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 Pf6N2E2_512 5-keto-2-deoxygluconokinase (EC 2.7.1.92) / uncharacterized domain
Query= SwissProt::Q704D0 (325 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_512 Length = 645 Score = 117 bits (294), Expect = 6e-31 Identities = 106/352 (30%), Positives = 157/352 (44%), Gaps = 42/352 (11%) Query: 1 MAEGRCSQGKEPAEAMISLVALGEPLIQLNAVTPGP-LRYVAYFEKHVAGSEANFCIAAT 59 M + R + G++ + ++ LG + L A G L VA F K++ GS AN Sbjct: 1 MGQTRFASGRQ-----LDVICLGRLGVDLYAQQVGARLEDVASFAKYLGGSSANIAFGTA 55 Query: 60 MAGARCSLIARVGDDEFGRNIVEYLRGRGVDVSHVKVDPGAPTGIYFV----QRHFPVPG 115 G R ++++RVGDD GR +VE L G DVS +KVDP T + + + FP Sbjct: 56 RLGLRSAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTAMVLLGIKDRETFP--- 112 Query: 116 RSRLIYYRKGSAGSRVGPDDVDSSLISSADAVHSTGITLALSDSANRAVHKAFGEAKRR- 174 L++YR+ A + +D+D + I+S+ A+ TG T +D +A +A A++ Sbjct: 113 ---LVFYRENCADMALRVEDIDETFIASSKALLITG-THFSTDGVYKASTQALDYAEKHN 168 Query: 175 ---TFDTNIRPALWPDLAAARRAILDVLNYGV-----------DVLVTDPDDTQILLGVR 220 D + RP LW A V + V D++V ++ I G Sbjct: 169 VKCVLDIDYRPVLWGLAGKADGETRFVADQKVSQHVQGILPRFDLIVGTEEEFLIAGGSE 228 Query: 221 DPEEAYRKYRELGVQTLVYKLGAEGAYVFW--------NGGSYFRDALKVAVEDPTGAGD 272 D A R R L TLV KLGA+G V +G Y ++V V + GAGD Sbjct: 229 DLLSALRTVRSLTAATLVVKLGAQGCTVIHGAIPARLEDGALY--PGVRVEVLNVLGAGD 286 Query: 273 AVAGYFVALYLSGVDPRRALDLAVAASALVVGVRGDNEALPSPREAEELLKA 324 A F+A +L R LA A LVV A+P+ E + L K+ Sbjct: 287 AFMSGFLAGWLEDASDERCCQLANACGGLVVSRHACAPAMPTRAELDYLFKS 338 Lambda K H 0.319 0.137 0.401 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: 467 Number of extensions: 25 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: 325 Length of database: 645 Length adjustment: 33 Effective length of query: 292 Effective length of database: 612 Effective search space: 178704 Effective search space used: 178704 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 (21.7 bits) S2: 51 (24.3 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