Align BadK (characterized)
to candidate GFF2094 PS417_10680 enoyl-CoA hydratase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__WCS417:GFF2094 Length = 263 Score = 130 bits (327), Expect = 3e-35 Identities = 94/265 (35%), Positives = 130/265 (49%), Gaps = 20/265 (7%) Query: 4 NPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAA 63 +P+LT+ Q V ITLNR NAL+ + L L F+ D + +V+ GN R+F A Sbjct: 5 SPVLTQVQAGVAWITLNRGPQRNALDIPTLKHLHALLDTFNTDPAVRVVVLTGNGRSFCA 64 Query: 64 GADIASMAAWSYS---DVYGSNFITRNWET-IRQIRKPVLAAVAGLAYGGGCELALACDI 119 GAD+A AA + YG T + + KP +AA+ G A G G +L L CD+ Sbjct: 65 GADLAEWAAAEARGALETYGWTDTAHALMTRLHTLDKPTIAAINGTAVGAGMDLTLCCDL 124 Query: 120 VIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSR 179 +A +SA+F + P AG + LPR IG +A + +A+ A GLV Sbjct: 125 RVAAQSARFKAGYTSMAYSPDAGASWHLPRLIGSEQAKRLLFLDELWSADRALAAGLVGE 184 Query: 180 VVDDDRLRDETVALATTIA-----AFSAPALM---ALKESLNRAFESTLAEGILFERREL 231 VV DD L T ALAT +A AF+ + + SL ++ LA G+L R Sbjct: 185 VVTDDHLHAHTNALATRLANGPTFAFAQTKTLIRDGAERSLPAQLQAELAAGLLCGR--- 241 Query: 232 HARFASADAREGIQAFLEKRAPCFS 256 SAD E ++A LEKR P FS Sbjct: 242 -----SADGTEALRASLEKRLPIFS 261 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: 126 Number of extensions: 6 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: 263 Length adjustment: 25 Effective length of query: 233 Effective length of database: 238 Effective search space: 55454 Effective search space used: 55454 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