Align Cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase (characterized, see rationale)
to candidate WP_041787733.1 RVAN_RS15320 prephenate/arogenate dehydrogenase family protein
Query= uniprot:Q92MG1 (307 letters) >NCBI__GCF_000166055.1:WP_041787733.1 Length = 310 Score = 386 bits (991), Expect = e-112 Identities = 189/306 (61%), Positives = 235/306 (76%) Query: 2 AQQFQTIALIGIGLIGSSIARDIREKQLAGTIVVTTRSEATLKRAGELGLGDRYTLSAAE 61 A F+ +ALIG+GLIGSS++ +R LA TI + R+EAT LGL D AA+ Sbjct: 4 APMFEKVALIGVGLIGSSLSHAMRRANLARTIAASARTEATRAAVRRLGLADEVYEHAAD 63 Query: 62 AVEGADLVVVSVPVGASGAVAAEIAAHLKPGAIVTDVGSTKGSVIAQMAPHLPKDVHFVP 121 AV+GADLV++ PVG A+A EIA HLK GAI++D GS K +V+ +APHLP VHF+P Sbjct: 64 AVKGADLVILCTPVGTFDALAQEIAPHLKDGAILSDAGSVKQAVVDAVAPHLPPHVHFIP 123 Query: 122 GHPIAGTEHSGPDAGFAGLFRGRWCILTPPAGTDEEAVARLRLFWETLGSMVDEMDPKHH 181 GHPIAGTE SGP++GFA LF GRW ILTP DE AVA+L+ FWE G+ V+ M+PKHH Sbjct: 124 GHPIAGTEFSGPESGFAELFDGRWTILTPLPDADEAAVAKLKAFWEACGAHVEIMEPKHH 183 Query: 182 DKVLAIVSHLPHIIAYNIVGTADDLETVTESEVIKYSASGFRDFTRLAASDPTMWRDVCL 241 D VLAI SHLPH+IAYNIVGT DLE +SEVIK+SASGFRDFTR+AASDPTMWRD+ + Sbjct: 184 DLVLAITSHLPHLIAYNIVGTVADLEEEKKSEVIKFSASGFRDFTRIAASDPTMWRDIFI 243 Query: 242 HNKDAILEMLARFSEDLASLQRAIRWGDGDKLFDLFTRTRAIRRSIVQAGQDTAMPDFGR 301 +NK+A+LE+L RF+EDLA++QR IRWG+GDKLFD FTRTRA+RRSI+ AGQ++ P+FGR Sbjct: 244 NNKEAVLEILGRFTEDLAAMQRHIRWGEGDKLFDKFTRTRAVRRSIIDAGQESPEPNFGR 303 Query: 302 HAMDQK 307 +K Sbjct: 304 TPAPKK 309 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: 317 Number of extensions: 11 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: 310 Length adjustment: 27 Effective length of query: 280 Effective length of database: 283 Effective search space: 79240 Effective search space used: 79240 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