GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Shewanella amazonensis SB2B

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate 6935814 Sama_0032 multifunctional fatty acid oxidation complex subunit alpha (RefSeq)

Query= BRENDA::D3RXI0
         (252 letters)



>FitnessBrowser__SB2B:6935814
          Length = 716

 Score = 93.6 bits (231), Expect = 1e-23
 Identities = 65/191 (34%), Positives = 103/191 (53%), Gaps = 12/191 (6%)

Query: 12  ERVARIKIANP-PVNVLDMETMKEIISAIDEVEGVDV---IVFSGEGKSFSAGAEIKEH- 66
           +++AR+    P  VN  D ET+  + +A+D ++  D    ++ SG+  +F  GA+I E  
Sbjct: 15  DKIARLCFNAPGSVNKFDRETLASLNAALDVLKDSDAKAAVLTSGKD-TFIVGADITEFL 73

Query: 67  --FPDKAPEMIRWFTQ---LIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAK 121
             F ++  +++ W  Q   + +K+      TV+A+KGFALGGG E  +A DF +A  +AK
Sbjct: 74  ALFAEEDAKLMEWIAQANVVFNKLEDLPFPTVSAIKGFALGGGCEAILATDFRVADTSAK 133

Query: 122 LGVPEITLAHYPPV-AIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDENFE 180
           +G+PE  L   P       LPR+IG  NA E I TG+    E A ++G ++ V   EN E
Sbjct: 134 IGLPETKLGLIPGFGGTVRLPRLIGADNALEWITTGKDQRPEDALKVGAIDAVVAPENLE 193

Query: 181 ESVNDFVNSLL 191
            +    +N  L
Sbjct: 194 AAAIQMLNDAL 204


Lambda     K      H
   0.318    0.136    0.382 

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: 408
Number of extensions: 21
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: 252
Length of database: 716
Length adjustment: 32
Effective length of query: 220
Effective length of database: 684
Effective search space:   150480
Effective search space used:   150480
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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