Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_011764045.1 AZO_RS01570 3-oxoadipyl-CoA thiolase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000061505.1:WP_011764045.1 Length = 400 Score = 552 bits (1422), Expect = e-162 Identities = 278/401 (69%), Positives = 329/401 (82%), Gaps = 2/401 (0%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M +VFICD IRTPIGR+GGAL+GVR DDLAA+P+KALI N V W VD++++GCANQA Sbjct: 1 MTEVFICDGIRTPIGRYGGALSGVRTDDLAALPIKALIARNSGVDWAAVDDIYYGCANQA 60 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GEDNR+VARMA LLAGLP +PG T+NRLC SGMDA+GTA RAI +GE +L IAGGVESM Sbjct: 61 GEDNRDVARMAGLLAGLPIDVPGSTINRLCGSGMDAVGTAARAIRTGETQLMIAGGVESM 120 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 SRAPFVMGKA++ +SR+ K+EDTTIGWRF+NPLMK++YG+DSMPETA+NVA D+ ++RAD Sbjct: 121 SRAPFVMGKADTAFSRSAKIEDTTIGWRFVNPLMKAKYGIDSMPETAENVATDFNINRAD 180 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETI-VERDEHLRPETTLEALTKLKP 239 QDAFALRSQ + AAA GF+ E+VPV IA KKG+ + V DEH R TTLEAL KLK Sbjct: 181 QDAFALRSQLRYAAAAERGFYEGELVPVEIAQKKGDPLRVTADEHPR-VTTLEALAKLKG 239 Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299 V PD TVTAGNASGVNDG+ AL+LAS A KHGL PRAR++ MA+ GV PR+MGIGP Sbjct: 240 VVRPDGTVTAGNASGVNDGSVALLLASEAAAAKHGLKPRARIVAMATAGVEPRIMGIGPA 299 Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359 PA RKL G+++ DVIELNEAFA+Q LAV R+LG+ADD +VNPNGGAI+LGHPLG Sbjct: 300 PASRKLLALTGLSLDQMDVIELNEAFAAQALAVTRQLGLADDDARVNPNGGAISLGHPLG 359 Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 SGARLVLTAL QLE +GGR GL TMC+GVGQG+A+ IERV Sbjct: 360 ASGARLVLTALRQLEATGGRYGLCTMCIGVGQGIAMIIERV 400 Lambda K H 0.318 0.134 0.383 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: 520 Number of extensions: 10 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 WP_011764045.1 AZO_RS01570 (3-oxoadipyl-CoA thiolase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))
# 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/TIGR01930.hmm # target sequence database: /tmp/gapView.11412.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01930 [M=385] Accession: TIGR01930 Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase 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-134 434.9 2.2 1.4e-134 434.8 2.2 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011764045.1 AZO_RS01570 3-oxoadipyl-CoA thio Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000061505.1:WP_011764045.1 AZO_RS01570 3-oxoadipyl-CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 434.8 2.2 1.4e-134 1.4e-134 1 385 [] 6 398 .. 6 398 .. 0.95 Alignments for each domain: == domain 1 score: 434.8 bits; conditional E-value: 1.4e-134 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaala 67 i d++Rtpig++gg+l+ ++ +dL+a ik+l++r+ g+d +++d++++G++ qage+ ++aR+a l lcl|NCBI__GCF_000061505.1:WP_011764045.1 6 ICDGIRTPIGRYGGALSGVRTDDLAALPIKALIARNsGVDWAAVDDIYYGCANQAGEDnRDVARMAGLL 74 789*******99**********************************************9********** PP TIGR01930 68 aglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakl 136 aglp +vp+ t+nr+C+Sg++Av +aa++i++Ge ++++aGGvEsmSr+p+++ ++ +++ ++ak lcl|NCBI__GCF_000061505.1:WP_011764045.1 75 AGLPIDVPGSTINRLCGSGMDAVGTAARAIRTGETQLMIAGGVESMSRAPFVMGKA---DTAFSRSAKI 140 ***************************************************99997...4444455666 PP TIGR01930 137 edqllkdl..........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivp 195 ed+++ + ++ sm etAen+a++++i+R +qD++alrS+ + a+A e+g+ + e+vp lcl|NCBI__GCF_000061505.1:WP_011764045.1 141 EDTTI--GwrfvnplmkaKYGIDSMPETAENVATDFNINRADQDAFALRSQLRYAAAAERGFYEGELVP 207 66333..13467888987667779********************************************* PP TIGR01930 196 vevkgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakel 261 ve+ +k + v+ De++r ttle+LakLk + + ++g tvtAgN+s++nDG++alll+se++a+++ lcl|NCBI__GCF_000061505.1:WP_011764045.1 208 VEIAQKkgdPLRVTADEHPR-VTTLEALAKLKGVVR-PDG-TVTAGNASGVNDGSVALLLASEAAAAKH 273 ***99999989999******.89************9.69*.6*************************** PP TIGR01930 262 gltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.l 329 gl+p ariv++a+agv+p++mg+gp+pA++k+L+ +gls++++d++E+nEAFAaq+lav+++lg+ d + lcl|NCBI__GCF_000061505.1:WP_011764045.1 274 GLKPRARIVAMATAGVEPRIMGIGPAPASRKLLALTGLSLDQMDVIELNEAFAAQALAVTRQLGLADdD 342 ****************************************************************86679 PP TIGR01930 330 ekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 ++vN nGGAi+lGHPlGasGar+vlt l++L+ g++yGl t+C+g GqG+A+i+e lcl|NCBI__GCF_000061505.1:WP_011764045.1 343 ARVNPNGGAISLGHPLGASGARLVLTALRQLEATGGRYGLCTMCIGVGQGIAMIIE 398 ******************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.29 // [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