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 RR42_RS15485 RR42_RS15485 serine hydroxymethyltransferase
Query= curated2:D3DKC4 (427 letters) >FitnessBrowser__Cup4G11:RR42_RS15485 Length = 415 Score = 498 bits (1282), Expect = e-145 Identities = 250/403 (62%), Positives = 311/403 (77%), Gaps = 1/403 (0%) Query: 8 DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67 D E++ AI KE +RQ H+ELIASEN+TS AVM AQGS +TNKYAEG P KRYYGGCE+V Sbjct: 13 DPELFAAIQKEDQRQEEHIELIASENYTSPAVMAAQGSQLTNKYAEGYPGKRYYGGCEYV 72 Query: 68 DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127 DI E LAI+R K LF AE ANVQP+SG+QAN V+ A LKPGDTIMGM L+ GGHLTHG Sbjct: 73 DIVEQLAIDRVKQLFGAEAANVQPNSGSQANQGVFFAALKPGDTIMGMSLAEGGHLTHGM 132 Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187 +N SGK +N V YG+ IDYD L +LA+E KPKLI+ GASA+ ID+ ++ ++A Sbjct: 133 ALNMSGKWFNVVSYGLDANED-IDYDALEKLAQEKKPKLIIAGASAFALRIDFERISKVA 191 Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEFAKDID 247 S+GA MVDMAHYAGLIA G YPNPVP+A FVT+TTHK+LRGPR G IL K E K I+ Sbjct: 192 KSIGALFMVDMAHYAGLIAAGEYPNPVPHADFVTTTTHKSLRGPRGGVILMKAEHEKAIN 251 Query: 248 KSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVVSGG 307 ++FPGIQGGPLMHVIA KAVAFKEA+S EFK Y +QVV NARVLAE I+ G ++VSG Sbjct: 252 SAIFPGIQGGPLMHVIAGKAVAFKEALSPEFKTYQQQVVKNARVLAETLIERGLRIVSGR 311 Query: 308 TDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMTTRG 367 T+SH++L+DLR +TG+E E+ LG+A+ITVNKNA+P DP P TSGIRLG+PAMTTRG Sbjct: 312 TESHVMLVDLRAMQITGKEAEKVLGEAHITVNKNAIPNDPEKPFVTSGIRLGSPAMTTRG 371 Query: 368 MKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 KE++ R++A L++ V++N D I VR++V + ++FP+Y Sbjct: 372 FKEEEARLVANLVADVLENPHDLANIARVREQVAALTKRFPVY 414 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: 540 Number of extensions: 23 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: 415 Length adjustment: 32 Effective length of query: 395 Effective length of database: 383 Effective search space: 151285 Effective search space used: 151285 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