BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0586.0013.p (363 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KIG6.1 B3KIG6_9BACI Transcription termination factor NusA 677 0.0 B1DM55.1 B1DM55_9BACL NusA antitermination factor 634 e-180 C0ZF54.1 C0ZF54_BREBN Transcription elongation protein NusA 542 e-152 Q9KA74.1 NUSA_BACHD Transcription elongation protein nusA 530 e-148 Q5WFT9.1 Q5WFT9_BACSK Transcriptional elongation protein 515 e-144 >B3KIG6.1 B3KIG6_9BACI Transcription termination factor NusA Length = 365 Score = 677 bits (1747), Expect = 0.0, Method: Compositional matrix adjust. Identities = 329/363 (90%), Positives = 348/363 (95%) Query: 1 MDFIEAMNELEREKGISKDVLFEAIEAALISSYKRNFNAAQNVRVDMNRNTGVIKVFARK 60 MDFIEAMNELEREKGISKDVLFEAIEAALISSYKRNFN AQNVRVDMNRNTGVIKVFARK Sbjct: 3 MDFIEAMNELEREKGISKDVLFEAIEAALISSYKRNFNTAQNVRVDMNRNTGVIKVFARK 62 Query: 61 LIVEEVLDARTEISLMSAREINPHFQLEDIAELEVTPRDFGRIAAQTAKQVVTQRIREAE 120 LIV+EVLD RTEISL +AREINPHFQ+EDIAE+EVTPRDFGRIAAQTAKQVVTQRIREAE Sbjct: 63 LIVDEVLDPRTEISLHAAREINPHFQIEDIAEIEVTPRDFGRIAAQTAKQVVTQRIREAE 122 Query: 121 RGLIYNAFIDKEDDIVTGLVQRQDMRNIYVDLGKIEAVLPLSELMPGEKFKQSERIKAYI 180 RGLIY+AFIDKEDDIVTG +QRQD+RNIY+DLGKIEA LPL+ELMP EKFK +RIKAYI Sbjct: 123 RGLIYSAFIDKEDDIVTGTLQRQDLRNIYIDLGKIEAALPLTELMPNEKFKHGDRIKAYI 182 Query: 181 TKVENTTKGPQIMLSRSHPGLLKRLFELEVPEIFDGVVEIRSVAREAGFRSKIAVFSRNP 240 TKVENTTKGPQIMLSR+HPGLLKRLFELEVPEIFDGVVEIRSVAREAGFRSKIAV+SRN Sbjct: 183 TKVENTTKGPQIMLSRTHPGLLKRLFELEVPEIFDGVVEIRSVAREAGFRSKIAVYSRND 242 Query: 241 EVDPVGSCVGPRGTRVQTIVTELRGEKIDIVRYSDTVQEYVANALSPSKVLEVQVFEAEK 300 EVDPVGSCVGP+G RVQTIV ELRGEKIDIVRYSD V+EYVANALSPSKVLEVQVFE EK Sbjct: 243 EVDPVGSCVGPKGLRVQTIVNELRGEKIDIVRYSDQVEEYVANALSPSKVLEVQVFEDEK 302 Query: 301 MARVIVPDYQLSLAIGIKGQNARLAAKLTGWKIDIKSESQAEQEYGRPRTSNDEMHQDSV 360 MARVIVPDYQLSLAIGIKGQNARLAAKLTGWKIDIKSESQAEQE+GRP++ + EMHQDSV Sbjct: 303 MARVIVPDYQLSLAIGIKGQNARLAAKLTGWKIDIKSESQAEQEFGRPKSQSGEMHQDSV 362 Query: 361 SID 363 S+D Sbjct: 363 SVD 365 >B1DM55.1 B1DM55_9BACL NusA antitermination factor Length = 365 Score = 634 bits (1635), Expect = e-180, Method: Compositional matrix adjust. Identities = 