Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate WP_012466794.1 CLIM_RS09480 3-dehydroquinate synthase
Query= curated2:Q3A2N6 (362 letters) >NCBI__GCF_000020465.1:WP_012466794.1 Length = 354 Score = 184 bits (466), Expect = 4e-51 Identities = 105/302 (34%), Positives = 175/302 (57%), Gaps = 8/302 (2%) Query: 42 VVSNPLVQSLYGQALADALQSSGYDHHFISIPDGEEHKNWTTLQTIYDGLIAKGFDRHCG 101 ++ + +V+ LY + L DAL + H FI I E+ K++ ++++ + LI GF ++ Sbjct: 35 IIIDNIVKDLYDEYLQDALDT----HKFIGIDANEKTKSYQGVESVIEELIQNGFRKNHR 90 Query: 102 LIALGGGVTGDMGGFAAATFLRGIPYIQVPTTLLAQVDSSVGGKTAINHPQGKNLIGAFY 161 L+A+GGG+T D+ F ++ RG+ +I PTT+LAQ DS +G KT+IN + KN +G FY Sbjct: 91 LVAIGGGITQDVTAFISSIMYRGVNWIFYPTTMLAQGDSCIGSKTSINFGRFKNQVGGFY 150 Query: 162 QPRHVHIDVDTLQSLDAREFATGMAEVIKYGIIKDKAFFDWLY-THREALQRRDTEALIS 220 P +++I +L +E +GM E++ Y I+ K FD+ T + A +D AL Sbjct: 151 PPSYIYIFPPFKDTLKEKEIRSGMGEMLHYFIVSGKEDFDFYRDTFKAAFTEKD--ALSG 208 Query: 221 AVKRACQIKANIVEVDEKEQALRAILNFGHTFGHAIENLSGYQTYRHGEAVAIGMMVAAH 280 + ++ +IK +E+DE ++ R + N+GHTFGHAIE+L+ Y+ HG AV+ GM ++ Sbjct: 209 IINKSLEIKKRYIEIDEFDKKERQVFNYGHTFGHAIESLTQYR-IPHGIAVSYGMDMSNF 267 Query: 281 VSRRMDLCTADEVGAIERLLQVFDLPVTPPDYSLEAYLEAMQRDKKVQQGKLRLVLNKGI 340 VS +M L ++ I + D ++ Y+ A+ +DKK +L L+LNKG Sbjct: 268 VSVKMGLIPSEVRDEIREVTSYIWEGYPIDDIDIDTYINALSKDKKNVGMQLGLILNKGY 327 Query: 341 GD 342 G+ Sbjct: 328 GN 329 Lambda K H 0.322 0.138 0.409 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: 341 Number of extensions: 17 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: 362 Length of database: 354 Length adjustment: 29 Effective length of query: 333 Effective length of database: 325 Effective search space: 108225 Effective search space used: 108225 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 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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