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= 0265.0003.p (386 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 499 e-139 C2W8S3.1 C2W8S3_BACCE UvrD/Rep helicase 306 2e-81 C2WNJ5.1 C2WNJ5_BACCE UvrD/Rep helicase 305 4e-81 C2XCM7.1 C2XCM7_BACCE UvrD/Rep helicase 305 4e-81 C3ELR0.1 C3ELR0_BACTK UvrD/Rep helicase 305 5e-81 >B3KFJ9.1 B3KFJ9_9BACI UvrD/Rep helicase family protein Length = 725 Score = 499 bits (1285), Expect = e-139, Method: Compositional matrix adjust. Identities = 247/387 (63%), Positives = 294/387 (75%), Gaps = 10/387 (2%) Query: 1 VLHRSMILRWHNEEYAPYPPAKRKERVMARIHRWIEMELKKSPSAAAMKDRKKKSAAREK 60 VL + + W +EY PYP AKRKER++AR+HRW MELKKSPSAA +K+RKKK+A REK Sbjct: 345 VLKQETMAEWFYQEYKPYPLAKRKERLLARLHRWALMELKKSPSAAVLKERKKKAAQREK 404 Query: 61 AYSAKWPKYDPLTIYKQIFRAVKVPEDWPAEAPESIPPEVLASTVKELKKGILHEEDLPP 120 AY+ +WPK++P+++YKQ+F AVK W E IPPEVLA+T K+LKK ++ EEDLP Sbjct: 405 AYANRWPKFEPISLYKQLFGAVKAAGSWVEELSALIPPEVLAATRKDLKKNVVREEDLPA 464 Query: 121 LLYIHYLLNGNEGGSGFDHIVIDEAQDFSPFQIAVLDLYVKGHSFTILGDLSQGIHAYKG 180 LLY H LLN FDHIVIDEAQDFSPFQ+AVLDL+V+GHSFTILGDLSQGIHAY+G Sbjct: 465 LLYFHCLLNDISSEQRFDHIVIDEAQDFSPFQVAVLDLFVRGHSFTILGDLSQGIHAYRG 524 Query: 181 VHAWEEMQTLFAPEHTAYHALTRSYRSTMEIIEFANGILSAGVGSSLLAVPVFRSGNPVR 240 VHAWEEM +LF E TAY ALTRSYRSTMEIIEFANGIL GV S LLAVPVFRSG+ VR Sbjct: 525 VHAWEEMSSLFKEEETAYFALTRSYRSTMEIIEFANGILEKGVESDLLAVPVFRSGDAVR 584 Query: 241 LISYGQPLPASAAGGDRRIQAVRTALASLSGREYRTLAVLTRSLREAAELYTELAGHFED 300 LI Y + R + + A+ +L +EYRT+A+LTR+LREA EL+ EL+ + Sbjct: 585 LIPYD--------AANARRKDLERAMGALIAKEYRTVAILTRTLREAKELHEELSPSWPM 636 Query: 301 IHLIDGSMTEYRGGLSVLPVYLSKGLEFDAVILADADSDHYGGAAWDAKLMYVGCTRALH 360 ++LIDGS Y+GG SVLPVYLSKGLEFDAV++ADAD HY AWDAKLMYVGCTRALH Sbjct: 637 LNLIDGSKGTYQGGYSVLPVYLSKGLEFDAVVVADADRAHYAEKAWDAKLMYVGCTRALH 696 Query: 361 ELWILHGEGLPPYL--QNGEGTVQGWP 385 ELW+LHGE LP Y+ + E GWP Sbjct: 697 ELWLLHGEPLPSYIMAETSEIMASGWP 723 >C2W8S3.1 C2W8S3_BACCE UvrD/Rep helicase Length = 698 Score = 306 bits (784), Expect = 2e-81, Method: Compositional matrix adjust. Identities = 159/369 (43%), Positives = 221/369 (59%), Gaps = 21/369 (5%) Query: 7 ILRWHNEEYAPYPPAKRKERVMARIHRWIEMELKKSPSAAAMKDRKKKSAAREKAYSAKW 66 I +W EY YP AKR+ER++ RI RWIE+ELKK K+ KK++ R AY W Sbjct: 341 IRKWIQVEYKHYPLAKRRERLVGRIKRWIEIELKKFEGTNKKKELKKEATKRLSAYMKFW 400 Query: 67 PKYDPLTIYKQIFRAVKVPEDWPAEAPESIPPEVLASTVKELKKGILHEEDLPPLLYIHY 126 PK PL++Y + + + E +P E++ T K +K ++ EDL PL+YIH+ Sbjct: 401 PKMTPLSLYSSLMKQQAILE--------VLPKELVQETEKNCRKKEIYAEDLAPLIYIHH 452 Query: 127 LLNGNEGGSGFDHIVIDEAQDFSPFQIAVLDLYVKGHSFTILGDLSQGIHAYKGVHAWEE 186 L G E G F H+VIDEAQDFSP QI +L G+SFTILGDLSQ I+ Y+G+ W + Sbjct: 453 QLAGIEIGQKFHHVVIDEAQDFSPLQIYILKEITMGNSFTILGDLSQAIYDYQGIEDWND 512 Query: 187 MQTLFAPEHTAYHALTRSYRSTMEIIEFANGILSAGVGSSLLAVPVFRSGNPVRLISYGQ 246 + +F + T Y+ LTRSYRST EIIEFAN ++ LA PVFRSG V++IS Sbjct: 513 FKEVF--QETGYYELTRSYRSTKEIIEFANEVIKNAEVPVGLATPVFRSGEKVKVIS--- 567 Query: 247 PLPASAAGGDRRIQAVRTALASLSGREYRTLAVLTRSLREAAELYTELAGHFEDIHLIDG 306 D + + L + +T+AV+ R+ E +Y +L +++I+ Sbjct: 568 --------TDDQFTEIIKTLEDMQNENVKTIAVIGRTDDECRNIYEKLTAAGITVNVIEA 619 Query: 307 SMTEYRGGLSVLPVYLSKGLEFDAVILADADSDHYGGAAWDAKLMYVGCTRALHELWILH 366 + ++Y GG+SV+PVYL+KGLEFDAV+L D D+ HY G DAKL+YVGCTR+LH+L I + Sbjct: 620 NQSKYEGGISVVPVYLAKGLEFDAVLLIDVDAMHYKGTKHDAKLLYVGCTRSLHDLRIFY 679 Query: 367 GEGLPPYLQ 375 P +Q Sbjct: 680 SGEASPLIQ 688 >C2WNJ5.1 C2WNJ5_BACCE UvrD/Rep helicase Length = 691 Score = 305 bits (782), Expect = 4e-81, Method: Compositional matrix adjust. Identities = 160/366 (43%), Positives = 220/366 (60%), Gaps = 22/366 (6%) Query: 7 ILRWHNEEYAPYPPAKRKERVMARIHRWIEMELKKSPSAAAMKDRKKKSAAREKAYSAKW 66 I +W EY YP KR+ER++ R+ RWIE+ELKK K KK++ R AY W Sbjct: 341 IKKWMQVEYKHYPLQKRRERLVGRMKRWIEIELKKFGETNEKKLLKKEATKRLNAYMKFW 400 Query: 67 PKYDPLTIYKQIFRAVKVPEDWPAEAPESIPPEVLASTVKELKKGILHEEDLPPLLYIHY 126 PK L++Y I ++ E E +P E++ T K +K ++ EDLP L+YIH+ Sbjct: 401 PKMSALSLYSSIVKS--------KEILEVLPEELVKETEKSCRKKEVYVEDLPALIYIHH 452 Query: 127 LLNGNEGGSGFDHIVIDEAQDFSPFQIAVLDLYVKGHSFTILGDLSQGIHAYKGVHAWEE 186 + G E G F H+VIDEAQDFSPFQ+ VL G+SFTILGDLSQ I+ Y+G+ W Sbjct: 453 RITGIEIGQKFHHVVIDEAQDFSPFQVYVLKEITLGNSFTILGDLSQAIYDYQGIEDWNA 512 