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 5208561 Shew_1072 chorismate mutase (RefSeq)
Query= BRENDA::O30012 (620 letters) >FitnessBrowser__PV4:5208561 Length = 654 Score = 150 bits (378), Expect = 2e-40 Identities = 108/376 (28%), Positives = 195/376 (51%), Gaps = 28/376 (7%) Query: 262 KAESIEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEVMSK 321 K + R I ++D+ +L L+ +R + +AR K PI E+E L ++ + Sbjct: 3 KPHPLSHTREQITALDNELLALLAKRRALSLDVARSKEVDIRPIRDTQREKELLARLVKQ 62 Query: 322 TT---LNPVKLKEIFEGIM--SLAKEEEY-------KVAGVKYTIAVLGPQGSFSEEMAL 369 L+ + +++ I+ S+ ++ Y + +Y IA LG +GS+S A Sbjct: 63 GREQGLDAHYVLSLYQSIIEDSVLNQQAYLQGRANPDLQKQQYNIAYLGARGSYSYLAAT 122 Query: 370 KLVGSR---VPLRYCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVF 426 + R + C + DEI++ VESG DYG +PIEN+ +G++ V D L + + + Sbjct: 123 RYCERRQVGMQDLGCKSFDEIVQAVESGHADYGFLPIENTSSGSINEVYDVLQHTSLAIV 182 Query: 427 GEAKLEVNHCLVAKRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARM 486 GE +EV HCL+AK +K+IKTIY+HPQ ++QC +++ + + Y +S+++A Sbjct: 183 GETTIEVGHCLLAKPGTNVKQIKTIYAHPQPISQCSRYLSQH-GEFKLEYCSSSAEAMER 241 Query: 487 L----DDYSAAIMSENAARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEGKI---TS 539 + D+ AAI S Y+L + + + K N +RF ++ R++ ++ T+ Sbjct: 242 VLEADDNSVAAIGSVEGGALYQLEAVEHELANQK-INQSRFIVVARKAIAVPEQLPAKTT 300 Query: 540 LFFGVEDKPGALKDVLEVFHKKGFNLRKLESRPAGTGLGDYVFFVEVEAPLREED----L 595 L KPGAL + L + N+ KLESRP + +F+++++A L ++ L Sbjct: 301 LIMATGQKPGALVEALLILKAHDLNMSKLESRPIPGTPWEEMFYLDLDANLASDEMQQAL 360 Query: 596 LDLKQVTTFYKVVGVF 611 +L+++T F KV+G + Sbjct: 361 KELERITRFIKVLGCY 376 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: 745 Number of extensions: 34 Number of successful extensions: 4 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: 654 Length adjustment: 38 Effective length of query: 582 Effective length of database: 616 Effective search space: 358512 Effective search space used: 358512 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: 54 (25.4 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