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_012044666.1 BBTA_RS21765 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_000015165.1:WP_012044666.1 Length = 434 Score = 463 bits (1192), Expect = e-135 Identities = 237/414 (57%), Positives = 303/414 (73%), Gaps = 7/414 (1%) Query: 4 LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63 L D EI AI E RQ + +ELIASEN S AV+EAQGSVMTNKYAEG P RYYGG Sbjct: 20 LAEADPEIAAAIKGELGRQRHEIELIASENIVSRAVLEAQGSVMTNKYAEGYPGARYYGG 79 Query: 64 CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123 CE+VD+AE+LAI+RAK LF A ANVQP+SG+Q N AV++A+L+PGDT MG+DL+ GGHL Sbjct: 80 CEWVDVAENLAIDRAKKLFGANFANVQPNSGSQMNQAVFLALLQPGDTFMGLDLAAGGHL 139 Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183 THG+ VN SGK + A +Y V + HLID D + + A+E KPKLI+ G SAY R D+ + Sbjct: 140 THGSPVNMSGKWFKAAHYTVRRDDHLIDMDAVAKQAEEVKPKLIIAGGSAYSRPWDFKRF 199 Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKE-F 242 REIAD VGAYL+VDMAH+AGL+AGG + +PVP+AH VT+TTHK+LRGPR G IL E F Sbjct: 200 REIADHVGAYLLVDMAHFAGLVAGGAHASPVPHAHIVTTTTHKSLRGPRGGLILWNDEQF 259 Query: 243 AKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFK 302 K ++ ++FPG+QGGPLMHVIAAKAVAF EA+ EFK YA+ +V NA+ LAE +GF Sbjct: 260 TKKLNSAIFPGLQGGPLMHVIAAKAVAFAEALRPEFKTYAKNIVENAKALAESLRAQGFD 319 Query: 303 VVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPA 362 +VSGGTD+H++L+DLR GL G E+AL +A IT NKN +PFDP P TSG+RLGTPA Sbjct: 320 IVSGGTDNHLMLVDLRPKGLKGNVSEKALVRAGITCNKNGIPFDPEKPFVTSGLRLGTPA 379 Query: 363 MTTRGMKEDQMRIIARLISKVIKNI-----GDEKVIE-YVRQEVIEMCEQFPLY 410 TTRG + + + LI++V+ I G ++E V+ +V + ++FP+Y Sbjct: 380 ATTRGFGVAEFQQVGSLIAEVLNAIAQAPDGSAPLVEAAVKAKVKALTDRFPIY 433 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: 579 Number of extensions: 26 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: 434 Length adjustment: 32 Effective length of query: 395 Effective length of database: 402 Effective search space: 158790 Effective search space used: 158790 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