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= 0001.2229.p (184 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,... 72 2e-14 gi|300311653|ref|YP_003775745.1| ferric regulator sigma-24 subun... 67 1e-12 gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor ... 65 4e-12 gi|300313763|ref|YP_003777855.1| RNA polymerase sigma-70 factor,... 59 2e-10 gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor ... 59 3e-10 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 72.4 bits (176), Expect = 2e-14, Method: Compositional matrix adjust. Identities = 53/167 (31%), Positives = 87/167 (52%), Gaps = 8/167 (4%) Query: 16 NVITRYYRELLQFCLRKVKNPETAADLVQDSFVRVLTMERAGQAILDPRALLRQVALHLK 75 + + ++ L Q+ R+V + AADL QD+F+RVL A + +PRA L ++A L Sbjct: 14 TLYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVREPRAWLSRIAHGLV 73 Query: 76 IDMDRRAAIRQH--EDLDSLPETEMPAVPAHLQPEQACAAIQSAHAYLEAIDSLPTRCRE 133 +D RR + + E + LPE E+ + A L +A I + ++ L R R+ Sbjct: 74 VDKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCMIDAL------LEGLGERARQ 127 Query: 134 AFQLYAFEGLPNKEIAERMGISLSMVNQYISRGKLACAACREALEAA 180 AF L + + EIA +G+SLS V +Y++ C R++L+AA Sbjct: 128 AFLLSRLDEMSYPEIARHLGVSLSSVEKYMAAAIRHCYLMRQSLQAA 174 >gi|300311653|ref|YP_003775745.1| ferric regulator sigma-24 subunit [Herbaspirillum seropedicae SmR1] Length = 178 Score = 66.6 bits (161), Expect = 1e-12, Method: Compositional matrix adjust. Identities = 52/150 (34%), Positives = 76/150 (50%), Gaps = 14/150 (9%) Query: 36 PETAADLVQDSFVRVLTMERAGQAILDPRALLRQVALHLKIDMDRRAAIRQHEDLDSLPE 95 P A D+VQD+F+++ + I P A L ++ +L ID RR+A + D E Sbjct: 34 PHRADDVVQDTFIKIAEVPDDFD-IKQPVAYLYRIVRNLAIDRHRRSAF----ECDVFTE 88 Query: 96 TEMPAVPAHLQPEQACAAIQSAHAYLE----AIDSLPTRCREAFQLYAFEGLPNKEIAER 151 E + H Q + AI + YL A++ LP R R AF+LY GL +EIA Sbjct: 89 EE-DGLDVH-QEGDSPEAIAISRQYLSMIGRALEGLPARTRRAFELYRLSGLTQREIAAE 146 Query: 152 MGISLSMVNQYISRGKLACAACREALEAAP 181 + IS ++VN ++ R LAC CR L+ P Sbjct: 147 LNISTTLVN-FMIRDALAC--CRNLLQNEP 173 >gi|300309381|ref|YP_003773473.1| RNA polymerase sigma-70 factor protein [Herbaspirillum seropedicae SmR1] Length = 181 Score = 64.7 bits (156), Expect = 4e-12, Method: Compositional matrix adjust. Identities = 45/140 (32%), Positives = 76/140 (54%), Gaps = 4/140 (2%) Query: 31 RKVKNPETAADLVQDSFVRVLTMERAGQAILDPRALLRQVALHLKIDMDRRAAIRQHEDL 90 R++ N E AADL QD+F+R+L ER I +PRA L VA L ++ RR + Q L Sbjct: 37 RRLGNSEQAADLAQDTFLRLLGSERVPSVIHEPRAYLTTVAQRLVSNLWRREKLEQ-AYL 95 Query: 91 DSLPETEMPAVPAHLQPEQACAAIQSAHAYLEAIDSLPTRCREAFQLYAFEGLPNKEIAE 150 ++L + + P+ P++ +++ + +D LP+ R AF L +GL + ++A Sbjct: 96 EALAQAPVALAPS---PQEQAILLETLLELDQLLDELPSIVRRAFLLSQLDGLTHAQVAA 152 Query: 151 RMGISLSMVNQYISRGKLAC 170 +GIS+ V +Y+ + C Sbjct: 153 ALGISIPTVKRYLVKALQRC 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 = 58.9 bits (141), Expect = 2e-10, Method: Compositional matrix adjust. Identities = 46/151 (30%), Positives = 71/151 (47%), Gaps = 9/151 (5%) Query: 15 GNVITRYYRELLQFCLRKVKNPETAADLVQDSFVRVLTMERAGQAILDPRALLRQVALHL 74 G + ++ L+ + R++ ADL QD+FVR+L R + +PRA L +A L Sbjct: 15 GGLYREHHGWLVAWLSRRLACRHLGADLAQDTFVRLLG-HRPPPDLREPRAYLTTIAKGL 73 Query: 75 KIDMDRRAAIRQH--EDLDSLPETEMPAVPAHLQPEQACAAIQSAHAYLEAIDSLPTRCR 132 RR + E L +LPE P+ E+ + + +D LP R R Sbjct: 74 VASHLRRRQLETAYLEALAALPEPSQPSA------EERLLVLDTLCEIDRILDQLPARAR 127 Query: 133 EAFQLYAFEGLPNKEIAERMGISLSMVNQYI 163 + F L +GLP IA +GISLS V +++ Sbjct: 128 QVFLLAQLDGLPYASIAGLLGISLSTVKRHM 158 >gi|300312131|ref|YP_003776223.1| RNA polymerase sigma 24 factor protein [Herbaspirillum seropedicae SmR1] Length = 173 Score = 58.5 bits (140), Expect = 3e-10, Method: Compositional matrix adjust. Identities = 49/159 (30%), Positives = 77/159 (48%), Gaps = 8/159 (5%) Query: 18 ITRYYRELLQFCLRKVKNPETAADLVQDSFVRVLTMERAGQAILDPRALLRQVALHLKID 77 T Y L Q+ R+VK+ A D+ +FV + ++ I +PRALL ++ L D Sbjct: 22 FTNSYSWLKQYLRRQVKSLADAEDVASAAFVEMASLPDVS-IIREPRALLTTISQRLVFD 80 Query: 78 MDRRAAIRQHEDLDSLPETEMPAVPAHLQPEQACAAIQSAHAYLEAIDSLPTRCREAFQL 137 + RR + +L TE P+ PE +Q+ + L R+AF Sbjct: 81 LWRRRDLEAAYLA-ALATTEEATTPS---PEVVLEVVQTLVNIDRLLYGLSKNARQAFLY 136 Query: 138 YAFEGLPNKEIAERMGISLSMVNQYISRGKLACAACREA 176 +GL +EIAE +G+S+SMV +YI++ A A C E+ Sbjct: 137 SQLDGLTYREIAELLGVSVSMVRKYIAQ---ALAKCYES 172 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 0.134 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: 515,001 Number of extensions: 19936 Number of successful extensions: 110 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 107 Number of HSP's successfully gapped: 6 Length of query: 184 Length of database: 1,619,870 Length adjustment: 80 Effective length of query: 104 Effective length of database: 1,241,070 Effective search space: 129071280 Effective search space used: 129071280 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)