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_014027034.1 PYRFU_RS07375 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_000223395.1:WP_014027034.1 Length = 441 Score = 201 bits (511), Expect = 4e-56 Identities = 141/393 (35%), Positives = 203/393 (51%), Gaps = 16/393 (4%) Query: 26 LELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFVDIAEDLAIERAKALFDAE 85 + LIASEN S A + M ++YAEG P KRYY G +VD+ E+L ++ L Sbjct: 33 INLIASENVMSPLAEAAYLNDMMHRYAEGKPRKRYYQGLRYVDVVEELVMKYMGELLGGA 92 Query: 86 HANVQPHSGTQANMAVYMAVLKPGDT-----IMGMDLSHGGHLTHGAKVNFSGKIYNAVY 140 +P SGT AN V+ A+ + + + G H++H + Sbjct: 93 FIEPRPVSGTIANATVFRALASCPSSEGRPKALIAPVQAGAHVSHTKFGTLGALCIEHIE 152 Query: 141 YGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIADSVGAYLMVDMAH 200 P+ +D D+ ++ ++ KP +V G S Y ++ E A SVGA L+ D AH Sbjct: 153 LPYDPDNLNVDVDKAVKMIEDVKPVFVVLGGSLYLFPHPVREIAEAAHSVGAKLVYDAAH 212 Query: 201 YAGLIAGGVYPNPVPY-AHFVTSTTHKTLRGPRSGFILCKKE-FAKDIDKSVFPGIQGGP 258 GLI G + NP+ + A +T++THKT GP+ G I ++E K + + VFP Sbjct: 213 VLGLIVGKRWRNPLDHGADIMTASTHKTFPGPQGGIIATRQEDLYKAVSRIVFPYFVSNH 272 Query: 259 LMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVVS---GGTDSHIVLL 315 +H + A A+ E M + YA QVV NA+ LAE EGFKV+ G T SH V + Sbjct: 273 HLHRLPALAITALE-MKYYGEAYADQVVRNAKALAEALAAEGFKVLGEHLGYTRSHQVAV 331 Query: 316 DLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKT-SGIRLGTPAMTTRGMKEDQMR 374 D+R+ G G + + L +ANI VNKN +P+DP +K SG+RLG MT GMKED MR Sbjct: 332 DVREYG-GGAKAAQLLEEANIIVNKNLLPYDPPDAIKNPSGLRLGVQEMTRWGMKEDDMR 390 Query: 375 IIARLISKVIKNIGDEKVIEYVRQEVIEMCEQF 407 IAR + +V+ + D VR+EV+E F Sbjct: 391 EIARFMRRVVIDGEDP---AKVRKEVVEFRRNF 420 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: 517 Number of extensions: 35 Number of successful extensions: 6 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: 441 Length adjustment: 32 Effective length of query: 395 Effective length of database: 409 Effective search space: 161555 Effective search space used: 161555 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: 51 (24.3 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