Align 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase (EC 2.2.1.10) (characterized)
to candidate 209396 DVU0460 predicted phospho-2-dehydro-3-deoxyheptonate aldolase
Query= BRENDA::Q57843 (273 letters) >MicrobesOnline__882:209396 Length = 266 Score = 308 bits (790), Expect = 6e-89 Identities = 145/259 (55%), Positives = 199/259 (76%) Query: 9 NLGKLVRLERIFNRESEKTVIVPMDHGVSNGPIKGLIDIRKTVNDVAEGGANAVLLHKGI 68 ++GK +R+ER+FNR + ++VIVP+DHGVS GPI GL+D+R TVN VAEGGA+AVL+HKG+ Sbjct: 2 HIGKKIRMERLFNRTTGRSVIVPLDHGVSVGPIDGLVDMRDTVNQVAEGGADAVLMHKGL 61 Query: 69 VRHGHRGYGKDVGLIIHLSGGTAISPNPLKKVIVTTVEEAIRMGADAVSIHVNVGSDEDW 128 VR GHR G+DVGLI+HLS T++SP P K + TVE+AI+ GAD VS+HVN+G + + Sbjct: 62 VRCGHREGGRDVGLIVHLSASTSLSPLPNAKTLTATVEDAIKHGADGVSVHVNLGDETER 121 Query: 129 EAYRDLGMIAETCEYWGMPLIAMMYPRGKHIQNERDPELVAHAARLGAELGADIVKTSYT 188 + DLG +A WG+PL+AMMY RG I+++ DP++VAH AR+G ELGAD+VK YT Sbjct: 122 DMLADLGRVATIANDWGVPLLAMMYARGPRIRDQYDPQVVAHCARVGVELGADVVKVPYT 181 Query: 189 GDIDSFRDVVKGCPAPVVVAGGPKTNTDEEFLQMIKDAMEAGAAGVAVGRNIFQHDDVVG 248 GD+D+F VV+ C PVV+AGGPK ++ +FLQM+ DA+ AG +G++VGRNIFQH Sbjct: 182 GDMDTFAHVVQSCCVPVVIAGGPKLDSTRDFLQMVHDAVRAGGSGLSVGRNIFQHARPSQ 241 Query: 249 ITRAVCKIVHENADVEEAL 267 + +AV +VHE+ DVE+A+ Sbjct: 242 LVKAVRGLVHEDWDVEQAI 260 Lambda K H 0.318 0.138 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: 310 Number of extensions: 13 Number of successful extensions: 3 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: 273 Length of database: 266 Length adjustment: 25 Effective length of query: 248 Effective length of database: 241 Effective search space: 59768 Effective search space used: 59768 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: 47 (22.7 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