Align Serine acetyltransferase; SAT; EC 2.3.1.30 (characterized)
to candidate WP_018231431.1 THITHI_RS0102180 serine O-acetyltransferase
Query= SwissProt::Q06750 (217 letters) >NCBI__GCF_000378965.1:WP_018231431.1 Length = 270 Score = 208 bits (530), Expect = 7e-59 Identities = 103/201 (51%), Positives = 144/201 (71%), Gaps = 12/201 (5%) Query: 3 FRMLKEDIDTVFDQDPAARSYFEVILTYSGLHAIWAHRIAHALYKRKFYFLARLISQVSR 62 F ++EDI VFD+DPAAR+ FEV+ TY G+HA+ HR +H L++ + +LAR+ S + R Sbjct: 2 FDRIREDIRCVFDRDPAARNAFEVLTTYPGVHAVLMHRFSHRLWRWRLCWLARIFSNLGR 61 Query: 63 FFTGIEIHPGATIGRRFFIDHGMGVVIGETCEIGNNVTVFQGVTLGGTGKEKGKRHPTIK 122 + TGIEIHPGA IGRRFFIDHGMGVVIGET EIG + T++ GVTLGGT ++GKRHPT+ Sbjct: 62 WLTGIEIHPGARIGRRFFIDHGMGVVIGETAEIGEDCTLYHGVTLGGTSWKQGKRHPTLG 121 Query: 123 DDALIATGAKVLGSITVGEGSKIGAGSVVLHDVPDFSTVVGIPGRVVVQNG-KKVRRDLN 181 + ++ GAK+LG + VG+ +++G+ +VVL DVP +TVVGIPGRV+ + + RR+ Sbjct: 122 NRVVVGAGAKILGPLHVGDDARVGSNAVVLKDVPAGATVVGIPGRVISKRTVDEARREAM 181 Query: 182 -----------HQDLPDPVAD 191 +++PDPVA+ Sbjct: 182 AERIGFDAYGLSKEMPDPVAN 202 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: 241 Number of extensions: 6 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: 270 Length adjustment: 23 Effective length of query: 194 Effective length of database: 247 Effective search space: 47918 Effective search space used: 47918 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_018231431.1 THITHI_RS0102180 (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.26498.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-81 256.0 0.1 9.4e-81 255.7 0.1 1.1 1 lcl|NCBI__GCF_000378965.1:WP_018231431.1 THITHI_RS0102180 serine O-acetyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000378965.1:WP_018231431.1 THITHI_RS0102180 serine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 255.7 0.1 9.4e-81 9.4e-81 1 162 [] 5 166 .. 5 166 .. 0.99 Alignments for each domain: == domain 1 score: 255.7 bits; conditional E-value: 9.4e-81 TIGR01172 1 ikedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaak 69 i+ed++ v++rDPaa++a+evl +y+g+ha+l++r++h+l++++l +lar++s+l r+ltg++ihP+a+ lcl|NCBI__GCF_000378965.1:WP_018231431.1 5 IREDIRCVFDRDPAARNAFEVLTTYPGVHAVLMHRFSHRLWRWRLCWLARIFSNLGRWLTGIEIHPGAR 73 689****************************************************************** PP TIGR01172 70 igrgvliDhatGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgena 138 igr+++iDh++GvviGeta+ig+d+++y+gvtLGgt++++gkRhPt++++vv+gagak+LG+++vg++a lcl|NCBI__GCF_000378965.1:WP_018231431.1 74 IGRRFFIDHGMGVVIGETAEIGEDCTLYHGVTLGGTSWKQGKRHPTLGNRVVVGAGAKILGPLHVGDDA 142 ********************************************************************* PP TIGR01172 139 kiGansvvlkdvpaeatvvGvpar 162 ++G+n+vvlkdvpa+atvvG+p+r lcl|NCBI__GCF_000378965.1:WP_018231431.1 143 RVGSNAVVLKDVPAGATVVGIPGR 166 **********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (162 nodes) Target sequences: 1 (270 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 6.88 // [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