GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdA in Azospirillum brasilense Sp245

Align 2-oxoisovalerate dehydrogenase subunit alpha 2, mitochondrial; Branched-chain alpha-keto acid dehydrogenase E1 component alpha chain; BCKDE1A; BCKDH E1-alpha; EC 1.2.4.4 (characterized)
to candidate AZOBR_RS25395 AZOBR_RS25395 acetoin dehydrogenase

Query= SwissProt::Q84JL2
         (472 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS25395 AZOBR_RS25395 acetoin
           dehydrogenase
          Length = 316

 Score =  138 bits (348), Expect = 2e-37
 Identities = 98/313 (31%), Positives = 151/313 (48%), Gaps = 5/313 (1%)

Query: 133 IYSDMVTLQIMDNIFYEAQRQGRLSFYA-TAIGEEAINIASAAALTPQDVIFPQYREPGV 191
           +Y+ M  +++ + +  EA + G+++ Y   +IG+EAI  A  A L   DV+   +R  G 
Sbjct: 3   LYATMQRIRVFETLADEAHKAGQVAGYIHLSIGQEAIAAAVGANLRADDVLTSTHRGHGH 62

Query: 192 LLWRGFTLQEFANQCFGNKSDYGKGRQMPVHYGSNKLNYFTVSATIATQLPNAVGAAYSL 251
            + +G        +  G       G+   +H     +     +  +A  LP AVGAA+++
Sbjct: 63  TIAKGADPLAMFRELCGRAGGTCGGKGGSMHIADFSVGMLGANGVVAAGLPIAVGAAHAI 122

Query: 252 KMDKKDACAVTYFGDGGTSEGDFHAALNIAAVMEAPVLFICRNNGWAISTPTSDQFRSDG 311
            +  +D  AV +FGDG T+ G F  ALN AA    PVLF+C +NG+  +T T       G
Sbjct: 123 ALKGEDRIAVCFFGDGATNRGPFLEALNWAAAFRLPVLFVCEDNGYGATTRTGSVSAGGG 182

Query: 312 VVVKGRAYGIRSIRVDGNDALAMYSAVHTAREMAIRE-QRPILIEALTYRVGHHSTSDDS 370
             V+  + GI    VDGND LA   A   A   A+R+   P  + A TYR   H++SD +
Sbjct: 183 PGVRAESLGIPVTVVDGND-LAAVDAAAAALVRAVRDGGGPQFLHARTYRFRGHTSSDPA 241

Query: 371 TRYRSAGEIEWWNKARNPLSRFRTWIESNGWWSDKTESDLRSRIKKEMLEALRVAEKTEK 430
           T YR A E+       +PL R    +   G   D  E   R   ++ +  AL  A  +  
Sbjct: 242 T-YRDAAEVRAQLAGNDPLQRAAATLAELGVTPDALERVERHE-RETLAAALATALDSPW 299

Query: 431 PNLQNMFSDVYDV 443
           P+L+  F+DV D+
Sbjct: 300 PDLRTAFTDVQDI 312


Lambda     K      H
   0.318    0.132    0.394 

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: 329
Number of extensions: 17
Number of successful extensions: 5
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: 472
Length of database: 316
Length adjustment: 30
Effective length of query: 442
Effective length of database: 286
Effective search space:   126412
Effective search space used:   126412
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