Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate PfGW456L13_4129 Oxidoreductase, short chain dehydrogenase/reductase family
Query= SwissProt::O93868 (262 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4129 Length = 248 Score = 104 bits (260), Expect = 2e-27 Identities = 82/260 (31%), Positives = 113/260 (43%), Gaps = 24/260 (9%) Query: 6 TISFVNKTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKA 65 T + K ++ GG+RGIG A + +AA GA VA Y S+ E + G K A Sbjct: 3 TQNLSGKVALIQGGSRGIGAAIVKRLAAEGATVAFTYVSSTAKAEELQDSITAKGGKALA 62 Query: 66 YQCDVSNTDIVTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVF 125 + D ++ D + + G + L+ NAGV V P E EDF +NV VF Sbjct: 63 IKADSADADAIRSAVSATVEAFGRLDILVNNAGVLAVAPLAEFKLEDFDQTLAINVRSVF 122 Query: 126 NTCRAVAKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVF----YNSSKAACSNLVK 181 +A A+ + +IIN S N Y SK+A L K Sbjct: 123 IATQAAARHMTE-------------GGRIINIGSTNADRMPFAGGGPYAMSKSALVGLTK 169 Query: 182 GLAAEWASAGIRVNALSPGYVNTDQTAHMDKKIRDHQASNIPL---NRFAQPEEMTGQAI 238 GLA + GI +N + PG V+TD M+ D S IPL R+ + EE+ Sbjct: 170 GLARDLGPQGITINNVQPGPVDTD----MNPAEGDFAESLIPLMAVGRYGKAEEIASFVA 225 Query: 239 LLLSDHATYMTGGEYFIDGG 258 L+S A Y+TG IDGG Sbjct: 226 YLVSPEAGYITGASLTIDGG 245 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: 133 Number of extensions: 5 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: 248 Length adjustment: 24 Effective length of query: 238 Effective length of database: 224 Effective search space: 53312 Effective search space used: 53312 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