Align Arogenate dehydratase 1; PhADT1; EC 4.2.1.91 (characterized)
to candidate WP_057506775.1 ABB28_RS00665 chorismate mutase
Query= SwissProt::D3U715 (424 letters) >NCBI__GCF_001431535.1:WP_057506775.1 Length = 398 Score = 132 bits (333), Expect = 1e-35 Identities = 93/287 (32%), Positives = 143/287 (49%), Gaps = 22/287 (7%) Query: 130 LRVAYQGVPGAYSEAAAGKAYPNCE-AIPCDQFEVAFQAVELWIADRAVLPVENSLGGSI 188 L++ Y G G +S+ A K + +P E FQ VE AD V+PVENS G+I Sbjct: 128 LKIGYLGPEGTFSQQAVLKHFGRSALGLPMASIEEVFQEVEAGNADFGVVPVENSGQGTI 187 Query: 189 HRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYLTRVISHPQALAQCELTITKLGLN 248 D+ L L I GE +L V +++ G E + R+ +HPQ+ Q T L N Sbjct: 188 QITLDMFLTSNLKICGEAELRVQQYIMSRSG-HLEDIERIYAHPQSFMQ---TSAWLRAN 243 Query: 249 VAR-EAVDDTAGAAEYIAANNLRDTAAVASARAAELYGLQ-ILAEGIQDDSSNVTRFVML 306 + + E + ++ A A N D AA+ A +Y L+ ++ + IQ+D+ N TRF+++ Sbjct: 244 LPKAEKIPVSSNAEGARRARNADDAAAIGGENAGHVYNLKKVVTKPIQNDADNTTRFLVI 303 Query: 307 AREPIIPRMDRPFKTSIVFAHEGTGVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDA 366 R + P + +V H+ G LF VLS FA IS+ +IESRP + Sbjct: 304 GRS-LFPSSGHDRTSVLVLIHDKPGALFDVLSPFARHGISMNRIESRPSHH--------- 353 Query: 367 NVGTAKHFEYMFYVDFDASMADVRAQNALAEVQEFTSFLRVLGSYPM 413 +EY F++D + D Q ALAE++ + ++VLGSYP+ Sbjct: 354 -----GKWEYGFFIDLSGHIDDAPMQAALAELEGHAAQIKVLGSYPV 395 Lambda K H 0.319 0.133 0.388 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: 357 Number of extensions: 22 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: 398 Length adjustment: 31 Effective length of query: 393 Effective length of database: 367 Effective search space: 144231 Effective search space used: 144231 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: 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