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= 0013.0004.p (873 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF 2,715,099 sequences; 757,237,578 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value ref|NP_387936.1| transcription-repair coupling factor [Bacillus ... 1061 0.0 ref|NP_976379.1| transcription-repair coupling factor [Bacillus ... 1051 0.0 ref|NP_829955.1| Transcription-repair coupling factor [Bacillus ... 1051 0.0 ref|NP_654001.1| DEAD, DEAD/DEAH box helicase [Bacillus anthraci... 1051 0.0 ref|NP_690984.1| transcription-repair coupling factor [Oceanobac... 1039 0.0 >ref|NP_387936.1| transcription-repair coupling factor [Bacillus subtilis] sp|P37474|MFD_BACSU Transcription-repair coupling factor (TRCF) pir||S66085 transcription-repair coupling factor mfd - Bacillus subtilis dbj|BAA05290.1| transcription-repair coupling factor [Bacillus subtilis] emb|CAB11831.1| transcription-repair coupling factor [Bacillus subtilis subsp. subtilis str. 168] Length = 1177 Score = 1061 bits (2743), Expect = 0.0, Method: Compositional matrix adjust. Identities = 529/842 (62%), Positives = 645/842 (76%), Gaps = 19/842 (2%) Query: 4 DTLLVLDEPARLLETAKQLERDESEWNLHLLQNGKTLPDLQLSVESDAVMYQRPFQSLFM 63 +TLL+LDE +R+ E +QL+++E+E+ +LL+ GK L D++LS ++ ++ L+ Sbjct: 304 NTLLILDEVSRIHEMEEQLQKEEAEFITNLLEEGKILHDIRLSFSFQKIVAEQKRPLLYY 363 Query: 64 SIFLRQVPHIQPQNILGFISRGMQDFHGQMNVLKSEMERWHKSGVKVIMLANGEERMERV 123 S+FLR V H PQNI+ R MQ FHGQMNVL EMER+ KS V+ L +ER +++ Sbjct: 364 SLFLRHVHHTSPQNIVNVSGRQMQSFHGQMNVLAGEMERFKKSNFTVVFLGANKERTQKL 423 Query: 124 RRVLYDYGIEEPT-------------ILQGNLGSGFELPSIHLAVITEGEMFSQKQRKAR 170 VL DY IE I++G L SGFELP + LAVITE E+F + +K Sbjct: 424 SSVLADYDIEAAMTDSKKALVQGQVYIMEGELQSGFELPLMKLAVITEEELFKNRVKKKP 483 Query: 171 KVSKGIDNAERIKSYTELKIGDYVVHQNHGIGKYMGIGTLEVSGIHRDYMHILYAGGDKL 230 + K + NAERIKSY+EL+IGDYVVH NHGIGKY+GI TLE++GIH+DY++I Y G DKL Sbjct: 484 RKQK-LTNAERIKSYSELQIGDYVVHINHGIGKYLGIETLEINGIHKDYLNIHYQGSDKL 542 Query: 231 SVPIDQIDLIQKYVGSEDKEPKVYKLGGNEWTRVTSKVRSSVQDIADDLIKLYAERQSAL 290 VP++QID +QKYVGSE KEPK+YKLGG+EW RV KV +SVQDIADDLIKLYAER+++ Sbjct: 543 YVPVEQIDQVQKYVGSEGKEPKLYKLGGSEWKRVKKKVETSVQDIADDLIKLYAEREASK 602 Query: 291 GYGFEKDTQEQREFEEMFPYEETRDQLRAIEEIKKDMEQNRPMDRLLCGDVGYGKTEVAI 