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= 0001.3481.p
         (312 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...   600   e-173
gi|300311849|ref|YP_003775941.1| LysR family transcription regul...   100   2e-22
gi|300313602|ref|YP_003777694.1| LysR family transcription regul...    60   2e-10

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

 Score =  600 bits (1547), Expect = e-173,   Method: Compositional matrix adjust.
 Identities = 298/312 (95%), Positives = 305/312 (97%)

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

Query: 61  PAGLQLLQEGRHLLLAASDLEQRVKRTATGRETELHIVLNSLIPFDKMLPVIAAFDREQS 120
           PAGLQLLQEGRHLLLAA+DLEQRVKRTATGRETELHIVLNSLIPFDKMLP+IAAFDREQS
Sbjct: 61  PAGLQLLQEGRHLLLAANDLEQRVKRTATGRETELHIVLNSLIPFDKMLPIIAAFDREQS 120

Query: 121 GTRLRFTPGVLTGAWEKLIEGRANLVIGVTLDGPEVVRTSGRFQMQELGAVDWVFAVAPQ 180
           GTRLRFTPGVLTGAWEKLIEGRANLVIGVTLDGPEVVRTSGRFQMQELGAVDWVF VAPQ
Sbjct: 121 GTRLRFTPGVLTGAWEKLIEGRANLVIGVTLDGPEVVRTSGRFQMQELGAVDWVFVVAPQ 180

Query: 181 HPLASVIEPLSAELVRSHRAIAVGDNSQSLPTLTMGLLSGQETLTVATVADKLQAQLAGL 240
           HPLA V EPLSAELVRSHRAIAVGDNSQSLPTLTMGLLSGQETLTVATVADKLQAQLAGL
Sbjct: 181 HPLAGVEEPLSAELVRSHRAIAVGDNSQSLPTLTMGLLSGQETLTVATVADKLQAQLAGL 240

Query: 241 GCGHLPRIWAAPYLASGALVEKQTLAAKPNDNFMVAWPKAEQGKSLKWFIQYLAQPHVRQ 300
           GCGHLPRIWA PYLASGALVEKQTLAAKPNDNFMVAWPKAEQGKSLKWFIQ+LAQPHVRQ
Sbjct: 241 GCGHLPRIWAEPYLASGALVEKQTLAAKPNDNFMVAWPKAEQGKSLKWFIQHLAQPHVRQ 300

Query: 301 SLMGPITPQEPA 312
           SL+GP+  + PA
Sbjct: 301 SLIGPVPMRGPA 312


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

 Score =  100 bits (249), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 89/300 (29%), Positives = 142/300 (47%), Gaps = 14/300 (4%)

Query: 2   NLTLESLLILDMIDRKGSFAAAAVALDRVPSALTYSVRKLEDDLDVLLFDRRGHRAQLTP 61
            L+L+ L +   +   GSF AAA  L R  SA++Y++  LE+ L +LLFDR G+R QLT 
Sbjct: 5   RLSLDQLRVFVQVADSGSFLAAARKLARAQSAVSYAIASLEEQLGLLLFDRSGYRPQLTA 64

Query: 62  AGLQLLQEGRHLLLAASDLEQRVKRTATGRETELHIVLNSLIPFDKMLPVIAAFDREQSG 121
            G  LL + R +L     L+ R    A G+E E+ + ++   P D ++ ++  F      
Sbjct: 65  PGEALLADARQVLDHVDSLQVRASSYARGQELEMALAVDVFFPLDCLVDLLQRFRAAFPA 124

Query: 122 TRLRFTPGVLTGAWEKLIEGRANLVIGVTLDG--PEVVRTSGRFQMQELGAVDWVFAVAP 179
             +R     L    E++I+GRA L I  TL    P ++R +       L +V  V  VAP
Sbjct: 125 VTVRLEVEALGAVAERVIDGRAMLGILGTLPTTPPNLMRIT-------LPSVRLVAVVAP 177

Query: 180 QHPLASVIEPLSAELVRSHRAIAVGDNSQSLPTLTMGLLSGQETLTVATVADKLQAQLAG 239
            HPLA V   ++ +++     + + D S+        + S + T  ++ +  K     AG
Sbjct: 178 HHPLAKVKGRIAEKMLLQQTQLVLSDRSELTARQDFSVHS-RLTWRMSDLGTKHALLRAG 236

Query: 240 LGCGHLPRIWAAPYLASGALVEKQTLAAKPNDNFM----VAWPKAEQGKSLKWFIQYLAQ 295
           +G G++P       LA+G LV   T+   P    +    V  P    G +L W++  LA 
Sbjct: 237 MGWGNMPLHVVKEDLAAGRLVSISTIHHPPQGAELPIQCVYKPDHRAGPALSWWLDALAN 296


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

 Score = 60.1 bits (144), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 57/185 (30%), Positives = 93/185 (50%), Gaps = 12/185 (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-VIAAFDREQ 119
            +G QLL + RH+L AA  +E++      G  +ELHI  ++ I    MLP +IAA+ ++ 
Sbjct: 61  DSGRQLLPQARHMLDAAQTIERQFSDPEAG--SELHIGASTTIG-SYMLPAMIAAYRKDH 117

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

Query: 179 PQHPL 183
           P+HPL
Sbjct: 171 PRHPL 175


  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    0.135    0.392 

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: 947,459
Number of extensions: 38322
Number of successful extensions: 188
Number of sequences better than 1.0e-08: 7
Number of HSP's gapped: 187
Number of HSP's successfully gapped: 7
Length of query: 312
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 227
Effective length of database: 1,217,395
Effective search space: 276348665
Effective search space used: 276348665
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)