Align D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate Ga0059261_3694 Ga0059261_3694 threonine ammonia-lyase, medium form
Query= BRENDA::Q54HH2 (324 letters) >FitnessBrowser__Korea:Ga0059261_3694 Length = 420 Score = 190 bits (482), Expect = 6e-53 Identities = 106/318 (33%), Positives = 182/318 (57%), Gaps = 7/318 (2%) Query: 7 VTLKDIKEAHKRIEKYIHKTPVLTNSTINELAGKELYFKCENLQKTGSFKMRGACNAIFS 66 VTL D++ A RI + TP L + T+++L G +Y K ENLQ T ++K RGA N + Sbjct: 20 VTLADVQAAAARIMGAVVHTPTLHSKTLSDLTGATVYLKFENLQFTAAYKERGALNTLLQ 79 Query: 67 LDEEELSKGVVTHSSGNHGQALSYASKVRCVKCYVVVPEDAPSVKLNAICGYGATVTKCK 126 LD+ +KGV+ S+GNH Q L+Y + +V+P+ P+VK+ +GAT+ Sbjct: 80 LDDAARAKGVIAASAGNHAQGLAYHGNRLGIPVTIVMPKSTPTVKVMQTESHGATIILEG 139 Query: 127 ATLEARESNTKQLIEQHSCKLIHPFDNLQVIAGQGTASLELMEQVENLDAIITPVGGGGL 186 T + ++ +QL + +HPFD+ ++IAGQGT LE++ +D +I P+GGGGL Sbjct: 140 ETFDEAYAHARQLEASNGYTFVHPFDDPRIIAGQGTVFLEMLADAPAIDTLIVPIGGGGL 199 Query: 187 LSGTCITAKSLNPNIKVFAAEPLGADDTYRSLLSGEIQKHTPGKPNTIADGL-LTTVGSL 245 +SG AK+ + I+V + + + S+ + H P +T+A+G+ + G L Sbjct: 200 ISGALTVAKAADKPIEVVGVQA----ELFPSMFNRFTGAHEPIGGDTLAEGIAVKEPGGL 255 Query: 246 TFPIIKENCDGVILVTEDEIKYAMKLVWERMKIIIEPSSATTLAAILKQEFKDKKDIKKV 305 T I++ D ++LV+E ++ A+ L+ + K ++E + A LAA++ Q + + K V Sbjct: 256 TAQIVEALVDEIMLVSERSLEEAVSLLLQIEKTVVEGAGAAGLAALMTQPERFRG--KTV 313 Query: 306 GIIISGGNVDLSSISKIL 323 G+I++GGN+D ++ +L Sbjct: 314 GVILTGGNIDTRLLANVL 331 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: 263 Number of extensions: 14 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: 420 Length adjustment: 30 Effective length of query: 294 Effective length of database: 390 Effective search space: 114660 Effective search space used: 114660 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