Align Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.1 (characterized)
to candidate WP_013011589.1 DACET_RS11705 serine hydroxymethyltransferase
Query= SwissProt::P39148 (415 letters) >NCBI__GCF_000025725.1:WP_013011589.1 Length = 412 Score = 484 bits (1245), Expect = e-141 Identities = 239/407 (58%), Positives = 300/407 (73%) Query: 1 MKHLPAQDEQVFNAIKNERERQQTKIELIASENFVSEAVMEAQGSVLTNKYAEGYPGKRY 60 M+HL D +V IK E +RQ KI LIASEN+VS AV+EA G+VLTNKY+EGYPGKRY Sbjct: 1 MEHLSNFDPEVSGLIKQEEQRQIDKIRLIASENYVSHAVLEATGNVLTNKYSEGYPGKRY 60 Query: 61 YGGCEHVDVVEDIARDRAKEIFGAEHVNVQPHSGAQANMAVYFTILEQGDTVLGMNLSHG 120 Y G + +D +E IA +RAKE+FGAEH NVQP+SG+ ANMAVY ++ GDTV+GM+LSHG Sbjct: 61 YEGQQFIDPIETIAIERAKELFGAEHANVQPYSGSPANMAVYLAFVKPGDTVMGMSLSHG 120 Query: 121 GHLTHGSPVNFSGVQYNFVEYGVDKETQYIDYDDVREKALAHKPKLIVAGASAYPRTIDF 180 GHLTHGSPV+ +G +N V Y +D++T ++Y+ +RE A+ KPK+I+AG SAYPR IDF Sbjct: 121 GHLTHGSPVSITGKYFNIVSYELDRDTGLLNYETIRELAVKSKPKMIIAGHSAYPRQIDF 180 Query: 181 KKFREIADEVGAYFMVDMAHIAGLVAAGLHPNPVPYADFVTTTTHKTLRGPRGGMILCRE 240 +KFREIADEVGA VDMAH AGLVA G+HP+PVPYAD V+TTTHKTLRGPRGGM+LC+ Sbjct: 181 RKFREIADEVGAVLFVDMAHFAGLVAGGVHPSPVPYADVVSTTTHKTLRGPRGGMLLCKA 240 Query: 241 EFGKKIDKSIFPGIQGGPLMHVIAAKAVSFGEVLQDDFKTYAQNVISNAKRLAEALTKEG 300 E+ IDK++FPGIQGGP H A AV+ E L +FK YA V+ NA ++A+ LT G Sbjct: 241 EYAAAIDKAVFPGIQGGPHNHTTAGIAVALKEALLPEFKEYAAQVVKNAGKMADCLTSMG 300 Query: 301 IQLVSGGTDNHLILVDLRSLGLTGKVAEHVLDEIGITSNKNAIPYDPEKPFVTSGIRLGT 360 QLV+GGT+NHL+L+DL + +TGK A LD+ GI N NA+PYD KPF SGIR+G Sbjct: 301 YQLVTGGTENHLLLIDLSNKNITGKQAAKALDKAGIVLNCNAVPYDTRKPFDPSGIRMGL 360 Query: 361 AAVTSRGFDGDALEEVGAIIALALKNHEDEGKLEEARQRVAALTDKF 407 AAVTSRGF +E+ I A++N E+E LE + V L KF Sbjct: 361 AAVTSRGFKEAEVEKTAQWINKAIENFENEEVLENISKEVKELCVKF 407 Lambda K H 0.317 0.136 0.388 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: 561 Number of extensions: 23 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: 415 Length of database: 412 Length adjustment: 31 Effective length of query: 384 Effective length of database: 381 Effective search space: 146304 Effective search space used: 146304 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 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