GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Rhodococcus qingshengii djl-6-2

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_003941541.1 C1M55_RS07980 3-hydroxybutyryl-CoA dehydrogenase

Query= BRENDA::P9WNP7
         (286 letters)



>NCBI__GCF_002893965.1:WP_003941541.1
          Length = 298

 Score =  407 bits (1046), Expect = e-118
 Identities = 208/285 (72%), Positives = 240/285 (84%)

Query: 2   SDAIQRVGVVGAGQMGSGIAEVSARAGVEVTVFEPAEALITAGRNRIVKSLERAVSAGKV 61
           S+ IQRVGV+GAG MG+GIAEV ARA V+V VFE    L  AGR+RI++SL+R VS+GK+
Sbjct: 3   SEKIQRVGVIGAGIMGAGIAEVCARAHVDVLVFEQTRELAAAGRSRILRSLDRGVSSGKI 62

Query: 62  TERERDRALGLLTFTTDLNDLSDRQLVIEAVVEDEAVKSEIFAELDRVVTDPDAVLASNT 121
           TERER++A   L FT+DL D +DRQLV+EAVVEDE +KSEIFAELD VVTDPDAVLASNT
Sbjct: 63  TEREREQAAWRLRFTSDLGDFADRQLVVEAVVEDEKIKSEIFAELDAVVTDPDAVLASNT 122

Query: 122 SSIPIMKVAAATKQPQRVLGLHFFNPVPVLPLVELVRTLVTDEAAAARTEEFASTVLGKQ 181
           SSIPIMK+  +TK+P+RV+G+HFFNPVPVLPLVELV TL T  + + R E FAS +LGKQ
Sbjct: 123 SSIPIMKLGISTKRPERVIGMHFFNPVPVLPLVELVTTLKTSASVSQRAEAFASDILGKQ 182

Query: 182 VVRCSDRSGFVVNALLVPYLLSAIRMVEAGFATVEDVDKAVVAGLSHPMGPLRLSDLVGL 241
           VVR +DRSGFVVNALLVPYLLSAIRMVE+GFAT ED+DKA V GL+HPMGPL L+DLVGL
Sbjct: 183 VVRSADRSGFVVNALLVPYLLSAIRMVESGFATKEDIDKATVLGLAHPMGPLALTDLVGL 242

Query: 242 DTLKLIADKMFEEFKEPHYGPPPLLLRMVEAGQLGKKSGRGFYTY 286
           DT+K IAD M+EEFKEP Y  PPLLLRMVEAG  GKKSG GFY Y
Sbjct: 243 DTVKSIADSMYEEFKEPLYSAPPLLLRMVEAGLTGKKSGAGFYEY 287


Lambda     K      H
   0.318    0.135    0.369 

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: 335
Number of extensions: 10
Number of successful extensions: 1
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: 286
Length of database: 298
Length adjustment: 26
Effective length of query: 260
Effective length of database: 272
Effective search space:    70720
Effective search space used:    70720
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 (21.7 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