Align Serine acetyltransferase; SAT; EC 2.3.1.30 (characterized)
to candidate PP_0840 PP_0840 serine acetyltransferase
Query= SwissProt::Q06750 (217 letters) >FitnessBrowser__Putida:PP_0840 Length = 261 Score = 227 bits (579), Expect = 1e-64 Identities = 118/224 (52%), Positives = 160/224 (71%), Gaps = 18/224 (8%) Query: 3 FRMLKEDIDTVFDQDPAARSYFEVILTYSGLHAIWAHRIAHALYKRKFYFLARLISQVSR 62 F L+EDI +VF +DPAAR+ FEV+ Y G+HAIW HR+ +AL++R F +LARL+S R Sbjct: 2 FERLREDIQSVFHRDPAARNAFEVLTCYPGMHAIWLHRLGNALWRRDFKWLARLVSNFGR 61 Query: 63 FFTGIEIHPGATIGRRFFIDHGMGVVIGETCEIGNNVTVFQGVTLGGTGKEKGKRHPTIK 122 + TGIEIHPGATIGRRFFIDHGMG+VIGET EIG++VT++QGVTLGGT KGKRHPT++ Sbjct: 62 WLTGIEIHPGATIGRRFFIDHGMGIVIGETAEIGDDVTLYQGVTLGGTSWNKGKRHPTLE 121 Query: 123 DDALIATGAKVLGSITVGEGSKIGAGSVVLHDVPDFSTVVGIPGRVVVQN---------- 172 + ++ GAKVLG TVG G+KIG+ +VV VP +T VGIPGR++V++ Sbjct: 122 NGVVVGAGAKVLGPFTVGAGAKIGSNAVVTKAVPAGATAVGIPGRIIVKSEDTEVEAKRK 181 Query: 173 --GKKVRRDLN--HQDLPDPVADRFKSLEQQILELKAELEDRKE 212 +K+ D D+PDPVA +++ Q + L+A +++R E Sbjct: 182 AMAEKIGFDAYGVSGDMPDPVA---RAIGQMLDHLQA-VDERLE 221 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: 227 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: 217 Length of database: 261 Length adjustment: 23 Effective length of query: 194 Effective length of database: 238 Effective search space: 46172 Effective search space used: 46172 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 PP_0840 PP_0840 (serine 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.10892.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-81 256.5 0.1 6.6e-81 256.2 0.1 1.1 1 lcl|FitnessBrowser__Putida:PP_0840 PP_0840 serine acetyltransferase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_0840 PP_0840 serine acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 256.2 0.1 6.6e-81 6.6e-81 2 162 .] 6 166 .. 5 166 .. 0.99 Alignments for each domain: == domain 1 score: 256.2 bits; conditional E-value: 6.6e-81 TIGR01172 2 kedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaakigrgvli 76 +ed+++v++rDPaa++a+evl +y+g+ha++ +rl +al++r++k+larl+s++ r+ltg++ihP+a+igr+++i lcl|FitnessBrowser__Putida:PP_0840 6 REDIQSVFHRDPAARNAFEVLTCYPGMHAIWLHRLGNALWRRDFKWLARLVSNFGRWLTGIEIHPGATIGRRFFI 80 79************************************************************************* PP TIGR01172 77 DhatGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenakiGansvvlkdvp 151 Dh++G+viGeta+igddv++yqgvtLGgt+++kgkRhPt+++gvv+gagakvLG+++vg++akiG+n+vv+k vp lcl|FitnessBrowser__Putida:PP_0840 81 DHGMGIVIGETAEIGDDVTLYQGVTLGGTSWNKGKRHPTLENGVVVGAGAKVLGPFTVGAGAKIGSNAVVTKAVP 155 *************************************************************************** PP TIGR01172 152 aeatvvGvpar 162 a+at+vG+p+r lcl|FitnessBrowser__Putida:PP_0840 156 AGATAVGIPGR 166 *********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (162 nodes) Target sequences: 1 (261 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: 11.13 // [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