Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate WP_049904537.1 C447_RS14190 sugar kinase
Query= metacyc::MONOMER-12748 (320 letters) >NCBI__GCF_000336675.1:WP_049904537.1 Length = 318 Score = 229 bits (583), Expect = 9e-65 Identities = 133/303 (43%), Positives = 174/303 (57%), Gaps = 2/303 (0%) Query: 6 ILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGNDSLGR 65 +++ GETM + G + F K +AGA++NVAIGLARLG V W S++G D G Sbjct: 5 VVTLGETMVLVYPSTTGPMKHAHEFEKSLAGAETNVAIGLARLGHDVGWYSKLGTDPHGE 64 Query: 66 FVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAISDLD-P 124 ++ +R EG+D V PTG K R + G+ P V Y+R GSAAS ++ DL Sbjct: 65 YLEFFVRGEGVDTTTVEFTDEAPTGIMFKERREFGE-PAVHYYRHGSAASLMSPDDLPVD 123 Query: 125 ALLRARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPSEALMIREI 184 L A +LH TGI PALS+S R+ + AG +VSFDPN+R LW S+ M + Sbjct: 124 YLTNAEYLHLTGITPALSESCRDATLLAAERATEAGMTVSFDPNVRRKLWESDERMRETM 183 Query: 185 NRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYYRTQLDAGF 244 L +L+ VLPG+ EG L G DDP IAA LD GA V+KLGA GA Sbjct: 184 LDLVSLSDIVLPGIEEGAALFGTDDPEAIAAACLDHGAGTAVVKLGAAGAVVADGSTTER 243 Query: 245 VEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRGDMEGLPLR 304 V G V +VVD VGAGDGFA G +++ +E +G +EA + AN +G+ A GD EGLP R Sbjct: 244 VSGYDVERVVDPVGAGDGFAAGFLASRIEGQGPVEATETANAVGAFATTVAGDTEGLPTR 303 Query: 305 HEL 307 EL Sbjct: 304 KEL 306 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: 308 Number of extensions: 15 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: 318 Length adjustment: 28 Effective length of query: 292 Effective length of database: 290 Effective search space: 84680 Effective search space used: 84680 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