GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapB in Echinicola vietnamensis KMM 6221, DSM 17526

Align Dihydrodipicolinate reductase (characterized, see rationale)
to candidate Echvi_2395 Echvi_2395 dihydrodipicolinate reductase

Query= uniprot:L0G028_ECHVK
         (240 letters)



>FitnessBrowser__Cola:Echvi_2395
          Length = 240

 Score =  483 bits (1242), Expect = e-141
 Identities = 240/240 (100%), Positives = 240/240 (100%)

Query: 1   MNILILGYGKMGKIISQIAEERGHTIAAKIDESNIHELDKLDTTKVDAAIEFSQPDAAVQ 60
           MNILILGYGKMGKIISQIAEERGHTIAAKIDESNIHELDKLDTTKVDAAIEFSQPDAAVQ
Sbjct: 1   MNILILGYGKMGKIISQIAEERGHTIAAKIDESNIHELDKLDTTKVDAAIEFSQPDAAVQ 60

Query: 61  NLSWAIKHNIPVVCGTTGWLDKKPEIERLTLSNGGAFFYASNYSIGVNILFKVNSFLAKI 120
           NLSWAIKHNIPVVCGTTGWLDKKPEIERLTLSNGGAFFYASNYSIGVNILFKVNSFLAKI
Sbjct: 61  NLSWAIKHNIPVVCGTTGWLDKKPEIERLTLSNGGAFFYASNYSIGVNILFKVNSFLAKI 120

Query: 121 MNEQPAYTVKMEEIHHTEKKDAPSGTAITLAESIIDRVDRVKRWDLDKDVNGNEHSLPIT 180
           MNEQPAYTVKMEEIHHTEKKDAPSGTAITLAESIIDRVDRVKRWDLDKDVNGNEHSLPIT
Sbjct: 121 MNEQPAYTVKMEEIHHTEKKDAPSGTAITLAESIIDRVDRVKRWDLDKDVNGNEHSLPIT 180

Query: 181 AKRIDPAPGTHIVTYQSEIDDIEIKHTAHSRKGFALGAVLVAEWIKDKKGVLSMDDYLTF 240
           AKRIDPAPGTHIVTYQSEIDDIEIKHTAHSRKGFALGAVLVAEWIKDKKGVLSMDDYLTF
Sbjct: 181 AKRIDPAPGTHIVTYQSEIDDIEIKHTAHSRKGFALGAVLVAEWIKDKKGVLSMDDYLTF 240


Lambda     K      H
   0.317    0.134    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: 370
Number of extensions: 11
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: 240
Length of database: 240
Length adjustment: 23
Effective length of query: 217
Effective length of database: 217
Effective search space:    47089
Effective search space used:    47089
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 (21.6 bits)
S2: 46 (22.3 bits)

Align candidate Echvi_2395 Echvi_2395 (dihydrodipicolinate reductase)
to HMM TIGR00036 (dapB: 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8))

Software error:

../bin/blast/fastacmd -i /tmp/list.1692.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1692.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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