GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Cupriavidus basilensis 4G11

Align BadK (characterized)
to candidate RR42_RS18250 RR42_RS18250 enoyl-CoA hydratase

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



>FitnessBrowser__Cup4G11:RR42_RS18250
          Length = 258

 Score =  337 bits (865), Expect = 1e-97
 Identities = 166/253 (65%), Positives = 206/253 (81%)

Query: 6   ILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGA 65
           IL ET+GRVG++TLNRP  LNALNDALMD LG ALLAFDAD+ IG+IVI G+ RAFAAGA
Sbjct: 6   ILVETRGRVGLVTLNRPKALNALNDALMDELGVALLAFDADEAIGSIVITGSERAFAAGA 65

Query: 66  DIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRS 125
           DI  MA +SY DVY  ++ITRNWETIR+IRKPV+AAVAG A GGGCELA+ CDI+IA  +
Sbjct: 66  DIGMMAKYSYMDVYKGDYITRNWETIRRIRKPVIAAVAGYALGGGCELAMMCDIIIAADT 125

Query: 126 AKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDR 185
           A+F  PE+KLG +PGAGGTQRLPRA+ KAKAMD+CL++R ++A EA+R GLVSRVV  D+
Sbjct: 126 ARFGQPEVKLGTMPGAGGTQRLPRAVSKAKAMDLCLTSRMMDAAEAERAGLVSRVVAADK 185

Query: 186 LRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQ 245
           L D+ +A A TIA FS P +M +KES+N A+E++L+EG+  ERR  H+ FA+ D +EG+ 
Sbjct: 186 LLDDALAAAETIAGFSLPVVMMIKESINAAYETSLSEGVHLERRLFHSTFATEDQKEGMA 245

Query: 246 AFLEKRAPCFSHR 258
           AF+EKRAP F HR
Sbjct: 246 AFVEKRAPDFKHR 258


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: 169
Number of extensions: 4
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: 258
Length adjustment: 24
Effective length of query: 234
Effective length of database: 234
Effective search space:    54756
Effective search space used:    54756
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