GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdC in Klebsiella michiganensis M5al

Align Dihydrolipoyllysine-residue (2-methylpropanoyl)transferase (EC 2.3.1.168) (characterized)
to candidate BWI76_RS14150 BWI76_RS14150 dihydrolipoyllysine-residue acetyltransferase

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



>lcl|FitnessBrowser__Koxy:BWI76_RS14150 BWI76_RS14150
           dihydrolipoyllysine-residue acetyltransferase
          Length = 509

 Score =  168 bits (426), Expect = 3e-46
 Identities = 110/327 (33%), Positives = 169/327 (51%), Gaps = 8/327 (2%)

Query: 100 VAATKVETVVESKPVAAPAPKAAVCQGPMVAREADERPLASPAVRKHALDLGIQLRLVRG 159
           VA  +   V     VA+P P     + P  +   D +  A+P  R+ A  LGI L   R 
Sbjct: 180 VADLESAIVAAGGRVASPPPPVRSGKAPR-SHTDDSQVSATPLARRLANKLGINLHDCRK 238

Query: 160 TGPAGRVLHEDL--DAYLAQGQSNASAPVAAAYAQRTDEQQIPVIGMRRKIAQRMQDATQ 217
           +G  GRV  +D+   A L  G   A AP A +    T  + +P+  MRR IA R+Q + Q
Sbjct: 239 SGSLGRVSRDDVLAAALLLDGLHQAGAPQATS---ATAFETLPMSSMRRAIAGRLQMSKQ 295

Query: 218 RAAHFSYVEEIDVTAVEELRAHLNEKHGATRGKLTLLPFLVRALVVALRDFPQINARYDD 277
            A HF    ++D+  +  LR  +N +      K+++   LV+A  +AL   P +N ++D+
Sbjct: 296 HAPHFRLTVDLDLDRLLALRKEINSEVPGV--KISVNDMLVKACAMALIAVPDVNIQFDE 353

Query: 278 EAQVITRLGAVHVGIATQADIGLMVPVVRHAEARSLWDSAAEISRLATAARNGKASRDEL 337
             Q I R     + +A     GL+ P+VR A +RS+ D + E+  L T AR G    +E 
Sbjct: 354 ATQSIRRFADADISVAVALPDGLITPIVRSANSRSISDISNEVHSLITKARAGMLKPEEF 413

Query: 338 SGSTITLTSLGALGGIVSTPVLNLPEVAIVGVNKIVERPMVIKGQIVIRKMMNLSSSFDH 397
            G T ++++LG LG      ++N P+ AI+ +     R +V  GQIV+R  + +S S DH
Sbjct: 414 QGGTFSVSNLGMLGVRQFDAIINPPQGAILAIGAGEPRAVVRDGQIVVRHQLTVSLSCDH 473

Query: 398 RVVDGMDAALFIQAIRGLLEQPATLFV 424
           RV+DG   A F+QA++ L+E P  LF+
Sbjct: 474 RVIDGASGAAFLQALKRLVETPTLLFI 500


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: 387
Number of extensions: 12
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 425
Length of database: 509
Length adjustment: 33
Effective length of query: 392
Effective length of database: 476
Effective search space:   186592
Effective search space used:   186592
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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