Align xylitol 2-dehydrogenase (EC 1.1.1.9) (characterized)
to candidate Synpcc7942_0459 Synpcc7942_0459 glutathione-dependent formaldehyde dehydrogenase
Query= reanno::WCS417:GFF3461 (359 letters) >FitnessBrowser__SynE:Synpcc7942_0459 Length = 369 Score = 106 bits (264), Expect = 1e-27 Identities = 100/366 (27%), Positives = 159/366 (43%), Gaps = 45/366 (12%) Query: 20 LERIGKPQARANELVIRIAACGICASDCKCHSGAAMFWGGDNPWVKAPVVPGHEFFGYVV 79 +E + +A E+++++ A G+C +D SGA +P P + GHE G VV Sbjct: 17 IEEVDVQAPQAGEVMVKLVATGVCHTDAFTLSGA-------DPEGIFPCILGHEGAGIVV 69 Query: 80 EAGEGAEEHFEVAVGDKVIAEQIVPCGKCRFCKSGKYWMCEVHNIFGFQREVAEGG---- 135 E GEG VAVGD VI CG+C+FCKSGK +C+ + + +G Sbjct: 70 EVGEGVTS---VAVGDHVIPLYTPECGECKFCKSGKTNLCQAIRATQGKGLMPDGTSRFS 126 Query: 136 --------------MAQYMRIPKTAIVHKIPESVSLEDSALVEPMACSIHT-----VNRG 176 ++Y +P+ AI KI + +L+ L + C I T +N Sbjct: 127 LNGQPIYHFMGTSTFSEYTVLPEIAIA-KINPAAALDKVCL---LGCGITTGIGAVLNTA 182 Query: 177 DIQLDDVVVIAGAGTLGLCMVQVAALKTPKKLVVIDMVDERLELAKKFGADVVINPSRDN 236 ++ V + G G +GL ++Q A L +++ ID+ ++ E AK+ GA INP + Sbjct: 183 KVEPGSTVAVFGLGGVGLSVIQGAVLAKASRILAIDINPDKAEFAKQLGATDFINPKDYD 242 Query: 237 --AREIINGLTDNYGCDVYIETTGVPAGVTQGLDLIRK-LGRFVEFSVFGAETSVDWS-- 291 +E+I LTD G D E G + L+ K G V GA + Sbjct: 243 RPIQEVIVELTDG-GVDYSFEAIGNVNTMRAALESCHKGWGESTIIGVAGAGQEISTRPF 301 Query: 292 --IIGDRKELDVRGAHLGPYCYPIAIDLFERGLVTSKGIVTHDFPLDDWAEAFELANSTK 349 + G G G P ++ + G + VT PL++ EAFE ++ K Sbjct: 302 QLVTGRVWRGSAFGGVKGRSQLPGYVEQYLNGQIKVDEFVTETRPLEEINEAFEDMHAGK 361 Query: 350 SIKVLL 355 I+ ++ Sbjct: 362 VIRTVI 367 Lambda K H 0.322 0.139 0.432 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: 292 Number of extensions: 18 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: 359 Length of database: 369 Length adjustment: 29 Effective length of query: 330 Effective length of database: 340 Effective search space: 112200 Effective search space used: 112200 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: 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