Align FadA (EC 2.3.1.16) (characterized)
to candidate PP_2137 PP_2137 beta-ketoadipyl CoA thiolase, beta component
Query= metacyc::G1G01-2278-MONOMER (391 letters) >FitnessBrowser__Putida:PP_2137 Length = 391 Score = 780 bits (2014), Expect = 0.0 Identities = 391/391 (100%), Positives = 391/391 (100%) Query: 1 MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNGKVDPKEVEDVIWG 60 MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNGKVDPKEVEDVIWG Sbjct: 1 MSLNPRDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNGKVDPKEVEDVIWG 60 Query: 61 CVNQTLEQGWNIARMASLMTPIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG 120 CVNQTLEQGWNIARMASLMTPIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG Sbjct: 61 CVNQTLEQGWNIARMASLMTPIPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVG 120 Query: 121 GVEHMGHVSMMHGVDPNPHLSLHAAKASGMMGLTAEMLGKMHGITREQQDLFGLRSHQLA 180 GVEHMGHVSMMHGVDPNPHLSLHAAKASGMMGLTAEMLGKMHGITREQQDLFGLRSHQLA Sbjct: 121 GVEHMGHVSMMHGVDPNPHLSLHAAKASGMMGLTAEMLGKMHGITREQQDLFGLRSHQLA 180 Query: 181 HKATVEGKFKDEIIPMQGYDENGFLKVFDFDETIRPETTLEGLASLKPAFNPKGGTVTAG 240 HKATVEGKFKDEIIPMQGYDENGFLKVFDFDETIRPETTLEGLASLKPAFNPKGGTVTAG Sbjct: 181 HKATVEGKFKDEIIPMQGYDENGFLKVFDFDETIRPETTLEGLASLKPAFNPKGGTVTAG 240 Query: 241 TSSQITDGASCMIVMSGQRAMDLGIQPLAVIRSMAVAGVDPAIMGYGPVPSTQKALKRAG 300 TSSQITDGASCMIVMSGQRAMDLGIQPLAVIRSMAVAGVDPAIMGYGPVPSTQKALKRAG Sbjct: 241 TSSQITDGASCMIVMSGQRAMDLGIQPLAVIRSMAVAGVDPAIMGYGPVPSTQKALKRAG 300 Query: 301 LTMADIDFIELNEAFAAQALPVLKDLKVLDKMDEKVNLHGGAIALGHPFGCSGARISGTL 360 LTMADIDFIELNEAFAAQALPVLKDLKVLDKMDEKVNLHGGAIALGHPFGCSGARISGTL Sbjct: 301 LTMADIDFIELNEAFAAQALPVLKDLKVLDKMDEKVNLHGGAIALGHPFGCSGARISGTL 360 Query: 361 LNVMKQNGGTLGVATMCVGLGQGITTVFERV 391 LNVMKQNGGTLGVATMCVGLGQGITTVFERV Sbjct: 361 LNVMKQNGGTLGVATMCVGLGQGITTVFERV 391 Lambda K H 0.319 0.134 0.392 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: 716 Number of extensions: 17 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 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate PP_2137 PP_2137 (beta-ketoadipyl CoA thiolase, beta component)
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.28667.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-235 766.7 8.1 2.4e-235 766.5 8.1 1.0 1 lcl|FitnessBrowser__Putida:PP_2137 PP_2137 beta-ketoadipyl CoA thio Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_2137 PP_2137 beta-ketoadipyl CoA thiolase, beta component # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 766.5 8.1 2.4e-235 2.4e-235 1 385 [] 7 391 .] 7 391 .] 1.00 Alignments for each domain: == domain 1 score: 766.5 bits; conditional E-value: 2.4e-235 TIGR02445 1 dvvivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfniarnaallae 75 dvvivd++rtpmgrskgg++rntraed+sahl++kll+rn kv++ eved++wgcv+qtleqg+niar+a+l++ lcl|FitnessBrowser__Putida:PP_2137 7 DVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNGKVDPKEVEDVIWGCVNQTLEQGWNIARMASLMTP 81 79************************************************************************* PP TIGR02445 76 vphevaavtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdfhpglskhvakaagmmgltae 150 +ph++aa+tv+rlcgssm+alh+aa+aimtg+++v+++ggvehmghvsm+hgvd++p+ls h+aka+gmmgltae lcl|FitnessBrowser__Putida:PP_2137 82 IPHTSAAQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHVSMMHGVDPNPHLSLHAAKASGMMGLTAE 156 *************************************************************************** PP TIGR02445 151 mlgklhgisreqqdafaarsharahaatlegkfkneiiptegydadgvlkvldydevirpettvealaalrpafd 225 mlgk+hgi+reqqd f++rsh++ah+at+egkfk+eiip++gyd++g+lkv+d+de+irpett+e+la+l+paf+ lcl|FitnessBrowser__Putida:PP_2137 157 MLGKMHGITREQQDLFGLRSHQLAHKATVEGKFKDEIIPMQGYDENGFLKVFDFDETIRPETTLEGLASLKPAFN 231 *************************************************************************** PP TIGR02445 226 pkngtvtagtssalsdgasamlvmseeraqelgvkprarirsmavagvdpsimgygpvpatkkalkraglsisdi 300 pk+gtvtagtss+++dgas+m+vms +ra +lg++p+a+irsmavagvdp+imgygpvp+t+kalkragl++ di lcl|FitnessBrowser__Putida:PP_2137 232 PKGGTVTAGTSSQITDGASCMIVMSGQRAMDLGIQPLAVIRSMAVAGVDPAIMGYGPVPSTQKALKRAGLTMADI 306 *************************************************************************** PP TIGR02445 301 dvlelneafaaqalpvlkdlglldkldekvnlnggaialghplgcsgaristtllnlmerkdakfglatmciglg 375 d++elneafaaqalpvlkdl++ldk+dekvnl+ggaialghp+gcsgaris+tlln+m++++++ g+atmc+glg lcl|FitnessBrowser__Putida:PP_2137 307 DFIELNEAFAAQALPVLKDLKVLDKMDEKVNLHGGAIALGHPFGCSGARISGTLLNVMKQNGGTLGVATMCVGLG 381 *************************************************************************** PP TIGR02445 376 qgiatvferv 385 qgi+tvferv lcl|FitnessBrowser__Putida:PP_2137 382 QGITTVFERV 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.53 // [ok]
This GapMind analysis is from Sep 17 2021. 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