Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate GFF1234 Psest_1267 serine O-acetyltransferase
Query= BRENDA::Q0ZB96 (273 letters) >FitnessBrowser__psRCH2:GFF1234 Length = 264 Score = 272 bits (696), Expect = 5e-78 Identities = 135/262 (51%), Positives = 178/262 (67%) Query: 1 MPCEELDIVWNNIKAEARALADCEPMLASFYHATLLKHENLGSALSYMLANKLASPIMPA 60 MP + +WN+++ +A+ D EP LA+ + +L + G AL+Y + + LA + Sbjct: 1 MPSHSVSALWNDLRNQAQHALDTEPTLATVFRQAILDRPDFGCALAYRIGHALAENADQS 60 Query: 61 IAIREVVEEAYAADPEMIASAACDIQAVRTRDPAVDKYSTPLLYLKGFHALQAYRIGHWL 120 + + + P + +A D+QA+ +RDPA D L+ KGF ALQAYR+GH L Sbjct: 61 HTLADRFAGIHHHAPRLAEAACSDLQAIVSRDPAFDTALEVFLFSKGFLALQAYRVGHDL 120 Query: 121 WTQGRRALAIFLQNQVSVSFQVDIHPAAKIGRGIMLDHATGIVVGETAVIEDDVSILQSV 180 +G R LA+F+Q + + +DI+PA++IG GIMLDH TGIV+GETAV+ DDVSILQ V Sbjct: 121 QARGERLLAMFIQARCNERLGIDINPASRIGNGIMLDHGTGIVIGETAVVGDDVSILQGV 180 Query: 181 TLGGTGKTSGDRHPKIREGVMIGAGAKILGNIEVGRGAKIGAGSVVLQPVPPHTTAAGVP 240 TLGGTGK GDRHPK+R GVMIGAGAKILGNIE+G GAK+GAGS+VL PV PHTT G P Sbjct: 181 TLGGTGKEGGDRHPKVRSGVMIGAGAKILGNIEIGEGAKVGAGSIVLHPVAPHTTVVGNP 240 Query: 241 ARIVGKPESDKPAMDMDQHFNG 262 AR VG P +PA+DMDQ F+G Sbjct: 241 ARQVGTPRHARPALDMDQSFDG 262 Lambda K H 0.319 0.136 0.405 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: 320 Number of extensions: 12 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: 273 Length of database: 264 Length adjustment: 25 Effective length of query: 248 Effective length of database: 239 Effective search space: 59272 Effective search space used: 59272 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 (21.8 bits) S2: 47 (22.7 bits)
Align candidate GFF1234 Psest_1267 (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.27750.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-69 219.6 2.2 1.9e-69 218.9 1.2 1.7 2 lcl|FitnessBrowser__psRCH2:GFF1234 Psest_1267 serine O-acetyltransf Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF1234 Psest_1267 serine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? -0.8 0.0 0.075 0.075 6 44 .. 18 57 .. 13 71 .. 0.71 2 ! 218.9 1.2 1.9e-69 1.9e-69 3 162 .] 83 242 .. 81 242 .. 0.99 Alignments for each domain: == domain 1 score: -0.8 bits; conditional E-value: 0.075 TIGR01172 6 kavlerDPaaesal.evlllykglhallayrlahalykrk 44 +++l+ +P +++ + +l + + layr+ hal ++ lcl|FitnessBrowser__psRCH2:GFF1234 18 QHALDTEPTLATVFrQAILDRPDFGCALAYRIGHALAENA 57 55666677766655256778889999999***99997654 PP == domain 2 score: 218.9 bits; conditional E-value: 1.9e-69 TIGR01172 3 edlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaakigrgvliD 77 +dl+a+++rDPa+++alev+l+ kg+ al+ayr+ h l r+ +lla++++ + + g+di Pa++ig+g+++D lcl|FitnessBrowser__psRCH2:GFF1234 83 SDLQAIVSRDPAFDTALEVFLFSKGFLALQAYRVGHDLQARGERLLAMFIQARCNERLGIDINPASRIGNGIMLD 157 69************************************************************************* PP TIGR01172 78 hatGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenakiGansvvlkdvpa 152 h+tG+viGetav+gddvsi+qgvtLGgtgke g+RhP+v+ gv+igagak+LGnie+ge+ak+Ga+s+vl++v++ lcl|FitnessBrowser__psRCH2:GFF1234 158 HGTGIVIGETAVVGDDVSILQGVTLGGTGKEGGDRHPKVRSGVMIGAGAKILGNIEIGEGAKVGAGSIVLHPVAP 232 *************************************************************************** PP TIGR01172 153 eatvvGvpar 162 ++tvvG par lcl|FitnessBrowser__psRCH2:GFF1234 233 HTTVVGNPAR 242 ********97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (162 nodes) Target sequences: 1 (264 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: 9.90 // [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