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= 0001.2420.p (202 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300310115|ref|YP_003774207.1| RNA polymerase sigma-24 factor ... 272 1e-74 gi|300311253|ref|YP_003775345.1| RNA polymerase sigma-E factor (... 74 8e-15 gi|300311653|ref|YP_003775745.1| ferric regulator sigma-24 subun... 55 3e-09 gi|300312008|ref|YP_003776100.1| RNA polymerase sigma-E factor [... 55 3e-09 gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor,... 55 5e-09 >gi|300310115|ref|YP_003774207.1| RNA polymerase sigma-24 factor protein [Herbaspirillum seropedicae SmR1] Length = 244 Score = 272 bits (695), Expect = 1e-74, Method: Compositional matrix adjust. Identities = 127/162 (78%), Positives = 147/162 (90%) Query: 31 IDVVKLYTEHRSHLLRFVQRYVGSYEDAEDVVQNTFIEASKCAHRFSGLSKPSTWLFGIA 90 ID+V LYT+HR+HLLRFV RYVG++EDAEDVVQNTFIEA KCAHRFSGLSKPSTWLFGI Sbjct: 67 IDIVALYTKHRTHLLRFVLRYVGNHEDAEDVVQNTFIEAVKCAHRFSGLSKPSTWLFGIG 126 Query: 91 LNLARNQVRRNIADRCDAVDENFMEQIVDTHADPAVLYEMRQMAEKVEGLLNELPVKIRA 150 LNLARNQVRRN ADR + V+ENFMEQ+VD ADPA++YE+RQ+A+KV+ +L+ELP IR Sbjct: 127 LNLARNQVRRNSADRYEMVEENFMEQLVDASADPAMVYELRQIAQKVDDMLSELPPHIRH 186 Query: 151 TFEAVLDGDATYEQAAEHLHIPIGTVRSRVSRVRATVRSKYG 192 TFEAVLDGDATYE+AA+HL+IPIGTVRSRVSRVRA VR +YG Sbjct: 187 TFEAVLDGDATYEEAAQHLNIPIGTVRSRVSRVRAAVRQEYG 228 >gi|300311253|ref|YP_003775345.1| RNA polymerase sigma-E factor (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 200 Score = 73.9 bits (180), Expect = 8e-15, Method: Compositional matrix adjust. Identities = 51/163 (31%), Positives = 83/163 (50%), Gaps = 9/163 (5%) Query: 36 LYTEHRSHLLRFVQRYVGSYEDAEDVVQNTFIEASKCAHRFSGLSKPSTWLFGIALNLAR 95 L +++ L+R V R V +AEDVVQ FI+A + +F G S TWL+ I +N A+ Sbjct: 26 LVVKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAYRALPQFRGDSAFYTWLYRIGINTAK 85 Query: 96 NQV-----RRNIADRCDAVD-ENF--MEQIVDTHADPAVLYEMRQMAEKVEGLLNELPVK 147 N + R + DA + E F + + D + P + +Q+A+ V + LP + Sbjct: 86 NYLVTMGRRAPTSTEADAEEAETFDDADHLRDINT-PESMLATKQIAQTVNVAMEALPEE 144 Query: 148 IRATFEAVLDGDATYEQAAEHLHIPIGTVRSRVSRVRATVRSK 190 +R +Y++ A+ ++ PIGTVRSR+ R R + K Sbjct: 145 LRTAITLREIEGLSYDEIADAMNCPIGTVRSRIFRAREAIAEK 187 >gi|300311653|ref|YP_003775745.1| ferric regulator sigma-24 subunit [Herbaspirillum seropedicae SmR1] Length = 178 Score = 55.5 bits (132), Expect = 3e-09, Method: Compositional matrix adjust. Identities = 47/162 (29%), Positives = 72/162 (44%), Gaps = 7/162 (4%) Query: 37 YTEHRSHLLRFVQRYVGSYEDAEDVVQNTFIEASKCAHRFSGLSKPSTWLFGIALNLARN 96 + EHR+ L R +G A+DVVQ+TFI+ ++ F + +P +L+ I NLA + Sbjct: 16 