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= 0002.0004.p (1384 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... 2664 0.0 >gi|300309448|ref|YP_003773540.1| DNA-directed RNA polymerase subunit beta [Herbaspirillum seropedicae SmR1] Length = 1413 Score = 2664 bits (6904), Expect = 0.0, Method: Compositional matrix adjust. Identities = 1310/1376 (95%), Positives = 1348/1376 (97%), Gaps = 3/1376 (0%) Query: 11 KKPETINYRTFKPERDGLFCAKIFGPIKDYECLCGKYKRLKHRGVICEKCGVEVTLAKVR 70 KKPETINYRTFKPERDGLFCAKIFGPIKDYECLCGKYKRLKHRGVICEKCGVEVTLAKVR Sbjct: 39 KKPETINYRTFKPERDGLFCAKIFGPIKDYECLCGKYKRLKHRGVICEKCGVEVTLAKVR 98 Query: 71 RERMGHIELASPTAHIWFLKSLPSRLGMVLDMTLRDIERVLYFEAYVVTDPGMTPLKKCQ 130 RERMGHIELASPTAHIWFLKSLPSRLGMVLDMTLRDIERVLYFEAYVVTDPGMTPLKKCQ Sbjct: 99 RERMGHIELASPTAHIWFLKSLPSRLGMVLDMTLRDIERVLYFEAYVVTDPGMTPLKKCQ 158 Query: 131 IMSEDDYAAKYEEYGDDFTAFMGAEGIRELLRSIDIDRDAETLRVELKESKSEAKIKKYA 190 IMSEDDYAAKYEEYGDDF AFMGAEGIRELLRSIDIDR+AETLR ELK+SKSEAKIKKYA Sbjct: 159 IMSEDDYAAKYEEYGDDFIAFMGAEGIRELLRSIDIDREAETLRQELKDSKSEAKIKKYA 218 Query: 191 KRLKVLEAFQRSGIKPDWMIMEVLPVLPPELRPLVPLDGGRFATSDLNDLYRRVINRNNR 250 KRLKVLEAFQRSGIKP+WMIMEVLPVLPPELRPLVPLDGGRFATSDLNDLYRRVINRNNR Sbjct: 219 KRLKVLEAFQRSGIKPEWMIMEVLPVLPPELRPLVPLDGGRFATSDLNDLYRRVINRNNR 278 Query: 251 LKRLMELRAPEIITRNEKRMLQEAVDSLLDNGRRGKAMTGANKRPLKSLAEMIKGKGGRF 310 LKRLMELRAPEIITRNEKRMLQEAVDSLLDNGRRGKAMTGANKRPLKSLAEMIKGKGGRF Sbjct: 279 LKRLMELRAPEIITRNEKRMLQEAVDSLLDNGRRGKAMTGANKRPLKSLAEMIKGKGGRF 338 Query: 311 RQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFIFNKLELMGLATTIKAAK 370 RQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFIFNKLELMGL+TTIKAAK Sbjct: 339 RQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFIFNKLELMGLSTTIKAAK 398 Query: 371 KLVEIQEPVVWDILEDVIREHPVMLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAFN 430 KLVE QEPVVWDILE+VIREHPVMLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAFN Sbjct: 399 KLVEAQEPVVWDILEEVIREHPVMLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAFN 458 Query: 431 ADFDGDQMAVHVPLSIEAQMEARTLMLASNNILFPSNGEPSIVPSQDIVLGLYYATREAI 490 ADFDGDQMAVHVPLSIEAQMEARTLMLASNNILFPSNGEPSIVPSQDIVLGLYYATREAI Sbjct: 459 ADFDGDQMAVHVPLSIEAQMEARTLMLASNNILFPSNGEPSIVPSQDIVLGLYYATREAI 518 Query: 491 NAKNEGMLFQDVSEVIRAYDNKEVELATRVTVRIVENPKDPVTGEFVRTVKRYETTVGRA 550 N KNEGM+FQDVSEVIRAYDNKEVELATR+TVRIVE+PKDPVTGEFVRTVKRYETT+GRA Sbjct: 519 NGKNEGMMFQDVSEVIRAYDNKEVELATRITVRIVEHPKDPVTGEFVRTVKRYETTIGRA 578 Query: 551 ILSEILPKGLPFSVLNRALKKKEISKLINTSFRKCGLRATVVFADQLMQSGFRLATRAGI 610 ILSEILPKGLPFSVLNRALKKKEISKLINTSFRKCGLRATVVFADQLMQSGFRLATRAGI Sbjct: 579 ILSEILPKGLPFSVLNRALKKKEISKLINTSFRKCGLRATVVFADQLMQSGFRLATRAGI 638 Query: 611 SICVDDMLVPPQKATIIATAESEVKQIEQQYSSGLVTAGERYNKVVDIWGKAGDDVGKAM 670 SICVDDMLVPPQKAT+IA AESEVKQIEQQYSSGLVTAGERYNKVVDIWGKAGD+VGKAM Sbjct: 639 SICVDDMLVPPQKATLIAAAESEVKQIEQQYSSGLVTAGERYNKVVDIWGKAGDEVGKAM 698 Query: 671 MDQLKVEDVVRRDGTKGTQESFNAIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIET 730 MDQLKVEDV+ R+G K TQESFNAIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIET Sbjct: 