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 HSERO_RS06140 HSERO_RS06140 serine hydroxymethyltransferase
Query= curated2:D3DKC4 (427 letters) >FitnessBrowser__HerbieS:HSERO_RS06140 Length = 414 Score = 502 bits (1293), Expect = e-147 Identities = 255/407 (62%), Positives = 308/407 (75%), Gaps = 1/407 (0%) Query: 4 LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63 L D +++ AI KE RQ H+ELIASEN+TS AVMEAQGS +TNKYAEG P KRYYGG Sbjct: 8 LAKVDPDLWSAIQKENARQQDHIELIASENYTSPAVMEAQGSQLTNKYAEGYPGKRYYGG 67 Query: 64 CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123 CE+VD+AE LAI+R KALF AE ANVQP+SG+QAN V+ A+LKPGDTIMGM L+ GGHL Sbjct: 68 CEYVDVAEQLAIDRLKALFGAEAANVQPNSGSQANQGVFFAMLKPGDTIMGMSLAEGGHL 127 Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183 THG +N SGK +N V YG++ + IDY+ + RLA+E KPKLI+ GASAY ID+ + Sbjct: 128 THGMALNMSGKWFNVVSYGLNDKEE-IDYEAMERLAREKKPKLIIAGASAYSLRIDFERF 186 Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEFA 243 +IA VGAY MVDMAHYAGLIA GVYPNPVP+A FVTSTTHK+LRGPR G IL K E Sbjct: 187 AKIAKEVGAYFMVDMAHYAGLIAAGVYPNPVPFADFVTSTTHKSLRGPRGGVILMKAEHE 246 Query: 244 KDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKV 303 K I+ ++FPGIQGGPLMHVIAAKAVAFKEA S EFK Y +QVV NA VLA+ IK G ++ Sbjct: 247 KAINSAIFPGIQGGPLMHVIAAKAVAFKEAASPEFKAYQQQVVKNADVLAKTLIKRGLRI 306 Query: 304 VSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAM 363 VSGGT+SH++L+DLR GLTG+E E LG A++T NKN +P DP P TSGIRLG+PAM Sbjct: 307 VSGGTESHVMLVDLRPKGLTGKEAEAILGSAHMTCNKNGIPNDPEKPFVTSGIRLGSPAM 366 Query: 364 TTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 TTRG KE + + I+ V+ N D IE V+ EV ++ + FP+Y Sbjct: 367 TTRGFKEAEAEKVGNFIADVLDNPHDAATIERVKAEVKKLTDAFPVY 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: 546 Number of extensions: 19 Number of successful extensions: 2 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: 414 Length adjustment: 32 Effective length of query: 395 Effective length of database: 382 Effective search space: 150890 Effective search space used: 150890 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