Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate Ac3H11_3445 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= SwissProt::Q8NK50 (266 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3445 Length = 257 Score = 149 bits (375), Expect = 8e-41 Identities = 93/252 (36%), Positives = 140/252 (55%), Gaps = 7/252 (2%) Query: 14 LFSLKGKVVVVTGASGPRGMGIEAARGCAEMGADLAITYSSRKEGAEKNAEELTKEYGVK 73 LF L G+V +VTG G RG+G++ A EMGA LAIT E AE + Y V Sbjct: 6 LFDLTGQVALVTG--GSRGLGLQMAEALGEMGAKLAITARKADELAEAKKHLEAQGYEVL 63 Query: 74 VKVYKVNQSDYNDVERFVNQVVSDFGKIDAFIANAGATANSGVVDGSASDWDHVIQVDLS 133 V + +++ D+ V+QVV FG ID + NAGAT + D + W V+ +++S Sbjct: 64 TVVNDLQKTE--DIPGLVDQVVERFGTIDILVNNAGATWGAKAEDYPDAAWHKVMDLNVS 121 Query: 134 GTAYCAKAVGAHFK-KQGHGSLVITASMSGHVANYPQEQT-SYNVAKAGCIHLARSLANE 191 + ++ VG +G GS+++TAS++ P T +YN +KA +H AR+LA+E Sbjct: 122 APFFLSREVGKRCMIPRGKGSIIVTASVAALKGTPPGMNTIAYNTSKAAALHFARTLASE 181 Query: 192 WRDFA-RVNSISPGYIDTGLSDFIDEKTQELWRSMIPMGRNGDAKELKGAYVYLVSDASS 250 W + RVN+I PG+ + ++ + EK P+ R G ++LKGA V+L S+AS Sbjct: 182 WGHYGVRVNAICPGFFPSKMASGLIEKLGPAMIERTPLRRIGGEEDLKGAVVFLASNASR 241 Query: 251 YTTGADIVIDGG 262 + TG IV+DGG Sbjct: 242 HITGESIVVDGG 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: 167 Number of extensions: 10 Number of successful extensions: 5 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: 257 Length adjustment: 25 Effective length of query: 241 Effective length of database: 232 Effective search space: 55912 Effective search space used: 55912 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