Align BadK (characterized)
to candidate 5208024 Shew_0540 enoyl-CoA hydratase/isomerase (RefSeq)
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__PV4:5208024 Length = 245 Score = 126 bits (316), Expect = 5e-34 Identities = 86/248 (34%), Positives = 129/248 (52%), Gaps = 4/248 (1%) Query: 3 SNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFA 62 SN + QG V IIT+NRPD NALN + L L+ ++D+GI A ++ G F Sbjct: 2 SNIQFQDEQG-VRIITINRPDKRNALNLEMYARLTEYLIQGESDNGINAFLLKGEGDCFT 60 Query: 63 AGADIASMAAWSYSDVYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIA 122 +G D+A SD+ ++ R T+ + KP++AAVAG A G G L L CD+V A Sbjct: 61 SGNDVADFL--KNSDLGQNHPTVRFLFTLLDLTKPLVAAVAGPAVGIGTTLLLHCDLVYA 118 Query: 123 GRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVD 182 +AKF LP + L L+P AG + LPR +G+ KA ++ L P +A+ A GL++ ++ Sbjct: 119 DNTAKFQLPFVNLALVPEAGASLLLPRLVGQTKASELLLLGEPFDAQSALSMGLINDLLP 178 Query: 183 DDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADARE 242 D L ++ + +A AL A + L R + E + E E R S +A+ Sbjct: 179 SDELMSHAMSQSIKLAKKPPQALRASRR-LIRGDSELIREQMQKELEEFAVRLQSDEAKA 237 Query: 243 GIQAFLEK 250 AFL + Sbjct: 238 QFNAFLSR 245 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: 86 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: 245 Length adjustment: 24 Effective length of query: 234 Effective length of database: 221 Effective search space: 51714 Effective search space used: 51714 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: 46 (22.3 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