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= 0002.0002.p (1356 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309447|ref|YP_003773539.1| DNA-directed RNA polymerase sub... 2663 0.0 >gi|300309447|ref|YP_003773539.1| DNA-directed RNA polymerase subunit beta [Herbaspirillum seropedicae SmR1] Length = 1368 Score = 2663 bits (6903), Expect = 0.0, Method: Compositional matrix adjust. Identities = 1290/1345 (95%), Positives = 1321/1345 (98%) Query: 1 MHYSFTEKKRIRKSFAKRANVHNVPFLLATQIESYQTFLQTDKTTSQRKNEGLQSAFTSI 60 MHYSFTEKKRIRKSFAKRANVHNVPFLLATQIESYQ FLQ ++ S+RKNEGLQSAFTSI Sbjct: 1 MHYSFTEKKRIRKSFAKRANVHNVPFLLATQIESYQNFLQPERAASERKNEGLQSAFTSI 60 Query: 61 FPIVSHNGFARLEFLSYVLGAPPFDVKECQQRGLTFASPLRAKVRLVILDKESPTKPVIK 120 FPIVSHNGFARLEFLSYVLGAPPFDVKECQQRGLTFASPLRAKVRLVILDKESPTKPV+K Sbjct: 61 FPIVSHNGFARLEFLSYVLGAPPFDVKECQQRGLTFASPLRAKVRLVILDKESPTKPVVK 120 Query: 121 EMKEQEVYMGELPLMTTTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSAR 180 EMKEQEVYMGELPLMTTTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSAR Sbjct: 121 EMKEQEVYMGELPLMTTTGSFVINGTERVIVSQLHRSPGVFFEHDRGKTHSSGKLLFSAR 180 Query: 181 IIPYRGSWLDFEFDPKDILFFRVDRRRKMPVTILLKAIGMTSEQILANFFVFDNFTLRAE 240 IIPYRGSWLDFEFDPKDILFFRVDRRRKMPVTILLKAIGMTSEQILANFFVFDNF L AE Sbjct: 181 IIPYRGSWLDFEFDPKDILFFRVDRRRKMPVTILLKAIGMTSEQILANFFVFDNFNLHAE 240 Query: 241 GAEMEFVSERLRGEVARFDILDKAGKPLVAKDKRINAKHVRDIEAAGIKQISVPEDYLLG 300 GA+MEFVSERLRGEVARFDI DK+GK +VAKDKRINAKHVRDIEAAGIK ISVPEDYLLG Sbjct: 241 GADMEFVSERLRGEVARFDITDKSGKVMVAKDKRINAKHVRDIEAAGIKHISVPEDYLLG 300 Query: 301 RVLAKNIVDGDTGEVIASANDELTEELLARLREANIDAVQTLYTNDLDQGGYISQTLRTD 360 RVLAKNIVD +TGEV+ASANDELTEELLA+LREANI A+QTLYTNDLDQGGYISQTLRTD Sbjct: 301 RVLAKNIVDPETGEVVASANDELTEELLAKLREANISAIQTLYTNDLDQGGYISQTLRTD 360 Query: 361 DTADQTAARVAIYRMMRPGEPPTEDSVEALFNGLFYSEDRYDLSAVGRMKFNRRIGRDEL 420 DTADQTAARVAIYRMMRPGEPPTE+SVEALFNGLFYSEDRYDLSAVGRMKFNRR+GRDEL Sbjct: 361 DTADQTAARVAIYRMMRPGEPPTEESVEALFNGLFYSEDRYDLSAVGRMKFNRRVGRDEL 420 Query: 421 TGAMTLSNEDILAVIKILVELRNGRGEVDDIDHLGNRRVRCVGELAENQFRAGLVRVERA 480 TG MTLSN+DILAVIKILVELRNGRGEVDDIDHLGNRRVRCVGELAENQFRAGLVRVERA Sbjct: 421 TGTMTLSNDDILAVIKILVELRNGRGEVDDIDHLGNRRVRCVGELAENQFRAGLVRVERA 480 Query: 481 VKERLGQAEADNLMPHDLINSKPISAAIREFFGSSQLSQFMDQTNPLSEITHKRRVSALG 540 VKERLGQAEADNLMPHDLINSKPISAAIREFFGSSQLSQFMDQTNPLSEITHKRRVSALG Sbjct: 481 VKERLGQAEADNLMPHDLINSKPISAAIREFFGSSQLSQFMDQTNPLSEITHKRRVSALG 540 Query: 541 PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFLETPYRKV 600 PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFLETPYRKV Sbjct: 541 PGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYARLNEYGFLETPYRKV 600 Query: 601 EGSKVTNQIDYLSAIEEGRYIIAQANATIDASLKLSDELVSAREAGETILVSPERVQYMD 660 EGSKVTNQIDYLSAIEEGRY+IAQANATID KLSDELVSAREAGETILVSPERVQYMD Sbjct: 601 EGSKVTNQIDYLSAIEEGRYVIAQANATIDGEGKLSDELVSAREAGETILVSPERVQYMD 660 Query: 661 VAPGQVVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPLVGTGIERTVAVDSGT 720 VAPGQVVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPLVGTGIERTVAVDSGT