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 SMa2135 SMa2135 GlyA2 serine hydroxymethyltransferase, SHMT
Query= curated2:D3DKC4 (427 letters) >FitnessBrowser__Smeli:SMa2135 Length = 422 Score = 474 bits (1221), Expect = e-138 Identities = 239/407 (58%), Positives = 299/407 (73%), Gaps = 4/407 (0%) Query: 8 DAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEFV 67 D+ I AI +E RQ +ELIASEN S AV+ AQGSVMTNKYAEG P RYYGGC++V Sbjct: 12 DSVIAGAIAREMGRQRSEIELIASENIVSPAVLAAQGSVMTNKYAEGYPGHRYYGGCQYV 71 Query: 68 DIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHGA 127 D+ E AIERA LFDA NVQPHSG QAN AV +A+LKPGDT MG+ L+ GGHLTHGA Sbjct: 72 DLVEAAAIERAGMLFDASFVNVQPHSGAQANGAVMLALLKPGDTFMGLSLAAGGHLTHGA 131 Query: 128 KVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREIA 187 + SGK +NAV YGV LIDYD+L A +PKLI+ G SAYPR+ID+ ++R IA Sbjct: 132 RPTMSGKWFNAVQYGVRESDCLIDYDELEVKAIATRPKLIITGGSAYPRLIDFKRIRAIA 191 Query: 188 DSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILC-KKEFAKDI 246 DSVGA +MVDMAH+AGL+AGGV+PNPV A VT+TTHKTLRGPR G IL ++ AK + Sbjct: 192 DSVGAAMMVDMAHFAGLVAGGVHPNPVEIADIVTTTTHKTLRGPRGGMILTNNQDVAKKV 251 Query: 247 DKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVVSG 306 + +VFPG+QGGPLMHVIAAKAVA EA+ F++YARQ+VANAR LA + G+ +VSG Sbjct: 252 NSAVFPGLQGGPLMHVIAAKAVALGEALEDNFRQYARQMVANARALASALTERGYDIVSG 311 Query: 307 GTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMTTR 366 GTD+H++L+DLR G++G++ EEALG+A +T NKN +PFDP PP TSGIRLGTPA T+R Sbjct: 312 GTDTHLILVDLRSKGVSGKDAEEALGRAGLTCNKNGIPFDPAPPAVTSGIRLGTPAATSR 371 Query: 367 GMKEDQMRIIARLISKVIKNIGDEKVIEY---VRQEVIEMCEQFPLY 410 G +E + + LI+ V+ +G E+ E R V ++C FP+Y Sbjct: 372 GFREAEFNEVGALIANVLDALGTEQSGEQERRARMSVHDLCAAFPIY 418 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: 567 Number of extensions: 26 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 427 Length of database: 422 Length adjustment: 32 Effective length of query: 395 Effective length of database: 390 Effective search space: 154050 Effective search space used: 154050 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 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