GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Cupriavidus basilensis 4G11

Align BadK (characterized)
to candidate RR42_RS23710 RR42_RS23710 enoyl-CoA hydratase

Query= metacyc::MONOMER-943
         (258 letters)



>FitnessBrowser__Cup4G11:RR42_RS23710
          Length = 249

 Score =  340 bits (873), Expect = 1e-98
 Identities = 168/247 (68%), Positives = 206/247 (83%)

Query: 12  GRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADIASMA 71
           GRV +I LNRP  +NALNDALMDALG ALLA + DDG+GAIVI GN +AFAAGADIA+M 
Sbjct: 3   GRVAVIRLNRPRQMNALNDALMDALGLALLACEQDDGVGAIVITGNDKAFAAGADIAAMR 62

Query: 72  AWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAKFALP 131
            W Y DV+ SN+ITRNWET+R +RKPV+AAVAG A GGGCELA+ACDI+IA  +A F LP
Sbjct: 63  GWDYMDVFKSNYITRNWETLRNVRKPVIAAVAGYALGGGCELAMACDILIAADNAVFGLP 122

Query: 132 EIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRDETV 191
           E+KL ++PGAGGTQRLPRAI KAKAMDMC++AR ++A+EA+R GLVSRVV   RL DE +
Sbjct: 123 ELKLAVIPGAGGTQRLPRAISKAKAMDMCMTARNMDADEAERSGLVSRVVAAGRLMDEAM 182

Query: 192 ALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAFLEKR 251
           A+A TIA FS P++MA+KE++NRA ES+L+EG+LFERR+LHA FA+ D +EG+ AFLE+R
Sbjct: 183 AVAQTIAGFSLPSMMAVKEAINRACESSLSEGMLFERRQLHALFATEDLKEGMNAFLERR 242

Query: 252 APCFSHR 258
           A  F HR
Sbjct: 243 AAVFRHR 249


Lambda     K      H
   0.321    0.135    0.389 

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: 172
Number of extensions: 1
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: 258
Length of database: 249
Length adjustment: 24
Effective length of query: 234
Effective length of database: 225
Effective search space:    52650
Effective search space used:    52650
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 17 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