GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Methylocystis bryophila S285

Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate WP_085770280.1 B1812_RS02990 3-oxoacyl-[acyl-carrier-protein] reductase

Query= BRENDA::Q99714
         (261 letters)



>NCBI__GCF_002117405.1:WP_085770280.1
          Length = 246

 Score =  110 bits (274), Expect = 4e-29
 Identities = 83/252 (32%), Positives = 117/252 (46%), Gaps = 15/252 (5%)

Query: 10  GLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEK 69
           G  A++TG +SGLGLA A  L   GA+  L        E  A +L       P +++   
Sbjct: 6   GKTALVTGASSGLGLAIARTLHQAGATVGLSGTRREALETLAGELKERAHILPCNLSDRA 65

Query: 70  DVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVI 129
           +    +  A+G  G VD+ VN AGI        +K       ED+  VL VNL   F + 
Sbjct: 66  ETDKLIPAAEGAMGGVDILVNNAGITRDMLFMRMKD------EDWDAVLAVNLTAAFRLS 119

Query: 130 RLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPI 189
           R V   M +       + G IIN  SVA   G  GQA YSA+K G+ GMT  +A ++A  
Sbjct: 120 RAVLRGMMRK------RHGRIINITSVAGAVGNPGQANYSAAKAGLTGMTKSLANEVASR 173

Query: 190 GIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEY--AHLVQAIIENPFLN 247
           G+ V  +APG+  +P+   L E     L   +P   R G   E   A L  A  E  F+ 
Sbjct: 174 GVTVNCVAPGVIESPMTQVLNEAQRERLLKLIPM-ERFGSADEIGAAVLYLASDEAAFIT 232

Query: 248 GEVIRLDGAIRM 259
           G+ + ++G + M
Sbjct: 233 GQTLHINGGMAM 244


Lambda     K      H
   0.318    0.135    0.385 

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: 134
Number of extensions: 5
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: 261
Length of database: 246
Length adjustment: 24
Effective length of query: 237
Effective length of database: 222
Effective search space:    52614
Effective search space used:    52614
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 (21.7 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