GapMind for catabolism of small carbon sources

 

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

Align crotonase (EC 4.2.1.150) (characterized)
to candidate Ac3H11_2719 Enoyl-CoA hydratase (EC 4.2.1.17)

Query= metacyc::MONOMER-13469
         (259 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2719
          Length = 271

 Score =  157 bits (396), Expect = 3e-43
 Identities = 97/262 (37%), Positives = 146/262 (55%), Gaps = 8/262 (3%)

Query: 6   IILEKDGNVASITLNRPKALNAL-NAATLKEIDAAINDIAEDDNVYAVIITGSGKAFVAG 64
           +++E+DG V +  LNRP+  NAL + A + E+ A    I  D ++ A+++TG G AF AG
Sbjct: 10  LLIERDGPVLTARLNRPETRNALTDPAHMDELVALCRQIRADHSIKALVLTGEGSAFCAG 69

Query: 65  ADIAEMKDLTAV-EGRKFSVLGN------KIFRKLENLEKPVIAAINGFALGGGCELSLS 117
            ++ +M+    +  G  + V  +      +I   L  L+ PVIAA+NG A+G G +L+  
Sbjct: 70  GNVKDMQQRGGIFAGSPYEVRDSYRDTIQRIPLALYELDVPVIAAVNGPAIGAGLDLACM 129

Query: 118 CDIRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGL 177
           CDIRIAS KA F +  V +GI PG GG   L R IG+  A  L +TG  I+A +AL  GL
Sbjct: 130 CDIRIASDKALFAESFVKVGIVPGDGGAWLLPRVIGMPKASLLAFTGDTIDAAKALSWGL 189

Query: 178 VNKVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFA 237
           V  V   D+LL +A+AL   I +N   A+R+ K  + +G    +DT +   +        
Sbjct: 190 VADVFPADQLLGQAQALAQRIALNPSHALRLTKRLLREGQHVRLDTLLELSSAYQALSHH 249

Query: 238 TEDRVEGMTAFVEKRDKAFKNK 259
           TED +E + AF++KR   F  +
Sbjct: 250 TEDHLEAVNAFLDKRPAQFTGR 271


Lambda     K      H
   0.318    0.136    0.376 

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: 158
Number of extensions: 7
Number of successful extensions: 3
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: 259
Length of database: 271
Length adjustment: 25
Effective length of query: 234
Effective length of database: 246
Effective search space:    57564
Effective search space used:    57564
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 (21.7 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