Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_011764038.1 AZO_RS01535 phenylacetate--CoA ligase
Query= SwissProt::Q9L9C1 (440 letters) >NCBI__GCF_000061505.1:WP_011764038.1 Length = 440 Score = 787 bits (2032), Expect = 0.0 Identities = 383/440 (87%), Positives = 410/440 (93%) Query: 1 MPVKTPSPGDLEPIEKASQDELRALQLERLKWSVRHAYENVPHYRKAFDAKGVHPDDLKS 60 MP+ + +P LEPIE AS DELRALQLERLKWSVRHAYENVPHYRK FD KGVHPDDLKS Sbjct: 1 MPINSYAPPQLEPIETASIDELRALQLERLKWSVRHAYENVPHYRKKFDEKGVHPDDLKS 60 Query: 61 LADLAKFPFTAKGDLRDNYPFGMFAVPREKVARVHASSGTTGKPTVVGYTLKDIDTWATV 120 LADLAKFPFT+K DLRDNYPFGMFAVP +++ARVHASSGTTGKPTVVGYTLKDIDTWATV Sbjct: 61 LADLAKFPFTSKYDLRDNYPFGMFAVPMDRIARVHASSGTTGKPTVVGYTLKDIDTWATV 120 Query: 121 VARSIRASGGRAGDMVHIAYGYGLFTGGLGAHYGAEKLGCTVVPMSGGQTEKQIQLIQDF 180 VARSIRA+GGR GDMVH++YGYGLFTGGLGAHYGAEKLGCTVVPMSGGQTEKQIQ+IQDF Sbjct: 121 VARSIRAAGGRPGDMVHVSYGYGLFTGGLGAHYGAEKLGCTVVPMSGGQTEKQIQIIQDF 180 Query: 181 KPDIIMVTPSYMLTVLDEMERMGIDPHQTSLKVGIFGAEPWTQAMRAAMEARAGIDAVDI 240 KP IIMVTPSYMLT+LDEMERMGIDP TSL++GIFGAEPWT AMR AME RAGIDAVDI Sbjct: 181 KPKIIMVTPSYMLTILDEMERMGIDPKSTSLRIGIFGAEPWTPAMRVAMEQRAGIDAVDI 240 Query: 241 YGLSEVMGPGVANECIEAKDGPVIWEDHFYPEIIDPHTGEVLPDGSEGELVFTTLTKEAM 300 YGLSEVMGPGVANEC+E KDGP IWEDHFYPEIIDP+TGEVLPDGSEGELVFT+L+KEAM Sbjct: 241 YGLSEVMGPGVANECVETKDGPTIWEDHFYPEIIDPNTGEVLPDGSEGELVFTSLSKEAM 300 Query: 301 PVIRYRTRDLTRLLPPTARSMRRMAKITGRSDDMLIIRGVNLFPTQVEELICKNPKLAPQ 360 PVIRYRTRDLTRLLPP+ARSMRRMAKITGRSDDMLIIRGVN+FPTQ+EELICK PKLAP Sbjct: 301 PVIRYRTRDLTRLLPPSARSMRRMAKITGRSDDMLIIRGVNVFPTQIEELICKIPKLAPH 360 Query: 361 YLLEVDKDGHMDTLTVKVEINPEANVGRHPEQKEALAKELQHDIKTFIGVSAKVHVCEPF 420 YLLEVDK GHMDTLTVKVEIN EA VGRHPE KEALA+EL H IK+ IGVSAKV V EPF Sbjct: 361 YLLEVDKQGHMDTLTVKVEINAEAEVGRHPEHKEALARELTHSIKSLIGVSAKVLVGEPF 420 Query: 421 AIERVTIGKAKRVVDRRPKE 440 +IERVT+GKAKRV+DRRPK+ Sbjct: 421 SIERVTVGKAKRVIDRRPKD 440 Lambda K H 0.318 0.137 0.406 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: 803 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: 440 Length of database: 440 Length adjustment: 32 Effective length of query: 408 Effective length of database: 408 Effective search space: 166464 Effective search space used: 166464 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: 51 (24.3 bits)