350 GY F D + QREFE FPY+ET DQLR+I EIKKDME+ RPMDRLLCGDVGYGKTEVAI Sbjct: 603 GYAFSPDHEMQREFESAFPYQETEDQLRSIHEIKKDMERERPMDRLLCGDVGYGKTEVAI 662 Query: 351 RAAFKSAIEGKQVAVLVPTTILAQQHYETFRERFANYPLNIQVLSRFRSRKEQNETIKGV 410 RAAFK+ +GKQVA+LVPTTILAQQHYET +ERF +YP+NI +LSRFR+RKE NETIKG+ Sbjct: 663 RAAFKAIGDGKQVALLVPTTILAQQHYETIKERFQDYPINIGLLSRFRTRKEANETIKGL 722 Query: 411 RQGTVDVVIGTHRLLSQDMVFKDLGLLIVDEEQRFGVTHKEKLKKLKTNVDVLTLTATPI 470 + GTVD+VIGTHRLLS+D+V+KDLGLLI+DEEQRFGVTHKEK+K++K NVDVLTLTATPI Sbjct: 723 KNGTVDIVIGTHRLLSKDVVYKDLGLLIIDEEQRFGVTHKEKIKQIKANVDVLTLTATPI 782 Query: 471 PRTLHMSMLGVRDLSVIETPPENRFPVQTYVVEHSQTLIREAVERELARGGQVYYLYNRV 530 PRTLHMSMLGVRDLSVIETPPENRFPVQTYVVE++ L+REA+ERELARGGQVY+LYNRV Sbjct: 783 PRTLHMSMLGVRDLSVIETPPENRFPVQTYVVEYNGALVREAIERELARGGQVYFLYNRV 842 Query: 531 QGIQEMAAQISMLVPEARVGIGHGQMSESELEKTILDFLDGEYDVLVSTSIIETGVDIPN 590 + I+ A +ISMLVP+A+V HG+M+E+ELE +L FL+GE DVLVST+IIETGVDIPN Sbjct: 843 EDIERKADEISMLVPDAKVAYAHGKMTENELETVMLSFLEGESDVLVSTTIIETGVDIPN 902 Query: 591 VNTLIVHDADKMGLSQLYQLRGRVGRSNRIAYAYFTYQRDKVLTEVAEKRLQSIKEFTEL 650 VNTLIV DADKMGLSQLYQLRGRVGRSNR+AYAYFTY+RDKVLTEVAEKRLQ+IKEFTEL Sbjct: 903 VNTLIVFDADKMGLSQLYQLRGRVGRSNRVAYAYFTYRRDKVLTEVAEKRLQAIKEFTEL 962 Query: 651 GSGFKIAMRDLSIRGAGNLLGAEQHGFIASVGFDLYSQMLAEEIRKRKVSVLGEEDTSLK 710 GSGFKIAMRDL+IRGAGNLLGA+QHGFI SVGFDLYSQML E I +RK E Sbjct: 963 GSGFKIAMRDLTIRGAGNLLGAQQHGFIDSVGFDLYSQMLKEAIEERKGDTAKTE----- 1017 Query: 711 QGNTVIDLSIDAYLPSEYIYDSIQKIEIYKKXXXXXXXXXXXXXXXXXXXRFGELPEAVV 770 Q T ID+ +DAY+P YI D QKI++YK+ RFG P+ V Sbjct: 1018 QFETEIDVELDAYIPETYIQDGKQKIDMYKRFRSVATIEEKNELQDEMIDRFGNYPKEVE 1077 Query: 771 NLLTVARLKVYGKLYGMESMVRRGDEVSLNFHEGSTGAFDTAKLAKVGNSFERRVQFDRD 830 L TVA +KVY + +E + + D V L E ++ D KL ++GN + R++ + Sbjct: 1078 YLFTVAEMKVYARQERVELIKQDKDAVRLTISEEASAEIDGQKLFELGNQYGRQIGLGME 1137 Query: 831 AK 832 K Sbjct: 1138 GK 1139 >ref|NP_976379.1| transcription-repair coupling factor [Bacillus cereus ATCC 10987] gb|AAS38987.1| transcription-repair coupling factor [Bacillus cereus ATCC 10987] Length = 1176 Score = 1051 bits (2719), Expect = 0.0, Method: Compositional matrix adjust. Identities = 518/838 (61%), Positives = 650/838 (77%), Gaps = 19/838 (2%) Query: 1 MAQDTLLVLDEPARLLETAKQLERDESEWNLHLLQNGKTLPDLQLSVESDAVMYQRPFQS 