302/363 (83%), Positives = 344/363 (94%) Query: 1 MDFIEAMNELEREKGISKDVLFEAIEAALISSYKRNFNAAQNVRVDMNRNTGVIKVFARK 60 MDFIEA++E+ER+KGI+K+VL EAIEAALISSYKRNFNAAQNVRVD+NR++GVIKV+ARK Sbjct: 3 MDFIEALSEIERDKGIAKEVLLEAIEAALISSYKRNFNAAQNVRVDINRHSGVIKVYARK 62 Query: 61 LIVEEVLDARTEISLMSAREINPHFQLEDIAELEVTPRDFGRIAAQTAKQVVTQRIREAE 120 +V+EVLD R EI++ ++REINPH+QL+DIA++EVTPRDFGRIAAQTAKQVVTQRIREAE Sbjct: 63 TVVDEVLDPRLEITVDASREINPHYQLDDIADIEVTPRDFGRIAAQTAKQVVTQRIREAE 122 Query: 121 RGLIYNAFIDKEDDIVTGLVQRQDMRNIYVDLGKIEAVLPLSELMPGEKFKQSERIKAYI 180 RGLIYNAFIDKE+DIV G+VQRQD RN++VDLGK+EAVLPL+ELMP +KFK +R+K+YI Sbjct: 123 RGLIYNAFIDKEEDIVNGIVQRQDTRNLFVDLGKVEAVLPLTELMPTDKFKHGDRVKSYI 182 Query: 181 TKVENTTKGPQIMLSRSHPGLLKRLFELEVPEIFDGVVEIRSVAREAGFRSKIAVFSRNP 240 TKVENTTKGPQI+LSR+HPGLLKRLFELEVPEI+DGVVEIRSVAREAGFRSKIAV+SRN Sbjct: 183 TKVENTTKGPQIILSRTHPGLLKRLFELEVPEIYDGVVEIRSVAREAGFRSKIAVYSRNE 242 Query: 241 EVDPVGSCVGPRGTRVQTIVTELRGEKIDIVRYSDTVQEYVANALSPSKVLEVQVFEAEK 300 EVDPVGSCVGP+G RVQTIV EL GEKIDIVR+S++V+EYVANALSPSKVLEV VFE EK Sbjct: 243 EVDPVGSCVGPKGMRVQTIVNELTGEKIDIVRWSESVEEYVANALSPSKVLEVIVFEQEK 302 Query: 301 MARVIVPDYQLSLAIGIKGQNARLAAKLTGWKIDIKSESQAEQEYGRPRTSNDEMHQDSV 360 MARVIVPDYQLSLAIGIKGQNARLAAKLTGWKIDIKSE+QAEQEYGRP+T+ MHQDSV Sbjct: 303 MARVIVPDYQLSLAIGIKGQNARLAAKLTGWKIDIKSETQAEQEYGRPKTTASTMHQDSV 362 Query: 361 SID 363 SID Sbjct: 363 SID 365 >C0ZF54.1 C0ZF54_BREBN Transcription elongation protein NusA Length = 363 Score = 542 bits (1397), Expect = e-152, Method: Compositional matrix adjust. Identities = 264/343 (76%), Positives = 308/343 (89%) Query: 2 DFIEAMNELEREKGISKDVLFEAIEAALISSYKRNFNAAQNVRVDMNRNTGVIKVFARKL 61 DFIEA+ +EREKGI+KDVL EAIEAALIS YKRNFN+AQNVRVD+NR++G+++V+ARK Sbjct: 4 DFIEALEAIEREKGITKDVLIEAIEAALISGYKRNFNSAQNVRVDVNRHSGMVRVYARKS 63 Query: 62 IVEEVLDARTEISLMSAREINPHFQLEDIAELEVTPRDFGRIAAQTAKQVVTQRIREAER 121 +VEEVLD R EIS +A+EI+P+F+LEDI E+EVTPRDFGRIAAQTAKQVVTQRIREAER Sbjct: 64 VVEEVLDPRLEISQEAAQEIDPNFRLEDIVEIEVTPRDFGRIAAQTAKQVVTQRIREAER 123 Query: 122 GLIYNAFIDKEDDIVTGLVQRQDMRNIYVDLGKIEAVLPLSELMPGEKFKQSERIKAYIT 181 GLIY+ FI++EDDIVTG+VQR D RN Y+DLGK EAV+P++E MP E FK +R+KAYI Sbjct: 124 GLIYSEFIEREDDIVTGVVQRMDARNYYIDLGKAEAVMPITEKMPSEDFKSQDRVKAYII 183 Query: 182 KVENTTKGPQIMLSRSHPGLLKRLFELEVPEIFDGVVEIRSVAREAGFRSKIAVFSRNPE 241 KVE TTKGPQI++SR+HPGLLKRLFELEVPEI+DGVVEI+SVAREAG RSKIAV S N + Sbjct: 184 KVEKTTKGPQIVVSRTHPGLLKRLFELEVPEIYDGVVEIKSVAREAGDRSKIAVHSINAD 243 Query: 242 VDPVGSCVGPRGTRVQTIVTELRGEKIDIVRYSDTVQEYVANALSPSKVLEVQVFEAEKM 301 VDPVG+CVGP+G RVQTIVTEL+GEKIDIVR+S+ EYVANALSP+KVL V+V AEK+ Sbjct: 244 VDPVGACVGPKGMRVQTIVTELKGEKIDIVRWSEDPAEYVANALSPAKVLHVEVNVAEKV 303 Query: 302 ARVIVPDYQLSLAIGIKGQNARLAAKLTGWKIDIKSESQAEQE 344 RVIVPDYQLSLAIG +GQNARLAAKLTGWKIDIKSESQA+QE Sbjct: 304 TRVIVPDYQLSLAIGKRGQNARLAAKLTGWKIDIKSESQADQE 346 >Q9KA74.1 NUSA_BACHD Transcription elongation protein nusA Length = 382 Score = 530 bits (1364), Expect = e-148, Method: Compositional matrix adjust. Identities = 256/345 (74%), Positives = 305/345 (88%), Gaps = 1/345 (0%) Query: 2 DFIEAMNELEREKGISKDVLFEAIEAALISSYKRNFNAAQNVRVDMNRNTGVIKVFARKL 61 +F++A+ LE+EKGISK+V+ EAIEAALIS YKRNFN AQNVRVD+NR G I+VFARK Sbjct: 4 EFMDALTTLEKEKGISKEVIIEAIEAALISGYKRNFNQAQNVRVDVNRENGSIRVFARKE 63 Query: 62 IVEEVLDARTEISLMSAREINPHFQLEDIAELEVTPRDFGRIAAQTAKQVVTQRIREAER 121 +VEEV DAR EISL A+ INP+++++D+ E+EVTP+DFGRIAAQTAKQVVTQR+REAER Sbjct: 64 VVEEVFDARLEISLDEAKGINPNYEVDDVVEIEVTPKDFGRIAAQTAKQVVTQRVREAER 123 Query: 122 GLIYNAFIDKEDDIVTGLVQRQDMRNIYVDLGKIEAVLPLSELMPGEKFKQSERIKAYIT 181 G+IY FID+E+DI+TG+VQRQD R IYVDLGK+EA+LPLSE MP E ++ ++RIKAYIT Sbjct: 124 GIIYADFIDREEDIMTGIVQRQDNRFIYVDLGKVEALLPLSEQMPNESYRHNDRIKAYIT 183 Query: 182 KVENTTKGPQIMLSRSHPGLLKRLFELEVPEIFDGVVEIRSVAREAGFRSKIAVFSRNPE 241 KVE TTKGPQIM+SR+HPGLLKRLFELEVPEI+DG VE++SVAREAG RSKI+V + NPE Sbjct: 184 KVEKTTKGPQIMISRTHPGLLKRLFELEVPEIYDGTVELKSVAREAGDRSKISVHAENPE 243 Query: 242 VDPVGSCVGPRGTRVQTIVTELRGEKIDIVRYSDTVQEYVANALSPSKVLEVQVFEAEKM 301 VDPVG+CVGP+G+RVQTIV EL+GEKIDIVR+S+ EYVANALSPSKV++V V E EK Sbjct: 244 VDPVGACVGPKGSRVQTIVNELKGEKIDIVRWSEDPVEYVANALSPSKVVKVNVNEEEKT 303 Query: 302 ARVIVPDYQLSLAIGIKGQNARLAAKLTGWKIDIKSESQAEQEYG 346 +VIVPDYQLSLAIG +GQNARLAAKLTGWKIDIKSES+A QE G Sbjct: 304 TQVIVPDYQLSLAIGKRGQNARLAAKLTGWKIDIKSESEA-QELG 347 >Q5WFT9.1 Q5WFT9_BACSK Transcriptional elongation