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= 0265.0004.p (337 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KFJ9.1 B3KFJ9_9BACI UvrD/Rep helicase family protein 484 e-135 C3AM21.1 C3AM21_BACMY UvrD/Rep helicase 347 7e-94 C3B4A6.1 C3B4A6_BACMY UvrD/Rep helicase 347 7e-94 C2W8S3.1 C2W8S3_BACCE UvrD/Rep helicase 347 9e-94 C3BL40.1 C3BL40_9BACI UvrD/Rep helicase 346 2e-93 >B3KFJ9.1 B3KFJ9_9BACI UvrD/Rep helicase family protein Length = 725 Score = 484 bits (1245), Expect = e-135, Method: Compositional matrix adjust. Identities = 238/318 (74%), Positives = 266/318 (83%), Gaps = 2/318 (0%) Query: 1 LEDNFQSAYQEEEDRLNSALTEIDTVLERLRGIPVYTGHDYTEQALEVSREQRRKDLAKL 60 + ++FQSAYQEEE RLN + EID LERLRGIPVYTGHD+TEQ LE RE++R+ LAK Sbjct: 1 MSESFQSAYQEEESRLNEVIVEIDRQLERLRGIPVYTGHDFTEQVLEAGREEKRQALAKS 60 Query: 61 RQEPYFGRLDFQGKDEDGRKALYIGKIGVDREQVSDRPLVIDWRAPVASLFYSFTGGTEP 120 EPYFGRLDFQ +K LYIGKIG D+ D P+VIDWRAPVASLFYSFTGGT+P Sbjct: 61 LPEPYFGRLDFQENGTGAKKPLYIGKIGFDKADAGDHPMVIDWRAPVASLFYSFTGGTDP 120 Query: 121 ASYEAPEGLIEGLVYLKRNVVIRKQILERVADTYNRDSDGPAVSDEFLVYRLGENKDNRL 180 AS+EAPEG+IEGLVYLKRNVVIRKQILERV+DTYNR+S GPAVSDEFLVYRLGENKDNRL Sbjct: 121 ASFEAPEGIIEGLVYLKRNVVIRKQILERVSDTYNRESGGPAVSDEFLVYRLGENKDNRL 180 Query: 181 RDIVSTIQEEQDKIIRAAKNTALIIQGVAGSGKTTVALHRLAFLLYQYKEQVSAEKMIIF 240 RDIVSTIQ EQDKIIRAAKNTALIIQGVAGSGKTTVALHRLA+LLYQYKEQV+AEKMIIF Sbjct: 181 RDIVSTIQAEQDKIIRAAKNTALIIQGVAGSGKTTVALHRLAYLLYQYKEQVTAEKMIIF 240 Query: 241 APNRMFLDYISDVLPELGVGNIAQSTFPDWAADVLGVVLPEQNAAETMSYWFERE--GGM 298 APN MFLDYISDVLPELGVG+I Q TF DWAA +L + L ++ A+T+ WFE E G Sbjct: 241 APNLMFLDYISDVLPELGVGDIQQRTFGDWAAKLLDIQLSSEDHAQTLHQWFETEPGQGT 300 Query: 299 PEITEETPGRFKGSTALM 316 P+I + GR+KGS LM Sbjct: 301 PDIDDNVSGRYKGSLRLM 318 >C3AM21.1 C3AM21_BACMY UvrD/Rep helicase Length = 698 Score = 347 bits (891), Expect = 7e-94, Method: Compositional matrix adjust. Identities = 168/286 (58%), Positives = 216/286 (75%), Gaps = 1/286 (0%) Query: 7 SAYQEEEDRLNSALTEIDTVLERLRGIPVYTGHDYTEQALEVSREQRRKDLAKLRQEPYF 66 + ++EE R+ L+ +D L++L IPVY G D+ EQ LE RE R++L QEPYF Sbjct: 3 TIFEEELQRMKKTLSTMDEQLDKLEKIPVYYGEDFKEQILESMRESNRQNLRIGVQEPYF 62 Query: 67 GRLDFQGKDEDGRKALYIGKIGVDREQVSDRPLVIDWRAPVASLFYSFTGGTEPASYEAP 126 GRLDFQ + +YIGK+GV E+ +P+VIDWRAPVAS+FYSFTGG EPA Y +P Sbjct: 63 GRLDFQEDGQPEPNPIYIGKVGVSDEETM-KPIVIDWRAPVASMFYSFTGGEEPAFYHSP 121 Query: 127 