GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapD in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_3077 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117)

Query= SwissProt::G3XD76
         (344 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3077
          Length = 344

 Score =  589 bits (1519), Expect = e-173
 Identities = 295/344 (85%), Positives = 321/344 (93%)

Query: 1   MSQSLFSLAFGVGTQNRQEAWLEVFYALPLLKPSSEIVAAVAPILGYAAGNQALTFTSQQ 60
           MS +LFSLAFGVGTQNRQ AWLEVFYA PLL PS+E+VAA+AP+LGY  GNQA+ F++ Q
Sbjct: 1   MSTTLFSLAFGVGTQNRQGAWLEVFYAQPLLNPSAELVAAIAPVLGYTDGNQAIAFSTAQ 60

Query: 61  AYQLADALKGIDAAQSALLSRLAESQKPLVATLLAEDAAPSSTAEAYLKLHLLSHRLVKP 120
           A QLA+ALK +DAAQ+ALL+RLAES KPLVATLLAEDA  SST EAYLKLHLLSHRLVKP
Sbjct: 61  ASQLAEALKSVDAAQAALLTRLAESHKPLVATLLAEDAQLSSTPEAYLKLHLLSHRLVKP 120

Query: 121 HAVNLSGIFPLLPNVAWTNIGAVDLAELAELQLEARLKGKLLEVFSVDKFPKMTDYVVPA 180
           H +NL+GIFPLLPNVAWT+ GA+DLAELAE QLEARL+G+LLEVFSVDKFPKMTDYVVPA
Sbjct: 121 HGLNLAGIFPLLPNVAWTSQGAIDLAELAEHQLEARLRGELLEVFSVDKFPKMTDYVVPA 180

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

Query: 241 STMGTLSGGGNIVISVGEGCLIGANAGIGIPLGDRNIVEAGLYITAGTKVALLDEQNALV 300
           STMGTLSGGGNIVI VGEGCLIGANAGIGIPLGDRN VE+GLY+TAGTKVALLDE N LV
Sbjct: 241 STMGTLSGGGNIVIKVGEGCLIGANAGIGIPLGDRNTVESGLYVTAGTKVALLDENNKLV 300

Query: 301 KVVKARDLAGQPDLLFRRNSQNGAVECKTNKTAIELNEALHAHN 344
           KVVKAR+LAGQPDLLFRRNS+ GAVECKT+K+AIELNEALHAHN
Sbjct: 301 KVVKARELAGQPDLLFRRNSETGAVECKTHKSAIELNEALHAHN 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: 462
Number of extensions: 15
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 Pf1N1B4_3077 (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (EC 2.3.1.117))
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.16618.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16618.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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