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 WP_051185063.1 H567_RS0117035 serine hydroxymethyltransferase
Query= SwissProt::D3DKC4 (427 letters) >NCBI__GCF_000422285.1:WP_051185063.1 Length = 433 Score = 498 bits (1281), Expect = e-145 Identities = 246/412 (59%), Positives = 309/412 (75%) Query: 2 RHLFNTDAEIYEAIVKEYERQFYHLELIASENFTSLAVMEAQGSVMTNKYAEGLPHKRYY 61 R L D+E++EAI +E R+ L +IASEN+ S AVMEAQGSVMTNKYAEG P RYY Sbjct: 17 RSLKEADSEVFEAIGREVAREQDGLVMIASENYASRAVMEAQGSVMTNKYAEGYPGARYY 76 Query: 62 GGCEFVDIAEDLAIERAKALFDAEHANVQPHSGTQANMAVYMAVLKPGDTIMGMDLSHGG 121 GGCE+VD E LAIERA+ LF AE+ANVQPHSG+QANM +Y++ L+PGDTI+GM L+ GG Sbjct: 77 GGCEYVDTVEHLAIERARTLFGAEYANVQPHSGSQANMGIYISFLEPGDTILGMGLAQGG 136 Query: 122 HLTHGAKVNFSGKIYNAVYYGVHPETHLIDYDQLYRLAKEHKPKLIVGGASAYPRVIDWA 181 HLTHG+ V+FSGK+YNAV YGVHPE+H IDYDQ+ L + HKP+LI+ GASAYPR ID+ Sbjct: 137 HLTHGSAVSFSGKLYNAVSYGVHPESHRIDYDQVRDLTRRHKPRLIIAGASAYPRYIDFD 196 Query: 182 KLREIADSVGAYLMVDMAHYAGLIAGGVYPNPVPYAHFVTSTTHKTLRGPRSGFILCKKE 241 EIA AYLM DMAH AGL+A G++P P+ A FVT+TTHKTLRGPR G IL Sbjct: 197 LFAEIAHENDAYLMADMAHIAGLVAAGLHPTPIGRADFVTTTTHKTLRGPRGGLILSDAR 256 Query: 242 FAKDIDKSVFPGIQGGPLMHVIAAKAVAFKEAMSQEFKEYARQVVANARVLAEEFIKEGF 301 + + +DK +FPGIQGGPLMHVIAAKAVA EA+ EF Y +QVV NA+VL E I GF Sbjct: 257 YGEKLDKGIFPGIQGGPLMHVIAAKAVALGEALGTEFTAYQKQVVQNAKVLGEALIGFGF 316 Query: 302 KVVSGGTDSHIVLLDLRDTGLTGREVEEALGKANITVNKNAVPFDPLPPVKTSGIRLGTP 361 ++VSGGTD+H++LL+L + LTG++ E AL +A I NKNA+P+D P TSG+RLGTP Sbjct: 317 ELVSGGTDNHLLLLNLSNRSLTGKDAEAALVRAGIVANKNAIPYDRRGPKITSGLRLGTP 376 Query: 362 AMTTRGMKEDQMRIIARLISKVIKNIGDEKVIEYVRQEVIEMCEQFPLYPEL 413 A+TTRGM ++MR+IA I V++ E+ + V +EV E+C +FP+Y L Sbjct: 377 ALTTRGMGAEEMRLIAGWIRNVLERPESEETLAAVGREVRELCRRFPVYAHL 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: 635 Number of extensions: 25 Number of successful extensions: 1 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: 433 Length adjustment: 32 Effective length of query: 395 Effective length of database: 401 Effective search space: 158395 Effective search space used: 158395 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 10 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