GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapD in Shewanella loihica PV-4

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (characterized)
to candidate 5210195 Shew_2638 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (RefSeq)

Query= CharProtDB::CH_024869
         (274 letters)



>FitnessBrowser__PV4:5210195
          Length = 274

 Score =  456 bits (1172), Expect = e-133
 Identities = 225/274 (82%), Positives = 247/274 (90%)

Query: 1   MQQLQNIIETAFERRAEITPANADTVTREAVNQVIALLDSGALRVAEKIDGQWVTHQWLK 60
           M+ L+  IETAFE RAEITP   +   R  V + IA+LD+G  RVAEKIDGQW  HQWLK
Sbjct: 1   MEALRQRIETAFEARAEITPTTVEPSVRADVEKAIAMLDTGEARVAEKIDGQWNVHQWLK 60

Query: 61  KAVLLSFRINDNQVIEGAESRYFDKVPMKFADYDEARFQKEGFRVVPPAAVRQGAFIARN 120
           KAVLLSFRI DNQVI+GAE+++FDKVPMKFADYDEARF++E  RVVPPAAVR+G+FI +N
Sbjct: 61  KAVLLSFRIFDNQVIDGAETKFFDKVPMKFADYDEARFKQEAIRVVPPAAVRKGSFIGKN 120

Query: 121 TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED 180
           TVLMPSYVN+GAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQA PTIIED
Sbjct: 121 TVLMPSYVNLGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQAGPTIIED 180

Query: 181 NCFIGARSEVVEGVIVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS 240
           NCFIGARSE+VEGV+VEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSG LPS
Sbjct: 181 NCFIGARSEIVEGVVVEEGSVISMGVYIGQSTRIYDRETGEIHYGRVPAGSVVVSGTLPS 240

Query: 241 KDGKYSLYCAVIVKKVDAKTRGKVGINELLRTID 274
           + GKY+LY A+IVKKVDAKTRGKVGINELLR +D
Sbjct: 241 QCGKYNLYAAIIVKKVDAKTRGKVGINELLRIVD 274


Lambda     K      H
   0.318    0.136    0.391 

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: 339
Number of extensions: 5
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: 274
Length of database: 274
Length adjustment: 25
Effective length of query: 249
Effective length of database: 249
Effective search space:    62001
Effective search space used:    62001
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: 47 (22.7 bits)

Align candidate 5210195 Shew_2638 (2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (RefSeq))
to HMM TIGR00965 (dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117))

Software error:

../bin/blast/fastacmd -i /tmp/list.17449.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17449.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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