Align 3-dehydroquinate synthase; DHQS; EC 4.2.3.4 (uncharacterized)
to candidate WP_011605755.1 FRAAL_RS20255 cupin domain-containing protein
Query= curated2:Q8RB14 (356 letters) >NCBI__GCF_000058485.1:WP_011605755.1 Length = 515 Score = 154 bits (390), Expect = 4e-42 Identities = 99/323 (30%), Positives = 166/323 (51%), Gaps = 12/323 (3%) Query: 33 VRSSKTFVITDSNVYPLYFEKIEESLRKSGFDVLYEVIPAGETSKTMEMAQRLLEVAYDS 92 V + FV+ D+N++ LY I L + D V+PA E +K M+ L++ Sbjct: 28 VHRVRRFVVVDANIHALYGRDIHRYLDSNDCDYELCVLPASEEAKNMQSVLTLVQGLDSF 87 Query: 93 GLLR-DSSIIALGGGVVGDIAGFVAATYMRGIDFIQIPTTLLAQVDSSVGGKVAVNLKKG 151 G+ R + II +GGG++ D+ G ++ Y R +I++PT+LL VD+ VG K VN Sbjct: 88 GISRRNEPIIGIGGGIILDVVGLASSLYRRSTPYIRVPTSLLGLVDAGVGIKTGVNFNGH 147 Query: 152 KNIVGAFYQPKMVYIDTSVLGTLNKREVLGGLAEVIKYGVIWDFDLFTYIEENLGDILRL 211 KN +G+++ P + +D L TL R V GLAE++K ++ D LF +EE+ +L Sbjct: 148 KNRLGSYFAPSVALLDRGFLATLGDRYVSNGLAEILKISLVLDAHLFDLLEEHAETLLAE 207 Query: 212 KKEDLT--------YIVKRSCEIKAKVVSLDEKEENLRAILNFGHTIGHAIEALTGYERY 263 + T +++R+ + + + + E NL +++GH+ +E + Sbjct: 208 RLTGRTAVGDAVGREVIRRAVDGMLRELQPNLWERNLERRVDYGHSFSPTLE-MRALPAL 266 Query: 264 IHGEAVAIGMAYEARLAFNLGYIDEGYLERILNLIKRAGLPADYEGIEKTDML-NAIKLD 322 +HGEAV++ MA +A G I R+ NL+KR LP + + TD+L +A++ Sbjct: 267 LHGEAVSVDMALTTIVAERRGLISAPDRARVFNLMKRLRLPV-WHPLCGTDLLAHALRET 325 Query: 323 KKMREGRINFVLPVGLGKVDIVS 345 + R+G LPVG+G VS Sbjct: 326 TRHRDGLQRIPLPVGIGDARFVS 348 Lambda K H 0.320 0.141 0.393 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: 452 Number of extensions: 23 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: 356 Length of database: 515 Length adjustment: 32 Effective length of query: 324 Effective length of database: 483 Effective search space: 156492 Effective search space used: 156492 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 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