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= 0034.0011.p (175 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311653|ref|YP_003775745.1| ferric regulator sigma-24 subun... 222 1e-59 gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor,... 62 3e-11 gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor ... 61 6e-11 gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor,... 59 2e-10 gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor ... 56 2e-09 >gi|300311653|ref|YP_003775745.1| ferric regulator sigma-24 subunit [Herbaspirillum seropedicae SmR1] Length = 178 Score = 222 bits (566), Expect = 1e-59, Method: Compositional matrix adjust. Identities = 114/175 (65%), Positives = 133/175 (76%), Gaps = 4/175 (2%) Query: 1 MHHATAPTG--LQQHFIGQRQRLREAAQRILGCPHRADDVVQDAYLKIREVQDQENCAIR 58 M+H T+ L++ FI R RLR+ A RILGCPHRADDVVQD ++KI EV D + I+ Sbjct: 1 MNHTTSTQAARLREQFIEHRARLRDVATRILGCPHRADDVVQDTFIKIAEVPDDFD--IK 58 Query: 59 QPQAYLMRIVRNLAIDRHRRCRFESDVFAEEEAGEDIHEEAQGPEAIAIGRQTLALVSQA 118 QP AYL RIVRNLAIDRHRR FE DVF EEE G D+H+E PEAIAI RQ L+++ +A Sbjct: 59 QPVAYLYRIVRNLAIDRHRRSAFECDVFTEEEDGLDVHQEGDSPEAIAISRQYLSMIGRA 118 Query: 119 LDGLPARTRRAFELYRLTGLSQREIAAELGISVTLVNFLIRDAQASCRQCLALTP 173 L+GLPARTRRAFELYRL+GL+QREIAAEL IS TLVNF+IRDA A CR L P Sbjct: 119 LEGLPARTRRAFELYRLSGLTQREIAAELNISTTLVNFMIRDALACCRNLLQNEP 173 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 62.0 bits (149), Expect = 3e-11, Method: Compositional matrix adjust. Identities = 49/149 (32%), Positives = 76/149 (51%), Gaps = 8/149 (5%) Query: 21 LREAAQRILGCPHRADDVVQDAYLKIREVQDQENCAIRQPQAYLMRIVRNLAIDRHRRCR 80 L++ +R +G A D+ QD +L++ + +R+P+A+L RI L +D+ RR Sbjct: 23 LQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALD-GVREPRAWLSRIAHGLVVDKLRREE 81 Query: 81 FESDVFAEEEAGEDIHE-EAQGPEAIAIGRQTLALVSQALDGLPARTRRAFELYRLTGLS 139 E EA + E E PEA I + L ++ L+GL R R+AF L RL +S Sbjct: 82 VERTCL---EAIAHLPEPEVVSPEARLILVEALCMIDALLEGLGERARQAFLLSRLDEMS 138 Query: 140 QREIAAELGISVTLVNFLIRDAQASCRQC 168 EIA LG+S++ V + A+ R C Sbjct: 139 YPEIARHLGVSLSSVE---KYMAAAIRHC 164 >gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor protein [Herbaspirillum seropedicae SmR1] Length = 173 Score = 60.8 bits (146), Expect = 6e-11, Method: Compositional matrix adjust. Identities = 52/161 (32%), Positives = 76/161 (47%), Gaps = 8/161 (4%) Query: 10 LQQHFIGQRQRLREAAQRILGCPHRADDVVQDAYLKIREVQDQENCAIRQPQAYLMRIVR 69 L F L++ +R + A+DV A++++ + D IR+P+A L I + Sbjct: 18 LVTEFTNSYSWLKQYLRRQVKSLADAEDVASAAFVEMASLPDV--SIIREPRALLTTISQ 75 Query: 70 NLAIDRHRRCRFESDVFAEEEAGEDIHEEAQ--GPEAIAIGRQTLALVSQALDGLPARTR 127 L D RR D+ A A EEA PE + QTL + + L GL R Sbjct: 76 RLVFDLWRR----RDLEAAYLAALATTEEATTPSPEVVLEVVQTLVNIDRLLYGLSKNAR 131 Query: 128 RAFELYRLTGLSQREIAAELGISVTLVNFLIRDAQASCRQC 168 +AF +L GL+ REIA LG+SV++V I A A C + Sbjct: 132 QAFLYSQLDGLTYREIAELLGVSVSMVRKYIAQALAKCYES 172 >gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 169 Score = 59.3 bits (142), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 50/146 (34%), Positives = 71/146 (48%), Gaps = 9/146 (6%) Query: 26 QRILGCPHRADDVVQDAYLKIREVQDQENCAIRQPQAYLMRIVRNLAIDRHRRCRFESDV 85 R L C H D+ QD + +R + + +R+P+AYL I + L RR + E+ Sbjct: 30 SRRLACRHLGADLAQDTF--VRLLGHRPPPDLREPRAYLTTIAKGLVASHLRRRQLET-- 85 Query: 86 FAEEEAGEDIHEEAQ-GPEAIAIGRQTLALVSQALDGLPARTRRAFELYRLTGLSQREIA 144 A EA + E +Q E + TL + + LD LPAR R+ F L +L GL IA Sbjct: 86 -AYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPARARQVFLLAQLDGLPYASIA 144 Query: 145 AELGISVTLVNFLIRDAQASCRQCLA 170 LGIS++ V R + R CLA Sbjct: 145 GLLGISLSTVK---RHMVLALRHCLA 167 >gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor protein [Herbaspirillum seropedicae SmR1] Length = 181 Score = 56.2 bits (134), Expect = 2e-09, Method: Compositional matrix adjust. Identities = 49/157 (31%), Positives = 80/157 (50%), Gaps = 4/157 (2%) Query: 7 PTGLQQHFIGQRQRLREAAQRILGCPHRADDVVQDAYLKIREVQDQENCAIRQPQAYLMR 66 P ++ + L+ QR LG +A D+ QD +L++ ++ I +P+AYL Sbjct: 17 PMSIEALYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLG-SERVPSVIHEPRAYLTT 75 Query: 67 IVRNLAIDRHRRCRFESDVFAEEEAGEDIHEEAQGPEAIAIGRQTLALVSQALDGLPART 126 + + L + RR + E E + A P+ AI +TL + Q LD LP+ Sbjct: 76 VAQRLVSNLWRREKLEQAYL--EALAQAPVALAPSPQEQAILLETLLELDQLLDELPSIV 133 Query: 127 RRAFELYRLTGLSQREIAAELGISV-TLVNFLIRDAQ 162 RRAF L +L GL+ ++AA LGIS+ T+ +L++ Q Sbjct: 134 RRAFLLSQLDGLTHAQVAAALGISIPTVKRYLVKALQ 170 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 0.324 0.136 0.398 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: 470,016 Number of extensions: 15812 Number of successful extensions: 90 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 88 Number of HSP's successfully gapped: 7 Length of query: 175 Length of database: 1,619,870 Length adjustment: 79 Effective length of query: 96 Effective length of database: 1,245,805 Effective search space: 119597280 Effective search space used: 119597280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 127 (53.5 bits)