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_014450291.1 LFE_RS10975 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_000284315.1:WP_014450291.1 Length = 413 Score = 491 bits (1264), Expect = e-143 Identities = 235/410 (57%), Positives = 313/410 (76%) Query: 4 LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63 L TD E++EAI +E +R+ L LIASEN+ S +++EA GSVMTNKYAEG P +RYY G Sbjct: 4 LNQTDPEVHEAIAQELKREQEKLVLIASENYVSRSILEAVGSVMTNKYAEGYPGRRYYAG 63 Query: 64 CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123 CE VD E LAIERA+ LF AEH NVQPHSG+QANMAVY++ ++PGDTI+GMDLSHGGHL Sbjct: 64 CEAVDQVETLAIERARLLFGAEHVNVQPHSGSQANMAVYLSSIRPGDTILGMDLSHGGHL 123 Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183 THG+ V+FSG YNAV+YGVH +T LID Q+ LAK+H+P +I+ GASAYPR+ID+A Sbjct: 124 THGSPVSFSGHYYNAVFYGVHRDTGLIDEQQVEALAKQHRPAIIIAGASAYPRIIDFAFF 183 Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEFA 243 R +A+ VGA L+VDMAH++GL+A G +P+P P+A FVT++THKTLRGPR G K +A Sbjct: 184 RRVANEVGAILLVDMAHFSGLVATGHHPSPFPHADFVTTSTHKTLRGPRGGMAFSKSNWA 243 Query: 244 KDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKV 303 K +DK+VFP +QGGPLMHVIA KAV KEA+S +FK+Y+ + NA++LA E + G+++ Sbjct: 244 KALDKAVFPMMQGGPLMHVIAGKAVMLKEALSPDFKQYSENTLKNAKLLASELSEAGYRI 303 Query: 304 VSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAM 363 +GGTD+H++LLDLR+ LTG+E E L +A I NKN VP+D PP TSGIRLGTPA+ Sbjct: 304 STGGTDNHLMLLDLRNKNLTGKEAESYLAQAGIICNKNGVPYDDKPPTVTSGIRLGTPAI 363 Query: 364 TTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLYPEL 413 TTRG+ E ++ IA +I +++ + G VI+ V+ E++ + + FP+Y L Sbjct: 364 TTRGLGEKEVVKIASMIHRILDSKGQGSVIDSVKSELVSLLKDFPIYAGL 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: 570 Number of extensions: 24 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: 413 Length adjustment: 32 Effective length of query: 395 Effective length of database: 381 Effective search space: 150495 Effective search space used: 150495 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 Jul 25 2024. The underlying query database was built on Jul 25 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