Align Serine hydroxymethyltransferase; SHMT; Serine methylase; L-threonine/L-allo-threonine aldolase; EC 2.1.2.1; EC 4.1.2.48 (characterized)
to candidate Pf1N1B4_2161 Serine hydroxymethyltransferase (EC 2.1.2.1)
Query= SwissProt::D3DKC4 (427 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2161 Length = 421 Score = 474 bits (1221), Expect = e-138 Identities = 236/409 (57%), Positives = 302/409 (73%), Gaps = 6/409 (1%) Query: 8 DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67 DAE+ EAI E RQ H+ELIASEN+ S VM+ Q +V+TNKYAEG P KRYY GCE+V Sbjct: 12 DAELCEAIHNEEHRQEDHVELIASENYASPLVMKIQSTVLTNKYAEGYPGKRYYSGCEYV 71 Query: 68 DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127 D+AE LAIER KALF+ ++ANVQPH+G QAN AV++A++ PGDT+MGM+L+ GGHLTHG Sbjct: 72 DVAERLAIERVKALFNCDYANVQPHAGAQANAAVFLALINPGDTVMGMNLAQGGHLTHGN 131 Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187 NFSG+ Y V YG+ PET +DYD++ R+A E +PK+++GG SAY R DWA++R IA Sbjct: 132 PSNFSGRHYKIVPYGLDPETGFLDYDEMERIALETRPKMLIGGFSAYSRYKDWARMRAIA 191 Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCK---KEFAK 244 D VGA VDMAH AGLIA G YP+P+P+AH VTSTTHKTLRGPR G IL K + F K Sbjct: 192 DKVGAIFWVDMAHVAGLIAAGEYPDPLPHAHVVTSTTHKTLRGPRGGLILSKGQDEAFYK 251 Query: 245 DIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVV 304 +D +VFPG+QGGPLMH IAAKAVAFKEA+ EFK Y QVV NAR +A + G+K+V Sbjct: 252 KLDSAVFPGVQGGPLMHQIAAKAVAFKEALRPEFKTYQTQVVINARAMAAVLQERGYKIV 311 Query: 305 SGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMT 364 SGGTD+H++L+DL D TG+E + AL A IT NKN+VP DP P TSG+R+GTPA+T Sbjct: 312 SGGTDNHMMLIDLSDRPYTGKEADAALSNAYITANKNSVPNDPRSPFVTSGLRIGTPAIT 371 Query: 365 TRGMKEDQMRIIARLISKV---IKNIGDEKVIEYVRQEVIEMCEQFPLY 410 TRG + +A + V ++N E+V +VR++V+E+C + P+Y Sbjct: 372 TRGFGVIECEQLAGWLCDVLDALENGDSERVGHHVREQVVELCRRHPVY 420 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: 592 Number of extensions: 27 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: 421 Length adjustment: 32 Effective length of query: 395 Effective length of database: 389 Effective search space: 153655 Effective search space used: 153655 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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