Align Serine acetyltransferase; SAT; EC 2.3.1.30 (characterized)
to candidate WP_013553992.1 NITSA_RS05295 serine O-acetyltransferase
Query= SwissProt::Q06750 (217 letters) >NCBI__GCF_000186245.1:WP_013553992.1 Length = 234 Score = 195 bits (496), Expect = 5e-55 Identities = 97/202 (48%), Positives = 137/202 (67%), Gaps = 2/202 (0%) Query: 3 FRMLKEDIDTVFDQDPAARSYFEVILTYSGLHAIWAHRIAHALYKRKFYFLARLISQVSR 62 +++++ED TV DPA +S FE+ Y G+ A++ +RIAH+LY ++F LAR IS + + Sbjct: 4 WQLIREDFATVKRNDPALKSKFELFFNYPGVWALFFYRIAHSLYSKEFKRLARFISAMGQ 63 Query: 63 FFTGIEIHPGATIGRRFFIDHGMGVVIGETCEIGNNVTVFQGVTLGGTGKEKGKRHPTIK 122 F T ++IHPGA IGRR FIDH GVVIGET +GN+V ++Q VTLGG +GKRHPT++ Sbjct: 64 FLTAVDIHPGARIGRRVFIDHATGVVIGETAIVGNDVLIYQQVTLGGVSLSRGKRHPTVE 123 Query: 123 DDALIATGAKVLGSITVGEGSKIGAGSVVLHDVPDFSTVVGIPGRVVVQNGKKVRRDLNH 182 D +I GAKVLG+IT+G SK+GA SVV+ DVP T VG+P R+ + K L+H Sbjct: 124 DGVIIGAGAKVLGNITIGRESKVGANSVVIRDVPPGCTAVGVPARIAQRVDNKA--PLSH 181 Query: 183 QDLPDPVADRFKSLEQQILELK 204 +PD + F+ L ++I L+ Sbjct: 182 NVMPDVNREVFEYLLKRIAVLE 203 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: 199 Number of extensions: 9 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: 234 Length adjustment: 22 Effective length of query: 195 Effective length of database: 212 Effective search space: 41340 Effective search space used: 41340 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_013553992.1 NITSA_RS05295 (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.19115.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-77 244.7 0.2 2.9e-77 244.3 0.2 1.1 1 lcl|NCBI__GCF_000186245.1:WP_013553992.1 NITSA_RS05295 serine O-acetyltra Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000186245.1:WP_013553992.1 NITSA_RS05295 serine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 244.3 0.2 2.9e-77 2.9e-77 1 162 [] 7 168 .. 7 168 .. 0.99 Alignments for each domain: == domain 1 score: 244.3 bits; conditional E-value: 2.9e-77 TIGR01172 1 ikedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaak 69 i+ed+ +v+++DPa +s++e++++y+g++al yr+ah ly++++k lar++s + ++lt vdihP+a+ lcl|NCBI__GCF_000186245.1:WP_013553992.1 7 IREDFATVKRNDPALKSKFELFFNYPGVWALFFYRIAHSLYSKEFKRLARFISAMGQFLTAVDIHPGAR 75 689****************************************************************** PP TIGR01172 70 igrgvliDhatGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgena 138 igr+v+iDhatGvviGeta++g+dv+iyq+vtLGg + ++gkRhPtv++gv+igagakvLGni++g ++ lcl|NCBI__GCF_000186245.1:WP_013553992.1 76 IGRRVFIDHATGVVIGETAIVGNDVLIYQQVTLGGVSLSRGKRHPTVEDGVIIGAGAKVLGNITIGRES 144 ********************************************************************* PP TIGR01172 139 kiGansvvlkdvpaeatvvGvpar 162 k+Gansvv++dvp++ t+vGvpar lcl|NCBI__GCF_000186245.1:WP_013553992.1 145 KVGANSVVIRDVPPGCTAVGVPAR 168 **********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (162 nodes) Target sequences: 1 (234 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 7.40 // [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