GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Phaeobacter inhibens BS107

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate GFF3587 PGA1_c36420 succinyl-diaminopimelate desuccinylase DapE

Query= SwissProt::Q9JYL2
         (381 letters)



>FitnessBrowser__Phaeo:GFF3587
          Length = 385

 Score =  259 bits (662), Expect = 9e-74
 Identities = 152/371 (40%), Positives = 205/371 (55%), Gaps = 8/371 (2%)

Query: 8   ELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKNIWLRRGTKAP--VVCF 65
           +L  +LI   SVTP++     LL + L   GF    +  G+  N+  R G K     + F
Sbjct: 10  QLTADLIRCASVTPEEGGALVLLDKVLSAAGFTCTRVDRGEVSNLIARWGDKGHPRTMGF 69

Query: 66  AGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHPNHQG 125
            GHTDVVP G    W   PF   E+DG LYGRGA DMK+ +A FV A    V   P   G
Sbjct: 70  NGHTDVVPVGDTNAWTVDPFGAEEKDGFLYGRGATDMKSGVAAFVAAAIDLVQTTPP-DG 128

Query: 126 SIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRRGSLSG 185
           +I L IT DEEGDA+DGTT ++D +    E +  C+VGEPT  DK+G+MIK GRRGSLS 
Sbjct: 129 AILLTITGDEEGDAIDGTTALLDHMDREGEQMAVCLVGEPTCPDKMGEMIKIGRRGSLSA 188

Query: 186 NLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGGTGAT 245
             TV G QGH AYPH A NP++     +  L     D+G E+F  ++  +  I+ G  AT
Sbjct: 189 WFTVTGVQGHSAYPHRAKNPLNAMVRLMDRLASHELDQGTEHFDASTLAVVTIDTGNPAT 248

Query: 246 NVIPGELNVKFNFRFSTESTEAGLKQRVHA----ILDKHGVQYDLQWSCSGQPFLTQAGK 301
           NVIP +     N RF+   T A L   + A         GV   ++   SG+ F+T  G 
Sbjct: 249 NVIPAQTRSTVNIRFNDAHTGAELSDWLRAEAARAAKDFGVDIAVEIKVSGESFITPPGP 308

Query: 302 LTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLNDI 361
           L+D+  AA+    G + +LSTTGGTSD RF+K     ++E+G    T+HQ++E V +  I
Sbjct: 309 LSDLVSAAVETETGRKPQLSTTGGTSDARFVKNHC-PVVEVGLVGKTMHQVDERVEIAQI 367

Query: 362 PKLSAVYEGIL 372
            +L ++Y  IL
Sbjct: 368 HQLKSIYGRIL 378


Lambda     K      H
   0.317    0.135    0.400 

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: 424
Number of extensions: 22
Number of successful extensions: 5
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: 381
Length of database: 385
Length adjustment: 30
Effective length of query: 351
Effective length of database: 355
Effective search space:   124605
Effective search space used:   124605
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: 50 (23.9 bits)

Align candidate GFF3587 PGA1_c36420 (succinyl-diaminopimelate desuccinylase DapE)
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))

Software error:

../bin/blast/fastacmd -i /tmp/list.12880.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12880.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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