Align Benzoyl-CoA-dihydrodiol lyase; EC 4.1.2.44 (characterized)
to candidate Ac3H11_3085 Benzoyl-CoA-dihydrodiol lyase (EC 4.1.2.44)
Query= SwissProt::Q84HH6 (555 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3085 Length = 556 Score = 736 bits (1901), Expect = 0.0 Identities = 366/546 (67%), Positives = 429/546 (78%), Gaps = 3/546 (0%) Query: 13 VDYRTEPSKYRHWSLATDGEIATLTLNIDEDGGIRPGYKLKLNSYDLGVDIELHDALQRV 72 VDYRT+P++YRHW LA DG +A L+L+I EDGGIRPGYKLKLNSYDLGVDIELHDAL R+ Sbjct: 11 VDYRTDPTQYRHWKLAVDGAVARLSLDIAEDGGIRPGYKLKLNSYDLGVDIELHDALNRI 70 Query: 73 RFEHPEVRTVVVTSGKPKIFCSGANIYMLGLSTHAWKVNFCKFTNETRNGIEDSSQYSGL 132 RFEHP+VR+V+VTS + +IFCSGANI+MLG+S+HAWKVNFCKFTNETRNGIEDSS++SGL Sbjct: 71 RFEHPQVRSVIVTSARDRIFCSGANIFMLGVSSHAWKVNFCKFTNETRNGIEDSSKHSGL 130 Query: 133 KFLAACNGTTAGGGYELALACDEIVLVDDRNSSVSLPEVPLLGVLPGTGGLTRVTDKRRV 192 KF+AA NG AGGGYELALACDEIVLVDDR+S+VSLPEVPLLGVLPGTGGLTRVTDKR V Sbjct: 131 KFVAAVNGACAGGGYELALACDEIVLVDDRSSAVSLPEVPLLGVLPGTGGLTRVTDKRHV 190 Query: 193 RRDHADIFCTISEGVRGQRAKDWRLVDDVVKQQQFAEHIQARAKALAQTSDRPAGAKGVK 252 R D ADIFCT EGVRGQRA DWRLVD + K QFA + A L + S RP+ A+GV Sbjct: 191 RHDLADIFCTSVEGVRGQRAVDWRLVDRIAKPAQFAAAVDDTAARLTEGSPRPSHAQGVA 250 Query: 253 LTTLERTVDEKGYHYEFVDATIDADGRTVTLTVRAPAAVTAKTAAEIEAQGIKWWPLQMA 312 L +ER Y V +ID RT TLT++AP A+IEA G WWPL +A Sbjct: 251 LPRVEREETADSLRYTHVSVSIDRTRRTATLTLKAPTGPQPTDIADIEAAGAAWWPLALA 310 Query: 313 RELDDAILNLRTNHLDVGLWQLRTEGDAQVVLDIDATIDANRDNWFVRETIGMLRRTLAR 372 R+LDDAILNLRTN LD+G W L+TEGDAQ VL DAT+ A++ +W VRETIG LRRT AR Sbjct: 311 RQLDDAILNLRTNELDIGTWLLKTEGDAQAVLASDATLIAHQGHWLVRETIGALRRTFAR 370 Query: 373 IDVSSRSLYALIEPGSCFAGTLLEIALAADRSYML---DAAEAKNVVGLSAMNFGTFPMV 429 +DVSSRSL+AL+EPGS FAG+L E++ AADR+YML D E + L+ NFG PMV Sbjct: 371 LDVSSRSLFALVEPGSAFAGSLAELSFAADRTYMLALPDDTERAPKITLNEFNFGLLPMV 430 Query: 430 NGLSRIDARFYQEEAPVAAVKAKQGSLLSPAEAMELGLVTAIPDDLDWAEEVRIAIEERA 489 N SR+ RFY+E AP+ A +A G A+ LGLVTA PDD+DW +E+RIAIEERA Sbjct: 431 NDQSRLQRRFYEEAAPLEAARAAAGKPQDADAALALGLVTAAPDDIDWDDEIRIAIEERA 490 Query: 490 ALSPDALTGLEANLRFGPVETMNTRIFGRLSAWQNWIFNRPNAVGENGALKLFGSGKKAQ 549 A+SPD+LTGLEANLRF E MNTRIFGRL+AWQNWIFNRPNAVG+ GALK++G+G+KA Sbjct: 491 AMSPDSLTGLEANLRFASKENMNTRIFGRLTAWQNWIFNRPNAVGDKGALKVYGTGQKAG 550 Query: 550 FDWNRV 555 FD NRV Sbjct: 551 FDLNRV 556 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: 800 Number of extensions: 29 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: 556 Length adjustment: 36 Effective length of query: 519 Effective length of database: 520 Effective search space: 269880 Effective search space used: 269880 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 Ac3H11_3085 (Benzoyl-CoA-dihydrodiol lyase (EC 4.1.2.44))
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.11647.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-292 957.2 0.3 1.7e-292 957.0 0.3 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 Benzoyl-CoA-dihydrodiol lyase (E Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 Benzoyl-CoA-dihydrodiol lyase (EC 4.1.2.44) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 957.0 0.3 1.7e-292 1.7e-292 1 548 [] 11 556 .] 11 556 .] 