Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate BPHYT_RS14900 BPHYT_RS14900 prephenate dehydrogenase
Query= uniprot:D8IR44_HERSS (295 letters) >FitnessBrowser__BFirm:BPHYT_RS14900 Length = 313 Score = 330 bits (845), Expect = 3e-95 Identities = 178/290 (61%), Positives = 213/290 (73%), Gaps = 8/290 (2%) Query: 2 FKKVVIFGVGLIGGSFALALRRAGQA---AHIVGVGRSLQSLERARELGIIDAVAT---D 55 F K+VIFGVGLIGGS A ALR G+A ++GVGRS S ERA ELG+ID A+ D Sbjct: 9 FNKLVIFGVGLIGGSLARALRERGEADGARKVIGVGRSSASTERALELGVIDGSASLNDD 68 Query: 56 AA--SAVQGADLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDR 113 AA A++GAD +L+AAPVAQT P+L IAP L+ IVTDAGSTKSDVVAAAR ALG R Sbjct: 69 AALSEALKGADFVLLAAPVAQTQPLLERIAPFLDAATIVTDAGSTKSDVVAAARAALGAR 128 Query: 114 IVQFIPAHPIAGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHR 173 I QF+P HPIAGRE G EAAL +LY G+ VV+ LPEN ADVE VAA WRA GA++ Sbjct: 129 IGQFVPGHPIAGREASGVEAALPDLYVGRNVVLCPLPENAPADVERVAAMWRATGALVRD 188 Query: 174 LSPQEHDAVFASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWR 233 ++P++HD V ASVSHLPHVL+FALV+ I P AA F +AA GFRDFTRIAASSPEMWR Sbjct: 189 MAPEQHDRVLASVSHLPHVLSFALVEQILNSPDAALKFSFAAGGFRDFTRIAASSPEMWR 248 Query: 234 DITLANRDALLTEVDAYLLQLQNIRAMIAAGDGPGIEKIYASAQHARQQW 283 D+ +ANR ALL E+DAY L +RA I A DG +E ++A ++ AR +W Sbjct: 249 DVCVANRVALLDELDAYTAVLARLRAAIEAADGAALEAVFARSRVARTEW 298 Lambda K H 0.320 0.132 0.376 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: 302 Number of extensions: 9 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: 295 Length of database: 313 Length adjustment: 27 Effective length of query: 268 Effective length of database: 286 Effective search space: 76648 Effective search space used: 76648 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 (21.9 bits) S2: 48 (23.1 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