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= 0378.0006.p (465 letters) Database: COG 115,334 sequences; 38,378,431 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value CAC0516 [L] COG0587 DNA polymerase III, alpha subunit 486 e-137 all3578 [L] COG0587 DNA polymerase III, alpha subunit 406 e-113 slr0603 [L] COG0587 DNA polymerase III, alpha subunit 398 e-111 PA3640 [L] COG0587 DNA polymerase III, alpha subunit 361 1e-99 BS_dnaE [L] COG0587 DNA polymerase III, alpha subunit 360 3e-99 >CAC0516 [L] COG0587 DNA polymerase III, alpha subunit Length = 1167 Score = 486 bits (1252), Expect = e-137, Method: Compositional matrix adjust. Identities = 235/447 (52%), Positives = 304/447 (68%), Gaps = 19/447 (4%) Query: 4 FVHLHVHSEYSLLDGAARITDLVRRAGEYGMTTLALTDHGVMYGAIPFYKACKASGIKPI 63 FVHLHVH+EYSLLDG+ ++ LV RA E GM ++A+TDHG MYG + FYKA K GIKPI Sbjct: 11 FVHLHVHTEYSLLDGSGKVKKLVERAKELGMKSIAITDHGAMYGCVEFYKAAKEVGIKPI 70 Query: 64 IGWEAXXXGCEAYLTAGSRRERGSRKDQPIYHLILLAKNETGYRNLMRLVTIGHLEGQHY 123 IG CE Y+ S + + YHL+LL KNE GY+NLM +V+ +EG +Y Sbjct: 71 IG-------CEIYVAGKSMHIKHPDAENETYHLVLLVKNEIGYKNLMEIVSTASIEGFYY 123 Query: 124 KPRIDMESLAAHAEGVICLXXXXACLGGEVPQHLLHGREEEARKAALRYKEIFGGDFYLE 183 KPR+D E L +H+EG+I AC GGEV ++L E+A+KAAL YKE F FYLE Sbjct: 124 KPRVDHEYLMSHSEGLIA---SSACFGGEVQSYILKDNLEKAKKAALFYKETFKDGFYLE 180 Query: 184 LQDHGMPEQKRVNPQLIALAAECGIPLVATNDVHYLAKEDAEVQDVLICIGTGKTVDDEE 243 LQ H + + +VN L+ ++ E IPL+ATNDVHY+ KED+ D+L+CI TGKT+D+E Sbjct: 181 LQYHALKDDMKVNDTLVNMSKELDIPLIATNDVHYINKEDSIAHDILLCIQTGKTIDEEN 240 Query: 244 RLKIGTDQLFLKSGEQMAALFPHVPEAIANTLNIAEKCNLELTFGEHILPAYSPLPEGMD 303 R++ +Q +LKS E+M F +V EA+ NT IA++CN E F E LP + PLPEG D Sbjct: 241 RMRYAPEQFYLKSQEEMYEQFSYVKEALLNTSKIADECNFEYKFHESKLPNF-PLPEGED 299 Query: 304 AAAYLRELCWSGLEARYADTPRWSSPEEKDAAGKRLAYELGVIESMGFSDYFLIVWDFIA 363 YL++LC+ GL RY D +RL YELG+I+ MG+ DYFLIVWDFI Sbjct: 300 HYEYLKKLCYEGLNERYNPIT--------DTIKERLEYELGIIKEMGYVDYFLIVWDFIK 351 Query: 364 FCHRQGIVTGPGRGSSAGSLTAYCLRITDVDPLKYNLLFERFLNPERITMPDIDIDFSDE 423 F G+ TGPGRGS+AGS+ AY L IT +DP+KY+L+FERFLNP+R++MPDID DF E Sbjct: 352 FARENGVPTGPGRGSAAGSIVAYTLGITKIDPIKYSLIFERFLNPDRVSMPDIDSDFCYE 411 Query: 424 RRDEVIAYVVDKYGKQHVAQIITFGTM 450 R +VI YVV+KYGK V+QI+TFGTM Sbjct: 412 NRQKVIDYVVEKYGKDCVSQIVTFGTM 438 >all3578 [L] COG0587 DNA polymerase III, alpha subunit Length = 877 Score = 406 bits (1044), Expect = e-113, Method: Compositional matrix adjust. Identities = 220/461 (47%), Positives = 294/461 (63%), Gaps = 34/461 (7%) Query: 4 