Align D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate WP_057509300.1 ABB28_RS14485 threonine dehydratase
Query= BRENDA::Q54HH2 (324 letters) >NCBI__GCF_001431535.1:WP_057509300.1 Length = 366 Score = 142 bits (358), Expect = 1e-38 Identities = 96/318 (30%), Positives = 168/318 (52%), Gaps = 20/318 (6%) Query: 7 VTLKDIKEAHKRIEKYIHKTPVLTNSTINELAGKELYFKCENLQKTGSFKMRGACNAIFS 66 VT+ D+ A R+ +++ TP ++ + K ENLQ+TGS+K+RGA NA+ + Sbjct: 16 VTVADVLAAQARLRRFLPPTP------LHHAERFGTWLKLENLQRTGSYKVRGALNALLA 69 Query: 67 LDEEELSKGVVTHSSGNHGQALSYASKVRCVKCYVVVPEDAPSVKLNAICGYGATVTKCK 126 E + ++ S+GNH Q +++A+ V+ V+P AP+ K+ + +GATV + Sbjct: 70 GRERGDLRPIICASAGNHAQGVAWAAHRLGVQAITVMPHGAPANKIAGVAHWGATVRQHG 129 Query: 127 ATLEARESNTKQLIEQHSCKLIHPFDNLQVIAGQGTASLELMEQVENLDAIITPVGGGGL 186 + + + +L ++H + + FD+ VIAGQGT +EL + D +I P+GGGGL Sbjct: 130 ESYDDAWAFAVELAQRHDYRFLSAFDDADVIAGQGTVGIELAP--HSPDVVIVPIGGGGL 187 Query: 187 LSGTCITAKSLNPNIKVFAAEPLGADDTYRSLLSGEIQKHTPGKPNTIADGLLTTV-GSL 245 SG + KS +++ A+ G D R+ +SG+I+ P ++ADG+ + G L Sbjct: 188 ASGVALALKS--QGVRIVGAQVEGVDSMARA-ISGDIRPIAP--VPSLADGVRVKIPGFL 242 Query: 246 TFPIIKENCDGVILVTEDEIKYAMKLVWERMKIIIEPSSATTLAAILKQEFKDKKDIKKV 305 T + D V++V E E++ + + +I E + A LAA + + K Sbjct: 243 TRRLCASLLDDVVIVREAELRETLVRLALEENLIAEGAGALALAAGRRVAGRRK------ 296 Query: 306 GIIISGGNVDLSSISKIL 323 ++SGGN+D S ++ +L Sbjct: 297 FAVVSGGNIDASVLAGLL 314 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: 236 Number of extensions: 9 Number of successful extensions: 3 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: 366 Length adjustment: 29 Effective length of query: 295 Effective length of database: 337 Effective search space: 99415 Effective search space used: 99415 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: 49 (23.5 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