GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Vagococcus penaei CD276

Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_077275131.1 BW732_RS01515 glucose 1-dehydrogenase

Query= uniprot:B2T9V3
         (247 letters)



>NCBI__GCF_001998885.1:WP_077275131.1
          Length = 261

 Score =  113 bits (283), Expect = 3e-30
 Identities = 83/259 (32%), Positives = 126/259 (48%), Gaps = 25/259 (9%)

Query: 1   MTQRLAGKTALITAAGQGIGLATAELFAREGARVIATDIRIDGLAGKPVEARKLDVRDDA 60
           M Q L GK A+IT   +GIG A +E   +E  +V+      +  A + VEA K    D  
Sbjct: 1   MYQDLNGKVAVITGGSKGIGTAISERLGKEKMKVVVNYHSDEAGANQAVEAVKAAGGDGI 60

Query: 61  AIKA--------------LAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAM 106
           A++A                +E G +D+  N AG  +     +   EDW+   ++N+  +
Sbjct: 61  AVQANVGSEEGVQKLVDVALSEYGTLDLWINNAGMENQCETHKLPLEDWERVINVNLTGV 120

Query: 107 YRMIRAFLPAMLDKGG-GSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITR 165
           +   +A L   ++    G+IIN+SS    +   P    YSASK  V  LT++VA ++  R
Sbjct: 121 FLGTKAALSYFVENNKKGNIINISSVHEQIPW-PTFAHYSASKGGVKLLTETVAMEYANR 179

Query: 166 GVRCNAICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALY 225
            +R N I PG + +P   ++     Q Q  T + +        PM RIG PEE+AA A +
Sbjct: 180 NIRVNNIGPGAIKTPINAEKFADPEQLQ-TTKETI--------PMQRIGNPEEVAAAAAW 230

Query: 226 LGSDESSFTTGHAHVIDGG 244
           L SDE+S+ TG    +DGG
Sbjct: 231 LASDEASYVTGITLFVDGG 249


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: 144
Number of extensions: 10
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: 261
Length adjustment: 24
Effective length of query: 223
Effective length of database: 237
Effective search space:    52851
Effective search space used:    52851
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 Sep 24 2021. 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