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_050463875.1 AKL27_RS16115 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_001189915.1:WP_050463875.1 Length = 415 Score = 498 bits (1282), Expect = e-145 Identities = 252/405 (62%), Positives = 307/405 (75%), Gaps = 1/405 (0%) Query: 6 NTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCE 65 N D +++ AI KE RQ H+ELIASEN+TS AVMEAQGS +TNKYAEG P KRYYGGCE Sbjct: 10 NIDPDLWSAIQKENHRQQEHIELIASENYTSPAVMEAQGSQLTNKYAEGYPGKRYYGGCE 69 Query: 66 FVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTH 125 FVDIAE LAI+R K LF AE ANVQP+SG+QAN V+ A+LKPGDTIMGM L+ GGHLTH Sbjct: 70 FVDIAEQLAIDRLKQLFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLAEGGHLTH 129 Query: 126 GAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLRE 185 G +N SGK +N V YG++ + IDYD + RLA+E KPK+I+ GASAY ID+ + Sbjct: 130 GMALNMSGKWFNVVSYGLNDKEE-IDYDAMERLAREKKPKMIIAGASAYALRIDFERFAR 188 Query: 186 IADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEFAKD 245 IA VGAY MVDMAHYAGLIA GVYPNPVP+A FVTSTTHK+LRGPR GFIL K E K Sbjct: 189 IAKEVGAYFMVDMAHYAGLIAAGVYPNPVPHADFVTSTTHKSLRGPRGGFILSKAEHEKA 248 Query: 246 IDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVVS 305 I+ ++FPGIQGGPLMHVIA KA+AFKEA+S EFK Y +QVV NA LA+ I+ G ++VS Sbjct: 249 INSAIFPGIQGGPLMHVIAGKAIAFKEALSPEFKTYQQQVVKNADALAKTLIERGLRIVS 308 Query: 306 GGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMTT 365 G T+SH++L+DLR +TG+E E LG A++T NKNA+P DP P TSGIR+G+PAMTT Sbjct: 309 GRTESHVMLVDLRAKKITGKEAEAILGSAHMTCNKNAIPNDPEKPFVTSGIRIGSPAMTT 368 Query: 366 RGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 RG KE + +A LI+ V+ N D IE V+ EV ++ + FP+Y Sbjct: 369 RGFKEAEAVKVAHLIADVLDNPHDAATIERVKAEVKKLTDAFPVY 413 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: 556 Number of extensions: 20 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: 427 Length of database: 415 Length adjustment: 32 Effective length of query: 395 Effective length of database: 383 Effective search space: 151285 Effective search space used: 151285 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: 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