Align Benzoyl-CoA-dihydrodiol lyase; EC 4.1.2.44 (characterized)
to candidate RR42_RS07510 RR42_RS07510 benzoyl-CoA-dihydrodiol lyase
Query= SwissProt::Q84HH6 (555 letters) >FitnessBrowser__Cup4G11:RR42_RS07510 Length = 566 Score = 789 bits (2037), Expect = 0.0 Identities = 390/546 (71%), Positives = 449/546 (82%), Gaps = 3/546 (0%) Query: 13 VDYRTEPSKYRHWSLATDGEIATLTLNIDEDGGIRPGYKLKLNSYDLGVDIELHDALQRV 72 V + +P++YRHW L G +ATL+++IDEDGG+RPGY LKLNSYDLGVDIELHDA+QR+ Sbjct: 21 VTFERDPAQYRHWKLTFAGPVATLSMDIDEDGGLRPGYALKLNSYDLGVDIELHDAVQRI 80 Query: 73 RFEHPEVRTVVVTSGKPKIFCSGANIYMLGLSTHAWKVNFCKFTNETRNGIEDSSQYSGL 132 RFEHPEVRTV++TS K +IFCSGANI+MLG S+HAWKVNFCKFTNETRNGIED+S++SGL Sbjct: 81 RFEHPEVRTVILTSAKDRIFCSGANIFMLGKSSHAWKVNFCKFTNETRNGIEDASRHSGL 140 Query: 133 KFLAACNGTTAGGGYELALACDEIVLVDDRNSSVSLPEVPLLGVLPGTGGLTRVTDKRRV 192 KF+AACNGTTAGGGYELALACDEIVLVDDR+S+VSLPEVPLLGVLPGTGGLTR+TDKRRV Sbjct: 141 KFIAACNGTTAGGGYELALACDEIVLVDDRSSAVSLPEVPLLGVLPGTGGLTRLTDKRRV 200 Query: 193 RRDHADIFCTISEGVRGQRAKDWRLVDDVVKQQQFAEHIQARAKALAQTSDRPAGAKGVK 252 RRDHADIFCT +EGVRGQRA DW+LVD VVK +FAEH+Q RA ALA SDRPAG GVK Sbjct: 201 RRDHADIFCTTTEGVRGQRAHDWKLVDAVVKPARFAEHVQQRALALAAQSDRPAGHDGVK 260 Query: 253 LTTLERTVDEKGYHYEFVDATIDADGRTVTLTVRAPAAVTAKTAAEIEAQGIKWWPLQMA 312 LT L R+ + GY Y+ V ID R TLTV PA + A I A G WWPL+MA Sbjct: 261 LTPLSRSQEAHGYRYDTVQVHIDPRARKATLTVFGPAKHQPQALAAILAAGADWWPLKMA 320 Query: 313 RELDDAILNLRTNHLDVGLWQLRTEGDAQVVLDIDATIDANRDNWFVRETIGMLRRTLAR 372 RELDDAIL LR NHLD+G+W L+TEGD VL DA +DA+ +WFVRETIGMLRRTLAR Sbjct: 321 RELDDAILTLRANHLDIGIWILKTEGDPHQVLATDALLDAHASHWFVRETIGMLRRTLAR 380 Query: 373 IDVSSRSLYALIEPGSCFAGTLLEIALAADRSYML---DAAEAKNVVGLSAMNFGTFPMV 429 ++VSSR+L+ALIEP SCFAGTLLE+ALAADRSYML DA + V S NFG +P V Sbjct: 381 LEVSSRTLFALIEPDSCFAGTLLELALAADRSYMLHLPDAPDDAPRVFASTANFGRYPAV 440 Query: 430 NGLSRIDARFYQEEAPVAAVKAKQGSLLSPAEAMELGLVTAIPDDLDWAEEVRIAIEERA 489 NGL+R+ ARF Q+E + AV+ G+ L A LGLVTA PDD+DW +E+RIAIEERA Sbjct: 441 NGLTRLAARFCQDEVAIQAVQDHIGAPLDAINAASLGLVTATPDDIDWEDEIRIAIEERA 500 Query: 490 ALSPDALTGLEANLRFGPVETMNTRIFGRLSAWQNWIFNRPNAVGENGALKLFGSGKKAQ 549 +LSPDALTGLEANLRFGPVETM TRIFGRL+AWQNWIFNRPNAVGE GALK+FGSG KA+ Sbjct: 501 SLSPDALTGLEANLRFGPVETMETRIFGRLTAWQNWIFNRPNAVGEQGALKVFGSGNKAR 560 Query: 550 FDWNRV 555 FDW+RV Sbjct: 561 FDWDRV 566 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: 909 Number of extensions: 31 Number of successful extensions: 2 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: 566 Length adjustment: 36 Effective length of query: 519 Effective length of database: 530 Effective search space: 275070 Effective search space used: 275070 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 RR42_RS07510 RR42_RS07510 (benzoyl-CoA-dihydrodiol lyase)
