Align BadK (characterized)
to candidate WP_108402835.1 B9Z44_RS06720 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >NCBI__GCF_003063475.1:WP_108402835.1 Length = 268 Score = 145 bits (366), Expect = 8e-40 Identities = 89/258 (34%), Positives = 136/258 (52%), Gaps = 11/258 (4%) Query: 8 TETQGRVGIITLNRPDVLNALNDAL-MDALGGALLAFDADDGIGAIVIAG-NTRAFAAGA 65 T+ V + LNRP+V NALN + +D L + D + +V+ G + F G Sbjct: 15 TQVSDHVLQVCLNRPEVGNALNTQMGVDLLDLWVRLTDVPGDLRCVVLTGAGAKIFCGGG 74 Query: 66 DIASM-----AAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIV 120 D+ AW Y R + + + PV+ A+ G AYGGG E+AL CD + Sbjct: 75 DLKERNGMTPQAWQYQH----EIFERLYWALIDLPLPVIGAINGHAYGGGLEMALCCDFL 130 Query: 121 IAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRV 180 A + A+FALPE+ LG++PG GGTQ LPRA+G+ +A ++ L+ RP +AE+A +GLV++V Sbjct: 131 YASQDARFALPEVTLGIMPGMGGTQNLPRALGERRAKELALTGRPFSAEQALAWGLVNQV 190 Query: 181 VDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADA 240 D + + A IAA + ++ +K+S+ + L FE + + D Sbjct: 191 AAPDAVLALALETAQRIAANAPLSVRQIKKSIRYGGQMELRTAYRFEVEAYNRLVDTDDR 250 Query: 241 REGIQAFLEKRAPCFSHR 258 REG+ AF +KR P F R Sbjct: 251 REGVAAFNDKRPPVFKGR 268 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: 141 Number of extensions: 4 Number of successful extensions: 1 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: 268 Length adjustment: 25 Effective length of query: 233 Effective length of database: 243 Effective search space: 56619 Effective search space used: 56619 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