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= 0001.2443.p (196 letters) Database: BlastDatabases/690/690 3295 sequences; 1,000,347 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|134096429|ref|YP_001101504.1| putative RNA polymerase sigma f... 76 1e-15 gi|134095261|ref|YP_001100336.1| RNA polymerase sigma factor Rpo... 74 6e-15 gi|134094095|ref|YP_001099170.1| RNA polymerase sigma factor [He... 63 8e-12 gi|134094707|ref|YP_001099782.1| ECF family RNA polymerase sigma... 62 1e-11 >gi|134096429|ref|YP_001101504.1| putative RNA polymerase sigma factor [Herminiimonas arsenicoxydans] Length = 168 Score = 76.3 bits (186), Expect = 1e-15, Method: Compositional matrix adjust. Identities = 45/148 (30%), Positives = 76/148 (51%), Gaps = 9/148 (6%) Query: 46 FPRLTSFLRRLTAHPHLIDEIINDTMLVVWQKAHTYNQTCKVSTWIFAIAYRQGLKALRN 105 PRL + R L D+++ DTM W+K ++ + + W+F I + + +R Sbjct: 12 IPRLRRYARALIGERTGADDLVQDTMERGWKKLSSWQRGSDMRAWLFGIMHNLHIDQVRR 71 Query: 106 LRQEIEIVSDEDDPCDTPGPEQ---QMSRLQMRKVLESALSELSTEQRSVIALSYYHGMA 162 E++ D DTP P Q L+MR L+SAL+ L EQR ++ L M+ Sbjct: 72 PGIMTEVLDD-----DTPLPTSKATQADGLEMRD-LQSALATLPPEQREILLLVALEEMS 125 Query: 163 YDEIARAMKCPINTIKTRMFHARRKLKS 190 Y+E+A + P+ T+ +R+ AR+KL++ Sbjct: 126 YEEVATTLGLPLGTVMSRLSRARQKLRA 153 >gi|134095261|ref|YP_001100336.1| RNA polymerase sigma factor RpoE [Herminiimonas arsenicoxydans] Length = 200 Score = 73.6 bits (179), Expect = 6e-15, Method: Compositional matrix adjust. Identities = 51/185 (27%), Positives = 86/185 (46%), Gaps = 15/185 (8%) Query: 23 DAEVMEAIAGGNRAVFEKLYKQYFPRLTSFLRRLTAHPHLIDEIINDTMLVVWQKAHTYN 82 D ++E + G++ FE L +Y +L + RL ++++ + + ++ + Sbjct: 8 DQLLVERVQRGDKKAFELLVIKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAYRALPQFR 67 Query: 83 QTCKVSTWIFAIAYR--------QGLKALRNLRQEIEIVSDEDDPC---DTPGPEQQMSR 131 TW++ I QG +A + +IE DD D PE ++ Sbjct: 68 GDSAFYTWLYRIGINTAKNYLVTQGRRAPTSTEADIEEAETFDDGEHLRDINTPESLLAT 127 Query: 132 LQMRKVLESALSELSTEQRSVIALSYYHGMAYDEIARAMKCPINTIKTRMFHAR----RK 187 Q+ + L A+ EL E R I L G++YDEIA +M CPI T+++R+F AR K Sbjct: 128 KQIAQTLNLAMEELPEELRMAITLREIEGLSYDEIAVSMGCPIGTVRSRIFRAREAISEK 187 Query: 188 LKSLL 192 L+ LL Sbjct: 188 LRPLL 192 >gi|134094095|ref|YP_001099170.1| RNA polymerase sigma factor [Herminiimonas arsenicoxydans] Length = 184 Score = 63.2 bits (152), Expect = 8e-12, Method: Compositional matrix adjust. Identities = 35/157 (22%), Positives = 75/157 (47%), Gaps = 4/157 (2%) Query: 27 MEAIAGGNRAVFEKLYKQYFPRLTSFLRRLTAHPHLIDEIINDTMLVVWQKAHTYN-QTC 85 + A A G+ +++Y RL R+ HL +++++D + +W KA +++ + Sbjct: 14 LHACALGDEHALQRIYIHDSKRLLGVALRIVRQRHLAEDVVHDAFVSIWNKAASFDAKRG 73 Query: 86 KVSTWIFAIAYRQGLKALRNLRQEIEIVSDEDDPCDTPGPEQQMSRLQMRKV---LESAL 142 + WI+++ L LR+ +E+ D D E + + ++ L+ L Sbjct: 74 EGRGWIYSVVRHHALNMLRDRDREVYADEDAIDNMQHQNQELIIDQFELNDSLGQLQDCL 133 Query: 143 SELSTEQRSVIALSYYHGMAYDEIARAMKCPINTIKT 179 S L + +R+ I +Y G ++ EIA+ + P+ ++K Sbjct: 134 SHLDSAKRNSILCAYVDGCSHSEIAQRLNAPLGSVKA 170 >gi|134094707|ref|YP_001099782.1| ECF family RNA polymerase sigma factor [Herminiimonas arsenicoxydans] Length = 231 Score = 62.4 bits (150), Expect = 1e-11, Method: Compositional matrix adjust. Identities = 43/185 (23%), Positives = 83/185 (44%), Gaps = 15/185 (8%) Query: 23 DAEVMEAIAGGNRAVFEKLYKQYFPRLTSFLRRLTAHPHLIDEIINDTMLVVWQKAHTYN 82 D E+ + IA G+++ FE + +++ L R + ++++ + L+ ++ + Sbjct: 15 DIEIAQRIARGDQSAFEFMMRRHNRPLYRTARSILKDDAEAEDVLQEAYLLAYRNIEKFR 74 Query: 83 QTCKVSTWIFAIAYRQGLKALRNLRQEIEIV---SDEDDPCD------------TPGPEQ 127 +STW+ I + + R R+ EI+ SD P + T PE Sbjct: 75 GESALSTWLTRIVINEAIGRSRKSRRRAEIIRLDSDNTSPLEYEVAEVNMNEATTEQPES 134 Query: 128 QMSRLQMRKVLESALSELSTEQRSVIALSYYHGMAYDEIARAMKCPINTIKTRMFHARRK 187 R + R++LE + L R+V L M+ +E++R + P T+++R F AR Sbjct: 135 AALRAEARRMLERQIDALPDVFRTVFVLRALEEMSVEEVSRCLDVPEATVRSRFFRARGM 194 Query: 188 LKSLL 192 L+ L Sbjct: 195 LREAL 199 Database: BlastDatabases/690/690 Posted date: Apr 9, 2011 4:48 AM Number of letters in database: 1,000,347 Number of sequences in database: 3295 Lambda K H 0.322 0.133 0.388 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 3295 Number of Hits to DB: 333,202 Number of extensions: 11126 Number of successful extensions: 42 Number of sequences better than 1.0e-08: 4 Number of HSP's gapped: 41 Number of HSP's successfully gapped: 4 Length of query: 196 Length of database: 1,000,347 Length adjustment: 77 Effective length of query: 119 Effective length of database: 746,632 Effective search space: 88849208 Effective search space used: 88849208 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: 126 (53.1 bits)