60 + +D +++LDE +R+ ETA LE +E+EW + LL G + DL S + ++ + Sbjct: 301 LPEDGVVILDEISRIQETASHLETEEAEWYISLLGEGTIIQDLSFSHSFEEFLHHKKRSF 360 Query: 61 LFMSIFLRQVPHIQPQNILGFISRGMQDFHGQMNVLKSEMERWHKSGVKVIMLANGEERM 120 +++++FLR + H PQNI+ + MQDFHGQM +LK+E++RW++ ++L +ER+ Sbjct: 361 VYLTLFLRHIAHTHPQNIVNVTCKTMQDFHGQMQLLKTEIDRWNEGHFTTVVLGTDDERV 420 Query: 121 ERVRRVLYDYGIEE----------PTILQ---GNLGSGFELPSIHLAVITEGEMFSQKQR 167 ++++ +L DY IE P LQ G+L +GFE+P L VITE E+F +K + Sbjct: 421 KKLQHILSDYDIEADIVEGTDILLPGRLQIAVGDLHAGFEMPMQKLVVITEKELFHKKVK 480 Query: 168 KARKVSKGIDNAERIKSYTELKIGDYVVHQNHGIGKYMGIGTLEVSGIHRDYMHILYAGG 227 K+++ K + NAERIKSY+ELK+GDYVVH NHGIGK++GI TLE++G+H+DY++I Y G Sbjct: 481 KSQRKQK-LSNAERIKSYSELKVGDYVVHVNHGIGKFLGIETLEINGVHKDYLNIKYQGN 539 Query: 228 DKLSVPIDQIDLIQKYVGSEDKEPKVYKLGGNEWTRVTSKVRSSVQDIADDLIKLYAERQ 287 DKL VPI+QID +QKYVGSE K+PKVYKLGGN+W +V +KV SVQDIADDLIKLYAER+ Sbjct: 540 DKLYVPIEQIDQVQKYVGSEGKDPKVYKLGGNDWKKVKTKVEKSVQDIADDLIKLYAERE 599 Query: 288 SALGYGFEKDTQEQREFEEMFPYEETRDQLRAIEEIKKDMEQNRPMDRLLCGDVGYGKTE 347 ++ GY + DT EQ+EFE FPY+ET DQLR+IEEIKKDME+ RPMDRLLCGDVGYGKTE Sbjct: 600 ASKGYAYTPDTAEQQEFESSFPYQETEDQLRSIEEIKKDMERGRPMDRLLCGDVGYGKTE 659 Query: 348 VAIRAAFKSAIEGKQVAVLVPTTILAQQHYETFRERFANYPLNIQVLSRFRSRKEQNETI 407 VAIRAAFK+ ++ KQVA+LVPTTILAQQHYET RERF +YP+NI +LSRFR+RK+QNETI Sbjct: 660 VAIRAAFKAIMDEKQVAILVPTTILAQQHYETIRERFQDYPINIGLLSRFRTRKQQNETI 719 Query: 408 KGVRQGTVDVVIGTHRLLSQDMVFKDLGLLIVDEEQRFGVTHKEKLKKLKTNVDVLTLTA 467 KG++ GTVD+VIGTHR+LS+D+ +KDLGLLI+DEEQRFGVTHKEK+K+LK NVDVLTLTA Sbjct: 720 KGLKDGTVDIVIGTHRILSKDVTYKDLGLLIIDEEQRFGVTHKEKIKQLKANVDVLTLTA 779 Query: 468 TPIPRTLHMSMLGVRDLSVIETPPENRFPVQTYVVEHSQTLIREAVERELARGGQVYYLY 527 TPIPRTLHMSMLGVRDLSVIETPPENRFPVQTYVVE++ L+REA+ERELARGGQVY+LY Sbjct: 780 TPIPRTLHMSMLGVRDLSVIETPPENRFPVQTYVVEYNPALMREAIERELARGGQVYFLY 839 Query: 528 NRVQGIQEMAAQISMLVPEARVGIGHGQMSESELEKTILDFLDGEYDVLVSTSIIETGVD 587 NRV+ I+ A +ISMLVP+ARV HG+M+ESELE +L FL+G++DVLVST+IIETGVD Sbjct: 840 NRVEDIERKADEISMLVPDARVTYAHGKMNESELESVMLSFLEGQHDVLVSTTIIETGVD 899 Query: 588 IPNVNTLIVHDADKMGLSQLYQLRGRVGRSNRIAYAYFTYQRDKVLTEVAEKRLQSIKEF 647 IPNVNTLIV DAD+MGLSQLYQLRGRVGRSNR+AYAYF Y+RDKVL+EVAEKRLQ+IKEF Sbjct: 900 IPNVNTLIVFDADRMGLSQLYQLRGRVGRSNRVAYAYFAYKRDKVLSEVAEKRLQAIKEF 959 