Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate GFF760 PGA1_c07740 putative gluconate 5-dehydrogenase
Query= SwissProt::Q8NK50 (266 letters) >FitnessBrowser__Phaeo:GFF760 Length = 253 Score = 102 bits (255), Expect = 6e-27 Identities = 77/256 (30%), Positives = 121/256 (47%), Gaps = 12/256 (4%) Query: 14 LFSLKGKVVVVTGASGPRGMGIEAARGCAEMGADLAITYSSRKEGAEKNAEELTKEYGVK 73 LF L G +TGAS G+G AA A GA + + + R E E L E Sbjct: 7 LFDLTGHTACITGASS--GLGRRAAIALAAAGAQV-VAVARRAEALES----LCAEIRTS 59 Query: 74 VKVYKVNQSDYNDVERFVNQVVSDFGKIDAFIANAGATANSGVVDGSASDWDHVIQVDLS 133 + +D + ++ ++V + FG D I AG +A WD I ++LS Sbjct: 60 AAHVTADVADRSTLDTLRDRVSAPFGPPDILIHAAGVNTRQPADQVTAEGWDQTIALNLS 119 Query: 134 GTAYCAKAVGAHFKKQGHGSLVITASMSGHVANYPQEQTSYNVAKAGCIHLARSLANEWR 193 + ++A+ K +G G +V AS+ A +P SY +K G L R++A W Sbjct: 120 APFFLSQALVPAMKDRGWGRIVNFASLQTSRA-FPGGM-SYGASKGGIGQLTRAMAEAWS 177 Query: 194 DFA-RVNSISPGYIDTGLSDFIDEKTQELWRSMIP--MGRNGDAKELKGAYVYLVSDASS 250 F N+I PG+ T L+ + E R+ +GRNG ++L G ++L S+AS+ Sbjct: 178 SFGITANAIGPGFFPTELTQAVFEDDARAARNAAQTCIGRNGLMEDLDGPLLFLCSEASA 237 Query: 251 YTTGADIVIDGGYTTR 266 Y TG +++DGG+T + Sbjct: 238 YVTGQLLMVDGGFTAK 253 Lambda K H 0.314 0.131 0.379 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: 146 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: 266 Length of database: 253 Length adjustment: 24 Effective length of query: 242 Effective length of database: 229 Effective search space: 55418 Effective search space used: 55418 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: 42 (22.0 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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