GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etfA in Bacteroides thetaiotaomicron VPI-5482

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109) (characterized)
to candidate 351333 BT1805 electron transfer flavoprotein alpha-subunit (NCBI ptt file)

Query= BRENDA::Q18AQ5
         (336 letters)



>FitnessBrowser__Btheta:351333
          Length = 339

 Score =  260 bits (664), Expect = 4e-74
 Identities = 147/333 (44%), Positives = 209/333 (62%), Gaps = 14/333 (4%)

Query: 1   MGNVLVVIEQRENVIQTVSLELLGKATEIAKDYDTKVSALLLGSKVEGLIDTLAHYGADE 60
           M N+ V  E  E ++  VSLELL K   +A + + ++ A++ G+ ++ +   +  YG D+
Sbjct: 1   MNNLFVYCEIEEGIVADVSLELLTKGRSLANELNCQLEAVVAGTGLKEIEKQILPYGVDK 60

Query: 61  VIVVDDEALAVYTTEPYTKAAYEAIKAADPIVVLFGATSIGRDLAPRVSARIHTGLTADC 120
           + V D E L  YT+ P+T       K   P + L GAT IGRDL PRVS+ + +GLTADC
Sbjct: 61  LHVFDAEGLYPYTSLPHTSILVNLFKEEQPQICLMGATVIGRDLGPRVSSALTSGLTADC 120

Query: 121 TGLAVA--EDTK-------LLLMTRPAFGGNIMATIVCKDFRPQMSTVRPGVMKKN--EP 169
           T L +   ED K       LL   RPAFGGNI+ATIV  + RPQM+TVR GVMKK    P
Sbjct: 121 TSLEIGDHEDKKEGKVYKNLLYQIRPAFGGNIVATIVNPEHRPQMATVREGVMKKEIVSP 180

Query: 170 DETKEAVINRFKVEFNDADKLVQVVQV-IKEAKKQVKIEDAKILVSAGRGMGGKENLDIL 228
               E + +  K    D D +V+V++  +++AK  +K   + I+++ G G+G KEN D+L
Sbjct: 181 AYQGEVIRHDVKKYVADTDYVVKVIERHVEKAKNNLK--GSPIIIAGGYGVGSKENFDLL 238

Query: 229 YELAEIIGGEVSGSRATIDAGWLDKARQVGQTGKTVRPDLYIACGISGAIQHIAGMEDAE 288
           + LA+ +  EV  SRA +DAG+ +  RQ+GQTG TVRP LYIACGISG IQHIAGM+++ 
Sbjct: 239 FSLAKELHAEVGASRAAVDAGFAEHDRQIGQTGVTVRPKLYIACGISGQIQHIAGMQESG 298

Query: 289 FIVAINKNPEAPIFKYADVGIVGDVHKVLPELI 321
            I++IN +P+API   AD  I G + +V+P++I
Sbjct: 299 IIISINNDPDAPINTIADYVINGTIEEVVPKMI 331


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: 309
Number of extensions: 17
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: 336
Length of database: 339
Length adjustment: 28
Effective length of query: 308
Effective length of database: 311
Effective search space:    95788
Effective search space used:    95788
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.

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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