Align BadK (characterized)
to candidate WP_042119745.1 RHE_RS23495 carnitinyl-CoA dehydratase
Query= metacyc::MONOMER-943 (258 letters) >NCBI__GCF_000092045.1:WP_042119745.1 Length = 260 Score = 114 bits (284), Expect = 3e-30 Identities = 89/262 (33%), Positives = 135/262 (51%), Gaps = 9/262 (3%) Query: 3 SNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG-NTRAF 61 S+ + T G V + ++RP NA++ A A+G F D + +I+G + F Sbjct: 2 SDYVRTRRDGAVLEVVIDRPKA-NAIDLATSRAMGLIFRDFRDDPELRVAIISGAGEKFF 60 Query: 62 AAGADIASMAAWSYSDV-YGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIV 120 AG D+ + A+ D YG + +R + KPV+ AV GL GGG E+AL+ D++ Sbjct: 61 CAGWDLKAAASGDAVDGDYGVGGFG-GLQELRDLNKPVICAVNGLCCGGGLEIALSTDLI 119 Query: 121 IAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRV 180 IA A FALPEI+ G + A +LP+ I AMDM L+ R L+ EA R+G V+ V Sbjct: 120 IAAEHATFALPEIRSGTVADAASI-KLPKRIPYHIAMDMLLTGRWLDVHEAHRWGFVNEV 178 Query: 181 VDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTL--AEGILFERR--ELHARFA 236 V +RL + LA + + A+KE + A ST A + +R+ + ++ Sbjct: 179 VPAERLMERAWELARLLESGPPLVYAAIKEIVREAEGSTFQTAMNKITKRQFATVDRLYS 238 Query: 237 SADAREGIQAFLEKRAPCFSHR 258 S D EG +AF EKR+P + R Sbjct: 239 SEDQLEGARAFAEKRSPIWKGR 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: 114 Number of extensions: 8 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: 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 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