Align Serine acetyltransferase; SAT; EC 2.3.1.30 (characterized)
to candidate WP_019866882.1 METMI_RS0113810 serine O-acetyltransferase
Query= SwissProt::Q06750 (217 letters) >NCBI__GCF_000384075.1:WP_019866882.1 Length = 252 Score = 217 bits (552), Expect = 2e-61 Identities = 112/226 (49%), Positives = 155/226 (68%), Gaps = 12/226 (5%) Query: 3 FRMLKEDIDTVFDQDPAARSYFEVILTYSGLHAIWAHRIAHALYKRKFYFLARLISQVSR 62 F LKED+ VF +DPAA+++FEVI TY G+HA+ HR++H +K F +LAR I+ VSR Sbjct: 2 FTRLKEDVACVFARDPAAQTWFEVITTYPGVHAVIIHRLSHWCWKAGFRWLARFIAYVSR 61 Query: 63 FFTGIEIHPGATIGRRFFIDHGMGVVIGETCEIGNNVTVFQGVTLGGTGKEKGKRHPTIK 122 ++TGIEIHPGA IGRRFFIDHGMGVVIGET IG++ T++ GVTLGGT +KGKRHPT+ Sbjct: 62 WWTGIEIHPGAEIGRRFFIDHGMGVVIGETAVIGDDCTLYHGVTLGGTTWKKGKRHPTLH 121 Query: 123 DDALIATGAKVLGSITVGEGSKIGAGSVVLHDVPDFSTVVGIPGRVV----------VQN 172 + +I GAKVLG I +G+G+++G+ SVVL VP +TVVGIP ++ V+ Sbjct: 122 NGVVIGAGAKVLGPIDIGDGARVGSNSVVLKPVPAGTTVVGIPAHIIGGQKASKPEPVET 181 Query: 173 GKKVRRDL--NHQDLPDPVADRFKSLEQQILELKAELEDRKERINQ 216 G+ V + D+PDPVA + I +L ++E ++ +N+ Sbjct: 182 GRPVNFNAYGASADMPDPVALAINRMLDHINDLDKQIETMQKALNE 227 Lambda K H 0.323 0.141 0.413 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: 209 Number of extensions: 9 Number of successful extensions: 2 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: 217 Length of database: 252 Length adjustment: 23 Effective length of query: 194 Effective length of database: 229 Effective search space: 44426 Effective search space used: 44426 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 (21.9 bits) S2: 46 (22.3 bits)
Align candidate WP_019866882.1 METMI_RS0113810 (serine O-acetyltransferase)
to HMM TIGR01172 (cysE: serine O-acetyltransferase (EC 2.3.1.30))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01172.hmm # target sequence database: /tmp/gapView.9328.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01172 [M=162] Accession: TIGR01172 Description: cysE: serine O-acetyltransferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-80 254.9 0.9 2.1e-80 254.6 0.9 1.1 1 lcl|NCBI__GCF_000384075.1:WP_019866882.1 METMI_RS0113810 serine O-acetylt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384075.1:WP_019866882.1 METMI_RS0113810 serine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 254.6 0.9 2.1e-80 2.1e-80 2 161 .. 6 165 .. 5 166 .. 0.99 Alignments for each domain: == domain 1 score: 254.6 bits; conditional E-value: 2.1e-80 TIGR01172 2 kedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaaki 70 ked+ v++rDPaa++++ev+ +y+g+ha++++rl+h+ +k ++++lar++++++r+ tg++ihP+a+i lcl|NCBI__GCF_000384075.1:WP_019866882.1 6 KEDVACVFARDPAAQTWFEVITTYPGVHAVIIHRLSHWCWKAGFRWLARFIAYVSRWWTGIEIHPGAEI 74 79******************************************************************* PP TIGR01172 71 grgvliDhatGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenak 139 gr+++iDh++GvviGetavigdd+++y+gvtLGgt+++kgkRhPt+++gvvigagakvLG+i +g++a+ lcl|NCBI__GCF_000384075.1:WP_019866882.1 75 GRRFFIDHGMGVVIGETAVIGDDCTLYHGVTLGGTTWKKGKRHPTLHNGVVIGAGAKVLGPIDIGDGAR 143 ********************************************************************* PP TIGR01172 140 iGansvvlkdvpaeatvvGvpa 161 +G+nsvvlk+vpa++tvvG+pa lcl|NCBI__GCF_000384075.1:WP_019866882.1 144 VGSNSVVLKPVPAGTTVVGIPA 165 *********************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (162 nodes) Target sequences: 1 (252 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 7.51 // [ok]
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