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= 0103.0005.p
         (157 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311134|ref|YP_003775226.1| transcription regulator protein...   159   7e-41
gi|300313928|ref|YP_003778020.1| GntR family transcription regul...    80   9e-17
gi|300312337|ref|YP_003776429.1| transcription regulator protein...    68   4e-13
gi|300312133|ref|YP_003776225.1| transcription regulator protein...    59   2e-10

>gi|300311134|ref|YP_003775226.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 500

 Score =  159 bits (403), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 83/126 (65%), Positives = 96/126 (76%), Gaps = 9/126 (7%)

Query: 20  PLLSRESGDSLVDQIVRTVQSRIDDKLLRTGARMPSIRQFADLHGVSRFTVVEAYDRLVA 79
           PLL RESGDSLV+QIVR +++RIDDKLLR+G RMPSIRQFAD + +SRFTVVEAYDRLVA
Sbjct: 30  PLLLRESGDSLVEQIVRGIRARIDDKLLRSGMRMPSIRQFADTNQISRFTVVEAYDRLVA 89

Query: 80  QGFLESRRGSGFFVRERSPVANPSMTGTVLSAAGHNPSGDGTPQPQQLDVVWLVRNMFRQ 139
           QG+LESRRGSGF+V+ER+P+          S        D  P  + LDVVWLVRNMFRQ
Sbjct: 90  QGYLESRRGSGFYVKERAPLGG--------SYGAAQAELDTEPG-RGLDVVWLVRNMFRQ 140

Query: 140 MPAQKM 145
           MP  KM
Sbjct: 141 MPPAKM 146


>gi|300313928|ref|YP_003778020.1| GntR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 472

 Score = 79.7 bits (195), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 52/139 (37%), Positives = 74/139 (53%), Gaps = 17/139 (12%)

Query: 12  PAAVPTTLPLLSRESGDSLVDQIVRTVQSRIDDKLLRTGARMPSIRQFADLHGVSRFTVV 71
           PA  P  L L  R++   LV+Q+   +   I+   LR+G R+PS+RQFA  H +   TVV
Sbjct: 4   PARAPLQLDL-KRKTSARLVEQVANGLAGLIETGELRSGERLPSVRQFAQHHDIGSSTVV 62

Query: 72  EAYDRLVAQGFLESRRGSGFFVRERSPVANPSMTGTVLSAAGHNPSGDGTPQPQQLDVVW 131
           EAY++LVA+G L++RRG+GFFV  R   A  S    V             P+P  +D  W
Sbjct: 63  EAYEQLVARGMLQARRGAGFFVAAR---AGQSGQHAVFVP----------PEP-VIDSAW 108

Query: 132 LVRNMF--RQMPAQKMXSW 148
           L+  MF   ++P +    W
Sbjct: 109 LLSEMFADERVPIKAGCGW 127


>gi|300312337|ref|YP_003776429.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 469

 Score = 67.8 bits (164), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 38/119 (31%), Positives = 59/119 (49%), Gaps = 15/119 (12%)

Query: 25  ESGDSLVDQIVRTVQSRIDDKLLRTGARMPSIRQFADLHGVSRFTVVEAYDRLVAQGFLE 84
           E+  +L   +V+ ++ +I + +   G+R+PSIR+ A  HG ++ T+V  +D L A G  E
Sbjct: 3   EASTTLTSTLVQLIRRQIAEGVYAPGSRLPSIREMAARHGCAKNTIVNVFDELTALGLAE 62

Query: 85  SRRGSGFFVRERSPVANPSMTGTVLSAAGHNPSGDGTPQPQQLDVVWLVRNMFRQMPAQ 143
            RRG+GFFV    P       G +  A               +DVVWL+R   +  P Q
Sbjct: 63  PRRGAGFFVCVAPPRPKEDEEGNLSRA---------------MDVVWLMREQLKHDPGQ 106


>gi|300312133|ref|YP_003776225.1| transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 491

 Score = 58.9 bits (141), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 33/78 (42%), Positives = 47/78 (60%)

Query: 24  RESGDSLVDQIVRTVQSRIDDKLLRTGARMPSIRQFADLHGVSRFTVVEAYDRLVAQGFL 83
           + S   LVD+I   V   +  + L  G ++PS+R  A+   VSR TV  AY++LVA G +
Sbjct: 26  KHSARLLVDRIFTAVLEGVRTRRLAHGDKLPSLRVVAESAQVSRDTVARAYEKLVAHGHV 85

Query: 84  ESRRGSGFFVRERSPVAN 101
            +R G+GFFVR  + VAN
Sbjct: 86  YTRPGAGFFVRVDNQVAN 103


  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    0.132    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: 459,056
Number of extensions: 18513
Number of successful extensions: 88
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 86
Number of HSP's successfully gapped: 4
Length of query: 157
Length of database: 1,619,870
Length adjustment: 78
Effective length of query: 79
Effective length of database: 1,250,540
Effective search space: 98792660
Effective search space used: 98792660
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: 126 (53.1 bits)