GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bcd in Azospirillum brasilense Sp245

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 AZOBR_RS22300 AZOBR_RS22300 acyl-CoA dehydrogenase

Query= BRENDA::D2RL84
         (383 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS22300 AZOBR_RS22300 acyl-CoA
           dehydrogenase
          Length = 377

 Score =  360 bits (923), Expect = e-104
 Identities = 173/375 (46%), Positives = 261/375 (69%)

Query: 5   LTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYGGMGL 64
           LTE+Q+M++DMA +FA + LAPT  ERD+   + ++ + +MG  G  G+  PEE+ G G 
Sbjct: 3   LTEEQRMVRDMARDFAAERLAPTAAERDRTGAFPKEELAEMGRLGLMGMLVPEEFDGAGT 62

Query: 65  DVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHVGAFG 124
           D ++Y LA+EE++  D      +S + S+   PI  FG+ EQK+++L P+A G  +G F 
Sbjct: 63  DHIAYALAIEEIAAGDGAISTIMSVHNSVGCMPILKFGSAEQKERFLKPMARGEQLGCFC 122

Query: 125 LTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHGISAF 184
           LTEP AG+DA+A +T A   G+ ++LNG+K FIT+GK AD  +VFA++D   G  GI+AF
Sbjct: 123 LTEPQAGSDAAAIKTRARRDGNHWVLNGTKQFITSGKNADVAIVFAVSDPEAGKKGITAF 182

Query: 185 ILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLDGGRI 244
           ++    PGF+  ++E+K+G   S T +++ EDC +P + +LG EG G+++A+  L+GGRI
Sbjct: 183 VVPTDTPGFQVARVEEKLGQSCSDTCQIVLEDCRIPADLMLGAEGGGYRVALANLEGGRI 242

Query: 245 GVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVYHAAM 304
           G+A+Q++G+A  AL  A +Y++ER+  G  I + QA+ F +ADMATK+EAAR LV HAA 
Sbjct: 243 GIASQSVGMARAALDHATRYAQERQSMGLPIIQHQAVAFRLADMATKVEAARQLVLHAAS 302

Query: 305 LKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQIYEG 364
           L++ G+P  + AAMAK FAS++A  V +DA+QI GGYGY  D+P ER  R+ ++ QIYEG
Sbjct: 303 LRDAGEPCLKEAAMAKLFASEIAERVCSDAIQIHGGYGYLNDFPVERIYRDVRVCQIYEG 362

Query: 365 TNQVMRIVTSRALLR 379
           T+ + R+V SRAL++
Sbjct: 363 TSDIQRLVISRALMQ 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: 375
Number of extensions: 11
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: 377
Length adjustment: 30
Effective length of query: 353
Effective length of database: 347
Effective search space:   122491
Effective search space used:   122491
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 paper from 2022 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