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= 0001.2195.p (173 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... 228 2e-61 gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor,... 71 6e-14 gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor ... 66 2e-12 gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor,... 64 8e-12 gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor,... 55 4e-09 >gi|300311653|ref|YP_003775745.1| ferric regulator sigma-24 subunit [Herbaspirillum seropedicae SmR1] Length = 178 Score = 228 bits (581), Expect = 2e-61, Method: Compositional matrix adjust. Identities = 116/168 (69%), Positives = 131/168 (77%), Gaps = 4/168 (2%) Query: 5 SIQAAGFDLSLHQHFIGQRQRLREAAQRILGCPYRAEDVVQDAYLKIHEVPASFDIRQPQ 64 S QAA L + FI R RLR+ A RILGCP+RA+DVVQD ++KI EVP FDI+QP Sbjct: 6 STQAA----RLREQFIEHRARLRDVATRILGCPHRADDVVQDTFIKIAEVPDDFDIKQPV 61 Query: 65 AYLLRIVRNLAIDHHRRSAFESDVFAAEEDGLAVHEEAQGPEAIAIGRQTLACISQALDS 124 AYL RIVRNLAID HRRSAFE DVF EEDGL VH+E PEAIAI RQ L+ I +AL+ Sbjct: 62 AYLYRIVRNLAIDRHRRSAFECDVFTEEEDGLDVHQEGDSPEAIAISRQYLSMIGRALEG 121 Query: 125 LPARTRRAFELYRLAGLSQREIAAELGVSVTLVNFLIRDALASCRQHL 172 LPARTRRAFELYRL+GL+QREIAAEL +S TLVNF+IRDALA CR L Sbjct: 122 LPARTRRAFELYRLSGLTQREIAAELNISTTLVNFMIRDALACCRNLL 169 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 70.9 bits (172), Expect = 6e-14, Method: Compositional matrix adjust. Identities = 55/167 (32%), Positives = 79/167 (47%), Gaps = 7/167 (4%) Query: 3 PESIQAAGFDLSLHQHFIGQRQRLREAAQRILGCPYRAEDVVQDAYLKIHEVPASFD-IR 61 P ++ A F +H +Q LR R +G + A D+ QD +L++ P + D +R Sbjct: 4 PHTVHAQRFHTLYSEHHGWLQQWLR----RRVGSSFDAADLAQDTFLRVLGKPGALDGVR 59 Query: 62 QPQAYLLRIVRNLAIDHHRRSAFESDVFAAEEDGLAVHEEAQGPEAIAIGRQTLACISQA 121 +P+A+L RI L +D RR E E E PEA I + L I Sbjct: 60 EPRAWLSRIAHGLVVDKLRREEVERTCL--EAIAHLPEPEVVSPEARLILVEALCMIDAL 117 Query: 122 LDSLPARTRRAFELYRLAGLSQREIAAELGVSVTLVNFLIRDALASC 168 L+ L R R+AF L RL +S EIA LGVS++ V + A+ C Sbjct: 118 LEGLGERARQAFLLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHC 164 >gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor protein [Herbaspirillum seropedicae SmR1] Length = 173 Score = 65.9 bits (159), Expect = 2e-12, Method: Compositional matrix adjust. Identities = 57/156 (36%), Positives = 77/156 (49%), Gaps = 6/156 (3%) Query: 15 LHQHFIGQRQRLREAAQRILGCPYRAEDVVQDAYLKIHEVPASFDIRQPQAYLLRIVRNL 74 L F L++ +R + AEDV A++++ +P IR+P+A L I + L Sbjct: 18 LVTEFTNSYSWLKQYLRRQVKSLADAEDVASAAFVEMASLPDVSIIREPRALLTTISQRL 77 Query: 75 AIDHHRRSAFESDVFAAEEDGLAVHEEAQ--GPEAIAIGRQTLACISQALDSLPARTRRA 132 D RR D+ AA LA EEA PE + QTL I + L L R+A Sbjct: 78 VFDLWRRR----DLEAAYLAALATTEEATTPSPEVVLEVVQTLVNIDRLLYGLSKNARQA 133 Query: 133 FELYRLAGLSQREIAAELGVSVTLVNFLIRDALASC 168 F +L GL+ REIA LGVSV++V I ALA C Sbjct: 134 FLYSQLDGLTYREIAELLGVSVSMVRKYIAQALAKC 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 = 63.5 bits (153), Expect = 8e-12, Method: Compositional matrix adjust. Identities = 50/141 (35%), Positives = 70/141 (49%), Gaps = 10/141 (7%) Query: 32 RILGCPYRAEDVVQDAYLKI--HEVPASFDIRQPQAYLLRIVRNLAIDHHRRSAFESDVF 89 R L C + D+ QD ++++ H P D+R+P+AYL I + L H RR E+ Sbjct: 31 RRLACRHLGADLAQDTFVRLLGHRPPP--DLREPRAYLTTIAKGLVASHLRRRQLET--- 85 Query: 90 AAEEDGLAVHEEAQGPEAI--AIGRQTLACISQALDSLPARTRRAFELYRLAGLSQREIA 147 A + LA E P A + TL I + LD LPAR R+ F L +L GL IA Sbjct: 86 -AYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPARARQVFLLAQLDGLPYASIA 144 Query: 148 AELGVSVTLVNFLIRDALASC 168 LG+S++ V + AL C Sbjct: 145 GLLGISLSTVKRHMVLALRHC 165 >gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 178 Score = 54.7 bits (130), Expect = 4e-09, Method: Compositional matrix adjust. Identities = 43/150 (28%), Positives = 70/150 (46%), Gaps = 1/150 (0%) Query: 19 FIGQRQRLREAAQRILGCPYRAEDVVQDAYLKIHEVPASFDIRQPQAYLLRIVRNLAIDH 78 FI LR +R +G + AEDV + + ++ P ++R+P+A L I R + + Sbjct: 20 FIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPPQEVREPRALLTTISRRIVYEL 79 Query: 79 HRRSAFESDVFAAEEDGLAVHEEAQGPEAIAIGRQTLACISQALDSLPARTRRAFELYRL 138 RR E A ++ +A PE Q L + QAL L A+ AF LY+L Sbjct: 80 WRRRDLEEACLQALAH-VSGDVQAISPEDQLQLLQALRAMDQALAGLSAKECAAFLLYKL 138 Query: 139 AGLSQREIAAELGVSVTLVNFLIRDALASC 168 GL+ + I A+L ++ ++ + L C Sbjct: 139 DGLTYQAIGAQLRITPSVARRYVAKGLLQC 168 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 0.325 0.136 0.388 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: 521,646 Number of extensions: 20421 Number of successful extensions: 106 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: 173 Length of database: 1,619,870 Length adjustment: 79 Effective length of query: 94 Effective length of database: 1,245,805 Effective search space: 117105670 Effective search space used: 117105670 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)