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_012332880.1 M446_RS14695 sugar kinase
Query= SwissProt::P45416 (310 letters) >NCBI__GCF_000019365.1:WP_012332880.1 Length = 312 Score = 256 bits (655), Expect = 4e-73 Identities = 146/309 (47%), Positives = 194/309 (62%), Gaps = 14/309 (4%) Query: 6 IAIIGECMIELSQK--GADLNRGFGGDTLNTAVYISRQVKPDALDVHYVTALGTDSFSSE 63 +A +GECM+EL+++ GA L+RGFGGDTLNTA+Y++R + V YVTALG D +S E Sbjct: 3 VACLGECMVELAERPDGA-LSRGFGGDTLNTALYLARL----GVTVDYVTALGDDPWSDE 57 Query: 64 MMASWQKEGVKTDLIQRLDNKLPGLYFIETDATGERTFYYWRNDAAARYWLESPDADTIS 123 M +W +EG+ ++RL ++PGLY I TDA GER+F+YWR+ AAAR P A Sbjct: 58 MTQAWAREGIGLGRVRRLPGRMPGLYIIRTDAAGERSFHYWRDSAAARDLFTEPLAGATR 117 Query: 124 QQLAQFDYIYLSGISLAILNQASRARLLTVLRACRANGGKVIFDNNYRPRLWQSKEETRQ 183 + LA +D +YLSGISL++ A RA L L A + GG+V FD NYRPR W +EE R Sbjct: 118 EALAGYDLVYLSGISLSLYGPAGRAALDETLAALQGRGGRVAFDTNYRPRGWPDREEARA 177 Query: 184 AYSDMLACTDIAFLTLDDEDMLWGELPVDEVLKRTHGAGVMEVVIKRGADACLVS--IQG 241 + LA D+ F +++D D L+GE EVL+ G E+V+K + + + G Sbjct: 178 VFRAALARADLIFASVEDLDWLYGETGEAEVLRH---RGRAEIVLKESSARVPAARLLHG 234 Query: 242 EALLEVPAIKLPKEKVVDTTAAGDSFSAGYLSVRLNGGSAQDAAKRGHLTASTVIQYRGA 301 + VPA P E VVDTTAAGDSF+AGY++ RL G DAA GH A VI +RGA Sbjct: 235 DREETVPA--SPVETVVDTTAAGDSFAAGYIAARLAGLPPSDAAACGHRLAGAVIGHRGA 292 Query: 302 IIPLEAMPA 310 +IP AMPA Sbjct: 293 VIPPAAMPA 301 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: 308 Number of extensions: 17 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: 312 Length adjustment: 27 Effective length of query: 283 Effective length of database: 285 Effective search space: 80655 Effective search space used: 80655 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 Sep 24 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