Align BadK (characterized)
to candidate Ga0059261_0837 Ga0059261_0837 3-hydroxyacyl-CoA dehydrogenase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__Korea:Ga0059261_0837 Length = 676 Score = 144 bits (363), Expect = 5e-39 Identities = 102/253 (40%), Positives = 132/253 (52%), Gaps = 18/253 (7%) Query: 3 SNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFA 62 + PI TE QG + +IT N P V NAL A+ L A+ DD + A VI + R F Sbjct: 2 TGPITTERQGDILVITSNNPPV-NALGAAVRQGLDAAIKELAGDDSLKAAVIRCDGRTFF 60 Query: 63 AGADIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIA 122 AGADI + + + I KPV+AAV G A GGGCE+ALAC IA Sbjct: 61 AGADITE-----FGKPMQEPSLPVLVDLIEASEKPVVAAVHGTALGGGCEVALACHYRIA 115 Query: 123 GRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVD 182 SAKF LPE+KLG+LPGAGGTQRLPR G A+++ P++A A GLV R+ Sbjct: 116 VPSAKFGLPEVKLGILPGAGGTQRLPRVGGVEFALELATKGDPVSASAAKDAGLVDRLAG 175 Query: 183 DDRLRDETVALATTIAAFSAPALMALKESLNRAFES--TLAEGILFERRELHA-RFASAD 239 +D L + +A A IAA L R E T+ G+ R+ +A RF + D Sbjct: 176 EDSLTADAIAYANEIAA---------ARPLPRTSEKPVTVEAGVFEAFRKTNAKRFRNMD 226 Query: 240 AREGIQAFLEKRA 252 A I A +E+ A Sbjct: 227 APAEIIAVIEETA 239 Lambda K H 0.321 0.135 0.389 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: 277 Number of extensions: 11 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: 258 Length of database: 676 Length adjustment: 31 Effective length of query: 227 Effective length of database: 645 Effective search space: 146415 Effective search space used: 146415 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 50 (23.9 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