Align Mannitol 2-dehydrogenase; Short=M2DH; Short=MDH; EC 1.1.1.67 (characterized, see rationale)
to candidate 3607557 Dshi_0969 Mannitol dehydrogenase domain (RefSeq)
Query= uniprot:P33216 (477 letters) >FitnessBrowser__Dino:3607557 Length = 499 Score = 513 bits (1321), Expect = e-150 Identities = 264/473 (55%), Positives = 314/473 (66%), Gaps = 1/473 (0%) Query: 4 SVTRPSYDRKALTPGIVHIGVGNFHRAHQAVYLDDLFALGEGHDWAILGAGVRPTDARMR 63 ++ RP YDR LTPGIVHIGVGNFHRAHQA YL L G+ DWAI+GAGVRP DA MR Sbjct: 16 AIERPRYDRSRLTPGIVHIGVGNFHRAHQAWYLHRLMQAGQALDWAIIGAGVRPYDAAMR 75 Query: 64 EALAAQDNLSTVIELDPAGHRARQVGAMVGFLPVEADNAALIEAMSDPRIRIVSLTVTEG 123 + L AQD L+T+IEL P A VG+M+ +LP+ N LI M+DP IRIV++TVTE Sbjct: 76 DKLLAQDCLTTLIELAPDNVSAEVVGSMIDYLPIVDGNGPLIAQMADPAIRIVAMTVTES 135 Query: 124 GYYVD-ASGAFDPTHPDIVADAAHPARPATAFGAILAALRARRDAGVTPFTVMSCDNLPG 182 GYY+D + FD +HPD+V DAA P RP TAFGAI+AALRARR AG PFT +SCDNL G Sbjct: 136 GYYIDPVTKGFDASHPDLVHDAAQPDRPRTAFGAIVAALRARRAAGHGPFTCLSCDNLQG 195 Query: 183 NGHVTRNAVVGLAELYDAELAGWVKAQVAFPNGMVDRITPATGPHERELAQGFGLADPVP 242 NG + R VV LA L D LA W+ +FPN MVD I PATGP E LA FG+ D Sbjct: 196 NGDILRQTVVSLARLTDPALADWIDTHASFPNSMVDCIAPATGPKELALAAQFGIRDVAV 255 Query: 243 VTCEPFRQWVIEDHFPAGRPALEKVGVTFTPHVHAYEAMKIRILNGGHAVIAYPSALMDI 302 VT E FRQWVIED F AGRP + VG TF+ VHAYE MKIRILN GH V+A + I Sbjct: 256 VTHEAFRQWVIEDEFCAGRPNWDAVGATFSDDVHAYETMKIRILNAGHQVLANAGENLGI 315 Query: 303 QLVHAAMAHPLIAAFLHKVEVEEILPHVPPVPDTSIPDYLTLIESRFSNPEIADTTRRLC 362 + + MAHP IAAF KV+ EEI P V PVP + Y+ LIE+RF+NP I DTTRR+ Sbjct: 316 ETISGCMAHPGIAAFFGKVQREEIAPTVAPVPGKTPASYVNLIETRFANPRIVDTTRRVA 375 Query: 363 LDGSNRQPKFIVPSLRDNLAAGTVPKGLVLLSALWCRYCFGTTDSGVVVEPNDPNWTALQ 422 DGS R P F++P +RD LAAG +GL L+ ALW R C G + G + PNDP W L Sbjct: 376 FDGSARHPGFVLPIVRDQLAAGRSVEGLALVEALWARMCAGVREDGTEIAPNDPLWDRLA 435 Query: 423 DRARRAKETPAEWLAMTEVYGDLAQNDLLAAEFAAALEAVWRDGAEAVLRRFL 475 AR A+ PA WL T +YGDL Q++ A F A L +W G EA LRR++ Sbjct: 436 PVARAARTDPALWLGQTGLYGDLKQSEPFADAFCAWLVLIWDKGCEAALRRYI 488 Lambda K H 0.321 0.136 0.418 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: 703 Number of extensions: 24 Number of successful extensions: 2 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: 477 Length of database: 499 Length adjustment: 34 Effective length of query: 443 Effective length of database: 465 Effective search space: 205995 Effective search space used: 205995 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: 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