Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate WP_012332582.1 M446_RS13105 amino acid ABC transporter
Query= BRENDA::Q01269 (268 letters) >NCBI__GCF_000019365.1:WP_012332582.1 Length = 256 Score = 209 bits (533), Expect = 4e-59 Identities = 110/238 (46%), Positives = 143/238 (60%), Gaps = 1/238 (0%) Query: 19 ASASLQAQESRLDRILESGVLRVATTGDYKPFSYRTEEGGYAGFDVDMAQRLAESLGAKL 78 A A+ A L I E+GVLRV TGDY P+S R EG G DV MA+ LA SLG L Sbjct: 15 ALAAAPAAARPLAAIREAGVLRVGLTGDYAPYSLRRSEGDVKGADVTMARDLARSLGVSL 74 Query: 79 VVVPTSWPNLMRDFADDRFDIAMSGISINLERQRQAYFSIPYLRDGKTPITLCSEEARFQ 138 +VPT+W L D DRFDIAM G+S+ +R A FS+P + DGK PI C++ + Sbjct: 75 EIVPTTWKGLKDDLLADRFDIAMGGVSVTSDRAAVADFSVPVMTDGKRPIVRCADAGTYT 134 Query: 139 TLEQIDQPGVTAIVNPGGTNEKFARANLKKARILVHPDNVTIFQQIVDGKADLMMTDAIE 198 ++ ID+P V +VNPGGTNE+FA A+ A + +HPDN TIF+++ +G+ADLM+TD E Sbjct: 135 SIAAIDRPEVRVVVNPGGTNERFAAAHFPHAAVRLHPDNRTIFEEVAEGRADLMVTDGAE 194 Query: 199 ARLQSRLH-PELCAVHPQQPFDFAEKAYLLPRDEAFKRYVDQWLHIAEQSGLLRQRME 255 Q+R H LC FD A+K Y + RD A K VD WL A SG + +E Sbjct: 195 VDYQARRHRGVLCPATVADSFDHADKGYWMSRDPALKAAVDGWLKAALASGAYDRALE 252 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: 173 Number of extensions: 4 Number of successful extensions: 2 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: 256 Length adjustment: 25 Effective length of query: 243 Effective length of database: 231 Effective search space: 56133 Effective search space used: 56133 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