Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate Synpcc7942_0684 Synpcc7942_0684 3-oxoacyl-[acyl-carrier-protein] reductase
Query= BRENDA::Q1J2J0 (255 letters) >FitnessBrowser__SynE:Synpcc7942_0684 Length = 249 Score = 146 bits (368), Expect = 5e-40 Identities = 103/250 (41%), Positives = 141/250 (56%), Gaps = 24/250 (9%) Query: 16 LDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFE-------- 67 L R ALVTG ++GIG IA LA AGA+V + N GAA E+ Sbjct: 6 LTDRIALVTGASRGIGRAIALELAAAGAKVAV---NYASSAGAADEVVAAIAAAGGEAFA 62 Query: 68 -RLNVTDADAV----ADLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVF 122 + +V+ V A + R +DVLVNNAGI R+ DDW++VL +NL GVF Sbjct: 63 VKADVSQESEVEALFAAVIERWGRLDVLVNNAGITRDTLLLRMKRDDWQSVLDLNLGGVF 122 Query: 123 WCCREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRG 182 C R + ML + G I++ AS+ G + N QA Y+A+KA VI LT+++A E ASRG Sbjct: 123 LCSRAAAKIMLKQRSGRIINIASVVGEMGN--PGQANYSAAKAGVIGLTKTVAKELASRG 180 Query: 183 VRVNAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASD-AASFV 241 + VNAVAPG+ AT +T + E L+ PLGR E E+A V +LA+D AA+++ Sbjct: 181 ITVNAVAPGFIATDMT-----SELAAEKLLEVIPLGRYGEAAEVAGVVRFLAADPAAAYI 235 Query: 242 TGHTLVVDGG 251 TG + +DGG Sbjct: 236 TGQVINIDGG 245 Lambda K H 0.319 0.134 0.408 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: 174 Number of extensions: 6 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: 255 Length of database: 249 Length adjustment: 24 Effective length of query: 231 Effective length of database: 225 Effective search space: 51975 Effective search space used: 51975 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: 46 (22.3 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