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_083780266.1 BTUS_RS16125 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_000092905.1:WP_083780266.1 Length = 438 Score = 534 bits (1375), Expect = e-156 Identities = 263/408 (64%), Positives = 316/408 (77%) Query: 3 HLFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYG 62 HL D E+ AI KE RQ +ELIASENF S AV+EA G+V+TNKYAEG P KRYYG Sbjct: 25 HLRLIDPEVAAAIEKELNRQRNKIELIASENFVSRAVLEAMGTVLTNKYAEGYPGKRYYG 84 Query: 63 GCEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGH 122 GCE+VDI E+LA ERAK LF AEHANVQPHSG QAN AVY A+L+PGDT++GM+LSHGGH Sbjct: 85 GCEYVDIVENLARERAKQLFGAEHANVQPHSGAQANTAVYFALLQPGDTVLGMNLSHGGH 144 Query: 123 LTHGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAK 182 LTHG+ VN SGK+Y+ V YGV T IDYD + RLA+EH+PK+IV GASAYPR+ID+ K Sbjct: 145 LTHGSPVNISGKLYHFVPYGVDEHTQRIDYDHVARLAREHRPKMIVAGASAYPRIIDFPK 204 Query: 183 LREIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEF 242 LREIAD VGAYLMVDMAH AGL+A G +PNPVPYA VTSTTHKTLRGPR G ILCK+ F Sbjct: 205 LREIADEVGAYLMVDMAHIAGLVATGHHPNPVPYADVVTSTTHKTLRGPRGGLILCKERF 264 Query: 243 AKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFK 302 AKDIDK++FPGIQGGPLMH+IAAKAVAF EA+ EF++Y++ VV NA+ LA+ I GF Sbjct: 265 AKDIDKAIFPGIQGGPLMHIIAAKAVAFGEALRPEFRDYSQAVVDNAQALAKALIDRGFN 324 Query: 303 VVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPA 362 +VSGGTD+H++L+D+R+ LTGRE E L + +TVNKN +PFDP P TSGIR+GTPA Sbjct: 325 LVSGGTDNHLMLVDVRNLRLTGREAERLLDEVGVTVNKNTIPFDPESPFVTSGIRIGTPA 384 Query: 363 MTTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 +TTRGM M IA +I +++ ++ I V +CEQFPLY Sbjct: 385 VTTRGMGTKAMETIAEIIDLTLRHQDEQPAINRAMSLVRGLCEQFPLY 432 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: 637 Number of extensions: 22 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: 438 Length adjustment: 32 Effective length of query: 395 Effective length of database: 406 Effective search space: 160370 Effective search space used: 160370 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