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= 0165.0012.p
         (128 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigm...    64   5e-11
BH0263 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    60   7e-10
lin0443 [K] COG1595 DNA-directed RNA polymerase specialized sigm...    56   1e-08
PA1776 [K] COG1595 DNA-directed RNA polymerase specialized sigma...    56   1e-08
AGc3605 [K] COG1595 DNA-directed RNA polymerase specialized sigm...    53   1e-07

>BS_sigW [K] COG1595 DNA-directed RNA polymerase specialized sigma
          subunit, sigma24 homolog
          Length = 187

 Score = 63.9 bits (154), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 48/75 (64%)

Query: 7  IETKIARIQAGEVYIFADIIDTYQNRIYKYCLRLLSNREEAEDAVQDIMLKVFEKVRYYQ 66
          I+ +I +++ G+   FADI+D Y+++IY+ C R+L N  EAED  Q+  ++ +  +  + 
Sbjct: 5  IKKRIKQVKKGDQDAFADIVDIYKDKIYQLCYRMLGNVHEAEDIAQEAFIRAYVNIDSFD 64

Query: 67 PKGSFTSWLYKVAYN 81
              F++WLY++A N
Sbjct: 65 INRKFSTWLYRIATN 79


>BH0263 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog
          Length = 187

 Score = 60.1 bits (144), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 28/115 (24%), Positives = 60/115 (52%), Gaps = 18/115 (15%)

Query: 4   IESIETKIAR-IQAGEVYIFADIIDTYQNRIYKYCLRLLSNREEAEDAVQDIMLKVFEKV 62
           ++SI+ ++ R ++AG+   FA++++ Y++++Y+   R++ N  EA+D  Q+  L+ +  +
Sbjct: 1   MDSIDKRLVREVRAGDEQAFAELVELYKDKVYQVAYRMVGNVHEAQDVAQEAFLRAYTNI 60

Query: 63  RYYQPKGSFTSWLYKVAYNHCXXXXXXXXXXXRSAACLAGRLRQRAPNLQQRTPC 117
             Y  +  F++WL+++A N                     RLR+R P+     P 
Sbjct: 61  DTYDIQRKFSTWLFRIATN-----------------VAIDRLRKRKPDFHLEDPV 98


>lin0443 [K] COG1595 DNA-directed RNA polymerase specialized sigma
          subunit, sigma24 homolog
          Length = 301

 Score = 56.2 bits (134), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 5/83 (6%), Positives = 18/83 (21%), Gaps = 1/83 (1%)

Query: 1  VNSIESIETKIARIQAGEVYIFADIIDTYQNRIYKYCLRLLSNREEAEDAVQDIMLKVFE 60
          ++  +S    IA +        + +++    +      R           +         
Sbjct: 1  MSIDKSYCGFIAIVGRPN-VGKSTLLNKLLGQKISITSRKAQTTRHRIVGIHTEGAYQAI 59

Query: 61 KVRYYQPKGSFTSWLYKVAYNHC 83
           V            + ++     
Sbjct: 60 YVDTPGLHMEEKRAINRLMNKAA 82


>PA1776 [K] COG1595 DNA-directed RNA polymerase specialized sigma
          subunit, sigma24 homolog
          Length = 165

 Score = 55.8 bits (133), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 37/62 (59%)

Query: 22 FADIIDTYQNRIYKYCLRLLSNREEAEDAVQDIMLKVFEKVRYYQPKGSFTSWLYKVAYN 81
          + +++  YQ  ++  C R L N  +A+D  Q++MLKV   ++ ++ K  F +WLY + YN
Sbjct: 5  YEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYN 64

Query: 82 HC 83
           C
Sbjct: 65 EC 66


>AGc3605 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog
          Length = 301

 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 8/78 (10%), Positives = 17/78 (21%), Gaps = 1/78 (1%)

Query: 7   IETKIARIQAGEVYIFADIIDTYQNRIYKYCLRLLSNREEAEDAVQDIMLKVFEKVRYYQ 66
                   QA  V      ++  +           S+  + E  +  +    +       
Sbjct: 49  GIHTEGAYQAIYVDTPGLHMEEKRAINRLMNKAASSSIGDVELVIFVVEGTRWTPDDEMV 108

Query: 67  -PKGSFTSWLYKVAYNHC 83
             K         +A N  
Sbjct: 109 LNKLREGKAPVILAVNKV 126


  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
   0.324    0.135    0.408 

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: 7,638,465
Number of extensions: 228212
Number of successful extensions: 537
Number of sequences better than 1.0e-05: 15
Number of HSP's gapped: 546
Number of HSP's successfully gapped: 15
Length of query: 128
Length of database: 38,378,431
Length adjustment: 94
Effective length of query: 34
Effective length of database: 27,537,035
Effective search space: 936259190
Effective search space used: 936259190
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 109 (46.6 bits)