Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate PP_3378 PP_3378 putative 2-ketogluconokinase
Query= metacyc::MONOMER-12748 (320 letters) >FitnessBrowser__Putida:PP_3378 Length = 316 Score = 424 bits (1089), Expect = e-123 Identities = 218/307 (71%), Positives = 245/307 (79%) Query: 1 MPDIDILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGN 60 M + D+L FGETMAMFVAE GDLA V F KRIAGADSNVAIGLARLGFKV WLSRVG+ Sbjct: 1 MHEHDVLCFGETMAMFVAEQAGDLAGVGQFGKRIAGADSNVAIGLARLGFKVRWLSRVGD 60 Query: 61 DSLGRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAIS 120 DSLGRFVLD+LR EGLDC V D +PTGFQLK+R + G DP VEYFRRGSAAS L+ + Sbjct: 61 DSLGRFVLDSLRCEGLDCSGVEVDANYPTGFQLKARSEDGSDPAVEYFRRGSAASRLSAA 120 Query: 121 DLDPALLRARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVSFDPNLRPALWPSEALM 180 + P L+ARH+HATGIP ALSDS R LS L+ R+AG S+SFDPNLRP+LWP ++ M Sbjct: 121 MVSPVWLQARHVHATGIPLALSDSCRALSHALLDGMRAAGRSISFDPNLRPSLWPDQSSM 180 Query: 181 IREINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYYRTQL 240 +REIN LAA A WVLPGL EGRLLTG+ PADIAAFYLDQG E VVIKLG GAY+R+ Sbjct: 181 VREINALAAKADWVLPGLEEGRLLTGQHTPADIAAFYLDQGVELVVIKLGDAGAYFRSAK 240 Query: 241 DAGFVEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRGDMEG 300 G V VPV++VVDTVGAGD FAVG++SALLE R + EAV R NW GSRAVQSRGDMEG Sbjct: 241 GEGQVAPVPVSRVVDTVGAGDAFAVGVLSALLEGRPVAEAVARGNWCGSRAVQSRGDMEG 300 Query: 301 LPLRHEL 307 LPLRHEL Sbjct: 301 LPLRHEL 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: 426 Number of extensions: 15 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: 316 Length adjustment: 27 Effective length of query: 293 Effective length of database: 289 Effective search space: 84677 Effective search space used: 84677 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