GapMind for Amino acid biosynthesis

 

Alignments for a candidate for split_metH_1 in Hydrogenophaga taeniospiralis NBRC 102512

Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate WP_084235998.1 HTA01S_RS09875 methionine synthase

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



>NCBI__GCF_001592305.1:WP_084235998.1
          Length = 917

 Score = 99.0 bits (245), Expect = 3e-25
 Identities = 61/190 (32%), Positives = 99/190 (52%), Gaps = 11/190 (5%)

Query: 16  EDLVQQMFDDLYDGLKEEIEESVNILLERGWAPYKVLTEALVGGMTIVGADFRDGILFVP 75
           E L   +   + + + E+ EE    +   G  P  V+   L+ GM +VG  F  G +F+P
Sbjct: 338 ERLAHALVRGMNEFISEDTEEMWREIEAEGGRPLNVIEGPLMDGMNVVGDLFGQGKMFLP 397

Query: 76  EVLLAANAMKGGMAILKPLL---------AETGAPRMGSMVIGTVKGDIHDIGKNLVSMM 126
           +V+ +A  MK  +A L P +         A       G +VI TVKGD+HDIGKN+V+++
Sbjct: 398 QVVKSARVMKQAVAHLLPYIEAEKLAQQAAGADVKPKGKIVIATVKGDVHDIGKNIVTVV 457

Query: 127 MEGAGFEVVDIGINNPVENYLEALEEHQPDILGMSALLTTTMPYMKVVIDTMIEQG--KR 184
           ++   FEVV++G+  P    L   +E   DI+G+S L+T ++  M+ V   M +    + 
Sbjct: 458 LQCNNFEVVNMGVMVPCHEILAKAKEEGADIVGLSGLITPSLEEMQYVAGEMQKDAHFRE 517

Query: 185 DDYIVLVGGA 194
               +L+GGA
Sbjct: 518 KGIPLLIGGA 527


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: 457
Number of extensions: 23
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: 917
Length adjustment: 33
Effective length of query: 200
Effective length of database: 884
Effective search space:   176800
Effective search space used:   176800
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: 51 (24.3 bits)

This GapMind analysis is from Apr 10 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