Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate Ac3H11_13 Cyclohexadienyl dehydratase (EC 4.2.1.51)(EC 4.2.1.91)
Query= BRENDA::Q01269 (268 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_13 Length = 261 Score = 167 bits (422), Expect = 3e-46 Identities = 95/257 (36%), Positives = 150/257 (58%), Gaps = 11/257 (4%) Query: 11 ALACLALLASASLQAQES----RLDRILESGVLRVATTGDYKPFSYRTEEGGYAGFDVDM 66 A+A L+A+ SL +Q + RLD+I+E+ V+RV T GDY+PF+ +T+ GY+G D+D+ Sbjct: 8 AVAAAVLVAALSLFSQAAQAGPRLDKIMEAKVIRVGTPGDYRPFAIKTD-AGYSGHDIDV 66 Query: 67 AQRLAESLGAKLVVVPTSWPNLMRDFADDRFDIAMSGISINLERQRQAYFSIPYLRDGKT 126 + +A+ LG K+ V TSWPNL++D D+FD+A+ GI+ N+ R R Y GK Sbjct: 67 IETMAKELGVKIEYVQTSWPNLVKDLQGDKFDVAVGGITRNVNRMRIFDMLPGYAPFGKV 126 Query: 127 PITLCSEEARFQTLEQIDQPGVTAIVNPGGTNEKFARANLKKARILVHPDNVTIFQQIVD 186 + +++A++ +++ ++QP V I NPGGTNE + ANLK A++ H N I D Sbjct: 127 ALVRAADKAKYTSVDAMNQPTVRVIKNPGGTNETYVLANLKAAQVSTHDKNAENPALIAD 186 Query: 187 GKADLMMTDAIEARLQSRLHPELCAVHPQQPFDFAEKAYL---LPRDEA-FKRYVDQWLH 242 GK D+M+T+ EA ++ P L A P K YL LP D+A + R + Sbjct: 187 GKGDVMITETYEALHYAKADPRLHAAFVDAP--LTPKNYLGFMLPTDDADYVRVMGFVWG 244 Query: 243 IAEQSGLLRQRMEHWLE 259 + + G ++Q + WL+ Sbjct: 245 LVDSRGTIKQAADKWLK 261 Lambda K H 0.322 0.135 0.406 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: 166 Number of extensions: 6 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 268 Length of database: 261 Length adjustment: 25 Effective length of query: 243 Effective length of database: 236 Effective search space: 57348 Effective search space used: 57348 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: 47 (22.7 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