Align Serine racemase; D-serine ammonia-lyase; D-serine dehydratase; L-serine ammonia-lyase; L-serine dehydratase; EC 4.3.1.17; EC 4.3.1.18; EC 5.1.1.18 (characterized)
to candidate WP_104913117.1 C3B54_RS02615 threonine ammonia-lyase
Query= SwissProt::Q7XSN8 (339 letters) >NCBI__GCF_002950575.1:WP_104913117.1 Length = 419 Score = 197 bits (500), Expect = 5e-55 Identities = 108/311 (34%), Positives = 180/311 (57%), Gaps = 11/311 (3%) Query: 27 AQARIAPYVHKTPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALDDDEASK 86 A+A ++ TP+ S ++ ++G +F KCE Q+ G++KIRGA N + L ++E ++ Sbjct: 24 ARATVSAVAQVTPMEVSRYLEELLGVPVFMKCENLQRTGSYKIRGAFNRMSKLSEEERAR 83 Query: 87 GVVTHSSGNHAAAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSDVSIESRES 146 GVV S+GNHA VA AAK GI A I P K+ + YG ++ + ++ Sbjct: 84 GVVAASAGNHAQGVAFAAKELGIKATIFTPTGVALPKLQATRAYGAEVVLTGDTMIGPLR 143 Query: 147 VAKRVQEETGAILVHPFNNKNTISGQGTVSLELLEEVPEIDTIIVPISGGGLISGVALAA 206 A ++TGA+ + PF++ + ++GQGTV LE+L+++PE++T++VPI GGGL++GVA Sbjct: 144 AASEFAKQTGAVRIPPFDHHDVVAGQGTVGLEILDQMPEVETVVVPIGGGGLMAGVASVM 203 Query: 207 K----AINPSIRILAAEPKGADDSAQSKAAGKIITLPSTNTIADGLRAFL-GDLTWPVVR 261 K SI+++ + A S AGKI+ + TIADG+ G+L + +++ Sbjct: 204 KQRAALEGRSIKVIGVQATNAAPYPLSIEAGKIVEVSVKPTIADGIAVSKPGELNFDIIK 263 Query: 262 DLVDDIIVVDDNAIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSAWHESSKIGII 321 VD+++ VDD+ A+ + E K+ VEP+GA+ +AA +S K + +I Sbjct: 264 HTVDEVVTVDDDETARAILVLLERAKMVVEPAGAVAVAAVMSGLVK------ATGPTAVI 317 Query: 322 VSGGNVDLGVL 332 +SGGN+D +L Sbjct: 318 LSGGNIDPMIL 328 Lambda K H 0.316 0.133 0.381 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: 12 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: 339 Length of database: 419 Length adjustment: 30 Effective length of query: 309 Effective length of database: 389 Effective search space: 120201 Effective search space used: 120201 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 (21.6 bits) S2: 50 (23.9 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