Align Serine acetyltransferase; SAT; EC 2.3.1.30 (characterized)
to candidate GFF1216 Psest_1249 serine O-acetyltransferase
Query= SwissProt::Q06750 (217 letters) >FitnessBrowser__psRCH2:GFF1216 Length = 258 Score = 225 bits (573), Expect = 7e-64 Identities = 110/219 (50%), Positives = 151/219 (68%), Gaps = 13/219 (5%) Query: 3 FRMLKEDIDTVFDQDPAARSYFEVILTYSGLHAIWAHRIAHALYKRKFYFLARLISQVSR 62 F ++EDI +VF +DPAAR+ FEV+ Y GLHAIW HR++H L+ ++ +LAR+ S + R Sbjct: 2 FERMREDIQSVFHRDPAARNAFEVLTCYPGLHAIWIHRLSHWLWMHEWKWLARMSSNLGR 61 Query: 63 FFTGIEIHPGATIGRRFFIDHGMGVVIGETCEIGNNVTVFQGVTLGGTGKEKGKRHPTIK 122 + TG+EIHPGA IGRRFFIDHGMG+VIGET EIG++VT++ GVTLGGT KGKRHPT++ Sbjct: 62 WLTGVEIHPGARIGRRFFIDHGMGIVIGETAEIGDDVTLYHGVTLGGTSWNKGKRHPTLE 121 Query: 123 DDALIATGAKVLGSITVGEGSKIGAGSVVLHDVPDFSTVVGIPGRVVVQNG-------KK 175 D ++ GAK+LG TVG G+KIG+ +VV +VP +T VGIPGRV+V++ K Sbjct: 122 DGVIVGAGAKILGPFTVGAGAKIGSNAVVTREVPPGATAVGIPGRVIVKSSDEQEAKRKA 181 Query: 176 VRRDLN------HQDLPDPVADRFKSLEQQILELKAELE 208 + + +D+PDPVA L + ++ LE Sbjct: 182 IAEKIGFDAYGVSEDMPDPVARAIGQLLDHVQAVEERLE 220 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: 232 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: 217 Length of database: 258 Length adjustment: 23 Effective length of query: 194 Effective length of database: 235 Effective search space: 45590 Effective search space used: 45590 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 GFF1216 Psest_1249 (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.11699.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-82 260.5 0.1 3.9e-82 260.2 0.1 1.1 1 lcl|FitnessBrowser__psRCH2:GFF1216 Psest_1249 serine O-acetyltransf Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF1216 Psest_1249 serine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 260.2 0.1 3.9e-82 3.9e-82 1 162 [] 5 166 .. 5 166 .. 0.99 Alignments for each domain: == domain 1 score: 260.2 bits; conditional E-value: 3.9e-82 TIGR01172 1 ikedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaakigrgvl 75 ++ed+++v++rDPaa++a+evl +y+glha++++rl+h+l+ +++k+lar+ s+l r+ltgv+ihP+a+igr+++ lcl|FitnessBrowser__psRCH2:GFF1216 5 MREDIQSVFHRDPAARNAFEVLTCYPGLHAIWIHRLSHWLWMHEWKWLARMSSNLGRWLTGVEIHPGARIGRRFF 79 589************************************************************************ PP TIGR01172 76 iDhatGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenakiGansvvlkdv 150 iDh++G+viGeta+igddv++y+gvtLGgt+++kgkRhPt+++gv++gagak+LG+++vg++akiG+n+vv+++v lcl|FitnessBrowser__psRCH2:GFF1216 80 IDHGMGIVIGETAEIGDDVTLYHGVTLGGTSWNKGKRHPTLEDGVIVGAGAKILGPFTVGAGAKIGSNAVVTREV 154 *************************************************************************** PP TIGR01172 151 paeatvvGvpar 162 p++at+vG+p+r lcl|FitnessBrowser__psRCH2:GFF1216 155 PPGATAVGIPGR 166 **********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (162 nodes) Target sequences: 1 (258 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 6.15 // [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