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 6936711 Sama_0898 prephenate dehydratase / chorismate mutase / phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)
Query= BRENDA::O30012 (620 letters) >FitnessBrowser__SB2B:6936711 Length = 659 Score = 162 bits (411), Expect = 3e-44 Identities = 114/378 (30%), Positives = 198/378 (52%), Gaps = 30/378 (7%) Query: 261 KKAESIEELRGLIKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEVMS 320 +K + + E R I ID+ +L+L+ RR + + ++AR K P+ E E L ++ Sbjct: 2 EKPQPLSETREQITDIDNTVLQLLARRRELSLEVARSKEVDVRPVRDTQRERELLSRLVQ 61 Query: 321 KTT---LNPVKLKEIFEGIM--SLAKEEEY-------KVAGVKYTIAVLGPQGSFSEEMA 368 K L+P + ++++ I+ S+ ++ Y + +Y IA LG +GS+S A Sbjct: 62 KGREQGLDPHFVMQLYQSIIEDSVLNQQAYLHGRANPETQKQQYCIAYLGARGSYSYLAA 121 Query: 369 LKLVGSR----VPLRYCSTTDEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVE 424 + R V L C + DEI+ VESG DYG +PIEN+ +G++ V D L + + Sbjct: 122 NRYCQRRQVDMVDLG-CQSFDEIVHAVESGHADYGFLPIENTSSGSINEVYDVLQHTSLA 180 Query: 425 VFGEAKLEVNHCLVAKRKIELKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAA 484 + GE +EV HCL+AK + +IKT+Y+HPQ ++QC ++ + P + + Y S+++A Sbjct: 181 IVGETTIEVGHCLLAKPGTKASDIKTLYAHPQPISQCSRYLARH-PGLRLEYCASSAEAM 239 Query: 485 RMLDDYS----AAIMSENAARFYRLHVLRKGIQDLKGRNITRFYLIRRRSGRSEGKI--- 537 + AAI S Y+L + KG+ + K N +RF ++ R++ ++ Sbjct: 240 EKVQAADSKDVAAIGSAEGGGLYQLEAIEKGLANQK-VNQSRFIVVARKAVAVPEQLPAK 298 Query: 538 TSLFFGVEDKPGALKDVLEVFHKKGFNLRKLESRPAGTGLGDYVFFVEVEAPL----REE 593 +L KPGAL + L V N+ KLESRP + +F+++++A L + Sbjct: 299 CTLIMATGQKPGALVEALLVLKANNLNMSKLESRPIPGTPWEEMFYLDIDANLASVPMQL 358 Query: 594 DLLDLKQVTTFYKVVGVF 611 L +L+++T F KV+G + Sbjct: 359 ALKELERITRFIKVLGCY 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: 698 Number of extensions: 33 Number of successful extensions: 2 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: 659 Length adjustment: 38 Effective length of query: 582 Effective length of database: 621 Effective search space: 361422 Effective search space used: 361422 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