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 GFF2427 PGA1_c24580 putative serine hydroxymethyltransferase
Query= curated2:D3DKC4 (427 letters) >FitnessBrowser__Phaeo:GFF2427 Length = 435 Score = 143 bits (360), Expect = 1e-38 Identities = 109/337 (32%), Positives = 163/337 (48%), Gaps = 8/337 (2%) Query: 54 GLPHKRYYGGCEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIM 113 G P +Y G E ++ E +A A +FDAE + ++ SG AN+ +MA +PGDTI+ Sbjct: 80 GHPGDKYEMGLEAIEEIEVIAARLACEVFDAEFSEIRVPSGALANLYGFMATCRPGDTII 139 Query: 114 GMDLSHGGHLTHGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASA 173 S GGH+TH A ++ V + + +D + L +LA+ +PKLI G S Sbjct: 140 APPASIGGHVTHHAAGCAGLYGLRSIEAPVLEDGYTVDLEALQQLAERERPKLITIGGSL 199 Query: 174 YPRVIDWAKLREIADSVGAYLMVDMAHYAGLIAGGVYPNPVPY-AHFVTSTTHKTLRGPR 232 A +R IAD +GA +M D AH G+IAG + +P+ AHF+T +T+K+L GP Sbjct: 200 NLFEHPVAGVRAIADQIGAKVMFDAAHQCGIIAGKAWADPLAEGAHFMTMSTYKSLGGPA 259 Query: 233 SGFILCK-KEFAKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARV 291 G I+ E AK +D FPG+ + AA AV + + YA +++A A+ Sbjct: 260 GGLIVSNDAEIAKALDSIAFPGMTANFDVAKSAALAVTLLD-WRDHGRAYASEMIAMAKS 318 Query: 292 LAEEFIKEG---FKVVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPL 348 LA EG FK G T SH L G+ + L K +P P Sbjct: 319 LAAALEAEGLPLFKTADGITMSHQFAL-CAAPYCGGQAASKLLRKNGFLACGIGLPI-PA 376 Query: 349 PPVKTSGIRLGTPAMTTRGMKEDQMRIIARLISKVIK 385 +G+R+GTP + GM +A LI+ ++ Sbjct: 377 VEGDMNGLRIGTPELVRWGMTSKDAAALAALIAAALR 413 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: 408 Number of extensions: 21 Number of successful extensions: 4 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: 435 Length adjustment: 32 Effective length of query: 395 Effective length of database: 403 Effective search space: 159185 Effective search space used: 159185 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 17 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