Align Serine acetyltransferase; SAT; EC 2.3.1.30 (characterized)
to candidate Synpcc7942_2420 Synpcc7942_2420 serine O-acetyltransferase
Query= SwissProt::Q06750 (217 letters) >FitnessBrowser__SynE:Synpcc7942_2420 Length = 244 Score = 216 bits (549), Expect = 4e-61 Identities = 106/206 (51%), Positives = 146/206 (70%), Gaps = 1/206 (0%) Query: 3 FRMLKEDIDTVFDQDPAARSYFEVILTYSGLHAIWAHRIAHALYKRKFYFLARLISQVSR 62 F+ L D +F++DPAAR+ EV+L Y G A+ HR+AH LY+++ + RL+S +SR Sbjct: 2 FKTLAADFRIIFERDPAARNGLEVLLCYPGFQALVCHRVAHWLYQQRLPVIPRLLSHLSR 61 Query: 63 FFTGIEIHPGATIGRRFFIDHGMGVVIGETCEIGNNVTVFQGVTLGGTGKEKGKRHPTIK 122 TG+EIHPGA +G+ FIDHGMGVVIGET +G+ ++QGVTLGGTGK+ GKRHPT+ Sbjct: 62 LLTGVEIHPGARLGQGIFIDHGMGVVIGETAIVGDYCLIYQGVTLGGTGKQSGKRHPTLA 121 Query: 123 DDALIATGAKVLGSITVGEGSKIGAGSVVLHDVPDFSTVVGIPGRVVVQNGKKVRRDLNH 182 ++ ++ GAKVLG+I +GE +IGAGSVVL DVP TVVGIPGRV+ ++G +V L+H Sbjct: 122 NNVVVGAGAKVLGNIQIGENVRIGAGSVVLRDVPSDCTVVGIPGRVIYRSGVRV-DPLDH 180 Query: 183 QDLPDPVADRFKSLEQQILELKAELE 208 +PD A + L +I L+ +LE Sbjct: 181 SQMPDSEARVIRMLLDRIEALEDQLE 206 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: 220 Number of extensions: 10 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: 244 Length adjustment: 23 Effective length of query: 194 Effective length of database: 221 Effective search space: 42874 Effective search space used: 42874 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 Synpcc7942_2420 Synpcc7942_2420 (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.9875.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-80 255.1 0.4 1.7e-80 254.8 0.4 1.1 1 lcl|FitnessBrowser__SynE:Synpcc7942_2420 Synpcc7942_2420 serine O-acetylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_2420 Synpcc7942_2420 serine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 254.8 0.4 1.7e-80 1.7e-80 2 162 .] 6 166 .. 5 166 .. 0.99 Alignments for each domain: == domain 1 score: 254.8 bits; conditional E-value: 1.7e-80 TIGR01172 2 kedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaaki 70 ++d++ ++erDPaa++ levll+y+g++al+++r+ah+ly+++l ++ rlls+l+r+ltgv+ihP+a++ lcl|FitnessBrowser__SynE:Synpcc7942_2420 6 AADFRIIFERDPAARNGLEVLLCYPGFQALVCHRVAHWLYQQRLPVIPRLLSHLSRLLTGVEIHPGARL 74 689****************************************************************** PP TIGR01172 71 grgvliDhatGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenak 139 g+g++iDh++GvviGeta++gd ++iyqgvtLGgtgk++gkRhPt+ ++vv+gagakvLGni++gen++ lcl|FitnessBrowser__SynE:Synpcc7942_2420 75 GQGIFIDHGMGVVIGETAIVGDYCLIYQGVTLGGTGKQSGKRHPTLANNVVVGAGAKVLGNIQIGENVR 143 ********************************************************************* PP TIGR01172 140 iGansvvlkdvpaeatvvGvpar 162 iGa+svvl+dvp++ tvvG+p+r lcl|FitnessBrowser__SynE:Synpcc7942_2420 144 IGAGSVVLRDVPSDCTVVGIPGR 166 *********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (162 nodes) Target sequences: 1 (244 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: 6.37 // [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