Align BadK (characterized)
to candidate BPHYT_RS25360 BPHYT_RS25360 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__BFirm:BPHYT_RS25360 Length = 256 Score = 148 bits (373), Expect = 1e-40 Identities = 92/243 (37%), Positives = 126/243 (51%), Gaps = 1/243 (0%) Query: 14 VGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADIASMA-A 72 VG +TL+RP +N+LN + L L A+ DD + +V+ GN RAF AGAD+ A A Sbjct: 11 VGWLTLDRPAAMNSLNREMATGLIAQLKAWRNDDAVRVLVVTGNGRAFCAGADLIEAAEA 70 Query: 73 WSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAKFALPE 132 I ++T+R KPV+AAV GLA GG E+ LACD+V+A SA+ Sbjct: 71 TQPGRREFLELIVEFFDTLRAFPKPVIAAVNGLALAGGLEVVLACDVVLAAESARLGDAH 130 Query: 133 IKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRDETVA 192 G+ PGAGG LPR + A + + ++A E YGLV+ V+ D LR A Sbjct: 131 SNFGVFPGAGGAAILPRKVPANVARYLLFTGDAMSAAELKGYGLVNEVLADAELRPRAQA 190 Query: 193 LATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAFLEKRA 252 LA A S L +K N + + A+ + E EL S D +EG++AF EKR Sbjct: 191 LAHKFAKKSPLVLARMKRVANETADKSAADALRHELLELRNHQRSYDVQEGLRAFAEKRE 250 Query: 253 PCF 255 P F Sbjct: 251 PQF 253 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: 107 Number of extensions: 2 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: 256 Length adjustment: 24 Effective length of query: 234 Effective length of database: 232 Effective search space: 54288 Effective search space used: 54288 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 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