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_011766527.1 AZO_RS14080 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_000061505.1:WP_011766527.1 Length = 416 Score = 468 bits (1203), Expect = e-136 Identities = 243/408 (59%), Positives = 295/408 (72%), Gaps = 2/408 (0%) Query: 4 LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63 L D E++ AI E RQ H+ELIASEN+ S AVMEAQGS +TNKYAEG P KRYYGG Sbjct: 8 LAKVDPELWSAIQAENRRQEDHIELIASENYVSHAVMEAQGSQLTNKYAEGYPGKRYYGG 67 Query: 64 CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123 CE VD+ E LAI+R K LF A+ ANVQP+SG+QAN AV MA KPGDTIMGM L+ GGHL Sbjct: 68 CEHVDVVEQLAIDRLKKLFGADAANVQPNSGSQANQAVLMAFAKPGDTIMGMSLAEGGHL 127 Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183 THG +N SGK +N V YG+ E I+Y + LA+EHKPK+I+ GASAY ID+ + Sbjct: 128 THGMPLNMSGKWFNVVAYGLD-EKEEINYAAMEALAREHKPKIIIAGASAYALRIDFERF 186 Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEFA 243 IA VGA VDMAHYAGLIA G YPNPVP+A VTSTTHKTLRGPR G IL K E Sbjct: 187 ARIAREVGAIFWVDMAHYAGLIAAGYYPNPVPHADVVTSTTHKTLRGPRGGIILMKAEHE 246 Query: 244 KDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKE-GFK 302 K I+ ++FPG+QGGPL HVIAAKAVAFKEA + F++Y QV+ANARV+A +E G + Sbjct: 247 KAINSAIFPGLQGGPLEHVIAAKAVAFKEAATPAFRDYQEQVIANARVMARVLGEERGLR 306 Query: 303 VVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPA 362 +VSG T+SH+ L+DLR +TG+E E LG A+ITVNKN++P DP P TSGIR+G+PA Sbjct: 307 IVSGRTESHVFLVDLRSKNITGKEAEAVLGSAHITVNKNSIPNDPQKPFVTSGIRIGSPA 366 Query: 363 MTTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 MTTRG E + IA LI+ V+ D V+E VR +V E+C +FP+Y Sbjct: 367 MTTRGFTEIEAEQIAHLIADVLDAPQDAAVLERVRGKVGELCAKFPVY 414 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: 576 Number of extensions: 27 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: 416 Length adjustment: 32 Effective length of query: 395 Effective length of database: 384 Effective search space: 151680 Effective search space used: 151680 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