Align BadK (characterized)
to candidate WP_011881868.1 3-hydroxybutyryl-CoA dehydratase
Query= metacyc::MONOMER-943 (258 letters) >NCBI__GCF_000016205.1:WP_011881868.1 Length = 261 Score = 170 bits (431), Expect = 2e-47 Identities = 102/254 (40%), Positives = 144/254 (56%), Gaps = 6/254 (2%) Query: 9 ETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGN-TRAFAAGADI 67 E + + +T++RP LNALN + + A DD + +++ G+ +AF AGADI Sbjct: 10 EKKSGIAYVTVDRPKSLNALNFQTLTEITAAFEDARDDDAVHGVIVTGSGNKAFVAGADI 69 Query: 68 ASMAAWSYSDVYGSNFITRNWETIRQIR---KPVLAAVAGLAYGGGCELALACDIVIAGR 124 + +AA S V F T+ I KPV+AAV G A GGGCELA+AC + IA Sbjct: 70 SEIAA--LSAVAAEKFAGLGHSTMNLIETLGKPVIAAVNGFALGGGCELAMACTMRIASE 127 Query: 125 SAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDD 184 AKF PE+KLG++PG GGTQRLPR +GK AM + L+A ++A EA R GLV+ VV+ D Sbjct: 128 HAKFGQPEVKLGIIPGFGGTQRLPRLVGKGIAMQLILTAALIDANEAHRIGLVNEVVEAD 187 Query: 185 RLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGI 244 +L + IAA + A ++N+ E++L + + ER A+ D EG Sbjct: 188 KLIARAEQILNQIAANAPIATRLAITAVNQGVEASLEQALSLERALFAVCAATEDKAEGT 247 Query: 245 QAFLEKRAPCFSHR 258 AFL+KRAP F + Sbjct: 248 AAFLDKRAPTFQSK 261 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: 132 Number of extensions: 4 Number of successful extensions: 2 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: 261 Length adjustment: 24 Effective length of query: 234 Effective length of database: 237 Effective search space: 55458 Effective search space used: 55458 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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