Align 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 (characterized)
to candidate Pf1N1B4_4765 2-ketogluconate kinase (EC 2.7.1.13)
Query= SwissProt::P50845 (324 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4765 Length = 339 Score = 311 bits (797), Expect = 1e-89 Identities = 164/314 (52%), Positives = 215/314 (68%), Gaps = 4/314 (1%) Query: 2 KLDAVTFGESMAMFYANEYGGLHEVSTFSKGLAGAESNVACGLARLGFRMGWMSKVGNDQ 61 ++D ++FGE+MAMF A + G L +V F K +AGA+SNVA GL+RLGF + W+S+VG D Sbjct: 3 EIDILSFGETMAMFVAEQNGELADVDHFHKRIAGADSNVAIGLSRLGFNVAWLSRVGADS 62 Query: 62 LGTFILQELKKEGVDVSRVIRSQDENPTGLLLKSKVKEG-DPQVTYYRKNSAASTLTTAE 120 LG F++ L+K+G+D S V +PTG LKS+ +G DP V Y+R+ SAAS L+ Sbjct: 63 LGRFVIDTLEKQGLDCSHV-DIDPAHPTGFQLKSRTDDGSDPAVEYFRRGSAASHLSVQS 121 Query: 121 YPRDYFQCAGHLHVTGIPPALSAEMKDFTYHVMNDMRNAGKTISFDPNVRPSLWPDQATM 180 + A HLH TGIPPALSA ++ ++ +M MRNAG+++SFDPN+RPSLW + M Sbjct: 122 IAPQLLE-ARHLHATGIPPALSAAAREMSFELMTRMRNAGRSVSFDPNLRPSLWTSEQQM 180 Query: 181 VHTINDLAGLADWFFPGIAEGELLTGEKTPEGIADYYLKKGASFVAIKLGKEGAYFKTGT 240 + IN LA LA W PG++EG LLTG + P IA +YL +GA VAIKLG GAY++T Sbjct: 181 IREINRLAALAHWVLPGLSEGRLLTGFEDPADIAAFYLDQGAEAVAIKLGPAGAYYRTHL 240 Query: 241 SEGFLEGCRVDRVVDTVGAGDGFAVGVISGILDGLSYKDAVQRGNAIGALQVQAPGDMDG 300 EGF+ G V+ VVDTVGAGDGFAVG+IS +L+ S AVQR N IG+ VQ+ GDM+G Sbjct: 241 DEGFVAGVPVETVVDTVGAGDGFAVGLISALLENHSVAQAVQRANWIGSRAVQSRGDMEG 300 Query: 301 LPTR-EKLASFLSA 313 LPTR E A F A Sbjct: 301 LPTRLEMFAEFEGA 314 Lambda K H 0.317 0.135 0.399 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: 348 Number of extensions: 19 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: 324 Length of database: 339 Length adjustment: 28 Effective length of query: 296 Effective length of database: 311 Effective search space: 92056 Effective search space used: 92056 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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