Align D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate HSERO_RS00265 HSERO_RS00265 threonine dehydratase
Query= BRENDA::Q54HH2 (324 letters) >FitnessBrowser__HerbieS:HSERO_RS00265 Length = 401 Score = 196 bits (498), Expect = 8e-55 Identities = 108/318 (33%), Positives = 192/318 (60%), Gaps = 8/318 (2%) Query: 8 TLKDIKEAHKRIEKYIHKTPVLTNSTINELAGKELYFKCENLQKTGSFKMRGACNAIFSL 67 TL DI+ A +R++ I +TP + + T++++ G +++ K ENLQ T SFK RGACN + + Sbjct: 3 TLNDIEAAARRLQGQILETPCVESRTLSQIVGAQVFLKFENLQFTASFKERGACNKLVDV 62 Query: 68 DEEEL-SKGVVTHSSGNHGQALSYASKVRCVKCYVVVPEDAPSVKLNAICGYGATVTKCK 126 ++GVV S+GNH Q ++Y ++ + +V+P P VK+ G+GA V Sbjct: 63 AASGGGARGVVAMSAGNHAQGVAYHAQRLGLPATIVMPRFTPGVKIERTRGFGANVVLHG 122 Query: 127 ATLEARESNTKQLIEQHSCKLIHPFDNLQVIAGQGTASLELMEQVENLDAIITPVGGGGL 186 TLEA ++ +L E+ +HP+D+ +IAGQGT +LE+M+ V +LD ++ +GGGGL Sbjct: 123 DTLEAARTHAYELAEKEGLTFVHPYDDEAIIAGQGTVALEMMKAVPDLDCLVVSIGGGGL 182 Query: 187 LSGTCITAKSLNPNIKVFAAEPLGADDTYRSLLSGEIQKHTPGKPNTIADGL-LTTVGSL 245 L+G + A+++ P I++ + + ++++ P +TIA+G+ + T G+L Sbjct: 183 LAGMAVAARAIKPEIEIVGVQ----TRRFPTMVNAVKGTEHPVGASTIAEGIAVGTPGTL 238 Query: 246 TFPIIKENCDGVILVTEDEIKYAMKLVWERMKIIIEPSSATTLAAILKQEFKDKKDIKKV 305 T II D ++LV E +I+ A+ ++ E K ++E + A LAA+++ + D+ K+V Sbjct: 239 TRAIIAREADELLLVDEGDIEQAVLMLLEIEKTLVEGAGAAGLAALVR--YPDRFRGKRV 296 Query: 306 GIIISGGNVDLSSISKIL 323 G+++SGGN+D ++ I+ Sbjct: 297 GLVLSGGNIDPLLLTAII 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: 275 Number of extensions: 10 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: 401 Length adjustment: 29 Effective length of query: 295 Effective length of database: 372 Effective search space: 109740 Effective search space used: 109740 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 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