GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Pseudomonas simiae WCS417

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate GFF1354 PS417_06885 dihydrodipicolinate synthase

Query= BRENDA::A9CFV4
         (303 letters)



>FitnessBrowser__WCS417:GFF1354
          Length = 290

 Score =  148 bits (374), Expect = 1e-40
 Identities = 99/284 (34%), Positives = 145/284 (51%), Gaps = 4/284 (1%)

Query: 5   GIYTPAITPLGHDGE-IDRDAFAAVLESLMEARVHGIIIGGSTGEYYAQTAQERFDLAAY 63
           GI    ITP   DG+ ID +     ++ L+E  VH I   GSTGE    +  E  +++AY
Sbjct: 8   GIIGYTITPFSTDGQRIDLNTLGRSIDRLIEGGVHAIAPLGSTGEGAYLSDAEWDEVSAY 67

Query: 64  ARQVIGTRLPLVVGTGATRTEDSIEYAKAAKEIGADAILVSSPPYALPTERENAVHALAV 123
           +   I  R+P +V      T  ++  A+ A+  GAD ++V    Y   +E E   H  A+
Sbjct: 68  SLAKIARRVPTIVSVSDLTTAKAVRRARYAEANGADVVMVLPTSYWKLSEAEILAHYAAI 127

Query: 124 DRAANLPIMLYNYPARMGVVMGEEYFSRVGKS-KNVVAIKESSGDMGNLHLLARKFPQIA 182
             +  +PIMLYN PA  G  M  +   R+ K   NV  +KES+GD+  +H L R+   + 
Sbjct: 128 GDSIGVPIMLYNNPATSGTDMSVDLILRIIKQVPNVTMVKESTGDIQRMHHLHRQ-SDVP 186

Query: 183 LSCGWDDQALEFFAWGAKSWVCAGSNFLPREHVALYEACVVEKNFDKGRAIMTAMLPLMD 242
              G +  ALE FA GAK W  A  N +P  ++ALYEA V+  +  + R +    LPL+D
Sbjct: 187 FYNGCNPLALEAFAAGAKGWCTAAPNLIPELNLALYEA-VLANDLTQAREVFYRQLPLLD 245

Query: 243 FLECGKFVQSIKHGCEIIGLRAGSVRAPLRPLNSDEKRTLQTVV 286
           F+  G    +IK G  + GL AG  R P+ PL       L+T++
Sbjct: 246 FILKGGLPATIKAGLRLTGLEAGDPRLPVFPLGEVGIEQLKTLL 289


Lambda     K      H
   0.320    0.135    0.397 

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: 195
Number of extensions: 11
Number of successful extensions: 4
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: 303
Length of database: 290
Length adjustment: 26
Effective length of query: 277
Effective length of database: 264
Effective search space:    73128
Effective search space used:    73128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory