Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate Ac3H11_3647 Serine acetyltransferase (EC 2.3.1.30)
Query= BRENDA::A0A0H2UNY1 (205 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3647 Length = 259 Score = 162 bits (410), Expect = 5e-45 Identities = 86/194 (44%), Positives = 121/194 (62%), Gaps = 2/194 (1%) Query: 5 RETIDIVKENDPAARTTLEVLLTYPGVKALAAHRLSHFLWKHGFKLLARMYSQFWRFWTQ 64 R I + + DPAAR+T EV+ YPG+ A+ HR +H+ W +G K R S F R+ T Sbjct: 6 RSDIQCILDRDPAARSTWEVITCYPGLHAIWLHRPAHWCWNNGLKWPGRFISNFSRWLTG 65 Query: 65 IEIHPGAQIDSGVFIDHGSGLVIGETAIVEKGVLLYHGVTLGGTGKDCG-KRHPTVRKGA 123 IEIHPGA+I VF DH G+V+GETA + G +Y GVTLGGT G KRHPT+ K Sbjct: 66 IEIHPGAKIGERVFFDHAMGVVVGETAEIGDGCTIYQGVTLGGTSLYKGAKRHPTLGKDV 125 Query: 124 LISAHAQVIGPVEIGENAKVGAAAVVVADVPSDVTVVGIPAKIVRLHGKKDEPVIHEVEE 183 ++SA A+V+G E+G+ AK+G+ AVV+ VP+ T VGIPA+I+ + V E ++ Sbjct: 126 VVSAGAKVLGGFEVGDGAKIGSNAVVIKPVPAGATAVGIPARIIPSKEGQSADVT-EPQQ 184 Query: 184 KREYYVNKLEQAKD 197 +R++ + Q D Sbjct: 185 QRKFTAYGITQEDD 198 Lambda K H 0.319 0.137 0.418 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: 164 Number of extensions: 8 Number of successful extensions: 2 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: 205 Length of database: 259 Length adjustment: 23 Effective length of query: 182 Effective length of database: 236 Effective search space: 42952 Effective search space used: 42952 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: 46 (22.3 bits)
Align candidate Ac3H11_3647 (Serine acetyltransferase (EC 2.3.1.30))
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.9135.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-75 238.3 0.0 2.6e-75 238.0 0.0 1.1 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3647 Serine acetyltransferase (EC 2.3 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3647 Serine acetyltransferase (EC 2.3.1.30) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 238.0 0.0 2.6e-75 2.6e-75 2 162 .] 6 167 .. 5 167 .. 0.99 Alignments for each domain: == domain 1 score: 238.0 bits; conditional E-value: 2.6e-75 TIGR01172 2 kedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvd 63 ++d++ +l+rDPaa+s++ev+ +y+glha++ +r ah+ ++++lk+ +r++s+++r+ltg++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3647 6 RSDIQCILDRDPAARSTWEVITCYPGLHAIWLHRPAHWCWNNGLKWPGRFISNFSRWLTGIE 67 78************************************************************ PP TIGR01172 64 ihPaakigrgvliDhatGvviGetavigddvsiyqgvtLGgtgkekg.kRhPtvkegvviga 124 ihP+akig++v++Dha+Gvv+Geta+igd ++iyqgvtLGgt+ kg kRhPt++++vv++a lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3647 68 IHPGAKIGERVFFDHAMGVVVGETAEIGDGCTIYQGVTLGGTSLYKGaKRHPTLGKDVVVSA 129 **********************************************99************** PP TIGR01172 125 gakvLGnievgenakiGansvvlkdvpaeatvvGvpar 162 gakvLG +evg++akiG+n+vv+k+vpa+at+vG+par lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3647 130 GAKVLGGFEVGDGAKIGSNAVVIKPVPAGATAVGIPAR 167 ************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (162 nodes) Target sequences: 1 (259 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: 7.95 // [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