Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate PP_3280 PP_3280 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase
Query= metacyc::MONOMER-15952 (401 letters) >FitnessBrowser__Putida:PP_3280 Length = 406 Score = 703 bits (1815), Expect = 0.0 Identities = 353/399 (88%), Positives = 377/399 (94%) Query: 3 EALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQAGE 62 +ALIIDAVRTPIGRYAGAL+SVRADDL AIPLKALI RHP+LDW A+DDVI+GCANQAGE Sbjct: 8 DALIIDAVRTPIGRYAGALSSVRADDLAAIPLKALIQRHPELDWKAIDDVIFGCANQAGE 67 Query: 63 DNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMSR 122 DNRNVA MA+LLAGLP+ VPGTT+NRLCGSGLDA+G+AARALRCGEAGLMLAGGVESMSR Sbjct: 68 DNRNVAHMASLLAGLPLEVPGTTINRLCGSGLDAIGNAARALRCGEAGLMLAGGVESMSR 127 Query: 123 APFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRADQD 182 APFVMGKSEQAFGR+AE+FDTTIGWRFVN LM+ +GIDSMPETAENVA QF ISRADQD Sbjct: 128 APFVMGKSEQAFGRAAELFDTTIGWRFVNPLMKAAYGIDSMPETAENVAEQFGISRADQD 187 Query: 183 AFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGTPF 242 AFALRSQHKAAAA A GRLA+EIV VEI QRKGPAK+VEHDEHPRGDTTLEQLA+LGTPF Sbjct: 188 AFALRSQHKAAAAQARGRLAREIVPVEIPQRKGPAKVVEHDEHPRGDTTLEQLARLGTPF 247 Query: 243 RQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPVPA 302 R+GGSVTAGNASGVNDGACALLLASS AA+RHGLKAR R+VGMA AGVEPR+MGIGPVPA Sbjct: 248 REGGSVTAGNASGVNDGACALLLASSAAARRHGLKARGRIVGMAVAGVEPRLMGIGPVPA 307 Query: 303 TRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLGMS 362 TRKVL LTGLALAD+DVIELNEAFAAQGLAVLRELGLADDD RVN NGGAIALGHPLGMS Sbjct: 308 TRKVLALTGLALADLDVIELNEAFAAQGLAVLRELGLADDDPRVNRNGGAIALGHPLGMS 367 Query: 363 GARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401 GARLVTTALHELEE GRYALCTMCIGVGQGIA+IIER+ Sbjct: 368 GARLVTTALHELEETAGRYALCTMCIGVGQGIAMIIERL 406 Lambda K H 0.319 0.134 0.384 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: 665 Number of extensions: 18 Number of successful extensions: 1 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: 401 Length of database: 406 Length adjustment: 31 Effective length of query: 370 Effective length of database: 375 Effective search space: 138750 Effective search space used: 138750 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 (21.8 bits) S2: 50 (23.9 bits)
Align candidate PP_3280 PP_3280 (3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))
# 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/TIGR02430.hmm # target sequence database: /tmp/gapView.9757.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02430 [M=400] Accession: TIGR02430 Description: pcaF: 3-oxoadipyl-CoA thiolase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-222 722.5 9.5 8.2e-222 722.3 9.5 1.0 1 lcl|FitnessBrowser__Putida:PP_3280 PP_3280 3-oxoadipyl-CoA/3-oxo-5, Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_3280 PP_3280 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 722.3 9.5 8.2e-222 8.2e-222 2 400 .] 8 406 .] 7 406 .] 1.00 Alignments for each domain: == domain 1 score: 722.3 bits; conditional E-value: 8.2e-222 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaallaGl 76 ++ i+da+rtpiGry+G+lssvraddlaa+plkal++r+p+ld++aiddvi+GcanqaGednrnva ma llaGl lcl|FitnessBrowser__Putida:PP_3280 8 DALIIDAVRTPIGRYAGALSSVRADDLAAIPLKALIQRHPELDWKAIDDVIFGCANQAGEDNRNVAHMASLLAGL 82 578************************************************************************ PP TIGR02430 77 pvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwrfvnp 151 p +vpgtt+nrlcgsglda+g aara+++Gea l++aGGvesmsrapfv+Gk++ af+r a+l+dttiGwrfvnp lcl|FitnessBrowser__Putida:PP_3280 83 PLEVPGTTINRLCGSGLDAIGNAARALRCGEAGLMLAGGVESMSRAPFVMGKSEQAFGRAAELFDTTIGWRFVNP 157 *************************************************************************** PP TIGR02430 152 klkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvdkdehlr 226 +ka yG+dsmpetaenvae+fg+sr+dqdafalrsq+++aaaqa+G +a+eivpvei+q+kG ++vv++deh+r lcl|FitnessBrowser__Putida:PP_3280 158 LMKAAYGIDSMPETAENVAEQFGISRADQDAFALRSQHKAAAAQARGRLAREIVPVEIPQRKGPAKVVEHDEHPR 232 *************************************************************************** PP TIGR02430 227 aettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprvmGlgpvpa 301 +ttle+la+l +++re+g+vtaGnasGvndGa+alllas a++rhgl++r+ri+++a aGvepr+mG+gpvpa lcl|FitnessBrowser__Putida:PP_3280 233 GDTTLEQLARLGTPFREGGSVTAGNASGVNDGACALLLASSAAARRHGLKARGRIVGMAVAGVEPRLMGIGPVPA 307 *************************************************************************** PP TIGR02430 302 vkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlvltalkqleks 376 ++k+la +gl+l+dldvielneafaaq+lavlrelgladdd rvn nGGaialGhplG+sGarlv+tal++le++ lcl|FitnessBrowser__Putida:PP_3280 308 TRKVLALTGLALADLDVIELNEAFAAQGLAVLRELGLADDDPRVNRNGGAIALGHPLGMSGARLVTTALHELEET 382 *************************************************************************** PP TIGR02430 377 ggryalatlciGvGqGialvierv 400 gryal+t+ciGvGqGia++ier+ lcl|FitnessBrowser__Putida:PP_3280 383 AGRYALCTMCIGVGQGIAMIIERL 406 **********************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (400 nodes) Target sequences: 1 (406 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: 00:00:00.02 # Mc/sec: 7.94 // [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