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= 0011.0367.p (200 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... 361 e-101 gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor,... 74 1e-14 gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor,... 64 1e-11 gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor ... 63 1e-11 gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor,... 61 5e-11 >gi|300311653|ref|YP_003775745.1| ferric regulator sigma-24 subunit [Herbaspirillum seropedicae SmR1] Length = 178 Score = 361 bits (926), Expect = e-101, Method: Compositional matrix adjust. Identities = 177/178 (99%), Positives = 178/178 (100%) Query: 23 VNHTTSTQAARLREQFIEHRARLRDVATRILGCPHRADDVVQDTFIKIAEVPDDFDIKQP 82 +NHTTSTQAARLREQFIEHRARLRDVATRILGCPHRADDVVQDTFIKIAEVPDDFDIKQP Sbjct: 1 MNHTTSTQAARLREQFIEHRARLRDVATRILGCPHRADDVVQDTFIKIAEVPDDFDIKQP 60 Query: 83 VAYLYRIVRNLAIDRHRRSAFECDVFTEEEDGLDVHQEGDSPEAIAISRQYLSMIGRALE 142 VAYLYRIVRNLAIDRHRRSAFECDVFTEEEDGLDVHQEGDSPEAIAISRQYLSMIGRALE Sbjct: 61 VAYLYRIVRNLAIDRHRRSAFECDVFTEEEDGLDVHQEGDSPEAIAISRQYLSMIGRALE 120 Query: 143 GLPARTRRAFELYRLSGLTQREIAAELNISTTLVNFMIRDALACCRNLLQNEPELAGS 200 GLPARTRRAFELYRLSGLTQREIAAELNISTTLVNFMIRDALACCRNLLQNEPELAGS Sbjct: 121 GLPARTRRAFELYRLSGLTQREIAAELNISTTLVNFMIRDALACCRNLLQNEPELAGS 178 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 73.6 bits (179), Expect = 1e-14, Method: Compositional matrix adjust. Identities = 58/172 (33%), Positives = 81/172 (47%), Gaps = 5/172 (2%) Query: 23 VNHTTSTQAARLREQFIEHRARLRDVATRILGCPHRADDVVQDTFIKIAEVPDDFD-IKQ 81 V HT Q R + EH L+ R +G A D+ QDTF+++ P D +++ Sbjct: 3 VPHTVHAQ--RFHTLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVRE 60 Query: 82 PVAYLYRIVRNLAIDRHRRSAFECDVFTEEEDGLDVHQEGDSPEAIAISRQYLSMIGRAL 141 P A+L RI L +D+ RR E E E SPEA I + L MI L Sbjct: 61 PRAWLSRIAHGLVVDKLRREEVERTCL--EAIAHLPEPEVVSPEARLILVEALCMIDALL 118 Query: 142 EGLPARTRRAFELYRLSGLTQREIAAELNISTTLVNFMIRDALACCRNLLQN 193 EGL R R+AF L RL ++ EIA L +S + V + A+ C + Q+ Sbjct: 119 EGLGERARQAFLLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCYLMRQS 170 >gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 178 Score = 63.5 bits (153), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 52/162 (32%), Positives = 75/162 (46%), Gaps = 13/162 (8%) Query: 32 ARLREQFIEHRARLRDVATRILGCPHRADDVVQDTFIKIAEVPDDFDIKQPVAYLYRIVR 91 +R+ FIEH LR R +G A+DV +TF ++ P ++++P A L I R Sbjct: 14 SRIEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPPQEVREPRALLTTISR 73 Query: 92 NLAIDRHRRSAFECDVFTEEEDGLD--VHQEGD----SPEAIAISRQYLSMIGRALEGLP 145 + + RR EE L H GD SPE Q L + +AL GL Sbjct: 74 RIVYELWRRRDL-------EEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQALAGLS 126 Query: 146 ARTRRAFELYRLSGLTQREIAAELNISTTLVNFMIRDALACC 187 A+ AF LY+L GLT + I A+L I+ ++ + L C Sbjct: 127 AKECAAFLLYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQC 168 >gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor protein [Herbaspirillum seropedicae SmR1] Length = 173 Score = 63.2 bits (152), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 55/168 (32%), Positives = 77/168 (45%), Gaps = 9/168 (5%) Query: 25 HTTSTQAAR---LREQFIEHRARLRDVATRILGCPHRADDVVQDTFIKIAEVPDDFDIKQ 81 H+ + Q R L +F + L+ R + A+DV F+++A +PD I++ Sbjct: 6 HSYADQPFRHDFLVTEFTNSYSWLKQYLRRQVKSLADAEDVASAAFVEMASLPDVSIIRE 65 Query: 82 PVAYLYRIVRNLAIDRHRRSAFECDVFTEEEDGLDVHQEGD--SPEAIAISRQYLSMIGR 139 P A L I + L D RR D+ L +E SPE + Q L I R Sbjct: 66 PRALLTTISQRLVFDLWRRR----DLEAAYLAALATTEEATTPSPEVVLEVVQTLVNIDR 121 Query: 140 ALEGLPARTRRAFELYRLSGLTQREIAAELNISTTLVNFMIRDALACC 187 L GL R+AF +L GLT REIA L +S ++V I ALA C Sbjct: 122 LLYGLSKNARQAFLYSQLDGLTYREIAELLGVSVSMVRKYIAQALAKC 169 >gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 169 Score = 61.2 bits (147), Expect = 5e-11, Method: Compositional matrix adjust. Identities = 50/152 (32%), Positives = 67/152 (44%), Gaps = 6/152 (3%) Query: 38 FIEHRARLRDVATRILGCPHRADDVVQDTFIKIAEVPDDFDIKQPVAYLYRIVRNLAIDR 97 + EH L +R L C H D+ QDTF+++ D+++P AYL I + L Sbjct: 18 YREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGHRPPPDLREPRAYLTTIAKGLVASH 77 Query: 98 HRRSAFECDVFTEEEDGLDVHQEGDSPEAI--AISRQYLSMIGRALEGLPARTRRAFELY 155 RR E T + L E P A + L I R L+ LPAR R+ F L Sbjct: 78 LRRRQLE----TAYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPARARQVFLLA 133 Query: 156 RLSGLTQREIAAELNISTTLVNFMIRDALACC 187 +L GL IA L IS + V + AL C Sbjct: 134 QLDGLPYASIAGLLGISLSTVKRHMVLALRHC 165 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 0.137 0.407 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: 584,298 Number of extensions: 22399 Number of successful extensions: 108 Number of sequences better than 1.0e-08: 8 Number of HSP's gapped: 104 Number of HSP's successfully gapped: 8 Length of query: 200 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 119 Effective length of database: 1,236,335 Effective search space: 147123865 Effective search space used: 147123865 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: 128 (53.9 bits)