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 3608721 Dshi_2113 Glycine hydroxymethyltransferase (RefSeq)
Query= curated2:D3DKC4 (427 letters) >FitnessBrowser__Dino:3608721 Length = 424 Score = 465 bits (1196), Expect = e-135 Identities = 241/412 (58%), Positives = 294/412 (71%), Gaps = 6/412 (1%) Query: 7 TDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYYGGCEF 66 +D I EAI E +RQ +ELIASEN S+ V+ AQGSV+TNKYAEG P +RYYGGCE Sbjct: 11 SDTAIAEAIGHELDRQQTQIELIASENIVSVDVLRAQGSVLTNKYAEGYPGRRYYGGCEH 70 Query: 67 VDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGGHLTHG 126 VD E +AI+R LF + ANVQ HSG QAN AV++A+LKPGD IMG+DL+HGGHLTHG Sbjct: 71 VDTVEQIAIDRVCELFGSRFANVQAHSGAQANQAVFLALLKPGDRIMGLDLAHGGHLTHG 130 Query: 127 AKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWAKLREI 186 + V SGK ++ V Y V + HLID D + ++A + KPKLIV GASAYPR +D+A R I Sbjct: 131 SPVTMSGKWFDVVSYEVSRDDHLIDMDNVRKVALDTKPKLIVAGASAYPRHMDFAAFRAI 190 Query: 187 ADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKE-FAKD 245 AD VGA+LMVDMAHYAGLIA G YP+PVP+AH VTSTTHKTLRGPR G IL E AK Sbjct: 191 ADEVGAWLMVDMAHYAGLIAAGEYPDPVPHAHVVTSTTHKTLRGPRGGIILTNDEALAKK 250 Query: 246 IDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGFKVVS 305 + +VFPG QGGPLMHVIAAKAVAF EA+ FK+YA+ V+ANAR L+E + G VVS Sbjct: 251 FNSAVFPGNQGGPLMHVIAAKAVAFGEALEPSFKQYAKDVIANARALSEVLVAGGLGVVS 310 Query: 306 GGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTPAMTT 365 GGTD H+VL+DLR G+TG+ E AL +A +T NKNA+PFDP P TSG+RLGT A TT Sbjct: 311 GGTDCHMVLVDLRPKGVTGKAAENALERAGLTCNKNAIPFDPEKPFVTSGVRLGTSAGTT 370 Query: 366 RGMKEDQMRIIARLISKVIKNI-----GDEKVIEYVRQEVIEMCEQFPLYPE 412 RG E + R + L+ +VI + GD V V +EV +C P+Y + Sbjct: 371 RGFGEAEFRKVGALVLRVIDALAENAEGDAAVEAAVLEEVRALCAAHPIYAD 422 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: 561 Number of extensions: 18 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: 424 Length adjustment: 32 Effective length of query: 395 Effective length of database: 392 Effective search space: 154840 Effective search space used: 154840 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