Align Cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase (characterized, see rationale)
to candidate GFF2491 PGA1_c25230 protein TyrC
Query= uniprot:Q92MG1 (307 letters) >FitnessBrowser__Phaeo:GFF2491 Length = 306 Score = 362 bits (930), Expect = e-105 Identities = 185/297 (62%), Positives = 219/297 (73%) Query: 5 FQTIALIGIGLIGSSIARDIREKQLAGTIVVTTRSEATLKRAGELGLGDRYTLSAAEAVE 64 + IALIG+GLI SS+A IR LA I RS T A + L DR +AAEA + Sbjct: 6 YNRIALIGLGLIASSMAHAIRRGGLASEITGYARSAETRDTARRINLCDRVCDTAAEAAQ 65 Query: 65 GADLVVVSVPVGASGAVAAEIAAHLKPGAIVTDVGSTKGSVIAQMAPHLPKDVHFVPGHP 124 ADL+V+ VPVGA AV A+IA LKPGA V+DVGS K VI + PH+P+ VHFVP HP Sbjct: 66 DADLIVLCVPVGAMDAVMADIAPVLKPGATVSDVGSVKRHVIDAVQPHIPEGVHFVPAHP 125 Query: 125 IAGTEHSGPDAGFAGLFRGRWCILTPPAGTDEEAVARLRLFWETLGSMVDEMDPKHHDKV 184 +AGTEHSGP+AGFA L+ RWC+L P G+D V RLR WE +G+ VDEMD HHD V Sbjct: 126 LAGTEHSGPEAGFAELYDNRWCLLVPVEGSDRAPVDRLRQLWEGMGANVDEMDADHHDLV 185 Query: 185 LAIVSHLPHIIAYNIVGTADDLETVTESEVIKYSASGFRDFTRLAASDPTMWRDVCLHNK 244 LA+ SH PH+IAY +VG ADDL VT+SEVIKYSA+GFRDFTR+AASDPTMWRDV L NK Sbjct: 186 LAVTSHAPHLIAYTMVGVADDLRRVTDSEVIKYSAAGFRDFTRIAASDPTMWRDVFLTNK 245 Query: 245 DAILEMLARFSEDLASLQRAIRWGDGDKLFDLFTRTRAIRRSIVQAGQDTAMPDFGR 301 DA LE+L RF+E+L +LQRAIR GDG+ L FTRTRAIRR I++AGQDTA P+FGR Sbjct: 246 DATLEILGRFTEELFALQRAIRTGDGEHLHQYFTRTRAIRRGIIEAGQDTAAPNFGR 302 Lambda K H 0.320 0.135 0.398 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: 281 Number of extensions: 7 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: 307 Length of database: 306 Length adjustment: 27 Effective length of query: 280 Effective length of database: 279 Effective search space: 78120 Effective search space used: 78120 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 (21.8 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