Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate SMc02899 SMc02899 prephenate dehydratase
Query= BRENDA::Q9SA96 (392 letters) >FitnessBrowser__Smeli:SMc02899 Length = 284 Score = 187 bits (475), Expect = 3e-52 Identities = 115/289 (39%), Positives = 163/289 (56%), Gaps = 17/289 (5%) Query: 107 RISFQGIPGAYSETAALKAFPNCETVPCEQFEAAFQAVELWLVDKAVLPIENSVGGSIHR 166 RISFQG GA S+ A FP+ E +PC+ FE AF AVE D A++PIEN++ G + Sbjct: 7 RISFQGDYGANSDMACRDMFPSMEPLPCQTFEDAFLAVENGEADLAMIPIENTIAGRVAD 66 Query: 167 NYDLLLRHRLHIVQEVHLPVNHCLLGVPGVKKEDIKCVLSHPQALDQCVNSLNNLGIQRI 226 + LL RLHIV E +P+ L+ +PGV +E+I+ V SH AL QC + G + + Sbjct: 67 IHHLLPESRLHIVGEYFMPIRFQLMVLPGVGREEIRTVHSHIHALGQCRKIVRANGWKPV 126 Query: 227 SAKDTATAAQTVSSSGKIDVGAIASVRAANIYGLDILAENIQDDVNNVTRFLILAR-EPM 285 A DTA AA+ V G + A+A AA++YGLDI+AEN++D +NVTRF++L+R E Sbjct: 127 VAGDTAGAAKLVKEVGDRSMAALAPRLAADLYGLDIIAENVEDTDSNVTRFVVLSREESR 186 Query: 286 IPRT--DRPYKTSIVFSLEEGPGVLFKALAVFALRSINLSKIESRPQRRRPLRVVDGSNN 343 + RT D T+ VF++ P L+KA+ FA IN++K+ES Sbjct: 187 VARTSKDELIITTFVFNVRNIPAALYKAMGGFATNGINMTKLESYQL------------- 233 Query: 344 GSAKYFDYLFYIDFEASMADTRAQHALGHLQEFASFIRILGCYPMDLVR 392 K+ FY D E D +HA+ L+ F+ +RILG YP +R Sbjct: 234 -GGKFVATQFYADIEGHPDDIGVRHAMDELRFFSENVRILGTYPAHPMR 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: 235 Number of extensions: 9 Number of successful extensions: 3 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: 284 Length adjustment: 28 Effective length of query: 364 Effective length of database: 256 Effective search space: 93184 Effective search space used: 93184 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 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