Align D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate WP_011513321.1 PCRYO_RS05055 pyridoxal-phosphate dependent enzyme
Query= BRENDA::Q54HH2 (324 letters) >NCBI__GCF_000013905.1:WP_011513321.1 Length = 326 Score = 302 bits (773), Expect = 8e-87 Identities = 154/316 (48%), Positives = 210/316 (66%), Gaps = 8/316 (2%) Query: 8 TLKDIKEAHKRIEKYIHKTPVLTNSTINELAGKELYFKCENLQKTGSFKMRGACNAIFSL 67 TL D+ EAH+RI+ YIH+TPVLT+ +NELAG E++FKCEN QK G+FK+RGA NA+F L Sbjct: 12 TLDDMLEAHERIKPYIHRTPVLTSRFLNELAGCEMFFKCENFQKAGAFKVRGASNAVFGL 71 Query: 68 DEEELSKGVVTHSSGNHGQALSYASKVRCVKCYVVVPEDAPSVKLNAICGYGATVTKCKA 127 +E+ GV THSSGNH +LSYA+ R + C VV+P AP K A+ GYG +T+C+ Sbjct: 72 SDEDAKNGVCTHSSGNHALSLSYAAGQRGIPCNVVMPHSAPEAKKAAVRGYGGIITECEP 131 Query: 128 TLEARESNTKQLIEQHSCKLIHPFDNLQVIAGQGTASLELMEQVENL----DAIITPVGG 183 + +RE ++ + +HP+++ +VIAGQ T S E +EQ+E + D ++ P+GG Sbjct: 132 STTSREEVFAKVQAETGGDFVHPYNDPRVIAGQATCSREFLEQMEEIGEKPDMVVAPIGG 191 Query: 184 GGLLSGTCITAKSLNPNIKVFAAEPLGADDTYRSLLSGEIQKHTPGKPNTIADGLLTTVG 243 GG++SGTC+T +L P++K++AAEPL ADD RS +G I PNT+ADGL + Sbjct: 192 GGMISGTCLTLSNLAPDVKIYAAEPLNADDAARSFKAGHI--IADDAPNTVADGLKVPLK 249 Query: 244 SLTFPIIKENCDGVILVTEDEIKYAMKLVWERMKIIIEPSSATTLAAILKQEFKDKKDIK 303 LT+ + ++ TE+EI AMKL W MKIIIEPS A LA ILK KD K Sbjct: 250 DLTWHFVSNYVTDILTATEEEIVEAMKLTWTHMKIIIEPSCAVPLAVILKN--KDVFAGK 307 Query: 304 KVGIIISGGNVDLSSI 319 KVG+II+GGNVDL + Sbjct: 308 KVGVIITGGNVDLDKL 323 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: 329 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: 326 Length adjustment: 28 Effective length of query: 296 Effective length of database: 298 Effective search space: 88208 Effective search space used: 88208 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