GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Methylocapsa aurea KYG

Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_036263857.1 DL86_RS15400 enoyl-CoA hydratase/isomerase family protein

Query= BRENDA::Q1D5Y4
         (258 letters)



>NCBI__GCF_000746085.1:WP_036263857.1
          Length = 259

 Score =  130 bits (328), Expect = 2e-35
 Identities = 86/239 (35%), Positives = 127/239 (53%), Gaps = 8/239 (3%)

Query: 23  RNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGADLKE-RATMAEDEVRAFL 81
           RNA++  M + L  +  +V +   ++ +++TGAGD+AF +G D+ E R   + D+V A+ 
Sbjct: 24  RNALTSGMYEGLAAICAKVDADPAIKVLILTGAGDQAFASGTDIAEFRQFASPDDVLAYE 83

Query: 82  DGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPAAELGLTEVK-LGIIPG 140
             +     A+E+     IAAI G   GGG  +A  CDLR+  P  +LG+   + LG    
Sbjct: 84  ARIEAALSALERCRASTIAAIAGVCTGGGAMIAACCDLRIGEPETKLGMPIARTLGNCLS 143

Query: 141 GGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPE-GHLLAVAYGLAESVVE 199
                RLA L+GP R KDLILTAR + A EA ++GL N    +   LL  A+ L   V  
Sbjct: 144 MSNYARLAGLIGPARVKDLILTARLVGAKEAIAMGLLNEAVDQTKELLPRAHDLGRRVAG 203

Query: 200 NAPIAVATAKHAIDEGTGLELDDALA-LELRKYEEILKTEDRLEGLRAFAEKRAPVYKG 257
           +AP+++   K A+    G     A   L L  Y     +ED  EG+ AF EKR+P ++G
Sbjct: 204 HAPLSLRATKEALLRMRGQAPQSAAEDLVLMCY----LSEDFREGVAAFLEKRSPRWRG 258


Lambda     K      H
   0.319    0.136    0.380 

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: 157
Number of extensions: 6
Number of successful extensions: 4
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 (21.7 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Apr 09 2024. 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