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 Ac3H11_2574 Chorismate mutase I (EC 5.4.99.5) / Prephenate dehydratase (EC 4.2.1.51)
Query= BRENDA::O30012 (620 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2574 Length = 351 Score = 169 bits (428), Expect = 2e-46 Identities = 121/358 (33%), Positives = 184/358 (51%), Gaps = 32/358 (8%) Query: 273 IKSIDSLILRLIERRIDAARQIARIKMERGEPIELKDVEEEKLWEVMSKTT-LNPVKLK- 330 I SID +L L+ +R A Q+ +K G P D ++ +V+ K T NP LK Sbjct: 3 IDSIDQQLLTLLNQRALVAEQVGEVKKREGTPFFRPD----RVAQVIDKITHANPGPLKG 58 Query: 331 ----EIFEGIMS--LAKEEEYKVAGVKYTIAVLGPQGSFSEEMALKLVGSRVPLRYCSTT 384 I+ IMS LA E +VA VLGP+G+F E+ A++ G L YC+ Sbjct: 59 PHVAAIWREIMSACLALESPQRVA-------VLGPEGTFCEQAAIEFFGGAADLMYCANF 111 Query: 385 DEIIKLVESGEVDYGLVPIENSVNGTVLPVIDALLNHDVEVFGEAKLEVNHCLVAKRKIE 444 DE+ +G YG+V +ENS G V +D L+ V GE L V H L+ + Sbjct: 112 DEVFHATAAGSAQYGVVGVENSTEGVVTRSLDLFLHTPTHVVGEVSLLVRHNLL-RTTNS 170 Query: 445 LKEIKTIYSHPQAVAQCMGFINNYLPSVAIRYTTSTSDAARM--LDDYSAAIMSENAARF 502 L I+ + +HPQA+AQC +++ +LP R +S ++ AR+ + AA+ SE AA Sbjct: 171 LDGIEAVLAHPQALAQCQAWLSKHLPHAERRPVSSNAEGARLATTNPAWAALSSERAATQ 230 Query: 503 YRLHVLRKGIQDLKGRNITRFYLI----RRRSGRSEGK-ITSLFFGVEDKPGALKDVLEV 557 + LH++ IQD N TRF +I ++ GK TSL V ++PGA+ D+L Sbjct: 231 FGLHIVSHAIQD-DAYNRTRFAIICLPHTLQTPPPSGKDCTSLVVSVPNQPGAVHDLLVP 289 Query: 558 FHKKGFNLRKLESRPAGTGLGDYVFFVEVEA----PLREEDLLDLKQVTTFYKVVGVF 611 G ++ + ESRPA TG +Y F+++++ P L +L+ + FYKV+G + Sbjct: 290 LKTHGVSMTRFESRPARTGQWEYYFYIDLDGHPAQPHVARALEELRSLCAFYKVLGTY 347 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: 365 Number of extensions: 19 Number of successful extensions: 6 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: 351 Length adjustment: 33 Effective length of query: 587 Effective length of database: 318 Effective search space: 186666 Effective search space used: 186666 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 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