Align Probable prephenate dehydrogenase NovF; EC 1.3.1.12; Novobiocin biosynthesis protein F (uncharacterized)
to candidate WP_058929409.1 AU252_RS02695 prephenate dehydrogenase
Query= curated2:Q9L9G2 (362 letters) >NCBI__GCF_001484605.1:WP_058929409.1 Length = 369 Score = 199 bits (507), Expect = 7e-56 Identities = 132/358 (36%), Positives = 187/358 (52%), Gaps = 13/358 (3%) Query: 5 VIIGTGMIGTSIGLALRKQGVDSYLMDTSPVALRIAEAVGAGTAEEP--PETVDLAVVAV 62 V+IGTG++G SIGL LR +GV +L D SP +A +GAG + E +L VVA Sbjct: 17 VVIGTGLLGASIGLGLRGRGVPVFLSDPSPTNQAVAVDIGAGQPLDQLGDEAPELVVVAA 76 Query: 63 PPVHVAPVIASHQSRGTARFYVDVAGVKVSTRRELDALGCDLATVVGGHPLVGRPGSGPL 122 PP A V+A + VD+A VK + EL G DLA VG HP+ GR SGP+ Sbjct: 77 PPDVTADVVARALADYPDSVVVDIASVKAAILAELGGRGADLARYVGTHPMAGREKSGPV 136 Query: 123 AARGDLFDGRPWALVPAVGTDAAALNRALELVAACGAIPVVLDAEAHDRAIALGTLVPQI 182 AARG+LF PW + P + AAA+ A L GA+ A+ HD A+AL + +PQI Sbjct: 137 AARGELFTSMPWVVCPGPESSAAAVQTARSLATDLGAVVSQFTADEHDEAVALVSHLPQI 196 Query: 183 ALTLVAARLTEADSGALRLLGSVWSEIPQLVGVDSATSWTQVLAANAAPVVGELEKLSRD 242 +L+A+RL AL L G+ ++ ++ D T W Q+L NA VV L + D Sbjct: 197 MSSLLASRLQGTPLHALSLAGNGLRDVTRIAASD-PTLWVQILGGNAGKVVEILYGVRED 255 Query: 243 LASLLETLRGVADGDGSLAEPDGR--LLEFIQRGIDGSNRVPGRYGIPTETALADVDVSV 300 L L+ TL + LA P R L + I G G R+PG++G P + A + + V V Sbjct: 256 LNRLIGTL------EEPLA-PGARLDLAQLISEGNAGQARIPGKHGGPPQ-AYSWLTVLV 307 Query: 301 DDRPAELARLFDDVAGAGVVMRGIDISQRPDSPDRTVTISVTPRDAENLLHELRRRKW 358 DDRP ++A+L ++ GV + + + V +SV P ++L+ L R W Sbjct: 308 DDRPGQIAQLLTEIGEIGVNVEDLRLDHSSGQNVGMVELSVLPNKHDHLIEALNDRGW 365 Lambda K H 0.317 0.135 0.390 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: 346 Number of extensions: 23 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: 362 Length of database: 369 Length adjustment: 30 Effective length of query: 332 Effective length of database: 339 Effective search space: 112548 Effective search space used: 112548 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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