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= 0004.0094.p
         (237 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,...   361   e-101
gi|300311253|ref|YP_003775345.1| RNA polymerase sigma-E factor (...    55   6e-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 =  361 bits (926), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 181/195 (92%), Positives = 186/195 (95%)

Query: 43  MQPISTLSPMSDQDREITATVMRERSRLGGFIRRRVADAGEAEDILQEVFYEFVQAYRLP 102
           MQPIS  SPMSDQDREITATVMRERSRLGGFIRRRVADAGEAEDILQEVFYEFVQAYRLP
Sbjct: 1   MQPISLSSPMSDQDREITATVMRERSRLGGFIRRRVADAGEAEDILQEVFYEFVQAYRLP 60

Query: 103 EPIEQVSAWLFRVARNRIIDRFRKKKEEPLPEAHDIEQVEGGEDSWRLDLVLPASDGGPE 162
           EPIEQVSAWLFRVARNRIIDRFRKKKEEPLPEAHDIEQV+G +D+WRLDL LPAS  GPE
Sbjct: 61  EPIEQVSAWLFRVARNRIIDRFRKKKEEPLPEAHDIEQVDGADDAWRLDLALPASADGPE 120

Query: 163 AAYARAALIEALQAALDELPPAQREVFIAHELDGLSFKEMSAASGTSLNTLLARKRYAVL 222
           AAYARAALI+ALQ AL ELP AQREVFIAHELDGLSFKEM+AASGTSLNTLLARKRYAVL
Sbjct: 121 AAYARAALIDALQEALGELPEAQREVFIAHELDGLSFKEMAAASGTSLNTLLARKRYAVL 180

Query: 223 HLRERLQAVYDELEM 237
           HLRERLQAVYDELEM
Sbjct: 181 HLRERLQAVYDELEM 195


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

 Score = 54.7 bits (130), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 48/178 (26%), Positives = 85/178 (47%), Gaps = 18/178 (10%)

Query: 63  VMRERSRLGGFIRRRVADAGEAEDILQEVFYEFVQAYRLPEPIEQVSA---WLFRV---- 115
           V++ + +L   + R V D  EAED++QE F   ++AYR        SA   WL+R+    
Sbjct: 27  VVKYQRKLMRLVSRLVRDQAEAEDVVQEAF---IKAYRALPQFRGDSAFYTWLYRIGINT 83

Query: 116 ARNRIIDRFRKKKEEPLPEAHDIEQVEGGEDSWRLDLVLPASDGGPEAAYARAALIEALQ 175
           A+N ++   R+    P     D E+ E  +D+  L  +       PE+  A   + + + 
Sbjct: 84  AKNYLVTMGRRA---PTSTEADAEEAETFDDADHLRDI-----NTPESMLATKQIAQTVN 135

Query: 176 AALDELPPAQREVFIAHELDGLSFKEMSAASGTSLNTLLARKRYAVLHLRERLQAVYD 233
            A++ LP   R      E++GLS+ E++ A    + T+ +R   A   + E+L+ + D
Sbjct: 136 VAMEALPEELRTAITLREIEGLSYDEIADAMNCPIGTVRSRIFRAREAIAEKLRPLLD 193


  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    0.397 

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: 647,845
Number of extensions: 23285
Number of successful extensions: 89
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 91
Number of HSP's successfully gapped: 3
Length of query: 237
Length of database: 1,619,870
Length adjustment: 82
Effective length of query: 155
Effective length of database: 1,231,600
Effective search space: 190898000
Effective search space used: 190898000
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: 129 (54.3 bits)