Align BadK (characterized)
to candidate Synpcc7942_0597 Synpcc7942_0597 naphthoate synthase
Query= metacyc::MONOMER-943 (258 letters) >FitnessBrowser__SynE:Synpcc7942_0597 Length = 279 Score = 102 bits (255), Expect = 7e-27 Identities = 84/248 (33%), Positives = 112/248 (45%), Gaps = 11/248 (4%) Query: 17 ITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG------NTRAFAAGADIASM 70 IT+NRP NA + L A D IG I++ G AF AG D + Sbjct: 27 ITINRPHKRNAFRPKTVVELYDAFCDAREDIAIGVILLTGAGPHTDGRYAFCAGGDQSVR 86 Query: 71 AAWSYSDVYGS---NFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAK 127 A Y D G N + IR I K V+A VAG A GGG L + CD+ IA +A Sbjct: 87 GAGGYIDEEGLPRLNVLDLQ-RLIRTIPKVVIALVAGYAIGGGHVLHILCDLTIAADNAV 145 Query: 128 FALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLR 187 F K+G G G L R +G+ KA ++ R A+EA + GLV+ VV + L Sbjct: 146 FGQTGPKVGSFDGGFGASYLARLVGQKKAREIWFLCRQYGAKEALQMGLVNTVVPVEELE 205 Query: 188 DETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAF 247 E + A I S A+ LK + N + +A H + + + EG QAF Sbjct: 206 AEGIRWALEILEKSPIAIRCLKAAFNAELDG-MAGIQELAGHATHLYYLTEEGSEGKQAF 264 Query: 248 LEKRAPCF 255 LEKR+P F Sbjct: 265 LEKRSPDF 272 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: 114 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: 279 Length adjustment: 25 Effective length of query: 233 Effective length of database: 254 Effective search space: 59182 Effective search space used: 59182 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