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 AZOBR_RS29860 AZOBR_RS29860 ketodeoxygluconokinase
Query= SwissProt::P45416 (310 letters) >FitnessBrowser__azobra:AZOBR_RS29860 Length = 310 Score = 262 bits (670), Expect = 7e-75 Identities = 146/308 (47%), Positives = 192/308 (62%), Gaps = 8/308 (2%) Query: 2 TTKNIAIIGECMIELSQK-GADLNRGFGGDTLNTAVYISRQVKPDALDVHYVTALGTDSF 60 + + +A +GECMIEL ++ GFGGDTLNTAVY++R + YVTALG D Sbjct: 4 SARRVAALGECMIELVRRPDGTFTMGFGGDTLNTAVYMARL----GVATDYVTALGDDGN 59 Query: 61 SSEMMASWQKEGVKTDLIQRLDNKLPGLYFIETDATGERTFYYWRNDAAARYWLESPDAD 120 S M+A+W+ EGV T + R+ N++PGLY IETD +GER F YWR+ A AR PD+ Sbjct: 60 SDAMVATWEAEGVGTGHVLRVPNRVPGLYMIETDDSGERRFLYWRDSAPARDLFVLPDSP 119 Query: 121 TISQQLAQFDYIYLSGISLAILNQASRARLLTVLRACRANGGKVIFDNNYRPRLWQSKEE 180 + L +D +Y+SGISLAI + R L +L R GG+V FD N+RPRLW +E Sbjct: 120 ALVADLEGYDLLYMSGISLAIWGERGREVLFPMLDRLRERGGRVAFDTNWRPRLWPDRET 179 Query: 181 TRQAYSDMLACTDIAFLTLDDEDMLWGELPVDEVLKRTHGAGVMEVVIKRGADACLVSIQ 240 ++AY ML TDIA ++D L+G+ D + R GAGV E+V+K C+VS Sbjct: 180 AQRAYDAMLERTDIALPGVEDLRGLYGDADADTAMARVRGAGVTEIVLKLEKPGCIVSAP 239 Query: 241 GEALLEVPAIKLPKEKVVDTTAAGDSFSAGYLSVRLNGGSAQDAAKRGHLTASTVIQYRG 300 G VP+ K+ KVVDTTAAGDSFSAGYLS RL G +AA+ H A+ VIQ+RG Sbjct: 240 G-VEETVPSEKV--AKVVDTTAAGDSFSAGYLSARLKGLGPVEAARSAHRIAAVVIQHRG 296 Query: 301 AIIPLEAM 308 A+IP +AM Sbjct: 297 AVIPRDAM 304 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: 306 Number of extensions: 11 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: 310 Length adjustment: 27 Effective length of query: 283 Effective length of database: 283 Effective search space: 80089 Effective search space used: 80089 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 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