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_055435026.1 ASC41_RS02340 3-oxoadipyl-CoA thiolase
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_001418085.1:WP_055435026.1 Length = 404 Score = 462 bits (1190), Expect = e-135 Identities = 234/402 (58%), Positives = 299/402 (74%), Gaps = 1/402 (0%) Query: 1 MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 M+EA+I DGIRTPIG Y G LS+VR DDL A+ + E++ RNP + E DDVI+GCANQA Sbjct: 1 MKEAYIIDGIRTPIGNYKGTLSAVRTDDLGALVISEIVKRNPSIPKEAYDDVIMGCANQA 60 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 GEDNRNVARM++LLAGLP +V G T+NRLC SGL A+ A RAIKAGDGD+ I+GGVE+M Sbjct: 61 GEDNRNVARMSSLLAGLPFTVPGETVNRLCSSGLSAIIHANRAIKAGDGDVFISGGVENM 120 Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRED 180 +R P+VM K ++AF ++M+D+T GWRF+NP M +GTD M TAEN+ E ISRED Sbjct: 121 TRGPYVMAKPSTAFGGDSKMYDSTFGWRFINPKMQALYGTDGMGNTAENLVEKYNISRED 180 Query: 181 QDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKA 240 QD FAL SQQ+ KAQ SG LA+EIV V + +K + DE ++P ++LE L L+A Sbjct: 181 QDKFALWSQQKATKAQESGRLAKEIVTVEIPQRKKDPIQFSKDEFIKPTSSLEVLGKLRA 240 Query: 241 PF-RANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGP 299 F + G +TAGN+SG+NDGAAA IIAS L P ARIV+ A GVEPR+MG+GP Sbjct: 241 AFKKEGGSVTAGNSSGLNDGAAATIIASADAVKKYNLKPLARIVSSAVVGVEPRIMGIGP 300 Query: 300 VPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPL 359 V A+ + L +AGL++ D+D+IELNEAFAAQAL +R G+ D+ P +NPNGGAIA+GHPL Sbjct: 301 VQASNKALAKAGLTMDDIDIIELNEAFAAQALACIRAWGIADNDPRINPNGGAIAIGHPL 360 Query: 360 GMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 G++GAR+A +A+ EL +N +YAL TMCIGVGQG A I+E V Sbjct: 361 GVTGARVAHSAALELQNQNKKYALITMCIGVGQGYAAIIENV 402 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: 446 Number of extensions: 11 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: 401 Length of database: 404 Length adjustment: 31 Effective length of query: 370 Effective length of database: 373 Effective search space: 138010 Effective search space used: 138010 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_055435026.1 ASC41_RS02340 (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.460726.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-185 602.2 3.2 2.8e-185 602.0 3.2 1.0 1 NCBI__GCF_001418085.1:WP_055435026.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001418085.1:WP_055435026.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 602.0 3.2 2.8e-185 2.8e-185 1 400 [] 2 402 .. 2 402 .. 0.99 Alignments for each domain: == domain 1 score: 602.0 bits; conditional E-value: 2.8e-185 TIGR02430 1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnvarmaall 73 ke+yi+d+irtpiG y G+ls+vr+ddl+a+ + ++++rnps+ +a ddvi+GcanqaGednrnvarm+ ll NCBI__GCF_001418085.1:WP_055435026.1 2 KEAYIIDGIRTPIGNYKGTLSAVRTDDLGALVISEIVKRNPSIPKEAYDDVIMGCANQAGEDNRNVARMSSLL 74 69*********************************************************************** PP TIGR02430 74 aGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafsrsakledttiGw 146 aGlp +vpg tvnrlc+sgl a+ a raikaG+ d+ i+GGve m+r p+v+ k +af+ + k+ d+t+Gw NCBI__GCF_001418085.1:WP_055435026.1 75 AGLPFTVPGETVNRLCSSGLSAIIHANRAIKAGDGDVFISGGVENMTRGPYVMAKPSTAFGGDSKMYDSTFGW 147 ************************************************************************* PP TIGR02430 147 rfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffaeeivpveikqkkGeetvv 219 rf+npk++alyG+d m++taen+ e++++sredqd+fal sqq++++aq++G +a+eiv+vei+q+k ++ + NCBI__GCF_001418085.1:WP_055435026.1 148 RFINPKMQALYGTDGMGNTAENLVEKYNISREDQDKFALWSQQKATKAQESGRLAKEIVTVEIPQRKKDPIQF 220 ************************************************************************* PP TIGR02430 220 dkdehlraettlealaklkavvred.gtvtaGnasGvndGaaalllaseeavkrhgltprarilaaasaGvep 291 +kde ++ ++le l kl+a ++++ g+vtaGn+sG+ndGaaa ++as++avk+++l+p ari+++a +Gvep NCBI__GCF_001418085.1:WP_055435026.1 221 SKDEFIKPTSSLEVLGKLRAAFKKEgGSVTAGNSSGLNDGAAATIIASADAVKKYNLKPLARIVSSAVVGVEP 293 ********************99865279********************************************* PP TIGR02430 292 rvmGlgpvpavkkllaraglsledldvielneafaaqalavlrelgladddarvnpnGGaialGhplGasGar 364 r+mG+gpv a +k+la+agl+++d+d+ielneafaaqala++r+ g+ad+d r+npnGGaia+GhplG++Gar NCBI__GCF_001418085.1:WP_055435026.1 294 RIMGIGPVQASNKALAKAGLTMDDIDIIELNEAFAAQALACIRAWGIADNDPRINPNGGAIAIGHPLGVTGAR 366 ************************************************************************* PP TIGR02430 365 lvltalkqleksggryalatlciGvGqGialvierv 400 ++ +a +l++++++yal t+ciGvGqG a +ie v NCBI__GCF_001418085.1:WP_055435026.1 367 VAHSAALELQNQNKKYALITMCIGVGQGYAAIIENV 402 *********************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (400 nodes) Target sequences: 1 (404 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 26.83 // [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