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= 0001.0115.p (1413 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309448|ref|YP_003773540.1| DNA-directed RNA polymerase sub... 2877 0.0 >gi|300309448|ref|YP_003773540.1| DNA-directed RNA polymerase subunit beta [Herbaspirillum seropedicae SmR1] Length = 1413 Score = 2877 bits (7458), Expect = 0.0, Method: Compositional matrix adjust. Identities = 1409/1413 (99%), Positives = 1410/1413 (99%) Query: 1 MKALLDLFKQVQQNEQFDAIKIGLASPDKIRSWSFGEVKKPETINYRTFKPERDGLFCAK 60 MKALLDLFKQVQQNEQFDAIKIGLASPDKIRSWSFGEVKKPETINYRTFKPERDGLFCAK Sbjct: 1 MKALLDLFKQVQQNEQFDAIKIGLASPDKIRSWSFGEVKKPETINYRTFKPERDGLFCAK 60 Query: 61 IFGPIKDYECLCGKYKRLKHRGVICEKCGVEVTLAKVRRERMGHIELASPTAHIWFLKSL 120 IFGPIKDYECLCGKYKRLKHRGVICEKCGVEVTLAKVRRERMGHIELASPTAHIWFLKSL Sbjct: 61 IFGPIKDYECLCGKYKRLKHRGVICEKCGVEVTLAKVRRERMGHIELASPTAHIWFLKSL 120 Query: 121 PSRLGMVLDMTLRDIERVLYFEAYVVTDPGMTPLKKCQIMSEDDYAAKYEEYGDDFIAFM 180 PSRLGMVLDMTLRDIERVLYFEAYVVTDPGMTPLKKCQIMSEDDYAAKYEEYGDDFIAFM Sbjct: 121 PSRLGMVLDMTLRDIERVLYFEAYVVTDPGMTPLKKCQIMSEDDYAAKYEEYGDDFIAFM 180 Query: 181 GAEGIRELLRSIDIDREAETLRQELKDSKSEAKIKKYAKRLKVLEAFQRSGIKPEWMIME 240 GAEGIRELLRSIDIDREAETLRQELKDSKSEAKIKKYAKRLKVLEAFQRSGIKPEWMIME Sbjct: 181 GAEGIRELLRSIDIDREAETLRQELKDSKSEAKIKKYAKRLKVLEAFQRSGIKPEWMIME 240 Query: 241 VLPVLPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLMELRAPEIITRNEKRMLQ 300 VLPVLPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLMELRAPEIITRNEKRMLQ Sbjct: 241 VLPVLPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLMELRAPEIITRNEKRMLQ 300 Query: 301 EAVDSLLDNGRRGKAMTGANKRPLKSLAEMIKGKGGRFRQNLLGKRVDYSGRSVIVVGPQ 360 EAVDSLLDNGRRGKAMTGANKRPLKSLAEMIKGKGGRFRQNLLGKRVDYSGRSVIVVGPQ Sbjct: 301 EAVDSLLDNGRRGKAMTGANKRPLKSLAEMIKGKGGRFRQNLLGKRVDYSGRSVIVVGPQ 360 Query: 361 LKLHQCGLPKLMALELFKPFIFNKLELMGLSTTIKAAKKLVEAQEPVVWDILEEVIREHP 420 LKLHQCGLPKLMALELFKPFIFNKLELMGLSTTIKAAKKLVEAQEPVVWDILEEVIREHP Sbjct: 361 LKLHQCGLPKLMALELFKPFIFNKLELMGLSTTIKAAKKLVEAQEPVVWDILEEVIREHP 420 Query: 421 VMLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAFNADFDGDQMAVHVPLSIEAQMEA 480 VMLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAFNADFDGDQMAVHVPLSIEAQMEA Sbjct: 421 VMLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAFNADFDGDQMAVHVPLSIEAQMEA 480 Query: 481 RTLMLASNNILFPSNGEPSIVPSQDIVLGLYYATREAINGKNEGMMFQDVSEVIRAYDNK 540 RTLMLASNNILFPSNGEPSIVPSQDIVLGLYYATREAINGKNEGMMFQDVSEVIRAYDNK Sbjct: 481 RTLMLASNNILFPSNGEPSIVPSQDIVLGLYYATREAINGKNEGMMFQDVSEVIRAYDNK 540 Query: 541 EVELATRITVRIVEHPKDPVTGEFVRTVKRYETTIGRAILSEILPKGLPFSVLNRALKKK 600 EVELATRITVRIVEHPKDPVTGEFVRTVKRYETTIGRAILSEILPKGLPFSVLNRALKKK Sbjct: 541 EVELATRITVRIVEHPKDPVTGEFVRTVKRYETTIGRAILSEILPKGLPFSVLNRALKKK 600 Query: 601 EISKLINTSFRKCGLRATVVFADQLMQSGFRLATRAGISICVDDMLVPPQKATLIAAAES 660 EISKLINTSFRKCGLRATVVFADQLMQSGFRLATRAGISICVDDMLVPPQKATLIAAAES Sbjct: 601 EISKLINTSFRKCGLRATVVFADQLMQSGFRLATRAGISICVDDMLVPPQKATLIAAAES 660 Query: 661 EVKQIEQQYSSGLVTAGERYNKVVDIWGKAGDEVGKAMMDQLKVEDVITREGKKTTQESF 720 EVKQIEQQYSSGLVTAGERYNKVVDIWGKAGDEVGKAMMDQLKVEDVITREGKKTTQESF Sbjct: 661 EVKQIEQQYSSGLVTAGERYNKVVDIWGKAGDEVGKAMMDQLKVEDVITREGKKTTQESF 