Align Serine acetyltransferase; SAT; EC 2.3.1.30 (characterized)
to candidate 6937121 Sama_1291 Serine O-acetyltransferase (RefSeq)
Query= SwissProt::Q06750 (217 letters) >FitnessBrowser__SB2B:6937121 Length = 273 Score = 228 bits (580), Expect = 1e-64 Identities = 113/226 (50%), Positives = 154/226 (68%), Gaps = 23/226 (10%) Query: 6 LKEDIDTVFDQDPAARSYFEVILTYSGLHAIWAHRIAHALYKRKFYFLARLISQVSRFFT 65 LKEDI +++ +DPAARS E++L Y G+HAIW HRI+H L+KR + FLAR +S SR+ T Sbjct: 7 LKEDIASIYHRDPAARSAIEILLNYPGMHAIWLHRISHKLWKRDWRFLARCLSTFSRWLT 66 Query: 66 GIEIHPGATIGRRFFIDHGMGVVIGETCEIGNNVTVFQGVTLGGTGKEKGKRHPTIKDDA 125 G+EIHPGATIGRRFFIDHGMG+VIGET EIG++ T++ GVTLGGT GKRHPT++++ Sbjct: 67 GVEIHPGATIGRRFFIDHGMGIVIGETAEIGDDCTLYHGVTLGGTSWNAGKRHPTLENNV 126 Query: 126 LIATGAKVLGSITVGEGSKIGAGSVVLHDVPDFSTVVGIPGRVVVQNGKKVRRDLNHQ-- 183 ++ GAK+LG IT+ EGS++G+ SVV+ DVP+ +TVVGIPGR V Q + + + Sbjct: 127 VVGAGAKILGPITMKEGSRVGSNSVVVKDVPEHTTVVGIPGRAVAQPSSQSKETTERRSA 186 Query: 184 --------------DLPDPVA-------DRFKSLEQQILELKAELE 208 D PDPVA D ++ ++ +L EL+ Sbjct: 187 MAKKYGFDAYAVSPDNPDPVANAIGQMLDHMHLMDSKVQDLCQELQ 232 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: 6 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: 273 Length adjustment: 23 Effective length of query: 194 Effective length of database: 250 Effective search space: 48500 Effective search space used: 48500 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 6937121 Sama_1291 (Serine O-acetyltransferase (RefSeq))
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.22319.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-81 258.1 0.1 2.2e-81 257.7 0.1 1.1 1 lcl|FitnessBrowser__SB2B:6937121 Sama_1291 Serine O-acetyltransfe Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6937121 Sama_1291 Serine O-acetyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.7 0.1 2.2e-81 2.2e-81 2 162 .] 8 168 .. 7 168 .. 0.99 Alignments for each domain: == domain 1 score: 257.7 bits; conditional E-value: 2.2e-81 TIGR01172 2 kedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaakigrgvliDh 78 ked+ ++++rDPaa+sa+e+ll+y+g+ha++ +r++h+l+kr++++lar+ls+++r+ltgv+ihP+a+igr+++iDh lcl|FitnessBrowser__SB2B:6937121 8 KEDIASIYHRDPAARSAIEILLNYPGMHAIWLHRISHKLWKRDWRFLARCLSTFSRWLTGVEIHPGATIGRRFFIDH 84 79*************************************************************************** PP TIGR01172 79 atGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenakiGansvvlkdvpaeat 155 ++G+viGeta+igdd+++y+gvtLGgt+++ gkRhPt++++vv+gagak+LG+i++ e++++G+nsvv+kdvp+++t lcl|FitnessBrowser__SB2B:6937121 85 GMGIVIGETAEIGDDCTLYHGVTLGGTSWNAGKRHPTLENNVVVGAGAKILGPITMKEGSRVGSNSVVVKDVPEHTT 161 ***************************************************************************** PP TIGR01172 156 vvGvpar 162 vvG+p+r lcl|FitnessBrowser__SB2B:6937121 162 VVGIPGR 168 *****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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 11.32 // [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