Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate SM_b20589 SM_b20589 beta-ketoadipyl CoA thiolase
Query= metacyc::MONOMER-3207 (400 letters) >FitnessBrowser__Smeli:SM_b20589 Length = 400 Score = 547 bits (1409), Expect = e-160 Identities = 280/401 (69%), Positives = 327/401 (81%), Gaps = 2/401 (0%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 MR+ +ICD IRTPIGRFGG+LA VRADDL A+PLKAL++ N +V W+ VD+V FGCANQA Sbjct: 1 MREAYICDYIRTPIGRFGGSLASVRADDLGAIPLKALMDRNRSVDWEAVDDVIFGCANQA 60 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GEDNRN+ARM+LLLAGLP ++PG T+NRLC SGMDA+ A RAI GE EL IAGGVESM Sbjct: 61 GEDNRNIARMSLLLAGLPVAVPGTTINRLCGSGMDAVIAAARAIKCGEAELMIAGGVESM 120 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 SRAPFV+ KAES +SRN ++ DTTIGWRF+NPLMK+QYGVDSMPET +NVA+DY+VSR D Sbjct: 121 SRAPFVLPKAESAFSRNAEIYDTTIGWRFVNPLMKAQYGVDSMPETGENVAEDYKVSRED 180 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKK-GETIVERDEHLRPETTLEALTKLKP 239 QDAFALRSQ KAAAAQA G A EIV V I +K G +++RDEH R TT+EAL LK Sbjct: 181 QDAFALRSQAKAAAAQANGRLASEIVAVTIPQRKGGPVVIDRDEHPR-ATTIEALAGLKT 239 Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299 TVTAGNASGVNDGAAALI+AS EA +KHGL P AR+LG AS GV PR+MG+GPV Sbjct: 240 PFREGGTVTAGNASGVNDGAAALIIASEEAARKHGLRPMARILGGASAGVPPRIMGMGPV 299 Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359 PA ++L RLG FDVIELNEAFASQGLAVLR LG+ADD P+VN NGGAIALGHPLG Sbjct: 300 PASQRLMTRLGATQDRFDVIELNEAFASQGLAVLRALGIADDDPRVNRNGGAIALGHPLG 359 Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 MSGAR+ TA +L ++GGR L+TMC+GVGQG+A+A+ERV Sbjct: 360 MSGARITGTAALELAETGGRTSLSTMCIGVGQGIAVALERV 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: 522 Number of extensions: 20 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 SM_b20589 SM_b20589 (beta-ketoadipyl 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.18136.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-136 440.7 2.5 2.5e-136 440.6 2.5 1.0 1 lcl|FitnessBrowser__Smeli:SM_b20589 SM_b20589 beta-ketoadipyl CoA th Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SM_b20589 SM_b20589 beta-ketoadipyl CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 440.6 2.5 2.5e-136 2.5e-136 1 385 [] 6 398 .. 6 398 .. 0.96 Alignments for each domain: == domain 1 score: 440.6 bits; conditional E-value: 2.5e-136 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglpe 72 i d++Rtpig++ggsl++++a+dL+a +k+l++r+ +d e++d+vi+G++ qage+ niaR+ +l aglp lcl|FitnessBrowser__Smeli:SM_b20589 6 ICDYIRTPIGRFGGSLASVRADDLGAIPLKALMDRNrSVDWEAVDDVIFGCANQAGEDnRNIARMSLLLAGLPV 79 7899******************************************************9*************** PP TIGR01930 73 svpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144 vp++t+nr+C+Sg++Av+ aa++ik+Gea++++aGGvEsmSr+p++l+++ es+ ++a+ +d+++ lcl|FitnessBrowser__Smeli:SM_b20589 80 AVPGTTINRLCGSGMDAVIAAARAIKCGEAELMIAGGVESMSRAPFVLPKA---ESAFSRNAEIYDTTIGWRfv 150 *************************************************97...56666777888854443378 PP TIGR01930 145 ......vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvskDe 209 ++ sm et en+a++y++sRe+qD++alrS+ kaa+A+++g++++eiv v+++++ ++v+++De lcl|FitnessBrowser__Smeli:SM_b20589 151 nplmkaQYGVDSMPETGENVAEDYKVSREDQDAFALRSQAKAAAAQANGRLASEIVAVTIPQRkggPVVIDRDE 224 999998778889*************************************************999********** PP TIGR01930 210 girpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemg 283 ++r tt+e+La+Lk+ f+e g tvtAgN+s++nDGAaal+++see+a+++gl+p+ari + a agv+p++mg lcl|FitnessBrowser__Smeli:SM_b20589 225 HPR-ATTIEALAGLKTPFRE-GG-TVTAGNASGVNDGAAALIIASEEAARKHGLRPMARILGGASAGVPPRIMG 295 ***.899***********96.68.7************************************************* PP TIGR01930 284 lgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGasGarivltl 356 +gpvpA+++++ + g + + +d++E+nEAFA+q lav ++lg d + +vN nGGAiAlGHPlG+sGari+ t lcl|FitnessBrowser__Smeli:SM_b20589 296 MGPVPASQRLMTRLGATQDRFDVIELNEAFASQGLAVLRALGIADdDPRVNRNGGAIALGHPLGMSGARITGTA 369 ******************************************866799************************** PP TIGR01930 357 lkeLkergkkyGlatlCvggGqGaAvile 385 + eL+e g++ l t+C+g GqG+Av le lcl|FitnessBrowser__Smeli:SM_b20589 370 ALELAETGGRTSLSTMCIGVGQGIAVALE 398 **************************987 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.83 // [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