Align mannitol 2-dehydrogenase (EC 1.1.1.67) (characterized)
to candidate Ga0059261_2975 Ga0059261_2975 Mannitol-1-phosphate/altronate dehydrogenases
Query= BRENDA::O08355 (493 letters) >FitnessBrowser__Korea:Ga0059261_2975 Length = 479 Score = 239 bits (611), Expect = 1e-67 Identities = 169/486 (34%), Positives = 229/486 (47%), Gaps = 13/486 (2%) Query: 2 KLNKQNLTQLAPEVKLPAYTLADTRQGIAHIGVGGFHRAHQAYYTDALMNTGEGLDWSIC 61 +L + L + + PAY A G+ H G G FHRAHQA Y D ++ W I Sbjct: 3 RLTLETLRDVPAAIVKPAYDPATVSTGVVHFGPGAFHRAHQASYFDTVLANDPR--WGIA 60 Query: 62 GVGLRSEDRKARDDLAGQDYLFTLYELGDTDDTEVRVIGSISDMLLAEDSAQALIDKLAS 121 V LRS + LA QD L+TL L + +RVIG+ + AQ LA Sbjct: 61 AVSLRSGGTV--EALAAQDGLYTLAVLDR--EPSMRVIGAHRTWIGPGGGAQVSA-LLAR 115 Query: 122 PEIRIVSLTITEGGYCIDDSNGEFMAHLPQIQHDLAHPSSPKTVFGFICAALTQRRAAGI 181 PE+RIV+ T+TE GYC+ M+H P I DL P++ G++ L RRAAG Sbjct: 116 PEVRIVTSTVTEKGYCLAGDGTLDMSH-PDIVADL-QGGEPRSFVGWLVQGLAARRAAGA 173 Query: 182 PAFTVMSCDNLPHNGAVTRKALLAFAALHNAELHDWIKAHVSFPNAMVDRITPMTSTAHR 241 F V+ CDNL NG R A +A AA +A+L WI +FP+ MVD ITP + A Sbjct: 174 DPFMVLCCDNLSGNGGKLRAATIALAAARDADLAKWIADTAAFPDTMVDSITPASDDALY 233 Query: 242 LQLHDEHGIDDAWPVVCEPFVQWVLEDKFVNGRPAWEKVGVQFTDDVTPYEEMKIGLLNG 301 ++ E G++D V E F QWV+ + P G T DV YE K+ +LNG Sbjct: 234 ARVAAELGVEDRATVQREAFTQWVIGPYTLADGPDLAGAGATLTSDVGGYERAKLRILNG 293 Query: 302 SHLALTYLGFLKGYRFVHETMNDPLFVAYMRAYMDLDVTPNLAPVPGIDLTDYKQTLVDR 361 H +L YLG G V + M A+ D+ P L PV G+D Y Q +++R Sbjct: 294 LHSSLAYLGLAMGLETVADAMGQAQLAAFAERLALQDIVPVLDPVAGLDHAGYTQAVLER 353 Query: 362 FSNQAIADQLERVCSDGSSKFPKFTVPTINRLIADGRETERAALVVAAWALYLKGVDENG 421 F N AI L ++ DGS K P + T I GR +R A+ VAAW ++ G Sbjct: 354 FRNPAIRHLLSQIAWDGSQKLPYRLLDTTAAAIRAGRPVDRLAVPVAAWMHFVARRAAAG 413 Query: 422 VSYTIP--DPRAEFCQGLVSDDALISQRLLAVEEIFGTAIPNSPEFVAAFERCYGSLRDN 479 + T P P A+ G + A + RL A E +F I + AA +L + Sbjct: 414 EAITDPLAAPLADAAAG--ASPAQLVDRLFAFEAVFRPEIAGHAAYRAAVTAGVEALAEG 471 Query: 480 GVTTTL 485 V L Sbjct: 472 RVEALL 477 Lambda K H 0.321 0.137 0.414 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: 560 Number of extensions: 26 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: 493 Length of database: 479 Length adjustment: 34 Effective length of query: 459 Effective length of database: 445 Effective search space: 204255 Effective search space used: 204255 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 (21.8 bits) S2: 52 (24.6 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