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= 0055.0018.p
         (219 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312594|ref|YP_003776686.1| 3-isopropylmalate dehydrogenase...   412   e-116
gi|300310800|ref|YP_003774892.1| tartrate dehydrogenase [Herbasp...   119   2e-28
gi|300310728|ref|YP_003774820.1| isocitrate dehydrogenase [Herba...    79   4e-16

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

 Score =  412 bits (1058), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 200/214 (93%), Positives = 206/214 (96%)

Query: 5   MREAPDGPFKGAREGFDTMRYSEPEIRRIAHVAFQAAAKRGNRLCSVDKANVLETFQFWK 64
           MREAPDGPFKGAREGFDTMRYSEPEIRRIAHVAFQAAAKRG RLCSVDKANVLETFQFWK
Sbjct: 142 MREAPDGPFKGAREGFDTMRYSEPEIRRIAHVAFQAAAKRGKRLCSVDKANVLETFQFWK 201

Query: 65  DIVTDVHKEYPQVELTHMYVDNAAMQLVKAPKNFDVIVTGNMFGDILSDAAAMLTGSIGM 124
           DIVT+V KEYP VEL+HMYVDNAAMQLVKAPKNFDVIVTGNMFGDILSDAAAMLTGSIGM
Sbjct: 202 DIVTEVGKEYPDVELSHMYVDNAAMQLVKAPKNFDVIVTGNMFGDILSDAAAMLTGSIGM 261

Query: 125 LPSASLDANNKGLYEPSHGSAPDIAGKGIANPLATILSAAMMLRFSLNKAEQADRIEAAV 184
           LPSASLDANNKGLYEPSHGSAPDIAG+GIANPLATILSAAMMLRFSLNKAEQADRIE AV
Sbjct: 262 LPSASLDANNKGLYEPSHGSAPDIAGRGIANPLATILSAAMMLRFSLNKAEQADRIENAV 321

Query: 185 KKVLAQGYRTGDIYEEGTTKVGTKEMGDAVVKAL 218
           KKVLAQG RT DIYEEG TKV T++MG+AVVKAL
Sbjct: 322 KKVLAQGLRTADIYEEGCTKVNTQQMGEAVVKAL 355


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

 Score =  119 bits (298), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 79/202 (39%), Positives = 106/202 (52%), Gaps = 12/202 (5%)

Query: 25  YSEPEIRRIAHVAFQAAAKRGNR-LCSVDKAN-VLETFQFWKDIVTDVHKEYPQVELTHM 82
           +S     RI   AF  A  R  + L S  K+N +  T  +W + V  +  +YP V     
Sbjct: 162 FSRKGTDRILKFAFDLAQSRPKKHLTSATKSNGIAITMPYWDERVEAMGAKYPDVRRDKY 221

Query: 83  YVDNAAMQLVKAPKNFDVIVTGNMFGDILSDAAAMLTGSIGMLPSASLDANNK--GLYEP 140
           ++D      V  P  FDV+V  N+FGDILSD      G+IG+ PSA+++   +   L+EP
Sbjct: 222 HIDILTAHFVLNPDRFDVVVASNLFGDILSDLGPACAGTIGIAPSANINPTRELPSLFEP 281

Query: 141 SHGSAPDIAGKGIANPLATILSAAMMLRF---SLNKAEQA-DRIEAAVKKVLAQGYRTGD 196
            HGSAPDI GK IANP+A I S AMML F      K  QA D + AA++ VL  G  T D
Sbjct: 282 VHGSAPDIFGKNIANPVAMIWSGAMMLDFLGDGQGKYRQAHDAMLAAIETVLVNGPTTPD 341

Query: 197 IYEEGTTKVGTKEMGDAVVKAL 218
           +      K  T E+G A+  A+
Sbjct: 342 L----GGKSNTAEVGQAIAAAI 359


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

 Score = 78.6 bits (192), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 48/131 (36%), Positives = 77/131 (58%), Gaps = 4/131 (3%)

Query: 90  QLVKAPKNFDVIVTGNMFGDILSDAAAMLTGSIGMLPSASLDANNKGLYEPSHGSAPDIA 149
           Q++  P  + VI T N+ GD +SDA A   G IG+ P A++ +++  ++E +HG+AP  A
Sbjct: 290 QVLMRPAEYSVIATLNLNGDYISDAVAAQVGGIGIAPGANM-SDSVAVFEATHGTAPKYA 348

Query: 150 GKGIANPLATILSAAMMLRFSLNKAEQADRIEAAVKKVLAQGYRTGDIYE--EGTTKVGT 207
           GK   NP ++ILSA MMLR  +   E AD I +A++K ++    T D     EG T+V  
Sbjct: 349 GKDYVNPGSSILSAEMMLR-HMGWIEAADLIISAMQKSVSSKRVTYDFARLLEGATQVSC 407

Query: 208 KEMGDAVVKAL 218
              G+ +++ +
Sbjct: 408 SGFGEVMIENM 418


  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
   0.317    0.133    0.377 

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: 674,050
Number of extensions: 26737
Number of successful extensions: 102
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 100
Number of HSP's successfully gapped: 3
Length of query: 219
Length of database: 1,619,870
Length adjustment: 82
Effective length of query: 137
Effective length of database: 1,231,600
Effective search space: 168729200
Effective search space used: 168729200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 128 (53.9 bits)