GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapF in Pseudomonas simiae WCS417

Align diaminopimelate epimerase (EC 5.1.1.7) (characterized)
to candidate GFF1919 PS417_09775 DeoR faimly transcriptional regulator

Query= BRENDA::E4NI20
         (295 letters)



>FitnessBrowser__WCS417:GFF1919
          Length = 324

 Score = 62.0 bits (149), Expect = 2e-14
 Identities = 69/220 (31%), Positives = 92/220 (41%), Gaps = 42/220 (19%)

Query: 84  NADGSIAEMCGNGVRVFARYLVHAGH-AGSGELAVATRGGVKRVRIAADAPDGTPGDVT- 141
           N DGS+AE  GNG+ +FA+ L   G  +G+ EL V          ++          V  
Sbjct: 86  NTDGSLAERSGNGLTIFAQALTDQGLLSGACELRVHHDKSDAVSPVSTWVEPAIREQVAG 145

Query: 142 --VDMGRAAFPGPD--GVTVTVD-------------GRSWPALN-VNMGNPHAVAFVEDL 183
             +++G   F GP+  G  + VD                W A   V +GNPH V  VE +
Sbjct: 146 FWLELGVPGF-GPEVVGAQMEVDETELSHVSELAAINPQWAASQFVRVGNPHCVTLVEQV 204

Query: 184 A--------HAGHLYEAPATA----PAGA---YPQGVNVEFVVDRGERHVAMRVHERGSG 228
           +            LYE   T     PAG     P GVN+++   +    +  RV ERG G
Sbjct: 205 SALPDNTQMQQPALYEPLKTIAFAPPAGGGRPCPAGVNLQWAARQPGNRIIARVFERGEG 264

Query: 229 ETRSCGTGACAVAVAAIRRDGADPAATGEAVRYTVDVPGG 268
            T S GT A AVA AA R      A   E+    V +PGG
Sbjct: 265 PTASSGTSASAVACAAWR------AGWVESGEVAVVMPGG 298



 Score = 24.6 bits (52), Expect = 0.003
 Identities = 12/26 (46%), Positives = 15/26 (57%)

Query: 107 AGHAGSGELAVATRGGVKRVRIAADA 132
           AG   SGE+AV   GG+  VR+   A
Sbjct: 283 AGWVESGEVAVVMPGGIAPVRLHTQA 308


Lambda     K      H
   0.318    0.135    0.408 

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: 258
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 295
Length of database: 324
Length adjustment: 27
Effective length of query: 268
Effective length of database: 297
Effective search space:    79596
Effective search space used:    79596
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: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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