Query: 648 TELGSGFKIAMRDLSIRGAGNLLGAEQHGFIASVGFDLYSQMLAEEIRKRKVSVLGEEDT 707 TELGSGFKIAMRDLSIRGAGNLLGAEQHGFI SVGFDLYSQML + I +R+ G E+T Sbjct: 960 TELGSGFKIAMRDLSIRGAGNLLGAEQHGFIDSVGFDLYSQMLKDAIEQRR-GTDGVENT 1018 Query: 708 SLKQGNTVIDLSIDAYLPSEYIYDSIQKIEIYKKXXXXXXXXXXXXXXXXXXXRFGELPE 767 N IDL +DAYLP YI DS QKI +YK+ RFG+ P+ Sbjct: 1019 V----NVEIDLEVDAYLPDAYISDSKQKIMMYKQFRGVSAIEDIEELQEEMIDRFGDYPQ 1074 Query: 768 AVVNLLTVARLKVYGKLYGMESMVRRGDEVSLNFHEGSTGAFDTAKLAKVGNSFERRV 825 V LL +A +KV +E + + EV++ F E ++ D KL +GNSF R + Sbjct: 1075 EVGYLLQIANIKVLAMKEQIELIKQNKFEVTILFSEQASQNIDGGKLFMLGNSFGRMI 1132 >ref|NP_829955.1| Transcription-repair coupling factor [Bacillus cereus ATCC 14579] gb|AAP07156.1| Transcription-repair coupling factor [Bacillus cereus ATCC 14579] Length = 1176 Score = 1051 bits (2719), Expect = 0.0, Method: Compositional matrix adjust. Identities = 516/838 (61%), Positives = 649/838 (77%), Gaps = 19/838 (2%) Query: 1 MAQDTLLVLDEPARLLETAKQLERDESEWNLHLLQNGKTLPDLQLSVESDAVMYQRPFQS 60 + +D +++LDE +R+ ETA LE +E+EW + LL G + DL S + ++ + Sbjct: 301 LPEDGVVILDEISRIQETASHLETEEAEWYISLLGEGTIIQDLSFSHPFEGFLHHKKRSF 360 Query: 61 LFMSIFLRQVPHIQPQNILGFISRGMQDFHGQMNVLKSEMERWHKSGVKVIMLANGEERM 120 +++++FLR + H PQNI+ + MQDFHGQMN+LK+E++RW++ ++L +ER+ Sbjct: 361 VYLTLFLRHIAHTHPQNIVNVTCKTMQDFHGQMNLLKTEIDRWNEGHFTTVVLGTDDERV 420 Query: 121 ERVRRVLYDYGIEE----------PTILQ---GNLGSGFELPSIHLAVITEGEMFSQKQR 167 ++++ +L DY IE P LQ G+L +GFE+P L VITE E+F +K + Sbjct: 421 KKLQHILSDYDIEADIVEGTDILLPGRLQIAVGDLHAGFEMPMQKLVVITEKELFHKKVK 480 Query: 168 KARKVSKGIDNAERIKSYTELKIGDYVVHQNHGIGKYMGIGTLEVSGIHRDYMHILYAGG 227 K+++ K + NAERIKSY+ELK+GDYVVH NHGIGK++GI TLE++G+H+DY++I Y G Sbjct: 481 KSQRKQK-LSNAERIKSYSELKVGDYVVHVNHGIGKFLGIETLEINGVHKDYLNIKYQGN 539 Query: 228 DKLSVPIDQIDLIQKYVGSEDKEPKVYKLGGNEWTRVTSKVRSSVQDIADDLIKLYAERQ 287 DKL VPI+QID +QKYVGSE K+PKVYKLGGN+W +V +KV SVQDIADDLIKLYAER+ Sbjct: 540 DKLYVPIEQIDQVQKYVGSEGKDPKVYKLGGNDWKKVKTKVEKSVQDIADDLIKLYAERE 599 Query: 288 SALGYGFEKDTQEQREFEEMFPYEETRDQLRAIEEIKKDMEQNRPMDRLLCGDVGYGKTE 347 ++ GY + DT EQ+EFE FPY+ET DQLR+I+EIKKDME+ RPMDRLLCGDVGYGKTE Sbjct: 600 ASKGYAYTPDTAEQQEFESSFPYQETEDQLRSIDEIKKDMERGRPMDRLLCGDVGYGKTE 659 Query: 348 VAIRAAFKSAIEGKQVAVLVPTTILAQQHYETFRERFANYPLNIQVLSRFRSRKEQNETI 407 