Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_011385134.1 AMB_RS13855 phenylacetate--CoA ligase
Query= SwissProt::Q9L9C1 (440 letters) >NCBI__GCF_000009985.1:WP_011385134.1 Length = 442 Score = 629 bits (1621), Expect = 0.0 Identities = 308/434 (70%), Positives = 358/434 (82%), Gaps = 3/434 (0%) Query: 6 PSPGDLEPIEKASQDELRALQLERLKWSVRHAYENVPHYRKAFDAKGVHPDDLKSLADLA 65 P+ L+PIE AS+D++ ALQ ER+KWS+ HAY NV HYR KGVHPDD K L DLA Sbjct: 11 PAKDLLDPIEIASRDQITALQTERMKWSLTHAYNNVEHYRNKCREKGVHPDDFKELKDLA 70 Query: 66 KFPFTAKGDLRDNYPFGMFAVPREKVARVHASSGTTGKPTVVGYTLKDIDTWATVVARSI 125 KFPFT K DLRD YPFGMFAVP ++V RVHASSGTTGKPTVVGYT DID WA V+ARSI Sbjct: 71 KFPFTTKSDLRDTYPFGMFAVPMDEVVRVHASSGTTGKPTVVGYTQNDIDMWANVMARSI 130 Query: 126 RASGGRAGDMVHIAYGYGLFTGGLGAHYGAEKLGCTVVPMSGGQTEKQIQLIQDFKPDII 185 RA+GGR D H++YGYGLFTGGLGAHYGAE+LGCTV+PMSGGQTEKQIQLI DFKP+II Sbjct: 131 RAAGGRRSDKCHVSYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQIQLIMDFKPEII 190 Query: 186 MVTPSYMLTVLDEMERMGIDPHQTSLKVGIFGAEPWTQAMRAAMEARAGIDAVDIYGLSE 245 MVTPSYML + DEM+R GID L+VGIFGAEPWT AMR +E R GI+AVDIYGLSE Sbjct: 191 MVTPSYMLAIADEMDRQGIDTKTCPLQVGIFGAEPWTGAMREEIEVRMGIEAVDIYGLSE 250 Query: 246 VMGPGVANECIEAKDGPVIWEDHFYPEIIDPHTGEVLPDGSEGELVFTTLTKEAMPVIRY 305 V+GPGVA EC+E KDG +WEDHFYPEIIDPHTGEVLPDGS GELVFT+LTKEA+P+IRY Sbjct: 251 VIGPGVACECVETKDGLHLWEDHFYPEIIDPHTGEVLPDGSMGELVFTSLTKEALPIIRY 310 Query: 306 RTRDLTRLLPPTARSMRRMAKITGRSDDMLIIRGVNLFPTQVEELICKNPKLAPQYLLEV 365 RTRDLT+LLP TARSMRRM KITGRSDDMLIIRGVN+FPTQ+EELI K+ +LAP Y LEV Sbjct: 311 RTRDLTQLLPGTARSMRRMGKITGRSDDMLIIRGVNVFPTQIEELILKDYRLAPHYQLEV 370 Query: 366 DKDGHMDTLTVKVEINPEANVGRHPEQKEALAKELQHDIKTFIGVSAKVHVCEPFAIERV 425 +DGH+D++ V VE+ A+ EA +K+LQH IK++IG+S KV+V P +IER Sbjct: 371 TRDGHLDSVAVNVEV--RADQPYDDSALEAASKDLQHHIKSYIGISTKVNVLAPNSIER- 427 Query: 426 TIGKAKRVVDRRPK 439 ++GKA+RV+D+RPK Sbjct: 428 SMGKARRVIDKRPK 441 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: 708 Number of extensions: 20 Number of successful extensions: 3 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: 442 Length adjustment: 32 Effective length of query: 408 Effective length of database: 410 Effective search space: 167280 Effective search space used: 167280 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_011385134.1 AMB_RS13855 (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.3050.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-225 734.6 0.1 1.5e-225 734.4 0.1 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011385134.1 AMB_RS13855 phenylacetate--CoA l Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011385134.1 AMB_RS13855 phenylacetate--CoA ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 734.4 0.1 1.5e-225 1.5e-225 1 422 [] 20 439 .. 20 439 .. 0.98 Alignments for each domain: == domain 1 score: 734.4 bits; conditional E-value: 1.5e-225 TIGR02155 1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdl 69 e +s+d+++alq+er+k+s+ +ay+nv +yr++ ++gv+pdd+kel+dlakfp+t+ksdlrd ypf++ lcl|NCBI__GCF_000009985.1:WP_011385134.1 20 EIASRDQITALQTERMKWSLTHAYNNVEHYRNKCREKGVHPDDFKELKDLAKFPFTTKSDLRDTYPFGM 88 679****************************************************************** PP TIGR02155 70 lavprekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvh 138 +avp+++vvrvhassGttGkptvv+ytq+d+d+w++v+ars+raaGGr+ d+ h++yGyGlftGGlG+h lcl|NCBI__GCF_000009985.1:WP_011385134.1 89 FAVPMDEVVRVHASSGTTGKPTVVGYTQNDIDMWANVMARSIRAAGGRRSDKCHVSYGYGLFTGGLGAH 157 ********************************************************************* PP TIGR02155 139 yGaeklGatvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepw 207 yGae+lG+tv+p+sGGqtekq+qli dfkp+ii+vtpsy+la+++e++r+gid++ + l+v+i+Gaepw lcl|NCBI__GCF_000009985.1:WP_011385134.1 158 YGAERLGCTVIPMSGGQTEKQIQLIMDFKPEIIMVTPSYMLAIADEMDRQGIDTKTCPLQVGIFGAEPW 226 ********************************************************************* PP TIGR02155 208 teamrkelearlgikaldiyGlseviGpGvanecvetkdGlviwedhfypeiidpetgevlpdGeeGel 276 t amr+e+e r+gi+a+diyGlseviGpGva ecvetkdGl++wedhfypeiidp+tgevlpdG+ Gel lcl|NCBI__GCF_000009985.1:WP_011385134.1 227 TGAMREEIEVRMGIEAVDIYGLSEVIGPGVACECVETKDGLHLWEDHFYPEIIDPHTGEVLPDGSMGEL 295 ********************************************************************* PP TIGR02155 277 vfttltkealpviryrtrdltrllpgtartmrrmdkikGrsddllilrGvnvfptqleevllkldklsp 345 vft+ltkealp+iryrtrdlt+llpgtar+mrrm ki+Grsdd+li+rGvnvfptq+ee++lk +l+p lcl|NCBI__GCF_000009985.1:WP_011385134.1 296 VFTSLTKEALPIIRYRTRDLTQLLPGTARSMRRMGKITGRSDDMLIIRGVNVFPTQIEELILKDYRLAP 364 ********************************************************************* PP TIGR02155 346 hyqleltreGaldeltlkvelkdesaalrlleqksllakkiekkikaevgvsvdvelvepgslerseGk 414 hyqle+tr+G+ld+++++ve++ ++ ++ ++ +k+++++ik+ +g+s++v++ +p s+ers+Gk lcl|NCBI__GCF_000009985.1:WP_011385134.1 365 HYQLEVTRDGHLDSVAVNVEVRADQPYDDSA--LEAASKDLQHHIKSYIGISTKVNVLAPNSIERSMGK 431 **********************888777644..445799****************************** PP TIGR02155 415 akrvvdkr 422 a+rv+dkr lcl|NCBI__GCF_000009985.1:WP_011385134.1 432 ARRVIDKR 439 *******8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (422 nodes) Target sequences: 1 (442 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: 9.60 // [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