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 YP_002826884.1 NGR_c23720 2-dehydro-3-deoxygluconokinase
Query= SwissProt::P37647 (309 letters) >NCBI__GCF_000018545.1:YP_002826884.1 Length = 308 Score = 189 bits (480), Expect = 7e-53 Identities = 115/310 (37%), Positives = 170/310 (54%), Gaps = 9/310 (2%) Query: 1 MSKKIAVIGECMIELSE-KGADVKRGFGGDTLNTSVYIARQVDPAALTVHYVTALGTDSF 59 M+ + IGECM+EL + +G +++G+ GDT NT+ Y AR PA TV Y+TA+GTD Sbjct: 1 MAGSMLSIGECMVELMQAEGGMLRKGYAGDTFNTAYY-ARLFAPAGWTVEYLTAVGTDVV 59 Query: 60 SQQMLDAWHGENVDTSLTQRMENRLPGLYYIETDSTGERTFYYWRNEAAAKFWLES-EQS 118 S ++L V T+ R+E R+PGLY I GER+F YWR+ +AAK + E+ Sbjct: 60 SDELLSFIDSTGVGTAHIARIEGRMPGLYMIHLKD-GERSFSYWRSTSAAKLLADDPERL 118 Query: 119 AAICEELANFDYLYLSGISLAILSPTSREKLLSLLRECRANGGKVIFDNNYRPRLWASKE 178 A E++ D ++ SGI+LAIL+P + E LL+ LR +A+G +V+FD N RPRLW Sbjct: 119 RAAIEKV---DVVFFSGITLAILAPDAVETLLAELRRAKASGTRVVFDPNIRPRLWDDAA 175 Query: 179 ETQQVYQQMLECTDIAFLTLDDEDALWGQQPVEDVIARTHNAGVKEVVVKRGADSCLVSI 238 + + + + DDE +G + I R GV ++ VK GA+ + Sbjct: 176 RMRATLEAGARSATMVLPSYDDEATHFGDASIGATIERYRGLGVADIAVKDGANGVTLQF 235 Query: 239 AGEGLVDVPAVKLPKEKVIDTTAAGDSFSAGYLAVRLTGGSAEDAAKRGHLTASTVIQYR 298 +PA + V+DTT+AGD F+ +LA G S DAA A+ VI + Sbjct: 236 GEAERQHIPAASV--SHVVDTTSAGDCFNGSFLARLAAGDSPADAAAFAARVAAAVIGHH 293 Query: 299 GAIIPREAMP 308 GA++ RE +P Sbjct: 294 GALVEREKLP 303 Lambda K H 0.317 0.132 0.384 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: 244 Number of extensions: 11 Number of successful extensions: 5 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: 309 Length of database: 308 Length adjustment: 27 Effective length of query: 282 Effective length of database: 281 Effective search space: 79242 Effective search space used: 79242 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: 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