Query: 187 MQTLFAPEHTAYHALTRSYRSTMEIIEFANGILSAGVGSSLLAVPVFRSGNPVRLISYGQ 246 + +F + T Y+ LTRSYRST EIIEFAN I+ LA PVFRSG V++I Sbjct: 513 FKEVF--QETGYYELTRSYRSTKEIIEFANEIIKNAEIPVGLATPVFRSGEDVKVIH--- 567 Query: 247 PLPASAAGGDRRIQAVRTALASLSGREYRTLAVLTRSLREAAELYTELAGHFEDIHLIDG 306 + + + + L + +T+AV+ R+ E ++Y EL +++I+ Sbjct: 568 --------AENQFTEIVKTVKHLQNADVKTIAVIGRTEDECRDIYVELTNAGLTVNVIEA 619 Query: 307 SMTEYRGGLSVLPVYLSKGLEFDAVILADADSDHYGGAAWDAKLMYVGCTRALHELWILH 366 + ++Y GG+SV+PVYL+KGLEFDAV+L D D +HY DAKL+YVGCTR+LH+LWI H Sbjct: 620 NQSKYEGGISVVPVYLAKGLEFDAVLLIDVDEEHYKDTKHDAKLLYVGCTRSLHDLWIFH 679 Query: 367 -GEGLP 371 GE P Sbjct: 680 SGEASP 685 >C2XCM7.1 C2XCM7_BACCE UvrD/Rep helicase Length = 691 Score = 305 bits (781), Expect = 4e-81, Method: Compositional matrix adjust. Identities = 160/366 (43%), Positives = 220/366 (60%), Gaps = 22/366 (6%) Query: 7 ILRWHNEEYAPYPPAKRKERVMARIHRWIEMELKKSPSAAAMKDRKKKSAAREKAYSAKW 66 I +W EY YP KR+ER++ R+ RWIE+ELKK K KK++ R AY W Sbjct: 341 IKKWMQVEYKHYPLQKRRERLVGRMKRWIEIELKKFGETNEKKLLKKEATKRLNAYMKFW 400 Query: 67 PKYDPLTIYKQIFRAVKVPEDWPAEAPESIPPEVLASTVKELKKGILHEEDLPPLLYIHY 126 PK L++Y I ++ E E +P E++ T K +K ++ EDLP L+YIH+ Sbjct: 401 PKMSALSLYSSIVKS--------KEILEVLPEELVKETEKSCRKKEVYVEDLPALIYIHH 452 Query: 127 LLNGNEGGSGFDHIVIDEAQDFSPFQIAVLDLYVKGHSFTILGDLSQGIHAYKGVHAWEE 186 + G E G F H+VIDEAQDFSPFQ+ VL G+SFTILGDLSQ I+ Y+G+ W Sbjct: 453 RITGIEIGQKFHHVVIDEAQDFSPFQVYVLKEITLGNSFTILGDLSQAIYDYQGIEDWNA 512 Query: 187 MQTLFAPEHTAYHALTRSYRSTMEIIEFANGILSAGVGSSLLAVPVFRSGNPVRLISYGQ 246 + +F + T Y+ LTRSYRST EIIEFAN I+ LA PVFRSG V++I Sbjct: 513 FKEVF--QETGYYELTRSYRSTKEIIEFANEIIKNAEIPVGLATPVFRSGEDVKVIH--- 567 Query: 247 PLPASAAGGDRRIQAVRTALASLSGREYRTLAVLTRSLREAAELYTELAGHFEDIHLIDG 306 + + + + L + +T+AV+ R+ E ++Y EL +++I+ Sbjct: 568 --------AENQFTEIVKTVKHLQNADVKTIAVIGRTEDECRDIYVELTNAGLTVNVIEA 619 Query: 307 SMTEYRGGLSVLPVYLSKGLEFDAVILADADSDHYGGAAWDAKLMYVGCTRALHELWILH 366 + ++Y GG+SV+PVYL+KGLEFDAV+L D D +HY DAKL+YVGCTR+LH+LWI H Sbjct: 620 NQSKYEGGISVVPVYLAKGLEFDAVLLIDVDEEHYKDTKHDAKLLYVGCTRSLHDLWIFH 679 Query: 367 -GEGLP 371 GE P Sbjct: 