Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate H281DRAFT_00541 H281DRAFT_00541 serine O-acetyltransferase (EC 2.3.1.30)
Query= BRENDA::P95231 (229 letters) >FitnessBrowser__Burk376:H281DRAFT_00541 Length = 318 Score = 204 bits (518), Expect = 2e-57 Identities = 101/169 (59%), Positives = 122/169 (72%), Gaps = 1/169 (0%) Query: 1 MLTAMRGDIRAARERDPAAPTALEVIFCYPGVHAVWGHRLAHWLWQRGARLLARAAAEFT 60 M T +R DI RERDPAA +A EV+ CYPG+HA+ HRLAH WQ R LAR ++ Sbjct: 1 MFTRLREDIATIRERDPAARSAWEVLTCYPGLHALVLHRLAHACWQARRRWLARFVSQMA 60 Query: 61 RILTGVDIHPGAVIGARVFIDHATGVVIGETAEVGDDVTIYHGVTLGGSGMV-GGKRHPT 119 R +TG++IHPGA +G RVFIDH GVVIGETA++GDD TIY GVTLGG+ + G KRHPT Sbjct: 61 RFMTGIEIHPGATVGRRVFIDHGMGVVIGETAQIGDDCTIYQGVTLGGTSLTRGAKRHPT 120 Query: 120 VGDRVIIGAGAKVLGPIKIGEDSRIGANAVVVKPVPPSAVVVGVPGQVI 168 + VI+GAGAKVLG IG D++IG+NAVV KPVP VG P +VI Sbjct: 121 LERGVIVGAGAKVLGGFTIGADAKIGSNAVVTKPVPAGGTAVGNPARVI 169 Lambda K H 0.321 0.141 0.443 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: 238 Number of extensions: 13 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: 229 Length of database: 318 Length adjustment: 25 Effective length of query: 204 Effective length of database: 293 Effective search space: 59772 Effective search space used: 59772 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 H281DRAFT_00541 H281DRAFT_00541 (serine O-acetyltransferase (EC 2.3.1.30))
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.31327.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-76 242.2 0.5 2e-76 241.6 0.5 1.3 1 lcl|FitnessBrowser__Burk376:H281DRAFT_00541 H281DRAFT_00541 serine O-acetylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_00541 H281DRAFT_00541 serine O-acetyltransferase (EC 2.3.1.30) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 241.6 0.5 2e-76 2e-76 2 162 .] 6 167 .. 5 167 .. 0.99 Alignments for each domain: == domain 1 score: 241.6 bits; conditional E-value: 2e-76 TIGR01172 2 kedlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPa 67 +ed+ +++erDPaa+sa+evl +y+glhal+ +rlaha ++ ++++lar++s+++r++tg++ihP+ lcl|FitnessBrowser__Burk376:H281DRAFT_00541 6 REDIATIRERDPAARSAWEVLTCYPGLHALVLHRLAHACWQARRRWLARFVSQMARFMTGIEIHPG 71 79**************************************************************** PP TIGR01172 68 akigrgvliDhatGvviGetavigddvsiyqgvtLGgtgkekg.kRhPtvkegvvigagakvLGni 132 a++gr+v+iDh++GvviGeta+igdd++iyqgvtLGgt+ ++g kRhPt++ gv++gagakvLG + lcl|FitnessBrowser__Burk376:H281DRAFT_00541 72 ATVGRRVFIDHGMGVVIGETAQIGDDCTIYQGVTLGGTSLTRGaKRHPTLERGVIVGAGAKVLGGF 137 ******************************************99********************** PP TIGR01172 133 evgenakiGansvvlkdvpaeatvvGvpar 162 ++g++akiG+n+vv+k+vpa+ t+vG par lcl|FitnessBrowser__Burk376:H281DRAFT_00541 138 TIGADAKIGSNAVVTKPVPAGGTAVGNPAR 167 ****************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (162 nodes) Target sequences: 1 (318 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: 12.71 // [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