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= 0543.0019.p (251 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B3KKX2.1 B3KKX2_9BACI Primosome, DnaD subunit 285 3e-75 B1DL96.1 B1DL96_9BACL Primosome, DnaD subunit 198 4e-49 C0ZCI5.1 C0ZCI5_BREBN DNA replication protein DnaD 159 2e-37 A4IQ53.1 A4IQ53_GEOTN DNA replication protein DnaD 147 1e-33 B4BM15.1 B4BM15_9BACI Primosome, DnaD subunit 147 1e-33 >B3KKX2.1 B3KKX2_9BACI Primosome, DnaD subunit Length = 248 Score = 285 bits (729), Expect = 3e-75, Method: Compositional matrix adjust. Identities = 149/245 (60%), Positives = 176/245 (71%), Gaps = 7/245 (2%) Query: 7 NAWGEGVSFGLQNGMAVIPYALLKYYRKLNLTGSEAMLLIHLLSFRQVEGMEFPSLEELQ 66 N W G + G+ GMA+IPYALL++YR L L+ EAML+IHL+ ++QVE FPSLEEL Sbjct: 11 NGWTAGAAAGMSQGMAIIPYALLRHYRSLGLSDREAMLVIHLIGYQQVEFKTFPSLEELA 70 Query: 67 TVTGRSIAAIAGELQKLMKEGFISIDEDIDELRDIHYERYNFSGLYGKLGAFLAGAAQDP 126 VTG A IA LQ+LMK G I IDE +DE + IHYERYN +GLY KL A LA +D Sbjct: 71 EVTGSPAAFIAASLQRLMKVGLIGIDEYVDEGQGIHYERYNLNGLYEKLAACLAQEGRDK 130 Query: 127 AQGSSKPAGTVPSLHAGAPAPDGGYGRAFTSAAGKDAEENRSLFTIFEKEFGRPLSPMEC 186 + ++K A P L+A PA G+ S +E R+LFTIFEKEFGRPLSPME Sbjct: 131 SPEAAKFAS--PLLNA-RPAS----GKTAASEKPAPEKEERNLFTIFEKEFGRPLSPMEL 183 Query: 187 ETISGWVDQDNYPEELILLALKESVFAGKIHFRYIDRILLEWARNRVKNAQDVKTYTQKF 246 ETISGWVD D YP+ELILLALKE+VFAGK+HFRYIDRILLEW+RNRV+ AQD K YTQKF Sbjct: 184 ETISGWVDADRYPDELILLALKEAVFAGKLHFRYIDRILLEWSRNRVRTAQDAKAYTQKF 243 Query: 247 RGGGR 251 R GR Sbjct: 244 RNIGR 248 >B1DL96.1 B1DL96_9BACL Primosome, DnaD subunit Length = 226 Score = 198 bits (503), Expect = 4e-49, Method: Compositional matrix adjust. Identities = 104/243 (42%), Positives = 148/243 (60%), Gaps = 26/243 (10%) Query: 6 WNAWGEGVSFGLQNGMAVIPYALLKYYRKLNLTGSEAMLLIHLLSFRQVEGMEFPSLEEL 65 W A+ G++ + G + LL+ YR+LNL+ +EAML++ L+ F + EG+EFP++E+L Sbjct: 7 WKAYSRGMAAVMSEGGVHVSALLLRSYRQLNLSDTEAMLMLQLMLFGESEGIEFPTMEQL 66 Query: 66 QTVTGRSIAAIAGELQKLMKEGFISIDEDIDELRDIHYERYNFSGLYGKLGAFLAGAAQD 125 +G + I + +LMKEGF++IDE ID I E+YN+SG +L AA+ Sbjct: 67 AERSGSTTRTIEQTIGRLMKEGFLTIDERIDPATGIQSEQYNWSG-------WLLKAAEW 119 Query: 126 PAQGSSKPAGTVPSLHAGAPAPDGGYGRAFTSAAGKDAEENRSLFTIFEKEFGRPLSPME 185 A+ + A P ++F++FE+EFGR LSPME Sbjct: 120 AAEEKRETRRAERRTVKRATDPG-------------------NIFSVFEQEFGRLLSPME 160 Query: 186 CETISGWVDQDNYPEELILLALKESVFAGKIHFRYIDRILLEWARNRVKNAQDVKTYTQK 245 CETISGW+DQD Y +ELI ALKE+VFAGK++FRYIDRIL+EW RNRV N + + ++QK Sbjct: 161 CETISGWLDQDRYADELIRFALKEAVFAGKLNFRYIDRILIEWGRNRVTNVDEARAHSQK 220 Query: 246 FRG 248 FRG Sbjct: 221 FRG 223 >C0ZCI5.1 C0ZCI5_BREBN DNA replication protein DnaD Length = 227 Score = 159 bits (403), Expect = 2e-37, Method: Compositional matrix adjust. Identities = 93/231 (40%), Positives = 127/231 (54%), Gaps = 24/231 (10%) Query: 17 LQNGMAVIPYALLKYYRKLNLTGSEAMLLIHLLSFRQVEGMEFPSLEELQTVTGRSIAAI 76 LQ G + LLK Y++++LT E MLLIHLLSF+Q EG FP+L EL+ + + Sbjct: 9 LQEGATSVSNLLLKMYKRMSLTDDEMMLLIHLLSFQQ-EGNRFPTLTELEERMSMTSRRL 67 Query: 77 AGELQKLMKEGFISIDEDIDELRDIHYERYNFSGLYGKLGAFLAGAAQDPAQGSSKPAGT 136 LQKL+KE +I+IDE ID + +E+YN + LY KL DP S P Sbjct: 68 IQSLQKLLKEDWITIDEFIDPQTGMRHEQYNLTPLYKKLYQTWREQQADP--RSIDPFME 125 Query: 137 VPSLHAGAPAPDGGYGRAFTSAAGKDAEENRSLFTIFEKEFGRPLSPMECETISGWVDQD 196 V A DAE +++ FE+ FGRPL+P E E I W +QD Sbjct: 126 V--------------------AVSLDAEPV-AIYARFEQAFGRPLAPFELENIHMWTEQD 164 Query: 197 NYPEELILLALKESVFAGKIHFRYIDRILLEWARNRVKNAQDVKTYTQKFR 247 Y E+LIL AL+E+ GK+H RYIDRILLEW + ++ ++ + Y+ FR Sbjct: 165 GYQEDLILTALREAATVGKLHIRYIDRILLEWQKQQITTVEEARLYSLNFR 215 >A4IQ53.1 A4IQ53_GEOTN DNA replication protein DnaD Length = 235 Score = 147 bits (370), Expect = 1e-33, Method: Compositional matrix adjust. Identities = 87/235 (37%), Positives = 130/235 (55%), Gaps = 33/235 (14%) Query: 13 VSFGLQNGMAVIPYALLKYYRKLNLTGSEAMLLIHLLSFRQVEGMEFPSLEELQTVTGRS 72 V+ L G V+P LL +Y++L L+ E +LL+H+ SF + EG+ FP+ EL S Sbjct: 6 VAEWLAQGSVVVPKLLLDHYKQLGLSEGELVLLLHMQSFLE-EGIVFPTPAELAEKMTVS 64 Query: 73 IAAIAGELQKLMKEGFISIDEDIDELRDIHYERYNFSGLYGKLGAFLAGAAQDPAQGSSK 132 A +++L+++G + I+E DE R + E+Y L+ +L Sbjct: 65 AAECMEMVRRLLQKGMVGIEEHTDE-RGVRGEKYTLEPLWEQL----------------- 106 Query: 133 PAGTVPSLHAGAPAPDGGYGRAFTSAAGKDAEENRSLFTIFEKEFGRPLSPMECETISGW 192 V L+A DG G+ +E SL+TIFE+EFGRPLSP ECET+S W Sbjct: 107 ----VHHLYAQT-VKDGQIGQ---------QKEEESLYTIFEQEFGRPLSPFECETLSMW 152 Query: 193 VDQDNYPEELILLALKESVFAGKIHFRYIDRILLEWARNRVKNAQDVKTYTQKFR 247 +DQD + +I AL+E+V +GK++FRYIDRIL EW +N ++ + Y +KFR Sbjct: 153 IDQDGHEPAIIKAALREAVLSGKLNFRYIDRILFEWKKNGIRTIEQAHDYGKKFR 207 >B4BM15.1 B4BM15_9BACI Primosome, DnaD subunit Length = 235 Score = 147 bits (370), Expect = 1e-33, Method: Compositional matrix adjust. Identities = 87/235 (37%), Positives = 130/235 (55%), Gaps = 33/235 (14%) Query: 13 VSFGLQNGMAVIPYALLKYYRKLNLTGSEAMLLIHLLSFRQVEGMEFPSLEELQTVTGRS 72 V+ L G V+P LL +Y++L L+ E +LL+H+ SF + EG+ FP+ EL S Sbjct: 6 VAEWLAQGSVVVPKLLLDHYKQLGLSEGELVLLLHMQSFLE-EGIVFPTPAELAEKMTVS 64 Query: 73 IAAIAGELQKLMKEGFISIDEDIDELRDIHYERYNFSGLYGKLGAFLAGAAQDPAQGSSK 132 A +++L+++G + I+E DE R + E+Y L+ +L Sbjct: 65 AAECMEMVRRLLQKGMVGIEEHTDE-RGVRGEKYTLEPLWEQL----------------- 106 Query: 133 PAGTVPSLHAGAPAPDGGYGRAFTSAAGKDAEENRSLFTIFEKEFGRPLSPMECETISGW 192 V L+A DG G+ +E SL+TIFE+EFGRPLSP ECET+S W Sbjct: 107 ----VHHLYAQT-VKDGQIGQ---------QKEEESLYTIFEQEFGRPLSPFECETLSMW 152 Query: 193 VDQDNYPEELILLALKESVFAGKIHFRYIDRILLEWARNRVKNAQDVKTYTQKFR 247 +DQD + +I AL+E+V +GK++FRYIDRIL EW +N ++ + Y +KFR Sbjct: 153 IDQDGHEPAIIKAALREAVLSGKLNFRYIDRILFEWKKNGIRTIEQAHDYGKKFR 207 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 0.137 0.407 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: 1,609,536,802 Number of extensions: 69581736 Number of successful extensions: 187007 Number of sequences better than 1.0e-05: 262 Number of HSP's gapped: 187010 Number of HSP's successfully gapped: 277 Length of query: 251 Length of database: 3,060,696,203 Length adjustment: 132 Effective length of query: 119 Effective length of database: 1,817,122,223 Effective search space: 216237544537 Effective search space used: 216237544537 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: 129 (54.3 bits)