680 SGEASP 685 >C3ELR0.1 C3ELR0_BACTK UvrD/Rep helicase Length = 691 Score = 305 bits (781), Expect = 5e-81, Method: Compositional matrix adjust. Identities = 160/366 (43%), Positives = 220/366 (60%), Gaps = 22/366 (6%) Query: 7 ILRWHNEEYAPYPPAKRKERVMARIHRWIEMELKKSPSAAAMKDRKKKSAAREKAYSAKW 66 I +W EY YP KR+ER++ R+ RWIE+ELKK K KK++ R AY W Sbjct: 341 IKKWMQVEYKHYPLQKRRERLVGRMKRWIEIELKKFGETNEKKLLKKEATKRLNAYMKFW 400 Query: 67 PKYDPLTIYKQIFRAVKVPEDWPAEAPESIPPEVLASTVKELKKGILHEEDLPPLLYIHY 126 PK L++Y I ++ E E +P E++ T K +K ++ EDLP L+YIH+ Sbjct: 401 PKMSALSLYSSIVKS--------KEILEVLPEELVKETEKSCRKKEVYVEDLPALIYIHH 452 Query: 127 LLNGNEGGSGFDHIVIDEAQDFSPFQIAVLDLYVKGHSFTILGDLSQGIHAYKGVHAWEE 186 + G E G F H+VIDEAQDFSPFQ+ VL G+SFTILGDLSQ I+ Y+G+ W Sbjct: 453 RITGIEIGQKFHHVVIDEAQDFSPFQVYVLKEITLGNSFTILGDLSQAIYDYQGIEDWNA 512 Query: 187 MQTLFAPEHTAYHALTRSYRSTMEIIEFANGILSAGVGSSLLAVPVFRSGNPVRLISYGQ 246 + +F + T Y+ LTRSYRST EIIEFAN I+ LA PVFRSG V++I Sbjct: 513 FKEVF--QETGYYELTRSYRSTKEIIEFANEIIKNAEIPVGLATPVFRSGEDVKVIH--- 567 Query: 247 PLPASAAGGDRRIQAVRTALASLSGREYRTLAVLTRSLREAAELYTELAGHFEDIHLIDG 306 + + + + L + +T+AV+ R+ E ++Y EL +++I+ Sbjct: 568 --------AENQFTEIVKTVKHLQNADVKTIAVIGRTEDECRDIYVELTNAGLTVNVIEA 619 Query: 307 SMTEYRGGLSVLPVYLSKGLEFDAVILADADSDHYGGAAWDAKLMYVGCTRALHELWILH 366 + ++Y GG+SV+PVYL+KGLEFDAV+L D D +HY DAKL+YVGCTR+LH+LWI H Sbjct: 620 NQSKYEGGISVVPVYLAKGLEFDAVLLIDVDEEHYKDTKHDAKLLYVGCTRSLHDLWIFH 679 Query: 367 -GEGLP 371 GE P Sbjct: 680 SGEASP 685 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 0.318 0.136 0.411 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: 2,460,088,433 Number of extensions: 105534280 Number of successful extensions: 278161 Number of sequences better than 1.0e-05: 504 Number of HSP's gapped: 277641 Number of HSP's successfully gapped: 509 Length of query: 386 Length of database: 3,060,696,203 Length adjustment: 137 Effective length of query: 249 Effective length of database: 1,770,017,148 Effective search space: 440734269852 Effective search space used: 440734269852 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)