Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate Pf6N2E2_2835 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)
Query= metacyc::MONOMER-3207 (400 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2835 Length = 400 Score = 709 bits (1831), Expect = 0.0 Identities = 358/400 (89%), Positives = 382/400 (95%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 MRDV+ICDAIRTPIGRFGG L+ VRADDLAAVP+KAL+E NP+V W VDEVF GCANQA Sbjct: 1 MRDVYICDAIRTPIGRFGGGLSAVRADDLAAVPIKALMERNPSVDWSAVDEVFLGCANQA 60 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GEDNRNVARMALLLAGLP+SIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM Sbjct: 61 GEDNRNVARMALLLAGLPDSIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 SRAPFVMGKA++ +SR+MKLEDTTIGWRFINPLMK+QYGVD+MP+TADNVADDY VSRAD Sbjct: 121 SRAPFVMGKADAAFSRSMKLEDTTIGWRFINPLMKAQYGVDAMPQTADNVADDYAVSRAD 180 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240 QDAFALRSQQ+ AAAQAAGFFAEEIV VRIAHKKGET+VE+DEH R +TTLE L KLKPV Sbjct: 181 QDAFALRSQQRTAAAQAAGFFAEEIVAVRIAHKKGETVVEQDEHPRADTTLETLGKLKPV 240 Query: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVP 300 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPR +VLGMAS GVAPRVMGIGPVP Sbjct: 241 NGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRGKVLGMASAGVAPRVMGIGPVP 300 Query: 301 AVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGM 360 AVRKLTERLG+AV+DFDVIELNEAFASQGLAVLR+LG+ADDAPQVNPNGGAIALGHPLGM Sbjct: 301 AVRKLTERLGLAVADFDVIELNEAFASQGLAVLRDLGLADDAPQVNPNGGAIALGHPLGM 360 Query: 361 SGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 SGARLVLTALH LEK+GG+KGLATMCVGVGQGLALAIERV Sbjct: 361 SGARLVLTALHHLEKTGGKKGLATMCVGVGQGLALAIERV 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: 664 Number of extensions: 15 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 Pf6N2E2_2835 (Beta-ketoadipyl CoA thiolase (EC 2.3.1.-))
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.32006.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-136 439.4 4.2 6.1e-136 439.3 4.2 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2835 Beta-ketoadipyl CoA thiolase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2835 Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 439.3 4.2 6.1e-136 6.1e-136 1 385 [] 6 398 .. 6 398 .. 0.94 Alignments for each domain: == domain 1 score: 439.3 bits; conditional E-value: 6.1e-136 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaR 62 i da+Rtpig++gg l+ ++a+dL+a ik+l+er+ +d +++dev lG++ qage+ n+aR lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2835 6 ICDAIRTPIGRFGGGLSAVRADDLAAVPIKALMERNpSVDWSAVDEVFLGCANQAGEDnRNVAR 69 789*******************************************************9***** PP TIGR01930 63 eaalaaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslr. 125 +a+l aglp+s+p++t+nr+CaSg++A+ +a ++i++Ge+++++aGGvEsmSr+p+++ ++ + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2835 70 MALLLAGLPDSIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRAPFVMGKADAa 133 ********************************************************99997442 PP TIGR01930 126 .reslklgkakledqllkdl........vktklsmgetAenlakkygisReeqDeyalrShqka 180 ++s+kl++++ ++ +m +tA+n+a++y++sR +qD++alrS+q++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2835 134 fSRSMKLEDTTIGW-----RfinplmkaQYGVDAMPQTADNVADDYAVSRADQDAFALRSQQRT 192 23333333333333.....245666888777789****************************** PP TIGR01930 181 akAieegkfkdeivpvevkgk..kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssq 242 a+A+++g+f++eiv v++ +k ++vv++De++r++ttle+L+kLkp+ + + tvtAgN+s+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2835 193 AAAQAAGFFAEEIVAVRIAHKkgETVVEQDEHPRADTTLETLGKLKPVNGP-DK-TVTAGNASG 254 ******************9999999************************95.77.7******** PP TIGR01930 243 lnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidl 306 +nDGAaal+l+s e++k++gltp +++ ++a agv p++mg+gpvpA++k+ ++ gl + d+d+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2835 255 VNDGAAALILASAEAVKKHGLTPRGKVLGMASAGVAPRVMGIGPVPAVRKLTERLGLAVADFDV 318 **************************************************************** PP TIGR01930 307 vEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGl 369 +E+nEAFA+q lav ++lg+ d +vN nGGAiAlGHPlG+sGar+vlt l++L++ g+k Gl lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2835 319 IELNEAFASQGLAVLRDLGLADdAPQVNPNGGAIALGHPLGMSGARLVLTALHHLEKTGGKKGL 382 *******************866789*************************************** PP TIGR01930 370 atlCvggGqGaAvile 385 at+Cvg GqG A+ +e lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2835 383 ATMCVGVGQGLALAIE 398 ************9886 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: 00:00:00.02 # Mc/sec: 7.69 // [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