Align Serine acetyltransferase; SAT; EC 2.3.1.30 (characterized)
to candidate 201412 SO2262 serine acetyltransferase (NCBI ptt file)
Query= SwissProt::Q06750 (217 letters) >FitnessBrowser__MR1:201412 Length = 273 Score = 218 bits (555), Expect = 9e-62 Identities = 108/202 (53%), Positives = 145/202 (71%), Gaps = 16/202 (7%) Query: 6 LKEDIDTVFDQDPAARSYFEVILTYSGLHAIWAHRIAHALYKRKFYFLARLISQVSRFFT 65 LKEDI++++ +DPAARS FE+++ Y G+HAIW HRI+H L+KR + +AR +S SR+ T Sbjct: 7 LKEDIESIYHRDPAARSAFEILVNYPGMHAIWLHRISHKLWKRDWRLMARCLSTFSRWLT 66 Query: 66 GIEIHPGATIGRRFFIDHGMGVVIGETCEIGNNVTVFQGVTLGGTGKEKGKRHPTIKDDA 125 G+EIHPGATIG RFFIDHGMGVVIGET EIG++ T++ GVTLGGT + GKRHPT+ ++ Sbjct: 67 GVEIHPGATIGNRFFIDHGMGVVIGETAEIGDDCTLYHGVTLGGTTWQAGKRHPTLGNNV 126 Query: 126 LIATGAKVLGSITVGEGSKIGAGSVVLHDVPDFSTVVGIPGRVVV-----QNGKKVRRDL 180 ++ GAK+LG IT+ +G+++G+ SVV+ DVP +TVVGIPGRVV K RR Sbjct: 127 VVGAGAKILGPITMHDGARVGSNSVVVKDVPKDTTVVGIPGRVVATPSPQSKEKSERRSA 186 Query: 181 NHQ-----------DLPDPVAD 191 + D PDPVA+ Sbjct: 187 MAKKYGFDAYAVSPDNPDPVAN 208 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: 237 Number of extensions: 8 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 201412 SO2262 (serine acetyltransferase (NCBI ptt file))
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.7397.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-81 257.7 0.2 2.8e-81 257.4 0.2 1.1 1 lcl|FitnessBrowser__MR1:201412 SO2262 serine acetyltransferase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:201412 SO2262 serine acetyltransferase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.4 0.2 2.8e-81 2.8e-81 2 162 .] 8 168 .. 7 168 .. 0.99 Alignments for each domain: == domain 1 score: 257.4 bits; conditional E-value: 2.8e-81 TIGR01172 2 kedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaakigrgvliDhat 80 ked++++++rDPaa+sa+e+l++y+g+ha++ +r++h+l+kr+++l+ar+ls+++r+ltgv+ihP+a+ig++++iDh++ lcl|FitnessBrowser__MR1:201412 8 KEDIESIYHRDPAARSAFEILVNYPGMHAIWLHRISHKLWKRDWRLMARCLSTFSRWLTGVEIHPGATIGNRFFIDHGM 86 89***************************************************************************** PP TIGR01172 81 GvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenakiGansvvlkdvpaeatvvGv 159 GvviGeta+igdd+++y+gvtLGgt+++ gkRhPt++++vv+gagak+LG+i+++++a++G+nsvv+kdvp+++tvvG+ lcl|FitnessBrowser__MR1:201412 87 GVVIGETAEIGDDCTLYHGVTLGGTTWQAGKRHPTLGNNVVVGAGAKILGPITMHDGARVGSNSVVVKDVPKDTTVVGI 165 ******************************************************************************* PP TIGR01172 160 par 162 p+r lcl|FitnessBrowser__MR1:201412 166 PGR 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: 9.26 // [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