Alignments for a candidate for metB in Amycolatopsis halophila YIM 93223

GapMind for Amino acid biosynthesis

Alignments for a candidate for metB in Amycolatopsis halophila YIM 93223

Align cystathionine gamma-synthase (EC 2.5.1.48) (characterized)
to candidate WP_034269948.1 AMYHA_RS09025 cystathionine gamma-synthase

Query= BRENDA::A0PKT3
         (388 letters)



>NCBI__GCF_000504245.1:WP_034269948.1
          Length = 384

 Score =  494 bits (1272), Expect = e-144
 Identities = 239/376 (63%), Positives = 294/376 (78%)

Query: 13  GLATRAIHSGYRPDPATGAVNAPIYASSTFAQDGVGGLRGGYEYARTGNPTRTALEAALA 72
           G  TRAIH+G  PDP TGAV  PI+ +ST+AQDGVGG R GYEY+RT NPTRT +E ALA
Sbjct: 9   GFETRAIHAGQEPDPRTGAVITPIFQTSTYAQDGVGGTREGYEYSRTANPTRTVMEDALA 68

Query: 73  AVEDAAFGRAFSSGMAAADCALRAMLRPGDHVVIPDDAYGGTFRLIDKVFTGWNVEYTPV 132
           A+EDAA   AF+SGMAA+D  LR  LRPGDH+V+ +DAYGGTFRLIDKV TGW V+YT  
Sbjct: 69  ALEDAAHCVAFASGMAASDAVLRIALRPGDHLVLGNDAYGGTFRLIDKVLTGWGVDYTVA 128

Query: 133 ALADLDAVRAAIRPTTRLIWVETPTNPLLSIADIAGIAQLGADSSAKVLVDNTFASPALQ 192
            ++ LD VRAA+RP T+L+W ETP+NPLL IADIAG+A +     A+++VDNTFA+P LQ
Sbjct: 129 DMSSLDEVRAALRPETKLVWCETPSNPLLGIADIAGLADVAHSGGAQLVVDNTFATPYLQ 188

Query: 193 QPLSLGADVVLHSTTKYIGGHSDVVGGALVTNDEELDQSFAFLQNGAGAVPGPFDAYLTM 252
           QP+ LGAD+V+HSTTKY+GGHSDVVGGA+VTN +E+ +   FL+N AGAVPGPFD++LT+
Sbjct: 189 QPIGLGADIVVHSTTKYLGGHSDVVGGAVVTNSDEMREELFFLRNSAGAVPGPFDSWLTL 248

Query: 253 RGLKTLVLRMQRHSENAAAVAEFLAEHPAISTVLYPGLPSHPGHAVAARQMRGFGGMVSV 312
           RG+KTL +RM+RH +NA  +A  LAEH  I+ V YPGL  HPGH +AA+QMR FGGMVS 
Sbjct: 249 RGMKTLAVRMERHCDNAERIARALAEHEGITEVYYPGLAEHPGHVLAAKQMRRFGGMVSF 308

Query: 313 RMRAGRTAAEQLCAKTNIFILAESLGSVESLIEHPSAMTHASTAGSQLEVPDDLVRLSVG 372
            +  G   A  + AKT +F+LAESLG +ESLIEHP  MTHAS  GSQL+VP  L+R+SVG
Sbjct: 309 TVAGGEQRALDVAAKTKLFLLAESLGGIESLIEHPGRMTHASVDGSQLQVPSGLLRISVG 368

Query: 373 IEDVADLLDDLKQALG 388
           IE+  DL+ DL  ALG
Sbjct: 369 IENADDLMADLTAALG 384


Lambda     K      H
   0.318    0.133    0.386 

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: 562
Number of extensions: 16
Number of successful extensions: 1
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: 388
Length of database: 384
Length adjustment: 30
Effective length of query: 358
Effective length of database: 354
Effective search space:   126732
Effective search space used:   126732
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: 50 (23.9 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the original publication.

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

GapMind for Amino acid biosynthesis