GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etfA in Echinicola vietnamensis KMM 6221, DSM 17526

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate Echvi_2952 Echvi_2952 Electron transfer flavoprotein, alpha subunit

Query= BRENDA::Q18AQ5
         (336 letters)



>FitnessBrowser__Cola:Echvi_2952
          Length = 321

 Score =  169 bits (428), Expect = 9e-47
 Identities = 104/326 (31%), Positives = 172/326 (52%), Gaps = 6/326 (1%)

Query: 3   NVLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHYGADEVI 62
           ++LV IE  E  I+  SLE +  A+ + +    +V+A+ LG+  EG +      GA +V+
Sbjct: 2   SILVYIEHAEGTIKKTSLEAVSYASALGEKEGKEVTAVALGAIEEGALAKAGAAGAKKVL 61

Query: 63  VVDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADCTG 122
            V D+ L     + +  A  +A + A    ++   +S+G  +A R+S ++  GL ++   
Sbjct: 62  HVADDKLNDGVIQAHASAVAQAFEQAGADTLVLAKSSLGDAVAARLSIKLKAGLASNV-- 119

Query: 123 LAVAEDTKLLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKNEPDETKEAVINRFKV 182
           +A+ E+     + R  + G      V       ++  +  V  K++     +A +  F+V
Sbjct: 120 VALPEEDGGYKVRRSIYTGKAFTDTVITTSNKILAVKKNAVPLKSDG---ADASVEAFQV 176

Query: 183 EFNDADKLVQVVQVIKEAKKQVKIEDAKILVSAGRGMGGKENLDILYELAEIIGGEVSGS 242
              ++D   ++    K A  ++ + +A I+VS GRGM G EN  ++  LA+ +G     S
Sbjct: 177 NLEESDFAAKITATDK-ATDEISLPEADIVVSGGRGMKGPENWHLIENLAKAMGAATGCS 235

Query: 243 RATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAEFIVAINKNPEAPIF 302
           +   D+ W      VGQTG  V P LY+A GISGAIQH+AG+  ++FI+ INK+PEAP F
Sbjct: 236 KPVSDSEWRPHHEHVGQTGVKVAPSLYVAVGISGAIQHLAGVNASKFILVINKDPEAPFF 295

Query: 303 KYADVGIVGDVHKVLPELISQLSVAK 328
           K AD GIVGD  ++LP+L   +   K
Sbjct: 296 KAADYGIVGDAFEILPKLTEAVKAIK 321


Lambda     K      H
   0.316    0.135    0.371 

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: 233
Number of extensions: 3
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: 336
Length of database: 321
Length adjustment: 28
Effective length of query: 308
Effective length of database: 293
Effective search space:    90244
Effective search space used:    90244
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 (21.6 bits)
S2: 49 (23.5 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