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_013259861.1 DEBA_RS15345 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_000143965.1:WP_013259861.1 Length = 413 Score = 442 bits (1137), Expect = e-129 Identities = 220/408 (53%), Positives = 289/408 (70%) Query: 1 MRHLFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRY 60 M L TD++I E I +E RQ L +I SEN+ S AV+ A GS++ NKY+EG P KRY Sbjct: 1 MDQLRETDSQIAELIQREAARQANVLRMIPSENYASAAVLTATGSILANKYSEGYPRKRY 60 Query: 61 YGGCEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHG 120 Y G EF+D E++A++RA+ALF AEHANVQP+SG+ ANMAVY+ +L +MGMDL+ G Sbjct: 61 YQGQEFIDQIEEVAVQRARALFGAEHANVQPYSGSPANMAVYLGLLGAEGRVMGMDLAAG 120 Query: 121 GHLTHGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDW 180 GHLTHGAKV+FSG Y+ YG+ E LIDY+ RLA+E +P+LI GAS+YPR+ID+ Sbjct: 121 GHLTHGAKVSFSGSYYDVRQYGLSRENGLIDYEAARRLAREFRPQLIFCGASSYPRIIDF 180 Query: 181 AKLREIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKK 240 A EIA VGA+L D++H +GL G++P+P+P+A +T+TTHK LRGPR G ILC+ Sbjct: 181 AIFGEIAREVGAFLAADISHISGLCVTGLHPHPLPHADVITTTTHKMLRGPRGGMILCRA 240 Query: 241 EFAKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEG 300 A IDK+VFPG+QGGP HV AA AVA KEA F EY RQ+VANA+ LA+E + G Sbjct: 241 GLAPAIDKAVFPGLQGGPHNHVTAAIAVALKEASGTAFVEYCRQIVANAKALADELMARG 300 Query: 301 FKVVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGT 360 FK+++GGTD+H+ L+D GLTG+ + +A+ KA I N N +PFDP SG+RLGT Sbjct: 301 FKLITGGTDNHLALIDASCRGLTGKILAQAMEKAGIVANANKIPFDPRSANDPSGVRLGT 360 Query: 361 PAMTTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFP 408 PA+T+RGMKE +MR +A LI +V +GDE + +R EV EMC FP Sbjct: 361 PALTSRGMKEPEMRRVAALIDRVTDVVGDEAALAKIRAEVEEMCAAFP 408 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: 560 Number of extensions: 18 Number of successful extensions: 1 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: 413 Length adjustment: 32 Effective length of query: 395 Effective length of database: 381 Effective search space: 150495 Effective search space used: 150495 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 09 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