Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate Echvi_4610 Echvi_4610 3-oxoacyl-(acyl-carrier-protein) reductase
Query= SwissProt::Q8NK50 (266 letters) >FitnessBrowser__Cola:Echvi_4610 Length = 248 Score = 150 bits (380), Expect = 2e-41 Identities = 92/250 (36%), Positives = 140/250 (56%), Gaps = 6/250 (2%) Query: 17 LKGKVVVVTGASGPRGMGIEAARGCAEMGADLAITYSSRKEGAEKNAEELTKEYGVKVKV 76 L GK ++TGAS +G+G A A+ GA++A T+ S E + +EL E+GVK K Sbjct: 4 LTGKTALITGAS--KGIGRAIALKYAQEGANVAFTFLSSVEKGQALEKELA-EFGVKAKG 60 Query: 77 YKVNQSDYNDVERFVNQVVSDFGKIDAFIANAGATANSGVVDGSASDWDHVIQVDLSGTA 136 ++ + SD+ E VN+VV +FG +D I NAG T ++ ++ + WD V+ ++L Sbjct: 61 FRSDASDFKAAEELVNEVVKEFGALDVLINNAGVTRDNLLMRMNEEAWDDVMNINLKSCF 120 Query: 137 YCAKAVGAHFKKQGHGSLVITASMSGHVANYPQEQTSYNVAKAGCIHLARSLANEWRDFA 196 KA KQ GS++ S+ G N Q +Y +KAG I +S+A E Sbjct: 121 NTVKAATRTLMKQKAGSIINITSVVGIKGN--AGQANYAASKAGIIGFTKSVALELGSRG 178 Query: 197 -RVNSISPGYIDTGLSDFIDEKTQELWRSMIPMGRNGDAKELKGAYVYLVSDASSYTTGA 255 R N+++PG+I+T +++ +DEKT + WR IPM R G +E+ A V+L SD SSY +G Sbjct: 179 IRSNAVAPGFIETEMTEVLDEKTVQGWRDAIPMKRGGQPEEVANACVFLGSDMSSYVSGQ 238 Query: 256 DIVIDGGYTT 265 I +DG T Sbjct: 239 VIQVDGAMLT 248 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: 137 Number of extensions: 6 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: 248 Length adjustment: 24 Effective length of query: 242 Effective length of database: 224 Effective search space: 54208 Effective search space used: 54208 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 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