Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate GFF1943 Psest_1986 3-phosphoshikimate 1-carboxyvinyltransferase
Query= uniprot:D8IR44_HERSS (295 letters) >FitnessBrowser__psRCH2:GFF1943 Length = 747 Score = 223 bits (569), Expect = 8e-63 Identities = 118/284 (41%), Positives = 165/284 (58%) Query: 1 MFKKVVIFGVGLIGGSFALALRRAGQAAHIVGVGRSLQSLERARELGIIDAVATDAASAV 60 + ++V+ G+GLIGGSFA LR AG +VG +S E A ELG++D A A A Sbjct: 13 ILNRLVVIGLGLIGGSFAKGLREAGLCREVVGFDLDARSRELAVELGVVDRCADTLAEAC 72 Query: 61 QGADLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFIPA 120 GAD+I +A P+ +L +A A++TD GS K +VV AR G+ +F+P Sbjct: 73 HGADVIQLATPILALERLLGELAKLELGGAVITDVGSAKGNVVRCARNVFGEMPSRFVPG 132 Query: 121 HPIAGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHRLSPQEHD 180 HPIAG E G AA + L+ KV++T L D + +V W A GA + + HD Sbjct: 133 HPIAGSELSGVTAANSTLFRRHKVILTPLENTDPQALALVTKLWSALGADVEHMGVAHHD 192 Query: 181 AVFASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWRDITLANR 240 V A+ SHLPH+LAF LVD +A + +F+YAA GFRDFTRIA S P MW DI LANR Sbjct: 193 EVLAATSHLPHLLAFGLVDSLAKRHENLEIFRYAAGGFRDFTRIAGSDPVMWHDIFLANR 252 Query: 241 DALLTEVDAYLLQLQNIRAMIAAGDGPGIEKIYASAQHARQQWA 284 +A+L +D + L +RA + GDG + ++ A+ AR+ ++ Sbjct: 253 EAVLHTLDDFRADLDALRAAVDEGDGHRLLGVFTRAKAAREHFS 296 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: 519 Number of extensions: 24 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: 747 Length adjustment: 33 Effective length of query: 262 Effective length of database: 714 Effective search space: 187068 Effective search space used: 187068 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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