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_086510497.1 BZY95_RS13805 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_002151265.1:WP_086510497.1 Length = 432 Score = 487 bits (1253), Expect = e-142 Identities = 243/410 (59%), Positives = 308/410 (75%), Gaps = 7/410 (1%) Query: 8 DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67 D+++ AI E RQ H+ELIASEN+ S AVMEAQG+ +TNKYAEG P KRYYGGCE V Sbjct: 10 DSQVAAAIADEVARQEAHVELIASENYASRAVMEAQGTQLTNKYAEGYPGKRYYGGCEHV 69 Query: 68 DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127 D+ E LAIERA LF A+ ANVQPHSG QAN AV+MA++ PGDT++GM L+HGGHLTHGA Sbjct: 70 DVVEKLAIERACDLFGADFANVQPHSGAQANAAVFMALVSPGDTVLGMSLAHGGHLTHGA 129 Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187 NFSGK Y+AV YG++PET IDY+++ RLA+ HKPKLI+ G SAY RV+DW + R IA Sbjct: 130 APNFSGKHYHAVQYGLNPETGEIDYEEVERLARSHKPKLIIAGFSAYSRVVDWRRFRNIA 189 Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILC---KKEFAK 244 D VGA+LMVDMAH AGL+A G+YP+PVP+AH VT+TTHKTLRGPR G IL E K Sbjct: 190 DEVGAWLMVDMAHVAGLVAAGLYPSPVPHAHVVTTTTHKTLRGPRGGLILSAHGDAELYK 249 Query: 245 DIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVV 304 ++ +VFPG QGGPLMHVIAAKAVAFKEAMSQ F +Y ++V+ NAR +A+ F++ G+ VV Sbjct: 250 KLNGAVFPGQQGGPLMHVIAAKAVAFKEAMSQAFVQYQQRVIDNARAMAKVFVERGYDVV 309 Query: 305 SGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMT 364 SGGTD H+ L+ L G+TG++ + ALG+A+ITVNKNAVP DP P TSG+R+GTPA+T Sbjct: 310 SGGTDDHLFLVSLIRQGVTGKDADAALGRAHITVNKNAVPNDPQSPFVTSGLRIGTPAVT 369 Query: 365 TRGMKEDQMRIIARLISKVIKNIGD----EKVIEYVRQEVIEMCEQFPLY 410 +RG +A I ++ + + + V VR +V E+CE+ P+Y Sbjct: 370 SRGFDVADCEALAGWICDILDVLAEQGNTDAVEAEVRTKVAELCERHPVY 419 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: 618 Number of extensions: 23 Number of successful extensions: 3 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: 432 Length adjustment: 32 Effective length of query: 395 Effective length of database: 400 Effective search space: 158000 Effective search space used: 158000 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