GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapD in Sphingomonas koreensis DSMZ 15582

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 Ga0059261_1374 Ga0059261_1374 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Query= SwissProt::P56220
         (274 letters)



>FitnessBrowser__Korea:Ga0059261_1374
          Length = 272

 Score =  335 bits (860), Expect = 5e-97
 Identities = 177/272 (65%), Positives = 208/272 (76%), Gaps = 2/272 (0%)

Query: 1   MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLK 60
           M  L   I++A+E RA+I+ A    V R+AV + + LLDSG  RVAE +   W  +QWLK
Sbjct: 1   MTDLAATIDAAWEDRANISLATTGAV-RDAVAEALNLLDSGEARVAEPVADGWQVNQWLK 59

Query: 61  KAVLLSFRINDNKVMDGAETRY-YDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIAR 119
           KAVLLSFR+NDN+V+      + +DKVP+K A +DEARF+  GFR VP + VR GAFI++
Sbjct: 60  KAVLLSFRLNDNEVIGTQAGDWGFDKVPLKTAGWDEARFRAAGFRQVPGSVVRHGAFISK 119

Query: 120 NTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIE 179
           N VLMPS+VNIGAYV EG+MVD WATVGSCAQIG+NVHLSGGVGIGGVLEPLQA+P II 
Sbjct: 120 NVVLMPSFVNIGAYVGEGSMVDGWATVGSCAQIGRNVHLSGGVGIGGVLEPLQADPVIIG 179

Query: 180 DNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLP 239
           D  FIGAR+EV EGV V EG+V+SMGVYLG ST+I DR TGE+H G VP  SVVV G LP
Sbjct: 180 DGAFIGARAEVAEGVRVGEGAVLSMGVYLGASTKIVDRATGEVHRGVVPPYSVVVPGTLP 239

Query: 240 SKDGSYSLYCAVIVKKVDAKTRGKVGINELLR 271
            KDG   LYCAVIVK VDA+TR K GINELLR
Sbjct: 240 GKDGGPGLYCAVIVKTVDAQTRSKTGINELLR 271


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: 277
Number of extensions: 7
Number of successful extensions: 2
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: 272
Length adjustment: 25
Effective length of query: 249
Effective length of database: 247
Effective search space:    61503
Effective search space used:    61503
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 Ga0059261_1374 Ga0059261_1374 (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase)
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.10261.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10261.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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