FVHLHVHSEYSLLDGAARITDLVRRAGEYGMTTLALTDHGVMYGAIPFYKACKASGIKPI 63 FV LH+HS+YSLLDGA+++ +L+ +A GM +A+TDHGVMYGAI K C++ IKPI Sbjct: 3 FVPLHIHSDYSLLDGASQLPELIDQAIALGMKAIAVTDHGVMYGAIELLKICRSKNIKPI 62 Query: 64 IGWEAXXXGCEAYLTAGS--RRERGSRKDQPIYHLILLAKNETGYRNLMRLVTIGHLEGQ 121 IG E Y+ G ++ERG +P YH ++LAKN GY+NL++L TI HL+G Sbjct: 63 IG-------NEMYILNGDLEKQERG----RPKYHQVVLAKNTKGYKNLVKLTTISHLQGV 111 Query: 122 HYK-----PRIDMESLAAHAEGVICLXXXXACLGGEVPQHLLHGREEEARKAALRYKEIF 176 K P I+ + L + EG+I ACLGGE+PQ +L R + ARK A YK++F Sbjct: 112 QGKGIFSRPCINKDLLKEYHEGLIV---TSACLGGEIPQAILSNRPDAARKVAKWYKDVF 168 Query: 177 GGDFYLELQDHGMPEQKRVNPQLIALAAECGIPLVATNDVHYLAKEDAEVQDVLICIGTG 236 G DFYLE+QDHG E + VN ++I +A E I VATND HY++ D E D L+CI TG Sbjct: 169 GDDFYLEIQDHGSQEDRIVNVEIIKIARELEIKFVATNDSHYISCFDVEAHDALLCIQTG 228 Query: 237 KTVDDEERLKI-GTDQLFLKSGEQMAALFPH------VPEAIANTLNIAEKCNLELTFGE 289 K + +++R++ GT+ +LKSGE+M LF + EAIA T +A+K GE Sbjct: 229 KLISEDKRMRYSGTE--YLKSGEEMKLLFRDHLTDDVIAEAIATTEEVADKVEPYHIMGE 286 Query: 290 HILPAYSPLPEGMDAAAYLRELCWSGLEARYADTPRWSSPEEKDAAGKRLAYELGVIESM 349 +P Y P+P G Y+ E+ W GL + R S E + +RL YEL +++ M Sbjct: 287 PRIPNY-PIPSGHTPDTYVEEVAWQGLLEKLN---RKSRNEVEPVYRERLEYELKMLQQM 342 Query: 350 GFSDYFLIVWDFIAFCHRQGIVTGPGRGSSAGSLTAYCLRITDVDPLKYNLLFERFLNPE 409 GFS YFL+VWD+I F I GPGRGS+AGSL AY + IT++DP+ + LLFERFLNPE Sbjct: 343 GFSSYFLVVWDYIKFARDNNIPVGPGRGSAAGSLVAYTMGITNIDPVHHGLLFERFLNPE 402 Query: 410 RITMPDIDIDFSDERRDEVIAYVVDKYGKQHVAQIITFGTM 450 R +MPDID DF E+RD+VI YV DKYGK+ VAQIITF + Sbjct: 403 RKSMPDIDTDFCIEQRDKVIEYVTDKYGKERVAQIITFNRL 443 >slr0603 [L] COG0587 DNA polymerase III, alpha subunit Length = 897 Score = 398 bits (1023), Expect = e-111, Method: Compositional matrix adjust. Identities = 216/460 (46%), Positives = 288/460 (62%), Gaps = 33/460 (7%) Query: 4 FVHLHVHSEYSLLDGAARITDLVRRAGEYGMTTLALTDHGVMYGAIPFYKACKASGIKPI 63 FV LH+HS+YSLLDGA+++ L+ RA E GM +ALTDHGVMYGA+ K C+ IKPI Sbjct: 3 FVGLHIHSDYSLLDGASQLPALIDRAIELGMPAIALTDHGVMYGAVELLKVCRGKPIKPI 62 Query: 64 IGWEAXXXGCEAYLTAGSRRERGSRKDQPIYHLILLAKNETGYRNLMRLVTIGHLEGQH- 122 IG E + + RR +H ++LAKN GYRNL++L TI +L+G Sbjct: 63 IGNEMYVINGDIEINKRHRR----------FHQVVLAKNNQGYRNLVKLTTISNLKGIQG 112 Query: 123 ----YKPRIDMESLAAHAEGVICLXXXXACLGGEVPQHLLHGREEEARKAALRYKEIFGG 178 +P I+ E L + EG+I ACLGGEVPQ +L G + AR+ A YK +FG Sbjct: 113 SGIFARPCINKELLEQYKEGLIV---TSACLGGEVPQAILKGDLDHARQVAKWYKNLFGD 169 Query: 179 DFYLELQDHGMPEQKRVNPQLIALAAECGIPLVATNDVHYLAKEDAEVQDVLICIGTGKT 238 D+YLE+QDHG E + VN L+ +A E I +VATND H+++ D E D L+CI TGK Sbjct: 170 