Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_086508931.1 BZY95_RS05310 prephenate dehydratase
Query= BRENDA::O22241 (424 letters) >NCBI__GCF_002151265.1:WP_086508931.1 Length = 363 Score = 147 bits (371), Expect = 5e-40 Identities = 102/287 (35%), Positives = 148/287 (51%), Gaps = 21/287 (7%) Query: 126 RVAYQGVPGAYSEAAAGKAY-PNCDAIPCDQFDVAFQAVELWIADRAVLPVENSLGGSIH 184 +VAY G G +++ AA K + + ++P D F+ VE + V+PVENS G + Sbjct: 94 KVAYLGPEGTFTQQAALKHFGQSAVSMPMAAIDEVFREVEAGAVNYGVVPVENSTEGVVS 153 Query: 185 RNYDLLLRHRLHIVGEVQIPVHHCLLALPGVRTDCVSRVISHPQALAQTEHSLDVLTPHA 244 D + + I GEV + +HH LL D VSRV SHPQ+LAQ LD P A Sbjct: 154 HTLDSFMDSSIRICGEVVLRIHHHLLVADTTLRDKVSRVYSHPQSLAQCRKWLDAHYPRA 213 Query: 245 AREAFHDTAAAAEYISANDLHDTAAVASARAAELYNLQILADGIQDDPGNVTRFLMLARE 304 R A AA+ I +AA+A AA+LY L+ +A+ I+D P N TRFL++ + Sbjct: 214 ERVPVSSNAEAAKMIKGE--WHSAAIAGDMAAKLYGLEKVAEKIEDRPDNSTRFLIIGSQ 271 Query: 305 PIIPRTDRPFKTSIVFAAQEHKGTSVLFKVLSAFAFRDISLTKIESRPHHNRPLRVVGDG 364 +P + KTSIV A + G L ++L F I LT++E+RP Sbjct: 272 H-VPMSGED-KTSIVVAMRNQPG--ALHELLEPFHRHSIDLTRLETRP------------ 315 Query: 365 SFGTSKNFEYMFYVDFEASMAEPRAQNALAEVQEYTSFLRVLGSYPM 411 + + Y+F++DF+ + EPR L EV+ S L+VLGSYP+ Sbjct: 316 --SRTGVWNYVFFIDFKGHVDEPRVAAVLEEVRLRASELKVLGSYPV 360 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: 321 Number of extensions: 14 Number of successful extensions: 4 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: 363 Length adjustment: 31 Effective length of query: 393 Effective length of database: 332 Effective search space: 130476 Effective search space used: 130476 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