Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate WP_020176769.1 A3OQ_RS0117705 serine O-acetyltransferase
Query= BRENDA::C4IRW0 (281 letters) >NCBI__GCF_000385335.1:WP_020176769.1 Length = 274 Score = 336 bits (862), Expect = 3e-97 Identities = 162/258 (62%), Positives = 200/258 (77%) Query: 20 LDQVDPIWHSIRAEAEEATRNDPVLGAFLYATILNQPSLEEAVMHRIAERLGHPDVSADI 79 ++ VDPI+ +R EAEE +P + + +TILN +LE A++HR+A RLGHP+V D+ Sbjct: 10 IESVDPIFARMRTEAEETIHREPEISGIMMSTILNHDTLESAIIHRLAARLGHPEVPGDL 69 Query: 80 LRQTFDTMLEANPEWSHVLRVDIQAVYDRDPAYSRFMDPVLYLKGFHAIQTHRLAHWLYK 139 +R+T+ +L +P + R D+ AV DRDPA R ++PVLY KGFHAIQTHRLAH L+ Sbjct: 70 IRKTYLDVLAHDPSIAEAFRADLVAVVDRDPACVRVIEPVLYFKGFHAIQTHRLAHALWN 129 Query: 140 QGRKDFAYYLQSRSSSIFQTDIHPAARLGSGLFLDHATGLVVGETAVVEDNVSILHGVTL 199 GR+DFA YLQSRSS +FQTDIHPAA+ G +FLDHATGLVVG TAV+ED VS+L VTL Sbjct: 130 AGRRDFALYLQSRSSEVFQTDIHPAAQFGKSIFLDHATGLVVGSTAVIEDGVSMLQDVTL 189 Query: 200 GGTGKSSGDRHPKIRQGVLIGAGAKILGNIQVGQCSKIAAGSVVLKSVPHNVTVAGVPAR 259 GGTGK GDRHPKIR GVLIGAGAKILGNI+VG C++IAAGSVVL VP+N TVAGVPA+ Sbjct: 190 GGTGKEKGDRHPKIRHGVLIGAGAKILGNIEVGHCARIAAGSVVLHPVPNNKTVAGVPAK 249 Query: 260 IIGETGCTEPSRVMDQML 277 I+GE GC EP+ MDQ+L Sbjct: 250 IVGEAGCAEPALSMDQIL 267 Lambda K H 0.320 0.135 0.403 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: 332 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: 281 Length of database: 274 Length adjustment: 25 Effective length of query: 256 Effective length of database: 249 Effective search space: 63744 Effective search space used: 63744 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: 47 (22.7 bits)
Align candidate WP_020176769.1 A3OQ_RS0117705 (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.16594.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-71 224.2 1.1 2.6e-70 221.7 1.0 1.9 2 lcl|NCBI__GCF_000385335.1:WP_020176769.1 A3OQ_RS0117705 serine O-acetyltr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000385335.1:WP_020176769.1 A3OQ_RS0117705 serine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 0.4 0.0 0.032 0.032 4 40 .. 23 60 .. 20 66 .. 0.79 2 ! 221.7 1.0 2.6e-70 2.6e-70 2 162 .] 89 249 .. 88 249 .. 0.99 Alignments for each domain: == domain 1 score: 0.4 bits; conditional E-value: 0.032 TIGR01172 4 dlkavlerDPaaes.alevlllykglhallayrlahal 40 + +++++r+P ++ +++ +l++ +l + +++rla++l lcl|NCBI__GCF_000385335.1:WP_020176769.1 23 EAEETIHREPEISGiMMSTILNHDTLESAIIHRLAARL 60 56778899998876156789999**********99876 PP == domain 2 score: 221.7 bits; conditional E-value: 2.6e-70 TIGR01172 2 kedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaaki 70 ++dl av++rDPa+ +++e++l++kg+ha++++rlahal++ +++ +a +l+++++ +++ dihPaa++ lcl|NCBI__GCF_000385335.1:WP_020176769.1 89 RADLVAVVDRDPACVRVIEPVLYFKGFHAIQTHRLAHALWNAGRRDFALYLQSRSSEVFQTDIHPAAQF 157 6799***************************************************************** PP TIGR01172 71 grgvliDhatGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenak 139 g+ +++DhatG+v+G+tavi+d vs++q+vtLGgtgkekg+RhP++++gv+igagak+LGnievg+ a+ lcl|NCBI__GCF_000385335.1:WP_020176769.1 158 GKSIFLDHATGLVVGSTAVIEDGVSMLQDVTLGGTGKEKGDRHPKIRHGVLIGAGAKILGNIEVGHCAR 226 ********************************************************************* PP TIGR01172 140 iGansvvlkdvpaeatvvGvpar 162 i a+svvl++vp++ tv+Gvpa+ lcl|NCBI__GCF_000385335.1:WP_020176769.1 227 IAAGSVVLHPVPNNKTVAGVPAK 249 *********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (162 nodes) Target sequences: 1 (274 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: 8.32 // [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