DYYLEIQDHGSVEDRLVNINLVKIAQELDIKIVATNDSHFISCNDVEAHDALLCIQTGKL 229 Query: 239 VDDEERLKI-GTDQLFLKSGEQMAALF-PHVPE-----AIANTLNIAEKCNLELTFGEHI 291 + +E+RL+ GT+ +LKS E+M LF H+P+ AIANTL +A+K GE Sbjct: 230 ITEEKRLRYSGTE--YLKSAEEMHLLFRDHLPDDIIETAIANTLEVADKVEAYSILGEPR 287 Query: 292 LPAYSPLPEGMDAAAYLRELCWSGLEARYADTPRWS-SPEEKDAAGKRLAYELGVIESMG 350 +P Y P+P Y+ ++ W GL R R +P K+ RL YEL ++E MG Sbjct: 288 IPHY-PIPPNHTPETYVEDIAWDGLLERLKCRERADITPVYKE----RLEYELRMLEKMG 342 Query: 351 FSDYFLIVWDFIAFCHRQGIVTGPGRGSSAGSLTAYCLRITDVDPLKYNLLFERFLNPER 410 F YFL+VWD+I + GI GPGRGS+AGSL AYC++IT++DP+ + L+FERFLNPER Sbjct: 343 FCTYFLVVWDYIKYARDHGIPVGPGRGSAAGSLVAYCMKITNIDPVHHGLIFERFLNPER 402 Query: 411 ITMPDIDIDFSDERRDEVIAYVVDKYGKQHVAQIITFGTM 450 +MPD+D DF +RRDE+I YV KYG+ VAQIITF M Sbjct: 403 KSMPDVDTDFCIDRRDEMIEYVTQKYGEDKVAQIITFNRM 442 >PA3640 [L] COG0587 DNA polymerase III, alpha subunit Length = 1173 Score = 361 bits (927), Expect = 1e-99, Method: Compositional matrix adjust. Identities = 204/458 (44%), Positives = 269/458 (58%), Gaps = 36/458 (7%) Query: 4 FVHLHVHSEYSLLDGAARITDLVRRAGEYGMTTLALTDHGVMYGAIPFYKACKASGIKPI 63 FVHL +H+E+SL+DG R+ L + GM +A+TD M + FYK +GIKPI Sbjct: 5 FVHLRLHTEFSLVDGLVRVKPLAKAVAGLGMPAVAVTDQSNMCSLVKFYKTAMGAGIKPI 64 Query: 64 IGWEAXXXGCEAYLTAGSRRERGSRKDQPIYHLILLAKNETGYRNLMRLVTIGHLEGQHY 123 C A + SR E G P+ L LLA N GYRNL L++ G EGQ Sbjct: 65 ---------CGADIWLASREEDG-----PLSRLSLLAMNAKGYRNLTELISRGWSEGQRN 110 Query: 124 -KPRIDMESLAAHAEGVICLXXXXACLGGEVPQHLLHGREEEARKAALRYKEIFGGDFYL 182 + I+ + + AEG+I L A GE+ LL G E +A + E+F FY+ Sbjct: 111 GEIIIERDWVKEAAEGLIALS---AAKEGEIGHALLDGEEAKAEALLREWMEVFPERFYV 167 Query: 183 ELQDHGMPEQKRVNPQ-----LIALAAECGIPLVATNDVHYLAKEDAEVQDVLICIGTGK 237 E+Q RVN + +ALA+ C PLVATNDV ++ +ED E + +CIG G+ Sbjct: 168 EVQ-----RTSRVNDEEHLHAAVALASRCNAPLVATNDVRFIKQEDFEAHETRVCIGEGR 222 Query: 238 TVDDEERLKIGTDQLFLKSGEQMAALFPHVPEAIANTLNIAEKCNLELTFGEHILPAYSP 297 T+DD R + +DQ +LKS +MA LF +PEA+ NT+ IA++CN+E+ G++ LP + P Sbjct: 223 TLDDPRRPRTYSDQQYLKSPAEMAELFSDLPEALENTVEIAKRCNIEVQLGKYFLPDF-P 281 Query: 298 LPEGMDAAAYLRELCWSGLEARY-----ADTPRWSSPEEKDAAGKRLAYELGVIESMGFS 352 P GM YLR + GLE R DTP + + ++ RL +EL +I MGF Sbjct: 282 TPNGMGIDDYLRHASFEGLEERLEVLLPKDTPDYEA--KRQVYVDRLNFELDIIIQMGFP 339 Query: 353 DYFLIVWDFIAFCHRQGIVTGPGRGSSAGSLTAYCLRITDVDPLKYNLLFERFLNPERIT 412 YFLIV DFI + G+ GPGRGS AGSL AY L+ITD+DPL Y+LLFERFLNPERI+ Sbjct: 340 GYFLIVMDFIKWAKNNGVPVGPGRGSGAGSLVAYVLKITDLDPLAYDLLFERFLNPERIS 399 Query: 413 MPDIDIDFSDERRDEVIAYVVDKYGKQHVAQIITFGTM 450 MPD D+DF E RD VI YV D YG+ V+QIITFGTM Sbjct: 400 