Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate AO353_26875 AO353_26875 2-dehydro-3-deoxygluconokinase
Query= metacyc::MONOMER-12748 (320 letters) >FitnessBrowser__pseudo3_N2E3:AO353_26875 Length = 326 Score = 470 bits (1210), Expect = e-137 Identities = 241/308 (78%), Positives = 258/308 (83%) Query: 1 MPDIDILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGN 60 M +IDILSFGETMAMFVAE GDLA V FHKRIAGADSNVAIGL+RLGFKV+WLSRVG Sbjct: 1 MSEIDILSFGETMAMFVAEQSGDLADVTQFHKRIAGADSNVAIGLSRLGFKVSWLSRVGA 60 Query: 61 DSLGRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAIS 120 DSLGRFV+DTL EGLDCRFV D HPTGFQLKSR D G DP VEYFRRGSAAS L++ Sbjct: 61 DSLGRFVVDTLEQEGLDCRFVETDHAHPTGFQLKSRADDGSDPHVEYFRRGSAASLLSVQ 120 Query: 121 DLDPALLRARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPSEALM 180 + P L ARHLHATGI PALS+SAR++S LM R AG SVSFDPNLRP LW SE M Sbjct: 121 SIVPEQLEARHLHATGIVPALSESARQMSFELMTRMRQAGRSVSFDPNLRPTLWGSEQQM 180 Query: 181 IREINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYYRTQL 240 I EINRLAALAHWVLPGL+EGRLL+G +DPADIAAFYLDQGAEAVVIKLG GAYYRTQ Sbjct: 181 IGEINRLAALAHWVLPGLSEGRLLSGFEDPADIAAFYLDQGAEAVVIKLGPDGAYYRTQH 240 Query: 241 DAGFVEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRGDMEG 300 D GFV GVPV VVDTVGAGDGFAVG+ISALLE+ + +AVQRANWIGSRAVQSRGDMEG Sbjct: 241 DQGFVPGVPVTTVVDTVGAGDGFAVGMISALLENLSVPDAVQRANWIGSRAVQSRGDMEG 300 Query: 301 LPLRHELP 308 LP R ELP Sbjct: 301 LPKRSELP 308 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: 449 Number of extensions: 21 Number of successful extensions: 1 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: 326 Length adjustment: 28 Effective length of query: 292 Effective length of database: 298 Effective search space: 87016 Effective search space used: 87016 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