GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ech in Porphyrobacter dokdonensis DSW-74

Align crotonase (EC 4.2.1.150) (characterized)
to candidate WP_068864712.1 I603_RS10325 crotonase/enoyl-CoA hydratase family protein

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



>NCBI__GCF_001677335.1:WP_068864712.1
          Length = 265

 Score =  171 bits (432), Expect = 2e-47
 Identities = 106/262 (40%), Positives = 143/262 (54%), Gaps = 8/262 (3%)

Query: 6   IILEKDGNVASITLNRPKALNALNAATLKEIDAAIND-IAEDDNVYAVIITGSGKAFVAG 64
           I + ++G V  +TL+R + +N L A    +  A+I D I  D     VI+TG+G+AF AG
Sbjct: 4   IRIAREGPVTILTLDRAETMNPLGAPGDGDAFASIADAINRDMECRVVILTGAGRAFSAG 63

Query: 65  ADIAEMKDLTAVEGRKFSVLGN-------KIFRKLENLEKPVIAAINGFALGGGCELSLS 117
            DI  M+D T   G     + +       ++ R L  L  PVIAA+NG A+G GC+++  
Sbjct: 64  GDIKAMRDKTGTFGGTAPAISDGYRDNIHRMLRALHGLRVPVIAAVNGPAIGLGCDVACL 123

Query: 118 CDIRIASSKAKFGQPEVGLGITPGFGGTQRLARAIGVGMAKELIYTGKVINAEEALRIGL 177
            DIRIAS  AKFG   + LGI PG GGT  L R IG+  A EL YTG VI+A  A   GL
Sbjct: 124 ADIRIASENAKFGVTFLKLGIIPGDGGTWILPRVIGMSRAAELFYTGDVIDAATAKEWGL 183

Query: 178 VNKVVEPDKLLEEAKALVDAIIVNAPIAVRMCKAAINQGLQCDIDTGVAYEAEVFGECFA 237
           V++VV PD L++EA+AL   I    P A+R  K  + QG Q   DT +   A        
Sbjct: 184 VSRVVAPDALMDEARALAGRIAAMPPHALRQSKMLLRQGQQVSYDTALEMAANTQAMMHT 243

Query: 238 TEDRVEGMTAFVEKRDKAFKNK 259
           T D  EG+ A + KR   F+ +
Sbjct: 244 TADHAEGVAALIAKRVPDFRGE 265


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: 179
Number of extensions: 10
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: 265
Length adjustment: 25
Effective length of query: 234
Effective length of database: 240
Effective search space:    56160
Effective search space used:    56160
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 24 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