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= 0068.0007.p
         (162 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310416|ref|YP_003774508.1| MocR family transcription regul...    97   8e-22
gi|300311139|ref|YP_003775231.1| MocR family transcription regul...    92   2e-20
gi|300313928|ref|YP_003778020.1| GntR family transcription regul...    58   3e-10

>gi|300310416|ref|YP_003774508.1| MocR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 516

 Score = 96.7 bits (239), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 59/163 (36%), Positives = 83/163 (50%), Gaps = 2/163 (1%)

Query: 2   RHVGPETRSQYDFMGGIPVRRQFPQEEWRQCVLYGLRQVNEARGFYAETEGVPALREAIA 61
           R  G   R    FM G+P     P + W +      R+ N     Y    G   LRE IA
Sbjct: 144 RQAGVGERQWGAFMPGVPDVTCVPYKIWGRLQNKHWRRSNADLLTYGPGAGYAGLREQIA 203

Query: 62  RHVSFSRGVQCTAADVLVTNGAQQALDLITRVLVEPGSVVAVEDPGYPPARMLFSAQGAR 121
            ++  +R V CT + VL+T G  Q+LD++ ++L E G    VEDP Y   R + ++ G +
Sbjct: 204 EYLRVARSVNCTPSQVLITTGIHQSLDIVVKLLGEHGDSAWVEDPCYWGTRSVLNSLGIQ 263

Query: 122 VESVPVDDEGMRVDL--IPDGTRLIYATPAHQFPLGMPMSPAR 162
              + VD EGMR+ L  +    R I  TP+HQ+PLGM MS +R
Sbjct: 264 SVPIAVDQEGMRMRLANLRRPPRFICTTPSHQYPLGMVMSLSR 306


>gi|300311139|ref|YP_003775231.1| MocR family transcription
           regulator protein [Herbaspirillum seropedicae SmR1]
          Length = 398

 Score = 91.7 bits (226), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 56/146 (38%), Positives = 80/146 (54%), Gaps = 4/146 (2%)

Query: 13  DFMGGIPVRRQFPQEEWRQCVLYGLRQVNEARGFYAETEGVPALREAIARHVSFSRGVQC 72
            F GG+P    FP E  +      L Q  +    Y  T+G   LRE IA  +S + G Q 
Sbjct: 39  SFAGGLPSPLTFPVEHMKTAFDRVLSQQGKMALQYGPTDGYLPLREWIAASLS-TNGAQI 97

Query: 73  TAADVLVTNGAQQALDLITRVLVEPGSVVAVEDPGYPPARMLFSAQGARVESVPVDDEGM 132
           +A  VL+ +G+QQ LDL+ +VL++ GS V VE P Y  A   F+  GA+ ESVP D+ G+
Sbjct: 98  SAEQVLMVSGSQQGLDLLGKVLIDEGSKVLVETPSYLGALQAFALYGAKFESVPSDEFGL 157

Query: 133 R---VDLIPDGTRLIYATPAHQFPLG 155
           +   ++ I  G R++Y+ P  Q P G
Sbjct: 158 QPETIEAIAGGARMLYSLPNFQNPTG 183


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

 Score = 58.2 bits (139), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 39/123 (31%), Positives = 56/123 (45%), Gaps = 12/123 (9%)

Query: 47  YAETEGVPALREAIAR---HVSFSRGVQCTAADVLVTNGAQQALDLITRVLVEPGSVVAV 103
           Y    G   LR+ I +   H S   G++     VL T+GA QALDL+ R + +PG  V +
Sbjct: 156 YGHPYGYAPLRQLITQFLGHWSLELGIE----QVLTTHGATQALDLVIRTMTQPGDTVLI 211

Query: 104 EDPGYPPARMLFSAQGARVESVPVDDEGMRVDLIPDGTR-----LIYATPAHQFPLGMPM 158
           +DPGY     +    G  V  VP    G+  D++    R     + + T   Q P G   
Sbjct: 212 DDPGYCNLIAMLRLAGLNVIGVPRTPGGVDTDVLETLARTHHPKMFFTTSVLQNPTGTSY 271

Query: 159 SPA 161
           +PA
Sbjct: 272 TPA 274


  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
   0.321    0.137    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: 587,574
Number of extensions: 24564
Number of successful extensions: 93
Number of sequences better than 1.0e-08: 4
Number of HSP's gapped: 92
Number of HSP's successfully gapped: 4
Length of query: 162
Length of database: 1,619,870
Length adjustment: 78
Effective length of query: 84
Effective length of database: 1,250,540
Effective search space: 105045360
Effective search space used: 105045360
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: 127 (53.5 bits)