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/690/690 
           3295 sequences; 1,000,347 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|134094539|ref|YP_001099614.1| sigma F (sigma 28) factor of RN...   343   4e-96
gi|134093713|ref|YP_001098788.1| putative sigma 70 factor of RNA...    66   2e-12

>gi|134094539|ref|YP_001099614.1| sigma F (sigma 28) factor of RNA
           polymerase, transcription of late flagellar genes (class
           3a and 3b operons) [Herminiimonas arsenicoxydans]
          Length = 216

 Score =  343 bits (880), Expect = 4e-96,   Method: Compositional matrix adjust.
 Identities = 165/218 (75%), Positives = 193/218 (88%), Gaps = 2/218 (0%)

Query: 28  LKAKLPPSVEVDDLIQAGMMGLLDAVNRYEETHGAQFETYAVQRIRGAMLDELRSSDWLP 87
           +KAKLPPSVEVDDLIQAGM+GLLDAV RYEETHGAQFETYAVQRIRGAMLDELRSSDW+P
Sbjct: 1   MKAKLPPSVEVDDLIQAGMIGLLDAVGRYEETHGAQFETYAVQRIRGAMLDELRSSDWMP 60

Query: 88  RSIRQNARKVEEAMQALLQQLGRQPQETEVAQHMKISLVEYQSLLTECGGHQLIYYEDFH 147
           RS+RQN RK+E AM +L Q+LGR P E+EVA+ +K+SL +YQ LL++ GGHQL+YYEDFH
Sbjct: 61  RSMRQNMRKIEVAMNSLQQKLGRPPNESEVAKQLKLSLADYQDLLSDGGGHQLVYYEDFH 120

Query: 148 DDEGGHEHFLDRYQTGEADDDPLQSLINGGFRDAVVDSIKALPEREQILMALYYEQEMNL 207
           D E  +EHFLDRY T E+  DPLQ+L+N GFR AV+ +I+ALPERE+ILM+LYYEQEMNL
Sbjct: 121 DSE-DNEHFLDRYCTDES-PDPLQNLMNTGFRSAVIAAIEALPEREKILMSLYYEQEMNL 178

Query: 208 KEIGAVMGVSESRVCQLHSQAISRMRTYLREHSWSGVA 245
           KEIGAVMGV+ESRV QLHSQAI+RMR  LRE +W+GVA
Sbjct: 179 KEIGAVMGVTESRVSQLHSQAIARMRANLREKAWTGVA 216


>gi|134093713|ref|YP_001098788.1| putative sigma 70 factor of RNA
           polymerase [Herminiimonas arsenicoxydans]
          Length = 858

 Score = 65.9 bits (159), Expect = 2e-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: 614 MKARKAKREMTEANLRLVISIAKKYTNR---GLQFLDLIQEGNIGLMKAVDKFEYRRGFK 670

Query: 64  FETYAVQRIRGAML----DELRSSDWLPRSIRQNARKVEEAMQALLQQLGRQPQETEVAQ 119
           F TYA   IR A+     D+ R+   +P  + +   K+    + +LQ+ G +P    +A 
Sbjct: 671 FSTYATWWIRQAITRSIADQARTIR-IPVHMIETINKMNRISRQILQETGAEPDPATLAI 729

Query: 120 HMKISLVEYQSLLTECGGHQLIYYEDFHDDEGGHEHFLDRYQTGEADDDPLQSLINGGFR 179
            M++   + + ++ +     +       DD+  H   L  +        P  + ++   R
Sbjct: 730 KMEMPEDKIRKIM-KIAKEPISMETPIGDDDDSH---LGDFIEDNNTLAPADAALHASMR 785

Query: 180 DAVVDSIKALPEREQILMALYYEQEMN----LKEIGAVMGVSESRVCQLHSQAISRMR 233
             V D + +L  RE  ++ + +  EM+    L+E+G    V+  R+ Q+ ++A+ ++R
Sbjct: 786 GVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 843


  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
   0.317    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: 3295
Number of Hits to DB: 452,755
Number of extensions: 17301
Number of successful extensions: 73
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 71
Number of HSP's successfully gapped: 2
Length of query: 245
Length of database: 1,000,347
Length adjustment: 79
Effective length of query: 166
Effective length of database: 740,042
Effective search space: 122846972
Effective search space used: 122846972
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: 127 (53.5 bits)