GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Lacinutrix algicola AKS293

Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_055437269.1 ASC41_RS13975 3-oxoacyl-[acyl-carrier-protein] reductase

Query= uniprot:B2T9V3
         (247 letters)



>NCBI__GCF_001418085.1:WP_055437269.1
          Length = 248

 Score =  130 bits (326), Expect = 3e-35
 Identities = 86/254 (33%), Positives = 137/254 (53%), Gaps = 26/254 (10%)

Query: 5   LAGKTALITAAGQGIGLATAELFAREGARVIAT-------------DIRIDGLAGKPVEA 51
           L GKTA+IT A +GIG   AE+FA++GA V  T             ++   G+  K  ++
Sbjct: 4   LEGKTAIITGASRGIGKGIAEVFAQQGANVAFTYSSSVEAANALEKELNALGVKAKGYKS 63

Query: 52  RKLDVRDDAAI-KALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMI 110
              +  +   + + + AE G++D+L N AG      ++   E D+D   ++N+K+++ M 
Sbjct: 64  NAANFDESQKLAEDVLAEFGSIDILINNAGITKDNLLMRMGEADFDKVIEVNLKSVFNMT 123

Query: 111 RAFLPAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCN 170
           +A    ML +  GSIINMSS    VKG   +  Y+ASKA +IG +KSVA +  +R +R N
Sbjct: 124 KAVQRTMLKQRKGSIINMSSVV-GVKGNAGQTNYAASKAGIIGFSKSVALELGSRNIRSN 182

Query: 171 AICPGTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDE 230
            I PG +     E  + A+   +  T+ + + A     P+ R G PE+IA + ++L SD 
Sbjct: 183 VIAPGFI-----ETEMTAKLDEE--TVKSWRNAI----PLKRGGTPEDIANVCVFLASDM 231

Query: 231 SSFTTGHAHVIDGG 244
           S++ TG    +DGG
Sbjct: 232 SAYVTGQTINVDGG 245


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: 146
Number of extensions: 5
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: 247
Length of database: 248
Length adjustment: 24
Effective length of query: 223
Effective length of database: 224
Effective search space:    49952
Effective search space used:    49952
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: 46 (22.3 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