GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapH in Pseudomonas simiae WCS417

Align 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase; Tetrahydrodipicolinate N-acetyltransferase; THP acetyltransferase; Tetrahydropicolinate acetylase; EC 2.3.1.89 (characterized)
to candidate GFF4893 PS417_25075 hypothetical protein

Query= SwissProt::O34981
         (236 letters)



>FitnessBrowser__WCS417:GFF4893
          Length = 188

 Score = 73.6 bits (179), Expect = 3e-18
 Identities = 48/154 (31%), Positives = 74/154 (48%), Gaps = 30/154 (19%)

Query: 92  ARIEPGAIIRDQVEIGDNAVIMMGASINIGSVIGEGTMIDMNVVLGGRATVGKNCHIGAG 151
           +R   G  +R +V + D+A +  G ++ I      G M         R  VG +C IG+ 
Sbjct: 39  SRFTAGVDLRIEV-LEDSACVTFGQNVKINDYCHIGAM--------SRVVVGDDCLIGSR 89

Query: 152 SVLA----GVIEPPS-----------------AKPVVIEDDVVIGANAVVLEGVTVGKGA 190
             +     GV   PS                  KP++IE +V IG+ A+++ GVT+G+G+
Sbjct: 90  VTIVDHEHGVYRKPSDHPASLPWTPPDERLLQGKPIIIEKNVWIGSGAIIVGGVTIGEGS 149

Query: 191 VVAAGAIVVNDVEPYTVVAGTPAKKIKDIDEKTK 224
           V+ A A+V  D+  Y++  G PAK IK  DE  K
Sbjct: 150 VIGANAVVTRDISRYSLAVGAPAKVIKTFDEGGK 183


Lambda     K      H
   0.313    0.134    0.364 

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: 145
Number of extensions: 14
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: 236
Length of database: 188
Length adjustment: 21
Effective length of query: 215
Effective length of database: 167
Effective search space:    35905
Effective search space used:    35905
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 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