Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate GFF3574 PGA1_c36290 putative phenylserine dehydratase
Query= BRENDA::Q04513 (436 letters) >FitnessBrowser__Phaeo:GFF3574 Length = 314 Score = 149 bits (376), Expect = 1e-40 Identities = 106/314 (33%), Positives = 156/314 (49%), Gaps = 24/314 (7%) Query: 25 DIQTAQARISSVIAPTPLQYCPRLSEETGA----EIYLKREDLQDVRSYKIRGALNSGAQ 80 DI+ A RI I TP+ E TG I LK E +Q S+K RGA N+ Sbjct: 6 DIRAADTRIRPYIQRTPIL------ETTGFGLDYPISLKLEHMQHTGSFKARGAFNT--L 57 Query: 81 LTQEQRDAGIVAASAGNHAQGVAYVCKSLGVQGRIYVPVQTPKQKRDRIMVHGGEFVSLV 140 L DAG+VAAS GNH VAY K LG++ R+YVP K I G + L Sbjct: 58 LGGSVPDAGLVAASGGNHGAAVAYAAKRLGMRARVYVPEMAGPAKIALIRACGAD---LK 114 Query: 141 VTGNNFDEASAAAHEDAERTGATLIEPFDARNTVIGQGTVAAEILSQLTSMGKSADHVMV 200 V + A A ++TGA + +DA TVIGQGT AE +Q G AD +++ Sbjct: 115 VVPGAYANALEQAQAYEQQTGAMQVHAYDAAATVIGQGTCFAEWDAQ----GLEADTLLI 170 Query: 201 PVGGGGLLAGVVSYMADMAPRTAIVGIEPAGAASMQAALHNGGPITLETVDPFVDGAAVK 260 VGGGGL+AG +++ IV +EP ++++ AAL G P+ +E + + Sbjct: 171 AVGGGGLIAGAMAWYGGSKK---IVAVEPETSSALNAALAVGRPVDVEVSGVAANALGAR 227 Query: 261 RVGDLNYTIVEKNQGRVHMMSATEGAVCTEMLDLYQNEGIIAEPAGALSIAGLKEMSF-- 318 R+G L Y + + V ++ ++ A+ L++ ++ EPAGA ++A L ++ Sbjct: 228 RIGTLCYELAQGQSDTVTSLTVSDEAISAAQNKLWKERRLLVEPAGATALAALTSGAYQP 287 Query: 319 APGSVVVCIISGGN 332 AP V ++ GGN Sbjct: 288 APDERVAVLLCGGN 301 Lambda K H 0.316 0.133 0.373 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: 314 Number of extensions: 16 Number of successful extensions: 4 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: 436 Length of database: 314 Length adjustment: 30 Effective length of query: 406 Effective length of database: 284 Effective search space: 115304 Effective search space used: 115304 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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