Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate WP_011384257.1 AMB_RS09365 serine O-acetyltransferase
Query= BRENDA::C4IRW0 (281 letters) >NCBI__GCF_000009985.1:WP_011384257.1 Length = 295 Score = 312 bits (799), Expect = 6e-90 Identities = 156/254 (61%), Positives = 190/254 (74%) Query: 24 DPIWHSIRAEAEEATRNDPVLGAFLYATILNQPSLEEAVMHRIAERLGHPDVSADILRQT 83 D +W +R EAEEA P+L IL QP+ E AV HRI++RL + V+ +L +T Sbjct: 30 DGLWAELRREAEEALAGAPMLRRLFIDNILEQPTFEAAVFHRISQRLKNEVVTLPLLTET 89 Query: 84 FDTMLEANPEWSHVLRVDIQAVYDRDPAYSRFMDPVLYLKGFHAIQTHRLAHWLYKQGRK 143 F + A P+ + LR DI AV DRDPA RF++P LY KGFHA+QTHRLAHWL+ +G + Sbjct: 90 FARAVAATPKIAQALRADIAAVLDRDPATQRFIEPFLYFKGFHAVQTHRLAHWLWSRGER 149 Query: 144 DFAYYLQSRSSSIFQTDIHPAARLGSGLFLDHATGLVVGETAVVEDNVSILHGVTLGGTG 203 DFA YLQSRSS +FQTDIHPAAR G G+FLDHATGLVVGETAVVED+VS+L VTLGGTG Sbjct: 150 DFALYLQSRSSDVFQTDIHPAARFGQGVFLDHATGLVVGETAVVEDDVSLLQNVTLGGTG 209 Query: 204 KSSGDRHPKIRQGVLIGAGAKILGNIQVGQCSKIAAGSVVLKSVPHNVTVAGVPARIIGE 263 K SGDRHPK+RQG +IGAGAKILGNI++G S+IAAGSVVLK+V + TVAG+PARII Sbjct: 210 KESGDRHPKVRQGAIIGAGAKILGNIEIGAHSRIAAGSVVLKAVEPHSTVAGIPARIIRT 269 Query: 264 TGCTEPSRVMDQML 277 T E R +++L Sbjct: 270 TNDPEVLRTKEEIL 283 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: 309 Number of extensions: 7 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: 295 Length adjustment: 26 Effective length of query: 255 Effective length of database: 269 Effective search space: 68595 Effective search space used: 68595 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_011384257.1 AMB_RS09365 (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.18530.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-72 227.7 0.2 2.8e-71 224.9 0.1 1.9 2 lcl|NCBI__GCF_000009985.1:WP_011384257.1 AMB_RS09365 serine O-acetyltrans Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011384257.1 AMB_RS09365 serine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 0.8 0.0 0.024 0.024 19 58 .. 55 93 .. 38 98 .. 0.76 2 ! 224.9 0.1 2.8e-71 2.8e-71 2 162 .] 105 265 .. 104 265 .. 0.99 Alignments for each domain: == domain 1 score: 0.8 bits; conditional E-value: 0.024 TIGR01172 19 levlllykglhallayrlahalykrklkllarllselvrv 58 ++ +l +++ a + +r++++l + ++ +l l ++++r lcl|NCBI__GCF_000009985.1:WP_011384257.1 55 IDNILEQPTFEAAVFHRISQRLKN-EVVTLPLLTETFARA 93 567889999**********99854.555666666666655 PP == domain 2 score: 224.9 bits; conditional E-value: 2.8e-71 TIGR01172 2 kedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaaki 70 ++d+ avl+rDPa+++ +e++l++kg+ha++++rlah+l++r+ + +a +l+++++ +++ dihPaa++ lcl|NCBI__GCF_000009985.1:WP_011384257.1 105 RADIAAVLDRDPATQRFIEPFLYFKGFHAVQTHRLAHWLWSRGERDFALYLQSRSSDVFQTDIHPAARF 173 78******************************************************************* PP TIGR01172 71 grgvliDhatGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenak 139 g+gv++DhatG+v+Getav++ddvs++q+vtLGgtgke+g+RhP+v++g++igagak+LGnie+g++++ lcl|NCBI__GCF_000009985.1:WP_011384257.1 174 GQGVFLDHATGLVVGETAVVEDDVSLLQNVTLGGTGKESGDRHPKVRQGAIIGAGAKILGNIEIGAHSR 242 ********************************************************************* PP TIGR01172 140 iGansvvlkdvpaeatvvGvpar 162 i a+svvlk v +++tv+G+par lcl|NCBI__GCF_000009985.1:WP_011384257.1 243 IAAGSVVLKAVEPHSTVAGIPAR 265 *********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (162 nodes) Target sequences: 1 (295 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: 7.72 // [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