Align Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.1; L-threonine/L-allo-threonine aldolase; EC 4.1.2.48 (uncharacterized)
to candidate WP_066603023.1 V473_RS09495 serine hydroxymethyltransferase
Query= curated2:D3DKC4 (427 letters) >NCBI__GCF_001046645.1:WP_066603023.1 Length = 433 Score = 486 bits (1250), Expect = e-142 Identities = 240/414 (57%), Positives = 311/414 (75%), Gaps = 7/414 (1%) Query: 4 LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63 L + D EI+ A E +RQ +ELIASEN S AV+EA GS+ TNKYAEG P KRYYGG Sbjct: 20 LASADPEIFGACRNELKRQQDKIELIASENIVSKAVLEAAGSIFTNKYAEGYPGKRYYGG 79 Query: 64 CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123 CE+ D+ E LAIERAK LF A ANVQP+SG+Q N AV++A+L+PGDT MG+DLS GGHL Sbjct: 80 CEYADVVETLAIERAKELFGANFANVQPNSGSQMNQAVFLALLQPGDTFMGLDLSSGGHL 139 Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183 THG+ VN SGK + V YGV + HLID D++ R+A+E KPKLI+ G +AY RV D+ + Sbjct: 140 THGSPVNMSGKWFKPVAYGVRADDHLIDMDEVARIARECKPKLIICGGTAYSRVWDFKRF 199 Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKE-F 242 REIAD VGAYL+ DM+H++GL+AGG +P+PVPYAH T+TTHK+LRGPRSG +L E Sbjct: 200 REIADEVGAYLLADMSHFSGLVAGGAHPSPVPYAHVTTTTTHKSLRGPRSGIVLTNDEAI 259 Query: 243 AKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFK 302 AK I+ ++FPG+QGGPLMH+IAAKAVAFKEA++ EFK YA Q+VANAR L+E G Sbjct: 260 AKKINSAIFPGMQGGPLMHIIAAKAVAFKEALTPEFKAYAHQIVANARALSETLADAGLS 319 Query: 303 VVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPA 362 +VSGGTD+H++L+DLR TG+ E+AL +A IT NKN VPFD P TSG+RLGTPA Sbjct: 320 IVSGGTDNHLMLVDLRAKNTTGKAAEKALDRAYITCNKNNVPFDTASPFVTSGVRLGTPA 379 Query: 363 MTTRGMKEDQMRIIARLISKVIKNI------GDEKVIEYVRQEVIEMCEQFPLY 410 TTRG +E++ R I RLI++V++ + GD +V ++VR++V+ + +FP+Y Sbjct: 380 GTTRGFREEEFREIGRLIAEVVEGLKRNGDEGDGQVEQHVREKVLGLTARFPIY 433 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: 593 Number of extensions: 22 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: 427 Length of database: 433 Length adjustment: 32 Effective length of query: 395 Effective length of database: 401 Effective search space: 158395 Effective search space used: 158395 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 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