Align BadK (characterized)
to candidate WP_058857482.1 AS188_RS02285 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >NCBI__GCF_001482365.1:WP_058857482.1 Length = 262 Score = 172 bits (435), Expect = 8e-48 Identities = 100/244 (40%), Positives = 142/244 (58%), Gaps = 2/244 (0%) Query: 13 RVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG-NTRAFAAGADIASMA 71 +V ++T++RP+V NALN A++D L AL + + A+V+ G +AF AGADI+ + Sbjct: 18 QVAVVTVDRPEVRNALNAAVLDGLEAALDECERRTDVRAVVLTGAGEKAFVAGADISQLV 77 Query: 72 AWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAKFALP 131 ++ D + + R W+ I + P +AAV G A GGG ELA+ACDI IA A+F LP Sbjct: 78 GYTLRDGLRAR-MQRLWDRIEDLELPTIAAVNGFALGGGTELAMACDIRIAAGGARFGLP 136 Query: 132 EIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRDETV 191 E LG++PGAGGTQRL R +G +A ++ L+ R ++AEEA R GLV+ VV L D + Sbjct: 137 EANLGIIPGAGGTQRLSRLVGLGRAQELILTGRLVDAEEALRIGLVTSVVPGPELLDAAL 196 Query: 192 ALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAFLEKR 251 A TI A A+ K + E+ G+L ER +A+ + EG AFLEKR Sbjct: 197 GTAATILAKGPLAVRMAKLVVRHGAETDQRTGLLLERLAQSLLYAADEKAEGAAAFLEKR 256 Query: 252 APCF 255 F Sbjct: 257 PARF 260 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: 127 Number of extensions: 9 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: 262 Length adjustment: 24 Effective length of query: 234 Effective length of database: 238 Effective search space: 55692 Effective search space used: 55692 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 Sep 24 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