BLASTP 2.2.22 [Sep-27-2009]


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= gi|254780611|ref|YP_003065024.1| RNA polymerase factor sigma-32
[Candidatus Liberibacter asiaticus str. psy62]
         (302 letters)

Database: las_proteome 
           1233 sequences; 328,796 total letters

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



>gi|254780611|ref|YP_003065024.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter asiaticus
           str. psy62]
          Length = 302

 Score =  618 bits (1594), Expect = e-179,   Method: Compositional matrix adjust.
 Identities = 302/302 (100%), Positives = 302/302 (100%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL
Sbjct: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS
Sbjct: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL
Sbjct: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER
Sbjct: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
           RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP
Sbjct: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300

Query: 301 RY 302
           RY
Sbjct: 301 RY 302


>gi|254780289|ref|YP_003064702.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter asiaticus
           str. psy62]
          Length = 682

 Score = 99.8 bits (247), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 85/289 (29%), Positives = 138/289 (47%), Gaps = 49/289 (16%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           SI V   I +S + H    + M+ K E E  +AK+            +V ++LRLV+ +A
Sbjct: 415 SISVETGISISEFRH---IVSMVRKGECEASIAKK-----------EMVEANLRLVISVA 460

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y   GL   +++ EGNIGLM+A +KFD   G++ +TY+MWW+K A+   I      ++
Sbjct: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520

Query: 126 IGTTANQK--RLFFNLRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVIS 175
           I      K  ++    RR+   ++        PE++          + K L +++ E IS
Sbjct: 521 IPVHMRDKIHKVVRTARRMSNKIK----REPTPEEIAKKLAMPVEGVRKVLKITK-EPIS 575

Query: 176 MNCRLAGDESLNALINS-SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
           +   + GDE  + L +   DKN+    D  +               + N R   TR ++ 
Sbjct: 576 LETPI-GDEDTSHLGDFIEDKNAVSPLDSAI---------------QANLRETTTRVLAS 619

Query: 235 LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668


>gi|254780766|ref|YP_003065179.1| recombination protein F [Candidatus Liberibacter asiaticus str.
           psy62]
          Length = 375

 Score = 26.2 bits (56), Expect = 0.80,   Method: Compositional matrix adjust.
 Identities = 9/24 (37%), Positives = 15/24 (62%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYS 105
           G   +++A+    P RGFR A+Y+
Sbjct: 39  GKTNILEAISFLSPGRGFRRASYA 62


>gi|254780799|ref|YP_003065212.1| DNA translocase FtsK [Candidatus Liberibacter asiaticus str. psy62]
          Length = 806

 Score = 24.3 bits (51), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 10/34 (29%), Positives = 19/34 (55%)

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           +P  +  F  + +Q N  TL+++ S+F +  E V
Sbjct: 320 SPVNQMTFSPKVMQNNACTLKSVLSDFGIQGEIV 353


>gi|254781024|ref|YP_003065437.1| electron transfer flavoprotein-ubiquinone oxidoreductase
           [Candidatus Liberibacter asiaticus str. psy62]
          Length = 554

 Score = 23.9 bits (50), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 4/35 (11%)

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           IG  A     F NL R+KG   AI    L  E++V
Sbjct: 327 IGCAAG----FVNLLRIKGSHNAIISGMLAAEKIV 357


>gi|254781029|ref|YP_003065442.1| chemotaxis sensory transducer [Candidatus Liberibacter asiaticus str.
            psy62]
          Length = 1828

 Score = 23.5 bits (49), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 14/34 (41%), Positives = 18/34 (52%)

Query: 252  PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             + LEN   E E S  RV    A +FK + +SIQ
Sbjct: 1022 TINLENNLKEQEKSLSRVVDTSASSFKYLSDSIQ 1055


>gi|254780779|ref|YP_003065192.1| 30S ribosomal protein S2 [Candidatus Liberibacter asiaticus str.
           psy62]
          Length = 278

 Score = 23.1 bits (48), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           RRL+  + A+ D N  P+ V  +    N   S  I++ C L    +++ +
Sbjct: 178 RRLRIPIVAVVDTNSNPDLVDYVIPG-NDDSSRSIALFCDLVASAAIDGI 226


>gi|254780514|ref|YP_003064927.1| type II restriction endonuclease [Candidatus Liberibacter asiaticus
           str. psy62]
          Length = 110

 Score = 22.7 bits (47), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 8/30 (26%), Positives = 18/30 (60%)

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAF 277
           +Q N + L+N+S+ +EV +  + ++    F
Sbjct: 1   MQFNEIILKNISNNYEVPKMLITELSTELF 30


  Database: las_proteome
    Posted date:  Jun 5, 2011  6:30 PM
  Number of letters in database: 328,796
  Number of sequences in database:  1233
  
Lambda     K      H
   0.318    0.132    0.371 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 178,652
Number of Sequences: 1233
Number of extensions: 6787
Number of successful extensions: 33
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 22
Number of HSP's gapped (non-prelim): 13
length of query: 302
length of database: 328,796
effective HSP length: 73
effective length of query: 229
effective length of database: 238,787
effective search space: 54682223
effective search space used: 54682223
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 38 (19.2 bits)