GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garR in Stenotrophomonas chelatiphaga DSM 21508

Align 2-hydroxy-3-oxopropionate reductase; Tartronate semialdehyde reductase; TSAR; EC 1.1.1.60 (characterized)
to candidate WP_057507560.1 ABB28_RS04900 3-hydroxyisobutyrate dehydrogenase

Query= SwissProt::P0ABQ2
         (294 letters)



>NCBI__GCF_001431535.1:WP_057507560.1
          Length = 296

 Score =  181 bits (459), Expect = 2e-50
 Identities = 103/286 (36%), Positives = 165/286 (57%), Gaps = 7/286 (2%)

Query: 2   KVGFIGLGIMGKPMSKNLLKAGYSLVVADRNPEAIADVIAAGAETASTAKAIAEQCDVII 61
           ++ FIGLG MG PM+ NL KAG+++ V D  P A+   + AGA  AS+A       +V+I
Sbjct: 3   RIAFIGLGNMGGPMAANLAKAGHAVRVFDLVPAAVQAAVDAGATAASSALDTLADAEVVI 62

Query: 62  TMLPNSPHVKEVALGENGIIEGAKPGTVLIDMSSIAPLASREISEALKAKGIDMLDAPVS 121
           +MLP S HV+ V LG++G++     G ++ID S+IAP  +R+++EA  A+G+ MLDAPVS
Sbjct: 63  SMLPASRHVEGVYLGDDGLLADIPGGALVIDCSTIAPATARKVAEAAAARGLQMLDAPVS 122

Query: 122 GGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGEIGAGNVTKLANQVIVALNI 181
           GG   A  GTL+ +VGG++   ++    ++AM  ++ H G  GAG V KL N + + + +
Sbjct: 123 GGTAGATAGTLTFIVGGEEDALERARPYLQAMGRNIFHVGASGAGQVAKLCNNMALGVIM 182

Query: 182 AAMSEALTLATKAGVNPDLVYQ--AIRGGLAGSTVLDAKAPMVMD-----RNFKPGFRID 234
           A   E++ L    G++P ++ Q  A+  G + +T +    P V++     R +  GF  D
Sbjct: 183 AVTGESIALGVAHGLDPKVLSQMMAVSTGRSWATEVCNPWPGVLENAPASRGYSGGFGSD 242

Query: 235 LHIKDLANALDTSHGVGAQLPLTAAVMEMMQALRADGLGTADHSAL 280
           L +KD+  A++ +  VGA +PL      +       G G  D S++
Sbjct: 243 LMLKDMGLAVEAAMSVGASIPLGELARNLYSMNHQAGRGKLDFSSV 288


Lambda     K      H
   0.316    0.133    0.366 

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: 206
Number of extensions: 6
Number of successful extensions: 2
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: 294
Length of database: 296
Length adjustment: 26
Effective length of query: 268
Effective length of database: 270
Effective search space:    72360
Effective search space used:    72360
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: 48 (23.1 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