Align prephenate dehydratase (EC 4.2.1.51) (characterized)
to candidate WP_049754093.1 HM1_RS08655 prephenate dehydratase
Query= BRENDA::P9WIC3 (321 letters) >NCBI__GCF_000019165.1:WP_049754093.1 Length = 290 Score = 163 bits (412), Expect = 5e-45 Identities = 115/284 (40%), Positives = 151/284 (53%), Gaps = 16/284 (5%) Query: 4 IAYLGPEGTFTEAALVRMVAAGLVPETGPDALQRMPVESAPAALAAVRDGGADYACVPIE 63 + YLGPEGTF+E A A +P+T P S A A+ + A +P+E Sbjct: 18 VGYLGPEGTFSEEA----ARAFFLPDT-----TLRPFSSISAVYEALSLWEIEAAILPLE 68 Query: 64 NSIDGSVLPTLDSLAIGVRLQVFAETTLDVTFSIVVKPGRNAADVRTLAAFPVAAAQVRQ 123 NSI+G++ TLD L L +F E L V ++V PG + V + + P AQ R+ Sbjct: 69 NSIEGTINQTLDELVENPGLFIFGELILPVHNHLLVPPGVDWTRVVEVYSHPQPLAQCRR 128 Query: 124 WLAAHLPAADLRPAYSNADAARQVADGLVD----AAVTSPLAAARWGLAALADGVVDESN 179 +L A LP A L S + A++ + V AAV S AA R GL + N Sbjct: 129 FLEAKLPNARLIATASTVEGAKKALELTVPEAPRAAVGSAFAARRLGLQIAQSDIQSRPN 188 Query: 180 ARTRFVLVGRPGPPPARTGADRTSAVLRI-DNQPGALVAALAEFGIRGIDLTRIESRPTR 238 +TRFV+VGR P TG D+TS V + ++PG L A L EF R I+LTRIESRPT+ Sbjct: 189 NKTRFVVVGRQLTEP--TGNDKTSLVCSLPQDRPGGLYAILKEFAEREINLTRIESRPTK 246 Query: 239 TELGTYLFFVDCVGHIDDEAVAEALKAVHRRCADVRYLGSWPTG 282 ELG YLFF+D VGH D VAEAL A+ + R LGS+ G Sbjct: 247 HELGQYLFFIDFVGHQRDRTVAEALNAIGQFTTLTRVLGSYLRG 290 Lambda K H 0.319 0.134 0.396 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: 212 Number of extensions: 9 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: 321 Length of database: 290 Length adjustment: 27 Effective length of query: 294 Effective length of database: 263 Effective search space: 77322 Effective search space used: 77322 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 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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