Align Probable prephenate dehydrogenase NovF; EC 1.3.1.12; Novobiocin biosynthesis protein F (uncharacterized)
to candidate WP_011603419.1 FRAAL_RS09830 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= curated2:Q9L9G2 (362 letters) >NCBI__GCF_000058485.1:WP_011603419.1 Length = 371 Score = 164 bits (414), Expect = 5e-45 Identities = 119/361 (32%), Positives = 172/361 (47%), Gaps = 8/361 (2%) Query: 1 MRTAVIIGTGMIGTSIGLALRKQGVDSYLMDTSPVALRIAEAVGAGTAEEPPETVDLAVV 60 +R ++GTG+IG SIGLAL QGV+ L D + IA +GAG E V+ AVV Sbjct: 14 LRRVGVVGTGLIGASIGLALSAQGVEVLLRDADEAQVAIAAKMGAGQPWAAGERVEHAVV 73 Query: 61 AVPPVHVAPVIASHQSRGTARFYVDVAGVKVSTRRELDALGCDLATVVGGHPLVGRPGSG 120 A P + + + G A D VKV E LGCDL+T HP+ GR G Sbjct: 74 ATPLPTIPAEVRALARAGLADTVSDAGSVKVRPLVEGVQLGCDLSTWCPAHPIAGRERHG 133 Query: 121 PLAARGDLFDGRPWALVPAVGTDAAALNRALELVAACGAIPVVLDAEAHDRAIALGTLVP 180 ++AR DLF R WA+ P T AAAL+ + L ACGA PV + HD A+A + VP Sbjct: 134 AVSARADLFAERVWAVCPVPHTGAAALHATVALALACGATPVRTTPQRHDEAMATVSHVP 193 Query: 181 QIALTLVAARLTEADSGALRLLGSVWSEIPQLVGVDSATSWTQVLAANAAPVVGELEKLS 240 Q+ + +A L G + L G + + +L D A W ++ N P+ + Sbjct: 194 QLVASALAGVLVGLAPGEVPLAGQGFRDTTRLADSD-AELWAGIVEGNRGPIARRV---- 248 Query: 241 RDLASLLETLRGVADGDGSLAEPDGRLLEFIQRGIDGSNRVPGRYGIPTETALADVDVSV 300 RDL S L L V D G+ + + ++ G G +P + G T + V V + Sbjct: 249 RDLGSRLTALADVLDAAGA-DDVTTAVTRLMRDGHAGRALLPRKAG-ATARSWGWVGVVL 306 Query: 301 DDRPAELARLFDDVAGAGVVMRGI-DISQRPDSPDRTVTISVTPRDAENLLHELRRRKWP 359 DDRP +LA + ++ V + + D+P V ++V P A++L+ L W Sbjct: 307 DDRPGQLAAIVGLISRWDVNIEDVGPFEHSLDAPAGIVELAVDPAVADSLVDRLTATGWT 366 Query: 360 A 360 A Sbjct: 367 A 367 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: 393 Number of extensions: 26 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: 362 Length of database: 371 Length adjustment: 30 Effective length of query: 332 Effective length of database: 341 Effective search space: 113212 Effective search space used: 113212 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