Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate WP_069664978.1 BCR25_RS17880 threonine synthase
Query= BRENDA::B1N2N4 (423 letters) >NCBI__GCF_001730305.1:WP_069664978.1 Length = 352 Score = 90.1 bits (222), Expect = 9e-23 Identities = 89/297 (29%), Positives = 133/297 (44%), Gaps = 28/297 (9%) Query: 50 NTISKKVGCKTYLKLENLQKTGSFKVRGAVNKIATLTEEEKKRGVVAASAGNHAQGVAFA 109 +++SK++G Y K E L TGSFK RG V +A EE K +V AS GN + A Sbjct: 35 HSLSKELGINLYGKYEGLNPTGSFKDRGMVMAVAKAVEEGAK-AIVCASTGNTSAAAAAY 93 Query: 110 STSAGCKATIVMPE-FASTAKVTATRGYGAEVVLHGKVFDESLAYAMQLCKEEGKTFVHP 168 +T AG KA +V+P+ + K+ YGA+++ FDE+L + K E V+ Sbjct: 94 ATRAGVKAYVVIPDGKIAMGKLAQAIIYGADIISIPGNFDEALKAVRDIAKTEAVALVNS 153 Query: 169 FNDPWVMAGQGTIALEILEQLEKC-DVIIGAIGGGGLMSGVAFAAKQIKPEIRIIGVQAA 227 N P+ + GQ T A E+ EQL + DV+ +G G +S K+ ++ Sbjct: 154 VN-PYRLEGQKTAAFEVCEQLGQAPDVLAIPVGNAGNISAYWKGFKEWH------DLKGT 206 Query: 228 ECPSMAVSKAEHKICCVK-----TAKTMADGIAVKAPGDKTAPVLLKYVDE----IVTVD 278 P M +AE VK +T+A I + P T + DE I V Sbjct: 207 SLPRMHGFEAEGAAAIVKGEAIDQPETIATAIRIGNPASWTLAEAAR--DESNGHIDAVT 264 Query: 279 EESIAQAMLLMLERCKIVSEGSGATPVAALL----SGKIKGLTEDTNVVCIVSGGNL 331 +E I A + + + E A +A ++ SGKIK VV + +G L Sbjct: 265 DEEILNAYRKVAAQDGVFVEPGSAASLAGVIQHVKSGKIK---PGETVVAVFTGNGL 318 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: 306 Number of extensions: 10 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: 352 Length adjustment: 30 Effective length of query: 393 Effective length of database: 322 Effective search space: 126546 Effective search space used: 126546 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 Jul 26 2024. The underlying query database was built on Jul 25 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