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= 0188.0029.p
         (182 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

BS_xpf [K] COG1595 DNA-directed RNA polymerase specialized sigma...    91   8e-19
lin2397 [K] COG1595 DNA-directed RNA polymerase specialized sigm...    70   1e-12

>BS_xpf [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog
          Length = 169

 Score = 91.3 bits (225), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 53/156 (33%), Positives = 84/156 (53%), Gaps = 4/156 (2%)

Query: 20  LFSYSEFVDDMLPDYQISLRGAEQLYRHADADDKKVIAGMISDCEYVVEWLSTGRQPGNK 79
           LF Y   +      Y+      E +    +  DKK+I  MI+D EYV EWL  GRQPG +
Sbjct: 5   LFEYKRTLKQTRIQYKPLAEADESVLSAEELKDKKIIRNMITDLEYVTEWLEKGRQPGIR 64

Query: 80  RGIERRAGYEREILLEPMRMQIFTRHTHTNAVNSEG-LSEDQQLRLEYIMALLSKREREC 138
           R I+RR  Y+R ++ +P   +I    +       +G +SE+ + R+   +ALL+ RE+E 
Sbjct: 65  RAIDRRDVYQRLMIKDP---RIIESFSSAMMFEPDGQVSEEDRDRIREALALLTDREKEM 121

Query: 139 YMLANGEGFSHVAIAEMLTISAGSVSEYIQRAQRKI 174
           ++L   E FS+  IA++L +   +V   I+RA  K+
Sbjct: 122 FLLHKVECFSYERIADLLGVKKSTVQTTIKRASLKM 157


>lin2397 [K] COG1595 DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog
          Length = 301

 Score = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 5/130 (3%), Positives = 14/130 (10%), Gaps = 5/130 (3%)

Query: 56  IAGMISDCEYVVEWLSTGRQPGNKRGIERRAGYEREIL---LEPMRMQIFTRH--THTNA 110
            A      +     +   R           +      L   +              +   
Sbjct: 54  GAYQAIYVDTPGLHMEEKRAINRLMNKAASSSIGDVELVIFVVEGTRWTPDDEMVLNKLR 113

Query: 111 VNSEGLSEDQQLRLEYIMALLSKRERECYMLANGEGFSHVAIAEMLTISAGSVSEYIQRA 170
                +                    +               AE         +   +  
Sbjct: 114 EGKAPVILAVNKVDNVQEKADLLPHLQFLASQMNFLDIVPISAETGLNVDTIAAIVRKHL 173

Query: 171 QRKICSIMNG 180
                     
Sbjct: 174 PEATHHFPED 183


  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    0.136    0.391 

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: 13,488,935
Number of extensions: 490885
Number of successful extensions: 823
Number of sequences better than 1.0e-05: 2
Number of HSP's gapped: 821
Number of HSP's successfully gapped: 2
Length of query: 182
Length of database: 38,378,431
Length adjustment: 100
Effective length of query: 82
Effective length of database: 26,845,031
Effective search space: 2201292542
Effective search space used: 2201292542
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: 112 (47.8 bits)