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 Dsui_1265 Dsui_1265 glycine/serine hydroxymethyltransferase
Query= curated2:D3DKC4 (427 letters) >FitnessBrowser__PS:Dsui_1265 Length = 416 Score = 483 bits (1243), Expect = e-141 Identities = 249/408 (61%), Positives = 303/408 (74%), Gaps = 2/408 (0%) Query: 4 LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63 L D E+++AI E RQ H+ELIASEN+ S AVMEAQGS +TNKYAEG P KRYYGG Sbjct: 8 LAKVDPELWKAIEDENRRQEEHIELIASENYVSNAVMEAQGSQLTNKYAEGYPGKRYYGG 67 Query: 64 CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123 CE+VD+AE LAIER K LF AE ANVQP+SG+QAN AV MA KPGDTIMGM L+ GGHL Sbjct: 68 CEYVDVAEQLAIERLKKLFGAEAANVQPNSGSQANQAVLMAFAKPGDTIMGMSLAEGGHL 127 Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183 THG +N SGK +N V YG++ E IDYD++ LA+EHKPK+IV GASAY ID+ + Sbjct: 128 THGMALNMSGKWFNVVSYGLN-EKEEIDYDKMEALAREHKPKIIVAGASAYALRIDFERF 186 Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKEFA 243 +IA VGA VDMAHYAGLIA G YPNPVP+A VTSTTHKTLRGPR G IL K E Sbjct: 187 AKIAKEVGAIFWVDMAHYAGLIAAGYYPNPVPFADVVTSTTHKTLRGPRGGVILMKAEHE 246 Query: 244 KDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKE-GFK 302 K ++ ++FPG+QGGPLMHVIAAKAVAFKEA S EFK+Y QV+ NARV+A+ +E G + Sbjct: 247 KALNSAIFPGLQGGPLMHVIAAKAVAFKEAASPEFKKYQEQVINNARVMAKVLGEERGLR 306 Query: 303 VVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPA 362 +VSG T+SH+ L+DLR +TG+E E ALGKA+ITVNKN +P DP P TSGIR+G+PA Sbjct: 307 IVSGRTESHVFLIDLRAKKITGKEAEAALGKAHITVNKNGIPNDPEKPFVTSGIRIGSPA 366 Query: 363 MTTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLY 410 MT+RG E + IA L++ V+ DE + VR +V +C +FP+Y Sbjct: 367 MTSRGFTEIEAEQIAHLVADVLDAPNDEAKLAEVRAKVAALCAKFPVY 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: 564 Number of extensions: 25 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: 416 Length adjustment: 32 Effective length of query: 395 Effective length of database: 384 Effective search space: 151680 Effective search space used: 151680 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