Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate Ac3H11_700 2-dehydro-3-deoxygluconate kinase (EC 2.7.1.45)
Query= metacyc::MONOMER-12748 (320 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_700 Length = 319 Score = 141 bits (355), Expect = 2e-38 Identities = 113/313 (36%), Positives = 152/313 (48%), Gaps = 17/313 (5%) Query: 5 DILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGNDSLG 64 D+++ GE + F G+ +Q F G SN I AR G + A+L+R+G+D+ G Sbjct: 10 DVVALGEALVEFNQTRPGEPQYLQGF----GGDTSNAVIAAARAGARTAYLTRLGSDAFG 65 Query: 65 RFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAISDL-- 122 + +LD EG+D V D HPTG + G + Y R GSAAS +A + L Sbjct: 66 QALLDLWAREGVDTTAVERDAQHPTGIYFVTHGAAGHE--FSYLRAGSAASRMAPAWLAD 123 Query: 123 ----DPA--LLRARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPS 176 PA L + R LH +GI A+S SA + + M R+AG V+FDPNLR LWP Sbjct: 124 ESVKGPAAVLQQCRILHVSGISLAVSASACDTAYEAMRVARAAGARVAFDPNLRLKLWPL 183 Query: 177 EALMIREINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYY 236 A I +L LPGL + L G D IA + QGA VV+KLGA G Sbjct: 184 -ARARACIAHAVSLCDIFLPGLDDMAALLGLSDADAIADWGHAQGAATVVVKLGADGVLL 242 Query: 237 RTQLDAGFVEGVPVAQV--VDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQS 294 + A + VP V VD GAGD F L++ L + AV+ AN S AVQ Sbjct: 243 SSADPAVPRQRVPGRSVALVDATGAGDCFDGNLLARLALGDDLAAAVRYANTAASLAVQG 302 Query: 295 RGDMEGLPLRHEL 307 G + LP ++ Sbjct: 303 FGAVAPLPTAQQV 315 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: 295 Number of extensions: 19 Number of successful extensions: 4 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: 319 Length adjustment: 28 Effective length of query: 292 Effective length of database: 291 Effective search space: 84972 Effective search space used: 84972 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 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