VAIRAAFK+ ++ KQVA+LVPTTILAQQHYET RERF +YP+NI +LSRFR+RK+QNETI Sbjct: 660 VAIRAAFKAIMDEKQVAILVPTTILAQQHYETIRERFQDYPINIGLLSRFRTRKQQNETI 719 Query: 408 KGVRQGTVDVVIGTHRLLSQDMVFKDLGLLIVDEEQRFGVTHKEKLKKLKTNVDVLTLTA 467 KG++ GTVD+VIGTHR+LS+D+ +KDLGLLI+DEEQRFGVTHKEK+K+LK NVDVLTLTA Sbjct: 720 KGLKDGTVDIVIGTHRILSKDVTYKDLGLLIIDEEQRFGVTHKEKIKQLKANVDVLTLTA 779 Query: 468 TPIPRTLHMSMLGVRDLSVIETPPENRFPVQTYVVEHSQTLIREAVERELARGGQVYYLY 527 TPIPRTLHMSMLGVRDLSVIETPPENRFPVQTYVVE++ L+REA+ERELARGGQVY+LY Sbjct: 780 TPIPRTLHMSMLGVRDLSVIETPPENRFPVQTYVVEYNPALMREAIERELARGGQVYFLY 839 Query: 528 NRVQGIQEMAAQISMLVPEARVGIGHGQMSESELEKTILDFLDGEYDVLVSTSIIETGVD 587 NRV+ I+ A +ISMLVP+ARV HG+M+ESELE +L FL+G++DVLVST+IIETGVD Sbjct: 840 NRVEDIERKADEISMLVPDARVTYAHGKMNESELESVMLSFLEGQHDVLVSTTIIETGVD 899 Query: 588 IPNVNTLIVHDADKMGLSQLYQLRGRVGRSNRIAYAYFTYQRDKVLTEVAEKRLQSIKEF 647 IPNVNTLIV DAD+MGLSQLYQLRGRVGRSNR+AYAYF Y+RDKVL+EVAEKRLQ+IKEF Sbjct: 900 IPNVNTLIVFDADRMGLSQLYQLRGRVGRSNRVAYAYFAYKRDKVLSEVAEKRLQAIKEF 959 Query: 648 TELGSGFKIAMRDLSIRGAGNLLGAEQHGFIASVGFDLYSQMLAEEIRKRKVSVLGEEDT 707 TELGSGFKIAMRDLSIRGAGNLLGAEQHGFI SVGFDLYSQML + I +R+ + D Sbjct: 960 TELGSGFKIAMRDLSIRGAGNLLGAEQHGFIDSVGFDLYSQMLKDAIEQRRGT-----DG 1014 Query: 708 SLKQGNTVIDLSIDAYLPSEYIYDSIQKIEIYKKXXXXXXXXXXXXXXXXXXXRFGELPE 767 + N IDL +DAYLP YI DS QKI +YK+ RFG+ P+ Sbjct: 1015 AENIVNVEIDLEVDAYLPDAYISDSKQKIMMYKQFRGVSAIEDIEELQEEMIDRFGDYPQ 1074 Query: 768 AVVNLLTVARLKVYGKLYGMESMVRRGDEVSLNFHEGSTGAFDTAKLAKVGNSFERRV 825 V LL +A +KV +E + + EV+ F E ++ D KL +GNSF R + Sbjct: 1075 EVGYLLQIANIKVLAMKEQIELIKQNKFEVTFLFSEQASQNIDGGKLFMLGNSFGRMI 1132 >ref|NP_654001.1| DEAD, DEAD/DEAH box helicase [Bacillus anthracis A2012] ref|NP_842621.1| transcription-repair coupling factor [Bacillus anthracis str. Ames] gb|AAP24107.1| transcription-repair coupling factor [Bacillus anthracis str. Ames] Length = 1176 Score = 1051 bits (2717), Expect = 0.0, Method: Compositional matrix adjust. Identities = 517/838 (61%), Positives = 650/838 (77%), Gaps = 19/838 (2%) Query: 1 MAQDTLLVLDEPARLLETAKQLERDESEWNLHLLQNGKTLPDLQLSVESDAVMYQRPFQS 60 + +D +++LDE +R+ ETA LE +E+EW + LL G + DL S + ++ + Sbjct: 301 LPEDGVVILDEISRIQETASHLESEEAEWYISLLGEGTIIQDLSFSHSFEEFLHHKKRSF 360 Query: 61 LFMSIFLRQVPHIQPQNILGFISRGMQDFHGQMNVLKSEMERWHKSGVKVIMLANGEERM 