EGLIEGLVYLKRNVVIRKQILERVADTYNRDSDGPAVSDEFLVYRLGENKDNRLRDIVST 186 +GL+EG VYLKRN+ IRK+ LERV DTY + S+ +++D+FL+YRLGENKDN+L+DIVST Sbjct: 122 DGLVEGDVYLKRNIAIRKRELERVVDTYVKGSEDVSLADDFLLYRLGENKDNKLKDIVST 181 Query: 187 IQEEQDKIIRAAKNTALIIQGVAGSGKTTVALHRLAFLLYQYKEQVSAEKMIIFAPNRMF 246 IQ EQ+ IIRA KN L+IQGVAGSGKTT+ALHRLAFL+Y+Y+EQ+ AE+MI+FAPN +F Sbjct: 182 IQSEQNDIIRAEKNMPLLIQGVAGSGKTTIALHRLAFLIYEYREQLEAERMIVFAPNSLF 241 Query: 247 LDYISDVLPELGVGNIAQSTFPDWAADVLGVVLPEQNAAETMSYWF 292 LDYIS VLPELGVGNI Q+TF DWA + L + ++ E + F Sbjct: 242 LDYISSVLPELGVGNIRQTTFQDWALNTLDAAVKLKDTDEKLKEAF 287 >C3B4A6.1 C3B4A6_BACMY UvrD/Rep helicase Length = 698 Score = 347 bits (891), Expect = 7e-94, Method: Compositional matrix adjust. Identities = 168/286 (58%), Positives = 216/286 (75%), Gaps = 1/286 (0%) Query: 7 SAYQEEEDRLNSALTEIDTVLERLRGIPVYTGHDYTEQALEVSREQRRKDLAKLRQEPYF 66 + ++EE R+ L+ +D L++L IPVY G D+ EQ LE RE R++L QEPYF Sbjct: 3 TIFEEELQRMKKTLSTMDEQLDKLEKIPVYYGEDFKEQILESMRESNRQNLRIGVQEPYF 62 Query: 67 GRLDFQGKDEDGRKALYIGKIGVDREQVSDRPLVIDWRAPVASLFYSFTGGTEPASYEAP 126 GRLDFQ + +YIGK+GV E+ +P+VIDWRAPVAS+FYSFTGG EPA Y +P Sbjct: 63 GRLDFQEDGQPEPNPIYIGKVGVSDEETM-KPIVIDWRAPVASMFYSFTGGEEPAFYHSP 121 Query: 127 EGLIEGLVYLKRNVVIRKQILERVADTYNRDSDGPAVSDEFLVYRLGENKDNRLRDIVST 186 +GL+EG VYLKRN+ IRK+ LERV DTY + S+ +++D+FL+YRLGENKDN+L+DIVST Sbjct: 122 DGLVEGDVYLKRNIAIRKRELERVVDTYVKGSEDVSLADDFLLYRLGENKDNKLKDIVST 181 Query: 187 IQEEQDKIIRAAKNTALIIQGVAGSGKTTVALHRLAFLLYQYKEQVSAEKMIIFAPNRMF 246 IQ EQ+ IIRA KN L+IQGVAGSGKTT+ALHRLAFL+Y+Y+EQ+ AE+MI+FAPN +F Sbjct: 182 IQSEQNDIIRAEKNMPLLIQGVAGSGKTTIALHRLAFLIYEYREQLEAERMIVFAPNSLF 241 Query: 247 LDYISDVLPELGVGNIAQSTFPDWAADVLGVVLPEQNAAETMSYWF 292 LDYIS VLPELGVGNI Q+TF DWA + L + ++ E + F Sbjct: 242 LDYISSVLPELGVGNIRQTTFQDWALNTLDAAVKLKDTDEKLKEAF 287 >C2W8S3.1 C2W8S3_BACCE UvrD/Rep helicase Length = 698 Score = 347 bits (890), Expect = 9e-94, Method: Compositional matrix adjust. Identities = 169/286 (59%), Positives = 217/286 (75%), Gaps = 1/286 (0%) Query: 7 SAYQEEEDRLNSALTEIDTVLERLRGIPVYTGHDYTEQALEVSREQRRKDLAKLRQEPYF 66 + +QEE R+ L+ +D L++L PVY G D+ EQ LE RE R++L QEPYF Sbjct: 3 NIFQEELQRMKETLSTMDKHLDKLEKTPVYYGSDFKEQILESMRESNRQNLRIGVQEPYF 62 Query: 67 GRLDFQGKDEDGRKALYIGKIGVDREQVSDRPLVIDWRAPVASLFYSFTGGTEPASYEAP 126 GRLDFQ +D +YIGK+GV E+ + +P+VIDWRAPVAS+FYSFTGG E A Y +P Sbjct: 63 GRLDFQEDGKDEPMPIYIGKVGVSDEETT-KPIVIDWRAPVASMFYSFTGGEEMAFYHSP 121 Query: 127 