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= 0212.0002.p (176 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor,... 162 1e-41 gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor,... 157 3e-40 gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor ... 136 8e-34 gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor ... 121 3e-29 gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor,... 119 2e-28 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 162 bits (410), Expect = 1e-41, Method: Compositional matrix adjust. Identities = 83/163 (50%), Positives = 110/163 (67%) Query: 12 MHTLYADHHGWLQTWLRRKLGCAFTAEDLTHDTFLRLLVRPRELDTKRDPRAYLTTIAQG 71 HTLY++HHGWLQ WLRR++G +F A DL DTFLR+L +P LD R+PRA+L+ IA G Sbjct: 12 FHTLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVREPRAWLSRIAHG 71 Query: 72 LVVDHWRRREIERAWLDAIMELAEPLVPSAEHQAVILETLVEVDRILARLPSKPREAFLL 131 LVVD RR E+ER L+AI L EP V S E + +++E L +D +L L + R+AFLL Sbjct: 72 LVVDKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCMIDALLEGLGERARQAFLL 131 Query: 132 SHLHGLTYAEIAAQLGVSERMVKKYMAQAMLHCLTAGNAFRSA 174 S L ++Y EIA LGVS V+KYMA A+ HC + ++A Sbjct: 132 SRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCYLMRQSLQAA 174 >gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 169 Score = 157 bits (398), Expect = 3e-40, Method: Compositional matrix adjust. Identities = 81/153 (52%), Positives = 105/153 (68%), Gaps = 1/153 (0%) Query: 15 LYADHHGWLQTWLRRKLGCAFTAEDLTHDTFLRLLVRPRELDTKRDPRAYLTTIAQGLVV 74 LY +HHGWL WL R+L C DL DTF+RLL R R+PRAYLTTIA+GLV Sbjct: 17 LYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGH-RPPPDLREPRAYLTTIAKGLVA 75 Query: 75 DHWRRREIERAWLDAIMELAEPLVPSAEHQAVILETLVEVDRILARLPSKPREAFLLSHL 134 H RRR++E A+L+A+ L EP PSAE + ++L+TL E+DRIL +LP++ R+ FLL+ L Sbjct: 76 SHLRRRQLETAYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPARARQVFLLAQL 135 Query: 135 HGLTYAEIAAQLGVSERMVKKYMAQAMLHCLTA 167 GL YA IA LG+S VK++M A+ HCL A Sbjct: 136 DGLPYASIAGLLGISLSTVKRHMVLALRHCLAA 168 >gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor protein [Herbaspirillum seropedicae SmR1] Length = 181 Score = 136 bits (343), Expect = 8e-34, Method: Compositional matrix adjust. Identities = 79/162 (48%), Positives = 111/162 (68%) Query: 12 MHTLYADHHGWLQTWLRRKLGCAFTAEDLTHDTFLRLLVRPRELDTKRDPRAYLTTIAQG 71 + LY DHH WL+ WL+R+LG + A DL DTFLRLL R +PRAYLTT+AQ Sbjct: 20 IEALYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSERVPSVIHEPRAYLTTVAQR 79 Query: 72 LVVDHWRRREIERAWLDAIMELAEPLVPSAEHQAVILETLVEVDRILARLPSKPREAFLL 131 LV + WRR ++E+A+L+A+ + L PS + QA++LETL+E+D++L LPS R AFLL Sbjct: 80 LVSNLWRREKLEQAYLEALAQAPVALAPSPQEQAILLETLLELDQLLDELPSIVRRAFLL 139 Query: 132 SHLHGLTYAEIAAQLGVSERMVKKYMAQAMLHCLTAGNAFRS 173 S L GLT+A++AA LG+S VK+Y+ +A+ C A +F + Sbjct: 140 SQLDGLTHAQVAAALGISIPTVKRYLVKALQRCYFADISFSA 181 >gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor protein [Herbaspirillum seropedicae SmR1] Length = 173 Score = 121 bits (304), Expect = 3e-29, Method: Compositional matrix adjust. Identities = 72/164 (43%), Positives = 101/164 (61%), Gaps = 2/164 (1%) Query: 2 SYSD-PFTQPHMHTLYADHHGWLQTWLRRKLGCAFTAEDLTHDTFLRLLVRPRELDTKRD 60 SY+D PF + T + + + WL+ +LRR++ AED+ F+ + P ++ R+ Sbjct: 7 SYADQPFRHDFLVTEFTNSYSWLKQYLRRQVKSLADAEDVASAAFVEMASLP-DVSIIRE 65 Query: 61 PRAYLTTIAQGLVVDHWRRREIERAWLDAIMELAEPLVPSAEHQAVILETLVEVDRILAR 120 PRA LTTI+Q LV D WRRR++E A+L A+ E PS E +++TLV +DR+L Sbjct: 66 PRALLTTISQRLVFDLWRRRDLEAAYLAALATTEEATTPSPEVVLEVVQTLVNIDRLLYG 125 Query: 121 LPSKPREAFLLSHLHGLTYAEIAAQLGVSERMVKKYMAQAMLHC 164 L R+AFL S L GLTY EIA LGVS MV+KY+AQA+ C Sbjct: 126 LSKNARQAFLYSQLDGLTYREIAELLGVSVSMVRKYIAQALAKC 169 >gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 178 Score = 119 bits (297), Expect = 2e-28, Method: Compositional matrix adjust. Identities = 67/165 (40%), Positives = 101/165 (61%), Gaps = 2/165 (1%) Query: 6 PFTQPHMHTLYADHHGWLQTWLRRKLGCAFTAEDLTHDTFLRLLVRPRELDTKRDPRAYL 65 P + ++ +HHGWL+T LRR +G AFTAED+ +TF +LL P + R+PRA L Sbjct: 10 PPAMSRIEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSPPPQEV-REPRALL 68 Query: 66 TTIAQGLVVDHWRRREIERAWLDAIMELAEPL-VPSAEHQAVILETLVEVDRILARLPSK 124 TTI++ +V + WRRR++E A L A+ ++ + S E Q +L+ L +D+ LA L +K Sbjct: 69 TTISRRIVYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQALAGLSAK 128 Query: 125 PREAFLLSHLHGLTYAEIAAQLGVSERMVKKYMAQAMLHCLTAGN 169 AFLL L GLTY I AQL ++ + ++Y+A+ +L C A Sbjct: 129 ECAAFLLYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCYKAAG 173 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 0.135 0.417 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: 571,222 Number of extensions: 22013 Number of successful extensions: 140 Number of sequences better than 1.0e-08: 7 Number of HSP's gapped: 137 Number of HSP's successfully gapped: 7 Length of query: 176 Length of database: 1,619,870 Length adjustment: 79 Effective length of query: 97 Effective length of database: 1,245,805 Effective search space: 120843085 Effective search space used: 120843085 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)