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_012101671.1 CKL_RS06320 serine hydroxymethyltransferase
Query= curated2:D3DKC4 (427 letters) >NCBI__GCF_000016505.1:WP_012101671.1 Length = 411 Score = 542 bits (1397), Expect = e-159 Identities = 259/407 (63%), Positives = 330/407 (81%), Gaps = 2/407 (0%) Query: 4 LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63 L NTD +IY I +E+ERQ +ELIASENFTS +VMEA GS +TNKYAEG P KRYYGG Sbjct: 6 LKNTDKDIYGIIEEEWERQKNGIELIASENFTSKSVMEAMGSFLTNKYAEGYPGKRYYGG 65 Query: 64 CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123 C VD AEDLA +R K LF+AEH NVQPHSG+QANMAVYM+VLKPGDT++GM L+HGGHL Sbjct: 66 CYIVDKAEDLARDRMKKLFNAEHVNVQPHSGSQANMAVYMSVLKPGDTVLGMSLNHGGHL 125 Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183 THG+KV+FSGK+YN V YG++ +T +IDYD++ LA +HKPK+IV GASAYPR ID+ K+ Sbjct: 126 THGSKVSFSGKLYNFVSYGLNSDTEIIDYDEMRELALKHKPKMIVSGASAYPRKIDFKKI 185 Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEFA 243 REI D VGAY+MVDMAH AG+IA G + +PVPYA FVT+TTHKTLRGPR G I+CK+++ Sbjct: 186 REICDEVGAYMMVDMAHIAGIIAAGRHESPVPYADFVTTTTHKTLRGPRGGAIICKEKYG 245 Query: 244 KDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKV 303 +DK++FPGIQGGPLMH+IAAKAV F EA+ E+KEY Q++ NA+V EE +K GF++ Sbjct: 246 AALDKTIFPGIQGGPLMHIIAAKAVCFGEALKDEYKEYIDQIIKNAKVFGEELVKYGFRL 305 Query: 304 VSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAM 363 VSGGTD+H++L+DL + +TG+++EE L K NITVNKNA+PFD L P TSGIR+GTPA+ Sbjct: 306 VSGGTDNHLLLVDLTNKNITGKDLEELLDKVNITVNKNAIPFDKLKPNVTSGIRVGTPAV 365 Query: 364 TTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 TTRG KE++M+ +A I+K ++N E + +++EVIE+CE FPLY Sbjct: 366 TTRGFKEEEMKKVAYFINKAVEN--REGDLSAIKREVIELCEAFPLY 410 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: 649 Number of extensions: 24 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: 411 Length adjustment: 32 Effective length of query: 395 Effective length of database: 379 Effective search space: 149705 Effective search space used: 149705 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 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