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= 0502.0030.p
         (209 letters)

Database: COG 
           115,334 sequences; 38,378,431 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Rv1189 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    57   2e-08
MT1226 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    57   2e-08
SMb20030 [K] COG1595 DNA-directed RNA polymerase specialized sig...    49   5e-06

>Rv1189 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog
          Length = 301

 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 7/104 (6%), Positives = 17/104 (16%), Gaps = 4/104 (3%)

Query: 9   GDVS----DPECEALLADSVGLAMLVVLGSLNPAEQIAFVLHDVFALPFEEIAPIVGRSK 64
            ++     +        + V   +      +  A      + +   L           + 
Sbjct: 89  VELVIFVVEGTRWTPDDEMVLNKLREGKAPVILAVNKVDNVQEKADLLPHLQFLASQMNF 148

Query: 65  EXXXXXXXXXXXXVHGFDTARHADLARQRELVDAFLAATRAGNF 108
                        V          L              R+  F
Sbjct: 149 LDIVPISAETGLNVDTIAAIVRKHLPEATHHFPEDYITDRSQRF 192


>MT1226 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog
          Length = 290

 Score = 57.0 bits (136), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 33/104 (31%), Positives = 51/104 (49%), Gaps = 4/104 (3%)

Query: 9   GDVS----DPECEALLADSVGLAMLVVLGSLNPAEQIAFVLHDVFALPFEEIAPIVGRSK 64
           GD S    DP     L D V LA+L++L  L PAE++ FVLH++F LP+++IA  +G   
Sbjct: 89  GDASVSSVDPADRVTLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQA 148

Query: 65  EXXXXXXXXXXXXVHGFDTARHADLARQRELVDAFLAATRAGNF 108
                        ++    A   + A+ R +  AF+ A   G+ 
Sbjct: 149 STCRQLAHRARRKINESRIAASVEPAQHRVVTRAFIEACSNGDL 192


>SMb20030 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog
          Length = 285

 Score = 49.3 bits (116), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 41/83 (49%)

Query: 26  LAMLVVLGSLNPAEQIAFVLHDVFALPFEEIAPIVGRSKEXXXXXXXXXXXXVHGFDTAR 85
           L +++ L  L+P E+ AF+LHDVF L FEE+A  + R               V       
Sbjct: 102 LPLMLALERLSPLERAAFLLHDVFGLGFEEVAATIQRDAAACRQLAARARTHVREARPRF 161

Query: 86  HADLARQRELVDAFLAATRAGNF 108
           H +  R  EL +AF  A+R+G+ 
Sbjct: 162 HVEKERGLELAEAFFKASRSGDM 184


  Database: COG
    Posted date:  Aug 3, 2010  9:58 AM
  Number of letters in database: 38,378,431
  Number of sequences in database:  115,334
  
Lambda     K      H
   0.321    0.139    0.387 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 115334
Number of Hits to DB: 10,966,242
Number of extensions: 325145
Number of successful extensions: 504
Number of sequences better than 1.0e-05: 3
Number of HSP's gapped: 503
Number of HSP's successfully gapped: 3
Length of query: 209
Length of database: 38,378,431
Length adjustment: 102
Effective length of query: 107
Effective length of database: 26,614,363
Effective search space: 2847736841
Effective search space used: 2847736841
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: 113 (48.1 bits)