Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_020562931.1 A3OW_RS0108110 prephenate dehydratase
Query= BRENDA::O22241 (424 letters) >NCBI__GCF_000372865.1:WP_020562931.1 Length = 361 Score = 139 bits (350), Expect = 1e-37 Identities = 97/287 (33%), Positives = 142/287 (49%), Gaps = 22/287 (7%) Query: 125 LRVAYQGVPGAYSEAAAGKAYPNC-DAIPCDQFDVAFQAVELWIADRAVLPVENSLGGSI 183 L VA+ G G +++ AA K + + + +P + F +VEL V+PVENS G I Sbjct: 92 LEVAFLGPEGTFTQQAAFKHFGHAINTVPVASINEIFNSVELNKCHFGVVPVENSTEGVI 151 Query: 184 HRNYDLLLRHRLHIVGEVQIPVHHCLLALPGVRTDCVSRVISHPQALAQTEHSLDVLTPH 243 + D L L I GEV++ VH L+ ++ ++ V SH Q+LAQ + LD PH Sbjct: 152 NHTLDRFLTSPLKICGEVEVKVHQNLMGHTESLSE-ITEVFSHQQSLAQCRYWLDKYLPH 210 Query: 244 AAREAFHDTAAAAEYISANDLHDTAAVASARAAELYNLQILADGIQDDPGNVTRFLMLAR 303 A A A AA S N TAAVA AAE+Y L ++ I+D+P N TRF+++ + Sbjct: 211 ARLTAVASNAEAARLASVN--KSTAAVAGMVAAEVYQLPVIEKNIEDEPNNTTRFIVIGQ 268 Query: 304 EPIIPRTDRPFKTSIVFAAQEHKGTSVLFKVLSAFAFRDISLTKIESRPHHNRPLRVVGD 363 + + KTS+V + G L+K L FA I + IESRP Sbjct: 269 Q--TSSSTGKDKTSLVISTGNQPG--ALYKALEPFARFSIGMVNIESRP----------- 313 Query: 364 GSFGTSKNFEYMFYVDFEASMAEPRAQNALAEVQEYTSFLRVLGSYP 410 +EY+F++D E +P AL ++ S L++LGSYP Sbjct: 314 ---SRQGLWEYVFFIDIEGHSEDPNVAEALEILKGTVSMLKLLGSYP 357 Lambda K H 0.318 0.131 0.387 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: 301 Number of extensions: 15 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: 424 Length of database: 361 Length adjustment: 31 Effective length of query: 393 Effective length of database: 330 Effective search space: 129690 Effective search space used: 129690 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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