Align Cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase (characterized, see rationale)
to candidate WP_015932245.1 MNOD_RS27460 prephenate dehydrogenase/arogenate dehydrogenase family protein
Query= uniprot:Q92MG1 (307 letters) >NCBI__GCF_000022085.1:WP_015932245.1 Length = 309 Score = 391 bits (1005), Expect = e-114 Identities = 198/294 (67%), Positives = 227/294 (77%) Query: 8 IALIGIGLIGSSIARDIREKQLAGTIVVTTRSEATLKRAGELGLGDRYTLSAAEAVEGAD 67 +AL+G+GLIGSSIAR R L TIV R A L+R LGL D T A V AD Sbjct: 11 LALVGLGLIGSSIARGARANDLVDTIVAIDRDPAVLERVRTLGLADHVTDDLAAGVAEAD 70 Query: 68 LVVVSVPVGASGAVAAEIAAHLKPGAIVTDVGSTKGSVIAQMAPHLPKDVHFVPGHPIAG 127 LV++ VPVGA G V A +A LKPGAI++DVGS KG+V+A APH+P FVP HP+AG Sbjct: 71 LVILCVPVGAVGPVTAALAGALKPGAILSDVGSVKGAVMAAAAPHVPDHAAFVPAHPVAG 130 Query: 128 TEHSGPDAGFAGLFRGRWCILTPPAGTDEEAVARLRLFWETLGSMVDEMDPKHHDKVLAI 187 TE SGPDAGFA LF+GRWCILTPP GT EAVAR+R FWE LGS+V+ M HHD VLAI Sbjct: 131 TEQSGPDAGFATLFQGRWCILTPPEGTPPEAVARVRGFWEGLGSVVETMTAAHHDLVLAI 190 Query: 188 VSHLPHIIAYNIVGTADDLETVTESEVIKYSASGFRDFTRLAASDPTMWRDVCLHNKDAI 247 SH+PH+IAYNIVGTA DLETVT+SEVIK+SA GFRDFTR+AASDPTMWRDV L+NK+A+ Sbjct: 191 TSHVPHLIAYNIVGTAADLETVTQSEVIKFSAGGFRDFTRIAASDPTMWRDVFLNNKEAV 250 Query: 248 LEMLARFSEDLASLQRAIRWGDGDKLFDLFTRTRAIRRSIVQAGQDTAMPDFGR 301 LE+L RF+EDLA+L RAIRW DGD L LFTRTRAIRR IV GQ+TA PDFGR Sbjct: 251 LEVLGRFNEDLAALARAIRWDDGDALHALFTRTRAIRRGIVAMGQETAEPDFGR 304 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: 310 Number of extensions: 9 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: 309 Length adjustment: 27 Effective length of query: 280 Effective length of database: 282 Effective search space: 78960 Effective search space used: 78960 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 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