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= 0228.0013.p
         (127 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313525|ref|YP_003777617.1| AraC family transcription regul...   105   1e-24
gi|300310273|ref|YP_003774365.1| AraC family transcription regul...    83   6e-18
gi|300311011|ref|YP_003775103.1| AraC family transcription regul...    79   8e-17
gi|300310311|ref|YP_003774403.1| AraC family transcription regul...    77   3e-16

>gi|300313525|ref|YP_003777617.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 298

 Score =  105 bits (262), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 54/127 (42%), Positives = 78/127 (61%), Gaps = 8/127 (6%)

Query: 1   LAGVILDEI-----RTLPEEFLGLPMPQDARLLKIARALSDRPDDERRMEEWAMWAGIAP 55
           LA V+++E+       LP   L LP PQ +RL  IAR L++ P D R + +W     ++ 
Sbjct: 135 LAAVLVEELEHSQRHALP---LHLPAPQHSRLRAIARHLAEHPADRRTVAQWGQRHAMSE 191

Query: 56  RTLTRRFVAETGFSFTEWRQRVRLLKSLEMLAAGKSVTTIALDLGYGNVSAFIALFRRTF 115
           R+  R   AETG SF  WR+++ L+ +L+ LA+G SV  ++ DLGY +VSAFI +FR+T 
Sbjct: 192 RSFARFVQAETGMSFGRWRRQIHLMLALQRLASGSSVQRVSQDLGYDSVSAFITMFRKTL 251

Query: 116 GATPGRY 122
           G  P RY
Sbjct: 252 GKPPARY 258


>gi|300310273|ref|YP_003774365.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 271

 Score = 83.2 bits (204), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 43/125 (34%), Positives = 67/125 (53%), Gaps = 3/125 (2%)

Query: 1   LAGVILDEIRTLPEEFLGLPMPQ---DARLLKIARALSDRPDDERRMEEWAMWAGIAPRT 57
           L  ++++E+ T P     LP P    D  + ++ +AL D P D     EWA    +  +T
Sbjct: 140 LGALVMEEVLTQPTLPFHLPWPMSETDGPMARLCQALLDDPGDMATAAEWADRLAMGQKT 199

Query: 58  LTRRFVAETGFSFTEWRQRVRLLKSLEMLAAGKSVTTIALDLGYGNVSAFIALFRRTFGA 117
             RRF+  TG +F +WRQ++RL+ SL +L  G  +T +AL  GY + SA+   F + FG 
Sbjct: 200 FHRRFLQSTGMTFGKWRQQLRLMSSLPLLMQGMPITQVALASGYDSHSAYTTAFGKQFGK 259

Query: 118 TPGRY 122
            P  +
Sbjct: 260 PPSAF 264


>gi|300311011|ref|YP_003775103.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 273

 Score = 79.3 bits (194), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 42/113 (37%), Positives = 64/113 (56%)

Query: 4   VILDEIRTLPEEFLGLPMPQDARLLKIARALSDRPDDERRMEEWAMWAGIAPRTLTRRFV 63
           ++LDEI    E    +P+P + RL ++       P       +WA+   I+ RT +RRF+
Sbjct: 144 LLLDEIGRAEEIPAHVPLPPEPRLGELCHRFLAAPSIRSGPAQWALQLHISERTFSRRFL 203

Query: 64  AETGFSFTEWRQRVRLLKSLEMLAAGKSVTTIALDLGYGNVSAFIALFRRTFG 116
           A+TG  F +WR R  ++ ++  LA G+ VTTIA DLGY   +AF  +FR+  G
Sbjct: 204 AQTGMGFQQWRLRACVMYAISRLALGQPVTTIAYDLGYERPAAFSTMFRKMTG 256


>gi|300310311|ref|YP_003774403.1| AraC family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 274

 Score = 77.4 bits (189), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 44/122 (36%), Positives = 63/122 (51%)

Query: 1   LAGVILDEIRTLPEEFLGLPMPQDARLLKIARALSDRPDDERRMEEWAMWAGIAPRTLTR 60
           +A +IL E+   P   + +P P D RL  I  A+   P  +  + +WA   G + RT+ R
Sbjct: 139 VAELILSELARAPAIPVAIPWPGDRRLQAICEAILADPGRQFSLADWAGMGGASVRTVIR 198

Query: 61  RFVAETGFSFTEWRQRVRLLKSLEMLAAGKSVTTIALDLGYGNVSAFIALFRRTFGATPG 120
            F  ETG  F  W Q+V L ++L  L+ G  V  +A  LGY + SAF  +FR+    TP 
Sbjct: 199 LFPKETGLQFRHWVQQVHLSEALVRLSRGDPVGVVAQALGYRSQSAFSNMFRKALRTTPN 258

Query: 121 RY 122
            Y
Sbjct: 259 HY 260


  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    0.139    0.415 

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: 430,985
Number of extensions: 16530
Number of successful extensions: 112
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 120
Number of HSP's successfully gapped: 4
Length of query: 127
Length of database: 1,619,870
Length adjustment: 75
Effective length of query: 52
Effective length of database: 1,264,745
Effective search space: 65766740
Effective search space used: 65766740
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: 125 (52.8 bits)