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 GFF502 HP15_489 glycine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >FitnessBrowser__Marino:GFF502 Length = 417 Score = 516 bits (1328), Expect = e-151 Identities = 253/405 (62%), Positives = 316/405 (78%), Gaps = 2/405 (0%) Query: 8 DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67 D E++ A+ E +RQ H+ELIASEN+TS VMEAQGSV+TNKYAEG P KRYYGGCEFV Sbjct: 12 DDELWNAMQAEEKRQEAHIELIASENYTSPRVMEAQGSVLTNKYAEGYPGKRYYGGCEFV 71 Query: 68 DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127 DIAE+LAIERAK LF A +ANVQPHSG+QAN AV+MA+LKPGDT++GM L+HGGHLTHGA Sbjct: 72 DIAEELAIERAKELFGAAYANVQPHSGSQANSAVFMALLKPGDTVLGMSLAHGGHLTHGA 131 Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187 VNFSGKIYNAV YG++ +T L+DYD++ LA EHKPK+I+ G SAY + +D+A+ REIA Sbjct: 132 SVNFSGKIYNAVQYGINTDTGLLDYDEIESLALEHKPKMIIAGFSAYSQELDFARFREIA 191 Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILC--KKEFAKD 245 D VGAYL VDMAH AGL+A GVYP+PVP+AH V +TTHKTLRGPR G IL + K Sbjct: 192 DKVGAYLFVDMAHVAGLVAAGVYPDPVPHAHVVATTTHKTLRGPRGGLILACDDADLQKK 251 Query: 246 IDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVVS 305 ++ +VFPG QGGPLMHVIAAKAV FKEAMS +FK Y +QVV NA +A+ F+ G+ VVS Sbjct: 252 LNSAVFPGGQGGPLMHVIAAKAVCFKEAMSDDFKTYQQQVVKNASAMAQVFVDRGYDVVS 311 Query: 306 GGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMTT 365 GGT +H+ L+ L +TG++ + ALG+A+ITVNKNAVP DP P TSG+R+GTPA+TT Sbjct: 312 GGTKNHLFLVSLIKQDITGKDADAALGRAHITVNKNAVPNDPRSPFVTSGLRIGTPAITT 371 Query: 366 RGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 RG E + R +A I ++ N+ DE V VR++V +C +FP+Y Sbjct: 372 RGFGESECRDLAGWICDILDNLDDEAVNSRVREQVSALCARFPVY 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: 600 Number of extensions: 34 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: 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 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