Align candidate WP_011764038.1 AZO_RS01535 (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.30396.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-239 778.8 0.0 5.7e-239 778.6 0.0 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011764038.1 AZO_RS01535 phenylacetate--CoA l Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000061505.1:WP_011764038.1 AZO_RS01535 phenylacetate--CoA ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 778.6 0.0 5.7e-239 5.7e-239 1 422 [] 15 437 .. 15 437 .. 1.00 Alignments for each domain: == domain 1 score: 778.6 bits; conditional E-value: 5.7e-239 TIGR02155 1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdl 69 e++s delralqlerlk+sv++ayenvp+yrk+fd++gv+pddlk+l+dlakfp+t+k dlrdnypf++ lcl|NCBI__GCF_000061505.1:WP_011764038.1 15 ETASIDELRALQLERLKWSVRHAYENVPHYRKKFDEKGVHPDDLKSLADLAKFPFTSKYDLRDNYPFGM 83 899****************************************************************** PP TIGR02155 70 lavprekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvh 138 +avp+++++rvhassGttGkptvv+yt kd+dtw++vvars+raaGGr+gd++h++yGyGlftGGlG+h lcl|NCBI__GCF_000061505.1:WP_011764038.1 84 FAVPMDRIARVHASSGTTGKPTVVGYTLKDIDTWATVVARSIRAAGGRPGDMVHVSYGYGLFTGGLGAH 152 ********************************************************************* PP TIGR02155 139 yGaeklGatvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepw 207 yGaeklG+tvvp+sGGqtekq+q+iqdfkp+ii+vtpsy+l++l+e++r+gidp+++sl+++i+Gaepw lcl|NCBI__GCF_000061505.1:WP_011764038.1 153 YGAEKLGCTVVPMSGGQTEKQIQIIQDFKPKIIMVTPSYMLTILDEMERMGIDPKSTSLRIGIFGAEPW 221 ********************************************************************* PP TIGR02155 208 teamrkelearlgikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGel 276 t amr ++e+r+gi+a+diyGlsev+GpGvanecvetkdG++iwedhfypeiidp+tgevlpdG+eGel lcl|NCBI__GCF_000061505.1:WP_011764038.1 222 TPAMRVAMEQRAGIDAVDIYGLSEVMGPGVANECVETKDGPTIWEDHFYPEIIDPNTGEVLPDGSEGEL 290 ********************************************************************* PP TIGR02155 277 vfttltkealpviryrtrdltrllpgtartmrrmdkikGrsddllilrGvnvfptqleevllkldklsp 345 vft+l+kea+pviryrtrdltrllp++ar+mrrm+ki+Grsdd+li+rGvnvfptq+ee+++k++kl+p lcl|NCBI__GCF_000061505.1:WP_011764038.1 291 VFTSLSKEAMPVIRYRTRDLTRLLPPSARSMRRMAKITGRSDDMLIIRGVNVFPTQIEELICKIPKLAP 359 ********************************************************************* PP TIGR02155 346 hyqleltreGaldeltlkvelkdesaalrlleqksllakkiekkikaevgvsvdvelvepgsler.seG 413 hy le++++G++d+lt+kve++ e+ ++r+ e+k++la+++ ++ik+ +gvs++v + ep+s+er + G lcl|NCBI__GCF_000061505.1:WP_011764038.1 360 HYLLEVDKQGHMDTLTVKVEINAEAEVGRHPEHKEALARELTHSIKSLIGVSAKVLVGEPFSIERvTVG 428 *****************************************************************99** PP TIGR02155 414 kakrvvdkr 422 kakrv+d+r lcl|NCBI__GCF_000061505.1:WP_011764038.1 429 KAKRVIDRR 437 *******98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (422 nodes) Target sequences: 1 (440 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: 12.17 // [ok]
This GapMind analysis is from Sep 24 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