GapMind for catabolism of small carbon sources

 

Alignments for a candidate for srlD in Haloglycomyces albus DSM 45210

Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate WP_025272362.1 HALAL_RS0101795 3-oxoacyl-ACP reductase FabG

Query= curated2:P37079
         (267 letters)



>NCBI__GCF_000527155.1:WP_025272362.1
          Length = 236

 Score =  115 bits (289), Expect = 7e-31
 Identities = 79/256 (30%), Positives = 129/256 (50%), Gaps = 30/256 (11%)

Query: 11  VIIVTGGASGIGLAIVDELLSQGAHVQMIDIHGGDRHHNGDNYHFWSTDISSATEVQQTI 70
           V+++TGG  GIG A    L   G  V +      D  +  D +H+   D+S     +  I
Sbjct: 5   VVLITGGTRGIGRAAAQRLKDDGFTVAVASRSIPDAENRLDVHHY-QVDVSDGNACKDLI 63

Query: 71  DAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNINQKGVFFMSQAV 130
             +      ID L+N+AG+     L+          +    +  ++  N  G + M +++
Sbjct: 64  TTVEDEVGDIDVLINSAGIVRDSPLLT---------MTGDDWNDVIRTNLDGTYNMCRSM 114

Query: 131 ARQMVKQRAGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKYGIRVVGVAP 190
           A  M+K++ G I+N+SS +G++G+  QS Y+A+KA +  F+++ SKELG++ IRV  VAP
Sbjct: 115 AFSMMKRKNGSIINLSSVAGIQGNPTQSNYSASKAGIIGFSKALSKELGRFNIRVNVVAP 174

Query: 191 GILEKTGLRTPEYEEALAWTRNITVEQLREGYTKNA---IPIGRAGKLSEVADFVCYLLS 247
           G +E                 ++T + L E   K A   IP+GR G + +VA  V +L S
Sbjct: 175 GFIE----------------TDMTAD-LAESVKKKAVENIPLGRMGSVDDVAHLVGFLAS 217

Query: 248 ARASYITGVTTNIAGG 263
            RA+Y+TG    + GG
Sbjct: 218 PRATYMTGAVVPVDGG 233


Lambda     K      H
   0.316    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: 140
Number of extensions: 6
Number of successful extensions: 4
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: 267
Length of database: 236
Length adjustment: 24
Effective length of query: 243
Effective length of database: 212
Effective search space:    51516
Effective search space used:    51516
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 (21.6 bits)
S2: 46 (22.3 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