Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_078429991.1 BK574_RS21135 threonine synthase
Query= BRENDA::B1N2N4 (423 letters) >NCBI__GCF_002019605.1:WP_078429991.1 Length = 354 Score = 88.6 bits (218), Expect = 3e-22 Identities = 87/297 (29%), Positives = 141/297 (47%), Gaps = 32/297 (10%) Query: 52 ISKKVGCKTYLKLENLQKTGSFKVRGAVNKIATLTEEEKKRGVVAASAGNHAQGVAFAST 111 +SK+ G Y+K+E TGSFK RG V +A EE K ++ AS GN + A Sbjct: 39 LSKEWGVDVYVKVEGANPTGSFKDRGMVMAVAKAKEEGSKT-IICASTGNTSAAAAAYGA 97 Query: 112 SAGCKATIVMPE-FASTAKVTATRGYGAEVVLHGKVFDESLAYAMQLCKEEGKTFVHPFN 170 AG + +V+PE + K+ YGAEV+ FD +L ++ ++E T V+ N Sbjct: 98 RAGLRCIVVIPEGKIALGKLAQAVMYGAEVLEIKGNFDNALDIVRKISEQEPITLVNSVN 157 Query: 171 DPWVMAGQGTIALEILEQLEKC-DVIIGAIGGGGLMSGVAFAAKQIK-------PEIRII 222 P+ + GQ T A EI + L + DV+ +G G ++ K+ P++R Sbjct: 158 -PYRIEGQKTAAFEICDALGQAPDVLAIPVGNAGNITAYWKGFKEYNEAKQTGLPQMR-- 214 Query: 223 GVQAAECPSMAVSKAEHKICCVKTAKTMADGIAVKAPGDKTAPVLLKYVDE----IVTVD 278 G QA S A+ + E +++ +T+A I + P V + DE I +V Sbjct: 215 GFQA--WGSAAIVRNE----VIESPETIATAIRIGNPASWKQAVAAR--DESNGHIDSVT 266 Query: 279 EESIAQAMLLMLERCKIVSEGSGATPVAALL----SGKIKGLTEDTNVVCIVSGGNL 331 +E I A L+ R + +E + +A L+ +G+IK + VVC+++G L Sbjct: 267 DEEILAAYQLLASREGVFAEPASCASIAGLIKQINTGEIK---KGAKVVCVLTGNGL 320 Lambda K H 0.317 0.133 0.378 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: 325 Number of extensions: 16 Number of successful extensions: 2 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: 423 Length of database: 354 Length adjustment: 30 Effective length of query: 393 Effective length of database: 324 Effective search space: 127332 Effective search space used: 127332 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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