Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_011840691.1 RSPH17029_RS04715 threonine/serine dehydratase
Query= BRENDA::A0QY48 (316 letters) >NCBI__GCF_000015985.1:WP_011840691.1 Length = 325 Score = 207 bits (527), Expect = 3e-58 Identities = 137/317 (43%), Positives = 180/317 (56%), Gaps = 13/317 (4%) Query: 9 ISGAAARIAADIVRTPLLAADWGDPRCP--LWLKAETLQPIGAFKIRGAFNALGRLDTHT 66 I AAAR+A RTPLL++ + D + +KAE LQ G+FK RG ++AL L+ Sbjct: 7 IEAAAARLAGHARRTPLLSSPFLDEIAGRRVLVKAECLQHTGSFKFRGGWSALSALEPAR 66 Query: 67 RARGVVAYSSGNHAQAVAYAAAAYGVPAHIVMPEETPAVKVEATRRRGAHVVLCGAGERE 126 RA+GV+AYSSGNHAQ VA AAA +G PA IVMP + P +K+E TR GA VVL + Sbjct: 67 RAQGVIAYSSGNHAQGVALAAARHGAPAVIVMPADAPQLKIENTRALGAEVVLYDRATED 126 Query: 127 RTA--AELVEKTGAVLIPPFDHPDIIAGQGTIGIEIAEDLPE----LATVLIPVSGGGLA 180 R A A L ++ G LI PFD P +IAGQGT G+EIAE E A VL GGGL Sbjct: 127 RDAIGARLADERGLTLIRPFDEPLVIAGQGTTGLEIAEQAAEEGVTSADVLTCCGGGGLT 186 Query: 181 SGIGTAIRALRPKAKIFAVEPELAADTAESLALGSIVEWPVAKRNRTIADGL-RSTPSEL 239 +GI A+ A P ++ VEP DTA SLA G I A + +I D + P + Sbjct: 187 AGIALALEARAPGLRVRPVEPVGFDDTARSLAAGEIRS--NAALSGSICDAIVTPQPGRI 244 Query: 240 TFAHLRQVIDDVITVSEDEIRSAVRELALRARLVAEPSGAVSLAG--YRKAALPDGSAVA 297 TF L ++ + V++ E A+ LR ++V EP GAV+LA +R AL + + Sbjct: 245 TFPILARLCGPGLAVTDAEALRAMALAFLRLKIVLEPGGAVALAAALFRPEALDGDAVIC 304 Query: 298 IVSGGNIEPAQLAAILA 314 SGGN++P A LA Sbjct: 305 TASGGNVDPPLFARALA 321 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: 318 Number of extensions: 16 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: 325 Length adjustment: 28 Effective length of query: 288 Effective length of database: 297 Effective search space: 85536 Effective search space used: 85536 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 Apr 10 2024. 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