Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate RR42_RS35005 RR42_RS35005 L-idonate 5-dehydrogenase
Query= BRENDA::Q6ECH5 (336 letters) >FitnessBrowser__Cup4G11:RR42_RS35005 Length = 342 Score = 144 bits (362), Expect = 4e-39 Identities = 101/316 (31%), Positives = 153/316 (48%), Gaps = 15/316 (4%) Query: 15 EDIKEPEIKPD-----EVLIHTAYAGICGTDKALYA-GLPGSASAVPPIVLGHENSGVVT 68 ED++ +++P EV + AGICG+D Y G G+ P+ GHE +G+V+ Sbjct: 11 EDLRFTQVEPAAPGPFEVEVRLGAAGICGSDLHYYFHGKVGAFVIREPLTPGHEAAGIVS 70 Query: 69 KVGSEVTNVKPGDRVTVDPNIYCGQCKYCRTQRPELCEHLDAVGVTR-----NGGFEEYF 123 +VGS VT V PG++V ++P+ CGQC YCR R LC + +G G F E+F Sbjct: 71 RVGSAVTRVAPGNKVAINPSHACGQCDYCRAGRDNLCRSMRFLGSASIYPHVQGMFREHF 130 Query: 124 TAPAKVVYPIPDDVSLKAAAVVEPISCAMHGVDLLETHPYQKALVLGDGFEGQLFAQILK 183 + + P+ D+SL A EP+S A+HGV+ + LV G G G L + Sbjct: 131 LMHERQLTPVDSDISLGELAFAEPLSVALHGVNRAGELLGKTVLVTGGGTIGSLAVMAAR 190 Query: 184 ARGIHEVTLAGRSDEKLENNRKHFGVKTIDTTKEEIPA--DAYDIVVEAVGLPATQEQAL 241 G + +D LE + + I T +E A D D+ +EA G A + L Sbjct: 191 LAGAAHIIACDIADRPLEVALRVGADQVIRTDREPPRALQDLADVCLEAAGSGAALDTCL 250 Query: 242 AAAARGAQVLMFGVGNPDDKFSVNTYDVFQKQLTIQGAFVNPYTFEDSIALLSSGVVDPL 301 AA RGA+++ G P + ++ ++L GAF F+ ++ L+ G +D Sbjct: 251 LAARRGARIVQIGT-LPAEGLHFPANNIMARELEYVGAFRFGREFDWAVRYLTQGRLDVR 309 Query: 302 PLFSHELDL-DGVEDF 316 PL S +L L VE F Sbjct: 310 PLLSAQLPLAQAVEAF 325 Lambda K H 0.316 0.136 0.393 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: 226 Number of extensions: 13 Number of successful extensions: 4 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: 336 Length of database: 342 Length adjustment: 28 Effective length of query: 308 Effective length of database: 314 Effective search space: 96712 Effective search space used: 96712 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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