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_066329080.1 BLR17_RS14560 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_900100165.1:WP_066329080.1 Length = 424 Score = 484 bits (1245), Expect = e-141 Identities = 241/419 (57%), Positives = 309/419 (73%), Gaps = 16/419 (3%) Query: 8 DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67 D +I+E I++E +RQ + LELIASENF S VMEA GSV+TNKYAEG P KRYYGGCE V Sbjct: 4 DKQIFELILEEQDRQIHGLELIASENFVSDEVMEAAGSVLTNKYAEGYPGKRYYGGCEVV 63 Query: 68 DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127 DI E +AI+RAK LF AE+ANVQPHSG+QAN +V+ A LKPGD I+G DLSHGGHLTHG+ Sbjct: 64 DIVEQIAIDRAKELFGAEYANVQPHSGSQANASVFHACLKPGDKILGFDLSHGGHLTHGS 123 Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187 VNFSG++YN V+YGV ET +DYD++ +A + +PKLI+ GASAY R +D+A+ R+IA Sbjct: 124 PVNFSGRVYNPVFYGVDKETGRLDYDKIQEIATKEQPKLIIAGASAYSRDMDFARFRQIA 183 Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEFAKD-- 245 DSVGA LM D++H AGLIA G+ +P+P+ H VT+TTHKTLRGPR G IL K+F Sbjct: 184 DSVGAILMADISHPAGLIAKGLLSDPIPHCHIVTTTTHKTLRGPRGGLILMGKDFPNPWG 243 Query: 246 --------------IDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARV 291 +D +VFPG QGGPLMH+IAAKAVAF EA+ EF YARQ+ NA Sbjct: 244 LTTPKGEIRMMSALLDLAVFPGNQGGPLMHIIAAKAVAFGEALQDEFFTYARQLQKNANA 303 Query: 292 LAEEFIKEGFKVVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPV 351 +A+ F+K G+ ++SGGTD+H++L+DLR+ G++G++ E AL KA ITVNKN VPFD P Sbjct: 304 MADAFVKRGYNIISGGTDNHMMLIDLRNKGISGKDAENALVKAEITVNKNMVPFDDKSPF 363 Query: 352 KTSGIRLGTPAMTTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 TSGIR+GT A+TTRG+ E+ M I +I KV+ N +E VIE V +EV EM + ++ Sbjct: 364 VTSGIRVGTAAITTRGLVEEDMETIVAMIDKVLMNHTNEDVIEEVAEEVNEMMSERAIF 422 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: 546 Number of extensions: 21 Number of successful extensions: 2 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: 424 Length adjustment: 32 Effective length of query: 395 Effective length of database: 392 Effective search space: 154840 Effective search space used: 154840 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 Jul 26 2024. The underlying query database was built on Jul 25 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