GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Acidovorax sp. GW101-3H11

Align BadK (characterized)
to candidate Ac3H11_1055 Enoyl-CoA hydratase (EC 4.2.1.17)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_1055
          Length = 259

 Score =  124 bits (310), Expect = 3e-33
 Identities = 84/248 (33%), Positives = 129/248 (52%), Gaps = 4/248 (1%)

Query: 10  TQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADIAS 69
           +QG+  I+TL+ P+  NA++ ++  A   AL   ++   I ++VI G+   F +G ++  
Sbjct: 9   SQGQTLILTLSNPERRNAIDPSMYAAGVEALSVAESSADIRSVVITGSDGMFCSGGNLQR 68

Query: 70  MAAWSY--SDVYGSNFI-TRNW-ETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRS 125
           + A      DV   +     NW ETIR   KPV+AAV G A G G  LALACD ++A R+
Sbjct: 69  LLANRQLPPDVQAQSIEGLHNWIETIRTYPKPVIAAVEGAAAGAGFSLALACDFIVAARN 128

Query: 126 AKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDR 185
           A F +    + L P  G +  L +A+ +  A ++ +    + AE     GLV+RV +   
Sbjct: 129 AVFVMAYSNVALSPDGGASWSLSQALPRQIATEILMCGDRIGAERLHALGLVNRVAEAGS 188

Query: 186 LRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQ 245
             D  +ALA  + A +  AL ++KE LN A  ++L + +  ER         A+   GI 
Sbjct: 189 ALDAALALAEQLNAKAPNALASIKELLNEAPHASLTQHLGHERDHFVKNLHHANGGAGIS 248

Query: 246 AFLEKRAP 253
           AFLEKR P
Sbjct: 249 AFLEKRVP 256


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: 124
Number of extensions: 5
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: 258
Length of database: 259
Length adjustment: 24
Effective length of query: 234
Effective length of database: 235
Effective search space:    54990
Effective search space used:    54990
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