Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate WP_058931420.1 AU252_RS15070 phenylacetate--CoA ligase
Query= SwissProt::Q9L9C1 (440 letters) >NCBI__GCF_001484605.1:WP_058931420.1 Length = 454 Score = 511 bits (1316), Expect = e-149 Identities = 268/450 (59%), Positives = 325/450 (72%), Gaps = 17/450 (3%) Query: 2 PVKTPSPGDLEPI----EKASQDELRALQLERLKWSVRHAYENVPHYRKAFDAKGVHPDD 57 P+ P+ +PI E S+DEL ALQL RL+ +V +AY+ VP Y++ FD G+HP D Sbjct: 9 PMPQPTSQGTDPILDREETISRDELEALQLTRLQHTVAYAYDRVPLYKRKFDDAGIHPTD 68 Query: 58 LKSLADLAKFPFTAKGDLRDNYPFGMFAVPREKVARVHASSGTTGKPTVVGYTLKDIDTW 117 L+ L+DL FPFT K DLR YPFGMFAVP+ +VARVHASSGTTG+PTVVGYT +D+ W Sbjct: 69 LRELSDLGNFPFTTKEDLRAEYPFGMFAVPQSEVARVHASSGTTGRPTVVGYTKQDLADW 128 Query: 118 ATVVARSIRASGGRAGDMVHIAYGYGLFTGGLGAHYGAEKLGCTVVPMSGGQTEKQIQLI 177 A +VAR +RASG R G VH AYGYGLFTGGLGAH GAE LGCTV+PMSGGQTE+QIQLI Sbjct: 129 AKLVARCLRASGVRPGMKVHNAYGYGLFTGGLGAHAGAEALGCTVIPMSGGQTERQIQLI 188 Query: 178 QDFKPDIIMVTPSYMLTVLDEMERMGIDPHQTSLKVGIFGAEPWTQAMRAAMEARAGIDA 237 QDF+PD I+ TP+Y+LT+ D M MGIDP TSLK + GAEPWTQ MR +E I A Sbjct: 189 QDFQPDAILATPTYLLTIADAMAHMGIDPTSTSLKYAVLGAEPWTQEMRHELEVTMNIKA 248 Query: 238 VDIYGLSEVMGPGVANECIEAKDGPVIWEDHFYPEIID---PHTGE--VLPDGSEGELVF 292 DIYGLSEVMGPGVA E +E +DG IWEDHF PEIID P G+ VL DG GELVF Sbjct: 249 CDIYGLSEVMGPGVAGEAVETQDGSHIWEDHFRPEIIDAFNPAVGKENVLRDGEHGELVF 308 Query: 293 TTLTKEAMPVIRYRTRDLTRLLPPTAR-SMRRMAKITGRSDDMLIIRGVNLFPTQVEELI 351 T LTKEA+P+IRYRT+DLTRLLP TAR + RRM +ITGRSDDM+I+RGVNLFP+Q+EE+ Sbjct: 309 TALTKEALPIIRYRTKDLTRLLPGTARPAHRRMGRITGRSDDMIILRGVNLFPSQIEEIA 368 Query: 352 CKNPKLAPQYLLEVDK--DGHMDTLTVKVEINPEANVGRHPEQKEALAKELQHDIKTFIG 409 + P+L+P + LE+ + MD LTVK+E + EQ A+ LQ IK +G Sbjct: 369 LRIPELSPHFQLELTRPEGQRMDQLTVKIERRDAVTL----EQSTTAARTLQEQIKIHVG 424 Query: 410 VSAKVHVCEPFAIERVTIGKAKRVVDRRPK 439 S V V EP ++ER + GK +R+ D RPK Sbjct: 425 SSCAVDVVEPGSLER-SNGKLRRIYDLRPK 453 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: 668 Number of extensions: 24 Number of successful extensions: 4 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: 454 Length adjustment: 33 Effective length of query: 407 Effective length of database: 421 Effective search space: 171347 Effective search space used: 171347 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_058931420.1 AU252_RS15070 (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.4049526.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-200 650.2 0.0 6.4e-200 650.0 0.0 1.0 1 NCBI__GCF_001484605.1:WP_058931420.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001484605.1:WP_058931420.