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 6936832 Sama_1014 serine hydroxymethyltransferase (RefSeq)
Query= curated2:D3DKC4 (427 letters) >FitnessBrowser__SB2B:6936832 Length = 417 Score = 518 bits (1333), Expect = e-151 Identities = 254/406 (62%), Positives = 316/406 (77%), Gaps = 4/406 (0%) Query: 8 DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67 D E+++AI E RQ H+ELIASEN+TS VM+AQGS +TNKYAEG P KRYYGGCE+V Sbjct: 12 DPELFKAIEDETLRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYPGKRYYGGCEYV 71 Query: 68 DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127 DI E LAIERAK LF A ANVQPHSG+QAN AVYM +L+PGDT++GM+L+HGGHLTHG+ Sbjct: 72 DIVETLAIERAKELFGATFANVQPHSGSQANSAVYMTLLQPGDTVLGMNLAHGGHLTHGS 131 Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187 VNFSGK+YN + YG+ ET IDYD++ RLA EHKPK+++GG SAY ++DWA++REIA Sbjct: 132 PVNFSGKLYNIIPYGI-DETGKIDYDEMERLAVEHKPKMMIGGFSAYSGIVDWARMREIA 190 Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILC---KKEFAK 244 D +GAYL VDMAH AGL+A GVYPNPVP+AH VTSTTHKTL GPR G IL ++ K Sbjct: 191 DKIGAYLFVDMAHVAGLVAAGVYPNPVPHAHVVTSTTHKTLAGPRGGIILSAANDEDLYK 250 Query: 245 DIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVV 304 ++ +VFPG QGGPLMHVIA KAVAFKEA+ EFK Y +QVV NA+ + E F++ G+K+V Sbjct: 251 KLNSAVFPGGQGGPLMHVIAGKAVAFKEALEPEFKVYQQQVVTNAKAMVEVFLERGYKIV 310 Query: 305 SGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMT 364 SGGTD+H++L+DL LTG+E + ALG ANITVNKN+VP DP P TSGIR+GTPA+T Sbjct: 311 SGGTDNHLMLVDLIGRDLTGKEADAALGAANITVNKNSVPNDPRSPFITSGIRIGTPAIT 370 Query: 365 TRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 RG KE + R + I V+ N DE VI V+ +V+E+C +FP+Y Sbjct: 371 RRGFKEAEARELTHWICDVLDNAKDESVIARVKGQVLELCARFPVY 416 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: 619 Number of extensions: 26 Number of successful extensions: 3 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: 417 Length adjustment: 32 Effective length of query: 395 Effective length of database: 385 Effective search space: 152075 Effective search space used: 152075 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: 50 (23.9 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