Align NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; EC 1.1.1.138 (characterized)
to candidate CCNA_01747 CCNA_01747 3-oxoacyl-(acyl-carrier protein) reductase
Query= SwissProt::Q8NK50 (266 letters) >FitnessBrowser__Caulo:CCNA_01747 Length = 246 Score = 117 bits (293), Expect = 2e-31 Identities = 83/251 (33%), Positives = 127/251 (50%), Gaps = 11/251 (4%) Query: 14 LFSLKGKVVVVTGASGPRGMGIEAARGCAEMGADLAITYSSRKEGAEKNAEELTKEYGVK 73 +F L GK +VTGA+G G+G AR GA + + S +E A EL E G + Sbjct: 1 MFDLTGKTALVTGATG--GIGGAIARALHAQGAHVVL--SGTRESA---LAELKAELGER 53 Query: 74 VKVYKVNQSDYNDVERFVNQVVSDFGK-IDAFIANAGATANSGVVDGSASDWDHVIQVDL 132 N SD V+ V + G +D IANAG T + +V DWD VI+V+L Sbjct: 54 ASTVVANLSDAEQVDGLVAKAEEAAGAPLDIVIANAGVTRDGLIVRMKDEDWDTVIKVNL 113 Query: 133 SGTAYCAKAVGAHFKKQGHGSLVITASMSGHVANYPQEQTSYNVAKAGCIHLARSLANEW 192 G ++A K+ G ++ S+ G N QT+Y +KAG I +++LA E Sbjct: 114 EGYFRLSRAAAKGMMKRRAGRIIGITSIVGVTGN--PGQTNYAASKAGMIGFSKALAQEL 171 Query: 193 RDFA-RVNSISPGYIDTGLSDFIDEKTQELWRSMIPMGRNGDAKELKGAYVYLVSDASSY 251 VN ++PG+I + ++D ++E+ + S IP G+ G+ ++ A VYL SD + Y Sbjct: 172 ASRGVTVNCVAPGFIASPMTDALNEQQKAGILSTIPAGKLGEGADIAAACVYLASDQAGY 231 Query: 252 TTGADIVIDGG 262 TG + ++GG Sbjct: 232 VTGQTLHVNGG 242 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: 163 Number of extensions: 7 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: 266 Length of database: 246 Length adjustment: 24 Effective length of query: 242 Effective length of database: 222 Effective search space: 53724 Effective search space used: 53724 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