120 +++++FLR + H PQNI+ + MQDFHGQM +LK+E++RW++ ++L +ER+ Sbjct: 361 VYLTLFLRHIAHTHPQNIVNVTCKTMQDFHGQMQLLKTEIDRWNEGHFTTVVLGTDDERV 420 Query: 121 ERVRRVLYDYGIEE----------PTILQ---GNLGSGFELPSIHLAVITEGEMFSQKQR 167 ++++ +L DY I+ P LQ G+L +GFE+P L VITE E+F +K + Sbjct: 421 KKLQHILSDYDIDADIVEGTDILLPGRLQIAVGDLHAGFEMPMQKLVVITEKELFHKKVK 480 Query: 168 KARKVSKGIDNAERIKSYTELKIGDYVVHQNHGIGKYMGIGTLEVSGIHRDYMHILYAGG 227 K+++ K + NAERIKSY+ELK+GDYVVH NHGIGK++GI TLE++G+H+DY++I Y G Sbjct: 481 KSQRKQK-LSNAERIKSYSELKVGDYVVHVNHGIGKFLGIETLEINGVHKDYLNIKYQGN 539 Query: 228 DKLSVPIDQIDLIQKYVGSEDKEPKVYKLGGNEWTRVTSKVRSSVQDIADDLIKLYAERQ 287 DKL VPI+QID +QKYVGSE K+PKVYKLGGN+W +V +KV SVQDIADDLIKLYAER+ Sbjct: 540 DKLYVPIEQIDQVQKYVGSEGKDPKVYKLGGNDWKKVKTKVEKSVQDIADDLIKLYAERE 599 Query: 288 SALGYGFEKDTQEQREFEEMFPYEETRDQLRAIEEIKKDMEQNRPMDRLLCGDVGYGKTE 347 ++ GY + DT EQ+EFE FPY+ET DQLR+IEEIKKDME+ RPMDRLLCGDVGYGKTE Sbjct: 600 ASKGYAYTPDTAEQQEFESSFPYQETEDQLRSIEEIKKDMERGRPMDRLLCGDVGYGKTE 659 Query: 348 VAIRAAFKSAIEGKQVAVLVPTTILAQQHYETFRERFANYPLNIQVLSRFRSRKEQNETI 407 VAIRAAFK+ ++ KQVA+LVPTTILAQQHYET RERF +YP+NI +LSRFR+RK+QNETI Sbjct: 660 VAIRAAFKAIMDEKQVAILVPTTILAQQHYETIRERFQDYPINIGLLSRFRTRKQQNETI 719 Query: 408 KGVRQGTVDVVIGTHRLLSQDMVFKDLGLLIVDEEQRFGVTHKEKLKKLKTNVDVLTLTA 467 KG++ GTVD+VIGTHR+LS+D+ +KDLGLLI+DEEQRFGVTHKEK+K+LK NVDVLTLTA Sbjct: 720 KGLKDGTVDIVIGTHRILSKDVTYKDLGLLIIDEEQRFGVTHKEKIKQLKANVDVLTLTA 779 Query: 468 TPIPRTLHMSMLGVRDLSVIETPPENRFPVQTYVVEHSQTLIREAVERELARGGQVYYLY 527 TPIPRTLHMSMLGVRDLSVIETPPENRFPVQTYVVE++ L+REA+ERELARGGQVY+LY Sbjct: 780 TPIPRTLHMSMLGVRDLSVIETPPENRFPVQTYVVEYNPALMREAIERELARGGQVYFLY 839 Query: 528 NRVQGIQEMAAQISMLVPEARVGIGHGQMSESELEKTILDFLDGEYDVLVSTSIIETGVD 587 NRV+ I+ A +ISMLVP+ARV HG+M+ESELE +L FL+G++DVLVST+IIETGVD Sbjct: 840 NRVEDIERKADEISMLVPDARVTYAHGKMNESELESVMLSFLEGQHDVLVSTTIIETGVD 899 Query: 588 IPNVNTLIVHDADKMGLSQLYQLRGRVGRSNRIAYAYFTYQRDKVLTEVAEKRLQSIKEF 647 IPNVNTLIV DAD+MGLSQLYQLRGRVGRSNR+AYAYF Y+RDKVL+EVAEKRLQ+IKEF Sbjct: 900 IPNVNTLIVFDADRMGLSQLYQLRGRVGRSNRVAYAYFAYKRDKVLSEVAEKRLQAIKEF 959 Query: 648 TELGSGFKIAMRDLSIRGAGNLLGAEQHGFIASVGFDLYSQMLAEEIRKRKVSVLGEEDT 707 TELGSGFKIAMRDLSIRGAGNLLGAEQHGFI SVGFDLYSQML + I +R+ G E+T Sbjct: 960 TELGSGFKIAMRDLSIRGAGNLLGAEQHGFIDSVGFDLYSQMLKDAIEQRR-GTDGVENT 