Sbjct: 661 VAPGQVVSVAASLIPFLEHDDANRALMGANMQRQAVPCLRPEKPLVGTGIERTVAVDSGT 720 Query: 721 TVQALRGGIVDYVDAGRVVIRVNDEEAQAGEVGVDIYNLIKYTRSNQNTNINQRPIVKVG 780 TVQALRGG+VDYVDAGRVVIRVND+EAQAGEVGVDIYNLIKYTRSNQNTNINQRPIVK+G Sbjct: 721 TVQALRGGVVDYVDAGRVVIRVNDDEAQAGEVGVDIYNLIKYTRSNQNTNINQRPIVKIG 780 Query: 781 DRVAKHDVIADGASTDLGELALGQNMLVAFMPWNGYNFEDSILISEKVVADDRYTSIHIE 840 DRVAKHDVIADGASTD+GELALGQNMLVAFMPWNGYNFEDSILISEKVVADDRYTSIHIE Sbjct: 781 DRVAKHDVIADGASTDMGELALGQNMLVAFMPWNGYNFEDSILISEKVVADDRYTSIHIE 840 Query: 841 ELSVVARDTKLGAEEITRDISNLAENQLARLDESGITYIGAEVEAGDTLVGKVTPKGETQ 900 ELSVVARDTKLGAEEITRDISNLAENQLARLDESGI YIGAEVEAGDTLVGKVTPKGETQ Sbjct: 841 ELSVVARDTKLGAEEITRDISNLAENQLARLDESGIVYIGAEVEAGDTLVGKVTPKGETQ 900 Query: 901 LTPEEKLLRAIFGEKASDVKDTSLRVPSGMVGTVIDVQVFTREGIQRDKRAQQIIDDELK 960 LTPEEKLLRAIFGEKASDVKDTSLRVPSGMVGTVIDVQVFTREGIQRDKRAQQIIDDELK Sbjct: 901 LTPEEKLLRAIFGEKASDVKDTSLRVPSGMVGTVIDVQVFTREGIQRDKRAQQIIDDELK 960 Query: 961 RYRLDLNDQLRIVEGDAFQRLEKMLIGKVANGGPKKLVKGTKLDKAYLDDLDKYHWFDIR 1020 RYRLDLNDQLRIVEGDAFQRLE++LIGKVANGGPKKLVKGTKLDKAYLDDLDK+HWFDIR Sbjct: 961 RYRLDLNDQLRIVEGDAFQRLERLLIGKVANGGPKKLVKGTKLDKAYLDDLDKFHWFDIR 1020 Query: 1021 PADDDMATALEAIKESIAEKRHQFDLAFEEKRKKLTQGDELPPGVQKMVKVYLAVKRRLQ 1080 PADDD+A ALEAIKESIAEKRHQFDLAFEEKRKKLTQGDELPPGVQKMVKVYLAVKRRLQ Sbjct: 1021 PADDDIANALEAIKESIAEKRHQFDLAFEEKRKKLTQGDELPPGVQKMVKVYLAVKRRLQ 1080 Query: 1081 PGDKMAGRHGNKGVVSRILPIEDMPHMADGTPADIVLNPLGVPSRMNVGQVLEVHLGWAA 1140 PGDKMAGRHGNKGVVSRILPIEDMPHMADGTPADIVLNPLGVPSRMNVGQVLEVHLGWAA Sbjct: 1081 PGDKMAGRHGNKGVVSRILPIEDMPHMADGTPADIVLNPLGVPSRMNVGQVLEVHLGWAA 1140 Query: 1141 KGLGLRIGEMLTAQVKIAELRKFLTTIYNESGKKEALDEFSDQEILELAANLKKGVPFAT 1200 KGLGLR+GEM+ AQ K+AELRKFLTTIYNESGK+E LD F+D+EI+EL NLKKGVPFAT Sbjct: 1141 KGLGLRLGEMVQAQAKVAELRKFLTTIYNESGKQEELDSFTDEEIIELVENLKKGVPFAT 1200 Query: 1201 PVFDGAHEDETRRMLDLAYPDHIAKQLGMTPSKNQVTMYDGRTGEAFERTVTVGYMHYLK 1260 PVFDGAHE+ETRRMLDLAYPD IAKQLGMTPSKNQVTMYDGRTGEAFERTVTVGYMHYLK Sbjct: 1201 PVFDGAHEEETRRMLDLAYPDPIAKQLGMTPSKNQVTMYDGRTGEAFERTVTVGYMHYLK 1260 Query: 1261 LHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQEMLTVK 1320 LHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQEMLTVK Sbjct: 1261 LHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQEMLTVK 1320 Query: 1321 SDDVNGRTKVYENLVKGDHVIDAGM 1345 SDDVNGRTKVYENLVKGDHVIDAGM Sbjct: 1321 SDDVNGRTKVYENLVKGDHVIDAGM 1345 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.318 0.136 0.384 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 4,092,497 Number of extensions: 177838 Number of successful extensions: 469 Number of sequences better than 1.0e-08: 1 Number of HSP's gapped: 467 Number of HSP's successfully gapped: 1 Length of query: 1356 Length of database: 1,619,870 Length adjustment: 97 Effective length of query: 1259 Effective length of database: 1,160,575 Effective search space: 1461163925 Effective search space used: 1461163925 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: 137 (57.4 bits)