GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapD in Phaeobacter inhibens BS107

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase; Tetrahydrodipicolinate N-succinyltransferase; THDP succinyltransferase; THP succinyltransferase; Tetrahydropicolinate succinylase; EC 2.3.1.117 (characterized)
to candidate GFF3576 PGA1_c36310 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase DapD

Query= SwissProt::P56220
         (274 letters)



>FitnessBrowser__Phaeo:GFF3576
          Length = 275

 Score =  334 bits (856), Expect = 1e-96
 Identities = 174/272 (63%), Positives = 209/272 (76%), Gaps = 5/272 (1%)

Query: 3   QLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKID-GQWVTHQWLKK 61
           QL+  IE+A+E R  IT A      R+A+ + +  LDSG LRVAE+ D G W  +QW KK
Sbjct: 5   QLETAIEAAWEARDTITSATTGE-QRDAIEETLNALDSGKLRVAERQDSGNWHVNQWAKK 63

Query: 62  AVLLSFRINDNKVMDGAE--TRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIAR 119
           AVLL FRI D +   G    + ++DKV  KF  + EA +++ GFR VP   VR+ A+IA 
Sbjct: 64  AVLLGFRIKDMEEQSGGPQGSGWWDKVDSKFKGWGEAEWKEAGFRAVPNCVVRKSAYIAP 123

Query: 120 NTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIE 179
             VLMPS+VN+GA+VDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEP+QA PTIIE
Sbjct: 124 GVVLMPSFVNLGAHVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPMQAGPTIIE 183

Query: 180 DNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLP 239
           DNCFIGARSEVVEG IV EGSV+ MGV++GQST+I DRETGE+ YG VP  SVVV+G++P
Sbjct: 184 DNCFIGARSEVVEGCIVREGSVLGMGVFIGQSTKIVDRETGEVMYGEVPPYSVVVAGSMP 243

Query: 240 SKDGSYSLYCAVIVKKVDAKTRGKVGINELLR 271
           SK+G  +LYCAVIVK+VD +TR K GINELLR
Sbjct: 244 SKNG-INLYCAVIVKRVDERTRSKTGINELLR 274


Lambda     K      H
   0.318    0.136    0.393 

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: 260
Number of extensions: 8
Number of successful extensions: 4
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: 275
Length adjustment: 25
Effective length of query: 249
Effective length of database: 250
Effective search space:    62250
Effective search space used:    62250
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 GFF3576 PGA1_c36310 (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase DapD)
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.930.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.930.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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