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 CCNA_01110 CCNA_01110 2-dehydro-3-deoxygluconokinase
Query= SwissProt::P45416 (310 letters) >FitnessBrowser__Caulo:CCNA_01110 Length = 308 Score = 196 bits (499), Expect = 4e-55 Identities = 124/308 (40%), Positives = 170/308 (55%), Gaps = 17/308 (5%) Query: 6 IAIIGECMIELSQK----GADLNR-GFGGDTLNTAVYISRQVKPDALDVHYVTALGT-DS 59 I ++GECM+ELS + GA L R GF GDT NTA+Y++R V Y TALG D Sbjct: 4 ITVLGECMVELSPEAGDGGAPLYRMGFAGDTFNTAIYMARLGD----QVAYCTALGQGDP 59 Query: 60 FSSEMMASWQKEGVKTDLIQRLDNKLPGLYFIETDATGERTFYYWRNDAAARYWLESPDA 119 FS ++A+ ++EG+ T L+++++N+LPGLY I D GER F+YWR A R + A Sbjct: 60 FSEGVLAAMRREGMDTQLVRQVENRLPGLYAIVLDEHGERKFHYWRERAPIRDLFSAHTA 119 Query: 120 DTISQQLAQFDYIYLSGISLAILNQASRARLLTVLRACRANGGKVIFDNNYRPRLWQSKE 179 D + + D +YLSG++LA++ RARL +L ++G V D NYRP LW S E Sbjct: 120 DQLIEAAKASDLVYLSGVTLAVIGDIGRARLRDILAYVHSHGVAVALDFNYRPALWPSAE 179 Query: 180 ETRQAYSDMLACTDIAFLTLDDEDMLWGELPVDEVLKRTHGAGVMEVVIKRGADACLV-S 238 R A ++ L+ +D L+G D L A EVV + + A V + Sbjct: 180 AARAALDGVVPACRYISLSSEDSRPLYGREAED--LAAEWAAAGAEVVARDESHAVNVHT 237 Query: 239 IQGEALLEVPAIKLPKEKVVDTTAAGDSFSAGYLSVRLNGGSAQDAAKRGHLTASTVIQY 298 +G PA + K VDTT AGDSF+A YLS RL G + DA R H A V+ + Sbjct: 238 PEGRTATPAPA----RVKAVDTTGAGDSFNAAYLSSRLAGAAIPDAVARAHALAGIVVSH 293 Query: 299 RGAIIPLE 306 RGAI+P E Sbjct: 294 RGAIVPPE 301 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: 239 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: 308 Length adjustment: 27 Effective length of query: 283 Effective length of database: 281 Effective search space: 79523 Effective search space used: 79523 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