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= 0001.1889.p
         (245 letters)

Database: BlastDatabases/707/707 
           3697 sequences; 1,221,021 total letters

Searching..................................................done



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|152980386|ref|YP_001353773.1| RNA polymerase sigma factor for...   378   e-106
gi|152980761|ref|YP_001352183.1| RNA polymerase primary sigma fa...    65   3e-12

>gi|152980386|ref|YP_001353773.1| RNA polymerase sigma factor for
           flagellar operon [Janthinobacterium sp. Marseille]
          Length = 243

 Score =  378 bits (970), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 182/245 (74%), Positives = 213/245 (86%), Gaps = 2/245 (0%)

Query: 1   MYNVKGKKGKNDVLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYEETH 60
           MY   GK  KN ++ +HAPLVKKLAHQ+KAKLPPSVEVDDLIQAGM+GLLDAV+RYEETH
Sbjct: 1   MYTAAGKSDKNHLVGEHAPLVKKLAHQMKAKLPPSVEVDDLIQAGMIGLLDAVSRYEETH 60

Query: 61  GAQFETYAVQRIRGAMLDELRSSDWLPRSIRQNARKVEEAMQALLQQLGRQPQETEVAQH 120
           GAQFETYAVQRIRGAMLDELRSSDW+PRS+RQN RK+E AM  L Q+LGR P E+EVA+ 
Sbjct: 61  GAQFETYAVQRIRGAMLDELRSSDWMPRSMRQNMRKIEVAMNTLQQRLGRPPNESEVAKQ 120

Query: 121 MKISLVEYQSLLTECGGHQLIYYEDFHDDEGGHEHFLDRYQTGEADDDPLQSLINGGFRD 180
           +K+SL +YQ LL++ GGHQL+YYEDFHD E  +EHFLDRY T E+  DPLQ+L+N GFR 
Sbjct: 121 LKLSLADYQDLLSDGGGHQLVYYEDFHDSE-DNEHFLDRYCTDES-PDPLQNLMNTGFRA 178

Query: 181 AVVDSIKALPEREQILMALYYEQEMNLKEIGAVMGVSESRVCQLHSQAISRMRTYLREHS 240
           AV+++I+ALPERE+ILM LYYEQEMNLKEIGAVMGV+ESRV QLHSQAI+RMR  LRE +
Sbjct: 179 AVIEAIQALPEREKILMGLYYEQEMNLKEIGAVMGVTESRVSQLHSQAIARMRANLREKA 238

Query: 241 WSGVA 245
           W+GVA
Sbjct: 239 WTGVA 243


>gi|152980761|ref|YP_001352183.1| RNA polymerase primary sigma
           factor [Janthinobacterium sp. Marseille]
          Length = 826

 Score = 65.1 bits (157), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 56/238 (23%), Positives = 114/238 (47%), Gaps = 16/238 (6%)

Query: 4   VKGKKGKNDVLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYEETHGAQ 63
           +K +K K ++ E +  LV  +A +   +    ++  DLIQ G +GL+ AV+++E   G +
Sbjct: 582 MKARKAKREMTEANLRLVISIAKKYTNR---GLQFLDLIQEGNIGLMKAVDKFEYRRGFK 638

Query: 64  FETYAVQRIRGAML----DELRSSDWLPRSIRQNARKVEEAMQALLQQLGRQPQETEVAQ 119
           F TYA   IR A+     D+ R+   +P  + +   K+    + +LQ+ G +P    +A 
Sbjct: 639 FSTYATWWIRQAITRSIADQARTIR-IPVHMIETINKMNRISRQILQETGAEPDPATLAI 697

Query: 120 HMKISLVEYQSLLTECGGHQLIYYEDFHDDEGGHEHFLDRYQTGEADDDPLQSLINGGFR 179
            M++   + + ++ +     +       DD+  H   L  +        P  + ++   R
Sbjct: 698 KMEMPEDKIRKIM-KIAKEPISMETPIGDDDDSH---LGDFIEDNNTLAPADAALHASMR 753

Query: 180 DAVVDSIKALPEREQILMALYYEQEMN----LKEIGAVMGVSESRVCQLHSQAISRMR 233
             V D + +L  RE  ++ + +  EM+    L+E+G    V+  R+ Q+ ++A+ ++R
Sbjct: 754 GVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 811


  Database: BlastDatabases/707/707
    Posted date:  Apr 13, 2011 12:58 PM
  Number of letters in database: 1,221,021
  Number of sequences in database:  3697
  
Lambda     K      H
   0.317    0.133    0.380 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3697
Number of Hits to DB: 551,285
Number of extensions: 20992
Number of successful extensions: 88
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 86
Number of HSP's successfully gapped: 2
Length of query: 245
Length of database: 1,221,021
Length adjustment: 81
Effective length of query: 164
Effective length of database: 921,564
Effective search space: 151136496
Effective search space used: 151136496
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 128 (53.9 bits)