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= 0082.0040.p
         (207 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310728|ref|YP_003774820.1| isocitrate dehydrogenase [Herba...   373   e-105
gi|300312594|ref|YP_003776686.1| 3-isopropylmalate dehydrogenase...    76   2e-15
gi|300310800|ref|YP_003774892.1| tartrate dehydrogenase [Herbasp...    66   3e-12

>gi|300310728|ref|YP_003774820.1| isocitrate dehydrogenase
           [Herbaspirillum seropedicae SmR1]
          Length = 418

 Score =  373 bits (958), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 172/207 (83%), Positives = 193/207 (93%)

Query: 1   VRKAIQYAIDHDKPSVTIVHKGNIMKFTEGSFRDWAYALAQKEFGGVVIDDGPWVRIKNP 60
           VR+AIQYAIDHDKPSVT+VHKGNIMKFTEG+FRDW YALA +EFG  +IDDGPW+R+KNP
Sbjct: 212 VRQAIQYAIDHDKPSVTLVHKGNIMKFTEGAFRDWGYALAAREFGAELIDDGPWMRLKNP 271

Query: 61  KTGRDIIVKDVIADAFMQQILLRPAEYSVIATLNLNGDYISDALAAQVGGIGIAPGANMS 120
           KTGR II+KD I DAF QQ+L+RPAEYSVIATLNLNGDYISDA+AAQVGGIGIAPGANMS
Sbjct: 272 KTGRAIIIKDAITDAFFQQVLMRPAEYSVIATLNLNGDYISDAVAAQVGGIGIAPGANMS 331

Query: 121 DSVAMFEATHGTSPRYAGKDYVNPGSLILSAEMMLRHIGWTEAAALIIEAMQNTISSKKV 180
           DSVA+FEATHGT+P+YAGKDYVNPGS ILSAEMMLRH+GW EAA LII AMQ ++SSK+V
Sbjct: 332 DSVAVFEATHGTAPKYAGKDYVNPGSSILSAEMMLRHMGWIEAADLIISAMQKSVSSKRV 391

Query: 181 TYDFARLMEGATQVSCSGFGDAMIENL 207
           TYDFARL+EGATQVSCSGFG+ MIEN+
Sbjct: 392 TYDFARLLEGATQVSCSGFGEVMIENM 418


>gi|300312594|ref|YP_003776686.1| 3-isopropylmalate dehydrogenase
           oxidoreductase [Herbaspirillum seropedicae SmR1]
          Length = 356

 Score = 75.9 bits (185), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 48/145 (33%), Positives = 80/145 (55%), Gaps = 4/145 (2%)

Query: 65  DIIVKDVIADAFMQQILLRPAEYSVIATLNLNGDYISDALAAQVGGIGIAPGANM-SDSV 123
           D+ +  +  D    Q++  P  + VI T N+ GD +SDA A   G IG+ P A++ +++ 
Sbjct: 213 DVELSHMYVDNAAMQLVKAPKNFDVIVTGNMFGDILSDAAAMLTGSIGMLPSASLDANNK 272

Query: 124 AMFEATHGTSPRYAGKDYVNPGSLILSAEMMLR-HIGWTEAAALIIEAMQNTISSKKVTY 182
            ++E +HG++P  AG+   NP + ILSA MMLR  +   E A  I  A++  ++    T 
Sbjct: 273 GLYEPSHGSAPDIAGRGIANPLATILSAAMMLRFSLNKAEQADRIENAVKKVLAQGLRTA 332

Query: 183 DFARLMEGATQVSCSGFGDAMIENL 207
           D     EG T+V+    G+A+++ L
Sbjct: 333 DIYE--EGCTKVNTQQMGEAVVKAL 355


>gi|300310800|ref|YP_003774892.1| tartrate dehydrogenase
           [Herbaspirillum seropedicae SmR1]
          Length = 359

 Score = 65.9 bits (159), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 43/135 (31%), Positives = 68/135 (50%), Gaps = 12/135 (8%)

Query: 58  KNPKTGRDIIVKDVIADAFMQQILLRPAEYSVIATLNLNGDYISDALAAQVGGIGIAPGA 117
           K P   RD    D++   F    +L P  + V+   NL GD +SD   A  G IGIAP A
Sbjct: 212 KYPDVRRDKYHIDILTAHF----VLNPDRFDVVVASNLFGDILSDLGPACAGTIGIAPSA 267

Query: 118 NMSDS---VAMFEATHGTSPRYAGKDYVNPGSLILSAEMMLRHIG-----WTEAAALIIE 169
           N++ +    ++FE  HG++P   GK+  NP ++I S  MML  +G     + +A   ++ 
Sbjct: 268 NINPTRELPSLFEPVHGSAPDIFGKNIANPVAMIWSGAMMLDFLGDGQGKYRQAHDAMLA 327

Query: 170 AMQNTISSKKVTYDF 184
           A++  + +   T D 
Sbjct: 328 AIETVLVNGPTTPDL 342


  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
   0.319    0.134    0.393 

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: 646,570
Number of extensions: 26129
Number of successful extensions: 93
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 91
Number of HSP's successfully gapped: 3
Length of query: 207
Length of database: 1,619,870
Length adjustment: 81
Effective length of query: 126
Effective length of database: 1,236,335
Effective search space: 155778210
Effective search space used: 155778210
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: 128 (53.9 bits)