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_013683034.1 ARCVE_RS01615 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_000194625.1:WP_013683034.1 Length = 406 Score = 236 bits (601), Expect = 1e-66 Identities = 157/403 (38%), Positives = 223/403 (55%), Gaps = 23/403 (5%) Query: 10 EIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFVDI 69 +++ I + + L LIASEN TS+AV S + ++YA G +R Y GCE++D Sbjct: 6 QVFSIIEEHHRLMASSLPLIASENVTSMAVRRCYTSDLGHRYAMGEIGERAYEGCEYIDE 65 Query: 70 AEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGAKV 129 E A+E K LF+AEHANV+P SGT AN+AVY A+ GD+I + + GGH +H Sbjct: 66 IERKAVELTKRLFNAEHANVRPISGTVANIAVYHALTSCGDSIFSLPVECGGHTSHDDTA 125 Query: 130 NFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIADS 189 + N + E ID D R+ +E KP+LIV GAS + ++ EIA Sbjct: 126 RI--RCLNVHFLPFDSERFNIDIDAASRMIREVKPRLIVLGASVFLFPHPVKEIVEIAAE 183 Query: 190 VGAYLMVDMAHYAGLIAGGVYPNPVPY-AHFVTSTTHKTLRGPRSGFILCKKEFAKDIDK 248 VGA ++ D +H GLIAG + +PV A VT++THKT GP+ ILCK E A+ ID Sbjct: 184 VGANVIYDASHVLGLIAGKQFQDPVKEGADVVTASTHKTFFGPQRAIILCKSELAEKIDY 243 Query: 249 SVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKE-YARQVVANARVLAEEFIKEGFKVV--- 304 +V P + ++ +A +A E + EF E YA+Q V NA+ LAE + G KVV Sbjct: 244 AVMPCVVSNHHLNTLAGYVIACLEML--EFGESYAKQTVRNAKRLAERLYELGMKVVGEA 301 Query: 305 SGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMT 364 G T+SH V++D+ D G + + L KA I N+ +P+ K++GIR+G +T Sbjct: 302 EGFTESHQVVIDVDD----GEKAAKTLEKAGIITNRCLLPWS---EGKSAGIRIGVQEVT 354 Query: 365 TRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQF 407 GMK +M IA LISK + I VR EV+E+ +QF Sbjct: 355 RLGMKGGEMEYIAELISKALDGID-------VRSEVVELSKQF 390 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: 435 Number of extensions: 23 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: 406 Length adjustment: 31 Effective length of query: 396 Effective length of database: 375 Effective search space: 148500 Effective search space used: 148500 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