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 AO356_16850 AO356_16850 serine hydroxymethyltransferase
Query= curated2:D3DKC4 (427 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_16850 Length = 412 Score = 493 bits (1270), Expect = e-144 Identities = 240/407 (58%), Positives = 307/407 (75%) Query: 4 LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63 L N D I I +E RQ HLELIASEN+ S V++AQGSV+TNKYAEG P KRYYGG Sbjct: 3 LQNFDPAIARLIDRERNRQETHLELIASENYVSEEVLQAQGSVLTNKYAEGYPGKRYYGG 62 Query: 64 CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123 C+ VD E+LAIERA+ LF+ E+ NVQPHSG+QAN AV++AVL+PGDTI+GM L+HGGHL Sbjct: 63 CKVVDEIENLAIERARKLFNCEYVNVQPHSGSQANQAVFLAVLEPGDTILGMSLAHGGHL 122 Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183 THGA VNFSGK+Y A YG+ ET +DY+++ LA+EH+PK+I+ GASAY R +D+ + Sbjct: 123 THGASVNFSGKLYRAFSYGLDTETETLDYEEMEALAREHRPKMIIAGASAYSRTLDFQRF 182 Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEFA 243 R+I D VGAYLMVDMAHYAGLIA GVYP+PV A F+TSTTHKTLRGPR G IL K ++A Sbjct: 183 RKICDEVGAYLMVDMAHYAGLIAAGVYPSPVGIADFITSTTHKTLRGPRGGLILAKAQYA 242 Query: 244 KDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKV 303 +DK++FP QGGPLMHVIAAKAVAF EA+ FK Y ++V+ NARV+A+ + G +V Sbjct: 243 ALLDKTIFPVYQGGPLMHVIAAKAVAFNEALGDGFKHYQQRVIDNARVMADVLTRRGLRV 302 Query: 304 VSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAM 363 VSGGTD H+ LLDLR +TG++ E L A+IT+NKNA+P DP P TSGIR+GTPA+ Sbjct: 303 VSGGTDCHMFLLDLRSMNITGKDAEALLESAHITLNKNAIPNDPQKPAVTSGIRIGTPAL 362 Query: 364 TTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 TTRG E + +A LI+ +++ + ++ R+ V+ +CE FP+Y Sbjct: 363 TTRGFGEAECAEVANLIADLLEQPDNAARLDNTRRRVMHLCECFPVY 409 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: 575 Number of extensions: 28 Number of successful extensions: 1 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: 412 Length adjustment: 32 Effective length of query: 395 Effective length of database: 380 Effective search space: 150100 Effective search space used: 150100 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 Sep 17 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