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 AO356_00445 AO356_00445 ketodeoxygluconokinase
Query= SwissProt::P45416 (310 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_00445 Length = 306 Score = 285 bits (729), Expect = 1e-81 Identities = 155/300 (51%), Positives = 196/300 (65%), Gaps = 5/300 (1%) Query: 6 IAIIGECMIELSQKG-ADLNRGFGGDTLNTAVYISRQVKPDALDVHYVTALGTDSFSSEM 64 IA+IGECMIEL Q+ L + FGGDTLNTAVY+SR + V YVTALG DSFS M Sbjct: 10 IALIGECMIELQQRADGSLLQSFGGDTLNTAVYLSRALGNRGA-VDYVTALGDDSFSDAM 68 Query: 65 MASWQKEGVKTDLIQRLDNKLPGLYFIETDATGERTFYYWRNDAAARYWLESPDADTISQ 124 W +E + +QRL +LPGLY I+TDA GER F YWRN+AA R +P A I Sbjct: 69 CECWAEENIGLQRVQRLPGRLPGLYCIQTDAAGERRFLYWRNEAAVRECFTTPAAAPILA 128 Query: 125 QLAQFDYIYLSGISLAILNQASRARLLTVLRACRANGGKVIFDNNYRPRLWQSKEETRQA 184 L +D +Y SG++LA+L + RARL+ L R G +V+FDNNYRPRLW S E R A Sbjct: 129 ALPDYDVLYFSGVTLAVLGEQGRARLIETLVEARRRGAQVVFDNNYRPRLWASIEAARAA 188 Query: 185 YSDMLACTDIAFLTLDDEDMLWGELPVDEVLKRTHGAGVMEVVIKRGADACLVSIQGEAL 244 Y +L ++A LT++DE L+G D V G EVV+KRGA+ACL+ GE+ Sbjct: 189 YRSVLPYVELALLTVEDEQALFGYADTDAVFAAYGQLGTPEVVLKRGAEACLIRCDGES- 247 Query: 245 LEVPAIKLPKEKVVDTTAAGDSFSAGYLSVRLNGGSAQDAAKRGHLTASTVIQYRGAIIP 304 E+PA ++ E+VVDTTAAGDSFSA YL+ RL GG+ +AA+ GHL AS VIQ GA++P Sbjct: 248 YEIPAQRV--ERVVDTTAAGDSFSAAYLASRLLGGTPAEAAESGHLLASRVIQVPGALMP 305 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: 295 Number of extensions: 16 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: 306 Length adjustment: 27 Effective length of query: 283 Effective length of database: 279 Effective search space: 78957 Effective search space used: 78957 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