Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate WP_007680610.1 BN137_RS02010 sugar kinase
Query= metacyc::MONOMER-12748 (320 letters) >NCBI__GCF_000319285.1:WP_007680610.1 Length = 312 Score = 343 bits (879), Expect = 4e-99 Identities = 179/308 (58%), Positives = 218/308 (70%), Gaps = 2/308 (0%) Query: 4 IDILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGNDSL 63 +D+++ GE MAMFVA GDLAQV+HF KR+AGA+ NVA GLARLG V+W+SRVGNDS Sbjct: 5 LDVITIGEAMAMFVATEPGDLAQVEHFFKRVAGAELNVATGLARLGLNVSWVSRVGNDSF 64 Query: 64 GRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAISDLD 123 GRFVL L EG+ R V D PTGFQLKS+ G DP VEYFR+GSAASHL+ D + Sbjct: 65 GRFVLSQLEKEGISTRGVTIDDRFPTGFQLKSKVTDGTDPSVEYFRKGSAASHLSGEDFN 124 Query: 124 -PALLRARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPSEALMIR 182 P ARHLH +G+ ALS S+ EL H ++ G ++SFDPNLRP LW SEA M+ Sbjct: 125 APLFYSARHLHLSGVAAALSGSSYELLDHAARAMKTQGKTISFDPNLRPVLWKSEAEMVE 184 Query: 183 EINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYYRTQL-D 241 ++N LA LA WVLPGL EG +LTG+ P IA FYL +G +AVVIK GA GA+Y+T + Sbjct: 185 KLNHLATLADWVLPGLKEGHILTGQQHPEGIADFYLSRGVKAVVIKTGADGAWYQTASGE 244 Query: 242 AGFVEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRGDMEGL 301 G VE V V VVDTVGAGDGFAVG+ISALLE + + +A R N IG+ A+Q +GD EGL Sbjct: 245 QGTVEAVKVDNVVDTVGAGDGFAVGVISALLEGKTLHQAATRGNKIGALAIQVQGDSEGL 304 Query: 302 PLRHELPE 309 P R +L E Sbjct: 305 PTRAQLGE 312 Lambda K H 0.321 0.138 0.414 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: 361 Number of extensions: 16 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: 320 Length of database: 312 Length adjustment: 27 Effective length of query: 293 Effective length of database: 285 Effective search space: 83505 Effective search space used: 83505 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 (21.9 bits) S2: 48 (23.1 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