Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate WP_011384008.1 AMB_RS08070 NAD(P)-dependent oxidoreductase
Query= SwissProt::O93868 (262 letters) >NCBI__GCF_000009985.1:WP_011384008.1 Length = 245 Score = 96.7 bits (239), Expect = 4e-25 Identities = 81/263 (30%), Positives = 126/263 (47%), Gaps = 34/263 (12%) Query: 12 KTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKAYQC--- 68 KT++VTG +RGIG A R A G V R+ V KE + + + C Sbjct: 5 KTVVVTGASRGIGHAIARRFLAEGWRVITCARA---------DVPKECMID-RNWACHIV 54 Query: 69 -DVSNTDIVTKTIQQIDADLGA--ISGLIANAGVSVVKPATELTH------EDFKFVYDV 119 D+++ + Q +A LGA + L+ NAGVS P E + +K V+++ Sbjct: 55 ADLADPASAQDFVAQANAWLGAEPLHALVNNAGVSPKTPYKERLGVLNGPIDGWKDVFEL 114 Query: 120 NVFGVFNTCRAVAKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNL 179 N F R A + KG+IV +S++ ++ + GS Y++SKAA S L Sbjct: 115 NFFAPLRLARGFASAL--HRGKGAIVNITSIAGHYVHPFA--GSA----YSTSKAALSGL 166 Query: 180 VKGLAAEWASAGIRVNALSPGYVNTDQTAHMDKKIRDHQASNIPLNRFAQPEEMTGQAIL 239 + +AAE A G+RVNA++PG + T+ + + + IPL R PE++ G Sbjct: 167 TREMAAEMAQLGVRVNAVAPGEIRTEMISAEYEAL----VPRIPLERMGTPEDVAGTVFR 222 Query: 240 LLSDHATYMTGGEYFIDGGQLIW 262 L Y+TG E F+ GGQ ++ Sbjct: 223 LCGSDFDYVTGTEVFVTGGQHLY 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: 124 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: 245 Length adjustment: 24 Effective length of query: 238 Effective length of database: 221 Effective search space: 52598 Effective search space used: 52598 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