191 234 .. 21.7 3.1e-08 P31802|reviewed|Nitrate/nitrite 1/1 154 185 .. 191 222 .. 21.2 4.3e-08 P0A4H3|reviewed|Virulence 1/1 149 180 .. 191 222 .. 20.9 5.4e-08 P0A4H2|reviewed|Virulence 1/1 149 180 .. 191 222 .. 20.9 5.4e-08 P0A4H4|reviewed|Virulence 1/1 149 180 .. 191 222 .. 20.9 5.4e-08 Alignments of top-scoring domains: P11470|reviewed|Spore: domain 1 of 1, from 12 to 68: score 38.3, E = 1.9e-13 *->LsaREvdVLrrLaegKvYKQIaleLglStSTVRthlHNvygKlGAvD L++RE +V+++L + K K Ia+eL S+ TVR+h N+ +KlG++ P11470|rev 12 LTKREREVFELLVQDKTTKEIASELFISEKTVRNHISNAMQKLGVKG 58 RAQAV..LiA<-* R QAV +L++ P11470|rev 59 RSQAVveLLR 68 P0AGA6|reviewed|Transcriptional: domain 1 of 1, from 137 to 182: score 33.1, E = 8.4e-12 *->PLsaREvdVLrrLaegKvYKQIaleLglStSTVRthlHNvygKlGA< PL++RE +V ++La+g++ K Ia+eLglS TV+ h N +KlG+ P0AGA6|rev 137 PLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGV 182 -* P0AGA6|rev - - P0AGA8|reviewed|Transcriptional: domain 1 of 1, from 137 to 182: score 33.1, E = 8.4e-12 *->PLsaREvdVLrrLaegKvYKQIaleLglStSTVRthlHNvygKlGA< PL++RE +V ++La+g++ K Ia+eLglS TV+ h N +KlG+ P0AGA8|rev 137 PLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGV 182 -* P0AGA8|rev - - P0AGA9|reviewed|Transcriptional: domain 1 of 1, from 137 to 182: score 33.1, E = 8.4e-12 *->PLsaREvdVLrrLaegKvYKQIaleLglStSTVRthlHNvygKlGA< PL++RE +V ++La+g++ K Ia+eLglS TV+ h N +KlG+ P0AGA9|rev 137 PLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGV 182 -* P0AGA9|rev - - P0AGA7|reviewed|Transcriptional: domain 1 of 1, from 137 to 182: score 33.1, E = 8.4e-12 *->PLsaREvdVLrrLaegKvYKQIaleLglStSTVRthlHNvygKlGA< PL++RE +V ++La+g++ K Ia+eLglS TV+ h N +KlG+ P0AGA7|rev 137 PLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGV 182 -* P0AGA7|rev - - P27667|reviewed|Transcriptional: domain 1 of 1, from 137 to 182: score 32.0, E = 1.8e-11 *->PLsaREvdVLrrLaegKvYKQIaleLglStSTVRthlHNvygKlGA< PL++RE +V ++La+g++ K Ia+eLglS TV+ h N +KlG+ P27667|rev 137 PLTKRERQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLLEKLGV 182 -* P27667|rev - - P26319|reviewed|Fimbriae: domain 1 of 1, from 146 to 193: score 31.5, E = 2.7e-11 *->hhcPLsaREvdVLrrLaegKvYKQIaleLglStSTVRthlHNvygKl h PLs+REv VLr La g+ K Ia +L lS T+ h+ N+ +Kl P26319|rev 146 HDMPLSNREVTVLRYLANGMSNKEIAEQLLLSNKTISAHKANIFSKL 192 G<-* G P26319|rev 193 G 193 P55184|reviewed|Uncharacterized: domain 1 of 1, from 158 to 211: score 30.5, E = 5.2e-11 *->saREvdVLrrLaegKvYKQIaleLglStSTVRthlHNvygKlGAvDR ++RE++VL+++a g + +Ia +L S+STV th H + +K +A+DR P55184|rev 158 TKRELEVLQQMAYGLRNEDIAEKLFVSESTVKTHVHRILQKCNAQDR 204 AQAVLiA<-* QAV A P55184|rev 205 TQAVVFA 211 P56644|reviewed|Probable: domain 1 of 1, from 148 to 202: score 25.2, E = 2.4e-09 *->LsaREvdVLrrLaegKvYKQIaleLglStSTVRthlHNvygKlGAvD L+aRE + L La g QIa+ g S TV hl