699 MDQLKVEDVITREGKKTTQESFNAIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIET 758 Query: 731 PITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVTQDLVVIEDDCGTS 790 PITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVTQDLVVIEDDCGTS Sbjct: 759 PITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVTQDLVVIEDDCGTS 818 Query: 791 NGASMKAMVEGGEVIEALRDRILGRVAATDIINPETQATLYEAGTLMDEDTVEEVERLGI 850 NG++MKA+VEGGEVIEALRDRILGRVAATDI+NPE Q+TL+EAGTL+DED VEE+ER+GI Sbjct: 819 NGSAMKALVEGGEVIEALRDRILGRVAATDIVNPEDQSTLFEAGTLLDEDKVEEIERMGI 878 Query: 851 DEVKVRTPLTCDTRYGLCAKCYGRDLGRGVLVNSGEAVGVIAAQSIGEPGTQLTMRTFHI 910 DEVKVRTPLTCDTRYGLCAKCYGRDLGRG+LVNSGEAVGV+AAQSIGEPGTQLTMRTFHI Sbjct: 879 DEVKVRTPLTCDTRYGLCAKCYGRDLGRGLLVNSGEAVGVVAAQSIGEPGTQLTMRTFHI 938 Query: 911 GGAASRAAVASSVEAKSNGTIRFTATMRYVTNGKGELIVISRSGEVLITDDLGRERERHK 970 GGAASRAAVASSVEAKSNGT+RFTATMRYVTNGKGE IVISRSGEVLITDDLGRERERHK Sbjct: 939 GGAASRAAVASSVEAKSNGTVRFTATMRYVTNGKGEQIVISRSGEVLITDDLGRERERHK 998 Query: 971 VPYGATLIVKDGMVIKAGTALATWDPLTRPIITEYTGTVKFENVEEGSTVAKQIDEVTGL 1030 VPYGATLIVKDG+ IKAGTALATWDPLTRPIITEY+GTVKFENVEEGSTVAKQIDEVTGL Sbjct: 999 VPYGATLIVKDGLTIKAGTALATWDPLTRPIITEYSGTVKFENVEEGSTVAKQIDEVTGL 1058 Query: 1031 STLVVIDAKRRGSSAAKVLRPQVKLLNEQGEEVKIAGTEHAVTIGFQVGALITVKDGQQV 1090 STLVVIDAKRRG S +KV+RPQVKLLNEQGEEVKIAGTEH+VTIGFQVGALITVKDGQQV Sbjct: 1059 STLVVIDAKRRGPS-SKVMRPQVKLLNEQGEEVKIAGTEHSVTIGFQVGALITVKDGQQV 1117 Query: 1091 HVGEVLARIPTESQKTRDITGGLPRVAELFEARSPKDAGMLAEVTGTVAFGKETKGKQRL 1150 HVGEVLARIPTESQKTRDITGGLPRVAELFEARSPKDAGMLAEVTGTVAFGKETKGKQRL Sbjct: 1118 HVGEVLARIPTESQKTRDITGGLPRVAELFEARSPKDAGMLAEVTGTVAFGKETKGKQRL 1177 Query: 1151 EITDMDGAKHEFLITKDKQVLVHDGQVVNKGEMIVDGPADPQDILRLLGIEALARYIVDE 1210 EITDM+G KHEFLITKDKQVLVHDGQVVNKGEMIVDGPADPQDILRLLGIEALARYIVDE Sbjct: 1178 EITDMEGTKHEFLITKDKQVLVHDGQVVNKGEMIVDGPADPQDILRLLGIEALARYIVDE 1237 Query: 1211 VQDVYRLQGVKINDKHIEVIVRQMLRRVQVVDPGDTNYITGEQVERSELLDENDRVNAET 1270 VQDVYRLQGVKINDKHIEVIVRQMLRRVQVV+PGDTNYITGEQVERSELLDENDRV AE Sbjct: 1238 VQDVYRLQGVKINDKHIEVIVRQMLRRVQVVEPGDTNYITGEQVERSELLDENDRVTAEG 1297 Query: 1271 KIPATYENVLLGITKASLSTDSFISAASFQETTRVLTEAAIMGKKDGLRGLKENVIVGRL 1330 KIPATYENVLLGITKASLSTDSFISAASFQETTRVLTEAAIMGKKDGLRGLKENVIVGRL Sbjct: 1298 KIPATYENVLLGITKASLSTDSFISAASFQETTRVLTEAAIMGKKDGLRGLKENVIVGRL 1357 Query: 1331 IPAGTGLAFHRARKEKDAWEADERAALLESERQAR--VTETEAHSAETFGGADGEA 1384 IPAGTGLAFHRARKEKDAWEA+ERAALLE+ER +R + E S E+ GG +GEA Sbjct: 1358 IPAGTGLAFHRARKEKDAWEAEERAALLEAERASRSEFGDEEISSTESIGGGEGEA 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 0.381 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: 3,979,459 Number of extensions: 164933 Number of successful extensions: 494 Number of sequences better than 1.0e-08: 1 Number of HSP's gapped: 489 Number of HSP's successfully gapped: 1 Length of query: 1384 Length of database: 1,619,870 Length adjustment: 97 Effective length of query: 1287 Effective length of database: 1,160,575 Effective search space: 1493660025 Effective search space used: 1493660025 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)