Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate GFF1397 HP15_1364 3-phosphoshikimate 1-carboxyvinyltransferase
Query= uniprot:D8IR44_HERSS (295 letters) >FitnessBrowser__Marino:GFF1397 Length = 742 Score = 243 bits (621), Expect = 7e-69 Identities = 125/284 (44%), Positives = 173/284 (60%) Query: 1 MFKKVVIFGVGLIGGSFALALRRAGQAAHIVGVGRSLQSLERARELGIIDAVATDAASAV 60 +FK+V + G+GLIGGS A A+RR G A +VG + L+ +ELG+ID A+ + AV Sbjct: 7 LFKRVAVIGLGLIGGSLACAIRRKGLAVTVVGADHRTEELQLGKELGVIDQAASTVSDAV 66 Query: 61 QGADLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFIPA 120 +GADL+++A PV T +L I P LEP AI+TD GSTKS VA G IP Sbjct: 67 RGADLVVLAVPVRATRAVLEQIRPALEPDAILTDVGSTKSSFVADVEAVFGGLSPLVIPG 126 Query: 121 HPIAGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHRLSPQEHD 180 HPIAG EK G AA EL+ KV++T + + W CGA + +S HD Sbjct: 127 HPIAGSEKSGIRAANPELFANHKVILTPPDNVSQPHLARLKGLWEGCGATVLTMSVAYHD 186 Query: 181 AVFASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWRDITLANR 240 V A+ SHLPH++AF+LVD +A + +F+YAA GFRDFTRIAAS P MW DI L+NR Sbjct: 187 EVLAATSHLPHLIAFSLVDTLAGEDENMDIFRYAAGGFRDFTRIAASDPVMWHDIFLSNR 246 Query: 241 DALLTEVDAYLLQLQNIRAMIAAGDGPGIEKIYASAQHARQQWA 284 DA+L +D + L+ +R IA D + ++++ A+ AR+ ++ Sbjct: 247 DAVLRVIDHFTHDLEQLRTAIANQDSATLLRVFSRAKAAREHFS 290 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: 502 Number of extensions: 22 Number of successful extensions: 1 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: 742 Length adjustment: 33 Effective length of query: 262 Effective length of database: 709 Effective search space: 185758 Effective search space used: 185758 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: 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