Align Prephenate dehydrogenase [NADP(+)]; PRDH; EC 1.3.1.13 (characterized)
to candidate CA265_RS16955 CA265_RS16955 prephenate dehydrogenase
Query= SwissProt::P20049 (452 letters) >FitnessBrowser__Pedo557:CA265_RS16955 Length = 418 Score = 375 bits (964), Expect = e-108 Identities = 199/427 (46%), Positives = 280/427 (65%), Gaps = 18/427 (4%) Query: 16 IGIIGLGDMGLLYANKFTDAGWGVICCDREEYYDELKEKYASAKFELVKNGHLVSRQSDY 75 IGIIGLGDMG LYA F +AG+ V D + +LK + E++ +GH V+R+SD+ Sbjct: 3 IGIIGLGDMGKLYALSFINAGYKVCGADMPLRFTDLKNELEPKGIEVLIDGHEVARKSDF 62 Query: 76 IIYSVEASNISKIVATYGPSSKVGTIVGGQTSCKLPEIEAFEKYLPKDCDIITVHSLHGP 135 IIY VEA I ++VAT+ S+K G IV GQTS K PEI AFEK+LP+D I+T HSLHGP Sbjct: 63 IIYCVEAEKIDEVVATFARSTKYGAIVAGQTSVKHPEIAAFEKHLPEDTQIVTCHSLHGP 122 Query: 136 KVNTEGQPLVIINHRSQ---YPESFEFVNSVMACLKSKQVYL-TYEEHDKITADTQAVTH 191 + EGQ LV++ HR+ Y ++ E S LKS + + Y EHD+I ADTQAVTH Sbjct: 123 AFSPEGQTLVVVRHRATDAVYAKALEIYKS----LKSNIIEMDDYREHDRIVADTQAVTH 178 Query: 192 AAFLSMGSAWAKIKIYPWTLGVNKWY-GGLENVKVNISLRIYSNKWHVYAGLAITNPSAH 250 F SMGSAW +PW N Y GG++NVK+ +LRI+S K H+YAGLAI NP A Sbjct: 179 MGFESMGSAWKNAGFFPWD---NPAYAGGIDNVKILTTLRIFSYKSHIYAGLAILNPYAQ 235 Query: 251 QQILQYATSATELFSLMIDNKEQELTDRLLKAKQFVFGKHTGLLLLDDTILEKYSLSKSS 310 +Q+ YA + +ELF LMI E E +++ A+ FVF + LLLLDD I++++SLS +S Sbjct: 236 KQVKYYAQAESELFKLMICENETEFREKIYAARDFVFHESRALLLLDDNIMKEFSLSDAS 295 Query: 311 IGNSNNCKPVPNSHLSLLAIVDSWFQLGIDPYDHMICSTPLFRIFLGVSEYLFLKPGLLE 370 K PNSHLSLL++V +W+++G++PYD++IC TP F++ LG++EYLF +LE Sbjct: 296 ------HKQKPNSHLSLLSMVYAWYKMGVNPYDNLICQTPPFKLRLGIAEYLFKNEAMLE 349 Query: 371 QTIDAAIHDKSFIKDDLEFVISAREWSSVVSFANFDIYKKQFQSVQKFFEPMLPEANLIG 430 ++I+ A++DKS DDLEF + EW+S++ + + YK+ F++ + FF L + + Sbjct: 350 ESINTALYDKSIRGDDLEFHTAVHEWASIIGYGDLKGYKEHFEAAKSFFANRLNDGRDLS 409 Query: 431 NEMIKTI 437 EMIK + Sbjct: 410 AEMIKRL 416 Lambda K H 0.318 0.134 0.397 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: 475 Number of extensions: 25 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: 452 Length of database: 418 Length adjustment: 32 Effective length of query: 420 Effective length of database: 386 Effective search space: 162120 Effective search space used: 162120 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: 51 (24.3 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