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= 0013.0017.p
         (268 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310298|ref|YP_003774390.1| glycerol-3-phosphate regulon re...   546   e-157
gi|300313730|ref|YP_003777822.1| DeoR family transcription regul...    93   3e-20
gi|300310357|ref|YP_003774449.1| DeoR family transcription repre...    87   1e-18

>gi|300310298|ref|YP_003774390.1| glycerol-3-phosphate regulon
           repressor transcription regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 268

 Score =  546 bits (1406), Expect = e-157,   Method: Compositional matrix adjust.
 Identities = 267/268 (99%), Positives = 267/268 (99%)

Query: 1   MFIFDQNNYSSINYHTMLNPRQQTLLECVRKHGTISVEELAQQLNVTTQTVRRDVKAMVD 60
           MFIFDQNNYS INYHTMLNPRQQTLLECVRKHGTISVEELAQQLNVTTQTVRRDVKAMVD
Sbjct: 1   MFIFDQNNYSFINYHTMLNPRQQTLLECVRKHGTISVEELAQQLNVTTQTVRRDVKAMVD 60

Query: 61  ASLLARYHGGVGLLSSTENIAYPQRQVMHAEAKRRIGRTVAARVPDGCSLILNLGTTTEE 120
           ASLLARYHGGVGLLSSTENIAYPQRQVMHAEAKRRIGRTVAARVPDGCSLILNLGTTTEE
Sbjct: 61  ASLLARYHGGVGLLSSTENIAYPQRQVMHAEAKRRIGRTVAARVPDGCSLILNLGTTTEE 120

Query: 121 VALALQQHKNLHVVTNNLNVANSLASNPALEVIIAGGVVRARDRGIVGEATIDFIRQFKV 180
           VALALQQHKNLHVVTNNLNVANSLASNPALEVIIAGGVVRARDRGIVGEATIDFIRQFKV
Sbjct: 121 VALALQQHKNLHVVTNNLNVANSLASNPALEVIIAGGVVRARDRGIVGEATIDFIRQFKV 180

Query: 181 DIGIIGISSIEMDGVLRDFDAREVKVAQTIIEQSRQVWLVADASKFGRQALVKMAHLSQI 240
           DIGIIGISSIEMDGVLRDFDAREVKVAQTIIEQSRQVWLVADASKFGRQALVKMAHLSQI
Sbjct: 181 DIGIIGISSIEMDGVLRDFDAREVKVAQTIIEQSRQVWLVADASKFGRQALVKMAHLSQI 240

Query: 241 DVLFTDAPPPPELAKLLAETDVEVVIAK 268
           DVLFTDAPPPPELAKLLAETDVEVVIAK
Sbjct: 241 DVLFTDAPPPPELAKLLAETDVEVVIAK 268


>gi|300313730|ref|YP_003777822.1| DeoR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 267

 Score = 92.8 bits (229), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 67/251 (26%), Positives = 125/251 (49%), Gaps = 8/251 (3%)

Query: 21  RQQTLLECVRKHGTISVEELAQQLNVTTQTVRRDVKAMVDASLLARYHGGVGLLSSTENI 80
           R++ LL  + +H  ++VE+    LN +  TVRRD+  + +  +L R  GG   L+   + 
Sbjct: 6   RRKRLLSLLGEHTALTVEQFCHLLNASAATVRRDIAWLAERDMLTRTRGGAERLAQKRSA 65

Query: 81  AYPQRQVMHAE------AKRRIGRTVAARVPDGCSLILNLGTTTEEVALALQQHKNLHVV 134
                +   A        KR I R  A    +G ++I+N GTTT  +A  L Q K L ++
Sbjct: 66  FALSGETFQASLARQPAQKRAIARHAAEMCDNGETIIINGGTTTFLMAEYLAQ-KRLKIL 124

Query: 135 TNNLNVANSLASNPALEVIIAGGVVRARDRGIVGEATIDFIRQFKVDIGIIGISSIEMDG 194
           TN+  +A  L +    ++I+ GG +      I+     D  +        +GI  + M G
Sbjct: 125 TNSFLMAERLLTTSENQIIVPGGQIYREQNVILSPFENDITQHHYASKMFMGIYGVSMLG 184

Query: 195 VLRDFDAREVKVAQTIIEQSRQVWLVADASKFGRQALVKMAHLSQIDVLFTDAPPPPELA 254
           ++ + D   ++  + ++ Q+ Q+ ++AD+SKF R+A + +  L++++ L TD       A
Sbjct: 185 LM-EADPLLIQAEKRLLGQAEQLVVLADSSKFSRKAGLILCGLNRVNCLVTDTGISDAAA 243

Query: 255 KLLAETDVEVV 265
           +++ +  V+VV
Sbjct: 244 QMMEQAGVKVV 254


>gi|300310357|ref|YP_003774449.1| DeoR family transcription
           repressor protein [Herbaspirillum seropedicae SmR1]
          Length = 271

 Score = 87.4 bits (215), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 71/249 (28%), Positives = 116/249 (46%), Gaps = 7/249 (2%)

Query: 21  RQQTLLECVRKHGTISVEELAQQLNVTTQTVRRDVKAMVDASLLARYHGGVGLLSS---T 77
           R   + E +R HG   +  +A  L VT  TVRRD+ A  D+ L+    GG  L +S   +
Sbjct: 24  RLTRMQEMIRDHGPTPLSRIADVLGVTVMTVRRDL-AGEDSPLICL--GGHVLEASPGGS 80

Query: 78  ENIAYPQRQV-MHAEAKRRIGRTVAARVPDGCSLILNLGTTTEEVALALQQHKNLHVVTN 136
           EN     R+   HA+ KR   +  A RV +G SL ++ GTT   +A AL     L V+  
Sbjct: 81  ENRYSIDREADQHAQRKRLACQHAARRVVEGDSLFIDCGTTMTHLAEALPPEIGLSVICY 140

Query: 137 NLNVANSLASNPALEVIIAGGVVRARDRGIVGEATIDFIRQFKVDIGIIGISSIEMDGVL 196
           +LN+AN ++  P  +VI+ GG+          E  + ++++  V+   +    ++    +
Sbjct: 141 SLNIANIVSQRPNTQVILLGGLYHPSSASFASEEGVAYLKRLGVNKAFLSAGGVDARRGV 200

Query: 197 RDFDAREVKVAQTIIEQSRQVWLVADASKFGRQALVKMAHLSQIDVLFTDAPPPPELAKL 256
              +  EV + Q  IE + Q ++V D SK GR      + L     +     P  +   L
Sbjct: 201 SCSNFHEVPIKQAAIESAAQCYVVIDQSKLGRFRPAFYSTLEVFSGIVVGGTPEQDQLDL 260

Query: 257 LAETDVEVV 265
            ++  +EVV
Sbjct: 261 FSDFPLEVV 269


  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    0.134    0.370 

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: 644,328
Number of extensions: 22396
Number of successful extensions: 128
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 124
Number of HSP's successfully gapped: 3
Length of query: 268
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 184
Effective length of database: 1,222,130
Effective search space: 224871920
Effective search space used: 224871920
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)