Align Benzoyl-CoA-dihydrodiol lyase; EC 4.1.2.44 (characterized)
to candidate WP_011382621.1 AMB_RS00885 2,3-epoxybenzoyl-CoA dihydrolase
Query= SwissProt::Q84HH6 (555 letters) >NCBI__GCF_000009985.1:WP_011382621.1 Length = 550 Score = 613 bits (1582), Expect = e-180 Identities = 303/550 (55%), Positives = 388/550 (70%), Gaps = 6/550 (1%) Query: 12 LVDYRTEPSKYRHWSLATDGEIATLTLNIDEDGGIRPGYKLKLNSYDLGVDIELHDALQR 71 +++++T P YRHW LA DG +ATLT+++D + PGY+LK+NSYDLGVDIEL+DA+QR Sbjct: 1 MINFQTSPESYRHWKLAFDGPVATLTMDVDPASTLAPGYELKMNSYDLGVDIELYDAVQR 60 Query: 72 VRFEHPEVRTVVVTSGKPKIFCSGANIYMLGLSTHAWKVNFCKFTNETRNGIEDSSQYSG 131 +RFEHPEVR VV+ S PKIFC+GANI MLG+S+H KVNFCKFTNETRN IED+S+ S Sbjct: 61 LRFEHPEVRAVVMASANPKIFCAGANIKMLGVSSHGHKVNFCKFTNETRNSIEDASENSR 120 Query: 132 LKFLAACNGTTAGGGYELALACDEIVLVDDRNSSVSLPEVPLLGVLPGTGGLTRVTDKRR 191 +L A GT AGGGYELALA D I++VDD N++VSLPEVPLL VLPGTGGLTRV DKR+ Sbjct: 121 QTYLCAVTGTAAGGGYELALATDYIMMVDDGNTAVSLPEVPLLAVLPGTGGLTRVVDKRK 180 Query: 192 VRRDHADIFCTISEGVRGQRAKDWRLVDDVVKQQQFAEHIQARAKALAQTSDRPAGAKGV 251 VRRD ADIFC+I EGV+G+RA +WRLVD+V+ F + +A LA SDRP KGV Sbjct: 181 VRRDLADIFCSIEEGVKGKRAVEWRLVDEVIPSSAFKAAVAKKAAELAARSDRPTAEKGV 240 Query: 252 KLTTLERTVDEKGYHYEFVDATIDADGRTVTLTVRAPAAVTAKTAAEIEAQGIKWWPLQM 311 L+ + R + Y +D D R +T++ P A A I+AQG+ ++PL + Sbjct: 241 VLSQVSRVIGTDSVTYPHIDIAFDRATRAANITIKGPKAACPADLAGIKAQGVDFYPLAL 300 Query: 312 ARELDDAILNLRTNHLDVGLWQLRTEGDAQVVLDIDATIDA-NRDNWFVRETIGMLRRTL 370 ARELDDAIL+LR N + W RT+GDA +V+ DA + +W VRE + +RT+ Sbjct: 301 ARELDDAILHLRANETTIATWVFRTQGDADLVMGYDAALQTFGASDWLVREILLYWKRTM 360 Query: 371 ARIDVSSRSLYALIEPGSCFAGTLLEIALAADRSYMLDAAEAKN-----VVGLSAMNFGT 425 R+DV+SR+L+AL+EPGSCFAG + EI A DRS+MLD N + LSA+NF Sbjct: 361 KRLDVTSRTLFALVEPGSCFAGFVAEILFAVDRSFMLDGTFEDNPAPAAAIRLSALNFDG 420 Query: 426 FPMVNGLSRIDARFYQEEAPVAAVKAKQGSLLSPAEAMELGLVTAIPDDLDWAEEVRIAI 485 PM NG+SR+ RF E V + G L A +LGLVT PDD+DW +E+R+ I Sbjct: 421 LPMGNGISRLATRFLGEPDSVGKARDTIGKDLDAAACAKLGLVTGTPDDIDWEDEIRLMI 480 Query: 486 EERAALSPDALTGLEANLRFGPVETMNTRIFGRLSAWQNWIFNRPNAVGENGALKLFGSG 545 EERA+ SPD+LTG+EANLRF ETM T+IFGRL+AWQNWIF RPNAVG+ GALKL+G+G Sbjct: 481 EERASFSPDSLTGMEANLRFAGPETMETKIFGRLTAWQNWIFQRPNAVGDQGALKLYGTG 540 Query: 546 KKAQFDWNRV 555 K+A ++ RV Sbjct: 541 KRAAYNQERV 550 Lambda K H 0.318 0.134 0.397 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: 778 Number of extensions: 32 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: 555 Length of database: 550 Length adjustment: 36 Effective length of query: 519 Effective length of database: 514 Effective search space: 266766 Effective search space used: 266766 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: 53 (25.0 bits)
Align candidate WP_011382621.1 AMB_RS00885 (2,3-epoxybenzoyl-CoA dihydrolase)
to HMM TIGR03222 (boxC: benzoyl-CoA-dihydrodiol lyase (EC 4.1.2.44))
