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 H281DRAFT_00990 H281DRAFT_00990 serine hydroxymethyltransferase (EC 2.1.2.1)
Query= SwissProt::D3DKC4 (427 letters) >FitnessBrowser__Burk376:H281DRAFT_00990 Length = 431 Score = 464 bits (1193), Expect = e-135 Identities = 240/413 (58%), Positives = 296/413 (71%), Gaps = 6/413 (1%) Query: 4 LFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGG 63 L + D I I E RQ +ELIASEN S AVMEAQG+V+TNKYAEG P KRYYGG Sbjct: 12 LQSRDPVIASEIALELRRQQTQIELIASENIVSAAVMEAQGTVLTNKYAEGYPSKRYYGG 71 Query: 64 CEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHL 123 CE VD E LAI+R KALF+AE ANVQPHSG QAN AV +A++KPG+T+MGM L GGHL Sbjct: 72 CEHVDRVEALAIDRVKALFEAEFANVQPHSGAQANGAVMLALVKPGETVMGMSLDAGGHL 131 Query: 124 THGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKL 183 THGA+ SGK +NAV YGV+P+T+ +DY+Q+ LA+EH+PKLI+ G SAYPR +D+A Sbjct: 132 THGARPALSGKWFNAVQYGVNPQTYRVDYEQVRSLAQEHRPKLIIAGYSAYPRALDFAAF 191 Query: 184 REIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKK-EF 242 R+IADSVGA LMVDMAH AG++A G + NPV +A VTSTTHKTLRGPR GFIL + Sbjct: 192 RDIADSVGALLMVDMAHIAGIVAAGRHENPVRFADVVTSTTHKTLRGPRGGFILTNNGDI 251 Query: 243 AKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFK 302 AK I+ +VFPG+QGGPLMHVIA KAVAF EA+ EF Y QV+ NA+ L + G Sbjct: 252 AKKINSAVFPGLQGGPLMHVIAGKAVAFGEALRPEFTAYIDQVLRNAQALGDVLKSGGLS 311 Query: 303 VVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPA 362 +V+ GTD+H++L+DLR LTG + E+AL +A IT NKN +PFD P TSGIRLGTPA Sbjct: 312 LVTDGTDNHLLLVDLRSKRLTGTQAEKALERAGITCNKNGIPFDTESPTVTSGIRLGTPA 371 Query: 363 MTTRGMKEDQMRIIARLISKVIKNI-----GDEKVIEYVRQEVIEMCEQFPLY 410 TTRG Q I ++I +V+ + GDE+V VR V ++C QFP+Y Sbjct: 372 GTTRGFGTAQFEQIGQMILEVLSALEQEPAGDEQVERAVRSRVRDLCSQFPIY 424 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: 529 Number of extensions: 21 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: 431 Length adjustment: 32 Effective length of query: 395 Effective length of database: 399 Effective search space: 157605 Effective search space used: 157605 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