Align BadK (characterized)
to candidate Echvi_4069 Echvi_4069 Enoyl-CoA hydratase/carnithine racemase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__Cola:Echvi_4069 Length = 261 Score = 130 bits (326), Expect = 4e-35 Identities = 91/260 (35%), Positives = 130/260 (50%), Gaps = 12/260 (4%) Query: 3 SNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGN-TRAF 61 S IL+E + + +T+NR LNA+N ++ L + I +V+ G+ +AF Sbjct: 4 STNILSENKDGILYLTINRESKLNAINFDTLEELKNIFNEVSDNKSIRGVVLTGSGEKAF 63 Query: 62 AAGADIASMAAWSYSDVYGSNFITRNWET---IRQIRKPVLAAVAGLAYGGGCELALACD 118 AGADI+ +A +++ F E I KPV+A V G A GGGCEL++AC Sbjct: 64 VAGADISEIA--ELNELNARKFSENGQEVFSLIESCHKPVIAVVNGFALGGGCELSMACH 121 Query: 119 IVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVS 178 + IA +AKF PE+ LG++PG GGTQRL IG+ KA ++ ++ ++A EA GLV+ Sbjct: 122 MRIATSNAKFGQPEVNLGIIPGYGGTQRLTFLIGRTKANELLMTGDMVDAAEAKALGLVN 181 Query: 179 RVVDDDRLRDETVALATTI---AAFSAPALMALKESLNRAFESTLAEGILFERRELHARF 235 V + + E + A I AP + + A S G L E Sbjct: 182 YVT---QTKAEAIQKAEEILQKIMTKAPLSIGMIIDCVNAVYSNDENGYLIEANSFARCV 238 Query: 236 ASADAREGIQAFLEKRAPCF 255 S D EG AFLEKR P F Sbjct: 239 KSEDYSEGTSAFLEKRKPNF 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: 114 Number of extensions: 11 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: 261 Length adjustment: 24 Effective length of query: 234 Effective length of database: 237 Effective search space: 55458 Effective search space used: 55458 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