Align prephenate dehydrogenase (EC 1.3.1.12); prephenate dehydratase (EC 4.2.1.51); chorismate mutase (EC 5.4.99.5) (characterized)
to candidate WP_027721085.1 H589_RS0105335 prephenate dehydratase
Query= BRENDA::O30012 (620 letters) >NCBI__GCF_000425265.1:WP_027721085.1 Length = 367 Score = 164 bits (416), Expect = 5e-45 Identities = 116/359 (32%), Positives = 193/359 (53%), Gaps = 21/359 (5%) Query: 265 SIEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEVMSKTTL 324 ++ LR I S+DS IL L+ +R A+ + IK + I K E+++ + ++ Sbjct: 8 NLGSLREEIDSLDSEILELLNKRAAASLSVGAIKAGSSDQI-FKPFREQEVLQGLTGRNP 66 Query: 325 NPVK---LKEIFEGIMSLAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVPLRYC 381 P+ L+ I+ I+S ++ + + LGP+G+FS L+ +G + + Sbjct: 67 GPLPSEHLEAIYREIISSSRRLQRPER-----VVYLGPEGTFSYFAGLQHMGRQADMIPK 121 Query: 382 STTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCLVAKR 441 + ++I V GE D G++P+ENS+ GTV +D + + V + E ++H L++K Sbjct: 122 NNFEDIFVAVSKGEADLGIIPLENSLKGTVGQNVDLFMRYPVYIQAELYHRISHGLISK- 180 Query: 442 KIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML---DDYSAAIMSEN 498 + L EIKT+YSH +A+ QC G++ LP V + ST+ AA+M+ D+ AA+ Sbjct: 181 GVGLDEIKTVYSHSKALEQCTGWLRANLPGVPLVPVDSTAQAAQMVADSDEPIAALGHVK 240 Query: 499 AARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEGK--ITSLFFGVEDKPGALKDVLE 556 A + LHV+ + I+DL N TRF +I + G+ EGK T++ F D+PGAL VL Sbjct: 241 LANIFGLHVVAEAIEDLSD-NWTRFLIIGPKPGK-EGKRDKTTILFTTPDRPGALVSVLN 298 Query: 557 VFHKKGFNLRKLESRPAGTGLGDYVFFVEVEAPLREED----LLDLKQVTTFYKVVGVF 611 + K N+ KLESRP Y+FFV+++ LR E+ + DLK +K++G + Sbjct: 299 ELYGKDINMTKLESRPFLGEKWKYMFFVDLQGDLRAEEYESLIEDLKSRCLTFKILGSY 357 Lambda K H 0.320 0.137 0.380 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: 477 Number of extensions: 21 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: 620 Length of database: 367 Length adjustment: 33 Effective length of query: 587 Effective length of database: 334 Effective search space: 196058 Effective search space used: 196058 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: 51 (24.3 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