Align Serine acetyltransferase; SAT; EC 2.3.1.30 (characterized)
to candidate 5209866 Shew_2319 serine O-acetyltransferase (RefSeq)
Query= SwissProt::Q06750 (217 letters) >FitnessBrowser__PV4:5209866 Length = 273 Score = 205 bits (522), Expect = 6e-58 Identities = 98/202 (48%), Positives = 140/202 (69%), Gaps = 16/202 (7%) Query: 6 LKEDIDTVFDQDPAARSYFEVILTYSGLHAIWAHRIAHALYKRKFYFLARLISQVSRFFT 65 +K+DI +++ +DPAA E++L Y G+ AIW HR++H L+K K+ AR+IS SR+ T Sbjct: 7 IKDDIASIYHRDPAANGTLEILLNYPGMQAIWIHRVSHKLWKAKWCLTARMISTFSRWLT 66 Query: 66 GIEIHPGATIGRRFFIDHGMGVVIGETCEIGNNVTVFQGVTLGGTGKEKGKRHPTIKDDA 125 G+EIHPGATIG RFFIDHGMGVVIGET EIGN+ T++ GVTLGGT + GKRHPT+ ++ Sbjct: 67 GVEIHPGATIGDRFFIDHGMGVVIGETAEIGNDCTLYHGVTLGGTTWQAGKRHPTLGNNV 126 Query: 126 LIATGAKVLGSITVGEGSKIGAGSVVLHDVPDFSTVVGIPGRVVVQNGKKVRRDLNHQ-- 183 ++ GAK+LG IT+ +G+++G+ SVV+ +VP +TVVGIP R V + ++ + + + Sbjct: 127 VVGAGAKILGPITMHDGARVGSNSVVVKEVPKDTTVVGIPAREVARPSEEAKEHVQRRTE 186 Query: 184 --------------DLPDPVAD 191 D PDPVA+ Sbjct: 187 MAKKYGFDAYAVSPDNPDPVAN 208 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: 217 Number of extensions: 8 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: 217 Length of database: 273 Length adjustment: 23 Effective length of query: 194 Effective length of database: 250 Effective search space: 48500 Effective search space used: 48500 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 5209866 Shew_2319 (serine O-acetyltransferase (RefSeq))
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.2121.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-79 251.5 0.9 2.4e-79 251.1 0.9 1.1 1 lcl|FitnessBrowser__PV4:5209866 Shew_2319 serine O-acetyltransfe Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5209866 Shew_2319 serine O-acetyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 251.1 0.9 2.4e-79 2.4e-79 1 162 [] 7 168 .. 7 168 .. 0.99 Alignments for each domain: == domain 1 score: 251.1 bits; conditional E-value: 2.4e-79 TIGR01172 1 ikedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaakigrgvliDh 78 ik+d+ ++++rDPaa+ +le+ll+y+g++a++++r++h+l+k k+ l ar++s+++r+ltgv+ihP+a+ig +++iDh lcl|FitnessBrowser__PV4:5209866 7 IKDDIASIYHRDPAANGTLEILLNYPGMQAIWIHRVSHKLWKAKWCLTARMISTFSRWLTGVEIHPGATIGDRFFIDH 84 689*************************************************************************** PP TIGR01172 79 atGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenakiGansvvlkdvpaeatv 156 ++GvviGeta+ig+d+++y+gvtLGgt+++ gkRhPt++++vv+gagak+LG+i+++++a++G+nsvv+k+vp+++tv lcl|FitnessBrowser__PV4:5209866 85 GMGVVIGETAEIGNDCTLYHGVTLGGTTWQAGKRHPTLGNNVVVGAGAKILGPITMHDGARVGSNSVVVKEVPKDTTV 162 ****************************************************************************** PP TIGR01172 157 vGvpar 162 vG+par lcl|FitnessBrowser__PV4:5209866 163 VGIPAR 168 ****97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (162 nodes) Target sequences: 1 (273 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: 6.46 // [ok]
This GapMind analysis is from Apr 09 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