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= 0029.0063.p
         (128 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310488|ref|YP_003774580.1| LacI family transcription regul...   168   2e-43
gi|300311238|ref|YP_003775330.1| LacI family transcription regul...    89   9e-20
gi|300310423|ref|YP_003774515.1| GntR family transcription regul...    79   8e-17
gi|300311611|ref|YP_003775703.1| transcription regulator DNA-bin...    60   4e-11

>gi|300310488|ref|YP_003774580.1| LacI family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 365

 Score =  168 bits (425), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 85/123 (69%), Positives = 98/123 (79%)

Query: 5   GRTEVPQCMVPAPTTLGSGRTGLADLLGQDGAIDGVFCSSDILAMGVMIEAQVRGIAIPS 64
           GR  +P   V APTTLG GR GLA+LL     +D +FCSSD+LA+GVMIEAQ RGIAIP 
Sbjct: 242 GRAPLPMHHVTAPTTLGQGRQGLAELLQAQPDLDAIFCSSDLLALGVMIEAQSRGIAIPE 301

Query: 65  QLALMGFGDLSFSRDLHPQLTTVRIDGTGIGKAAARFIIERAEGREVPERVHDIGFTIIE 124
           QLA++GFGDL FSRDL P+LTTVRIDGTGIG+ AARFII+RA G EV ERV D+GF+II 
Sbjct: 302 QLAVVGFGDLEFSRDLQPRLTTVRIDGTGIGQRAARFIIDRAAGIEVAERVVDVGFSIIA 361

Query: 125 RQS 127
           R S
Sbjct: 362 RDS 364


>gi|300311238|ref|YP_003775330.1| LacI family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 340

 Score = 89.4 bits (220), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 46/123 (37%), Positives = 72/123 (58%)

Query: 5   GRTEVPQCMVPAPTTLGSGRTGLADLLGQDGAIDGVFCSSDILAMGVMIEAQVRGIAIPS 64
           G  E    ++P    L +GR  +  LL Q   +D  F S+D++A G  +E   RGIA+P 
Sbjct: 217 GAAEPVHLVMPMGAFLQAGREAIGRLLTQHPEVDAAFFSNDVIAAGAALECARRGIAVPG 276

Query: 65  QLALMGFGDLSFSRDLHPQLTTVRIDGTGIGKAAARFIIERAEGREVPERVHDIGFTIIE 124
           ++AL GF +L  + ++ P LTTV+I    IG  AA  ++ R +G  + + VHD+G++I+E
Sbjct: 277 RIALAGFANLEIATEVLPALTTVQISAHQIGLTAAEMLLTRFDGDPLDQAVHDLGYSILE 336

Query: 125 RQS 127
           R S
Sbjct: 337 RDS 339


>gi|300310423|ref|YP_003774515.1| GntR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 352

 Score = 79.3 bits (194), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 41/118 (34%), Positives = 67/118 (56%)

Query: 11  QCMVPAPTTLGSGRTGLADLLGQDGAIDGVFCSSDILAMGVMIEAQVRGIAIPSQLALMG 70
           + ++P PTT+  G   L  +L      D VFC +D LA+G + E Q +GI++P Q+A+ G
Sbjct: 235 EVLLPQPTTVDMGAQLLRRVLQDHPDCDSVFCCNDDLALGALFECQRQGISVPRQMAIAG 294

Query: 71  FGDLSFSRDLHPQLTTVRIDGTGIGKAAARFIIERAEGREVPERVHDIGFTIIERQSV 128
           F DLS++    P +TTV      IG  +A  ++ + +G E+ +   D+GF +  R+S 
Sbjct: 295 FNDLSWAACATPSITTVVTPRYDIGYQSAEMLVRQLKGEEIAKGRLDLGFELAVREST 352


>gi|300311611|ref|YP_003775703.1| transcription regulator
           DNA-binding repressor protein [Herbaspirillum
           seropedicae SmR1]
          Length = 337

 Score = 60.5 bits (145), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 48/77 (62%)

Query: 38  DGVFCSSDILAMGVMIEAQVRGIAIPSQLALMGFGDLSFSRDLHPQLTTVRIDGTGIGKA 97
           D +FC +D++A+GV+  A    I +P +L+++GF D+  ++ +HP LTTV  +   +G  
Sbjct: 240 DAIFCCNDMMAIGVLRAAGELQIEVPGELSVVGFDDIELAQFVHPPLTTVAQNTRKLGNL 299

Query: 98  AARFIIERAEGREVPER 114
            A+F++ER     +P R
Sbjct: 300 TAQFLLERIADPSLPAR 316


  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
   0.323    0.140    0.403 

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: 432,624
Number of extensions: 18388
Number of successful extensions: 118
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 118
Number of HSP's successfully gapped: 4
Length of query: 128
Length of database: 1,619,870
Length adjustment: 75
Effective length of query: 53
Effective length of database: 1,264,745
Effective search space: 67031485
Effective search space used: 67031485
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 (21.9 bits)
S2: 125 (52.8 bits)