Align BadK (characterized)
to candidate WP_035704417.1 BA79_RS18210 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >NCBI__GCF_000691145.1:WP_035704417.1 Length = 260 Score = 147 bits (371), Expect = 2e-40 Identities = 88/242 (36%), Positives = 128/242 (52%), Gaps = 2/242 (0%) Query: 14 VGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG-NTRAFAAGADIASMAA 72 +GI+TLNRP NAL+ A+++ + + D I +++ G + F AGAD+ Sbjct: 14 IGIMTLNRPAQANALSAAMLEEINQTIQEIKHDANIRCLLMTGAGAKVFCAGADLKERRL 73 Query: 73 WSYSDVYGSNF-ITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAKFALP 131 + + + I + + I + PV+A + G A GGG ELALACD+ IA A LP Sbjct: 74 MTEQEAKEAVLTIQQTFTDIESLPVPVIAVINGHALGGGLELALACDLRIARAGAALGLP 133 Query: 132 EIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRDETV 191 E L +LPGAGGTQRLPR IG KA +M + L AEEA + GL+ R+ D L ++ + Sbjct: 134 ETGLAILPGAGGTQRLPRLIGPGKAKEMIFTGTSLRAEEAVQIGLIERISTADSLMNDAI 193 Query: 192 ALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAFLEKR 251 LA I AL K+++ + + L G+ E + D EG++AF EKR Sbjct: 194 TLAKQITKNGPIALKEAKQAIQSSLDHDLQTGLTKEYEAYLRLIHTEDRLEGLKAFQEKR 253 Query: 252 AP 253 P Sbjct: 254 TP 255 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: 108 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: 260 Length adjustment: 24 Effective length of query: 234 Effective length of database: 236 Effective search space: 55224 Effective search space used: 55224 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