Align BadK (characterized)
to candidate BWI76_RS20065 BWI76_RS20065 1,4-dihydroxy-2-naphthoyl-CoA synthase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__Koxy:BWI76_RS20065 Length = 285 Score = 102 bits (253), Expect = 1e-26 Identities = 84/245 (34%), Positives = 116/245 (47%), Gaps = 7/245 (2%) Query: 17 ITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGN-TRAFAAGADIASMAAWS- 74 IT+NRP V NA + + AL DD IG IV+ G +AF AG D + Sbjct: 37 ITINRPQVRNAFRPLTVKEMIQALADARYDDNIGVIVLTGEGDKAFCAGGDQKVRGDYGG 96 Query: 75 YSDVYGSNFITRNWETIRQIR---KPVLAAVAGLAYGGGCELALACDIVIAGRSAKFALP 131 Y D G + + + RQIR KPVLA VAG + GGG L + CD+ IA +A F Sbjct: 97 YQDDSGVHHLNV-LDFQRQIRTCPKPVLAMVAGYSIGGGHVLHMMCDLTIAAENAIFGQT 155 Query: 132 EIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRDETV 191 K+G G G + R +G+ KA ++ R +A++A GLV+ VV L ETV Sbjct: 156 GPKVGSFDGGWGASYMARIVGQKKAREIWFLCRQYDAQQALDMGLVNTVVPLADLEKETV 215 Query: 192 ALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAFLEKR 251 + S AL LK +LN + L + + + + +EG AF +KR Sbjct: 216 RWCREMLQNSPMALRCLKAALNADCDGQAGLQELAGNATM-LFYMTEEGQEGRNAFNQKR 274 Query: 252 APCFS 256 P FS Sbjct: 275 QPDFS 279 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: 119 Number of extensions: 7 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: 285 Length adjustment: 25 Effective length of query: 233 Effective length of database: 260 Effective search space: 60580 Effective search space used: 60580 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