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_057506775.1 ABB28_RS00665 chorismate mutase
Query= BRENDA::O30012 (620 letters) >NCBI__GCF_001431535.1:WP_057506775.1 Length = 398 Score = 150 bits (379), Expect = 1e-40 Identities = 116/361 (32%), Positives = 189/361 (52%), Gaps = 25/361 (6%) Query: 266 IEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEE----KLWEVMSK 321 + ++RG I ID I LI R A Q+ + K + ++ E E ++ ++ Sbjct: 43 LADVRGKIDQIDRDIQSLIAERARFAHQVGKAKGKLAAAVDYYRPEREAQVLRMVVDRNE 102 Query: 322 TTLNPVKLKEIFEGIMS--LAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVPLR 379 L+ L ++ IMS LA++E K I LGP+G+FS++ LK G Sbjct: 103 GPLSDELLVHVYREIMSACLAQQEPLK-------IGYLGPEGTFSQQAVLKHFGRSALGL 155 Query: 380 YCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCLVA 439 ++ +E+ + VE+G D+G+VP+ENS GT+ +D L ++++ GEA+L V +++ Sbjct: 156 PMASIEEVFQEVEAGNADFGVVPVENSGQGTIQITLDMFLTSNLKICGEAELRVQQYIMS 215 Query: 440 KRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARML--DDYSAAIMSE 497 R L++I+ IY+HPQ+ Q ++ LP +S ++ AR D +AAI E Sbjct: 216 -RSGHLEDIERIYAHPQSFMQTSAWLRANLPKAEKIPVSSNAEGARRARNADDAAAIGGE 274 Query: 498 NAARFYRL-HVLRKGIQDLKGRNITRFYLIRRRSGRSEG-KITSLFFGVEDKPGALKDVL 555 NA Y L V+ K IQ+ N TRF +I R S G TS+ + DKPGAL DVL Sbjct: 275 NAGHVYNLKKVVTKPIQN-DADNTTRFLVIGRSLFPSSGHDRTSVLVLIHDKPGALFDVL 333 Query: 556 EVFHKKGFNLRKLESRPAGTGLGDYVFFVEV-----EAPLREEDLLDLKQVTTFYKVVGV 610 F + G ++ ++ESRP+ G +Y FF+++ +AP+ + L +L+ KV+G Sbjct: 334 SPFARHGISMNRIESRPSHHGKWEYGFFIDLSGHIDDAPM-QAALAELEGHAAQIKVLGS 392 Query: 611 F 611 + Sbjct: 393 Y 393 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: 450 Number of extensions: 21 Number of successful extensions: 3 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: 398 Length adjustment: 34 Effective length of query: 586 Effective length of database: 364 Effective search space: 213304 Effective search space used: 213304 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: 52 (24.6 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