Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate CCNA_03203 CCNA_03203 threo-3-hydroxyaspartate ammonia-lyase
Query= BRENDA::A0QY48 (316 letters) >FitnessBrowser__Caulo:CCNA_03203 Length = 325 Score = 204 bits (520), Expect = 2e-57 Identities = 133/323 (41%), Positives = 184/323 (56%), Gaps = 13/323 (4%) Query: 4 VTLDDISGAAARIAADIVRTPLLAADWGDPRCP--LWLKAETLQPIGAFKIRGAFNALGR 61 V+L DI AA R+ V TPL+ + + R ++LK ETLQ GAFK RGA+N L + Sbjct: 3 VSLADIQAAAVRLKGSAVETPLIESPALNDRLGGRIFLKPETLQRAGAFKFRGAYNRLSQ 62 Query: 62 LDTHTRARGVVAYSSGNHAQAVAYAAAAYGVPAHIVMPEETPAVKVEATRRRGAHVVLCG 121 L +ARGVVA+SSGNHAQ VA AA GVPA IVMP ++P+VKVE TR GA + Sbjct: 63 LSDEEKARGVVAFSSGNHAQGVALAARLLGVPALIVMPSDSPSVKVEGTRGFGADIRFYD 122 Query: 122 AGERERTAA--ELVEKTGAVLIPPFDHPDIIAGQGTIGIEI----AEDLPELATVLIPVS 175 +R A ++ + G V++P +D P IIAGQGT+G+EI A L ++ V Sbjct: 123 RFTEDRVAIADQIAAERGCVVVPSYDDPHIIAGQGTVGLEIVAQAAAQGATLDRLICCVG 182 Query: 176 GGGLASGIGTAIRALRPKAKIFAVEPELAADTAESLALGSIVEWPVAKRNRTIADGLRS- 234 GGGL +G TA++AL P +I+ VEP +T SL G + K R+I D L + Sbjct: 183 GGGLIAGTSTAVKALSPATEIWGVEPAGFDETRRSLESGR--RETIDKDARSICDALLTP 240 Query: 235 TPSELTFAHLRQVIDDVITVSEDEIRSAVRELALRARLVAEPSGAVSLAGYRKAALP-DG 293 P +LT+ ++ + V+ V++ E+ A+R +LV EP G V+L + G Sbjct: 241 IPGDLTWPINQKNLSGVVAVTDAEVAEAMRYAFSTLKLVVEPGGCVALTAALTGKVDVAG 300 Query: 294 SAVAIV-SGGNIEPAQLAAILAG 315 VAIV SGGN++P A +L G Sbjct: 301 KTVAIVLSGGNVDPGLFAQVLGG 323 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: 284 Number of extensions: 10 Number of successful extensions: 5 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 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