Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate Ga0059261_3754 Ga0059261_3754 Threonine dehydratase
Query= BRENDA::A0QY48 (316 letters) >FitnessBrowser__Korea:Ga0059261_3754 Length = 322 Score = 208 bits (530), Expect = 1e-58 Identities = 140/318 (44%), Positives = 185/318 (58%), Gaps = 22/318 (6%) Query: 9 ISGAAARIAADIVRTPLLAADWGDPRCPLWLKAETLQPIGAFKIRGAFNALGRLDTHTRA 68 + AAA++AA + TPLL A+ P+ KAE LQPIGAFKIRGA++ L +D R Sbjct: 12 VRDAAAKVAAILPPTPLLVAEIRG--IPVMFKAECLQPIGAFKIRGAWHRLTAIDPEQRE 69 Query: 69 RGVVAYSSGNHAQAVAYAAAAYGVPAHIVMPEETPAVKVEATRRRGAHVVLCGAGERERT 128 +GVVA+SSGNHAQ VA+AA G+PA IVMP + PA K ++T GA VV + +R Sbjct: 70 KGVVAFSSGNHAQGVAWAAKRLGIPAVIVMPADAPAAKRDSTLALGAEVVAYDRMKEDRV 129 Query: 129 --AAELVEKTGAVLIPPFDHPDIIAGQGTIGIEIAED-----LPELATVLIPVSGGGLAS 181 AA L GA L+PPFD P II GQG++ IE+ LP+ +++P GGGLAS Sbjct: 130 KIAAHLAHARGATLVPPFDDPWIIEGQGSMAIEVLTQAAEMRLPDPGRIVVPCGGGGLAS 189 Query: 182 GIGTAIRALRPKAKIFAVEPELAADTAESLALG---SIVEWPVAKRNRTIADGLRS-TPS 237 G+ A+ P+A+ VEPE D SLA G SI E P T D L++ P+ Sbjct: 190 GVTLAL----PEAQTTIVEPEGWDDMCRSLANGWIESIGESPPP----TACDALQTFQPA 241 Query: 238 ELTFAHLRQVIDDVITVSEDEIRSAVRELALRARLVAEPSGAVSLAGYRKAAL-PDGSAV 296 +LTF L + + VSE E+R+A R A + RLV EP GAV+LA + P + Sbjct: 242 QLTFDVLSRRGATGVAVSEAEVRAAQRWAARKLRLVVEPGGAVALAALLAGKVDPTPDTL 301 Query: 297 AIVSGGNIEPAQLAAILA 314 I+SGGN +P A +LA Sbjct: 302 VILSGGNADPDAYARVLA 319 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: 14 Number of successful extensions: 7 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: 322 Length adjustment: 28 Effective length of query: 288 Effective length of database: 294 Effective search space: 84672 Effective search space used: 84672 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