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 SMc01531 SMc01531 2-dehydro-3-deoxygluconokinase
Query= SwissProt::P37647 (309 letters) >FitnessBrowser__Smeli:SMc01531 Length = 305 Score = 197 bits (500), Expect = 3e-55 Identities = 122/309 (39%), Positives = 171/309 (55%), Gaps = 7/309 (2%) Query: 1 MSKKIAVIGECMIELSEKGADV-KRGFGGDTLNTSVYIARQVDPAALTVHYVTALGTDSF 59 M+ K+ IGECM+EL + D+ ++G+ GDT NT+ Y AR PA TV Y TA+GTD+ Sbjct: 1 MTGKLLSIGECMVELMQAERDMLRKGYAGDTFNTAYY-ARLFLPADWTVDYFTAVGTDTV 59 Query: 60 SQQMLDAWHGENVDTSLTQRMENRLPGLYYIETDSTGERTFYYWRNEAAAKFWLESEQSA 119 S ++L V T+ +R+E R PGLY I GER+F YWR+ +AAK + Sbjct: 60 SDELLAFIESTGVGTAHIRRIEGRTPGLYMIHLKD-GERSFSYWRSTSAAKLLADDPDRL 118 Query: 120 AICEELANFDYLYLSGISLAILSPTSREKLLSLLRECRANGGKVIFDNNYRPRLWASKEE 179 E AN ++ SGI+LAILSP + E LL+ LR +A G +V+FD N RPRLW Sbjct: 119 RAAIEAANV--VFFSGITLAILSPDAAETLLAELRRAKAGGRQVVFDPNIRPRLWDDAAR 176 Query: 180 TQQVYQQMLECTDIAFLTLDDEDALWGQQPVEDVIARTHNAGVKEVVVKRGADSCLVSIA 239 + + + + DDE +G VE I R G + V VK G + + A Sbjct: 177 MRATIEAGGRAATMVMPSFDDEATHFGDASVEATIERYRALGAENVAVKDGKNGVTLCFA 236 Query: 240 GEGLVDVPAVKLPKEKVIDTTAAGDSFSAGYLAVRLTGGSAEDAAKRGHLTASTVIQYRG 299 G+ V VPA ++ V+DTT+AGDSF+ +LA +G S DAA A+ VI + G Sbjct: 237 GKERVHVPASQV--SAVVDTTSAGDSFNGSFLARLASGDSPADAAAFAARIAAAVIGHHG 294 Query: 300 AIIPREAMP 308 A+I R+ +P Sbjct: 295 ALIGRDKLP 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: 246 Number of extensions: 8 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: 305 Length adjustment: 27 Effective length of query: 282 Effective length of database: 278 Effective search space: 78396 Effective search space used: 78396 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 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