Align prephenate dehydratase (EC 4.2.1.51) (characterized)
to candidate WP_017601478.1 D471_RS0126865 prephenate dehydratase
Query= BRENDA::P9WIC3 (321 letters) >NCBI__GCF_000341125.1:WP_017601478.1 Length = 315 Score = 244 bits (624), Expect = 2e-69 Identities = 146/316 (46%), Positives = 185/316 (58%), Gaps = 20/316 (6%) Query: 3 RIAYLGPEGTFTEAALVRMVAAGLVPETGPDALQRMPVESAPAALAAVRDGGADYACVPI 62 R AYLGPEGTFTEAAL R + G PD R+P + A AVR G D VP+ Sbjct: 4 RYAYLGPEGTFTEAAL-RALRPG-----APDGA-RVPCQGVAAVFDAVRSGSVDGGVVPL 56 Query: 63 ENSIDGSVLPTLDSLAIGVRLQVFAETTLDVTFSIVVKPGRNAADVRTLAAFPVAAAQVR 122 ENS++G V T+ L G L + ET + V F++ +PG DV+ +A P A AQ R Sbjct: 57 ENSVEGGVTATIAELINGDPLIITGETAVPVDFALFARPGTVLEDVKRVATHPHALAQCR 116 Query: 123 QWLAAHLPAADLRPAYSNADAARQVAD--GLVDAAVTSPLAAARWGLAALADGVVDESNA 180 WLA HLP AD S A AAR VA+ DAA+ + +A R+GL ALA GV D S+A Sbjct: 117 GWLARHLPDADTHTVSSTAAAARSVAEPGAPYDAAICAVIAGERYGLQALATGVGDRSDA 176 Query: 181 RTRFVLVGRPGPPPARTGADRTSAVLRI-DNQPGALVAALAEFGIRGIDLTRIESRPTRT 239 TRF+ + RPG P TG+D TS V I D+ PGAL+ L +F +RG++LTR+ESRPT Sbjct: 177 ATRFIYLSRPGALPEPTGSDLTSLVAFINDDHPGALIEVLNQFAVRGVNLTRLESRPTGD 236 Query: 240 ELGTYLFFVDCVGHIDDEAVAEALKAVHRRCADVRYLGSWPTGPAAGAQPPLV------- 292 LG+Y F +D GH+ + V EAL + R C DVR+LGS+P A PL+ Sbjct: 237 GLGSYCFCIDAEGHVAEARVGEALMGIRRVCRDVRFLGSYPRSGRATEVDPLLRPRPTTD 296 Query: 293 ---DEASRWLARLRAG 305 EA RWLAR+RAG Sbjct: 297 AVFAEAERWLARVRAG 312 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: 294 Number of extensions: 13 Number of successful extensions: 5 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: 315 Length adjustment: 27 Effective length of query: 294 Effective length of database: 288 Effective search space: 84672 Effective search space used: 84672 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 Apr 09 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