Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate WP_086510996.1 BZY95_RS16175 sugar kinase
Query= metacyc::MONOMER-12748 (320 letters) >NCBI__GCF_002151265.1:WP_086510996.1 Length = 334 Score = 365 bits (938), Expect = e-106 Identities = 195/311 (62%), Positives = 228/311 (73%), Gaps = 5/311 (1%) Query: 2 PDIDILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGND 61 P +IL+FGE M +FVA+ G LA+V+HF +RIAGAD+NVAIGLARLGF V WLSRVG D Sbjct: 12 PSPEILTFGEAMTLFVADAPGHLAEVEHFQRRIAGADTNVAIGLARLGFHVGWLSRVGAD 71 Query: 62 SLGRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAISD 121 S G F+ TL AEGL+CR + DP HPTG K R GG DPRVEYFRRGSAASHL+ D Sbjct: 72 SFGTFIRHTLEAEGLNCRHLGVDPDHPTGLLFKERALGGADPRVEYFRRGSAASHLSPKD 131 Query: 122 LDPALLRA-RHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPSEALM 180 A RHLHATGIPPALS SAR+LS H++ R G S+SFDPNLRP+LW SEA M Sbjct: 132 AAEVDFTALRHLHATGIPPALSPSARDLSRHMLAQARQVGASISFDPNLRPSLWKSEAEM 191 Query: 181 IREINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYYR--- 237 +N LAAL+ WVLPGLAEGRLLTG++ P IA FYL++GA AV+IKLG G++YR Sbjct: 192 RDTLNALAALSDWVLPGLAEGRLLTGQNTPEAIADFYLERGASAVIIKLGPEGSFYRGSL 251 Query: 238 -TQLDAGFVEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRG 296 +L+ V G V +VVDTVGAGDGFAVG +SALL+ R EAV+R N IGS AVQ G Sbjct: 252 GGKLETFSVPGFAVDEVVDTVGAGDGFAVGAVSALLDGRSPWEAVRRGNLIGSLAVQVVG 311 Query: 297 DMEGLPLRHEL 307 DMEGLP R +L Sbjct: 312 DMEGLPSREQL 322 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: 427 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: 334 Length adjustment: 28 Effective length of query: 292 Effective length of database: 306 Effective search space: 89352 Effective search space used: 89352 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 Apr 09 2024. 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