Align BadK (characterized)
to candidate WP_058929110.1 AU252_RS00885 enoyl-CoA hydratase/isomerase family protein
Query= metacyc::MONOMER-943 (258 letters) >NCBI__GCF_001484605.1:WP_058929110.1 Length = 258 Score = 128 bits (322), Expect = 1e-34 Identities = 90/258 (34%), Positives = 134/258 (51%), Gaps = 10/258 (3%) Query: 7 LTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG-NTRAFAAGA 65 LT + + I +NRP+ +NA + L + D I VI G +AF+AGA Sbjct: 5 LTVSDDGIATIVMNRPERMNAFDAEAYKQLSEVWIRVRDDHAIRVAVITGAGEKAFSAGA 64 Query: 66 DIASM--AAWSYSDVYGSNFITRNWETIR---QIRKPVLAAVAGLAYGGGCELALACDIV 120 D+ + A D++ +T+ + + +I KPV+AAV G GGG + A DI Sbjct: 65 DLKDLVPAPPELHDLW----LTQKDQLLNRGLEIWKPVIAAVNGYCLGGGLTMLFATDIR 120 Query: 121 IAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRV 180 IA A F L E+K G+LPG G TQR+ + +AM+M L+ P++A +A +GL++ V Sbjct: 121 IACHDATFGLSEVKRGVLPGNGATQRVIDNVSYPRAMEMLLTGEPIDASKALEWGLINEV 180 Query: 181 VDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADA 240 VD RL + ++ +A IAA + A+ A KE R+ LA G+ E+ S DA Sbjct: 181 VDRARLMERSLEIARQIAANAPLAVQATKELAVRSRSMDLASGLRLEQVLQRILQTSEDA 240 Query: 241 REGIQAFLEKRAPCFSHR 258 EG +AF E+R F R Sbjct: 241 VEGPKAFAERRPAVFGGR 258 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: 104 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: 258 Length adjustment: 24 Effective length of query: 234 Effective length of database: 234 Effective search space: 54756 Effective search space used: 54756 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