Align BadK (characterized)
to candidate Pf1N1B4_3903 Enoyl-CoA hydratase (EC 4.2.1.17) / Delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase (EC 5.3.3.8) / 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) / 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3)
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3903 Length = 715 Score = 95.5 bits (236), Expect = 3e-24 Identities = 59/186 (31%), Positives = 94/186 (50%), Gaps = 7/186 (3%) Query: 15 GIITLN---RPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADIASMA 71 GI+ L + + +N N ++ L A+ AD I ++++ F GADI Sbjct: 16 GIVELKFDLKGESVNKFNRLTLNELRQAVDTIKADASIKGVIVSSGKDVFIVGADITEFV 75 Query: 72 A-WSYSD---VYGSNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAK 127 + D V G+ + + + P +AA+ G+A GGG E+ LA D + +AK Sbjct: 76 DNFKLPDAELVAGNLEANKIFSDFEDLNVPTVAAINGIALGGGLEMCLAADFRVMANTAK 135 Query: 128 FALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLR 187 LPE+KLG+ PG GGT RLPR IG A++ + + AE+A + G V VV ++L+ Sbjct: 136 IGLPEVKLGIYPGFGGTVRLPRIIGADNAIEWIAAGKENRAEDALKVGAVDAVVAPEKLQ 195 Query: 188 DETVAL 193 + + L Sbjct: 196 EAALNL 201 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: 268 Number of extensions: 10 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: 715 Length adjustment: 32 Effective length of query: 226 Effective length of database: 683 Effective search space: 154358 Effective search space used: 154358 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: 51 (24.3 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