protein Length = 368 Score = 515 bits (1326), Expect = e-144, Method: Compositional matrix adjust. Identities = 249/342 (72%), Positives = 297/342 (86%) Query: 2 DFIEAMNELEREKGISKDVLFEAIEAALISSYKRNFNAAQNVRVDMNRNTGVIKVFARKL 61 +F+EA++ LE +KGI K+V+ EAIEAALIS YKRNF AQNVRVD+NR+ G I+VFARK+ Sbjct: 4 EFMEALSTLEADKGIKKEVIIEAIEAALISGYKRNFGQAQNVRVDVNRDNGSIRVFARKV 63 Query: 62 IVEEVLDARTEISLMSAREINPHFQLEDIAELEVTPRDFGRIAAQTAKQVVTQRIREAER 121 +VEEV D R EIS A+ INPH++++DI E+EVTP+DFGRIAAQTAKQVVTQR+REAER Sbjct: 64 VVEEVFDKRLEISEAEAQRINPHYEVDDIVEIEVTPKDFGRIAAQTAKQVVTQRVREAER 123 Query: 122 GLIYNAFIDKEDDIVTGLVQRQDMRNIYVDLGKIEAVLPLSELMPGEKFKQSERIKAYIT 181 G+IY+ FID+E+DI+ G+VQRQD R IYVDLGK+EA+LPLSE MP E +K ++RIKAYIT Sbjct: 124 GIIYSDFIDREEDIMNGIVQRQDHRFIYVDLGKVEALLPLSEQMPNETYKHNDRIKAYIT 183 Query: 182 KVENTTKGPQIMLSRSHPGLLKRLFELEVPEIFDGVVEIRSVAREAGFRSKIAVFSRNPE 241 KVE TTKGPQI++SR+HPGLLKRLFELEVPEI+DG VEI+SV+REAG RSKIAV S NPE Sbjct: 184 KVEKTTKGPQILISRTHPGLLKRLFELEVPEIYDGTVEIKSVSREAGDRSKIAVHSDNPE 243 Query: 242 VDPVGSCVGPRGTRVQTIVTELRGEKIDIVRYSDTVQEYVANALSPSKVLEVQVFEAEKM 301 VD VG+CVG RG RVQTIV EL+GEKIDIV +S+ YVANALSP+KV++V V E EKM Sbjct: 244 VDSVGACVGQRGQRVQTIVDELKGEKIDIVEWSEDPVVYVANALSPAKVMKVNVLEGEKM 303 Query: 302 ARVIVPDYQLSLAIGIKGQNARLAAKLTGWKIDIKSESQAEQ 343 +VIVPDYQLSLAIG +GQNARLAAKLTGWKIDIKSES+A + Sbjct: 304 TQVIVPDYQLSLAIGKRGQNARLAAKLTGWKIDIKSESEARE 345 Database: pfamseq Posted date: Aug 5, 2010 3:22 PM Number of letters in database: 3,060,696,203 Number of sequences in database: 9,421,015 Lambda K H 0.317 0.134 0.362 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 9421015 Number of Hits to DB: 1,850,563,510 Number of extensions: 70117921 Number of successful extensions: 206232 Number of sequences better than 1.0e-05: 1513 Number of HSP's gapped: 204055 Number of HSP's successfully gapped: 1514 Length of query: 363 Length of database: 3,060,696,203 Length adjustment: 137 Effective length of query: 226 Effective length of database: 1,770,017,148 Effective search space: 400023875448 Effective search space used: 400023875448 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 132 (55.5 bits)