Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate BWI76_RS21950 BWI76_RS21950 prephenate dehydratase/arogenate dehydratase
Query= BRENDA::Q01269 (268 letters) >FitnessBrowser__Koxy:BWI76_RS21950 Length = 257 Score = 149 bits (377), Expect = 4e-41 Identities = 83/240 (34%), Positives = 132/240 (55%), Gaps = 4/240 (1%) Query: 17 LLASASLQAQESRLDRILESGVLRVATTGDYKPFSYRTEEGGYAGFDVDMAQRLAESLGA 76 ++A+ + AQ ++ I +SG L+V GDY P ++ + G G+DVDMA+ L + LG Sbjct: 10 IIAAIAFGAQARDMNSIQQSGELKVGVPGDYAPLAFHNKAGELLGYDVDMAKDLGKRLGL 69 Query: 77 KLVVVPTSWPNLMRDFADDRFDIAMSGISINLERQRQAYFSIPYLRDGKTPITLCSEEAR 136 K+ VPTSWP L D D+FDIAM G++ R + S P + +GK + C+ Sbjct: 70 KVRFVPTSWPTLSADLQADKFDIAMGGVTETAARAKDFALSQPVVPNGKIALANCASAPA 129 Query: 137 FQTLEQIDQPGVTAIVNPGGTNEKFARANLKKARILVHPDNVTIFQQIVDGKADLMMTDA 196 +LE+IDQP V +VNPGGTN+ F ++K A+I+ +N+ + + AD+M+TD Sbjct: 130 LGSLEKIDQPNVKVVVNPGGTNQSFVDEHIKHAQIIRVKNNIDNLEALRQKTADMMVTDL 189 Query: 197 IEARLQSRLHPELCAVHPQQPF--DFAEKAYLLPRDE-AFKRYVDQWLHIAEQSGLLRQR 253 IE P + V + PF + K Y++ +D V+QWL ++ +L+Q+ Sbjct: 190 IEGVYYQSNEPGVFCVANETPFPGTASFKVYMMNKDNPQLLEKVNQWL-ASQDKNVLKQK 248 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: 167 Number of extensions: 5 Number of successful extensions: 1 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: 257 Length adjustment: 25 Effective length of query: 243 Effective length of database: 232 Effective search space: 56376 Effective search space used: 56376 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