1018 Query: 708 SLKQGNTVIDLSIDAYLPSEYIYDSIQKIEIYKKXXXXXXXXXXXXXXXXXXXRFGELPE 767 N IDL +DAYLP YI DS QKI +YK+ RFG+ P+ Sbjct: 1019 V----NVEIDLEVDAYLPDAYISDSKQKIMMYKQFRGVSAIEDIEELQEEMIDRFGDYPQ 1074 Query: 768 AVVNLLTVARLKVYGKLYGMESMVRRGDEVSLNFHEGSTGAFDTAKLAKVGNSFERRV 825 V LL +A +KV +E + + EV++ F E ++ D KL +GNSF R + Sbjct: 1075 EVGYLLQIANIKVLAMKEQIELIKQNKFEVTILFSEQASQNIDGGKLFMLGNSFGRMI 1132 >ref|NP_690984.1| transcription-repair coupling factor [Oceanobacillus iheyensis HTE831] dbj|BAC12019.1| transcription-repair coupling factor (TRCF) [Oceanobacillus iheyensis HTE831] Length = 1173 Score = 1039 bits (2687), Expect = 0.0, Method: Compositional matrix adjust. Identities = 506/843 (60%), Positives = 634/843 (75%), Gaps = 17/843 (2%) Query: 1 MAQDTLLVLDEPARLLETAKQLERDESEWNLHLLQNGKTLPDLQLSVESDAVMYQRPFQS 60 + + L+ DE +R+ ETA L+ +E+EW LL+ K + + + S D VM Q Sbjct: 301 LPSNGLVFFDEMSRIGETATNLDHEEAEWYASLLEGNKMVQNSRFSFSWDEVMEGMNQQR 360 Query: 61 LFMSIFLRQVPHIQPQNILGFISRGMQDFHGQMNVLKSEMERWHKSGVKVIMLANGEERM 120 ++MS+F+R +P+ P+N++ SR MQ+FHGQM++ K+E++RW K VI+LA E+R Sbjct: 361 VYMSVFMRHIPNTNPENVINLSSRTMQEFHGQMHLFKNELQRWEKGDYSVIILAADEQRA 420 Query: 121 ERVRRVLYDYGIEE-------------PTILQGNLGSGFELPSIHLAVITEGEMFSQKQR 167 E+V +L DY IE PTI+ GN+ SG E P LAV+TE E+F ++ + Sbjct: 421 EKVHSILDDYDIETQISKKEPVLPVKMPTIIVGNIQSGTEFPMHKLAVVTEQELFKKRMK 480 Query: 168 KARKVSKGIDNAERIKSYTELKIGDYVVHQNHGIGKYMGIGTLEVSGIHRDYMHILYAGG 227 RK K + NAERIKSY ELKIGDYVVH NHG+GKY+GI TLEVS +H+DYM I Y+G Sbjct: 481 HKRKQPK-VSNAERIKSYQELKIGDYVVHANHGVGKYLGIETLEVSNLHKDYMLIKYSGD 539 Query: 228 DKLSVPIDQIDLIQKYVGSEDKEPKVYKLGGNEWTRVTSKVRSSVQDIADDLIKLYAERQ 287 DKL VPIDQIDL+QK+VGSE KEPK+YKLGG EWT+V KV+SSV+DIADDLIKLYAER+ Sbjct: 540 DKLFVPIDQIDLVQKFVGSEAKEPKLYKLGGTEWTKVKRKVQSSVEDIADDLIKLYAERE 599 Query: 288 SALGYGFEKDTQEQREFEEMFPYEETRDQLRAIEEIKKDMEQNRPMDRLLCGDVGYGKTE 347 + GY F D++ Q EFE FPY+ET DQLR I+EIK+DME+ RPMDRLLCGDVGYGKTE Sbjct: 600 AKQGYAFSPDSELQHEFEASFPYQETDDQLRCIQEIKEDMEKERPMDRLLCGDVGYGKTE 659 Query: 348 VAIRAAFKSAIEGKQVAVLVPTTILAQQHYETFRERFANYPLNIQVLSRFRSRKEQNETI 407 VAIRAAFK+ +GKQVA+LVPTTILAQQHYET RERF +YP+NI +LSRFR++K+Q ET Sbjct: 660 VAIRAAFKAISDGKQVAILVPTTILAQQHYETIRERFQDYPINIGLLSRFRTKKQQTETT 719 Query: 408 KGVRQGTVDVVIGTHRLLSQDMVFKDLGLLIVDEEQRFGVTHKEKLKKLKTNVDVLTLTA 