Align Arogenate dehydratase 2; PhADT2; Prephenate dehydratase ADT3; EC 4.2.1.91; EC 4.2.1.51 (characterized)
to candidate WP_027177588.1 G496_RS0100775 prephenate dehydratase
Query= SwissProt::D3U716 (394 letters) >NCBI__GCF_000429985.1:WP_027177588.1 Length = 366 Score = 145 bits (365), Expect = 2e-39 Identities = 102/312 (32%), Positives = 161/312 (51%), Gaps = 29/312 (9%) Query: 87 PLPRPLTSADLSNMATEGSRL----RVAYQGVRGAYSESAA-EKAYPNCEAVPCEQFDTA 141 PLP A + + RL RV Y G G +S A E E P F+ Sbjct: 68 PLPAEHLEAIYREIISSSRRLQRPERVVYLGPEGTFSYFAGLEYLGRQAELQPRNNFEDI 127 Query: 142 FEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKLAIRHCLLANNGVKIED 201 F +V + D ++P+ENSL G++ +N DL +R+ + I EV I H ++ + Sbjct: 128 FVSVSKGESDLGIVPLENSLKGTVGQNVDLFMRYPVFIQAEVYSRISHGIMGQT-ADLSK 186 Query: 202 LKRVLSHPQALAQC----ENNLTKLGLVREAVDDTAGAAKYIAFQQLKDAGAVASLAAAR 257 +K V SH +AL QC +NL K + +VD TA AA+ ++ Q + AV ++ A Sbjct: 187 IKYVYSHSKALEQCSGWLRSNLPKAEQI--SVDSTAKAAEMVS-QGEDNCAAVGNVKLAN 243 Query: 258 IYGLNVLAQDIQDDSDNVTRFLMLAREPIIPGTDKPFKTSVVFSLDEGPGVLFKALAVFA 317 I+GLN+LA+ I+D DN TRFL++ +P G K KTS++F+ + PG L L V + Sbjct: 244 IFGLNILAEAIEDMPDNWTRFLIIGAKPGKEG--KRDKTSLLFTTPDRPGALVSVLNVLS 301 Query: 318 MRNINLTKIESRPLQKQALRVLDDSADGFPKYFPYLFYVDFEASMADQRAQNALGHLKEF 377 ++IN+TK+ESRP + + Y+F+VD + + ++ ++ + LK+ Sbjct: 302 GKDINMTKLESRPF--------------LGEKWKYMFFVDLQGDLGAEKQKSLIDDLKDR 347 Query: 378 ATFLRVLGSYPS 389 +R LGSYP+ Sbjct: 348 CLTMRFLGSYPA 359 Lambda K H 0.318 0.133 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: 295 Number of extensions: 14 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: 394 Length of database: 366 Length adjustment: 30 Effective length of query: 364 Effective length of database: 336 Effective search space: 122304 Effective search space used: 122304 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: 50 (23.9 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