GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Haloglycomyces albus DSM 45210

Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_025272126.1 HALAL_RS0100575 SDR family NAD(P)-dependent oxidoreductase

Query= uniprot:B2T9V3
         (247 letters)



>NCBI__GCF_000527155.1:WP_025272126.1
          Length = 290

 Score =  112 bits (280), Expect = 8e-30
 Identities = 79/255 (30%), Positives = 126/255 (49%), Gaps = 30/255 (11%)

Query: 5   LAGKTALITAAG--QGIGLATAELFAREGARV--IATDIRIDGLAGK-PVEARKLDVRDD 59
           L GKTAL+T AG   GIG+A A      GAR+  ++T  RI   A +        D+ D+
Sbjct: 46  LIGKTALVTGAGADDGIGMAIATRLRLAGARLALVSTTKRIHERANELDAVGFVADLTDE 105

Query: 60  AAIKALAAEI----GAVDVLFNCAGFVH------AGNILECSEEDWDFAFDLNVKAMYRM 109
           A +  L   +    G VD++ N AG            + +   +DW+     N+ + + +
Sbjct: 106 AEVAGLGDAVTEGLGEVDIVVNNAGMTSKTAPAVTKPVAQLGFDDWEAEITRNLHSTFLV 165

Query: 110 IRAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRC 169
            R F+ +M + G G I+N+S+ A     +P   AY+++KA V GLT+++A + +  GV  
Sbjct: 166 SRYFVQSMAESGWGRIVNVSATAGVSSVMPAEAAYASAKAGVAGLTRALATEVVADGVTV 225

Query: 170 NAICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSD 229
           NA+ PG + + S             +T+  +Q       P+GR G PEE+AA   +  S 
Sbjct: 226 NAVAPGLIHTGS-------------STVPELQRG--VDSPLGRPGTPEEVAAAVAFFCSP 270

Query: 230 ESSFTTGHAHVIDGG 244
            +S+ TG   V+DGG
Sbjct: 271 SASYVTGQTLVVDGG 285


Lambda     K      H
   0.320    0.133    0.381 

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: 165
Number of extensions: 12
Number of successful extensions: 3
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: 247
Length of database: 290
Length adjustment: 25
Effective length of query: 222
Effective length of database: 265
Effective search space:    58830
Effective search space used:    58830
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 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