Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_012402372.1 BPHY_RS15405 arogenate dehydratase
Query= BRENDA::Q01269 (268 letters) >NCBI__GCF_000020045.1:WP_012402372.1 Length = 260 Score = 263 bits (673), Expect = 2e-75 Identities = 130/261 (49%), Positives = 177/261 (67%), Gaps = 3/261 (1%) Query: 1 MPKSFRHLVQALACL-ALLASASLQAQESRLDRILESGVLRVATTGDYKPFSYRTEEGGY 59 M K+ V AL C A+ A + A SRLD IL G LR TTGDYKP+S+ ++G + Sbjct: 1 MKKATMLFVSALVCAGAVHAQTAAPAPASRLDEILARGTLRACTTGDYKPYSFYKQDGQF 60 Query: 60 AGFDVDMAQRLAESLGAKLVVVPTSWPNLMRDFADDRFDIAMSGISINLERQRQAYFSIP 119 G D+DM + LA SLG K V TSW NLM DF + D+ + G+S L+RQ++A+F++ Sbjct: 61 EGIDIDMTESLARSLGVKAEFVKTSWSNLMNDFVS-KCDVGVGGVSTTLDRQKRAFFTVA 119 Query: 120 YLRDGKTPITLCSEEARFQTLEQIDQPGVTAIVNPGGTNEKFARANLKKARILVHPDNVT 179 Y DGK+PI C + ++QT+ QIDQP I NPGGTNE+FAR L A++ V+PDNVT Sbjct: 120 YQVDGKSPIVRCDDVDKYQTVAQIDQPSTRVIFNPGGTNERFARQFLSHAKLTVYPDNVT 179 Query: 180 IFQQIVDGKADLMMTDAIEARLQSRLHPELCAVHPQQPFDFAEKAYLLPR-DEAFKRYVD 238 IF+QI+ GKAD+M+TDA E LQ +L+P LC+VHP +PF + EKA+L+PR D F++YVD Sbjct: 180 IFKQILAGKADVMVTDASETLLQQKLNPGLCSVHPDKPFQYGEKAWLVPRGDVVFQQYVD 239 Query: 239 QWLHIAEQSGLLRQRMEHWLE 259 QWLH+A +G + + WL+ Sbjct: 240 QWLHLARATGEYQSISDKWLK 260 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: 198 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: 268 Length of database: 260 Length adjustment: 25 Effective length of query: 243 Effective length of database: 235 Effective search space: 57105 Effective search space used: 57105 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 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