Align Mannitol 2-dehydrogenase; M2DH; MDH; EC 1.1.1.67 (uncharacterized)
to candidate HSERO_RS02215 HSERO_RS02215 D-arabinitol 4-dehydrogenase
Query= curated2:P33216 (477 letters) >FitnessBrowser__HerbieS:HSERO_RS02215 Length = 477 Score = 239 bits (610), Expect = 1e-67 Identities = 154/406 (37%), Positives = 214/406 (52%), Gaps = 12/406 (2%) Query: 1 MTRSVTRPSYDRK-ALTPGIVHIGVGNFHRAHQAVYLDDLFALGEGHDWAILGAGVRPTD 59 MTR+ T D +LT +HIG G+FHRAHQAVYL+ L G W + A +R Sbjct: 1 MTRTATSIDQDAADSLT--WLHIGAGSFHRAHQAVYLNALRESGADRRWQLALANIRADM 58 Query: 60 ARMREALAAQDNLSTVIELDPAGHRARQVGAMVG-FLPVEADNAALIEAMSDPRIRIVSL 118 + + EALA Q T+ + P G R+ Q A +G LP +A LI A ++ R RI+S Sbjct: 59 SPLLEALARQQGQYTLETVTPQGQRSYQRIASIGRILPWDAQLTQLIAAGAEERTRIISF 118 Query: 119 TVTEGGYYVDASGAFDPTHPDIVADAA----HPARPATAFGAILAALRARRDAGV-TPFT 173 TVTEGGYY+D D ++ D+ D P T +GAI A L AR A T Sbjct: 119 TVTEGGYYLDHQHQLDTSNADLAEDLRCALDGSGAPRTIYGAIAAILHARSQAHPQAALT 178 Query: 174 VMSCDNLPGNGHVTRNAVVGLAELY-DAELAGWVKAQVAFPNGMVDRITPA-TGPHEREL 231 +++CDNL NG R+ + L + L W++A PN MVDRITP T + + Sbjct: 179 LLNCDNLRHNGERFRDGLRQFLTLRGETALVSWMQANTTSPNAMVDRITPRPTAAVAQRV 238 Query: 232 AQGFGLADPVPVTCEPFRQWVIEDHFPAGRPALEKVGVTFTPHVHAYEAMKIRILNGGHA 291 + G+ DP + E F QWVIED F AGRP LE+ GV V YE KIRILN H+ Sbjct: 239 KEATGIDDPCALMGESFIQWVIEDDFKAGRPRLEEAGVEMVQSVLPYEEAKIRILNASHS 298 Query: 292 VIAYPSALMDIQLVHAAMAHPLIAAFLHKVEVEEILPHVPPVPDTSIPDYLTLIESRFSN 351 IA+ L +Q +H I + ++++ + P P + Y +RFSN Sbjct: 299 CIAWAGTLAGLQYIHEGTLRDDIRQMAYDYVTQDVIACLTPSP-IDLAAYRDTTLARFSN 357 Query: 352 PEIADTTRRLCLDGSNRQPKFIVPSLRDNLAAGTVPKGLVLLSALW 397 P I DT +R+ DG ++ P FI P+L++++AAG P+ +L AL+ Sbjct: 358 PAIQDTNQRVAADGYSKIPGFIRPTLQESMAAGRDPRATAMLPALF 403 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: 519 Number of extensions: 33 Number of successful extensions: 6 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: 477 Length adjustment: 33 Effective length of query: 444 Effective length of database: 444 Effective search space: 197136 Effective search space used: 197136 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: 51 (24.3 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