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= 0225.0060.p
         (194 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312377|ref|YP_003776469.1| RNA polymerase sigma-70 factor,...   226   8e-61
gi|300311653|ref|YP_003775745.1| ferric regulator sigma-24 subun...    54   7e-09

>gi|300312377|ref|YP_003776469.1| RNA polymerase sigma-70 factor,
           ECF subfamily (sigma-24) transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 195

 Score =  226 bits (576), Expect = 8e-61,   Method: Compositional matrix adjust.
 Identities = 121/197 (61%), Positives = 146/197 (74%), Gaps = 6/197 (3%)

Query: 1   METTLPSKPMAEADNNNAHITDMVLRERSRLRNFIRTRVPDPSDAEDILQDVFYELVEAC 60
           M+    S PM++ D     IT  V+RERSRL  FIR RV D  +AEDILQ+VFYE V+A 
Sbjct: 1   MQPISLSSPMSDQDRE---ITATVMRERSRLGGFIRRRVADAGEAEDILQEVFYEFVQAY 57

Query: 61  RLPEPIEQVGAWMFRVARNRIVDRFRKKREQALPVSGDGEE--DEDDGW-LEQLLPDTDA 117
           RLPEPIEQV AW+FRVARNRI+DRFRKK+E+ LP + D E+    DD W L+  LP +  
Sbjct: 58  RLPEPIEQVSAWLFRVARNRIIDRFRKKKEEPLPEAHDIEQVDGADDAWRLDLALPASAD 117

Query: 118 GPEAAYARSLLLAELHDALEELPAEQRDVFIAHELERRSFKELSAETGVGVNTLLARKRY 177
           GPEAAYAR+ L+  L +AL ELP  QR+VFIAHEL+  SFKE++A +G  +NTLLARKRY
Sbjct: 118 GPEAAYARAALIDALQEALGELPEAQREVFIAHELDGLSFKEMAAASGTSLNTLLARKRY 177

Query: 178 AVLHLRSRLQTLYDELE 194
           AVLHLR RLQ +YDELE
Sbjct: 178 AVLHLRERLQAVYDELE 194


>gi|300311653|ref|YP_003775745.1| ferric regulator sigma-24 subunit
           [Herbaspirillum seropedicae SmR1]
          Length = 178

 Score = 54.3 bits (129), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 48/173 (27%), Positives = 82/173 (47%), Gaps = 13/173 (7%)

Query: 18  AHITDMVLRERSRLRNFIRTRVPDPSDAEDILQDVFYELVEACRLPE--PIEQVGAWMFR 75
           A + +  +  R+RLR+     +  P  A+D++QD F ++ E   +P+   I+Q  A+++R
Sbjct: 10  ARLREQFIEHRARLRDVATRILGCPHRADDVVQDTFIKIAE---VPDDFDIKQPVAYLYR 66

Query: 76  VARNRIVDRFRKKREQALPVSGDGEEDEDDGWLEQLLPDTDAGPEAAYARSLLLAELHDA 135
           + RN  +DR R+          D   +E+DG       D+   PEA       L+ +  A
Sbjct: 67  IVRNLAIDRHRRS-----AFECDVFTEEEDGLDVHQEGDS---PEAIAISRQYLSMIGRA 118

Query: 136 LEELPAEQRDVFIAHELERRSFKELSAETGVGVNTLLARKRYAVLHLRSRLQT 188
           LE LPA  R  F  + L   + +E++AE  +    +    R A+   R+ LQ 
Sbjct: 119 LEGLPARTRRAFELYRLSGLTQREIAAELNISTTLVNFMIRDALACCRNLLQN 171


  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
   0.318    0.135    0.384 

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: 496,322
Number of extensions: 16329
Number of successful extensions: 54
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 56
Number of HSP's successfully gapped: 3
Length of query: 194
Length of database: 1,619,870
Length adjustment: 80
Effective length of query: 114
Effective length of database: 1,241,070
Effective search space: 141481980
Effective search space used: 141481980
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 128 (53.9 bits)