Align BadK (characterized)
to candidate WP_009546068.1 CCE_RS03960 1,4-dihydroxy-2-naphthoyl-CoA synthase
Query= metacyc::MONOMER-943 (258 letters) >NCBI__GCF_000017845.1:WP_009546068.1 Length = 277 Score = 99.4 bits (246), Expect = 7e-26 Identities = 86/259 (33%), Positives = 114/259 (44%), Gaps = 11/259 (4%) Query: 6 ILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG------NTR 59 IL + IT+NRP NA + L A D IG I++ G Sbjct: 14 ILYHKADGIAKITINRPHKRNAFRPKTVFELYDAFCDAREDSSIGVILLTGAGPHTDGKY 73 Query: 60 AFAAGADIASMAAWSYSDVYGS---NFITRNWETIRQIRKPVLAAVAGLAYGGGCELALA 116 AF +G D + Y D G N + IR + K V+A VAG A GGG L + Sbjct: 74 AFCSGGDQSVRGQAGYVDDAGIPRLNVLDLQ-RLIRSMPKVVIALVAGYAIGGGHVLHVI 132 Query: 117 CDIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGL 176 CD+ IA +A F K+G G G L R IG+ KA ++ R NAE+A GL Sbjct: 133 CDLTIAADNAVFGQTGPKVGSFDGGFGASYLARIIGQKKAREIWFLCRQYNAEQALEMGL 192 Query: 177 VSRVVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFA 236 V+ VV ++L E V A I + S A+ LK + N + L L + Sbjct: 193 VNCVVPVEQLETEGVQWAKEILSKSPIAIRCLKAAFNADCDGQAGLQELAGNATL-LYYM 251 Query: 237 SADAREGIQAFLEKRAPCF 255 + + EG QAFLEKR P F Sbjct: 252 TEEGAEGKQAFLEKRPPNF 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: 116 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: 277 Length adjustment: 25 Effective length of query: 233 Effective length of database: 252 Effective search space: 58716 Effective search space used: 58716 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 Apr 09 2024. 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