Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Cla h 8; EC 1.1.1.138 (characterized)
to candidate Pf1N1B4_451 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= SwissProt::P0C0Y5 (267 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_451 Length = 247 Score = 123 bits (308), Expect = 4e-33 Identities = 83/249 (33%), Positives = 131/249 (52%), Gaps = 7/249 (2%) Query: 16 LSLKGKVVVVTGASGPKGMGIEAARGCAEMGAAVAITYASRAQGAEENVKELEKTYGIKA 75 +SL+GKV +VTGAS +G+G A GA V T A+ A GAE L++ GI+ Sbjct: 1 MSLQGKVALVTGAS--RGIGQAIALELGRQGAVVIGT-ATSASGAERIAATLKEN-GIQG 56 Query: 76 KAYKCQVDSYESCEKLVKDVVADFGQIDAFIANAGATADSGILDGSVEAWNHVVQVDLNG 135 + V S ES ++ + FG + NAG T D+ ++ + W+ VV +LN Sbjct: 57 TGLELNVTSDESVAAVLASIQEQFGAPAILVNNAGITRDNLMMRMKDDEWHDVVDTNLNS 116 Query: 136 TFHCAKAVGHHFKERGTGSLVITASMSGHIANFPQEQTSYNVAKAGCIHMARSLANEWRD 195 F +K V + G ++ S+ G + N Q +Y AKAG +R+LA E Sbjct: 117 LFRLSKGVLRGMTKARWGRIISIGSVVGAMGN--AGQVNYAAAKAGLEGFSRALAREVGS 174 Query: 196 FA-RVNSISPGYIDTGLSDFVPKETQQLWHSMIPMGRDGLAKELKGAYVYFASDASTYTT 254 + VNS++PG+IDT ++ +P+ ++ + IP+GR G A+E+ + ASD + Y T Sbjct: 175 RSITVNSVAPGFIDTDMTRELPEAQREALQTQIPLGRLGQAQEIASVVAFLASDGAAYVT 234 Query: 255 GADLLIDGG 263 GA + ++GG Sbjct: 235 GATIPVNGG 243 Lambda K H 0.316 0.131 0.383 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: 159 Number of extensions: 8 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: 267 Length of database: 247 Length adjustment: 24 Effective length of query: 243 Effective length of database: 223 Effective search space: 54189 Effective search space used: 54189 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 (21.6 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