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_008482275.1 B3C1_RS00900 threonine ammonia-lyase, biosynthetic
Query= SwissProt::Q7XSN8 (339 letters) >NCBI__GCF_000299915.1:WP_008482275.1 Length = 500 Score = 182 bits (462), Expect = 2e-50 Identities = 111/304 (36%), Positives = 172/304 (56%), Gaps = 22/304 (7%) Query: 38 TPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALDDDEASKGVVTHSSGNHA 97 TPV + +G+ ++ K E Q +FK+RGA + I +L D GVV S+GNHA Sbjct: 23 TPVNRLARLSERLGQDVWLKREDLQPVHSFKLRGAYHKIASLPRD--CPGVVAASAGNHA 80 Query: 98 AAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSDVSIESRESVAKRVQEETGA 157 VAL+A+ G A IV+P APA KVD VK G ++ + ++ + A+ + + G Sbjct: 81 QGVALSARALGFKAIIVMPTQAPAIKVDAVKALGAEVVLFGDNFDAAKDHAQTLSSQQGF 140 Query: 158 ILVHPFNNKNTISGQGTVSLELLEEVPEIDTIIVPISGGGLISGVALAAKAINPSIRILA 217 V PF+++ I+GQGT+ LEL++E+P++D + +P+ GGGL +GVA K + P IR++A Sbjct: 141 AFVAPFDDEKVIAGQGTLGLELIKELPKLDVLFLPVGGGGLAAGVAAVIKQLKPEIRVVA 200 Query: 218 AEPKGADDSAQSKA---AGKIITLPSTNTIADGLRA-FLGDLTWPVVRDLVDDIIVVDDN 273 EP DD+A KA AG +TL T ADG+ +G T+ V+ VD+ I V ++ Sbjct: 201 VEP---DDAACFKAAFEAGAPVTLDEVGTFADGVAVKRIGTETFRVMSQFVDEAITVSND 257 Query: 274 AIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSAWHE-----SSKIGIIVSGGNVD 328 AI A+K +E ++ EP+GA+ LA AW E ++G ++SG N++ Sbjct: 258 AICAAIKDIFEDVRAVAEPAGALSLAGL--------KAWCEQHPEFKGQVGAVLSGANLN 309 Query: 329 LGVL 332 +L Sbjct: 310 FHLL 313 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: 326 Number of extensions: 17 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: 339 Length of database: 500 Length adjustment: 31 Effective length of query: 308 Effective length of database: 469 Effective search space: 144452 Effective search space used: 144452 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