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_014267265.1 ACIX8_RS20320 carbohydrate kinase family protein
Query= SwissProt::Q53W83 (309 letters) >NCBI__GCF_000178955.2:WP_014267265.1 Length = 310 Score = 80.1 bits (196), Expect = 6e-20 Identities = 80/280 (28%), Positives = 119/280 (42%), Gaps = 16/280 (5%) Query: 33 GGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDLTHFRRAPGFTGLYLRE 92 GG VN A ALARLG G GEDE A + RL + GV H + L + Sbjct: 42 GGGTVNTACALARLGHNSSIFGVFGEDE-EAWLRLRLSSFGVHAEHAASSELPNALTVSM 100 Query: 93 YLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEARAFSLWAMEE 152 + + Y A L P+ + + L E L ++ Sbjct: 101 STTSDRSFLSY---AGANRILEKYVALPETIAALSMAQHVHFAMPLEVELAKVLLPSLRA 157 Query: 153 AKRRGVRVSLDVNYRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFG--RVEEALR- 209 A G +S+D +R+ + + L VDL +E EA+LL G + E+ LR Sbjct: 158 A---GCTLSIDPGWRKDWFLSSGSLDILRM----VDLFLPNESEAQLLTGHKKPEQMLRS 210 Query: 210 --ALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPV 267 AL V+K G +GA F + R V+ +D GAGDAF AG++ + G + Sbjct: 211 CAALGLHHTVIKLGPRGAVTFQNDRLYTMVPPDVQVIDTTGAGDAFDAGFIDAWLSGADI 270 Query: 268 EERLRLANLLGASVAASRGDHEGAPYREDLEVLLKATQTF 307 EE+LR A + G+ +RG P+RE++ ++ F Sbjct: 271 EEQLRRACICGSLSTRARGALTALPFREEMRDFVQEKSIF 310 Lambda K H 0.320 0.139 0.407 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: 215 Number of extensions: 14 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 309 Length of database: 310 Length adjustment: 27 Effective length of query: 282 Effective length of database: 283 Effective search space: 79806 Effective search space used: 79806 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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