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= 0034.0328.p (1412 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... 2739 0.0 >gi|300309448|ref|YP_003773540.1| DNA-directed RNA polymerase subunit beta [Herbaspirillum seropedicae SmR1] Length = 1413 Score = 2739 bits (7100), Expect = 0.0, Method: Compositional matrix adjust. Identities = 1344/1414 (95%), Positives = 1384/1414 (97%), Gaps = 3/1414 (0%) Query: 1 MKALLDLFKQVQQNEQFDAIKIGLASPEKIRSWSYGEVKKPETINYRTFKPERDGLFCAK 60 MKALLDLFKQVQQNEQFDAIKIGLASP+KIRSWS+GEVKKPETINYRTFKPERDGLFCAK Sbjct: 1 MKALLDLFKQVQQNEQFDAIKIGLASPDKIRSWSFGEVKKPETINYRTFKPERDGLFCAK 60 Query: 61 IFGPIKDYECLCGKYKRLKHRGVICEKCGVEVTLAKVRRERMGHIELASPTAHIWFLKSL 120 IFGPIKDYECLCGKYKRLKHRGVICEKCGVEVTLAKVRRERMGHIELASPTAHIWFLKSL Sbjct: 61 IFGPIKDYECLCGKYKRLKHRGVICEKCGVEVTLAKVRRERMGHIELASPTAHIWFLKSL 120 Query: 121 PSRLGMVLDMTLRDIERVLYFEAYVVTDPGMTPLKKCQIMSEDDYAAKYEEYGDDFTAFM 180 PSRLGMVLDMTLRDIERVLYFEAYVVTDPGMTPLKKCQIMSEDDYAAKYEEYGDDF AFM Sbjct: 121 PSRLGMVLDMTLRDIERVLYFEAYVVTDPGMTPLKKCQIMSEDDYAAKYEEYGDDFIAFM 180 Query: 181 GAEGIRELLRSIDIDRDAETLRVELKESKSEAKIKKYAKRLKVLEAFQRSGIKPDWMIME 240 GAEGIRELLRSIDIDR+AETLR ELK+SKSEAKIKKYAKRLKVLEAFQRSGIKP+WMIME Sbjct: 181 GAEGIRELLRSIDIDREAETLRQELKDSKSEAKIKKYAKRLKVLEAFQRSGIKPEWMIME 240 Query: 241 VLPVLPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLMELRAPEIITRNEKRMLQ 300 VLPVLPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLMELRAPEIITRNEKRMLQ Sbjct: 241 VLPVLPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLMELRAPEIITRNEKRMLQ 300 Query: 301 EAVDSLLDNGRRGKAMTGANKRPLKSLAEMIKGKGGRFRQNLLGKRVDYSGRSVIVVGPQ 360 EAVDSLLDNGRRGKAMTGANKRPLKSLAEMIKGKGGRFRQNLLGKRVDYSGRSVIVVGPQ Sbjct: 301 EAVDSLLDNGRRGKAMTGANKRPLKSLAEMIKGKGGRFRQNLLGKRVDYSGRSVIVVGPQ 360 Query: 361 LKLHQCGLPKLMALELFKPFIFNKLELMGLATTIKAAKKLVEIQEPVVWDILEDVIREHP 420 LKLHQCGLPKLMALELFKPFIFNKLELMGL+TTIKAAKKLVE QEPVVWDILE+VIREHP Sbjct: 361 LKLHQCGLPKLMALELFKPFIFNKLELMGLSTTIKAAKKLVEAQEPVVWDILEEVIREHP 420 Query: 421 VMLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAFNADFDGDQMAVHVPLSIEAQMEA 480 VMLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAFNADFDGDQMAVHVPLSIEAQMEA Sbjct: 421 VMLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAFNADFDGDQMAVHVPLSIEAQMEA 480 Query: 481 RTLMLASNNILFPSNGEPSIVPSQDIVLGLYYATREAINAKNEGMLFQDVSEVIRAYDNK 540 RTLMLASNNILFPSNGEPSIVPSQDIVLGLYYATREAIN KNEGM+FQDVSEVIRAYDNK Sbjct: 481 RTLMLASNNILFPSNGEPSIVPSQDIVLGLYYATREAINGKNEGMMFQDVSEVIRAYDNK 540 Query: 541 EVELATRVTVRIVENPKDPVTGEFVRTVKRYETTVGRAILSEILPKGLPFSVLNRALKKK 600 EVELATR+TVRIVE+PKDPVTGEFVRTVKRYETT+GRAILSEILPKGLPFSVLNRALKKK Sbjct: 541 EVELATRITVRIVEHPKDPVTGEFVRTVKRYETTIGRAILSEILPKGLPFSVLNRALKKK 600 Query: 601 EISKLINTSFRKCGLRATVVFADQLMQSGFRLATRAGISICVDDMLVPPQKATIIATAEQ 660 EISKLINTSFRKCGLRATVVFADQLMQSGFRLATRAGISICVDDMLVPPQKAT+IA AE Sbjct: 601 EISKLINTSFRKCGLRATVVFADQLMQSGFRLATRAGISICVDDMLVPPQKATLIAAAES 660 Query: 661 EVKQIEQQYSSGLVTAGERYNKVVDIWGKAGDDVGKAMMDQLKVEDVVRRDGTKGTQESF 720 EVKQIEQQYSSGLVTAGERYNKVVDIWGKAGD+VGKAMMDQLKVEDV+ R+G K TQESF Sbjct: 661 EVKQIEQQYSSGLVTAGERYNKVVDIWGKAGDEVGKAMMDQLKVEDVITREGKKTTQESF 720 Query: 721 NAIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGA 780 NAIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGA Sbjct: 721 NAIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGA 780 Query: 781 RKGLADTALKTANSGYLTRRLVDVTQDLVVIEDDCGTSNGASMKAMVEGGEVIEALRDRI 840 RKGLADTALKTANSGYLTRRLVDVTQDLVVIEDDCGTSNG++MKA+VEGGEVIEALRDRI Sbjct: 781 RKGLADTALKTANSGYLTRRLVDVTQDLVVIEDDCGTSNGSAMKALVEGGEVIEALRDRI 840 Query: 841 LGRVAATDIINPETQATLYEAGTLMDEDTVEEVERLGIDEVKVRTPLTCDTRYGLCAKCY 900 LGRVAATDI+NPE Q+TL+EAGTL+DED VEE+ER+GIDEVKVRTPLTCDTRYGLCAKCY Sbjct: 841 LGRVAATDIVNPEDQSTLFEAGTLLDEDKVEEIERMGIDEVKVRTPLTCDTRYGLCAKCY 900 Query: 901 GRDLGRGVLVNSGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAVASSVEAKSNGTIR 960 GRDLGRG+LVNSGEAVGV+AAQSIGEPGTQLTMRTFHIGGAASRAAVASSVEAKSNGT+R Sbjct: 901 GRDLGRGLLVNSGEAVGVVAAQSIGEPGTQLTMRTFHIGGAASRAAVASSVEAKSNGTVR 960 Query: 961 FTATMRYVTNGKGELIVISRSGEVLITDDLGRERERHKVPYGATLIVKDGMVIKAGTALA 1020 FTATMRYVTNGKGE IVISRSGEVLITDDLGRERERHKVPYGATLIVKDG+ IKAGTALA Sbjct: 961 FTATMRYVTNGKGEQIVISRSGEVLITDDLGRERERHKVPYGATLIVKDGLTIKAGTALA 1020 Query: 1021 TWDPLTRPIITEYTGTVKFENVEEGSTVAKQIDEVTGLSTLVVIDAKRRGSSAAKVLRPQ 1080 TWDPLTRPIITEY+GTVKFENVEEGSTVAKQIDEVTGLSTLVVIDAKRRG S +KV+RPQ Sbjct: 1021 TWDPLTRPIITEYSGTVKFENVEEGSTVAKQIDEVTGLSTLVVIDAKRRGPS-SKVMRPQ 1079 Query: 1081 VKLLNEQGEEVKIAGTEHAVTIGFQVGALITVKDGQQVHVGEVLARIPTESQKTRDITGG 1140 VKLLNEQGEEVKIAGTEH+VTIGFQVGALITVKDGQQVHVGEVLARIPTESQKTRDITGG Sbjct: 1080 VKLLNEQGEEVKIAGTEHSVTIGFQVGALITVKDGQQVHVGEVLARIPTESQKTRDITGG 1139 Query: 1141 LPRVAELFEARSPKDAGMLAEVTGTVAFGKETKGKQRLEITDMDGAKHEFLITKDKQVLV 1200 LPRVAELFEARSPKDAGMLAEVTGTVAFGKETKGKQRLEITDM+G KHEFLITKDKQVLV Sbjct: 1140 LPRVAELFEARSPKDAGMLAEVTGTVAFGKETKGKQRLEITDMEGTKHEFLITKDKQVLV 1199 Query: 1201 HDGQVVNKGEMIVDGPADPQDILRLLGIEALARYIVDEVQDVYRLQGVKINDKHIEVIVR 1260 HDGQVVNKGEMIVDGPADPQDILRLLGIEALARYIVDEVQDVYRLQGVKINDKHIEVIVR Sbjct: 1200 HDGQVVNKGEMIVDGPADPQDILRLLGIEALARYIVDEVQDVYRLQGVKINDKHIEVIVR 1259 Query: 1261 QMLRRVQVVDPGDTNYITGEQVERSELLDENDRVNAATKIPATYENVLLGITKASLSTDS 1320 QMLRRVQVV+PGDTNYITGEQVERSELLDENDRV A KIPATYENVLLGITKASLSTDS Sbjct: 1260 QMLRRVQVVEPGDTNYITGEQVERSELLDENDRVTAEGKIPATYENVLLGITKASLSTDS 1319 Query: 1321 FISAASFQETTRVLTEAAIMGKKDGLRGLKENVIVGRLIPAGTGLAFHRARKEKDAWEAD 1380 FISAASFQETTRVLTEAAIMGKKDGLRGLKENVIVGRLIPAGTGLAFHRARKEKDAWEA+ Sbjct: 1320 FISAASFQETTRVLTEAAIMGKKDGLRGLKENVIVGRLIPAGTGLAFHRARKEKDAWEAE 1379 Query: 1381 ERAALLESERVAR--VTETEAHSAETFGGTDGEA 1412 ERAALLE+ER +R + E S E+ GG +GEA Sbjct: 1380 ERAALLEAERASRSEFGDEEISSTESIGGGEGEA 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 0.318 0.135 0.380 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: 4,106,424 Number of extensions: 170970 Number of successful extensions: 499 Number of sequences better than 1.0e-08: 1 Number of HSP's gapped: 494 Number of HSP's successfully gapped: 1 Length of query: 1412 Length of database: 1,619,870 Length adjustment: 97 Effective length of query: 1315 Effective length of database: 1,160,575 Effective search space: 1526156125 Effective search space used: 1526156125 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)