720 Query: 721 NAIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGA 780 NAIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGA Sbjct: 721 NAIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGA 780 Query: 781 RKGLADTALKTANSGYLTRRLVDVTQDLVVIEDDCGTSNGSAMKALVEGGEVIEALRDRI 840 RKGLADTALKTANSGYLTRRLVDVTQDLVVIEDDCGTSNGSAMKALVEGGEVIEALRDRI Sbjct: 781 RKGLADTALKTANSGYLTRRLVDVTQDLVVIEDDCGTSNGSAMKALVEGGEVIEALRDRI 840 Query: 841 LGRVAATDIVNPEDQSTLFEAGTLLDEDKVEEIERMGIDEVKVRTPLTCDTRYGLCAKCY 900 LGRVAATDIVNPEDQSTLFEAGTLLDEDKVEEIERMGIDEVKVRTPLTCDTRYGLCAKCY Sbjct: 841 LGRVAATDIVNPEDQSTLFEAGTLLDEDKVEEIERMGIDEVKVRTPLTCDTRYGLCAKCY 900 Query: 901 GRDLGRGLLVNSGEAVGVVAAQSIGEPGTQLTMRTFHIGGAASRAAVASSVEAKSNGTVR 960 GRDLGRGLLVNSGEAVGVVAAQSIGEPGTQLTMRTFHIGGAASRAAVASSVEAKSNGTVR Sbjct: 901 GRDLGRGLLVNSGEAVGVVAAQSIGEPGTQLTMRTFHIGGAASRAAVASSVEAKSNGTVR 960 Query: 961 FTATMRYVTNGKGEQIVISRSGEVLITDDLGRERERHKVPYGATLIVKDGLTIKAGTALA 1020 FTATMRYVTNGKGEQIVISRSGEVLITDDLGRERERHKVPYGATLIVKDGLTIKAGTALA Sbjct: 961 FTATMRYVTNGKGEQIVISRSGEVLITDDLGRERERHKVPYGATLIVKDGLTIKAGTALA 1020 Query: 1021 TWDPLTRPIITEYSGTVKFENVEEGSTVAKQIDEVTGLSTLVVIDAKRRGSSSKVMRPQV 1080 TWDPLTRPIITEYSGTVKFENVEEGSTVAKQIDEVTGLSTLVVIDAKRRG SSKVMRPQV Sbjct: 1021 TWDPLTRPIITEYSGTVKFENVEEGSTVAKQIDEVTGLSTLVVIDAKRRGPSSKVMRPQV 1080 Query: 1081 KLLNEQGEEVKIAGTEHSVTIGFQVGALITVKDGQQVHVGEVLARIPTESQKTRDITGGL 1140 KLLNEQGEEVKIAGTEHSVTIGFQVGALITVKDGQQVHVGEVLARIPTESQKTRDITGGL Sbjct: 1081 KLLNEQGEEVKIAGTEHSVTIGFQVGALITVKDGQQVHVGEVLARIPTESQKTRDITGGL 1140 Query: 1141 PRVAELFEARSPKDAGMLAEVTGTVAFGKETKGKQRLEITDMEGTKHEFLITKDKQVLVH 1200 PRVAELFEARSPKDAGMLAEVTGTVAFGKETKGKQRLEITDMEGTKHEFLITKDKQVLVH Sbjct: 1141 PRVAELFEARSPKDAGMLAEVTGTVAFGKETKGKQRLEITDMEGTKHEFLITKDKQVLVH 1200 Query: 1201 DGQVVNKGEMIVDGPADPQDILRLLGIEALARYIVDEVQDVYRLQGVKINDKHIEVIVRQ 1260 DGQVVNKGEMIVDGPADPQDILRLLGIEALARYIVDEVQDVYRLQGVKINDKHIEVIVRQ Sbjct: 1201 DGQVVNKGEMIVDGPADPQDILRLLGIEALARYIVDEVQDVYRLQGVKINDKHIEVIVRQ 1260 Query: 1261 MLRRVQVVEPGDTNYITGEQVERSELLDENDRVTAEGKIPATYENVLLGITKASLSTDSF 1320 MLRRVQVVEPGDTNYITGEQVERSELLDENDRVTAEGKIPATYENVLLGITKASLSTDSF Sbjct: 1261 MLRRVQVVEPGDTNYITGEQVERSELLDENDRVTAEGKIPATYENVLLGITKASLSTDSF 1320 Query: 1321 ISAASFQETTRVLTEAAIMGKKDGLRGLKENVIVGRLIPAGTGLAFHRARKEKDAWEAEE 1380 ISAASFQETTRVLTEAAIMGKKDGLRGLKENVIVGRLIPAGTGLAFHRARKEKDAWEAEE Sbjct: 1321 ISAASFQETTRVLTEAAIMGKKDGLRGLKENVIVGRLIPAGTGLAFHRARKEKDAWEAEE 1380 Query: 1381 RAALLEAERASRSEFADEEVSSTESIGGGESEA 1413 RAALLEAERASRSEF DEE+SSTESIGGGE EA Sbjct: 1381 RAALLEAERASRSEFGDEEISSTESIGGGEGEA 1413 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 0.317 0.135 0.378 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: 3,972,260 Number of extensions: 164928 Number of successful extensions: 489 Number of sequences better than 1.0e-08: 1 Number of HSP's gapped: 485 Number of HSP's successfully gapped: 1 Length of query: 1413 Length of database: 1,619,870 Length adjustment: 97 Effective length of query: 1316 Effective length of database: 1,160,575 Effective search space: 1527316700 Effective search space used: 1527316700 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)