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= 0008.0040.p
         (304 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312870|ref|YP_003776962.1| transcription regulator protein...   580   e-167
gi|300311849|ref|YP_003775941.1| LysR family transcription regul...   101   8e-23
gi|300313602|ref|YP_003777694.1| LysR family transcription regul...    58   8e-10

>gi|300312870|ref|YP_003776962.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 312

 Score =  580 bits (1495), Expect = e-167,   Method: Compositional matrix adjust.
 Identities = 286/298 (95%), Positives = 292/298 (97%)

Query: 1   VNLTLESLLILDMIDRKGSFAAAAVALDRVPSALTYSVRKLEDDLDVLLFDRRGHRAQLT 60
           +NLTLESLLILDMIDRKGSFAAAAVALDRVPSALTYSVRKLEDDLDVLLFDRRGHRAQLT
Sbjct: 1   MNLTLESLLILDMIDRKGSFAAAAVALDRVPSALTYSVRKLEDDLDVLLFDRRGHRAQLT 60

Query: 61  PAGLQLLQEGRHLLLAASDLEQRVKRTATGRETELHIVLNSLIPFDKMLPVIEAFDREES 120
           PAGLQLLQEGRHLLLAA+DLEQRVKRTATGRETELHIVLNSLIPFDKMLP+I AFDRE+S
Sbjct: 61  PAGLQLLQEGRHLLLAANDLEQRVKRTATGRETELHIVLNSLIPFDKMLPIIAAFDREQS 120

Query: 121 GTRLRFTPGVLTGAWEKLIEGRANLVIGVTLDGPEVVRTSGRFQMQELGSVDWVFAVAPT 180
           GTRLRFTPGVLTGAWEKLIEGRANLVIGVTLDGPEVVRTSGRFQMQELG+VDWVF VAP 
Sbjct: 121 GTRLRFTPGVLTGAWEKLIEGRANLVIGVTLDGPEVVRTSGRFQMQELGAVDWVFVVAPQ 180

Query: 181 HPLASATEPLSAELVRSHRAIAVGDNSQSLPTLTMGLLSGQETLTVATVADKLQAQLAGL 240
           HPLA   EPLSAELVRSHRAIAVGDNSQSLPTLTMGLLSGQETLTVATVADKLQAQLAGL
Sbjct: 181 HPLAGVEEPLSAELVRSHRAIAVGDNSQSLPTLTMGLLSGQETLTVATVADKLQAQLAGL 240

Query: 241 GCGHLPRIWAEPYLATGALVEKQTLAAKPNDNFMVAWPKAEQGKSLKWFIQHLAQPHV 298
           GCGHLPRIWAEPYLA+GALVEKQTLAAKPNDNFMVAWPKAEQGKSLKWFIQHLAQPHV
Sbjct: 241 GCGHLPRIWAEPYLASGALVEKQTLAAKPNDNFMVAWPKAEQGKSLKWFIQHLAQPHV 298


>gi|300311849|ref|YP_003775941.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 309

 Score =  101 bits (251), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 89/299 (29%), Positives = 142/299 (47%), Gaps = 14/299 (4%)

Query: 3   LTLESLLILDMIDRKGSFAAAAVALDRVPSALTYSVRKLEDDLDVLLFDRRGHRAQLTPA 62
           L+L+ L +   +   GSF AAA  L R  SA++Y++  LE+ L +LLFDR G+R QLT  
Sbjct: 6   LSLDQLRVFVQVADSGSFLAAARKLARAQSAVSYAIASLEEQLGLLLFDRSGYRPQLTAP 65

Query: 63  GLQLLQEGRHLLLAASDLEQRVKRTATGRETELHIVLNSLIPFDKMLPVIEAFDREESGT 122
           G  LL + R +L     L+ R    A G+E E+ + ++   P D ++ +++ F       
Sbjct: 66  GEALLADARQVLDHVDSLQVRASSYARGQELEMALAVDVFFPLDCLVDLLQRFRAAFPAV 125

Query: 123 RLRFTPGVLTGAWEKLIEGRANLVIGVTLDG--PEVVRTSGRFQMQELGSVDWVFAVAPT 180
            +R     L    E++I+GRA L I  TL    P ++R +       L SV  V  VAP 
Sbjct: 126 TVRLEVEALGAVAERVIDGRAMLGILGTLPTTPPNLMRIT-------LPSVRLVAVVAPH 178

Query: 181 HPLASATEPLSAELVRSHRAIAVGDNSQSLPTLTMGLLSGQETLTVATVADKLQAQLAGL 240
           HPLA     ++ +++     + + D S+        + S + T  ++ +  K     AG+
Sbjct: 179 HPLAKVKGRIAEKMLLQQTQLVLSDRSELTARQDFSVHS-RLTWRMSDLGTKHALLRAGM 237

Query: 241 GCGHLPRIWAEPYLATGALVEKQTLAAKPNDNFM----VAWPKAEQGKSLKWFIQHLAQ 295
           G G++P    +  LA G LV   T+   P    +    V  P    G +L W++  LA 
Sbjct: 238 GWGNMPLHVVKEDLAAGRLVSISTIHHPPQGAELPIQCVYKPDHRAGPALSWWLDALAN 296


>gi|300313602|ref|YP_003777694.1| LysR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 300

 Score = 58.2 bits (139), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 57/198 (28%), Positives = 97/198 (48%), Gaps = 12/198 (6%)

Query: 1   VNLTLESLLILDMIDRKGSFAAAAVALDRVPSALTYSVRKLEDDLDVLLFDRRGHRAQLT 60
           + +TL  L I   + + GS  AAA  +    SA + ++ +LE  L V LFDR G R  L 
Sbjct: 1   MKITLRQLQIFLAVAQSGSTTAAADLVALSQSAASAALNELEHLLGVQLFDRVGKRLVLN 60

Query: 61  PAGLQLLQEGRHLLLAASDLEQRVKRTATGRETELHIVLNSLIPFDKMLP-VIEAFDREE 119
            +G QLL + RH+L AA  +E++      G  +ELHI  ++ I    MLP +I A+ ++ 
Sbjct: 61  DSGRQLLPQARHMLDAAQTIERQFSDPEAG--SELHIGASTTIG-SYMLPAMIAAYRKDH 117

Query: 120 SGTRLRFTPGVLTGAWEKLIEGRANLVIGVTL-DGPEVVRTSGRFQMQELGSVDWVFAVA 178
           +G R+R     L      +++   N  +   L +GP     +   +++     + +   A
Sbjct: 118 AGARVR----ALVANTADIVDAVVNFEVDAGLIEGP---CHADDVEVEPWMMDELIVVAA 170

Query: 179 PTHPLASATEPLSAELVR 196
           P HPL  +   ++ + +R
Sbjct: 171 PRHPLVKSGRKITLKRLR 188


  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
   0.319    0.134    0.390 

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: 919,011
Number of extensions: 36982
Number of successful extensions: 187
Number of sequences better than 1.0e-08: 8
Number of HSP's gapped: 188
Number of HSP's successfully gapped: 8
Length of query: 304
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 219
Effective length of database: 1,217,395
Effective search space: 266609505
Effective search space used: 266609505
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)