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.19763.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-306 1003.6 0.0 1.4e-306 1003.4 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS07510 RR42_RS07510 benzoyl-CoA-dihydro Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS07510 RR42_RS07510 benzoyl-CoA-dihydrodiol lyase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1003.4 0.0 1.4e-306 1.4e-306 1 548 [] 21 566 .] 21 566 .] 1.00 Alignments for each domain: == domain 1 score: 1003.4 bits; conditional E-value: 1.4e-306 TIGR03222 1 vdfrtepskyrhwkltfdGpvatltldvdedgglrdGyklklnsydlGvdieladalqrlrfehpevrv 69 v+f+++p +yrhwkltf Gpvatl++d+dedgglr+Gy lklnsydlGvdiel+da+qr+rfehpevr+ lcl|FitnessBrowser__Cup4G11:RR42_RS07510 21 VTFERDPAQYRHWKLTFAGPVATLSMDIDEDGGLRPGYALKLNSYDLGVDIELHDAVQRIRFEHPEVRT 89 78******************************************************************* PP TIGR03222 70 vvltsakdkvfcaGanikmlglsthahkvnfckftnetrngiedaseesglkflaavnGtaaGGGyela 138 v+ltsakd++fc+Gani+mlg+s+ha+kvnfckftnetrngiedas++sglkf+aa+nGt+aGGGyela lcl|FitnessBrowser__Cup4G11:RR42_RS07510 90 VILTSAKDRIFCSGANIFMLGKSSHAWKVNFCKFTNETRNGIEDASRHSGLKFIAACNGTTAGGGYELA 158 ********************************************************************* PP TIGR03222 139 lacdeivlvddrssavslpevpllavlpGtGGltrvtdkrrvrrdladifctieeGvkGkrakewrlvd 207 lacdeivlvddrssavslpevpll+vlpGtGGltr+tdkrrvrrd+adifct++eGv+G+ra +w+lvd lcl|FitnessBrowser__Cup4G11:RR42_RS07510 159 LACDEIVLVDDRSSAVSLPEVPLLGVLPGTGGLTRLTDKRRVRRDHADIFCTTTEGVRGQRAHDWKLVD 227 ********************************************************************* PP TIGR03222 208 evvksskfdaavaeraaelaaksdrpadakGveltklertieedgvryetvdvaidraartatitvkgp 276 vvk+++f+++v++ra +laa+sdrpa + Gv+lt+l+r++e++g+ry+tv+v+id ar+at+tv gp lcl|FitnessBrowser__Cup4G11:RR42_RS07510 228 AVVKPARFAEHVQQRALALAAQSDRPAGHDGVKLTPLSRSQEAHGYRYDTVQVHIDPRARKATLTVFGP 296 ********************************************************************* PP TIGR03222 277 eaaapadlaaikaqGaefyplklarelddailhlrlneldiglwvlrteGdaelvlaadalleakedhw 345 ++++p+ laai a+Ga+++plk+arelddail+lr+n+ldig+w+l+teGd ++vla+dall a+++hw lcl|FitnessBrowser__Cup4G11:RR42_RS07510 297 AKHQPQALAAILAAGADWWPLKMARELDDAILTLRANHLDIGIWILKTEGDPHQVLATDALLDAHASHW 365 ********************************************************************* PP TIGR03222 346 lvreilgllkrtlkrldvssrslfalvepgscfaGtlaelvfaadrsymlegeleddedeeaaitlsel 414 +vre++g+l+rtl+rl+vssr+lfal+ep+scfaGtl+el++aadrsyml +l+d++d++++++ s + lcl|FitnessBrowser__Cup4G11:RR42_RS07510 366 FVRETIGMLRRTLARLEVSSRTLFALIEPDSCFAGTLLELALAADRSYML--HLPDAPDDAPRVFASTA 432 *************************************************9..9**************** PP TIGR03222 415 nfgayplsnglsrlaarflaeeaaveavrdkiGealdaaeaeklglvtaalddidwedeirilleeras 483 nfg+yp +ngl+rlaarf ++e a++av+d+iG lda +a++lglvta++ddidwedeiri++eeras lcl|FitnessBrowser__Cup4G11:RR42_RS07510 433 NFGRYPAVNGLTRLAARFCQDEVAIQAVQDHIGAPLDAINAASLGLVTATPDDIDWEDEIRIAIEERAS 501 ********************************************************************* PP TIGR03222 484 lspdaltGleanlrfagpetmetrifgrltawqnwifnrpnavGekGalklyGsGkkaqfdlerv 548 lspdaltGleanlrf+++etmetrifgrltawqnwifnrpnavGe+Galk++GsG+ka+fd++rv lcl|FitnessBrowser__Cup4G11:RR42_RS07510 502 LSPDALTGLEANLRFGPVETMETRIFGRLTAWQNWIFNRPNAVGEQGALKVFGSGNKARFDWDRV 566 ****************************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (548 nodes) Target sequences: 1 (566 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: 00:00:00.02 # Mc/sec: 12.79 // [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