Align 3-oxoadipyl-CoA thiolase; EC 2.3.1.174 (characterized, see rationale)
to candidate YP_001313805.1 Smed_5094 beta-ketoadipyl CoA thiolase
Query= uniprot:B2SYZ2 (400 letters) >NCBI__GCF_000017145.1:YP_001313805.1 Length = 400 Score = 568 bits (1465), Expect = e-167 Identities = 282/400 (70%), Positives = 333/400 (83%) Query: 1 MNDAFICDAIRTPIGRYGGALKDVRADDLGAVPIKALIERNPGVDWRTVDDVIYGCANQA 60 M DAFICD +RTPIGRYGGAL VRADDLG+VP+KAL+ER+P VDW VDDVI+GCANQA Sbjct: 1 MRDAFICDYVRTPIGRYGGALSSVRADDLGSVPLKALVERHPSVDWEAVDDVIFGCANQA 60 Query: 61 GEDNRNVARMSALLAGLPVEAPGSTINRLCGSGMDAVGTAARAIKAGEARLMIAGGVESM 120 GEDNRNVARMS LLAGLP + G+TINRLCGSGMDAV AARAIK+GEA LMIAGGVESM Sbjct: 61 GEDNRNVARMSLLLAGLPPQVSGTTINRLCGSGMDAVIAAARAIKSGEAELMIAGGVESM 120 Query: 121 TRAPFVMGKATSAFARQADIYDTTIGWRFINPLMKRQYGVDSMPETAENVAAEFSVSRAD 180 +RAP V+ KA +AF+R A+IYDTTIGWRF+NPLMK QYGVDSMPET ENVA +++VSR D Sbjct: 121 SRAPMVIPKADAAFSRNAEIYDTTIGWRFVNPLMKSQYGVDSMPETGENVAEDYNVSRED 180 Query: 181 QDAFALASQQKAARAQQDGTLAQEIVGVEIAQKKGDPVRALLDEHPRETSLESLGKLKGV 240 QDAFA+ SQ KAARAQ+DG LA+E+V V + Q+KG+P+ DEHPR T++E+L KL Sbjct: 181 QDAFAVLSQAKAARAQEDGRLAKEVVPVTVPQRKGEPIVVQKDEHPRATTIEALAKLPTP 240 Query: 241 VRPDGSVTAGNASGVNDGACALLLANQQAADQYGLRRRARVVGMATAGVEPRIMGIGPAP 300 R GSVTAGNASGV+DGA AL++A+ +AA +YGL+ AR++ ATAGV PR+MGIGPAP Sbjct: 241 FRKGGSVTAGNASGVSDGAAALIIASAEAAQKYGLKPVARIIAGATAGVSPRVMGIGPAP 300 Query: 301 ATQKLLKQLGMTLEQLDVIELNEAFASQGLAVLRTLGLRDDDPRVNPNGGAIALGHPLGA 360 A+QKL++ G+ EQ DVIELNEAFASQGLAVLR LG+ DDD RVN NGGAIALGHPLG Sbjct: 301 ASQKLMRLTGLKQEQFDVIELNEAFASQGLAVLRALGIADDDARVNRNGGAIALGHPLGM 360 Query: 361 SGARLITTALYQLERTNGRFALCTMCIGVGQGIALVIERL 400 SGAR+ TA +L T GR++L TMCIGVGQGIA+ +ER+ Sbjct: 361 SGARITGTAALELVETGGRYSLSTMCIGVGQGIAVALERV 400 Lambda K H 0.318 0.135 0.386 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: 548 Number of extensions: 14 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: 400 Length of database: 400 Length adjustment: 31 Effective length of query: 369 Effective length of database: 369 Effective search space: 136161 Effective search space used: 136161 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate YP_001313805.1 Smed_5094 (beta-ketoadipyl 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.2101.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-211 688.7 8.5 1.5e-211 688.5 8.5 1.0 1 lcl|NCBI__GCF_000017145.1:YP_001313805.1 Smed_5094 beta-ketoadipyl CoA th Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017145.1:YP_001313805.1 Smed_5094 beta-ketoadipyl CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 688.5 8.5 1.5e-211 1.5e-211 1 400 [] 2 400 .] 2 400 .] 1.00 Alignments for each domain: == domain 1 score: 688.5 bits; conditional E-value: 1.5e-211 TIGR02430 1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarm 69 ++++i+d +rtpiGrygG+lssvraddl++vplkal++r+ps+d++a+ddvi+GcanqaGednrnvarm lcl|NCBI__GCF_000017145.1:YP_001313805.1 2 RDAFICDYVRTPIGRYGGALSSVRADDLGSVPLKALVERHPSVDWEAVDDVIFGCANQAGEDNRNVARM 70 689****************************************************************** PP TIGR02430 70 aallaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsak 138 ++llaGlp +v+gtt+nrlcgsg+da+ aaraik+Gea+l+iaGGvesmsrap v+ kad+afsr+a+ lcl|NCBI__GCF_000017145.1:YP_001313805.1 71 SLLLAGLPPQVSGTTINRLCGSGMDAVIAAARAIKSGEAELMIAGGVESMSRAPMVIPKADAAFSRNAE 139 ********************************************************************* PP TIGR02430 139 ledttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpv 207 + dttiGwrfvnp +k++yGvdsmpet envae+++vsredqdafa+ sq+++a+aq+ G +a+e+vpv lcl|NCBI__GCF_000017145.1:YP_001313805.1 140 IYDTTIGWRFVNPLMKSQYGVDSMPETGENVAEDYNVSREDQDAFAVLSQAKAARAQEDGRLAKEVVPV 208 ********************************************************************* PP TIGR02430 208 eikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhglt 276 +++q+kGe+ vv+kdeh+r tt+ealakl +++r++g+vtaGnasGv dGaaal++as+ea++++gl+ lcl|NCBI__GCF_000017145.1:YP_001313805.1 209 TVPQRKGEPIVVQKDEHPR-ATTIEALAKLPTPFRKGGSVTAGNASGVSDGAAALIIASAEAAQKYGLK 276 *******************.89*********************************************** PP TIGR02430 277 prarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarv 345 p ari+a a+aGv+prvmG+gp+pa +kl++ +gl+ e++dvielneafa+q+lavlr+lg+adddarv lcl|NCBI__GCF_000017145.1:YP_001313805.1 277 PVARIIAGATAGVSPRVMGIGPAPASQKLMRLTGLKQEQFDVIELNEAFASQGLAVLRALGIADDDARV 345 ********************************************************************* PP TIGR02430 346 npnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400 n nGGaialGhplG+sGar+ ta +l ++ggry+l+t+ciGvGqGia+++erv lcl|NCBI__GCF_000017145.1:YP_001313805.1 346 NRNGGAIALGHPLGMSGARITGTAALELVETGGRYSLSTMCIGVGQGIAVALERV 400 ******************************************************8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (400 nodes) Target sequences: 1 (400 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: 6.92 // [ok]
This GapMind analysis is from Sep 24 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