BLASTP 2.2.17 [Aug-26-2007]

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 composition-based statistics:
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
Eugene V. Koonin, and Stephen F. Altschul (2001), 
"Improving the accuracy of PSI-BLAST protein database searches with 
composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.

Query= 0001.0812.p         (96 letters)

Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF excluding environmental samples
from WGS projects 
           15,459,386 sequences; 5,307,515,862 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

ref|YP_001353607.1| RNA polymerase sigma factor [Janthinobacteri...    84   6e-15
ref|YP_004153278.1| ECF subfamily RNA polymerase sigma-24 subuni...    78   4e-13
ref|YP_001099170.1| RNA polymerase sigma factor [Herminiimonas a...    78   4e-13
ref|ZP_03543519.1| RNA polymerase, sigma-24 subunit, ECF subfami...    74   1e-11
ref|YP_003277945.1| ECF subfamily RNA polymerase sigma-24 subuni...    72   3e-11

>ref|YP_001353607.1| RNA polymerase sigma factor [Janthinobacterium sp. Marseille]
 gb|ABR90334.1| RNA polymerase sigma-70 factor, ECF subfamily [Janthinobacterium
           sp. Marseille]
          Length = 216

 Score = 84.3 bits (207), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 45/82 (54%), Positives = 57/82 (69%), Gaps = 2/82 (2%)

Query: 2   QHEVSAGDDLEELADRAE--PAVDAPEWQADLGRLDECLGQLSDAKRASIVYAYVDGCTH 59
           Q EV   +D  E  D  +   A D  E   +LG+LD+CL  L  AKR S++YAYVDGC+H
Sbjct: 127 QQEVYTDEDTVEALDAQQGIEAQDPFETHVNLGKLDDCLSHLDHAKRNSLLYAYVDGCSH 186

Query: 60  GEIAERLQAPLGSVKAWIKRGL 81
            EIAER+++P+GSVKAWIKRGL
Sbjct: 187 REIAERMKSPVGSVKAWIKRGL 208


>ref|YP_004153278.1| ECF subfamily RNA polymerase sigma-24 subunit [Variovorax paradoxus
           EPS]
 gb|ADU35167.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Variovorax
           paradoxus EPS]
          Length = 203

 Score = 78.2 bits (191), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 39/59 (66%), Positives = 47/59 (79%)

Query: 23  DAPEWQADLGRLDECLGQLSDAKRASIVYAYVDGCTHGEIAERLQAPLGSVKAWIKRGL 81
           D  E +ADLGRL  CL  L  A+R  I+YAYV+GC+HGEIAERLQ PLG+VKAWI+RG+
Sbjct: 137 DPFELRADLGRLHGCLSGLEPARRDCILYAYVEGCSHGEIAERLQTPLGTVKAWIQRGM 195


>ref|YP_001099170.1| RNA polymerase sigma factor [Herminiimonas arsenicoxydans]
 emb|CAL61043.1| putative RNA polymerase sigma factor [Herminiimonas arsenicoxydans]
          Length = 184

 Score = 78.2 bits (191), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 39/64 (60%), Positives = 46/64 (71%)

Query: 19  EPAVDAPEWQADLGRLDECLGQLSDAKRASIVYAYVDGCTHGEIAERLQAPLGSVKAWIK 78
           E  +D  E    LG+L +CL  L  AKR SI+ AYVDGC+H EIA+RL APLGSVKAW+K
Sbjct: 114 ELIIDQFELNDSLGQLQDCLSHLDSAKRNSILCAYVDGCSHSEIAQRLNAPLGSVKAWVK 173

Query: 79  RGLG 82
           RGL 
Sbjct: 174 RGLA 177


>ref|ZP_03543519.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Comamonas
           testosteroni KF-1]
 gb|EED67805.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Comamonas
           testosteroni KF-1]
          Length = 192

 Score = 73.6 bits (179), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 38/54 (70%), Positives = 45/54 (83%)

Query: 28  QADLGRLDECLGQLSDAKRASIVYAYVDGCTHGEIAERLQAPLGSVKAWIKRGL 81
           QA LGRL  CL  L  A+RA +++AYVDGC+H EIAERLQAPLG+VKAWI+RGL
Sbjct: 131 QASLGRLGHCLDGLEPARRACLLHAYVDGCSHSEIAERLQAPLGTVKAWIQRGL 184


>ref|YP_003277945.1| ECF subfamily RNA polymerase sigma-24 subunit [Comamonas
           testosteroni CNB-2]
 gb|ACY32649.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Comamonas
           testosteroni CNB-2]
          Length = 192

 Score = 72.0 bits (175), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 36/54 (66%), Positives = 45/54 (83%)

Query: 28  QADLGRLDECLGQLSDAKRASIVYAYVDGCTHGEIAERLQAPLGSVKAWIKRGL 81
           QA LGRL  CL  L  A+RA +++AYVDGC+H EIAER++APLG+VKAWI+RGL
Sbjct: 131 QASLGRLGHCLDSLEPARRACLLHAYVDGCSHSEIAERVKAPLGTVKAWIQRGL 184