Align prephenate dehydrogenase (EC 1.3.1.12) (characterized)
to candidate WP_084056098.1 B9A12_RS02865 3-dehydroquinate synthase
Query= BRENDA::P43902 (377 letters) >NCBI__GCF_900176285.1:WP_084056098.1 Length = 677 Score = 165 bits (417), Expect = 4e-45 Identities = 90/265 (33%), Positives = 144/265 (54%), Gaps = 2/265 (0%) Query: 105 IVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERL 164 I+GG G +G +F R+ + G P+ I D+ + ++ +DVV+VSVP++ +E +E L Sbjct: 34 IIGGLGAMGRVFYRFFASRGMPVLISDQNTSLSNQDLIDRSDVVLVSVPLHRAVEILEEL 93 Query: 165 KPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPE 224 P L+ D+ S+K EP+ + L+ +GLHPM+G ++ Q ++ C GR P+ Sbjct: 94 CPCFRPRQLVLDICSLKVEPM-RALDRSAAWFVGLHPMYGPYVSDFHGQTMIACRGRVPD 152 Query: 225 R-YEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLAL 283 ++WL + G KI++ EHD MT IQ + H +T G L + + L Sbjct: 153 AVWDWLWSLFEGAGLKIHECTPEEHDRMMTVIQLIPHMATVVLGHCLRTLDVPVQESLRY 212 Query: 284 SSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFI 343 +SPIYRLEL +IGRLFAQD +LYA I M +E + ++ +L + FI Sbjct: 213 TSPIYRLELDLIGRLFAQDPQLYAAISMKNPFRKEALEAFQSAFERSLALVRQGNWHEFI 272 Query: 344 DAFHKVRDWFGDYSEQFLKESRQLL 368 + F + D+ G + Q L+E+ +LL Sbjct: 273 EDFRRTSDYLGGFCAQALQETNRLL 297 Lambda K H 0.321 0.137 0.390 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: 510 Number of extensions: 24 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: 377 Length of database: 677 Length adjustment: 34 Effective length of query: 343 Effective length of database: 643 Effective search space: 220549 Effective search space used: 220549 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: 52 (24.6 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