Align arogenate dehydratase (EC 4.2.1.91) (characterized)
to candidate AO353_17845 AO353_17845 ArtI protein
Query= BRENDA::Q01269 (268 letters) >FitnessBrowser__pseudo3_N2E3:AO353_17845 Length = 261 Score = 253 bits (645), Expect = 4e-72 Identities = 129/250 (51%), Positives = 171/250 (68%), Gaps = 3/250 (1%) Query: 12 LACLALLASASLQAQE--SRLDRILESGVLRVATTGDYKPFSYRTEEGGYAGFDVDMAQR 69 L C L S AQ S LD+++E G L+V TTGDYKP++Y EGGY G D+ MAQ Sbjct: 6 LLCSLLTFSVQAIAQNAPSHLDQVIERGHLKVCTTGDYKPYTYLRAEGGYEGIDIAMAQS 65 Query: 70 LAESLGAKLVVVPTSWPNLMRDFADDRFDIAMSGISINLERQRQAYFSIPYLRDGKTPIT 129 LA+SL + VPT+W NLM DF DR DI M GIS++LERQ++A FS DGK P+ Sbjct: 66 LAKSLNVDVQWVPTTWKNLMTDFLADRCDIGMGGISVSLERQKKAAFSDTLGVDGKIPLV 125 Query: 130 LCSEEARFQTLEQIDQPGVTAIVNPGGTNEKFARANLKKARILVHPDNVTIFQQIVDGKA 189 C ++ R+QT+EQ++Q V I GGTNE FAR +L A + + PDNVTIF+Q+++ KA Sbjct: 126 RCEDKQRYQTVEQLNQSSVRLIEPAGGTNEVFARTHLPNATLTLFPDNVTIFEQLLENKA 185 Query: 190 DLMMTDAIEARLQSRLHPELCAVHPQQPFDFAEKAYLLPRDE-AFKRYVDQWLHIAEQSG 248 D+M+TDA EAR Q +L P LCAV+P+Q ++EKAYLLPRD+ A+K YVDQWLH+++ +G Sbjct: 186 DVMITDASEARYQQKLKPGLCAVNPEQYLQYSEKAYLLPRDDVAWKAYVDQWLHLSKATG 245 Query: 249 LLRQRMEHWL 258 + WL Sbjct: 246 AYDAVLAQWL 255 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: 214 Number of extensions: 5 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: 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