Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate CA265_RS08355 CA265_RS08355 short-chain dehydrogenase
Query= SwissProt::O93868 (262 letters) >FitnessBrowser__Pedo557:CA265_RS08355 Length = 254 Score = 107 bits (268), Expect = 2e-28 Identities = 83/263 (31%), Positives = 127/263 (48%), Gaps = 29/263 (11%) Query: 8 SFVNKTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKAYQ 67 S NK +VTGG GIG A +A GA V +I + A + +++ GV +Y Sbjct: 3 SLKNKKAVVTGGGSGIGKAIATILAKQGAEVHIIELGTEHAQDTLDEIKTNGGVAF-SYG 61 Query: 68 CDVSNTDIVTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVFNT 127 CDVS+ V +I G I+ LI NAG++ + A DF V VNV GV+N Sbjct: 62 CDVSDHQAVAAVFNEI----GNINILINNAGIAHIGKADTTDEADFDRVMRVNVKGVYN- 116 Query: 128 CRAVAKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGLAAEW 187 C A ++ G I+ +S+++ I G + Y+++K A + +A ++ Sbjct: 117 CLHAAIPQIRLSGGGVIINMASIAALI-------GLPDRFVYSAAKGAVKAITMSVAKDY 169 Query: 188 ASAGIRVNALSPGYVNT------------DQTAHMDKKIRDHQASNIPLNRFAQPEEMTG 235 IR N++SP V+T D M +K+ Q P+ R A+PEE+ Sbjct: 170 IGENIRCNSISPARVHTPFVDGFLQKNYPDNIPEMFEKLSKTQ----PIGRMAKPEEVGA 225 Query: 236 QAILLLSDHATYMTGGEYFIDGG 258 A+ L SD A+++TG +Y IDGG Sbjct: 226 LALYLCSDEASFITGCDYPIDGG 248 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: 155 Number of extensions: 8 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: 262 Length of database: 254 Length adjustment: 24 Effective length of query: 238 Effective length of database: 230 Effective search space: 54740 Effective search space used: 54740 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: 47 (22.7 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