GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bcd in Shewanella sp. ANA-3

Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (subunit 1/2) (EC 1.3.8.1) (characterized)
to candidate 7025618 Shewana3_2769 acyl-CoA dehydrogenase domain-containing protein (RefSeq)

Query= BRENDA::D2RL84
         (383 letters)



>lcl|FitnessBrowser__ANA3:7025618 Shewana3_2769 acyl-CoA
           dehydrogenase domain-containing protein (RefSeq)
          Length = 385

 Score =  302 bits (774), Expect = 9e-87
 Identities = 164/379 (43%), Positives = 237/379 (62%), Gaps = 3/379 (0%)

Query: 1   MDFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYG 60
           MDFN  EDQ+   D+A +FA   LAP   + D+ H + + +I K GE GFC +  PE  G
Sbjct: 1   MDFNFNEDQRQFADLARQFAADELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEG 60

Query: 61  GMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHV 120
           GMGL  L   +  EELSK    T   L+ + ++    +  +GT+  +Q +  P+  G  +
Sbjct: 61  GMGLSRLDASIIFEELSKGCTATTAMLTIH-NMATWMVTTWGTDTLRQAWSEPLTTGQML 119

Query: 121 GAFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHG 180
            ++ LTEP AG+DA++ QT AV +GD+Y+++GSK+FI+     +  VV   T ++ G  G
Sbjct: 120 ASYCLTEPGAGSDAASLQTKAVREGDEYVVSGSKMFISGAGSTELLVVMCRTGQA-GPKG 178

Query: 181 ISAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLD 240
           ISA  +     G  +GK EDKMG +   T  + F++  VP  NLLG+EG+GF  AM+ LD
Sbjct: 179 ISAIAIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLD 238

Query: 241 GGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVY 300
           GGRI +A  ++G A+ AL  A +Y  ER+QFG+ ++ FQALQF +ADMAT++ AAR +V 
Sbjct: 239 GGRINIATCSVGTAQAALERATQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVR 298

Query: 301 HAAMLKNEGKPYSEA-AAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKIT 359
            AA   + G P + A  AMAK FA+DV  +V   A+QI GGYGY  +YP ER+ R+ ++ 
Sbjct: 299 LAAFKLDSGDPEATAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVH 358

Query: 360 QIYEGTNQVMRIVTSRALL 378
           QI EGTN++MR++ +R LL
Sbjct: 359 QILEGTNEIMRLIIARRLL 377


Lambda     K      H
   0.318    0.134    0.379 

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: 350
Number of extensions: 19
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: 383
Length of database: 385
Length adjustment: 30
Effective length of query: 353
Effective length of database: 355
Effective search space:   125315
Effective search space used:   125315
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.

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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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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