Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate Pf1N1B4_4765 2-ketogluconate kinase (EC 2.7.1.13)
Query= metacyc::MONOMER-12748 (320 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4765 Length = 339 Score = 479 bits (1233), Expect = e-140 Identities = 242/307 (78%), Positives = 260/307 (84%) Query: 1 MPDIDILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGN 60 M +IDILSFGETMAMFVAE G+LA V HFHKRIAGADSNVAIGL+RLGF VAWLSRVG Sbjct: 1 MSEIDILSFGETMAMFVAEQNGELADVDHFHKRIAGADSNVAIGLSRLGFNVAWLSRVGA 60 Query: 61 DSLGRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAIS 120 DSLGRFV+DTL +GLDC V DP HPTGFQLKSR D G DP VEYFRRGSAASHL++ Sbjct: 61 DSLGRFVIDTLEKQGLDCSHVDIDPAHPTGFQLKSRTDDGSDPAVEYFRRGSAASHLSVQ 120 Query: 121 DLDPALLRARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPSEALM 180 + P LL ARHLHATGIPPALS +ARE+S LM R+AG SVSFDPNLRP+LW SE M Sbjct: 121 SIAPQLLEARHLHATGIPPALSAAAREMSFELMTRMRNAGRSVSFDPNLRPSLWTSEQQM 180 Query: 181 IREINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYYRTQL 240 IREINRLAALAHWVLPGL+EGRLLTG +DPADIAAFYLDQGAEAV IKLG GAYYRT L Sbjct: 181 IREINRLAALAHWVLPGLSEGRLLTGFEDPADIAAFYLDQGAEAVAIKLGPAGAYYRTHL 240 Query: 241 DAGFVEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRGDMEG 300 D GFV GVPV VVDTVGAGDGFAVGLISALLE+ + +AVQRANWIGSRAVQSRGDMEG Sbjct: 241 DEGFVAGVPVETVVDTVGAGDGFAVGLISALLENHSVAQAVQRANWIGSRAVQSRGDMEG 300 Query: 301 LPLRHEL 307 LP R E+ Sbjct: 301 LPTRLEM 307 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: 480 Number of extensions: 16 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: 339 Length adjustment: 28 Effective length of query: 292 Effective length of database: 311 Effective search space: 90812 Effective search space used: 90812 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: 49 (23.5 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