Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate CCNA_01559 CCNA_01559 2-deoxy-D-gluconate 3-dehydrogenase
Query= SwissProt::O93868 (262 letters) >FitnessBrowser__Caulo:CCNA_01559 Length = 255 Score = 120 bits (300), Expect = 4e-32 Identities = 82/257 (31%), Positives = 134/257 (52%), Gaps = 13/257 (5%) Query: 8 SFVNKTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVT-EKVGKEFGVKTKAY 66 S K ++TG N GIG A+AAAGA++A RSA + E +G++F + Sbjct: 6 SLEGKVALITGANTGIGQGIAIALAAAGADIAAAGRSAPTETQAAVEALGRKF----LSI 61 Query: 67 QCDVSNTDIVTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVFN 126 + D S+ + V + + + A G + L+ NAG+ + E + D+ V D N+ VF Sbjct: 62 KADFSSIEPVQRVVDETVAAFGKVDILVNNAGIIRRADSIEFSEADWDAVMDTNLKVVFF 121 Query: 127 TCRAVAKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGLAAE 186 +A AK L++ +G +++S + S G + Y +SK+ + L K LA E Sbjct: 122 LTQAFAKQALKQGFEGGQAKVINIASLL----SFQGGIRVPSYTASKSGLAGLTKILANE 177 Query: 187 WASAGIRVNALSPGYVNTDQTAHMDKKIRDHQA---SNIPLNRFAQPEEMTGQAILLLSD 243 WA+ GI VNA++PGY +T+ T + + +D A + IP R+ +PE++ G A+ L S Sbjct: 178 WATKGINVNAIAPGYFDTNNTEAL-RADQDRNAAILARIPAGRWGRPEDIGGAAVFLASS 236 Query: 244 HATYMTGGEYFIDGGQL 260 + Y+ G +DGG L Sbjct: 237 ASDYVQGITLPVDGGWL 253 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: 135 Number of extensions: 9 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: 255 Length adjustment: 24 Effective length of query: 238 Effective length of database: 231 Effective search space: 54978 Effective search space used: 54978 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