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 650.0 0.0 6.4e-200 6.4e-200 1 422 [] 26 451 .. 26 451 .. 0.96 Alignments for each domain: == domain 1 score: 650.0 bits; conditional E-value: 6.4e-200 TIGR02155 1 eklsldelralqlerlkvsvkrayenvpayrkafdaagvkpddlkelsdlakfpltaksdlrdnypfdllavp 73 e++s+del+alql+rl+ +v+ ay++vp y+++fd+ag++p dl+elsdl +fp+t+k+dlr +ypf+++avp NCBI__GCF_001484605.1:WP_058931420.1 26 ETISRDELEALQLTRLQHTVAYAYDRVPLYKRKFDDAGIHPTDLRELSDLGNFPFTTKEDLRAEYPFGMFAVP 98 799********************************************************************** PP TIGR02155 74 rekvvrvhassGttGkptvvaytqkdldtwsevvarslraaGGrkgdllhnayGyGlftGGlGvhyGaeklGa 146 + +v+rvhassGttG+ptvv+yt++dl w+++var lra+G r+g+++hnayGyGlftGGlG+h Gae lG+ NCBI__GCF_001484605.1:WP_058931420.1 99 QSEVARVHASSGTTGRPTVVGYTKQDLADWAKLVARCLRASGVRPGMKVHNAYGYGLFTGGLGAHAGAEALGC 171 ************************************************************************* PP TIGR02155 147 tvvpisGGqtekqvqliqdfkpdiiavtpsyilalleelkrlgidpedislkvailGaepwteamrkelearl 219 tv+p+sGGqte+q+qliqdf+pd i +tp+y+l++++++ ++gidp+++slk+a+lGaepwt++mr+ele ++ NCBI__GCF_001484605.1:WP_058931420.1 172 TVIPMSGGQTERQIQLIQDFQPDAILATPTYLLTIADAMAHMGIDPTSTSLKYAVLGAEPWTQEMRHELEVTM 244 ************************************************************************* PP TIGR02155 220 gikaldiyGlseviGpGvanecvetkdGlviwedhfypeiid...petg..evlpdGeeGelvfttltkealp 287 +ika diyGlsev+GpGva e+vet+dG++iwedhf peiid p g +vl dGe+Gelvft+ltkealp NCBI__GCF_001484605.1:WP_058931420.1 245 NIKACDIYGLSEVMGPGVAGEAVETQDGSHIWEDHFRPEIIDafnPAVGkeNVLRDGEHGELVFTALTKEALP 317 *****************************************844455443269******************** PP TIGR02155 288 viryrtrdltrllpgtart.mrrmdkikGrsddllilrGvnvfptqleevllkldklsphyqleltr.eG.al 357 +iryrt+dltrllpgtar+ rrm +i+Grsdd++ilrGvn+fp+q+ee+ l++++lsph+qleltr eG ++ NCBI__GCF_001484605.1:WP_058931420.1 318 IIRYRTKDLTRLLPGTARPaHRRMGRITGRSDDMIILRGVNLFPSQIEEIALRIPELSPHFQLELTRpEGqRM 390 ******************9789********************************************954547* PP TIGR02155 358 deltlkvelkdesaalrlleqksllakkiekkikaevgvsvdvelvepgslerseGkakrvvdkr 422 d+lt+k+e +d +++l eq ++ a+ ++++ik +vg s v +vepgslers+Gk++r++d+r NCBI__GCF_001484605.1:WP_058931420.1 391 DQLTVKIERRD-AVTL---EQSTTAARTLQEQIKIHVGSSCAVDVVEPGSLERSNGKLRRIYDLR 451 ********994.3333...46667799************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (422 nodes) Target sequences: 1 (454 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: 18.57 // [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