Align Serine hydroxymethyltransferase; SHMT; Serine methylase; L-threonine/L-allo-threonine aldolase; EC 2.1.2.1; EC 4.1.2.48 (characterized)
to candidate WP_012966217.1 FERP_RS08690 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_000025505.1:WP_012966217.1 Length = 420 Score = 261 bits (666), Expect = 4e-74 Identities = 162/404 (40%), Positives = 234/404 (57%), Gaps = 12/404 (2%) Query: 10 EIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFVDI 69 E+YE I K E L LIASEN TS V S + ++YAEG +R+Y GC FVD Sbjct: 5 EVYEVIRKHTEFYKNSLPLIASENITSKFVRNCYISDLGHRYAEGKIGERFYEGCSFVDE 64 Query: 70 AEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGAKV 129 E +A+ K L A H NVQP SG ANMA + A+ PGD I + + GGH++H Sbjct: 65 IELMAVNLMKELVKAPHVNVQPISGVVANMAGFFALTNPGDKIFALSIPSGGHISHEKYS 124 Query: 130 NFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIADS 189 + ++Y E ID D+ +LA++ KPKL V G S + ++ EIA Sbjct: 125 AAGLRGLQVLHYPFDAEIMNIDVDETKKLAEKEKPKLFVLGGSLFLFPHPVKEISEIAAE 184 Query: 190 VGAYLMVDMAHYAGLIAGGVYPNPVPY-AHFVTSTTHKTLRGPRSGFILCKKEFAKDIDK 248 + A +M D +H GLIAGG + NP+ A +T++THKT GP+ I C++E A +DK Sbjct: 185 INAKVMYDGSHVLGLIAGGEFQNPMEEGADVLTASTHKTFFGPQRAIIACREELADRVDK 244 Query: 249 SVFPGIQGGPLMHVIAAKAVAFKEAMSQEF-KEYARQVVANARVLAEEFIKEGFKVVS-- 305 +VFPG+ ++ +A +A E +EF ++YA Q V NA+ LAEE +EG KV+ Sbjct: 245 AVFPGVVSNHHLNTLAGLVIAAME--FKEFGRDYAEQTVKNAKRLAEELAEEGLKVLGED 302 Query: 306 -GGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKT-SGIRLGTPAM 363 G T+SH V +D+R G G +V + L KANI +NKN +P+D + + SGIR+G + Sbjct: 303 LGFTESHQVAVDVRKQG-GGAKVAKKLEKANIILNKNLLPWDSIKDTENPSGIRIGVQEV 361 Query: 364 TTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQF 407 T GMKE +M +IA+LI+ VI D + ++ VR++VI + ++F Sbjct: 362 TRLGMKESEMDVIAKLIADVIL---DRRSVDKVRKDVISLKKEF 402 Lambda K H 0.319 0.136 0.395 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: 475 Number of extensions: 26 Number of successful extensions: 7 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: 427 Length of database: 420 Length adjustment: 32 Effective length of query: 395 Effective length of database: 388 Effective search space: 153260 Effective search space used: 153260 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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