Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate WP_011382581.1 AMB_RS00675 KR domain-containing protein
Query= SwissProt::O93868 (262 letters) >NCBI__GCF_000009985.1:WP_011382581.1 Length = 238 Score = 91.7 bits (226), Expect = 1e-23 Identities = 78/253 (30%), Positives = 114/253 (45%), Gaps = 23/253 (9%) Query: 8 SFVNKTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKAYQ 67 S K +VTGG RGIG A + A GA V V + G E + Sbjct: 3 SLAGKLALVTGGTRGIGAAIAARLLADGAKVMV----------TGTRPGGEGPAGSGYLA 52 Query: 68 CDVSNTDIVTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVFNT 127 D ++ T +Q A LG + L+ NAG++ V P E+ DF + VNV F Sbjct: 53 VDFADAAATTAFAEQA-AGLG-VDILVNNAGINKVSPFAEIDPADFARIQQVNVTAPFLL 110 Query: 128 CRAVAKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGLAAEW 187 RAV +Q + G IV SS+ +I + Y++SK A L LAAE Sbjct: 111 ARAVVP-GMQAKAWGRIVTVSSIWGRISRAG-------RGAYSASKFAVDGLTAALAAEV 162 Query: 188 ASAGIRVNALSPGYVNTDQTAHM--DKKIRDHQASNIPLNRFAQPEEMTGQAILLLSDHA 245 A GI N ++PG+++T+ T + + I++ A +P R +PEE+ L Sbjct: 163 AQFGILANCVAPGFIDTELTRQVLGEDGIKELTA-QVPARRLGRPEEIAAFVAWLAGPEN 221 Query: 246 TYMTGGEYFIDGG 258 +Y++G IDGG Sbjct: 222 SYISGQNLVIDGG 234 Lambda K H 0.317 0.130 0.372 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: 131 Number of extensions: 7 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: 262 Length of database: 238 Length adjustment: 24 Effective length of query: 238 Effective length of database: 214 Effective search space: 50932 Effective search space used: 50932 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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