GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucDH in Methylocystis bryophila S285

Align Short-chain dehydrogenase/reductase SDR (characterized, see rationale)
to candidate WP_085770280.1 B1812_RS02990 3-oxoacyl-[acyl-carrier-protein] reductase

Query= uniprot:B2T9V3
         (247 letters)



>NCBI__GCF_002117405.1:WP_085770280.1
          Length = 246

 Score =  138 bits (348), Expect = 9e-38
 Identities = 91/250 (36%), Positives = 130/250 (52%), Gaps = 22/250 (8%)

Query: 5   LAGKTALITAAGQGIGLATAELFAREGARVIATDIR---IDGLAGKPVEARKL------- 54
           L GKTAL+T A  G+GLA A    + GA V  +  R   ++ LAG+  E   +       
Sbjct: 4   LTGKTALVTGASSGLGLAIARTLHQAGATVGLSGTRREALETLAGELKERAHILPCNLSD 63

Query: 55  DVRDDAAIKALAAEIGAVDVLFNCAGFVHAGNILECSEEDWDFAFDLNVKAMYRMIRAFL 114
               D  I A    +G VD+L N AG       +   +EDWD    +N+ A +R+ RA L
Sbjct: 64  RAETDKLIPAAEGAMGGVDILVNNAGITRDMLFMRMKDEDWDAVLAVNLTAAFRLSRAVL 123

Query: 115 PAMLDKGGGSIINMSSAASSVKGVPNRFAYSASKAAVIGLTKSVAADFITRGVRCNAICP 174
             M+ K  G IIN++S A +V G P +  YSA+KA + G+TKS+A +  +RGV  N + P
Sbjct: 124 RGMMRKRHGRIINITSVAGAV-GNPGQANYSAAKAGLTGMTKSLANEVASRGVTVNCVAP 182

Query: 175 GTVASPSLEQRIVAQAQAQGATLDAVQAAFVARQPMGRIGKPEEIAALALYLGSDESSFT 234
           G + SP  +  ++ +AQ +           +   PM R G  +EI A  LYL SDE++F 
Sbjct: 183 GVIESPMTQ--VLNEAQRE---------RLLKLIPMERFGSADEIGAAVLYLASDEAAFI 231

Query: 235 TGHAHVIDGG 244
           TG    I+GG
Sbjct: 232 TGQTLHINGG 241


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: 147
Number of extensions: 7
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: 246
Length adjustment: 24
Effective length of query: 223
Effective length of database: 222
Effective search space:    49506
Effective search space used:    49506
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 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