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= 0001.1796.p
         (200 letters)

Database: BlastDatabases/707/707 
           3697 sequences; 1,221,021 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|152980473|ref|YP_001353052.1| RNA polymerase sigma factor Rpo...   380   e-107
gi|152980264|ref|YP_001355194.1| ECF subfamily RNA polymerase si...    56   1e-09
gi|152981847|ref|YP_001353607.1| RNA polymerase sigma factor [Ja...    54   5e-09

>gi|152980473|ref|YP_001353052.1| RNA polymerase sigma factor RpoE
           [Janthinobacterium sp. Marseille]
          Length = 200

 Score =  380 bits (977), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 184/200 (92%), Positives = 193/200 (96%)

Query: 1   LTTEREIDQQLVERVQRGDKKAFELLVVKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAY 60
           +TTER+IDQQLVERVQRGDKKAFELLV+KYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAY
Sbjct: 1   MTTERDIDQQLVERVQRGDKKAFELLVIKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAY 60

Query: 61  RALPQFRGDSAFYTWLYRIGINTAKNYLVTMGRRAPTSTEADAEEAETFDDADHLRDINT 120
           RALPQFRGDSAFYTWLYRIGINTAKNYLVT GRRAPTSTEAD EEAETFDD DHLRDINT
Sbjct: 61  RALPQFRGDSAFYTWLYRIGINTAKNYLVTQGRRAPTSTEADVEEAETFDDGDHLRDINT 120

Query: 121 PESMLATKQIAQTVNVAMEALPEELRTAITLREIEGLSYDEIADAMNCPIGTVRSRIFRA 180
           PES+LATKQIAQT+N+AME LPEELR AITLREIEGLSYDEIA++M CPIGTVRSRIFRA
Sbjct: 121 PESLLATKQIAQTLNLAMEELPEELRMAITLREIEGLSYDEIAESMGCPIGTVRSRIFRA 180

Query: 181 REAIAEKLRPLLDTAADKRW 200
           REAI+EKLRPLLDTA DKRW
Sbjct: 181 REAISEKLRPLLDTALDKRW 200


>gi|152980264|ref|YP_001355194.1| ECF subfamily RNA polymerase sigma
           factor [Janthinobacterium sp. Marseille]
          Length = 168

 Score = 56.2 bits (134), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 42/152 (27%), Positives = 72/152 (47%), Gaps = 14/152 (9%)

Query: 33  KLMRLVSRLVRDQAEAEDVVQEAFIKAYRALPQFRGDSAFYTWLYRIGINTAKNYLVTMG 92
           +L R    L+ D+  A+D+VQ+   + ++ L  ++  S    WL+ I      N  V   
Sbjct: 14  RLRRYARALLGDRTGADDLVQDTMERGWKKLSSWQRGSDMRAWLFGI----MHNLHVDQV 69

Query: 93  RRAPTSTEADAEEAETFDDADHLRDINTPESMLATKQIAQTVNVAMEALPEELRTAITLR 152
           R+    TE      E  DD      I    + ++     + +  A+ +LP E R  + L 
Sbjct: 70  RKPSLPTE------ELDDDTP----IPAAHTSVSDGLEMRDLESALHSLPTEQREILLLV 119

Query: 153 EIEGLSYDEIADAMNCPIGTVRSRIFRAREAI 184
            +E +SY+E+A  +  P+GTV SR+ RAR+ +
Sbjct: 120 ALEEMSYEEVAATLGLPLGTVMSRLSRARQKL 151


>gi|152981847|ref|YP_001353607.1| RNA polymerase sigma factor
           [Janthinobacterium sp. Marseille]
          Length = 216

 Score = 54.3 bits (129), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 41/177 (23%), Positives = 86/177 (48%), Gaps = 17/177 (9%)

Query: 17  RGDKKAFELLVVKYQRKLMRLVSRLVRDQAEAEDVVQEAFIKAYRALPQFRGDSAFYTWL 76
           RG++ A + +  +  ++L+ +  R+VR +A AEDV+ +AF+  +R    F  D+A     
Sbjct: 51  RGERAALQQIYQQDGKRLLGVALRIVRQRALAEDVLHDAFVNIWRKAGSF--DAAR---- 104

Query: 77  YRIGINTAKNYLVTMGRRAPTSTEADAEEAETFDDADHLRDINTPESMLATKQIAQTVNV 136
                 + + ++ ++ R    +   D ++ E + D D +  ++  + + A       VN+
Sbjct: 105 -----GSGRGWIHSVVRHQALNLVRDRQQ-EVYTDEDTVEALDAQQGIEAQDPFETHVNL 158

Query: 137 A-----MEALPEELRTAITLREIEGLSYDEIADAMNCPIGTVRSRIFRAREAIAEKL 188
                 +  L    R ++    ++G S+ EIA+ M  P+G+V++ I R   A+ E +
Sbjct: 159 GKLDDCLSHLDHAKRNSLLYAYVDGCSHREIAERMKSPVGSVKAWIKRGLLALRECM 215


  Database: BlastDatabases/707/707
    Posted date:  Apr 13, 2011 12:58 PM
  Number of letters in database: 1,221,021
  Number of sequences in database:  3697
  
Lambda     K      H
   0.319    0.132    0.366 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3697
Number of Hits to DB: 360,902
Number of extensions: 11598
Number of successful extensions: 68
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 70
Number of HSP's successfully gapped: 4
Length of query: 200
Length of database: 1,221,021
Length adjustment: 79
Effective length of query: 121
Effective length of database: 928,958
Effective search space: 112403918
Effective search space used: 112403918
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: 127 (53.5 bits)