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 SMc01770 SMc01770 serine hydroxymethyltransferase
Query= curated2:D3DKC4 (427 letters) >FitnessBrowser__Smeli:SMc01770 Length = 431 Score = 485 bits (1249), Expect = e-141 Identities = 242/417 (58%), Positives = 307/417 (73%), Gaps = 8/417 (1%) Query: 2 RHLFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYY 61 R L ++D EI+ AI KE RQ + +ELIASEN S AV+EAQGS+MTNKYAEG P KRYY Sbjct: 12 RSLADSDPEIFGAIEKELGRQRHEIELIASENIVSRAVLEAQGSIMTNKYAEGYPGKRYY 71 Query: 62 GGCEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGG 121 GGC++VDIAE LAIERAK LF ANVQP+SG+Q N AV++A+L+PGDT MG+DL+ GG Sbjct: 72 GGCQYVDIAEALAIERAKKLFGVNFANVQPNSGSQMNQAVFLALLQPGDTFMGLDLNSGG 131 Query: 122 HLTHGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWA 181 HLTHG+ VN SGK +N V YGV + HL+D D++ R A+E KPKLI+ G +AY R+ DW Sbjct: 132 HLTHGSPVNMSGKWFNVVSYGVREDDHLLDMDEVARKAREQKPKLIIAGGTAYSRIWDWK 191 Query: 182 KLREIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCK-K 240 + REIAD VGA+LMVDMAH AGL+AGG +P+P P+ H T+TTHK+LRGPR G IL + Sbjct: 192 RFREIADEVGAWLMVDMAHIAGLVAGGQHPSPFPHCHVATTTTHKSLRGPRGGMILTNDE 251 Query: 241 EFAKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEG 300 E AK I+ +VFPG+QGGPLMHVIAAKAVA EA+ FK+YA QVV NAR LAE G Sbjct: 252 EIAKKINSAVFPGLQGGPLMHVIAAKAVALGEALQPSFKDYAAQVVKNARTLAETLKANG 311 Query: 301 FKVVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGT 360 +VSGGTD+H++L+DLR TG+ E ALG+A +T NKN +PFDP P TSG+RLG Sbjct: 312 LDIVSGGTDNHLMLVDLRKKNATGKRAEAALGRAYVTCNKNGIPFDPEKPFVTSGVRLGA 371 Query: 361 PAMTTRGMKEDQMRIIARLISKVIKNI-------GDEKVIEYVRQEVIEMCEQFPLY 410 PA TTRG KE + + + LI +V+ + G+ V VR++VI++ ++FP+Y Sbjct: 372 PAGTTRGFKEAEFKEVGELIVEVLDGLKAANSDEGNAAVEAGVREKVIKLTDRFPMY 428 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: 577 Number of extensions: 19 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 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