Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_010437861.1 G7G_RS0102215 3-oxoadipyl-CoA thiolase
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_000192475.1:WP_010437861.1 Length = 400 Score = 541 bits (1394), Expect = e-158 Identities = 274/399 (68%), Positives = 317/399 (79%) Query: 3 EAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAGE 62 +AFICD RTPIGRYGG+LS VR DDLAAIP+ L+ RNP++D IDDVI G ANQAGE Sbjct: 2 DAFICDAQRTPIGRYGGSLSQVRTDDLAAIPIAALIARNPQVDWTGIDDVIYGDANQAGE 61 Query: 63 DNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSR 122 NRNVARMA LLAGLP V GTTINRLC SG+DA+G AARAI+AGD D+ IAGGVESMSR Sbjct: 62 SNRNVARMAALLAGLPVDVPGTTINRLCASGMDAVGMAARAIRAGDYDMAIAGGVESMSR 121 Query: 123 APFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISREDQD 182 APFVM KA SAFSR ++DTTIGWRFVNP M Q+FG DSMPETA+NVAE I+R DQD Sbjct: 122 APFVMPKATSAFSRANSVYDTTIGWRFVNPKMKQEFGIDSMPETADNVAEAYGINRSDQD 181 Query: 183 SFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKAPF 242 +FA RSQ R A A +G+ EEI PV + +KG + DEH RP TT E+L GLK Sbjct: 182 AFAERSQARWAAAHQTGVFREEITPVTIPQRKGDPVVVDTDEHPRPGTTAEKLSGLKGIN 241 Query: 243 RANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGPVPA 302 + +TAGNASGVNDGAAA+++A+E AA LTP AR+V M+ AGVEPR+MG+GPVPA Sbjct: 242 GLDKTVTAGNASGVNDGAAAILMANESAAAKNDLTPIARVVGMSVAGVEPRVMGIGPVPA 301 Query: 303 TRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPLGMS 362 +R+VL RAGLSI MDVIELNEAFA+Q L LRELG+PDDAPHVNPNGGAIA+GHPLGMS Sbjct: 302 SRKVLARAGLSIDQMDVIELNEAFASQGLATLRELGVPDDAPHVNPNGGAIAIGHPLGMS 361 Query: 363 GARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 GARL + A+++L R GRYALCTMC+GVGQG A+ILERV Sbjct: 362 GARLVMTAAYQLRRTGGRYALCTMCVGVGQGAALILERV 400 Lambda K H 0.319 0.135 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: 550 Number of extensions: 11 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: 400 Length adjustment: 31 Effective length of query: 370 Effective length of database: 369 Effective search space: 136530 Effective search space used: 136530 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 WP_010437861.1 G7G_RS0102215 (3-oxoadipyl-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.1052942.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-213 694.8 9.9 2e-213 694.6 9.9 1.0 1 NCBI__GCF_000192475.1:WP_010437861.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000192475.1:WP_010437861.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 694.6 9.9 2e-213 2e-213 2 400 .] 2 400 .] 1 400 [] 1.00 Alignments for each domain: == domain 1 score: 694.6 bits; conditional E-value: 2e-213 TIGR02430 2 evyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaalla 74 +++i+da rtpiGrygGsls+vr+ddlaa+p++al+arnp++d++ iddvi+G anqaGe nrnvarmaalla NCBI__GCF_000192475.1:WP_010437861.1 2 DAFICDAQRTPIGRYGGSLSQVRTDDLAAIPIAALIARNPQVDWTGIDDVIYGDANQAGESNRNVARMAALLA 74 69*********************************************************************** PP TIGR02430 75 GlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGwr 147 Glpv+vpgtt+nrlc+sg+da+g+aarai+aG+ d+ iaGGvesmsrapfv+ ka safsr + + dttiGwr NCBI__GCF_000192475.1:WP_010437861.1 75 GLPVDVPGTTINRLCASGMDAVGMAARAIRAGDYDMAIAGGVESMSRAPFVMPKATSAFSRANSVYDTTIGWR 147 ************************************************************************* PP TIGR02430 148 fvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvvd 220 fvnpk+k+ +G+dsmpeta+nvae +g++r+dqdafa rsq+r+aaa+++G+f eei+pv+i+q+kG+++vvd NCBI__GCF_000192475.1:WP_010437861.1 148 FVNPKMKQEFGIDSMPETADNVAEAYGINRSDQDAFAERSQARWAAAHQTGVFREEITPVTIPQRKGDPVVVD 220 ************************************************************************* PP TIGR02430 221 kdehlraettlealaklkavvredgtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGveprv 293 +deh+r+ tt e+l+ lk+++ d+tvtaGnasGvndGaaa+l+a e a+++++ltp ar+++++ aGveprv NCBI__GCF_000192475.1:WP_010437861.1 221 TDEHPRPGTTAEKLSGLKGINGLDKTVTAGNASGVNDGAAAILMANESAAAKNDLTPIARVVGMSVAGVEPRV 293 ************************************************************************* PP TIGR02430 294 mGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGarlv 366 mG+gpvpa +k+laragls++++dvielneafa+q+la+lrelg++dd+ +vnpnGGaia+GhplG+sGarlv NCBI__GCF_000192475.1:WP_010437861.1 294 MGIGPVPASRKVLARAGLSIDQMDVIELNEAFASQGLATLRELGVPDDAPHVNPNGGAIAIGHPLGMSGARLV 366 ************************************************************************* PP TIGR02430 367 ltalkqleksggryalatlciGvGqGialvierv 400 +ta +ql+++ggryal+t+c+GvGqG al++erv NCBI__GCF_000192475.1:WP_010437861.1 367 MTAAYQLRRTGGRYALCTMCVGVGQGAALILERV 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 27.24 // [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