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) >FitnessBrowser__Koxy:BWI76_RS14150 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.
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:
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:
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