1.00 Alignments for each domain: == domain 1 score: 957.0 bits; conditional E-value: 1.7e-292 TIGR03222 1 vdfrtepskyrhwkltfdGpvatltldvdedgglrdGyklklnsydlGvdieladalqrlrf 62 vd+rt+p +yrhwkl++dG+va l+ld++edgg+r+GyklklnsydlGvdiel+dal+r+rf lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 11 VDYRTDPTQYRHWKLAVDGAVARLSLDIAEDGGIRPGYKLKLNSYDLGVDIELHDALNRIRF 72 89************************************************************ PP TIGR03222 63 ehpevrvvvltsakdkvfcaGanikmlglsthahkvnfckftnetrngiedaseesglkfla 124 ehp+vr+v++tsa+d++fc+Gani+mlg+s+ha+kvnfckftnetrngied+s++sglkf+a lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 73 EHPQVRSVIVTSARDRIFCSGANIFMLGVSSHAWKVNFCKFTNETRNGIEDSSKHSGLKFVA 134 ************************************************************** PP TIGR03222 125 avnGtaaGGGyelalacdeivlvddrssavslpevpllavlpGtGGltrvtdkrrvrrdlad 186 avnG++aGGGyelalacdeivlvddrssavslpevpll+vlpGtGGltrvtdkr+vr+dlad lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 135 AVNGACAGGGYELALACDEIVLVDDRSSAVSLPEVPLLGVLPGTGGLTRVTDKRHVRHDLAD 196 ************************************************************** PP TIGR03222 187 ifctieeGvkGkrakewrlvdevvksskfdaavaeraaelaaksdrpadakGveltklerti 248 ifct +eGv+G+ra++wrlvd + k+++f+aav + aa l+ s+rp++a+Gv+l ++er + lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 197 IFCTSVEGVRGQRAVDWRLVDRIAKPAQFAAAVDDTAARLTEGSPRPSHAQGVALPRVEREE 258 ************************************************************** PP TIGR03222 249 eedgvryetvdvaidraartatitvkgpeaaapadlaaikaqGaefyplklarelddailhl 310 ++d++ry++v+v+idr+ rtat+t+k+p +p+d+a+i+a+Ga+++pl+lar+lddail+l lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 259 TADSLRYTHVSVSIDRTRRTATLTLKAPTGPQPTDIADIEAAGAAWWPLALARQLDDAILNL 320 ************************************************************** PP TIGR03222 311 rlneldiglwvlrteGdaelvlaadalleakedhwlvreilgllkrtlkrldvssrslfalv 372 r+neldig+w+l+teGda++vla da+l+a++ hwlvre++g l+rt++rldvssrslfalv lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 321 RTNELDIGTWLLKTEGDAQAVLASDATLIAHQGHWLVRETIGALRRTFARLDVSSRSLFALV 382 ************************************************************** PP TIGR03222 373 epgscfaGtlaelvfaadrsymlegeleddedeeaaitlselnfgayplsnglsrlaarfla 434 epgs faG lael faadr+yml +l+dd++ +++itl e nfg +p++n++srl++rf++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 383 EPGSAFAGSLAELSFAADRTYML--ALPDDTERAPKITLNEFNFGLLPMVNDQSRLQRRFYE 442 **********************9..9************************************ PP TIGR03222 435 eeaaveavrdkiGealdaaeaeklglvtaalddidwedeirilleeraslspdaltGleanl 496 e a++ea+r+ G+ da +a lglvtaa+ddidw+deiri++eera++spd+ltGleanl lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 443 EAAPLEAARAAAGKPQDADAALALGLVTAAPDDIDWDDEIRIAIEERAAMSPDSLTGLEANL 504 ************************************************************** PP TIGR03222 497 rfagpetmetrifgrltawqnwifnrpnavGekGalklyGsGkkaqfdlerv 548 rfa+ e m+trifgrltawqnwifnrpnavG+kGalk+yG+G+ka fdl+rv lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3085 505 RFASKENMNTRIFGRLTAWQNWIFNRPNAVGDKGALKVYGTGQKAGFDLNRV 556 ***************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (548 nodes) Target sequences: 1 (556 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: 9.27 // [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