GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapD in Pseudomonas simiae WCS417

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 GFF1216 PS417_06180 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase

Query= SwissProt::G3XD76
         (344 letters)



>FitnessBrowser__WCS417:GFF1216
          Length = 344

 Score =  585 bits (1509), Expect = e-172
 Identities = 294/344 (85%), Positives = 318/344 (92%)

Query: 1   MSQSLFSLAFGVGTQNRQEAWLEVFYALPLLKPSSEIVAAVAPILGYAAGNQALTFTSQQ 60
           MS SLFSL FGVGTQNRQ AWLEVFYA PLL PS+EIVAAVAPILGY  GNQA+TFT  Q
Sbjct: 1   MSHSLFSLGFGVGTQNRQGAWLEVFYAQPLLNPSAEIVAAVAPILGYTEGNQAITFTISQ 60

Query: 61  AYQLADALKGIDAAQSALLSRLAESQKPLVATLLAEDAAPSSTAEAYLKLHLLSHRLVKP 120
           A QLADALK +DA Q+ALL+RLAES  PLVATLLAEDAA +ST EAYLKLHLLSHRLVKP
Sbjct: 61  ALQLADALKNVDATQAALLNRLAESHTPLVATLLAEDAALTSTPEAYLKLHLLSHRLVKP 120

Query: 121 HAVNLSGIFPLLPNVAWTNIGAVDLAELAELQLEARLKGKLLEVFSVDKFPKMTDYVVPA 180
           H ++L+G+FP LPNVAWT+ GA+D+AELAE QLEARL+G+LLEVFSVDKFPKMTDYVVP+
Sbjct: 121 HGLSLAGVFPQLPNVAWTSQGAIDIAELAERQLEARLRGELLEVFSVDKFPKMTDYVVPS 180

Query: 181 GVRIADTARVRLGAYIGEGTTVMHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGC 240
           GVRIAD AR+RLGAY+GEGTTVMHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGC
Sbjct: 181 GVRIADAARIRLGAYVGEGTTVMHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGC 240

Query: 241 STMGTLSGGGNIVISVGEGCLIGANAGIGIPLGDRNIVEAGLYITAGTKVALLDEQNALV 300
           STMGTLSGGGNIVI VGEGCLIGANAGIGIPLGDRN VE+GLY+TAGTKVALLDEQN LV
Sbjct: 241 STMGTLSGGGNIVIKVGEGCLIGANAGIGIPLGDRNTVESGLYVTAGTKVALLDEQNQLV 300

Query: 301 KVVKARDLAGQPDLLFRRNSQNGAVECKTNKTAIELNEALHAHN 344
           KVVKAR+LAGQ DLLFRRNS+ GAVECKT+K+AIELNEALHAHN
Sbjct: 301 KVVKARELAGQSDLLFRRNSETGAVECKTHKSAIELNEALHAHN 344


Lambda     K      H
   0.317    0.134    0.380 

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: 455
Number of extensions: 14
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: 344
Length of database: 344
Length adjustment: 29
Effective length of query: 315
Effective length of database: 315
Effective search space:    99225
Effective search space used:    99225
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: 49 (23.5 bits)

Align candidate GFF1216 PS417_06180 (2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase)
to HMM TIGR03536 (dapD: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117))

Software error:

../bin/blast/fastacmd -i /tmp/list.5401.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5401.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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