EGLIEGLVYLKRNVVIRKQILERVADTYNRDSDGPAVSDEFLVYRLGENKDNRLRDIVST 186 +GL+EG VYLKRN+ IRK+ LERV DTY + S+ +++D+FL+YRLGENKDN+L+DIVST Sbjct: 122 DGLVEGDVYLKRNIAIRKRELERVVDTYVKGSEDVSLADDFLLYRLGENKDNKLKDIVST 181 Query: 187 IQEEQDKIIRAAKNTALIIQGVAGSGKTTVALHRLAFLLYQYKEQVSAEKMIIFAPNRMF 246 IQ EQ+ IIRA KN L+IQGVAGSGKTT+ALHRLAFL+Y+Y+EQ+ AE+MI+FAPN +F Sbjct: 182 IQSEQNDIIRAEKNMPLLIQGVAGSGKTTIALHRLAFLIYEYREQLEAERMIVFAPNSLF 241 Query: 247 LDYISDVLPELGVGNIAQSTFPDWAADVLGVVLPEQNAAETMSYWF 292 LDYIS VLPELGVGNI Q+TF DWA L + ++A E ++ F Sbjct: 242 LDYISSVLPELGVGNIKQTTFQDWALRTLDDAVKLKDAEEKLTAAF 287 >C3BL40.1 C3BL40_9BACI UvrD/Rep helicase Length = 698 Score = 346 bits (888), Expect = 2e-93, Method: Compositional matrix adjust. Identities = 169/272 (62%), Positives = 213/272 (78%), Gaps = 7/272 (2%) Query: 7 SAYQEEEDRLNSALTEIDTVLERLRGIPVYTGHDYTEQALEVSREQRRKDLAKLRQEPYF 66 + ++EE R+ L+ +D L++L IPVY G D+ EQ LE RE R++L QEPYF Sbjct: 3 TIFEEELQRMKKTLSTMDEQLDKLEKIPVYYGEDFKEQILESMRESNRQNLRIGVQEPYF 62 Query: 67 GRLDFQGKDEDGR---KALYIGKIGVDREQVSDRPLVIDWRAPVASLFYSFTGGTEPASY 123 GRLDFQ EDG+ +YIGK+GV E+ +P+VIDWRAPVAS+FYSFTGG EPA Y Sbjct: 63 GRLDFQ---EDGQPEPNPIYIGKVGVSDEETM-KPIVIDWRAPVASMFYSFTGGEEPAFY 118 Query: 124 EAPEGLIEGLVYLKRNVVIRKQILERVADTYNRDSDGPAVSDEFLVYRLGENKDNRLRDI 183 +P+GL+EG VYLKRN+ IRK+ LERV DTY + S+ +++D+FL+YRLGENKDN+L+DI Sbjct: 119 HSPDGLVEGDVYLKRNIAIRKRELERVVDTYVKGSEDVSLADDFLLYRLGENKDNKLKDI 178 Query: 184 VSTIQEEQDKIIRAAKNTALIIQGVAGSGKTTVALHRLAFLLYQYKEQVSAEKMIIFAPN 243 VSTIQ EQ+ IIRA KN L+IQGVAGSGKTT+ALHRLAFL+Y+Y+EQ+ AE+MI+FAPN Sbjct: 179 VSTIQSEQNDIIRAEKNMPLLIQGVAGSGKTTIALHRLAFLIYEYREQLEAERMIVFAPN 238 Query: 244 RMFLDYISDVLPELGVGNIAQSTFPDWAADVL 275 +FLDYIS VLPELGVGNI Q+TF DWA + L Sbjct: 239 SLFLDYISSVLPELGVGNIRQTTFQDWALNTL 270 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 0.137 0.394 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: 2,067,214,431 Number of extensions: 91282187 Number of successful extensions: 288804 Number of sequences better than 1.0e-05: 575 Number of HSP's gapped: 287645 Number of HSP's successfully gapped: 575 Length of query: 337 Length of database: 3,060,696,203 Length adjustment: 136 Effective length of query: 201 Effective length of database: 1,779,438,163 Effective search space: 357667070763 Effective search space used: 357667070763 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 (21.6 bits) S2: 131 (55.1 bits)