Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate GFF1745 PGA1_c17690 serine acetyltransferase CysE
Query= BRENDA::C4IRW0 (281 letters) >FitnessBrowser__Phaeo:GFF1745 Length = 271 Score = 297 bits (761), Expect = 1e-85 Identities = 142/261 (54%), Positives = 189/261 (72%) Query: 20 LDQVDPIWHSIRAEAEEATRNDPVLGAFLYATILNQPSLEEAVMHRIAERLGHPDVSADI 79 + VDP+W I EA++A R P++G ++A IL+ SLE+A+ +RIA +L ++S I Sbjct: 8 VSSVDPVWDQITTEAQDAVRRQPLMGGLIHACILHHTSLEKALSYRIAAKLCSNEMSMVI 67 Query: 80 LRQTFDTMLEANPEWSHVLRVDIQAVYDRDPAYSRFMDPVLYLKGFHAIQTHRLAHWLYK 139 LR+ D NP+ R D+ AVY+RDPA R + P+LY KG+ A+Q +R+AHWL++ Sbjct: 68 LREIVDKAYGENPDLIAAGRADLMAVYERDPACHRLLQPILYFKGYQAVQAYRVAHWLWQ 127 Query: 140 QGRKDFAYYLQSRSSSIFQTDIHPAARLGSGLFLDHATGLVVGETAVVEDNVSILHGVTL 199 +G D +Y+ Q R S IF DIHPAA++G G+ +DHA +V+GETAVV DNVS+LH VTL Sbjct: 128 KGDYDLSYFFQMRISEIFGVDIHPAAKIGRGIMIDHAHSIVIGETAVVGDNVSMLHSVTL 187 Query: 200 GGTGKSSGDRHPKIRQGVLIGAGAKILGNIQVGQCSKIAAGSVVLKSVPHNVTVAGVPAR 259 GGTGK DRHPKI GVLIGAGAK+LGNI+VG CS+IAAGSVVL+ +P TVAGVPA+ Sbjct: 188 GGTGKEEEDRHPKIGDGVLIGAGAKVLGNIKVGHCSRIAAGSVVLQEIPPCKTVAGVPAK 247 Query: 260 IIGETGCTEPSRVMDQMLGDG 280 I+GE GC +PS M+Q+LG G Sbjct: 248 IVGEAGCDQPSVSMNQVLGGG 268 Lambda K H 0.320 0.135 0.403 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: 282 Number of extensions: 10 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: 281 Length of database: 271 Length adjustment: 25 Effective length of query: 256 Effective length of database: 246 Effective search space: 62976 Effective search space used: 62976 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 GFF1745 PGA1_c17690 (serine acetyltransferase CysE)
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.24028.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-72 229.3 1.1 4.4e-72 227.5 0.5 1.8 2 lcl|FitnessBrowser__Phaeo:GFF1745 PGA1_c17690 serine acetyltransfe Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF1745 PGA1_c17690 serine acetyltransferase CysE # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ? 0.2 0.0 0.037 0.037 7 47 .. 24 65 .. 18 74 .. 0.73 2 ! 227.5 0.5 4.4e-72 4.4e-72 3 162 .] 88 247 .. 86 247 .. 0.99 Alignments for each domain: == domain 1 score: 0.2 bits; conditional E-value: 0.037 TIGR01172 7 avlerDPaaesal.evlllykglhallayrlahalykrklkl 47 +++r P + + +l +++l l+yr+a++l ++++ + lcl|FitnessBrowser__Phaeo:GFF1745 24 DAVRRQPLMGGLIhACILHHTSLEKALSYRIAAKLCSNEMSM 65 5566777666554156788899999999***99998887765 PP == domain 2 score: 227.5 bits; conditional E-value: 4.4e-72 TIGR01172 3 edlkavlerDPaaesalevlllykglhallayrlahalykrklkllarllselvrvltgvdihPaakigrgvliDh 78 +dl av+erDPa+++ l+++l++kg++a++ayr+ah+l++++ + l+++++ +++ ++gvdihPaakigrg++iDh lcl|FitnessBrowser__Phaeo:GFF1745 88 ADLMAVYERDPACHRLLQPILYFKGYQAVQAYRVAHWLWQKGDYDLSYFFQMRISEIFGVDIHPAAKIGRGIMIDH 163 799************************************************************************* PP TIGR01172 79 atGvviGetavigddvsiyqgvtLGgtgkekgkRhPtvkegvvigagakvLGnievgenakiGansvvlkdvpaea 154 a+ +viGetav+gd+vs++++vtLGgtgke+ +RhP++++gv+igagakvLGni+vg+ ++i a+svvl+++p+ lcl|FitnessBrowser__Phaeo:GFF1745 164 AHSIVIGETAVVGDNVSMLHSVTLGGTGKEEEDRHPKIGDGVLIGAGAKVLGNIKVGHCSRIAAGSVVLQEIPPCK 239 **************************************************************************** PP TIGR01172 155 tvvGvpar 162 tv+Gvpa+ lcl|FitnessBrowser__Phaeo:GFF1745 240 TVAGVPAK 247 ******97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (162 nodes) Target sequences: 1 (271 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: 7.47 // [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