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= 0001.3863.p
         (288 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313268|ref|YP_003777360.1| transcription regulator protein...   539   e-154
gi|300313081|ref|YP_003777173.1| transcription regulator protein...    56   4e-09
gi|300310394|ref|YP_003774486.1| AraC family transcription regul...    56   4e-09

>gi|300313268|ref|YP_003777360.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 288

 Score =  539 bits (1389), Expect = e-154,   Method: Compositional matrix adjust.
 Identities = 262/288 (90%), Positives = 271/288 (94%)

Query: 1   MSDIRKKAYIARFERVLDHIETHLHTPLDVEQLAAVAHFSRFHFQRQFADFVGVGVARYI 60
           MSD RKKAY ARFERVLDHIE HLH PL+VEQLA VAHFSRFHFQRQFADF GVGVARYI
Sbjct: 1   MSDERKKAYQARFERVLDHIEAHLHAPLEVEQLANVAHFSRFHFQRQFADFTGVGVARYI 60

Query: 61  LLMRLKQASLQLAFQAQRRIIDIALDAGFENPESFTRAFRSAFGQSPSQFRRAPDWPSWN 120
           LLMRLK ASLQLAFQ QRRIIDIAL+AGFENPESFTRAFRSAFGQSPSQFRRAPDWPSW+
Sbjct: 61  LLMRLKHASLQLAFQPQRRIIDIALEAGFENPESFTRAFRSAFGQSPSQFRRAPDWPSWH 120

Query: 121 ERYVFRIPERKVDVQVEIINVEPIRIALLAHRGPVNQLNATVAQFIAWRKSSGLSPMERC 180
           ER+VFRIPERKVDVQVEI +VEPIRIALLAHRGPVN LNATVAQFIAWRK+SGLSP+ERC
Sbjct: 121 ERFVFRIPERKVDVQVEITHVEPIRIALLAHRGPVNGLNATVAQFIAWRKASGLSPVERC 180

Query: 181 RTFGLAWDNPDTTPPEQFRFDICGELEGALPDNPQGVMEQSIPGGRCARVRHAGAHERLG 240
           RTFGLAWDNPDTTPPEQFRF ICGELEG LP N QGV+E  IPGGRCARVRH GAHERLG
Sbjct: 181 RTFGLAWDNPDTTPPEQFRFGICGELEGDLPGNAQGVVESLIPGGRCARVRHVGAHERLG 240

Query: 241 DSIYPLYRQWLPQSGEELRDFPLYFHYLNLLPDTPPGELLTDIYLPLK 288
           DSIYPLYRQWLP+SGEELRDFPLYFHYLNLLPDTPPGELLTDIYLPLK
Sbjct: 241 DSIYPLYRQWLPESGEELRDFPLYFHYLNLLPDTPPGELLTDIYLPLK 288


>gi|300313081|ref|YP_003777173.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 330

 Score = 55.8 bits (133), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 40/101 (39%), Positives = 48/101 (47%), Gaps = 1/101 (0%)

Query: 12  RFERVLDHIETHLHTPLDVEQLAAVAHFSRFHFQRQFADFVGVGVARYILLMRLKQASLQ 71
           R  R L     HLH  L V+ LA VA  SR  F R FA   G   AR I  MR + A L+
Sbjct: 212 RIRRALGFAREHLHQALTVDLLAEVACLSRRQFDRAFAAETGQTPARAIEQMRAEAARLR 271

Query: 72  LAFQAQRRIIDIALDAGFENPESFTRAFRSAFGQSPSQFRR 112
           +  Q+Q  +  IA   GF + +   RA    FGQ P   RR
Sbjct: 272 IE-QSQDTLESIARATGFGDADRMRRACLRLFGQPPQAMRR 311


>gi|300310394|ref|YP_003774486.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 294

 Score = 55.8 bits (133), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 32/101 (31%), Positives = 46/101 (45%)

Query: 13  FERVLDHIETHLHTPLDVEQLAAVAHFSRFHFQRQFADFVGVGVARYILLMRLKQASLQL 72
             R + ++  HL   +  + LA +   +   F R F    G  + RY   +R+  A L L
Sbjct: 183 LNRAIAYLREHLTDDIGEQDLADMVGQNLSSFSRAFKRHTGTTLVRYKNQLRVDLACLAL 242

Query: 73  AFQAQRRIIDIALDAGFENPESFTRAFRSAFGQSPSQFRRA 113
             + Q RI DI  + GF N  +F R F    G SPS+FR  
Sbjct: 243 LTRPQARITDICYETGFSNLSNFNRHFHKIKGMSPSEFRNT 283


  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
   0.325    0.140    0.440 

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: 997,570
Number of extensions: 44208
Number of successful extensions: 185
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 196
Number of HSP's successfully gapped: 3
Length of query: 288
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 204
Effective length of database: 1,222,130
Effective search space: 249314520
Effective search space used: 249314520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 130 (54.7 bits)