GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysE in Pseudomonas simiae WCS417

Align Serine O-acetyltransferase; EC 2.3.1.30 (characterized, see rationale)
to candidate GFF220 PS417_01115 serine acetyltransferase

Query= uniprot:Q72EB6_DESVH
         (323 letters)



>FitnessBrowser__WCS417:GFF220
          Length = 308

 Score =  261 bits (667), Expect = 2e-74
 Identities = 133/261 (50%), Positives = 168/261 (64%)

Query: 41  GSPMPSLEALTELMARLRAALFPGYFGASNIVLESMRYHLAANLDSIYRILAEQVRRGGC 100
           G  +PS EA+ +++  L  ALFP   G  ++  ES  +++   LD     L  Q R    
Sbjct: 37  GRELPSREAVAQILESLCGALFPMRLGPVDLREESEDFYVGHTLDVALNALLGQARLELR 96

Query: 101 FACADYATDCQNCESHSQETAMEFMRALPRIRQLLATDVKAAYEGDPAAKSPGETIFCYP 160
           +A    A D    +  +     +F  ALP +R LL TDV AAY GDPAA+S  E + CYP
Sbjct: 97  YAARQGAKDDSEVDVLAIRLIQDFALALPSLRSLLDTDVLAAYHGDPAARSVDEVLLCYP 156

Query: 161 SIYAMIHHRIAHELYRLDVPVIPRIISEMAHSRTGIDIHPGATVGEEFFIDHGTGVVIGE 220
            + A+IHHR+AH LYR  +P++ RI +E+AHS TGIDIHPGA +G  FFIDHGTGVVIGE
Sbjct: 157 GVLAVIHHRLAHHLYRAGLPLLARISAEIAHSATGIDIHPGAQIGPSFFIDHGTGVVIGE 216

Query: 221 TCIIGRGCRLYQGVTLGALSFPKDGGGALIKGIPRHPILQDGVTVYAGATILGRVTIGAG 280
           T IIG   R+YQ VTLGA  FP D  G L KG PRHPI++D V +YAGATILGR+TIG G
Sbjct: 217 TAIIGERVRIYQAVTLGAKRFPADEDGQLQKGHPRHPIVEDDVVIYAGATILGRITIGKG 276

Query: 281 AIVGGNVWVTHDVAPGAKVVQ 301
           + +GGNVW+T  V  GA + Q
Sbjct: 277 STIGGNVWLTRSVPAGANITQ 297


Lambda     K      H
   0.320    0.137    0.410 

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: 349
Number of extensions: 17
Number of successful extensions: 2
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: 323
Length of database: 308
Length adjustment: 27
Effective length of query: 296
Effective length of database: 281
Effective search space:    83176
Effective search space used:    83176
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