GapMind for Amino acid biosynthesis

 

Alignments for a candidate for split_metH_1 in Shewanella loihica PV-4

Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate 5208198 Shew_0710 B12-dependent methionine synthase (RefSeq)

Query= reanno::Phaeo:GFF1319
         (233 letters)



>FitnessBrowser__PV4:5208198
          Length = 1240

 Score = 99.4 bits (246), Expect = 3e-25
 Identities = 53/148 (35%), Positives = 86/148 (58%), Gaps = 2/148 (1%)

Query: 26  LYDGLKEEIEESVNILLERGWAPYKVLTEALVGGMTIVGADFRDGILFVPEVLLAANAMK 85
           L  G+ E I++      +    P  V+   L+ GM +VG  F  G +F+P+V+ +A  MK
Sbjct: 679 LVKGITEFIDQDTEEARQLASRPLDVIEGPLMDGMNVVGDLFGSGKMFLPQVVKSARVMK 738

Query: 86  GGMAILKPLLA--ETGAPRMGSMVIGTVKGDIHDIGKNLVSMMMEGAGFEVVDIGINNPV 143
             +A L P +   +      G +++ TVKGD+HDIGKN+V +++   G+EVVD+G+  PV
Sbjct: 739 KAVAYLNPYIEAEKVEGESNGKILMVTVKGDVHDIGKNIVGVVLACNGYEVVDLGVMVPV 798

Query: 144 ENYLEALEEHQPDILGMSALLTTTMPYM 171
           E  +E  +  + DI+GMS L+T ++  M
Sbjct: 799 EKIIEVAKAEKVDIIGMSGLITPSLDEM 826


Lambda     K      H
   0.318    0.138    0.390 

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: 645
Number of extensions: 40
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: 233
Length of database: 1240
Length adjustment: 35
Effective length of query: 198
Effective length of database: 1205
Effective search space:   238590
Effective search space used:   238590
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: 52 (24.6 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