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 WP_011952728.1 SWIT_RS09545 sugar kinase
Query= SwissProt::P45416 (310 letters) >NCBI__GCF_000016765.1:WP_011952728.1 Length = 309 Score = 220 bits (560), Expect = 4e-62 Identities = 133/305 (43%), Positives = 179/305 (58%), Gaps = 14/305 (4%) Query: 6 IAIIGECMIELSQKG-----ADLNRGFGGDTLNTAVYISRQVKPDALDVHYVTALGTDSF 60 IA+IGE M+ELS+ G A GGD LN+A++++R L+ +++ALG D Sbjct: 4 IAVIGEGMVELSRSGEHGGIAGWETHHGGDALNSAIHLARF----GLETGFISALGADPL 59 Query: 61 SSEMMASWQKEGVKTDLIQRLDNKLPGLYFIETDATGERTFYYWRNDAAARYWLESPDAD 120 S + SW +EG+ + ++ GLY IETDA GER+F YWR+D+AAR L+ P+A+ Sbjct: 60 SRALRRSWAEEGLDLTHLLTHPDRNAGLYAIETDAEGERSFAYWRSDSAARAMLDLPEAE 119 Query: 121 TISQQLAQFDYIYLSGISLAILNQASRARLLTVLRACRANGGKVIFDNNYRPRLWQSKEE 180 A+ D +YLS ISLAIL A R RL + R RA+GG+V FD+N+RPRLW S E Sbjct: 120 AALAHAARCDLLYLSLISLAILPPAGRERLAGLCRDVRAHGGRVAFDSNFRPRLWSSPAE 179 Query: 181 TRQAYSDMLACTDIAFLTLDDEDMLWGELPVDEVLKRTHGAGVMEVVIKRGADACLVSIQ 240 R A + DIA T DE L+G P+D V R G GV EV +K GAD CLV+ + Sbjct: 180 ARAAVEAIGPLVDIALPTQVDEAALFGPEPIDAVADRWVGWGVAEVAVKSGADGCLVATR 239 Query: 241 -GEALLEVPAIKLPKEKVVDTTAAGDSFSAGYLSVRLNGGSAQDAAKRGHLTASTVIQYR 299 G + P + VD++ AGD+F+AGYL+ RL G + AA GH A+ I R Sbjct: 240 DGRHRIAPPRAVV----AVDSSGAGDAFNAGYLAARLAGRAPAQAAPAGHELAAWTILRR 295 Query: 300 GAIIP 304 GAI P Sbjct: 296 GAIPP 300 Lambda K H 0.318 0.134 0.390 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: 257 Number of extensions: 9 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: 310 Length of database: 309 Length adjustment: 27 Effective length of query: 283 Effective length of database: 282 Effective search space: 79806 Effective search space used: 79806 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 (21.7 bits) S2: 48 (23.1 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