Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate PP_3279 PP_3279 phenylacetate-CoA ligase
Query= SwissProt::O33469 (439 letters) >FitnessBrowser__Putida:PP_3279 Length = 439 Score = 872 bits (2252), Expect = 0.0 Identities = 426/439 (97%), Positives = 433/439 (98%) Query: 1 MNMYHDADRALLDPMETASVDALRQHQLERLRWSLKHAYDNVPLYRQRFAECGAHPDDLT 60 MNMYHDADRALLDPMETASVDALRQHQLERLRWSLKHAYDNVPLYRQRFAE G HPDDL Sbjct: 1 MNMYHDADRALLDPMETASVDALRQHQLERLRWSLKHAYDNVPLYRQRFAEYGIHPDDLK 60 Query: 61 CLEDLAKFPFTGKNDLRDNYPYGMFAVPQEEVVRLHASSGTTGKPTVVGYTQNDINTWAN 120 CLEDLAKFPFTGKNDLRDNYPYGMFAVPQEEVVRLHASSGTTGKPTVVGYTQNDI+TWAN Sbjct: 61 CLEDLAKFPFTGKNDLRDNYPYGMFAVPQEEVVRLHASSGTTGKPTVVGYTQNDIDTWAN 120 Query: 121 VVARSIRAAGGRKGDKVHVSYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIRD 180 VVARSIRAAGGRKGDKVHVSYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIRD Sbjct: 121 VVARSIRAAGGRKGDKVHVSYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIRD 180 Query: 181 FQPDIIMVTPSYMLNLADEIERQGIDPHDLKLRLGIFGAEPWTDELRRSIEQRLGINALD 240 F PDIIMVTPSYMLNLADEIERQGIDPHDLKLRLGIFGAEPWTDELRRSIEQR+GINALD Sbjct: 181 FHPDIIMVTPSYMLNLADEIERQGIDPHDLKLRLGIFGAEPWTDELRRSIEQRMGINALD 240 Query: 241 IYGLSEIMGPGVAMECIETKDGPTIWEDHFYPEIIDPVTGEVLPDGQLGELVFTSLSKEA 300 IYGLSEIMGPGVAMECIETKDGPTIWEDHFYPEIIDP TGEVLPDGQLGELVFTSLSKEA Sbjct: 241 IYGLSEIMGPGVAMECIETKDGPTIWEDHFYPEIIDPATGEVLPDGQLGELVFTSLSKEA 300 Query: 301 LPMVRYRTRDLTRLLPGTARPMRRIGKITGRSDDMLIIRGVNVFPTQIEEQVLKIKQLSE 360 LPMVRYRTRDLTRLLPGTARPMRRIGKITGRSDDMLIIRGVNVFPTQIEEQVLKIKQLSE Sbjct: 301 LPMVRYRTRDLTRLLPGTARPMRRIGKITGRSDDMLIIRGVNVFPTQIEEQVLKIKQLSE 360 Query: 361 MYEIHLYRNGNLDSVEVHVELRAECQHLDEGQRKLVIGELSKQIKTYIGISTQVHLQACG 420 +YEIHLYRNGNLDSV+VHVELRAECQHLDEGQRKLV+GELSKQIKTYIGISTQVHLQ CG Sbjct: 361 LYEIHLYRNGNLDSVQVHVELRAECQHLDEGQRKLVVGELSKQIKTYIGISTQVHLQPCG 420 Query: 421 TLKRSEGKACHVYDKRLAS 439 TLKRSEGKACHV+D+RLAS Sbjct: 421 TLKRSEGKACHVFDRRLAS 439 Lambda K H 0.320 0.138 0.415 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: 911 Number of extensions: 22 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: 439 Length of database: 439 Length adjustment: 32 Effective length of query: 407 Effective length of database: 407 Effective search space: 165649 Effective search space used: 165649 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: 51 (24.3 bits)
Align candidate PP_3279 PP_3279 (phenylacetate-CoA ligase)
to HMM TIGR02155 (paaF: phenylacetate-CoA ligase (EC 6.2.1.30))