467 KG++ G VDVV+GTHR+LS+D+ +KDLGLLIVDEEQRFGV HKEK+K+LKTNVDVLTLTA Sbjct: 720 KGLKSGNVDVVVGTHRILSKDVEYKDLGLLIVDEEQRFGVKHKEKIKQLKTNVDVLTLTA 779 Query: 468 TPIPRTLHMSMLGVRDLSVIETPPENRFPVQTYVVEHSQTLIREAVERELARGGQVYYLY 527 TPIPRTLHMSMLGVRDLSVIETPPENRFP+QTYV E++ +REA+ERE+ RGGQV++LY Sbjct: 780 TPIPRTLHMSMLGVRDLSVIETPPENRFPIQTYVTEYNPIFMREAIEREMGRGGQVFFLY 839 Query: 528 NRVQGIQEMAAQISMLVPEARVGIGHGQMSESELEKTILDFLDGEYDVLVSTSIIETGVD 587 NRV+ I ++A + MLVPEA++ + HGQM+ESELE I FL+GE+D+LVST+IIETGVD Sbjct: 840 NRVESIDKIARDLGMLVPEAKIAVAHGQMNESELENVIFSFLEGEFDILVSTTIIETGVD 899 Query: 588 IPNVNTLIVHDADKMGLSQLYQLRGRVGRSNRIAYAYFTYQRDKVLTEVAEKRLQSIKEF 647 IPNVNTLIV+ AD MGLSQLYQLRGRVGRSNR+AYAYFTYQ+DKVLTEVAEKRLQ+IKEF Sbjct: 900 IPNVNTLIVNHADYMGLSQLYQLRGRVGRSNRVAYAYFTYQKDKVLTEVAEKRLQAIKEF 959 Query: 648 TELGSGFKIAMRDLSIRGAGNLLGAEQHGFIASVGFDLYSQMLAEEIRKRKVSVLGEEDT 707 TELGSGFKIAMRDLSIRG GNLLG++QHGFI SVGFD+YSQML + I RK G+E Sbjct: 960 TELGSGFKIAMRDLSIRGTGNLLGSQQHGFIDSVGFDMYSQMLKDAIDARKA---GKEIE 1016 Query: 708 SLKQGNTVIDLSIDAYLPSEYIYDSIQKIEIYKKXXXXXXXXXXXXXXXXXXXRFGELPE 767 + + L +DAY+P EY+ D QKIEIYK+ RFG+ P+ Sbjct: 1017 EITPFEPELSLKLDAYIPDEYLEDEKQKIEIYKQFQTLDSQEAIGDLKDELIDRFGDYPQ 1076 Query: 768 AVVNLLTVARLKVYGKLYGMESMVRRGDEVSLNFHEGSTGAFDTAKLAKVGNSFERRVQF 827 V +L TV+ +K+Y K +ES++ ++ + E + D +KL + N + R + Sbjct: 1077 EVEHLFTVSEMKMYAKTQRVESILETPKKIEMLIDESRSQEIDGSKLFALANEYGRDIGL 1136 Query: 828 DRD 830 D Sbjct: 1137 GTD 1139 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF Posted date: Mar 24, 2004 1:53 AM Number of letters in database: 757,237,578 Number of sequences in database: 2,715,099 Lambda K H 0.318 0.136 0.376 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 2715099 Number of Hits to DB: 1,161,669,951 Number of extensions: 47220009 Number of successful extensions: 141644 Number of sequences better than 1.0e-05: 1418 Number of HSP's gapped: 139895 Number of HSP's successfully gapped: 1427 Length of query: 873 Length of database: 757,237,578 Length adjustment: 135 Effective length of query: 738 Effective length of database: 390,699,213 Effective search space: 288336019194 Effective search space used: 288336019194 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: 130 (54.7 bits)