GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bcd in Burkholderia phytofirmans PsJN

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 BPHYT_RS02220 BPHYT_RS02220 butyryl-CoA dehydrogenase

Query= BRENDA::D2RL84
         (383 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS02220 BPHYT_RS02220 butyryl-CoA
           dehydrogenase
          Length = 376

 Score =  347 bits (889), Expect = e-100
 Identities = 171/373 (45%), Positives = 246/373 (65%)

Query: 5   LTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGGMGL 64
           L +D  M++D    F  + + P     D+   + + +  ++ E G  G+  PE YGG G+
Sbjct: 3   LDQDHLMVRDALRTFVREAITPHAAVWDRERTFPKDVHRQLAELGAYGVLVPEAYGGAGM 62

Query: 65  DVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVGAFG 124
           D L+  L +EE++  D GT   +S N     + +  +G + QK+ +L P+A G  +GAF 
Sbjct: 63  DALALALILEEIAAGDGGTSTAISVNNCPVCSILLTYGNDAQKRDWLTPLARGEMLGAFC 122

Query: 125 LTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGISAF 184
           LTEP AG+DASA +TTA   GD Y+LNG K FIT+GK  +  +V A+TDK+ G  GISAF
Sbjct: 123 LTEPQAGSDASALRTTATRDGDAYVLNGVKQFITSGKNGNVAIVMAVTDKAAGKRGISAF 182

Query: 185 ILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDGGRI 244
           I+     G+   ++EDK+G H+S TA++IFEDC VP  NL+G EGEG++IA+  L+GGRI
Sbjct: 183 IVPTDTKGYVVARVEDKLGQHSSDTAQIIFEDCRVPAANLIGAEGEGYRIALSGLEGGRI 242

Query: 245 GVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYHAAM 304
           G+AAQ++G+A  A  AA+ Y+KERE FG  +   QA+QF +ADMAT++EAAR L++HAA 
Sbjct: 243 GIAAQSVGMARAAFEAALSYAKERESFGAPLFSHQAVQFRLADMATQLEAARQLIWHAAS 302

Query: 305 LKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQIYEG 364
           LK+ G+P    AAMAK FAS+ A  + + A+QI GGYGY  D+P ER  R+ ++ QIYEG
Sbjct: 303 LKDAGQPCLTEAAMAKLFASEAAERICSAALQIHGGYGYLSDFPVERIYRDVRVCQIYEG 362

Query: 365 TNQVMRIVTSRAL 377
           T+ + +I+ +R L
Sbjct: 363 TSDIQKILIARGL 375


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: 371
Number of extensions: 12
Number of successful extensions: 1
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: 376
Length adjustment: 30
Effective length of query: 353
Effective length of database: 346
Effective search space:   122138
Effective search space used:   122138
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