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= 0034.0017.p (164 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor ... 327 3e-91 gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor,... 160 4e-41 gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor,... 139 1e-34 gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor,... 117 3e-28 gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor ... 112 1e-26 >gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor protein [Herbaspirillum seropedicae SmR1] Length = 181 Score = 327 bits (837), Expect = 3e-91, Method: Compositional matrix adjust. Identities = 163/164 (99%), Positives = 164/164 (100%) Query: 1 MSIEALYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSDRVPSVIHEPRAYLTTVA 60 MSIEALYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGS+RVPSVIHEPRAYLTTVA Sbjct: 18 MSIEALYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSERVPSVIHEPRAYLTTVA 77 Query: 61 QRLVSNLWRREKLEQAYLEALAQAPVALAPSPQEQAILLETLLELDQLLDELPSIVRRAF 120 QRLVSNLWRREKLEQAYLEALAQAPVALAPSPQEQAILLETLLELDQLLDELPSIVRRAF Sbjct: 78 QRLVSNLWRREKLEQAYLEALAQAPVALAPSPQEQAILLETLLELDQLLDELPSIVRRAF 137 Query: 121 LLSQLDGLTHAQVAAALGISIPTVKRYLVKALQRCYFADISFSA 164 LLSQLDGLTHAQVAAALGISIPTVKRYLVKALQRCYFADISFSA Sbjct: 138 LLSQLDGLTHAQVAAALGISIPTVKRYLVKALQRCYFADISFSA 181 >gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 169 Score = 160 bits (405), Expect = 4e-41, Method: Compositional matrix adjust. Identities = 85/156 (54%), Positives = 111/156 (71%), Gaps = 1/156 (0%) Query: 3 IEALYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSDRVPSVIHEPRAYLTTVAQR 62 I LY +HH WL WL RRL ADLAQDTF+RLLG R P + EPRAYLTT+A+ Sbjct: 14 IGGLYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLGH-RPPPDLREPRAYLTTIAKG 72 Query: 63 LVSNLWRREKLEQAYLEALAQAPVALAPSPQEQAILLETLLELDQLLDELPSIVRRAFLL 122 LV++ RR +LE AYLEALA P PS +E+ ++L+TL E+D++LD+LP+ R+ FLL Sbjct: 73 LVASHLRRRQLETAYLEALAALPEPSQPSAEERLLVLDTLCEIDRILDQLPARARQVFLL 132 Query: 123 SQLDGLTHAQVAAALGISIPTVKRYLVKALQRCYFA 158 +QLDGL +A +A LGIS+ TVKR++V AL+ C A Sbjct: 133 AQLDGLPYASIAGLLGISLSTVKRHMVLALRHCLAA 168 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 139 bits (349), Expect = 1e-34, Method: Compositional matrix adjust. Identities = 71/162 (43%), Positives = 106/162 (65%) Query: 3 IEALYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSDRVPSVIHEPRAYLTTVAQR 62 LY +HH WL+ WL+RR+G+S AADLAQDTFLR+LG + EPRA+L+ +A Sbjct: 12 FHTLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVREPRAWLSRIAHG 71 Query: 63 LVSNLWRREKLEQAYLEALAQAPVALAPSPQEQAILLETLLELDQLLDELPSIVRRAFLL 122 LV + RRE++E+ LEA+A P SP+ + IL+E L +D LL+ L R+AFLL Sbjct: 72 LVVDKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCMIDALLEGLGERARQAFLL 131 Query: 123 SQLDGLTHAQVAAALGISIPTVKRYLVKALQRCYFADISFSA 164 S+LD +++ ++A LG+S+ +V++Y+ A++ CY S A Sbjct: 132 SRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCYLMRQSLQA 173 >gi|300312828|ref|YP_003776920.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 178 Score = 117 bits (294), Expect = 3e-28, Method: Compositional matrix adjust. Identities = 69/157 (43%), Positives = 100/157 (63%), Gaps = 2/157 (1%) Query: 3 IEALYCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSDRVPSVIHEPRAYLTTVAQR 62 IEA++ +HH WL+ L+R +G++ A D+A +TF +LL S P + EPRA LTT+++R Sbjct: 16 IEAIFIEHHGWLRTRLRRSVGDAFTAEDVAAETFTQLLHSP-PPQEVREPRALLTTISRR 74 Query: 63 LVSNLWRREKLEQAYLEALAQAPVAL-APSPQEQAILLETLLELDQLLDELPSIVRRAFL 121 +V LWRR LE+A L+ALA + A SP++Q LL+ L +DQ L L + AFL Sbjct: 75 IVYELWRRRDLEEACLQALAHVSGDVQAISPEDQLQLLQALRAMDQALAGLSAKECAAFL 134 Query: 122 LSQLDGLTHAQVAAALGISIPTVKRYLVKALQRCYFA 158 L +LDGLT+ + A L I+ +RY+ K L +CY A Sbjct: 135 LYKLDGLTYQAIGAQLRITPSVARRYVAKGLLQCYKA 171 >gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor protein [Herbaspirillum seropedicae SmR1] Length = 173 Score = 112 bits (281), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 67/150 (44%), Positives = 100/150 (66%), Gaps = 1/150 (0%) Query: 7 YCDHHSWLKGWLQRRLGNSEQAADLAQDTFLRLLGSDRVPSVIHEPRAYLTTVAQRLVSN 66 + + +SWLK +L+R++ + A D+A F+ + V S+I EPRA LTT++QRLV + Sbjct: 22 FTNSYSWLKQYLRRQVKSLADAEDVASAAFVEMASLPDV-SIIREPRALLTTISQRLVFD 80 Query: 67 LWRREKLEQAYLEALAQAPVALAPSPQEQAILLETLLELDQLLDELPSIVRRAFLLSQLD 126 LWRR LE AYL ALA A PSP+ +++TL+ +D+LL L R+AFL SQLD Sbjct: 81 LWRRRDLEAAYLAALATTEEATTPSPEVVLEVVQTLVNIDRLLYGLSKNARQAFLYSQLD 140 Query: 127 GLTHAQVAAALGISIPTVKRYLVKALQRCY 156 GLT+ ++A LG+S+ V++Y+ +AL +CY Sbjct: 141 GLTYREIAELLGVSVSMVRKYIAQALAKCY 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 0.322 0.134 0.389 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: 411,610 Number of extensions: 12330 Number of successful extensions: 86 Number of sequences better than 1.0e-08: 9 Number of HSP's gapped: 80 Number of HSP's successfully gapped: 9 Length of query: 164 Length of database: 1,619,870 Length adjustment: 78 Effective length of query: 86 Effective length of database: 1,250,540 Effective search space: 107546440 Effective search space used: 107546440 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 127 (53.5 bits)