GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Desulfovibrio vulgaris Miyazaki F

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate 8499797 DvMF_0562 dihydrodipicolinate synthase (RefSeq)

Query= BRENDA::O67216
         (294 letters)



>FitnessBrowser__Miya:8499797
          Length = 292

 Score =  302 bits (774), Expect = 5e-87
 Identities = 139/284 (48%), Positives = 200/284 (70%)

Query: 2   FQGSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEF 61
           FQG+  AL+TPF+ GEVD E    L+E+ ++ G + ++ CGTTGES TLT +EH+ VI  
Sbjct: 3   FQGAFTALVTPFRNGEVDEERYRALVEWQIEQGINGLVPCGTTGESATLTHQEHKDVIRI 62

Query: 62  AVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTV 121
            V++  GR+ V+AG G N T EAV LT +AK+ GADGAL++ PYYNKPTQ GLY+HFK +
Sbjct: 63  CVEQVKGRVPVLAGAGSNNTREAVELTRYAKQAGADGALLITPYYNKPTQEGLYQHFKAI 122

Query: 122 AQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESF 181
           A EV +P I+YN+PSRT   +  +T+ ++  +   ++  KE+T N+ ++SEI++  G  F
Sbjct: 123 AAEVPMPFIVYNVPSRTGTNLCPETLARMKRDIPEVIGVKEATGNLIQVSEIIEYCGADF 182

Query: 182 SVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFK 241
            VLSGDD   LP++A+G  GVISV++NV+P ++ EL RA  EGD   AR +HY +  + +
Sbjct: 183 QVLSGDDFTVLPLLAVGGCGVISVSSNVVPAKMSELCRAFFEGDLATARRVHYEIASINR 242

Query: 242 VLFIETNPIPVKTACWMLGMCEKEFRLPLTEMSPENENKLREVL 285
            +F+ETNPIPVKTA  M+G  E E RLP+  + P N+++LR++L
Sbjct: 243 AMFLETNPIPVKTALSMMGRIELELRLPMVPLQPANQSRLRDIL 286


Lambda     K      H
   0.318    0.136    0.390 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 263
Number of extensions: 7
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 294
Length of database: 292
Length adjustment: 26
Effective length of query: 268
Effective length of database: 266
Effective search space:    71288
Effective search space used:    71288
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate 8499797 DvMF_0562 (dihydrodipicolinate synthase (RefSeq))
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.24500.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.24500.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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