Align BadK (characterized)
to candidate Dsui_0502 Dsui_0502 enoyl-CoA hydratase/carnithine racemase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__PS:Dsui_0502 Length = 263 Score = 135 bits (340), Expect = 9e-37 Identities = 90/265 (33%), Positives = 136/265 (51%), Gaps = 17/265 (6%) Query: 6 ILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGA 65 +L+ + V +TLNRP+ LNALN A+++ L A + D+ +GA+V+ G F AG Sbjct: 4 VLSHLEDGVLTLTLNRPEALNALNLAMIEDLRAATARAEHDEAVGAVVLRGGEH-FMAGG 62 Query: 66 DIASMAAWSYSDV----------YGSNFITRNWET--IRQIRKPVLAAVAGLAYGGGCEL 113 D+ W +S + + + T +R++ KPV+A+V+G A G G L Sbjct: 63 DLK----WFHSQLALPPAERQALFEQTIAAVHATTLQVRRMGKPVVASVSGAAAGFGLSL 118 Query: 114 ALACDIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADR 173 LACD+ +A +A F L +GL P G T LPRA+G +A ++ L +A +A Sbjct: 119 MLACDLAVAADNAYFTLAYCHIGLSPDGGATWFLPRAVGAKRAAEIALLGDRFDAAQARE 178 Query: 174 YGLVSRVVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHA 233 +GL++RVV L E+ LA +AA AL K L + ++L E + E+ A Sbjct: 179 WGLINRVVPAAELEAESAKLARRLAAGPRQALARTKALLQASSGNSLPEQLFAEQGNFAA 238 Query: 234 RFASADAREGIQAFLEKRAPCFSHR 258 D EG+ AFLEKR P F + Sbjct: 239 CSVHPDFAEGLGAFLEKRKPAFGQK 263 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: 124 Number of extensions: 5 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: 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