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= 0139.0003.p (420 letters) Database: pfamseq 9,421,015 sequences; 3,060,696,203 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value B1DGZ1.1 B1DGZ1_9BACL DNA-directed DNA polymerase EC=2.7.7.7 446 e-123 B3KJ48.1 B3KJ48_9BACI DNA-directed DNA polymerase EC=2.7.7.7 372 e-101 P54560.1 DPO42_BACSU DNA polymerase IV 2 EC=2.7.7.7 361 7e-98 C1PES5.1 C1PES5_BACCO DNA-directed DNA polymerase EC=2.7.7.7 350 2e-94 Q9K9A8.1 DPO42_BACHD DNA polymerase IV 2 EC=2.7.7.7 348 5e-94 >B1DGZ1.1 B1DGZ1_9BACL DNA-directed DNA polymerase EC=2.7.7.7 Length = 417 Score = 446 bits (1146), Expect = e-123, Method: Compositional matrix adjust. Identities = 220/418 (52%), Positives = 295/418 (70%), Gaps = 3/418 (0%) Query: 4 DRVILLSDCQAFYASVEKAAHPEYRDRPVAV-GDPSRMNGIVLAACPVAKAQGVTTASRV 62 +RVI+L DCQ+FYASVEKAAHPEY++ PV V GDPSR +GI+LAACP+AK GVTTA + Sbjct: 2 ERVIMLIDCQSFYASVEKAAHPEYKNDPVVVAGDPSRRSGIILAACPLAKQYGVTTAETL 61 Query: 63 GEALAKCPELIVIRPRMGTYIKVSLLISEIYRTYTDLVEPYSIDEQFLDVTGSLAYFGGS 122 GEAL KCP L++IRPRM YI VSL+I++I+R++TDLVEP+SIDEQFLDVTGSL+YFG S Sbjct: 62 GEALGKCPHLVIIRPRMQAYIDVSLMITDIFRSFTDLVEPFSIDEQFLDVTGSLSYFG-S 120 Query: 123 LKDMIQKIQHHVLLSTGVWTRIGIGSTKVMAKMATDNYAKKMKDGIYELTFNQLESTLWR 182 +++ +IQ ++ TGVW R+GI S K++AKMATD +AKK G + L ++++S LW Sbjct: 121 PEEIATQIQTKIMTYTGVWARVGISSNKILAKMATDIWAKKNDIGQFTLPKSEVQSLLWP 180 Query: 183 LPVQDMFMVASRMTRNFWRMGISTIGDIARMELPEFKQRMRTTMGKQSDIQAEYYWQTAR 242 LPV MF V SRMT +F RMGI+TIGD+ + LPEFK+R++ MG+ SDIQAE +WQTA Sbjct: 181 LPVNKMFGVGSRMTAHFQRMGITTIGDLGCLPLPEFKRRLQARMGRNSDIQAELFWQTAN 240 Query: 243 GLDPSPVVTGIRHQIKSVGHGKALRWNLYTRLTDXXXXXXXXXXXXCQRARRYRYMGSVV 302 G+DPSPV ++VGH L + Y++ + C+R+R YMGSVV Sbjct: 241 GIDPSPVKPSTHDAQQAVGHQMTLPRD-YSKPQEIDVVLLELSEEVCRRSRAKGYMGSVV 299 Query: 303 SISVLETDGESSCSYERQMTLPEPSSLTHEVAAAALALFMDNWSGLPVGRLAITLSRLSD 362 + D + + RQMT+P+P+++T EV AAA LF +W LPV +L +TLS+L Sbjct: 300 AAGAQGADFDHPTGFFRQMTVPDPTNITKEVFAAARTLFYAHWDRLPVRKLGVTLSKLVP 359 Query: 363 DGVIQLTLFDDRARSYNKEHAIDGIKARYGNQALIRASSLLESGVARERAEQIGGHYK 420 D QLTLF +R + + D I+ ++G +++RASSLLES ARER+ +IGGHYK Sbjct: 360 DDQYQLTLFGNREKERKLDRVTDAIRHKFGTTSILRASSLLESAQARERSVKIGGHYK 417 >B3KJ48.1 B3KJ48_9BACI DNA-directed DNA polymerase EC=2.7.7.7 Length = 421 Score = 372 bits (955), Expect = e-101, Method: Compositional matrix adjust. Identities = 194/419 (46%), Positives = 262/419 (62%), Gaps = 3/419 (0%) Query: 3 KDRVILLSDCQAFYASVEKAAHPEYRDRPVAV-GDPSRMNGIVLAACPVAKAQGVTTASR 61 K RV+ L+DCQ+FYASVEKAA+P Y+ RP+ V GDP+R +GI+LAACP+AK GVTTA Sbjct: 5 KQRVVFLADCQSFYASVEKAANPAYQHRPLVVSGDPARRSGIILAACPLAKDHGVTTAEP 64 Query: 62 VGEALAKCPELIVIRPRMGTYIKVSLLISEIYRTYTDLVEPYSIDEQFLDVTGSLAYFGG 121 + +A KCP+L+V++PRM YI+VSL I I +Y+DLVEP+SIDEQF+DVT SLA+FG Sbjct: 65 LWQAQQKCPDLVVMKPRMSAYIRVSLQIMSILESYSDLVEPFSIDEQFIDVTASLAHFGC 124 Query: 122 SLKDMIQKIQHHVLLSTGVWTRIGIGSTKVMAKMATDNYAKKMKDGIYELTFNQLESTLW 181 + K++ + IQ V TGV+TR+GIG KV+AK+A DN+AKK +DGI+EL +++ LW Sbjct: 125 TPKELARHIQMRVRRETGVYTRVGIGRNKVLAKLACDNFAKKNEDGIFELNEATMDA-LW 183 Query: 182 RLPVQDMFMVASRMTRNFWRMGISTIGDIARMELPEFKQRMRTTMGKQSDIQAEYYWQTA 241 P MF V SR T++ R+GI TIG++A LP+ K +M+ M K DI +E W+TA Sbjct: 184 ACPTHKMFGVGSRTTKHLARLGIQTIGELAHTPLPDLKFKMKRYMKKNCDIWSEVLWRTA 243 Query: 242 RGLDPSPVVTGIRHQIKSVGHGKALRWNLYTRLTDXXXXXXXXXXXXCQRARRYRYMGSV 301 G D SPV K +G L + Y D CQRAR YMG+V Sbjct: 244 NGYDDSPVTPDAFDGQKGIGRQTTLPVD-YHDQQDIDVVLNELSMLICQRARAKGYMGNV 302 Query: 302 VSISVLETDGESSCSYERQMTLPEPSSLTHEVAAAALALFMDNWSGLPVGRLAITLSRLS 361 V D + + RQM + EP+ L+ EV AAA LF +W G PV ++ ++L L Sbjct: 303 VHAGAQGADFDRPVGFSRQMKIAEPTHLSREVYAAAKELFRKHWDGGPVRKIWVSLGELQ 362 Query: 362 DDGVIQLTLFDDRARSYNKEHAIDGIKARYGNQALIRASSLLESGVARERAEQIGGHYK 420 D V QL+LF DR R EH +D I +YG ++ SSL ++ + +IGGHYK Sbjct: 363 SDAVYQLSLFGDRERLMYLEHTMDDINNQYGPSSVYFGSSLTKTSQLKFLNAKIGGHYK 421 >P54560.1 DPO42_BACSU DNA polymerase IV 2 EC=2.7.7.7 Length = 412 Score = 361 bits (927), Expect = 7e-98, Method: Compositional matrix adjust. Identities = 193/421 (45%), Positives = 257/421 (61%), Gaps = 10/421 (2%) Query: 1 MPKDRVILLSDCQAFYASVEKAAHPEYRDRPVAV-GDPSRMNGIVLAACPVAKAQGVTTA 59 M K++VI L D Q+FYASVEKA +P ++RPV V GDP + G+VLAACP+AK +GV A Sbjct: 1 MMKEKVIFLVDMQSFYASVEKAENPHLKNRPVIVSGDPEKRGGVVLAACPLAKQKGVVNA 60 Query: 60 SRVGEALAKCPELIVIRPRMGTYIKVSLLISEIYRTYTDLVEPYSIDEQFLDVTGSLAYF 119 SR+ EA KCPE +V+RPRM YI VSL I+ I YTDLVEPYSIDEQF+D+TGS F Sbjct: 61 SRLWEAQEKCPEAVVLRPRMQRYIDVSLQITAILEEYTDLVEPYSIDEQFMDITGSQKLF 120 Query: 120 GGSLKDMIQKIQHHVLLSTGVWTRIGIGSTKVMAKMATDNYAKKMKDGIYELTFNQLEST 179 G + ++ + IQ ++ GV+ R+GIG K +AK+A DN+AKK K+GI+ LT +++ Sbjct: 121 GTPM-EIAKSIQGRIMREIGVYARVGIGPNKALAKIACDNFAKKNKNGIFTLTKENMKTE 179 Query: 180 