GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysE in Shewanella loihica PV-4

Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate 5210146 Shew_2590 hexapaptide repeat-containing transferase (RefSeq)

Query= BRENDA::Q42588
         (314 letters)



>FitnessBrowser__PV4:5210146
          Length = 209

 Score = 57.8 bits (138), Expect = 2e-13
 Identities = 40/108 (37%), Positives = 56/108 (51%), Gaps = 6/108 (5%)

Query: 189 IGKGILLDHATG-VVIGETAVVGDNVSIL---HGVTLGGTGKQSGDRHPKI--GDGVLIG 242
           I  G  LD   G +VIG+   + +NV+I    HG+       Q   +   I  G  V IG
Sbjct: 102 INHGCSLDGGRGKIVIGDQTRIANNVTIYAFNHGMHPDTPIYQQSSQSKGIVIGRDVWIG 161

Query: 243 AGSCILGNITIGEGAKIGSGSVVVKDVPARTTAVGNPARLIGGKENPR 290
           A + I+  +TIG+ A IG G +V KDVP      GNPAR+IG + + +
Sbjct: 162 AQAGIVDGVTIGDCAVIGMGCIVTKDVPDYAIVAGNPARIIGDRRDKK 209


Lambda     K      H
   0.319    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: 214
Number of extensions: 18
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 314
Length of database: 209
Length adjustment: 24
Effective length of query: 290
Effective length of database: 185
Effective search space:    53650
Effective search space used:    53650
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: 47 (22.7 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