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_011973756.1 MAEO_RS05275 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_000017185.1:WP_011973756.1 Length = 429 Score = 251 bits (642), Expect = 2e-71 Identities = 156/409 (38%), Positives = 239/409 (58%), Gaps = 20/409 (4%) Query: 11 IYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFVDIA 70 + E +K++ ++LIASEN TS+ V EA + ++YAEGLP+ R Y GCE++D Sbjct: 10 VRETALKQHNWMRECIKLIASENITSIPVREACATDFMHRYAEGLPNNRLYQGCEYIDDI 69 Query: 71 EDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGAKVN 130 E+L IE ++ +F AEHANVQP SG AN+AV+ A KPGD +M MD+ +GGH++H KV+ Sbjct: 70 ENLCIELSEDIFKAEHANVQPTSGVVANLAVFFAEAKPGDKLMAMDVPNGGHISHW-KVS 128 Query: 131 FSGKIYNAVYYGVHP---ETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187 +G + HP E ID D++ + E KP+L++ G S +P + A Sbjct: 129 AAG--IRGLRASAHPFDAEEMNIDVDKMVKQILEEKPRLVLFGGSLFPFPHPVKDAVDAA 186 Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPV-PYAHFVTSTTHKTLRGPRSGFILCKKEFAKDI 246 + VGA + D AH GLIAGG + +P+ A ++ +THKTL G + G +L +K+ AK I Sbjct: 187 NEVGATIAYDGAHVLGLIAGGQFQDPLREGAEYMMGSTHKTLFGTQGGVVLTEKKNAKKI 246 Query: 247 DKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKE-YARQVVANARVLAEEFIKEGFKVV- 304 D +FPG+ +H A A+A E ++EF E YA+QVV NA+ L + + G V+ Sbjct: 247 DDKIFPGVVSNHHLHHKAGLAIALAE--TKEFGEAYAKQVVKNAKALGQALYERGCNVLC 304 Query: 305 --SGGTDSHIVLLDLRDT---GLTGREVEEALGKANITVNKNAVPFDPLP-PVKTSGIRL 358 G T+SH V+LD+ + + RE+ +ANI +NKN +P+D + SGIRL Sbjct: 305 EHKGFTESHQVILDIEKSECIEFSARELATMFEEANIILNKNLLPWDDVSNSDNPSGIRL 364 Query: 359 GTPAMTTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQF 407 G+ T GMKE +M IA + ++ D + I+ V+++++E + + Sbjct: 365 GSQECTRLGMKESEMDEIAEFMKRIAI---DGEDIKKVKEDIVEFAKSY 410 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: 527 Number of extensions: 29 Number of successful extensions: 7 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: 429 Length adjustment: 32 Effective length of query: 395 Effective length of database: 397 Effective search space: 156815 Effective search space used: 156815 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