Align 3-dehydroquinate dehydratase (EC 4.2.1.10) (characterized)
to candidate WP_028999905.1 H537_RS0124205 3-dehydroquinate dehydratase
Query= BRENDA::E4RLB7 (148 letters) >NCBI__GCF_000430725.1:WP_028999905.1 Length = 148 Score = 138 bits (347), Expect = 4e-38 Identities = 64/141 (45%), Positives = 90/141 (63%) Query: 3 KVAVIHGPNLNMLGLREPEIYGKNNLEMVNKNLKRKAKELDFEIEIMQSNHEGEIVDYLH 62 K+ V+HGPNLN+ G REP IYG L +N+ L A+EL E+E +QSNHEG +VD LH Sbjct: 2 KILVLHGPNLNLFGRREPHIYGTTTLAQINERLGLLAQELGVELETLQSNHEGVLVDKLH 61 Query: 63 QNFEQLDGVIINPGGLTHTSVILRDALAAVRLPVIEVHISNIHKREEFRHKSLTAAVAVG 122 + + +DG +INP GLT V L DA+ A+ PV+E+H+SN+ RE +RH S+ + G Sbjct: 62 ERIDSVDGALINPAGLTQHGVPLHDAIKAMPFPVLEIHLSNLATREPWRHHSIISPAVRG 121 Query: 123 QITGLGVKGYTLALEGLKSIL 143 + GLG + Y L L ++ Sbjct: 122 TVMGLGWRSYLAGLRALVELV 142 Lambda K H 0.318 0.138 0.382 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: 85 Number of extensions: 1 Number of successful extensions: 1 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: 148 Length of database: 148 Length adjustment: 16 Effective length of query: 132 Effective length of database: 132 Effective search space: 17424 Effective search space used: 17424 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: 42 (20.8 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