GapMind for Amino acid biosynthesis

 

Alignments for a candidate for split_metH_1 in Shewanella sp. ANA-3

Align Methionine synthase component, B12 binding and B12-binding cap domains (EC:2.1.1.13) (characterized)
to candidate 7026140 Shewana3_3282 B12-dependent methionine synthase (RefSeq)

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



>FitnessBrowser__ANA3:7026140
          Length = 1244

 Score =  110 bits (274), Expect = 2e-28
 Identities = 73/219 (33%), Positives = 113/219 (51%), Gaps = 10/219 (4%)

Query: 20  QQMFDDLYDGLKEEIEESVNILLERGWAPYKVLTEALVGGMTIVGADFRDGILFVPEVLL 79
           Q++   L  G+ E I+E      +    P  V+   L+ GM IVG  F  G +F+P+V+ 
Sbjct: 676 QRLAHALVKGITEFIDEDTEAARQLASRPLDVIEGPLMDGMNIVGDLFGSGKMFLPQVVK 735

Query: 80  AANAMKGGMAILKPLLAETGAPRM--GSMVIGTVKGDIHDIGKNLVSMMMEGAGFEVVDI 137
           +A  MK  +A L P + +        G +++ TVKGD+HDIGKN+V +++   GFEV D+
Sbjct: 736 SARVMKKAVAYLNPFIEQEKVEGQSNGRILMVTVKGDVHDIGKNIVGVVLACNGFEVFDL 795

Query: 138 GINNPVENYLEALEEHQPDILGMSALLTTTMPYMKVVIDTMIEQGKRDDYIVLVGGAPLN 197
           G+   VE  LEA++EH  DI+GMS L+T ++  M   + T   +G       ++GGA  +
Sbjct: 796 GVMVSVERILEAVKEHNIDIIGMSGLITPSLDEMVHNVKTFHREGL--TIPAIIGGATCS 853

Query: 198 EEFGKAIGADG------YCRDAAVAVEMAKDFVARKHNQ 230
           +       A        Y  DA+ AV M    V+ +  Q
Sbjct: 854 KIHTAVKIAPHYPHGAIYIADASRAVPMVSKLVSNETRQ 892


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: 648
Number of extensions: 34
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: 1244
Length adjustment: 35
Effective length of query: 198
Effective length of database: 1209
Effective search space:   239382
Effective search space used:   239382
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.

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