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 Ac3H11_2921 Serine hydroxymethyltransferase (EC 2.1.2.1)
Query= curated2:D3DKC4 (427 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2921 Length = 414 Score = 490 bits (1261), Expect = e-143 Identities = 246/404 (60%), Positives = 300/404 (74%), Gaps = 1/404 (0%) Query: 7 TDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEF 66 TD E++ AI E RQ +H+ELIASEN+ S AVM AQG+ +TNKYAEG P KRYYGGCE Sbjct: 11 TDPEVFAAIQAENARQEHHIELIASENYASPAVMWAQGTQLTNKYAEGYPGKRYYGGCEH 70 Query: 67 VDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHG 126 VD+AE LAI+R K +F A+ ANVQPH G AN AV++A LKPGDTIMGM L+ GGHLTHG Sbjct: 71 VDVAEQLAIDRVKKIFGADAANVQPHCGASANEAVFLAFLKPGDTIMGMSLAEGGHLTHG 130 Query: 127 AKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREI 186 +N SGK +N V YG+ + IDYD + A+EHKPKLIV GASAY ID+ + +I Sbjct: 131 MPLNMSGKWFNVVSYGLD-KNEAIDYDAMEAKAREHKPKLIVAGASAYSLHIDFERFAKI 189 Query: 187 ADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEFAKDI 246 A +GA MVDMAHYAGLIA GVYPNPVP+A VTSTTHK+LRGPR G IL K E K I Sbjct: 190 AKEIGAIFMVDMAHYAGLIAAGVYPNPVPHADVVTSTTHKSLRGPRGGIILMKAEHEKAI 249 Query: 247 DKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVVSG 306 + ++FPG+QGGPLMHVIAAKAVAFKEAM EFK Y QV NA+V+AE G ++VSG Sbjct: 250 NSAIFPGLQGGPLMHVIAAKAVAFKEAMQPEFKAYQEQVAKNAKVVAETLTARGLRIVSG 309 Query: 307 GTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMTTR 366 GT SH++L+DLR G+TG+E E LG A++T+NKNA+P DP P+ TSG+R+GTPAMTTR Sbjct: 310 GTQSHVMLVDLRAKGITGKEAEAVLGAAHMTINKNAIPNDPEKPMVTSGVRIGTPAMTTR 369 Query: 367 GMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 G KE++ RI A LI+ V+ N DE I VR +V + +FP+Y Sbjct: 370 GFKEEEARITANLIADVLDNPRDEANIAAVRAKVNALTARFPVY 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: 578 Number of extensions: 26 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