Align Serine acetyltransferase; SAT; EC 2.3.1.30 (characterized)
to candidate AZOBR_RS05825 AZOBR_RS05825 serine O-acetyltransferase
Query= SwissProt::Q06750 (217 letters) >FitnessBrowser__azobra:AZOBR_RS05825 Length = 276 Score = 212 bits (540), Expect = 5e-60 Identities = 107/212 (50%), Positives = 145/212 (68%), Gaps = 5/212 (2%) Query: 3 FRMLKEDIDTVFDQDPAARSYFEVILTYSGLHAIWAHRIAHALYKRKFYFLARLISQVSR 62 F+ L+E+ID + +DPAARS EV L Y G HAI HR+A + R+++ +AR +SQ++R Sbjct: 21 FKHLREEIDGIMARDPAARSRAEVALCYPGFHAIVLHRVARYCWDRRWHLMARAVSQIAR 80 Query: 63 FFTGIEIHPGATIGRRFFIDHGMGVVIGETCEIGNNVTVFQGVTLGGTGKEKGKRHPTIK 122 TGIEIHPGATIGRRFFIDHGMGVVIGET EIG++V ++ GVTLGGT +GKRHPT++ Sbjct: 81 ALTGIEIHPGATIGRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGTSLNQGKRHPTLE 140 Query: 123 DDALIATGAKVLGSITVGEGSKIGAGSVVLHDVPDFSTVVGIPGRVV-----VQNGKKVR 177 ++ GAKVLG+IT+G G+++GA +VV+ DV VVGIP + V V+ K + Sbjct: 141 SGVIVGAGAKVLGAITIGRGARVGANAVVVADVAPGIAVVGIPAKAVVTRDRVETQKFMP 200 Query: 178 RDLNHQDLPDPVADRFKSLEQQILELKAELED 209 D+PDPVA L Q+ L+ +E+ Sbjct: 201 YGTPCGDIPDPVARALNGLLDQVSTLRRRVEE 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: 217 Number of extensions: 7 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: 276 Length adjustment: 24 Effective length of query: 193 Effective length of database: 252 Effective search space: 48636 Effective search space used: 48636 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 AZOBR_RS05825 AZOBR_RS05825 (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.14016.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-75 239.3 3.8 1.3e-75 239.0 3.8 1.1 1 lcl|FitnessBrowser__azobra:AZOBR_RS05825 AZOBR_RS05825 serine O-acetyltra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS05825 AZOBR_RS05825 serine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 239.0 3.8 1.3e-75 1.3e-75 2 162 .] 25 185 .. 24 185 .. 0.99 Alignments for each domain: == domain 1 score: 239.0 bits; conditional E-value: 1.3e-75 TIGR01172 2 kedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaaki 70 +e+++ +++rDPaa+s+ ev l+y+g+ha++ +r+a + + r+++l+ar++s+++r ltg++ihP+a+i lcl|FitnessBrowser__azobra:AZOBR_RS05825 25 REEIDGIMARDPAARSRAEVALCYPGFHAIVLHRVARYCWDRRWHLMARAVSQIARALTGIEIHPGATI 93 689999*************************************************************** PP TIGR01172 71 grgvliDhatGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenak 139 gr+++iDh++GvviGeta+igddv++y+gvtLGgt+ ++gkRhPt++ gv++gagakvLG+i++g +a+ lcl|FitnessBrowser__azobra:AZOBR_RS05825 94 GRRFFIDHGMGVVIGETAEIGDDVMLYHGVTLGGTSLNQGKRHPTLESGVIVGAGAKVLGAITIGRGAR 162 ********************************************************************* PP TIGR01172 140 iGansvvlkdvpaeatvvGvpar 162 +Gan+vv+ dv+++++vvG+pa+ lcl|FitnessBrowser__azobra:AZOBR_RS05825 163 VGANAVVVADVAPGIAVVGIPAK 185 *********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (162 nodes) Target sequences: 1 (276 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.90 // [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