Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate 17668 b3607 serine acetyltransferase (NCBI)
Query= BRENDA::P0A9D4 (273 letters) >FitnessBrowser__Keio:17668 Length = 273 Score = 548 bits (1412), Expect = e-161 Identities = 273/273 (100%), Positives = 273/273 (100%) Query: 1 MSCEELEIVWNNIKAEARTLADCEPMLASFYHATLLKHENLGSALSYMLANKLSSPIMPA 60 MSCEELEIVWNNIKAEARTLADCEPMLASFYHATLLKHENLGSALSYMLANKLSSPIMPA Sbjct: 1 MSCEELEIVWNNIKAEARTLADCEPMLASFYHATLLKHENLGSALSYMLANKLSSPIMPA 60 Query: 61 IAIREVVEEAYAADPEMIASAACDIQAVRTRDPAVDKYSTPLLYLKGFHALQAYRIGHWL 120 IAIREVVEEAYAADPEMIASAACDIQAVRTRDPAVDKYSTPLLYLKGFHALQAYRIGHWL Sbjct: 61 IAIREVVEEAYAADPEMIASAACDIQAVRTRDPAVDKYSTPLLYLKGFHALQAYRIGHWL 120 Query: 121 WNQGRRALAIFLQNQVSVTFQVDIHPAAKIGRGIMLDHATGIVVGETAVIENDVSILQSV 180 WNQGRRALAIFLQNQVSVTFQVDIHPAAKIGRGIMLDHATGIVVGETAVIENDVSILQSV Sbjct: 121 WNQGRRALAIFLQNQVSVTFQVDIHPAAKIGRGIMLDHATGIVVGETAVIENDVSILQSV 180 Query: 181 TLGGTGKSGGDRHPKIREGVMIGAGAKILGNIEVGRGAKIGAGSVVLQPVPPHTTAAGVP 240 TLGGTGKSGGDRHPKIREGVMIGAGAKILGNIEVGRGAKIGAGSVVLQPVPPHTTAAGVP Sbjct: 181 TLGGTGKSGGDRHPKIREGVMIGAGAKILGNIEVGRGAKIGAGSVVLQPVPPHTTAAGVP 240 Query: 241 ARIVGKPDSDKPSMDMDQHFNGINHTFEYGDGI 273 ARIVGKPDSDKPSMDMDQHFNGINHTFEYGDGI Sbjct: 241 ARIVGKPDSDKPSMDMDQHFNGINHTFEYGDGI 273 Lambda K H 0.319 0.135 0.401 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: 445 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: 273 Length of database: 273 Length adjustment: 25 Effective length of query: 248 Effective length of database: 248 Effective search space: 61504 Effective search space used: 61504 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 (21.7 bits) S2: 47 (22.7 bits)
Align candidate 17668 b3607 (serine acetyltransferase (NCBI))
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.23701.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-79 250.4 1.5 5.6e-79 249.9 1.5 1.2 1 lcl|FitnessBrowser__Keio:17668 b3607 serine acetyltransferase ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:17668 b3607 serine acetyltransferase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 249.9 1.5 5.6e-79 5.6e-79 2 162 .] 82 242 .. 81 242 .. 0.99 Alignments for each domain: == domain 1 score: 249.9 bits; conditional E-value: 5.6e-79 TIGR01172 2 kedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaakigrgvliDhat 80 ++d++av++rDPa+++++++ll++kg+hal+ayr+ h+l+++++++la +l+++v+v+++vdihPaakigrg+++Dhat lcl|FitnessBrowser__Keio:17668 82 ACDIQAVRTRDPAVDKYSTPLLYLKGFHALQAYRIGHWLWNQGRRALAIFLQNQVSVTFQVDIHPAAKIGRGIMLDHAT 160 68***************************************************************************** PP TIGR01172 81 GvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenakiGansvvlkdvpaeatvvGv 159 G+v+Getavi++dvsi+q+vtLGgtgk+ g+RhP+++egv+igagak+LGnievg +akiGa+svvl++vp+++t++Gv lcl|FitnessBrowser__Keio:17668 161 GIVVGETAVIENDVSILQSVTLGGTGKSGGDRHPKIREGVMIGAGAKILGNIEVGRGAKIGAGSVVLQPVPPHTTAAGV 239 ******************************************************************************* PP TIGR01172 160 par 162 par lcl|FitnessBrowser__Keio:17668 240 PAR 242 *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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.46 // [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