Align Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.- (characterized)
to candidate WP_048061037.1 MTH_RS06600 serine hydroxymethyltransferase
Query= SwissProt::O27433 (423 letters) >NCBI__GCF_000008645.1:WP_048061037.1 Length = 423 Score = 844 bits (2181), Expect = 0.0 Identities = 423/423 (100%), Positives = 423/423 (100%) Query: 1 MVSNQDYTEKIRQLMKDHNSWMESSINLIASENITSSRVKEALLSDLSHRYAEGLPGERL 60 MVSNQDYTEKIRQLMKDHNSWMESSINLIASENITSSRVKEALLSDLSHRYAEGLPGERL Sbjct: 1 MVSNQDYTEKIRQLMKDHNSWMESSINLIASENITSSRVKEALLSDLSHRYAEGLPGERL 60 Query: 61 YEGCRYIDEIEELTIELSKRLFRAEHANVQPTSGVVANLACFFATAEVGDPIMAMEVPYG 120 YEGCRYIDEIEELTIELSKRLFRAEHANVQPTSGVVANLACFFATAEVGDPIMAMEVPYG Sbjct: 61 YEGCRYIDEIEELTIELSKRLFRAEHANVQPTSGVVANLACFFATAEVGDPIMAMEVPYG 120 Query: 121 GHISHARVSAAGVRGFQIYTHPFDFENMNIDADAMKKKILEVKPRIILFGGSLFLFPHPV 180 GHISHARVSAAGVRGFQIYTHPFDFENMNIDADAMKKKILEVKPRIILFGGSLFLFPHPV Sbjct: 121 GHISHARVSAAGVRGFQIYTHPFDFENMNIDADAMKKKILEVKPRIILFGGSLFLFPHPV 180 Query: 181 EEALEAAEEVGARIMYDGAHVLGLIAGGYFQDPLREGADMLVGSTHKTFPGPQGGIILCR 240 EEALEAAEEVGARIMYDGAHVLGLIAGGYFQDPLREGADMLVGSTHKTFPGPQGGIILCR Sbjct: 181 EEALEAAEEVGARIMYDGAHVLGLIAGGYFQDPLREGADMLVGSTHKTFPGPQGGIILCR 240 Query: 241 EELAADIDEAVFPGLVSNHHLHHVAGLGIATAEMLEFGAEYAAQTINNARKLAENLHELG 300 EELAADIDEAVFPGLVSNHHLHHVAGLGIATAEMLEFGAEYAAQTINNARKLAENLHELG Sbjct: 241 EELAADIDEAVFPGLVSNHHLHHVAGLGIATAEMLEFGAEYAAQTINNARKLAENLHELG 300 Query: 301 FNVLCEHLDFTESHQVVMDVSDIGRAAEISKRLEANNIILNKNLLPWDDVNRSDDPSGIR 360 FNVLCEHLDFTESHQVVMDVSDIGRAAEISKRLEANNIILNKNLLPWDDVNRSDDPSGIR Sbjct: 301 FNVLCEHLDFTESHQVVMDVSDIGRAAEISKRLEANNIILNKNLLPWDDVNRSDDPSGIR 360 Query: 361 IGTQEITRRGMKESEMSEVAEYIKRVVMDGKDVRDEVAEFMSSYTRVHYAFEDSEAYKYM 420 IGTQEITRRGMKESEMSEVAEYIKRVVMDGKDVRDEVAEFMSSYTRVHYAFEDSEAYKYM Sbjct: 361 IGTQEITRRGMKESEMSEVAEYIKRVVMDGKDVRDEVAEFMSSYTRVHYAFEDSEAYKYM 420 Query: 421 EIQ 423 EIQ Sbjct: 421 EIQ 423 Lambda K H 0.318 0.135 0.389 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: 808 Number of extensions: 24 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: 423 Length of database: 423 Length adjustment: 32 Effective length of query: 391 Effective length of database: 391 Effective search space: 152881 Effective search space used: 152881 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 (21.7 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