Align BadK (characterized)
to candidate PfGW456L13_3427 Enoyl-CoA hydratase (EC 4.2.1.17)
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3427 Length = 272 Score = 156 bits (395), Expect = 4e-43 Identities = 103/257 (40%), Positives = 130/257 (50%), Gaps = 3/257 (1%) Query: 3 SNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGN-TRAF 61 ++ + E VG + L RP +NA+ND + + AL D I IVI G R F Sbjct: 14 NDAVRLERDAMVGWVVLTRPRQINAINDEIRQGVPQALALLQQDPDIRVIVIRGEGDRGF 73 Query: 62 AAGADIASMAAWSYSDVYGSNFITRNW-ETIRQIRKPVLAAVAGLAYGGGCELALACDIV 120 AGADI S W ET+ I KPV+AA+ G GGG EL LACDI Sbjct: 74 CAGADIKERRGPESSLQVRQRMENVRWIETLDGITKPVIAAIHGYCMGGGLELVLACDIR 133 Query: 121 IAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRV 180 A A FALPE LGL+PG GGTQRL R + +A+DM L+ + AE+A R GLVSR+ Sbjct: 134 FAAPDAVFALPETGLGLIPGGGGTQRLSRVVAPGQALDMLLTGDRVGAEQAQRIGLVSRL 193 Query: 181 VDDD-RLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASAD 239 D L E A A IA+ A +K++ A E L G+ E + D Sbjct: 194 ASDSANLVQEVRAFAQRIASKPPTASAFVKQAARAALEMDLKRGLDLELDLFALLAPTKD 253 Query: 240 AREGIQAFLEKRAPCFS 256 ARE QAF E+R P F+ Sbjct: 254 AREAAQAFSERREPRFT 270 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: 136 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: 272 Length adjustment: 25 Effective length of query: 233 Effective length of database: 247 Effective search space: 57551 Effective search space used: 57551 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