Align D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate WP_025764552.1 X939_RS0117325 pyridoxal-phosphate dependent enzyme
Query= BRENDA::Q54HH2 (324 letters) >NCBI__GCF_000566685.1:WP_025764552.1 Length = 323 Score = 297 bits (761), Expect = 2e-85 Identities = 151/310 (48%), Positives = 217/310 (70%), Gaps = 5/310 (1%) Query: 11 DIKEAHKRIEKYIHKTPVLTNSTINELAGKELYFKCENLQKTGSFKMRGACNAIFSLDEE 70 D++EAH+RI +IH+TP++T+ +NEL G L+FK ENLQK G+FK+RGA NA+ SLD Sbjct: 16 DLREAHQRITPFIHRTPLMTSQMLNELTGAHLFFKPENLQKIGAFKIRGALNAMLSLDSA 75 Query: 71 ELSKGVVTHSSGNHGQALSYASKVRCVKCYVVVPEDAPSVKLNAICGYGATVTKCKATLE 130 L+ G+ THSSGNH QA++ A+ +R +K Y+V+P +AP VK++A+ GYGA++T C+ T E Sbjct: 76 VLANGLATHSSGNHAQAIACAAALRGIKAYIVMPHNAPKVKVSAVRGYGASITFCENTPE 135 Query: 131 ARESNTKQLIEQHSCKLIHPFDNLQVIAGQGTASLELME-QVENLDAIITPVGGGGLLSG 189 RE+ +++ + IHPF++ V+ GQ T + E++E E D ++ PVGGGGLLSG Sbjct: 136 DREAVVARIVAETGATFIHPFNHYGVMEGQATVAKEMIEDSTEPFDYLLAPVGGGGLLSG 195 Query: 190 TCITAKSLNPNIKVFAAEPLGADDTYRSLLSGEIQKHTPGKPNTIADGLLTTVGSLTFPI 249 T ++A + N V AEP GA D SL SG IQK +TIADGLLT +G TFP+ Sbjct: 196 TALSAHYFSKNTLVIGAEPEGAADAVLSLQSGSIQK--APYVDTIADGLLTYLGDKTFPV 253 Query: 250 IKENCDGVILVTEDEIKYAMKLVWERMKIIIEPSSATTLAAILKQEFKDKKDIKKVGIII 309 I + ++LV++ EI AM+L+WERMK+++EPS A TLAAI++ K + K+VG+I+ Sbjct: 254 IHKFVSEIVLVSDQEIVEAMRLIWERMKLVVEPSGAVTLAAIIRH--KKLFEGKRVGVIV 311 Query: 310 SGGNVDLSSI 319 SGGNVDL ++ Sbjct: 312 SGGNVDLGNL 321 Lambda K H 0.315 0.132 0.374 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: 14 Number of successful extensions: 4 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: 324 Length of database: 323 Length adjustment: 28 Effective length of query: 296 Effective length of database: 295 Effective search space: 87320 Effective search space used: 87320 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 (21.5 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