Align BadK (characterized)
to candidate PP_4030 PP_4030 Enoyl-CoA hydratase/isomerase family protein
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__Putida:PP_4030 Length = 280 Score = 126 bits (316), Expect = 6e-34 Identities = 86/260 (33%), Positives = 131/260 (50%), Gaps = 12/260 (4%) Query: 9 ETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADI- 67 E V + +NRP+ +NA+N A + + D D + +VI+G + F+AG D+ Sbjct: 20 ELTDSVAHVQINRPEKVNAMNAAFWEEIVDIFQWIDDTDAVRVVVISGAGKHFSAGIDLM 79 Query: 68 --ASMAAWSYSDV-YGSNFITR-------NWETIRQIRKPVLAAVAGLAYGGGCELALAC 117 AS+A DV + F+ + ++ + RKPVLAAV G GG +L AC Sbjct: 80 MLASLAGQMGKDVGRNARFLRKTIQRLQASFTAVDACRKPVLAAVQGYCIGGAIDLISAC 139 Query: 118 DIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLV 177 D+ R A+F++ EI +G+ G QRLPR IG ++ + R + A+EA R GLV Sbjct: 140 DMRYCSRDAQFSIKEIDMGMAADVGTLQRLPRIIGDGIMRELAFTGRNVEADEALRIGLV 199 Query: 178 SRVVDDD-RLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFA 236 +RV DD L D A+A IAA S A+ KE L+ + + +G+ + A Sbjct: 200 NRVYDDQAALMDGVFAIAREIAAKSPIAVAGTKEMLSYMRDHRIDDGLDYIATWNAAMLQ 259 Query: 237 SADAREGIQAFLEKRAPCFS 256 S D R + A + K+ P F+ Sbjct: 260 SEDLRVAVAAHMSKQKPTFA 279 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: 125 Number of extensions: 6 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: 280 Length adjustment: 25 Effective length of query: 233 Effective length of database: 255 Effective search space: 59415 Effective search space used: 59415 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