Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate Echvi_0125 Echvi_0125 Prephenate dehydrogenase
Query= uniprot:D8IR44_HERSS (295 letters) >FitnessBrowser__Cola:Echvi_0125 Length = 282 Score = 138 bits (348), Expect = 1e-37 Identities = 90/260 (34%), Positives = 134/260 (51%), Gaps = 12/260 (4%) Query: 3 KKVVIFGVGLIGGSFALALRRAGQAAHIVGVGRSLQSLERARELGIIDAVATDAASAVQG 62 K++ I G+GL+GGSF+L L++A + G + L+ A LGIID V+ + Sbjct: 2 KQIHIIGLGLLGGSFSLGLKKALTGLSVSGFDLNKGHLQEALSLGIIDRVSETVPA---D 58 Query: 63 ADLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDRIVQFIPAHP 122 DL++VA PV I++ + H+ P+ +V D GSTK + ++ + F+ AHP Sbjct: 59 TDLVIVATPVDTISGIVSRLLDHIPPETLVVDFGSTKEHICSSVSGHAHRQ--NFLAAHP 116 Query: 123 IAGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAV---IHRLSPQEH 179 IAG E GP AA +L +GK I L E D ++ A+RA A+ I + P EH Sbjct: 117 IAGTEYAGPSAAFPDLLKGK---IMILCETDKTGPDLCKKAYRAFEALEMQIRIMGPHEH 173 Query: 180 DAVFASVSHLPHVLAFALVDDIAAK-PHAATLFQYAASGFRDFTRIAASSPEMWRDITLA 238 D A VSHL H+ +F L + K + A SGF R+A SSP MW I Sbjct: 174 DNQLAFVSHLSHISSFMLGKTVLDKMEDDKHILNMAGSGFASTVRLAKSSPSMWTPIMKE 233 Query: 239 NRDALLTEVDAYLLQLQNIR 258 N++ +L ++ Y+ L + R Sbjct: 234 NKENILEALNGYIENLASFR 253 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: 173 Number of extensions: 13 Number of successful extensions: 5 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: 282 Length adjustment: 26 Effective length of query: 269 Effective length of database: 256 Effective search space: 68864 Effective search space used: 68864 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