LWRLPVQDMFMVASRMTRNFWRMGISTIGDIARMELPEFKQRMRTTMGKQSDIQAEYYWQ 239 +W LPV MF V SRM + RMGISTIG +A L K K+ I W Sbjct: 180 MWPLPVGSMFGVGSRMKHHLNRMGISTIGGLAAFPLDLLK--------KKWGINGHVLWM 231 Query: 240 TARGLDPSPVVTGIRHQIKSVGHGKALRWNLYTRLTDXXXXXXXXXXXXCQRARRYRYMG 299 TA G+D SPV T K++GHG L + + C+R+R MG Sbjct: 232 TANGIDYSPVSTSSLDGQKAIGHGMTLPRDYEHFDKEIKVVLLELSEEVCRRSRNAGVMG 291 Query: 300 SVVSISVLETDGESSCSYERQMTLPEPSSLTHEVAAAALALFMDNWSGLPVGRLAITLSR 359 VS+S D + + RQ+ L EP++ T +V A LF+ W G PV RL + LS+ Sbjct: 292 QTVSVSCRGADFDWPTGFNRQVKLAEPTNSTQDVYEAVRRLFLTFWDGKPVRRLGVNLSQ 351 Query: 360 LSDDGVIQLTLFDDRARSYNKEHAIDGIKARYGNQALIRASSLLESGVARERAEQIGGHY 419 LS D + QL LF D A+ + + +DGIK R+G+ A+IRA+SL +G A ERA +IGGHY Sbjct: 352 LSSDDIWQLNLFQDYAKKMSLGYVMDGIKNRFGDTAIIRAASLTAAGQAFERAAKIGGHY 411 Query: 420 K 420 K Sbjct: 412 K 412 >C1PES5.1 C1PES5_BACCO DNA-directed DNA polymerase EC=2.7.7.7 Length = 411 Score = 350 bits (897), Expect = 2e-94, Method: Compositional matrix adjust. Identities = 192/417 (46%), Positives = 257/417 (61%), Gaps = 10/417 (2%) Query: 5 RVILLSDCQAFYASVEKAAHPEYRDRPVAV-GDPSRMNGIVLAACPVAKAQGVTTASRVG 63 RVI L D Q+FYASVEKA HP YRD+PV V GDP+R +G+VLAACP+AK +GV A R+ Sbjct: 4 RVIFLVDMQSFYASVEKADHPAYRDKPVIVSGDPARRSGVVLAACPLAKKRGVKNALRLW 63 Query: 64 EALAKCPELIVIRPRMGTYIKVSLLISEIYRTYTDLVEPYSIDEQFLDVTGSLAYFGGSL 123 EA CP+ +++RPRM Y+ VS+ IS I YTD+VEPYS+DEQF+DVTGS FG Sbjct: 64 EAQQLCPDAVIVRPRMQRYLDVSVQISSILARYTDMVEPYSVDEQFMDVTGSRRLFG-EP 122 Query: 124 KDMIQKIQHHVLLSTGVWTRIGIGSTKVMAKMATDNYAKKMKDGIYELTFNQLESTLWRL 183 +++ +IQ ++ TGV+ R GIG KV+AKMA D++AKK K GI+EL + L++ LW L Sbjct: 123 REIAAQIQRDIMEETGVYARCGIGPNKVLAKMACDHFAKKNKTGIFELDHHHLKTHLWPL 182 Query: 184 PVQDMFMVASRMTRNFWRMGISTIGDIARMELPEFKQRMRTTMGKQSDIQAEYYWQTARG 243 PV MF V SRM ++ R+GI TIG +A L K+R I + W+TA G Sbjct: 183 PVGRMFGVGSRMEQHLKRLGIYTIGALACFPLSVLKKRW--------GIGGQVLWETANG 234 Query: 244 LDPSPVVTGIRHQIKSVGHGKALRWNLYTRLTDXXXXXXXXXXXXCQRARRYRYMGSVVS 303 +D SPV K++GH L + + C RAR MG+ VS Sbjct: 235 IDESPVSKESHVGQKAIGHAMTLPRDYADFEHEIKVALLELCEEVCFRARTSGVMGACVS 294 Query: 304 ISVLETDGESSCSYERQMTLPEPSSLTHEVAAAALALFMDNWSGLPVGRLAITLSRLSDD 363 + D + RQMTL P++ T +V AA LF+ W G PV R+++ LSRLS D Sbjct: 295 VGCQGADYAHPSGFHRQMTLLAPTNGTMDVYRAACRLFLSFWDGNPVRRISVGLSRLSRD 354 Query: 364 GVIQLTLFDDRARSYNKEHAIDGIKARYGNQALIRASSLLESGVARERAEQIGGHYK 420 + QL LF++R +A+D IK +YG+ A+IRA SLL++G