Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_009543287.1 CCE_RS21960 prephenate dehydratase
Query= BRENDA::Q9SA96 (392 letters) >NCBI__GCF_000017845.1:WP_009543287.1 Length = 288 Score = 131 bits (330), Expect = 2e-35 Identities = 105/299 (35%), Positives = 138/299 (46%), Gaps = 32/299 (10%) Query: 106 VRISFQGIPGAYSETAALKAFPNCET--------VPCEQFEAAFQAVELWLVDKAVLPIE 157 + I+ G G +ETAAL E PC +V +KAV+P+E Sbjct: 3 ISIAHLGPVGTNAETAALAYAHWLEENQGKSSLLCPCPSIAQTLHSVARGDTNKAVVPVE 62 Query: 158 NSVGGSIHRNYDLLLR-HRLHIVQEVHLPVNHCLLGVPGVKKEDIKCVLSHPQALDQCVN 216 NS GS+ D L + RL I QEV LP+ H G IK V SHPQAL QC Sbjct: 63 NSTEGSVASTLDTLWQLDRLQIQQEVVLPIIHAFFS-RGTSLNGIKTVYSHPQALAQCQR 121 Query: 217 SL--NNLGIQRISAKDTATAAQTVSSSGKIDVGAIASVRAANIYGLDILAENIQDDVNNV 274 L N + I TA A Q +S GAIA+ RA +Y + IL +I D +N Sbjct: 122 WLQHNLPNVALIPTNSTAEALQKISLEPT--AGAIAAPRAVKLYNVPILVNHINDYADNC 179 Query: 275 TRFLILAREPMIPRTDRPYKTSIVFSLEEG-PGVLFKALAVFALRSINLSKIESRPQRRR 333 TRF ++ P R S+ FS+ PG L K L VFA R+INLS+IESRP +R Sbjct: 180 TRFWVMTLNPTPTVGSR---ISLAFSVPANVPGSLMKPLQVFAQRNINLSRIESRPTKR- 235 Query: 334 PLRVVDGSNNGSAKYFDYLFYIDFEASMADTRAQHALGHLQEFASFIRILGCYPMDLVR 392 +Y+FY+D E + D AL L ++I G YP+ L++ Sbjct: 236 -------------SLGEYVFYLDVEGNQEDPNIIDALNALTHHTEVLKIYGSYPVLLLQ 281 Lambda K H 0.321 0.135 0.402 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: 252 Number of extensions: 16 Number of successful extensions: 6 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: 392 Length of database: 288 Length adjustment: 28 Effective length of query: 364 Effective length of database: 260 Effective search space: 94640 Effective search space used: 94640 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 (21.9 bits) S2: 49 (23.5 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