Align Serine hydroxymethyltransferase; SHMT; Serine methylase; EC 2.1.2.1; L-threonine/L-allo-threonine aldolase; EC 4.1.2.48 (uncharacterized)
to candidate WP_073042231.1 BUB04_RS18410 serine hydroxymethyltransferase
Query= curated2:D3DKC4 (427 letters) >NCBI__GCF_900129305.1:WP_073042231.1 Length = 425 Score = 523 bits (1346), Expect = e-153 Identities = 259/407 (63%), Positives = 316/407 (77%) Query: 4 LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63 L + D EI + + E RQ LELIASENF S AV AQGSV+TNKYAEG P +RYYGG Sbjct: 6 LQSMDPEIAQVLRDEEHRQRSKLELIASENFVSDAVRIAQGSVLTNKYAEGYPGRRYYGG 65 Query: 64 CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123 CEFVD+AE LA ERA LF AE+ANVQPHSG+QANMAVY A+L+PGDTIMGMDL GGHL Sbjct: 66 CEFVDVAERLAQERACRLFGAEYANVQPHSGSQANMAVYFALLEPGDTIMGMDLRQGGHL 125 Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183 THG+ V+FSG+++ V YGV P+T ID+D L RLA+EH+P+LIV GASAYPRVID+A+ Sbjct: 126 THGSPVSFSGRLFKVVSYGVKPDTETIDFDGLARLAREHRPRLIVAGASAYPRVIDFARF 185 Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEFA 243 REI D VGAYLMVDMAH AGLI+ G++PNPVP+AH VTSTTHKTLRGPR G IL E Sbjct: 186 REICDEVGAYLMVDMAHIAGLISAGLHPNPVPHAHVVTSTTHKTLRGPRGGLILAGAELG 245 Query: 244 KDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKV 303 + +D +FPGIQGGPLMHVIAAKAVAF+EAM FKEY R++V NAR LAE + G+++ Sbjct: 246 RKLDSQIFPGIQGGPLMHVIAAKAVAFQEAMQPCFKEYQRRIVQNARTLAEALLSHGYRL 305 Query: 304 VSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAM 363 VSGGTD+H++L+DLR+ GLTG++ EEAL KA ITVNKN++PFDP P TSGIR+GT A+ Sbjct: 306 VSGGTDNHMMLVDLRNKGLTGKQAEEALDKAGITVNKNSIPFDPQTPHVTSGIRIGTAAV 365 Query: 364 TTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 TTRGM+ M IAR I + + + D + + ++ +V CE FPL+ Sbjct: 366 TTRGMEPSHMVEIARFIHQALSAVDDSQRLAVLKADVAAFCESFPLH 412 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: 617 Number of extensions: 26 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: 425 Length adjustment: 32 Effective length of query: 395 Effective length of database: 393 Effective search space: 155235 Effective search space used: 155235 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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