# 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.carbon/TIGR02155.hmm # target sequence database: /tmp/gapView.21153.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02155 [M=422] Accession: TIGR02155 Description: PA_CoA_ligase: phenylacetate-CoA ligase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-223 725.6 0.0 8.1e-223 725.4 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_3279 PP_3279 phenylacetate-CoA ligase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_3279 PP_3279 phenylacetate-CoA ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 725.4 0.0 8.1e-223 8.1e-223 1 422 [] 16 436 .. 16 436 .. 0.99 Alignments for each domain: == domain 1 score: 725.4 bits; conditional E-value: 8.1e-223 TIGR02155 1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdllavpre 75 e++s+d lr+ qlerl++s+k+ay+nvp yr++f + g++pddlk l+dlakfp+t k+dlrdnyp++++avp+e lcl|FitnessBrowser__Putida:PP_3279 16 ETASVDALRQHQLERLRWSLKHAYDNVPLYRQRFAEYGIHPDDLKCLEDLAKFPFTGKNDLRDNYPYGMFAVPQE 90 799************************************************************************ PP TIGR02155 76 kvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyGaeklGatvvp 150 +vvr+hassGttGkptvv+ytq+d+dtw++vvars+raaGGrkgd++h++yGyGlftGGlG+hyGae+lG+tv+p lcl|FitnessBrowser__Putida:PP_3279 91 EVVRLHASSGTTGKPTVVGYTQNDIDTWANVVARSIRAAGGRKGDKVHVSYGYGLFTGGLGAHYGAERLGCTVIP 165 *************************************************************************** PP TIGR02155 151 isGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepwteamrkelearlgikald 225 +sGGqtekqvqli+df+pdii+vtpsy+l+l++e++r+gidp+d l+++i+Gaepwt+++r+ +e+r+gi+ald lcl|FitnessBrowser__Putida:PP_3279 166 MSGGQTEKQVQLIRDFHPDIIMVTPSYMLNLADEIERQGIDPHDLKLRLGIFGAEPWTDELRRSIEQRMGINALD 240 *************************************************************************** PP TIGR02155 226 iyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGelvfttltkealpviryrtrdltrll 300 iyGlse++GpGva+ec+etkdG++iwedhfypeiidp tgevlpdG+ Gelvft+l+kealp++ryrtrdltrll lcl|FitnessBrowser__Putida:PP_3279 241 IYGLSEIMGPGVAMECIETKDGPTIWEDHFYPEIIDPATGEVLPDGQLGELVFTSLSKEALPMVRYRTRDLTRLL 315 *************************************************************************** PP TIGR02155 301 pgtartmrrmdkikGrsddllilrGvnvfptqleevllkldklsphyqleltreGaldeltlkvelkdesaalrl 375 pgtar+mrr+ ki+Grsdd+li+rGvnvfptq+ee +lk+++ls y+++l r+G+ld++ ++vel+ e ++l+ lcl|FitnessBrowser__Putida:PP_3279 316 PGTARPMRRIGKITGRSDDMLIIRGVNVFPTQIEEQVLKIKQLSELYEIHLYRNGNLDSVQVHVELRAECQHLD- 389 ***********************************************************************999. PP TIGR02155 376 leqksllakkiekkikaevgvsvdvelvepgslerseGkakrvvdkr 422 + q++l+ +++k+ik+ +g+s++v+l+ +g+l+rseGka+ v+d+r lcl|FitnessBrowser__Putida:PP_3279 390 EGQRKLVVGELSKQIKTYIGISTQVHLQPCGTLKRSEGKACHVFDRR 436 667779***************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (422 nodes) Target sequences: 1 (439 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: 00:00:00.02 # Mc/sec: 7.58 // [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