Align Mannitol 2-dehydrogenase; Short=M2DH; Short=MDH; EC 1.1.1.67 (characterized, see rationale)
to candidate WP_011653611.1 RL_RS21725 mannitol dehydrogenase family protein
Query= uniprot:P33216 (477 letters) >NCBI__GCF_000009265.1:WP_011653611.1 Length = 493 Score = 539 bits (1388), Expect = e-158 Identities = 275/476 (57%), Positives = 332/476 (69%), Gaps = 2/476 (0%) Query: 1 MTRSVTRPSYDRKALTPGIVHIGVGNFHRAHQAVYLDDLFALGEGHDWAILGAGVRPTDA 60 + R+ P YDR +L GIVH GVGNFHRAHQA+YLDDLF G HDWAI+GAGV P+DA Sbjct: 13 VARTAAIPGYDRASLKAGIVHFGVGNFHRAHQAIYLDDLFNAGTDHDWAIVGAGVLPSDA 72 Query: 61 RMREALAAQDNLSTVIELDPAGHRARQVGAMVGFLPVEADNAALIEAMSDPRIRIVSLTV 120 MRE LAAQD L+TV+E D AR M+ LPV D AA+I ++DP IRIVS+T+ Sbjct: 73 AMREKLAAQDFLTTVVEQDNNKTAARVTAPMIDILPV-GDAAAIIARLADPEIRIVSMTI 131 Query: 121 TEGGYYVDASGAFDPTHPDIVADAAHPARPATAFGAILAALRARRDAGVTPFTVMSCDNL 180 TEGGY++DASG F+P HP I AD +P P T FG I+A L+AR+D G+ PFTVMSCDN+ Sbjct: 132 TEGGYFIDASGTFNPAHPAIAADGENPNAPKTVFGLIVAGLKARKDKGIGPFTVMSCDNI 191 Query: 181 PGNGHVTRNAVVGLAELYDAELAGWVKAQVAFPNGMVDRITPATGPHERE-LAQGFGLAD 239 P NG VT NAVVG A L D A W++A VAFPNGMVDRITPAT E + L F + D Sbjct: 192 PHNGIVTANAVVGTAALSDPAFADWIRANVAFPNGMVDRITPATSQREIDFLRDNFQIED 251 Query: 240 PVPVTCEPFRQWVIEDHFPAGRPALEKVGVTFTPHVHAYEAMKIRILNGGHAVIAYPSAL 299 PV CE F+QWV+ED F AGRPALEKVGVTF V YE MKIRILNGGHA IAYP+AL Sbjct: 252 SWPVYCEEFKQWVLEDKFTAGRPALEKVGVTFVADVTPYEHMKIRILNGGHAAIAYPAAL 311 Query: 300 MDIQLVHAAMAHPLIAAFLHKVEVEEILPHVPPVPDTSIPDYLTLIESRFSNPEIADTTR 359 MDI VH +M PLI AFL K+E +EI+P VPPVP+TS+ DY LIE R NP+IADT Sbjct: 312 MDIHFVHDSMEDPLIRAFLAKLEKDEIIPIVPPVPNTSLTDYFALIEHRLLNPKIADTIP 371 Query: 360 RLCLDGSNRQPKFIVPSLRDNLAAGTVPKGLVLLSALWCRYCFGTTDSGVVVEPNDPNWT 419 RL DGSNRQPKFI+PS DNL G GL L+SALWCRY G TDSG + ND + Sbjct: 372 RLAQDGSNRQPKFILPSTLDNLGQGRDVVGLALVSALWCRYFAGKTDSGKDIVFNDASAE 431 Query: 420 ALQDRARRAKETPAEWLAMTEVYGDLAQNDLLAAEFAAALEAVWRDGAEAVLRRFL 475 L A +AK+ P+ +L +++G++A+++L FA AL+ +W G L+ +L Sbjct: 432 RLHAAALKAKDDPSAFLVFDDIFGEVAKSELFRKRFAHALKTLWEKGTRETLQLYL 487 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: 690 Number of extensions: 24 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: 477 Length of database: 493 Length adjustment: 34 Effective length of query: 443 Effective length of database: 459 Effective search space: 203337 Effective search space used: 203337 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 24 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