GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapD in Cupriavidus basilensis 4G11

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 RR42_RS11935 RR42_RS11935 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase

Query= SwissProt::P56220
         (274 letters)



>FitnessBrowser__Cup4G11:RR42_RS11935
          Length = 275

 Score =  407 bits (1046), Expect = e-118
 Identities = 205/271 (75%), Positives = 229/271 (84%), Gaps = 1/271 (0%)

Query: 2   QQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKK 61
           Q LQ +I+ A+E RA ++P +     REAV  VIG LD+GALRVAEK   +W+ +QW+KK
Sbjct: 3   QALQALIDQAWEDRASLSPKSAPNDIREAVANVIGQLDTGALRVAEKQGKEWIVNQWIKK 62

Query: 62  AVLLSFRINDNKVMD-GAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARN 120
           AVLLSFR+ DN  M  G   ++YDKVP KFA++    F K GFRVVPPA  R+G+FIA+N
Sbjct: 63  AVLLSFRLEDNAPMSAGGFAQFYDKVPTKFANWTADDFAKGGFRVVPPAVARRGSFIAKN 122

Query: 121 TVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIED 180
            VLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANP IIED
Sbjct: 123 AVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPVIIED 182

Query: 181 NCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPS 240
           NCFIGARSEVVEGVIVEE SVISMGVYLGQST+IYDRETGEIHYGRVPAGSVVV+GNLPS
Sbjct: 183 NCFIGARSEVVEGVIVEENSVISMGVYLGQSTKIYDRETGEIHYGRVPAGSVVVAGNLPS 242

Query: 241 KDGSYSLYCAVIVKKVDAKTRGKVGINELLR 271
           KDG YSLYCAVIVKKVDA+TR K  +N+LLR
Sbjct: 243 KDGKYSLYCAVIVKKVDAQTRAKTSLNDLLR 273


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: 320
Number of extensions: 5
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: 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 RR42_RS11935 RR42_RS11935 (2,3,4,5-tetrahydropyridine-2,6-carboxylate 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.16253.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16253.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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