Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate GFF1490 PS417_07580 3-ketoacyl-CoA thiolase
Query= BRENDA::P28790 (391 letters) >FitnessBrowser__WCS417:GFF1490 Length = 391 Score = 739 bits (1909), Expect = 0.0 Identities = 367/391 (93%), Positives = 380/391 (97%) Query: 1 MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERNSKVDPGEVEDVIWG 60 MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERN+KVDP EVEDVIWG Sbjct: 1 MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERNTKVDPNEVEDVIWG 60 Query: 61 CVNQTLEQGWNIARMASLMTQIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG 120 CVNQTLEQGWNIARMASLMTQIPHT+A QTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG Sbjct: 61 CVNQTLEQGWNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG 120 Query: 121 GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGISREQQDAFAVRSHQLA 180 GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGI+RE QDAF +RSHQLA Sbjct: 121 GVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGITREAQDAFGLRSHQLA 180 Query: 181 HKATVEGKFKDEIIPMQGYDENGFLKIFDYDETIRPDTTLESLAALKPAFNPKGGTVTAG 240 HKAT+EGKFKDEIIPM GYDENGFLK+ DYDETIRPDTTLESLAALKPAFNPKGGTVTAG Sbjct: 181 HKATLEGKFKDEIIPMNGYDENGFLKLCDYDETIRPDTTLESLAALKPAFNPKGGTVTAG 240 Query: 241 TSSQITDGASCMIVMSAQRAKDLGLEPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAG 300 TSSQITDGASCMIVMSAQRA+DLG++PLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAG Sbjct: 241 TSSQITDGASCMIVMSAQRAQDLGIQPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAG 300 Query: 301 LNMADIDFIELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL 360 L + DIDF ELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL Sbjct: 301 LTINDIDFFELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTL 360 Query: 361 LNVMKQNGGTFGLSTMCIGLGQGIATVFERV 391 LNVMKQNGG G++TMCIGLGQGI+TVFERV Sbjct: 361 LNVMKQNGGNLGVATMCIGLGQGISTVFERV 391 Lambda K H 0.318 0.133 0.386 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: 668 Number of extensions: 14 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: 391 Length of database: 391 Length adjustment: 31 Effective length of query: 360 Effective length of database: 360 Effective search space: 129600 Effective search space used: 129600 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate GFF1490 PS417_07580 (3-ketoacyl-CoA thiolase)
to HMM TIGR02445 (fadA: acetyl-CoA C-acyltransferase FadA (EC 2.3.1.16))
# 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.carbon/TIGR02445.hmm # target sequence database: /tmp/gapView.1076371.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02445 [M=385] Accession: TIGR02445 Description: fadA: acetyl-CoA C-acyltransferase FadA 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.3e-237 771.7 8.3 7.1e-237 771.5 8.3 1.0 1 FitnessBrowser__WCS417:GFF1490 Domain annotation for each sequence (and alignments): >> FitnessBrowser__WCS417:GFF1490 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 771.5 8.3 7.1e-237 7.1e-237 1 385 [] 7 391 .] 7 391 .] 1.00 Alignments for each domain: == domain 1 score: 771.5 bits; conditional E-value: 7.1e-237 TIGR02445 1 dvvivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfniarnaallaevphe 79 dvvivd++rtpmgrskgg++rntraed+sahl++k+l+rn+kv++ eved++wgcv+qtleqg+niar+a+l++++ph+ FitnessBrowser__WCS417:GFF1490 7 DVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKVLERNTKVDPNEVEDVIWGCVNQTLEQGWNIARMASLMTQIPHT 85 79***************************************************************************** PP TIGR02445 80 vaavtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdfhpglskhvakaagmmgltaemlgklhgi 158 a +tv+rlcgssm+alh+aa+aimtg+++v+++ggvehmghvsm+hgvd++p++s +aka+gmmgltaemlgk+hgi FitnessBrowser__WCS417:GFF1490 86 AAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHVSMMHGVDPNPHMSLYAAKASGMMGLTAEMLGKMHGI 164 ******************************************************************************* PP TIGR02445 159 sreqqdafaarsharahaatlegkfkneiiptegydadgvlkvldydevirpettvealaalrpafdpkngtvtagtss 237 +re qdaf++rsh++ah+atlegkfk+eiip++gyd++g+lk dyde+irp+tt+e+laal+paf+pk+gtvtagtss FitnessBrowser__WCS417:GFF1490 165 TREAQDAFGLRSHQLAHKATLEGKFKDEIIPMNGYDENGFLKLCDYDETIRPDTTLESLAALKPAFNPKGGTVTAGTSS 243 ******************************************************************************* PP TIGR02445 238 alsdgasamlvmseeraqelgvkprarirsmavagvdpsimgygpvpatkkalkraglsisdidvlelneafaaqalpv 316 +++dgas+m+vms++raq+lg++p+a+irsmavagvdp+imgygpvpat+kalkragl+i+did++elneafaaqalpv FitnessBrowser__WCS417:GFF1490 244 QITDGASCMIVMSAQRAQDLGIQPLAVIRSMAVAGVDPAIMGYGPVPATQKALKRAGLTINDIDFFELNEAFAAQALPV 322 ******************************************************************************* PP TIGR02445 317 lkdlglldkldekvnlnggaialghplgcsgaristtllnlmerkdakfglatmciglgqgiatvferv 385 lkdl++ldk++ekvnl+ggaialghp+gcsgaris+tlln+m++++++ g+atmciglgqgi+tvferv FitnessBrowser__WCS417:GFF1490 323 LKDLKVLDKMNEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNGGNLGVATMCIGLGQGISTVFERV 391 ********************************************************************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (391 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 24.98 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
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