Align mannitol 2-dehydrogenase (NADP+) (EC 1.1.1.138) (characterized)
to candidate Echvi_3219 Echvi_3219 Zn-dependent alcohol dehydrogenases
Query= BRENDA::Q1ACW3 (345 letters) >FitnessBrowser__Cola:Echvi_3219 Length = 343 Score = 112 bits (279), Expect = 2e-29 Identities = 86/273 (31%), Positives = 126/273 (46%), Gaps = 15/273 (5%) Query: 3 LPATMKALRYDK-PESYAVVEVPLPTLRDNDVLIKVKACGVCGTDLHIHEGEFIAK--FP 59 LP TMKA + + + E+P+ +N +L++V A GVC TDLH +G++ K P Sbjct: 2 LPKTMKAAVVTEFGQPLKIEEIPVKAPNENQILVQVMASGVCHTDLHAADGDWPVKPRLP 61 Query: 60 LIPGHETVGVVAAIGKDVKGFTVGERVCAD-NSELCNECFYCRRGQLLLCEKFEAHGVTM 118 LIPGHE +G VAA+G +VK G+ V C C +C G LCE G ++ Sbjct: 62 LIPGHEGIGYVAAVGSNVKNTKEGDIVGVPWLYSACGHCEHCITGWETLCESQVNGGYSV 121 Query: 119 DGGFAEYCAYPAGKVFKIHNLSDVDATLLEPASCAA----HGLEKIAPKIGSSVLMFGAG 174 DGG+AEY V + +D + P CA GL++ + G V + G G Sbjct: 122 DGGYAEYVLADPNYVGRFSGA--IDFVQMAPILCAGVTVYKGLKETEVRPGQWVAISGIG 179 Query: 175 PTGLCLAQLPHNGASHVVIAAPEGLKMDLAKKLDCADIYVPLSRSNPQAQFDQIKSDNPY 234 G Q HV+ K++LAKKL + ++ NP + K Sbjct: 180 GLGHVAVQYAKAMGLHVLAVDVSDDKLNLAKKLGADRV---VNGKNPDEVMNARKETG-- 234 Query: 235 GFDIVVEATGSPKILEDAINYVRRGGKLVVYGV 267 G V+ SP A++ +RR G LV+ G+ Sbjct: 235 GVHGVLVTAVSPVAFRQALDLLRRKGTLVMNGL 267 Lambda K H 0.320 0.138 0.420 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: 279 Number of extensions: 16 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: 345 Length of database: 343 Length adjustment: 29 Effective length of query: 316 Effective length of database: 314 Effective search space: 99224 Effective search space used: 99224 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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