Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate WP_150110915.1 ACIX8_RS18080 sugar kinase
Query= BRENDA::Q9WXS2 (339 letters) >NCBI__GCF_000178955.2:WP_150110915.1 Length = 340 Score = 157 bits (398), Expect = 3e-43 Identities = 114/344 (33%), Positives = 168/344 (48%), Gaps = 21/344 (6%) Query: 10 MLRLSPPDHKRIFQTDSFDVTYGGAEANVAAFLAQ-MGLDAYFVTKLPNNPLGDAAAGHL 68 MLR P + RI + +F V GG E NVA L + L VT L +NP+G + Sbjct: 1 MLRFDPGEG-RIVGSRNFRVWEGGGEYNVARGLRRCFDLRTAIVTALVDNPVGRLVEDLM 59 Query: 69 RKFGVKTDYI-------ARGGNRIGIYFLEIGASQRPSKVVYDRAHSAISEAKREDFDWE 121 + GV ++ R GIYFLE G R + DR +AIS+ K D DW+ Sbjct: 60 LQGGVDLSHVLWRDFDGVGREARNGIYFLERGFGVRGGMGMMDRGSTAISQMKPGDVDWD 119 Query: 122 KIL--DGARWFHFSGITPPLGKELPLILEDALKVANEKGVTVSCDLNYRARLWTKEEAQK 179 +I +G +WFH G+ L ++ ++ +A+ A G VS D NYR LW +K Sbjct: 120 EIFQDEGVQWFHTGGVMAALSEDSTEVVREAMAAAKRHGTIVSFDCNYRPSLWKSRGGRK 179 Query: 180 VMIP----FMEYVDVLIANEEDIEKVLGISVEGLDLKTGKLNREAYAKIAEEVTRKY-NF 234 I M VDVL +E DI LG + +G T +++ +A VT ++ N Sbjct: 180 GSIDVNRSLMPLVDVLFGHEGDIAATLGEASQGPVWHT----LDSFRAMAGRVTAEFGNL 235 Query: 235 KTVGITLRESISATVNYWSVMVFENGQPHFSNRYE-IHIVDRVGAGDSFAGALIYGSLMG 293 K + T+R +A N WS + G+ + R++ + I+DRVG GDSFA LIYG L G Sbjct: 236 KVIASTVRRLHTANRNGWSAFGYAEGEAYEGLRFDDLEILDRVGGGDSFASGLIYGLLQG 295 Query: 294 FDSQKKAEFAAAASCLKHTIPGDFVVLSIEEIEKLASGATSGRV 337 + + A L T GD + ++ E+E+L +G ++G V Sbjct: 296 KGMRYALDCGIAHGALAMTTAGDSSMATLPEVERLMAGGSAGTV 339 Lambda K H 0.319 0.136 0.397 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: 307 Number of extensions: 14 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: 339 Length of database: 340 Length adjustment: 28 Effective length of query: 311 Effective length of database: 312 Effective search space: 97032 Effective search space used: 97032 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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