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_068167935.1 HTA01S_RS06365 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_001592305.1:WP_068167935.1 Length = 419 Score = 465 bits (1197), Expect = e-135 Identities = 235/408 (57%), Positives = 299/408 (73%), Gaps = 5/408 (1%) Query: 7 TDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEF 66 TD ++ + +E++RQ H+ELIASEN+TS AVM AQGS +TNKYAEG P +RYYGGCEF Sbjct: 12 TDPALWSIVQQEHQRQEQHIELIASENYTSPAVMMAQGSQLTNKYAEGYPGRRYYGGCEF 71 Query: 67 VDIAEDLAIERAKALFDAEH----ANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGH 122 VD AE LAI+R K LF A+ ANVQ HSG QAN AV+MA +KPGDT MGM+L+ GGH Sbjct: 72 VDQAEQLAIDRVKQLFGADQHGWAANVQAHSGAQANEAVFMAFMKPGDTFMGMNLAEGGH 131 Query: 123 LTHGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAK 182 L+HG +N SGK +N V YG++ + IDYD + R A E KPK+I+ GASAY ID+ + Sbjct: 132 LSHGMALNMSGKWFNVVSYGLNDKEE-IDYDAMERKAHESKPKIIIAGASAYALRIDFER 190 Query: 183 LREIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEF 242 ++A VGA LMVDMAHYAGLIA G YPNP+P+A VTSTTHK+LRGPR G IL + E Sbjct: 191 FAKVAKDVGALLMVDMAHYAGLIAAGEYPNPIPHADIVTSTTHKSLRGPRGGIILMRPEH 250 Query: 243 AKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFK 302 K I+ ++FPG+QGGPLMHVIAAKAVAF EA+S EF+ Y +QVV NA LA+ + G + Sbjct: 251 EKAINSAIFPGLQGGPLMHVIAAKAVAFGEALSPEFRAYQQQVVKNAAALADTLVARGLR 310 Query: 303 VVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPA 362 +VSG T+SH++L+DLR G+TG+ E LG A+ITVNKNA+P DP P+ TSG+RLG+PA Sbjct: 311 IVSGRTESHVMLVDLRAKGMTGKAAEALLGSAHITVNKNAIPNDPEKPMVTSGVRLGSPA 370 Query: 363 MTTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 MTTRG KE + + LI+ ++ + DE VI VR +V + FP+Y Sbjct: 371 MTTRGFKEAEAIQVGHLIADLLDHPEDEAVIARVRADVAALTAAFPVY 418 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: 535 Number of extensions: 19 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: 419 Length adjustment: 32 Effective length of query: 395 Effective length of database: 387 Effective search space: 152865 Effective search space used: 152865 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