# 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/TIGR03222.hmm # target sequence database: /tmp/gapView.24309.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03222 [M=548] Accession: TIGR03222 Description: benzo_boxC: benzoyl-CoA-dihydrodiol lyase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1021.9 0.1 0 1021.7 0.1 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011382621.1 AMB_RS00885 2,3-epoxybenzoyl-CoA Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011382621.1 AMB_RS00885 2,3-epoxybenzoyl-CoA dihydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1021.7 0.1 0 0 1 548 [] 2 550 .] 2 550 .] 1.00 Alignments for each domain: == domain 1 score: 1021.7 bits; conditional E-value: 0 TIGR03222 1 vdfrtepskyrhwkltfdGpvatltldvdedgglrdGyklklnsydlGvdieladalqrlrfehpevrv 69 ++f+t+p++yrhwkl+fdGpvatlt+dvd++++l++Gy+lk+nsydlGvdiel+da+qrlrfehpevr+ lcl|NCBI__GCF_000009985.1:WP_011382621.1 2 INFQTSPESYRHWKLAFDGPVATLTMDVDPASTLAPGYELKMNSYDLGVDIELYDAVQRLRFEHPEVRA 70 79******************************************************************* PP TIGR03222 70 vvltsakdkvfcaGanikmlglsthahkvnfckftnetrngiedaseesglkflaavnGtaaGGGyela 138 vv++sa++k+fcaGanikmlg+s+h+hkvnfckftnetrn+iedase+s++++l+av+GtaaGGGyela lcl|NCBI__GCF_000009985.1:WP_011382621.1 71 VVMASANPKIFCAGANIKMLGVSSHGHKVNFCKFTNETRNSIEDASENSRQTYLCAVTGTAAGGGYELA 139 ********************************************************************* PP TIGR03222 139 lacdeivlvddrssavslpevpllavlpGtGGltrvtdkrrvrrdladifctieeGvkGkrakewrlvd 207 la+d+i++vdd+++avslpevpllavlpGtGGltrv+dkr+vrrdladifc+ieeGvkGkra+ewrlvd lcl|NCBI__GCF_000009985.1:WP_011382621.1 140 LATDYIMMVDDGNTAVSLPEVPLLAVLPGTGGLTRVVDKRKVRRDLADIFCSIEEGVKGKRAVEWRLVD 208 ********************************************************************* PP TIGR03222 208 evvksskfdaavaeraaelaaksdrpadakGveltklertieedgvryetvdvaidraartatitvkgp 276 ev++ss+f+aava++aaelaa+sdrp+++kGv+l++++r+i +d+v+y ++d+a+dra+r+a+it+kgp lcl|NCBI__GCF_000009985.1:WP_011382621.1 209 EVIPSSAFKAAVAKKAAELAARSDRPTAEKGVVLSQVSRVIGTDSVTYPHIDIAFDRATRAANITIKGP 277 ********************************************************************* PP TIGR03222 277 eaaapadlaaikaqGaefyplklarelddailhlrlneldiglwvlrteGdaelvlaadalleakedh. 344 +aa+padla+ikaqG++fypl+larelddailhlr+ne++i++wv+rt+Gda+lv+++da+l+++ ++ lcl|NCBI__GCF_000009985.1:WP_011382621.1 278 KAACPADLAGIKAQGVDFYPLALARELDDAILHLRANETTIATWVFRTQGDADLVMGYDAALQTFGASd 346 ****************************************************************98766 PP TIGR03222 345 wlvreilgllkrtlkrldvssrslfalvepgscfaGtlaelvfaadrsymlegeleddedeeaaitlse 413 wlvreil ++krt+krldv+sr+lfalvepgscfaG++ae++fa+drs+ml+g++ed+++++aai+ls+ lcl|NCBI__GCF_000009985.1:WP_011382621.1 347 WLVREILLYWKRTMKRLDVTSRTLFALVEPGSCFAGFVAEILFAVDRSFMLDGTFEDNPAPAAAIRLSA 415 ********************************************************************* PP TIGR03222 414 lnfgayplsnglsrlaarflaeeaaveavrdkiGealdaaeaeklglvtaalddidwedeirilleera 482 lnf+ +p++ng+srla+rfl+e+++v ++rd+iG++ldaa+++klglvt ++ddidwedeir+++eera lcl|NCBI__GCF_000009985.1:WP_011382621.1 416 LNFDGLPMGNGISRLATRFLGEPDSVGKARDTIGKDLDAAACAKLGLVTGTPDDIDWEDEIRLMIEERA 484 ********************************************************************* PP TIGR03222 483 slspdaltGleanlrfagpetmetrifgrltawqnwifnrpnavGekGalklyGsGkkaqfdlerv 548 s+spd+ltG+eanlrfagpetmet+ifgrltawqnwif+rpnavG++GalklyG+Gk+a++++erv lcl|NCBI__GCF_000009985.1:WP_011382621.1 485 SFSPDSLTGMEANLRFAGPETMETKIFGRLTAWQNWIFQRPNAVGDQGALKLYGTGKRAAYNQERV 550 *****************************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (548 nodes) Target sequences: 1 (550 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03 # Mc/sec: 9.67 // [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