GapMind for Amino acid biosynthesis

 

Alignments for a candidate for split_metH_1 in Sphingomonas koreensis DSMZ 15582

Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate Ga0059261_0990 Ga0059261_0990 methionine synthase (B12-dependent) (EC 2.1.1.13)

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



>FitnessBrowser__Korea:Ga0059261_0990
          Length = 865

 Score =  110 bits (276), Expect = 7e-29
 Identities = 63/172 (36%), Positives = 100/172 (58%), Gaps = 5/172 (2%)

Query: 26  LYDGLKEEIEESVNILLERGWAPYKVLTEALVGGMTIVGADFRDGILFVPEVLLAANAMK 85
           L  G+ + + E      ++   P +V+   L+ GM +VG  F  G +F+P+V+ +A  MK
Sbjct: 316 LVKGIDQYVVEDTEECRQKADRPIEVIEGPLMDGMNVVGDLFGSGKMFLPQVVKSARVMK 375

Query: 86  GGMAILKPLLA---ETGAPRMGSMVIGTVKGDIHDIGKNLVSMMMEGAGFEVVDIGINNP 142
             +A L P +    E GA   G +V+ TVKGD+HDIGKN+V ++++  GFEVVD+G+  P
Sbjct: 376 KAVAHLLPYIEAAKEPGAKGKGKVVMATVKGDVHDIGKNIVGVVLQCNGFEVVDLGVMVP 435

Query: 143 VENYLEALEEHQPDILGMSALLTTTMPYMKVVIDTMIEQGKRDDYIVLVGGA 194
               LEA  E+  D++G+S L+T ++  M  V + M  +  R    +L+GGA
Sbjct: 436 WSKILEAANENDADMIGLSGLITPSLDEMVTVAEEM--KRARMTMPLLIGGA 485


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: 455
Number of extensions: 30
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: 233
Length of database: 865
Length adjustment: 32
Effective length of query: 201
Effective length of database: 833
Effective search space:   167433
Effective search space used:   167433
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 Jul 25 2024. The underlying query database was built on Jul 25 2024.

Links

Downloads

Related tools

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