Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_011648848.1 RL_RS33195 hydroxyectoine utilization dehydratase EutB
Query= BRENDA::A0QY48 (316 letters) >NCBI__GCF_000009265.1:WP_011648848.1 Length = 333 Score = 208 bits (530), Expect = 1e-58 Identities = 128/320 (40%), Positives = 187/320 (58%), Gaps = 11/320 (3%) Query: 4 VTLDDISGAAARIAADIVRTPLLAA-DWGD-PRCPLWLKAETLQPIGAFKIRGAFNALGR 61 V+L+DI AA RIA ++ TP++ + G+ P+ LK E Q G+FK+RGA NA+ Sbjct: 7 VSLEDIRAAARRIAGRVIGTPMVQSFSLGELAGVPVHLKLEHHQTTGSFKLRGATNAVLS 66 Query: 62 LDTHTRARGVVAYSSGNHAQAVAYAAAAYGVPAHIVMPEETPAVKVEATRRRGAHVVLCG 121 L R+RGVVA S+GNH +A+AYAA A G A I M P KV +RR GA V + G Sbjct: 67 LSPAERSRGVVAASTGNHGRALAYAAKAEGAVATICMSRLVPDNKVSESRRLGADVRIVG 126 Query: 122 AG--ERERTAAELVEKTGAVLIPPFDHPDIIAGQGTIGIEIAEDLPELATVLIPVSGGGL 179 E ++ LV + G V++PPFDHPD++AGQGT+G+EI + LPE A VL+P+SGGGL Sbjct: 127 GSQDEAQQEVERLVREEGLVMVPPFDHPDVVAGQGTLGLEIIDILPEAAIVLVPLSGGGL 186 Query: 180 ASGIGTAIRALRPKAKIFAVEPELAADTAESLALGSIVEWPVAKRNRTIADGLR---STP 236 A+G+ A++ + P K+ + E A SL G V+ + ++AD L Sbjct: 187 AAGVAAAVKGISPTTKVIGLTMEKGAAMKASLDAGRPVQ---VEEVSSLADSLGGGIGLD 243 Query: 237 SELTFAHLRQVIDDVITVSEDEIRSAVRELALRARLVAEPSGAVSLAGYRKAAL-PDGSA 295 + +TFA R+++DDVI ++E EI +R R + E +GAV +A + +G Sbjct: 244 NRVTFAMCRELLDDVILLTEVEIAVGMRHAYACERQIVEGAGAVGIAALLAGKIVGNGPI 303 Query: 296 VAIVSGGNIEPAQLAAILAG 315 VAI+SG N++ Q ++ G Sbjct: 304 VAILSGANVDMEQHRRVING 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: 301 Number of extensions: 17 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: 333 Length adjustment: 28 Effective length of query: 288 Effective length of database: 305 Effective search space: 87840 Effective search space used: 87840 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 24 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