FIEHRARLRDVATRILGCPHRADDVVQDTFIKIAEVPDDFD-IKQPVAYLYRIVRNLAID 74 Query: 97 QVRRNIADRCDAVDENFMEQIVDTHAD---PAVLYEMRQMAEKVEGLLNELPVKIRATFE 153 + RR+ A CD E E +D H + P + RQ + L LP + R FE Sbjct: 75 RHRRS-AFECDVFTEE--EDGLDVHQEGDSPEAIAISRQYLSMIGRALEGLPARTRRAFE 131 Query: 154 AVLDGDATYEQAAEHLHIPIGTVRSRVSRVRATVRSKYGSAP 195 T + A L+I V + A R+ + P Sbjct: 132 LYRLSGLTQREIAAELNISTTLVNFMIRDALACCRNLLQNEP 173 >gi|300312008|ref|YP_003776100.1| RNA polymerase sigma-E factor [Herbaspirillum seropedicae SmR1] Length = 163 Score = 55.5 bits (132), Expect = 3e-09, Method: Compositional matrix adjust. Identities = 47/146 (32%), Positives = 66/146 (45%), Gaps = 8/146 (5%) Query: 43 HLLRFVQRYVGSYEDAEDVVQNTFIEASKCAHRFSGLSKPSTWLFGIALNLARNQVRRNI 102 L R+ + G+ E A+D+VQ+T A + + S WLF I NL + RR Sbjct: 7 RLRRYARALTGAREAADDLVQDTLERAWQKLDSWQRGSPMRPWLFSIMHNLHAD-ARRRA 65 Query: 103 ADRCDAVDENFMEQIVDTHADPAVLYEMRQMAEKVEGLLNELPVKIRATFEAVLDGDATY 162 + A+DE DP VL ++ E L LP + R V+ + Y Sbjct: 66 SPATVALDEYGEIDQAQVALDPGVLLDL-------ETALQLLPPEQREVLLLVVLEEMRY 118 Query: 163 EQAAEHLHIPIGTVRSRVSRVRATVR 188 E+ A L IP GTV SR+SR R +R Sbjct: 119 EEVAVTLGIPTGTVMSRLSRARERLR 144 >gi|300311748|ref|YP_003775840.1| RNA polymerase sigma-70 factor, ECF subfamily (sigma-24) transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 174 Score = 54.7 bits (130), Expect = 5e-09, Method: Compositional matrix adjust. Identities = 44/157 (28%), Positives = 73/157 (46%), Gaps = 7/157 (4%) Query: 36 LYTEHRSHLLRFVQRYVGSYEDAEDVVQNTFIEASKCAHRFSGLSKPSTWLFGIALNLAR 95 LY+EH L ++++R VGS DA D+ Q+TF+ G+ +P WL IA L Sbjct: 15 LYSEHHGWLQQWLRRRVGSSFDAADLAQDTFLRVLGKPGALDGVREPRAWLSRIAHGLVV 74 Query: 96 NQVRRNIADR-CDAVDENFMEQIVDTHADPAVLYEMRQMAEKVEGLLNELPVKIRATFEA 154 +++RR +R C + E V + +L E M ++ LL L + R F Sbjct: 75 DKLRREEVERTCLEAIAHLPEPEVVSPEARLILVEALCM---IDALLEGLGERARQAFLL 131 Query: 155 VLDGDATYEQAAEHLHIPIGTVRSRVSRVRATVRSKY 191 + +Y + A HL + + +V ++ A +R Y Sbjct: 132 SRLDEMSYPEIARHLGVSLSSVEKYMA---AAIRHCY 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 0.319 0.132 0.379 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: 578,538 Number of extensions: 20890 Number of successful extensions: 91 Number of sequences better than 1.0e-08: 5 Number of HSP's gapped: 90 Number of HSP's successfully gapped: 5 Length of query: 202 Length of database: 1,619,870 Length adjustment: 81 Effective length of query: 121 Effective length of database: 1,236,335 Effective search space: 149596535 Effective search space used: 149596535 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 (21.8 bits) S2: 128 (53.9 bits)