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= 0165.0028.p
         (310 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312008|ref|YP_003776100.1| RNA polymerase sigma-E factor [...    64   1e-11
gi|300311253|ref|YP_003775345.1| RNA polymerase sigma-E factor (...    55   5e-09

>gi|300312008|ref|YP_003776100.1| RNA polymerase sigma-E factor
           [Herbaspirillum seropedicae SmR1]
          Length = 163

 Score = 64.3 bits (155), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 56/162 (34%), Positives = 77/162 (47%), Gaps = 17/162 (10%)

Query: 22  ALRPELHRYCARLMGSVFDGEDVVQDTLIRALEALPELDEATPLRPWLFRIAHNRALDLL 81
           A  P L RY   L G+    +D+VQDTL RA + L      +P+RPWLF I HN     L
Sbjct: 3   ACLPRLRRYARALTGAREAADDLVQDTLERAWQKLDSWQRGSPMRPWLFSIMHN-----L 57

Query: 82  RSRAVRKAEPIAAASD---VVDAANP--DPVEMLMRQEAVNTAVSRFAELPLVQRSVVIL 136
            + A R+A P   A D    +D A    DP  +L  + A+         LP  QR V++L
Sbjct: 58  HADARRRASPATVALDEYGEIDQAQVALDPGVLLDLETALQL-------LPPEQREVLLL 110

Query: 137 KDVLDESLVEIAVLLNLTVDAVKGHLARGRARLREINALAGQ 178
             + +    E+AV L +    V   L+R R RLR +    G+
Sbjct: 111 VVLEEMRYEEVAVTLGIPTGTVMSRLSRARERLRRVMQGQGE 152


>gi|300311253|ref|YP_003775345.1| RNA polymerase sigma-E factor
           (sigma-24) transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 200

 Score = 55.5 bits (132), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 47/165 (28%), Positives = 76/165 (46%), Gaps = 10/165 (6%)

Query: 10  DERRAEILAVAGALRPELHRYCARLMGSVFDGEDVVQDTLIRALEALPELDEATPLRPWL 69
           D++  E+L V    + +L R  +RL+    + EDVVQ+  I+A  ALP+    +    WL
Sbjct: 19  DKKAFELLVVK--YQRKLMRLVSRLVRDQAEAEDVVQEAFIKAYRALPQFRGDSAFYTWL 76

Query: 70  FRIAHNRALDLLRS---RAVRKAEPIAAASDVVDAANP-----DPVEMLMRQEAVNTAVS 121
           +RI  N A + L +   RA    E  A  ++  D A+       P  ML  ++   T   
Sbjct: 77  YRIGINTAKNYLVTMGRRAPTSTEADAEEAETFDDADHLRDINTPESMLATKQIAQTVNV 136

Query: 122 RFAELPLVQRSVVILKDVLDESLVEIAVLLNLTVDAVKGHLARGR 166
               LP   R+ + L+++   S  EIA  +N  +  V+  + R R
Sbjct: 137 AMEALPEELRTAITLREIEGLSYDEIADAMNCPIGTVRSRIFRAR 181


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.321    0.136    0.399 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 956,316
Number of extensions: 38402
Number of successful extensions: 133
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 134
Number of HSP's successfully gapped: 2
Length of query: 310
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 225
Effective length of database: 1,217,395
Effective search space: 273913875
Effective search space used: 273913875
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: 130 (54.7 bits)