Aligments for a candidate for bkdC in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for bkdC in Pseudomonas simiae WCS417

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate GFF3431 PS417_17555 branched-chain alpha-keto acid dehydrogenase subunit E2

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3542
         (425 letters)



>lcl|FitnessBrowser__WCS417:GFF3431 PS417_17555 branched-chain
           alpha-keto acid dehydrogenase subunit E2
          Length = 419

 Score =  680 bits (1754), Expect = 0.0
 Identities = 358/426 (84%), Positives = 383/426 (89%), Gaps = 8/426 (1%)

Query: 1   MGTHVIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVIAL 60
           MGTHVIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVI+L
Sbjct: 1   MGTHVIKMPDIGEGIAEVELSVWHVKVGDMVVEDQVLADVMTDKAMVDIPSPVHGKVISL 60

Query: 61  GGQPGEVMAVGSVLISIEVEGAGNVKESAQPAPVVKEAPVAATKVETVVESKPVAAPA-P 119
           GG+PGEVMAVGS+LISIEVEGAGN KE    AP  KE P AA  VE   +  PVA  + P
Sbjct: 61  GGEPGEVMAVGSILISIEVEGAGNAKE----APAAKETPKAAPVVEA--KPAPVAVESKP 114

Query: 120 KAAVCQGPMVAREADERPLASPAVRKHALDLGIQLRLVRGTGPAGRVLHEDLDAYLAQGQ 179
              V   P VAR ADERPLASPAVRKHALD GIQLRLV+G+GPAGR+LHEDLDAYL QG 
Sbjct: 115 APVVATQPPVARAADERPLASPAVRKHALDAGIQLRLVQGSGPAGRILHEDLDAYLQQGA 174

Query: 180 SNASAPVAAAYAQRTDEQQIPVIGMRRKIAQRMQDATQRAAHFSYVEEIDVTAVEELRAH 239
           S +S      YA+R  E+QIPVIGMRRKIAQRMQDAT+RAAHFSYVEEIDVTA++ELR H
Sbjct: 175 SKSST-ATNPYAERNTEEQIPVIGMRRKIAQRMQDATRRAAHFSYVEEIDVTALDELRVH 233

Query: 240 LNEKHGATRGKLTLLPFLVRALVVALRDFPQINARYDDEAQVITRLGAVHVGIATQADIG 299
           LNEKHGATRGKLTLLPF+VRA+VVALRDFPQINARYDDEAQVITRLGAVHVG+ATQ+D+G
Sbjct: 234 LNEKHGATRGKLTLLPFIVRAMVVALRDFPQINARYDDEAQVITRLGAVHVGVATQSDVG 293

Query: 300 LMVPVVRHAEARSLWDSAAEISRLATAARNGKASRDELSGSTITLTSLGALGGIVSTPVL 359
           LMVPVVRHAEARSLW +A EI+RLATAARNGKASRDELSGSTITLTSLGALGGIVSTPVL
Sbjct: 294 LMVPVVRHAEARSLWGNAEEIARLATAARNGKASRDELSGSTITLTSLGALGGIVSTPVL 353

Query: 360 NLPEVAIVGVNKIVERPMVIKGQIVIRKMMNLSSSFDHRVVDGMDAALFIQAIRGLLEQP 419
           NLPEVAIVGVN+IVERPMVIKGQIV+RKMMNLSSSFDHRVVDGMDAA FIQAIRGLLEQP
Sbjct: 354 NLPEVAIVGVNRIVERPMVIKGQIVVRKMMNLSSSFDHRVVDGMDAAQFIQAIRGLLEQP 413

Query: 420 ATLFVE 425
           A+LF+E
Sbjct: 414 ASLFLE 419


Lambda     K      H
   0.318    0.133    0.368 

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: 650
Number of extensions: 13
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: 425
Length of database: 419
Length adjustment: 32
Effective length of query: 393
Effective length of database: 387
Effective search space:   152091
Effective search space used:   152091
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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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources