Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate GFF448 PGA1_c04590 putative threonine dehydratase
Query= BRENDA::A0QY48 (316 letters) >FitnessBrowser__Phaeo:GFF448 Length = 324 Score = 200 bits (508), Expect = 4e-56 Identities = 130/314 (41%), Positives = 174/314 (55%), Gaps = 21/314 (6%) Query: 9 ISGAAARIAADIVRTPLLAADWGDPRCP--LWLKAETLQPIGAFKIRGAFNALGRLDTHT 66 I+ AA R++ TPLL++ + D + +KAE LQ G+FK RG + AL L Sbjct: 7 IAAAADRLSGHARETPLLSSPFLDEIAGRRVLIKAECLQHTGSFKFRGGWAALSALTDEQ 66 Query: 67 RARGVVAYSSGNHAQAVAYAAAAYGVPAHIVMPEETPAVKVEATRRRGAHVVLCGAGERE 126 R RGV+AYSSGNHAQ VA AAAA+ PA I+MP++ PA+K+ TR GA VVL + Sbjct: 67 RHRGVLAYSSGNHAQGVAAAAAAHTTPAVILMPQDAPAIKIANTRALGAEVVLFDRAKDN 126 Query: 127 RTA--AELVEKTGAVLIPPFDHPDIIAGQGTIGIEIAEDLPEL----ATVLIPVSGGGLA 180 R A AEL E G LI P+D +++AGQGT+G+EIA +L A VL+ GGGL Sbjct: 127 RDAIGAELAEARGLTLIKPYDDVEVVAGQGTVGLEIARQAADLDVTEADVLVCCGGGGLT 186 Query: 181 SGIGTAIRALRPKAKIFAVEPELAADTAESLALGSIVEWPVAKRNRTIADG-----LRST 235 +G+ A+ PK K+ EPE D SL G I RN A L Sbjct: 187 AGVALALEQTAPKMKVSPCEPERFDDVTRSLVAGKIC------RNEASAGSLCDAILTPA 240 Query: 236 PSELTFAHLRQVIDDVITVSEDEIRSAVRELALRARLVAEPSGAVSLAG--YRKAALPDG 293 P E+TF L ++ I VSE++ A+ LR ++V EP GAVSLA + L Sbjct: 241 PGEITFPILARLCGSGIVVSEEDAMRAMVLAFLRLKIVLEPGGAVSLAAALFHGDQLSGP 300 Query: 294 SAVAIVSGGNIEPA 307 +A+AI +GGN++ A Sbjct: 301 AAIAIATGGNVDAA 314 Lambda K H 0.318 0.134 0.384 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: 313 Number of extensions: 19 Number of successful extensions: 6 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: 316 Length of database: 324 Length adjustment: 28 Effective length of query: 288 Effective length of database: 296 Effective search space: 85248 Effective search space used: 85248 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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