Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate GFF2263 HP15_2213 3-ketoacyl-(acyl-carrier-protein) reductase
Query= SwissProt::O93868 (262 letters) >FitnessBrowser__Marino:GFF2263 Length = 247 Score = 113 bits (282), Expect = 4e-30 Identities = 77/252 (30%), Positives = 123/252 (48%), Gaps = 9/252 (3%) Query: 7 ISFVNKTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKAY 66 +S KT +VTG RGIG A RA+AA GA V S A +T + + G K Sbjct: 1 MSLEGKTALVTGATRGIGQAIARALAAQGAEVVGTATSEAGAESITNDL-QSAGYKGYGM 59 Query: 67 QCDVSNTDIVTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVFN 126 +V++ + ++++ GA L+ NAG++ L +D+ V + N+ V+ Sbjct: 60 VMNVADPASIEAGLKELTEKSGAPLILVNNAGITRDNLLMRLKDDDWASVLETNLSSVYR 119 Query: 127 TCRAVAKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGLAAE 186 T +AV + + K + G I+ SS+ + + N N Y ++KA + LA E Sbjct: 120 TSKAVLR-GMAKAKWGRIINISSVVAGMGNAGQGN-------YCAAKAGVEGFTRSLAKE 171 Query: 187 WASAGIRVNALSPGYVNTDQTAHMDKKIRDHQASNIPLNRFAQPEEMTGQAILLLSDHAT 246 ++ GI N ++PG+++TD T +D K R IP R +PEE+ L SD A Sbjct: 172 MSNRGITANCVAPGFIDTDMTKKLDDKQRGAMLEIIPAGRLGEPEEVAAVVAFLASDAAG 231 Query: 247 YMTGGEYFIDGG 258 Y+TG ++GG Sbjct: 232 YVTGETINVNGG 243 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: 142 Number of extensions: 5 Number of successful extensions: 2 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: 247 Length adjustment: 24 Effective length of query: 238 Effective length of database: 223 Effective search space: 53074 Effective search space used: 53074 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