A ERA++IGGHYK Sbjct: 355 DIRQLDLFENREGERKIGYAVDRIKQKYGSGAVIRAVSLLDAGQALERAKKIGGHYK 411 >Q9K9A8.1 DPO42_BACHD DNA polymerase IV 2 EC=2.7.7.7 Length = 409 Score = 348 bits (894), Expect = 5e-94, Method: Compositional matrix adjust. Identities = 180/418 (43%), Positives = 254/418 (60%), Gaps = 11/418 (2%) Query: 4 DRVILLSDCQAFYASVEKAAHPEYRDRPVAV-GDPSRMNGIVLAACPVAKAQGVTTASRV 62 D+VI + D ++F+ASVE+A HPE RP+ V GDP R +G++LAACPVAKA+GVT R+ Sbjct: 2 DKVIFMVDMESFFASVERANHPELSGRPLLVSGDPERRSGVILAACPVAKARGVTNGERL 61 Query: 63 GEALAKCPELIVIRPRMGTYIKVSLLISEIYRTYTDLVEPYSIDEQFLDVTGSLAYFGGS 122 EA KCPE +V+RP M Y+ VS+ I+EI +TDL+EP+SIDEQF+DVT S FG Sbjct: 62 WEAQQKCPEAVVVRPHMQQYVTVSVQITEILERFTDLIEPFSIDEQFMDVTHSQRLFGAP 121 Query: 123 LKDMIQKIQHHVLLSTGVWTRIGIGSTKVMAKMATDNYAKKMKDGIYELTFNQLESTLWR 182 +++ QK+Q + TGV RIG+G +KV+AKMA DN+AKKM G++ LT ++E LW Sbjct: 122 -REIAQKVQQAIWHETGVRARIGMGESKVLAKMACDNFAKKMPSGVFHLTKERMERLLWP 180 Query: 183 LPVQDMFMVASRMTRNFWRMGISTIGDIARMELPEFKQRMRTTMGKQSDIQAEYYWQTAR 242 LP++ ++ V +MT+ F GI TIG +A L +R++ G + W TA Sbjct: 181 LPIECLYGVGRQMTKYFRNQGIRTIGQLANTSL----ERIKGKWG----VNGHVLWLTAH 232 Query: 243 GLDPSPVVTGIRHQIKSVGHGKALRWNLYTRLTDXXXXXXXXXXXXCQRARRYRYMGSVV 302 G+DPSPV + K +GHG L + Y + D C+RARR MG V Sbjct: 233 GIDPSPVTPHSHDKQKGIGHGMTLPHD-YVKAEDIHVVLLELCEEVCKRARRAHLMGRTV 291 Query: 303 SISVLETDGESSCSYERQMTLPEPSSLTHEVAAAALALFMDNWSGLPVGRLAITLSRLSD 362 +I V + E+ + RQM L +++T EV A LF W G P+ RL + LS L+ Sbjct: 292 AIGVSGANMETPTGFHRQMKLTNHTNITMEVYEGAATLFERFWDGKPIRRLHVNLSNLTS 351 Query: 363 DGVIQLTLFDDRARSYNKEHAIDGIKARYGNQALIRASSLLESGVARERAEQIGGHYK 420 D QL+ F +R R++ + +D IK ++G+ A+ RA S L + A ERA++IGGHYK Sbjct: 352 DEAWQLSFFGNRDRAHQLGYTMDTIKEKFGDTAIRRAVSFLSASQAEERAKKIGGHYK 409 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 0.320 0.134 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: 2,295,268,135 Number of extensions: 88393820 Number of successful extensions: 209577 Number of sequences better than 1.0e-05: 2376 Number of HSP's gapped: 204987 Number of HSP's successfully gapped: 2382 Length of query: 420 Length of database: 3,060,696,203 Length adjustment: 138 Effective length of query: 282 Effective length of database: 1,760,596,133 Effective search space: 496488109506 Effective search space used: 496488109506 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 133 (55.8 bits)