N y KlG+ P56644|rev 148 LTARERELLAALANGWTNLQIAARTGISRNTVKYHLKNLYDKLGVSN 194 RAQAVLiA<-* RA+AV + P56644|rev 195 RAMAVALH 202 O07528|reviewed|Uncharacterized: domain 1 of 1, from 149 to 203: score 23.7, E = 7.1e-09 *->LsaREvdVLrrLaegKvYKQIaleLglStSTVRthlHNvygKlGAvD L++RE dVL + a gK K Ia+ L S+ TV th N +Kl ++D O07528|rev 149 LTRREKDVLTEIANGKSNKEIAAALFISEKTVKTHVSNLLAKLEVAD 195 RAQAVLiA<-* R QA L A O07528|rev 196 RTQAALFA 203 P0AEL8|reviewed|Fimbriae: domain 1 of 1, from 150 to 193: score 21.7, E = 3.1e-08 *->LsaREvdVLrrLaegKvYKQIaleLglStSTVRthlHNvygKlG<-* Ls+REv Lr L g K Ia +L lS TV h+ N+ygKlG P0AEL8|rev 150 LSNREVTILRYLVSGLSNKEIADKLLLSNKTVSAHKSNIYGKLG 193 P0AEL9|reviewed|Fimbriae: domain 1 of 1, from 150 to 193: score 21.7, E = 3.1e-08 *->LsaREvdVLrrLaegKvYKQIaleLglStSTVRthlHNvygKlG<-* Ls+REv Lr L g K Ia +L lS TV h+ N+ygKlG P0AEL9|rev 150 LSNREVTILRYLVSGLSNKEIADKLLLSNKTVSAHKSNIYGKLG 193 P31802|reviewed|Nitrate/nitrite: domain 1 of 1, from 154 to 185: score 21.2, E = 4.3e-08 *->LsaREvdVLrrLaegKvYKQIaleLglStSTV<-* L++RE+dVL +La+g KQIa+ L S+ TV P31802|rev 154 LTERELDVLHELAQGLSNKQIASVLNISEQTV 185 P0A4H3|reviewed|Virulence: domain 1 of 1, from 149 to 180: score 20.9, E = 5.4e-08 *->LsaREvdVLrrLaegKvYKQIaleLglStSTV<-* Ls+RE+ VL++La+g+ K+Ia + lS TV P0A4H3|rev 149 LSNRELTVLQLLAQGMSNKDIADSMFLSNKTV 180 P0A4H2|reviewed|Virulence: domain 1 of 1, from 149 to 180: score 20.9, E = 5.4e-08 *->LsaREvdVLrrLaegKvYKQIaleLglStSTV<-* Ls+RE+ VL++La+g+ K+Ia + lS TV P0A4H2|rev 149 LSNRELTVLQLLAQGMSNKDIADSMFLSNKTV 180 P0A4H4|reviewed|Virulence: domain 1 of 1, from 149 to 180: score 20.9, E = 5.4e-08 *->LsaREvdVLrrLaegKvYKQIaleLglStSTV<-* Ls+RE+ VL++La+g+ K+Ia + lS TV P0A4H4|rev 149 LSNRELTVLQLLAQGMSNKDIADSMFLSNKTV 180 Histogram of all scores: score obs exp (one = represents 1 sequences) ----- --- --- -13 8 3|==*===== -12 9 29|========= * -11 12 63|============ * -10 13 65|============= * -9 9 46|========= * -8 3 26|=== * -7 6 14|====== * -6 9 7|======*== -5 5 3|==*== -4 10 1|*========= -3 0 0| -2 6 0|====== -1 2 0|== 0 4 0|==== 1 2 0|== 2 4 0|==== 3 11 0|=========== 4 12 0|============ 5 15 0|=============== 6 21 0|===================== 7 13 0|============= 8 2 0|== 9 30 0|============================== 10 9 0|========= 11 2 0|== 12 19 0|=================== 13 4 0|==== 14 1 0|= 15 0 0| 16 3 0|=== 17 0 0| 18 2 0|== 19 2 0|== 20 3 0|=== 21 3 0|=== 22 0 0| 23 1 0|= 24 0 0| > 25 9 -|========= % Statistical details of theoretical EVD fit: mu = -9.9953 lambda = 0.7217 chi-sq statistic = 133.1386 P(chi-square) = 4.343e+08 Total sequences searched: 264 Whole sequence top hits: tophits_s report: Total hits: 16 Satisfying E cutoff: 16 Total memory: 21K Domain top hits: tophits_s report: Total hits: 16 Satisfying E cutoff: 16 Total memory: 26K