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= 0034.0141.p
         (318 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310311|ref|YP_003774403.1| AraC family transcription regul...   125   7e-30
gi|300311011|ref|YP_003775103.1| AraC family transcription regul...    89   4e-19
gi|300310273|ref|YP_003774365.1| AraC family transcription regul...    65   7e-12
gi|300313525|ref|YP_003777617.1| AraC family transcription regul...    65   9e-12

>gi|300310311|ref|YP_003774403.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 274

 Score =  125 bits (313), Expect = 7e-30,   Method: Compositional matrix adjust.
 Identities = 60/103 (58%), Positives = 72/103 (69%)

Query: 28  SPEAAQLQHLPHAVVAFSRDFDHDQLLAKHSHPRGQLLYAAEGVMQVRTAHGLWVIPPQR 87
           S E    QHLP +VVAF+R+     LL  HSH RGQLLYA EGVMQVRT  G+W++PP R
Sbjct: 11  SAEVDTFQHLPSSVVAFARELSARDLLTAHSHRRGQLLYAVEGVMQVRTPQGVWLVPPHR 70

Query: 88  ALWVPCSLAHEIRMLSAVRLRTLYIRPHESELIGAECRLLEVT 130
           ALWVP  + HEI MLS V +RTLYI   +   +G +CRLLEV+
Sbjct: 71  ALWVPPQVEHEILMLSKVSMRTLYINQAQGRELGEQCRLLEVS 113


>gi|300311011|ref|YP_003775103.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 273

 Score = 89.0 bits (219), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 48/116 (41%), Positives = 66/116 (56%), Gaps = 4/116 (3%)

Query: 41  VVAFSRDFDHDQLLAKHSHPRGQLLYAAEGVMQVRTAHGLWVIPPQRALWVPCSLAHEIR 100
           VVA    + H  +   HSH R QLLY   G+MQV TA G WV+PPQ A+W+P    H+ R
Sbjct: 26  VVAAGAQYRHGAVQPWHSHRRAQLLYGLSGLMQVITADGAWVVPPQHAVWIPSGREHQSR 85

Query: 101 MLSAVRLRTLYIRPHESELIGAECRLLEVTPLLRELILALLKEESDSESGYDLRGR 156
           ML AV   + +I P  +  + + C++L V PLLREL++    E +  +  Y L  R
Sbjct: 86  MLQAVTTCSAFIEPEHAPRVASSCQVLAVRPLLRELLI----EATRMDPHYVLHSR 137


>gi|300310273|ref|YP_003774365.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 271

 Score = 65.1 bits (157), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 34/114 (29%), Positives = 62/114 (54%)

Query: 41  VVAFSRDFDHDQLLAKHSHPRGQLLYAAEGVMQVRTAHGLWVIPPQRALWVPCSLAHEIR 100
           V   S  +    ++  H HP+G L+YA  G+++V+   G W++PP  A+W+   +AH + 
Sbjct: 25  VFGVSGRYPAGSVVPMHQHPQGHLIYADSGLLRVQAESGQWLVPPTAAVWLRSGVAHSLA 84

Query: 101 MLSAVRLRTLYIRPHESELIGAECRLLEVTPLLRELILALLKEESDSESGYDLR 154
           M   ++   L++R      + A   ++ V+PLLRELI+ L +   ++ S   +R
Sbjct: 85  MPVTLQAYGLFVRQDVCARLPAFDCVVHVSPLLRELIITLAQAREENMSAKRMR 138


>gi|300313525|ref|YP_003777617.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 298

 Score = 64.7 bits (156), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 32/90 (35%), Positives = 53/90 (58%), Gaps = 1/90 (1%)

Query: 57  HSHPRGQLLYAAEGVMQVRTAHGLWVIPPQRALWVPCSLAHEIRMLSAVRLRTLYIRPHE 116
           HSH +GQL+ A  G +   TA G+W++PPQ A+W+P  + H  R+    +L  L+I P  
Sbjct: 37  HSHRKGQLVVALRGAVTCETAQGMWIVPPQSAVWIPPGVPHSNRVTLDGQLCFLFIAPQA 96

Query: 117 SELIGAECRLLEVTPLLRELILALLKEESD 146
           + +   +C  L ++PLL ++I  L ++  D
Sbjct: 97  ASM-PEQCCTLALSPLLVQMICHLAEQRQD 125


  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
   0.320    0.133    0.409 

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: 872,729
Number of extensions: 30780
Number of successful extensions: 114
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 114
Number of HSP's successfully gapped: 4
Length of query: 318
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 233
Effective length of database: 1,217,395
Effective search space: 283653035
Effective search space used: 283653035
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: 130 (54.7 bits)