Align Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.1; L-threonine/L-allo-threonine aldolase; EC 4.1.2.48 (uncharacterized)
to candidate WP_015945493.1 DHAF_RS24045 serine hydroxymethyltransferase
Query= curated2:D3DKC4 (427 letters) >NCBI__GCF_000021925.1:WP_015945493.1 Length = 417 Score = 526 bits (1356), Expect = e-154 Identities = 260/406 (64%), Positives = 314/406 (77%), Gaps = 1/406 (0%) Query: 8 DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67 D E+ EAI +E +RQ Y +ELIASENF S AVM AQGSV+TNKYAEG P KRYYGGCE+V Sbjct: 12 DPEVAEAIAQEEQRQRYKIELIASENFVSRAVMAAQGSVLTNKYAEGYPGKRYYGGCEYV 71 Query: 68 DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127 DI EDLA ER K LF AEHANVQPHSG QAN AVY A+LKPGDT++GM+LSHGGHLTHG+ Sbjct: 72 DIVEDLARERVKKLFGAEHANVQPHSGAQANTAVYFAMLKPGDTVLGMNLSHGGHLTHGS 131 Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187 VN SG YN V YGV T IDYD + +LA EH+PKLIV GASAYPR ID+A+LREIA Sbjct: 132 PVNISGMYYNFVAYGVDQVTERIDYDVVRQLALEHRPKLIVAGASAYPRQIDFARLREIA 191 Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEFAKDID 247 D +Y MVDMAH AGL+A G++ NPVPYAHFVT+TTHKTLRGPR G ILC++EFAK ID Sbjct: 192 DEADSYFMVDMAHIAGLVAAGLHQNPVPYAHFVTTTTHKTLRGPRGGLILCQEEFAKAID 251 Query: 248 KSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVVSGG 307 K++FPGIQGGPLMHVIAAKAVAF EA+ EF EY +++V NA+VL+E ++GF++VSGG Sbjct: 252 KAIFPGIQGGPLMHVIAAKAVAFGEALKPEFVEYQKRIVENAKVLSETLAEKGFRIVSGG 311 Query: 308 TDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMTTRG 367 TD+H++L+D+R GLTG+E E L + ITVNKN +P+DP P+ TSGIR+GTPA+T+RG Sbjct: 312 TDNHLMLVDVRSKGLTGKEAEYILDEVGITVNKNTIPYDPASPMVTSGIRIGTPAVTSRG 371 Query: 368 MKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLYPEL 413 M M+ IA I + +E R V +C ++PLYP L Sbjct: 372 MDTLAMKKIAAAIDIALSE-PNEAGAAKARDMVAALCAEYPLYPNL 416 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: 612 Number of extensions: 23 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: 417 Length adjustment: 32 Effective length of query: 395 Effective length of database: 385 Effective search space: 152075 Effective search space used: 152075 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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