MPDFDVDFCMEGRDRVIDYVADAYGRNAVSQIITFGTM 437 >BS_dnaE [L] COG0587 DNA polymerase III, alpha subunit Length = 1115 Score = 360 bits (923), Expect = 3e-99, Method: Compositional matrix adjust. Identities = 206/449 (45%), Positives = 276/449 (61%), Gaps = 36/449 (8%) Query: 4 FVHLHVHSEYSLLDGAARITDLVRRAGEYGMTTLALTDHGVMYGAIPFYKACKASGIKPI 63 FVHL VHS YSLL+ AA + +LV A G +LALTD VMYGAI FYKACKA GI PI Sbjct: 3 FVHLQVHSGYSLLNSAAAVEELVSEADRLGYASLALTDDHVMYGAIQFYKACKARGINPI 62 Query: 64 IGWEAXXXGCEAYLTAGSRRERGSRKDQPIYHLILLAKNETGYRNLMRLVTIGHLEGQH- 122 IG A ++ L A Y L+LLAK+ TGY+NL+++ ++ + + Sbjct: 63 IGLTASVFTDDSELEA--------------YPLVLLAKSNTGYQNLLKISSVLQSKSKGG 108 Query: 123 YKPRIDMESLAAHAEGVICLXXXXACLGGEVPQHLLHGREEEARKAALRYKEIFG-GDFY 181 KP+ L ++ EG+I + G + L G E+A +A+L ++ IFG G FY Sbjct: 109 LKPKW----LHSYREGIIAITPGEK---GYIETLLEGGLFEQAAQASLEFQSIFGKGAFY 161 Query: 182 LELQDHGMPEQKRVNPQLIALAAECGIPLVATNDVHYLAKEDAEVQDVLICIGTGKTVDD 241 Q + ++ Q++ L+ E GIP+ AT DVHY+ KED L I G+ + D Sbjct: 162 FSYQP--FKGNQVLSEQILKLSEETGIPVTATGDVHYIRKEDKAAYRCLKAIKAGEKLTD 219 Query: 242 EERLKIGTDQLFLKSGEQMAALFPHVPEAIANTLNIAEKCNLELTFGEHILPAYSPLPEG 301 + L LK E+M ++ PEA+ ++ IAE+C ++++ G+ LP++ P P+G Sbjct: 220 APAEDL--PDLDLKPLEEMQNIYREHPEALQASVEIAEQCRVDVSLGQTRLPSF-PTPDG 276 Query: 302 MDAAAYLRELCWSGLEARYADTPRWSSPEEKDAAGKRLAYELGVIESMGFSDYFLIVWDF 361 A YL ++C GL +R+ P+E+ +RL YEL VI+ M FSDYFLIVWDF Sbjct: 277 TSADDYLTDICMEGLRSRFG------KPDERYL--RRLQYELDVIKRMKFSDYFLIVWDF 328 Query: 362 IAFCHRQGIVTGPGRGSSAGSLTAYCLRITDVDPLKYNLLFERFLNPERITMPDIDIDFS 421 + H +GIVTGPGRGS+AGSL AY L ITDVDP+K++LLFERFLNPER++MPDIDIDF Sbjct: 329 MKHAHEKGIVTGPGRGSAAGSLVAYVLYITDVDPIKHHLLFERFLNPERVSMPDIDIDFP 388 Query: 422 DERRDEVIAYVVDKYGKQHVAQIITFGTM 450 D RRDEVI YV KYG HVAQIITFGT+ Sbjct: 389 DTRRDEVIQYVQQKYGAMHVAQIITFGTL 417 Database: COG Posted date: Aug 3, 2010 9:58 AM Number of letters in database: 38,378,431 Number of sequences in database: 115,334 Lambda K H 0.321 0.139 0.424 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 115334 Number of Hits to DB: 35,134,970 Number of extensions: 1574080 Number of successful extensions: 2455 Number of sequences better than 1.0e-05: 32 Number of HSP's gapped: 2309 Number of HSP's successfully gapped: 34 Length of query: 465 Length of database: 38,378,431 Length adjustment: 110 Effective length of query: 355 Effective length of database: 25,691,691 Effective search space: 9120550305 Effective search space used: 9120550305 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 (21.9 bits) S2: 118 (50.1 bits)