Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate AO356_04930 AO356_04930 beta-ketoadipyl CoA thiolase
Query= metacyc::MONOMER-3207 (400 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_04930 Length = 400 Score = 715 bits (1846), Expect = 0.0 Identities = 359/400 (89%), Positives = 385/400 (96%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 MRDV+ICDAIRTPIGRFGG L+ VRADDLAAVP+KAL+E NP+V W+ VDEVF GCANQA Sbjct: 1 MRDVYICDAIRTPIGRFGGGLSAVRADDLAAVPIKALMERNPSVDWNAVDEVFLGCANQA 60 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GEDNRNVARMALLLAGLP+SIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM Sbjct: 61 GEDNRNVARMALLLAGLPQSIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 SRAPFVMGKA++ +SRNMKLEDTTIGWRFINPLMK+QYGVD+MP+TADNVADDY VSRAD Sbjct: 121 SRAPFVMGKADTAFSRNMKLEDTTIGWRFINPLMKAQYGVDAMPQTADNVADDYAVSRAD 180 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIVERDEHLRPETTLEALTKLKPV 240 QDAFALRSQQ+ AAAQAAGFFAEEIVPVRIAHKKGET+VE+DEH R +TTLE L+KLKPV Sbjct: 181 QDAFALRSQQRTAAAQAAGFFAEEIVPVRIAHKKGETVVEQDEHPRADTTLETLSKLKPV 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 SGARLV+TALH LEK+GG+KGLATMCVGVGQGLALAIERV Sbjct: 361 SGARLVMTALHHLEKTGGKKGLATMCVGVGQGLALAIERV 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: 668 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 AO356_04930 AO356_04930 (beta-ketoadipyl 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.403999.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-227 740.2 10.3 3.4e-227 740.0 10.3 1.0 1 FitnessBrowser__pseudo5_N2C3_1:AO356_04930 Domain annotation for each sequence (and alignments): >> FitnessBrowser__pseudo5_N2C3_1:AO356_04930 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 740.0 10.3 3.4e-227 3.4e-227 1 400 [] 2 400 .] 2 400 .] 1.00 Alignments for each domain: == domain 1 score: 740.0 bits; conditional E-value: 3.4e-227 TIGR02430 1 kevyivdairtpiGrygGslssvraddlaavplkallarnpsldaaaiddvilGcanqaGednrnva 67 ++vyi+dairtpiGr+gG+ls+vraddlaavp+kal++rnps+d++a+d+v+lGcanqaGednrnva FitnessBrowser__pseudo5_N2C3_1:AO356_04930 2 RDVYICDAIRTPIGRFGGGLSAVRADDLAAVPIKALMERNPSVDWNAVDEVFLGCANQAGEDNRNVA 68 689**************************************************************** PP TIGR02430 68 rmaallaGlpvsvpgttvnrlcgsgldalglaaraikaGeadlviaGGvesmsrapfvlGkadsafs 134 rma+llaGlp+s+pg+t+nrlc+sg+da+g+a+rai++Ge +l iaGGvesmsrapfv+Gkad+afs FitnessBrowser__pseudo5_N2C3_1:AO356_04930 69 RMALLLAGLPQSIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSRAPFVMGKADTAFS 135 ******************************************************************* PP TIGR02430 135 rsakledttiGwrfvnpklkalyGvdsmpetaenvaeefgvsredqdafalrsqqrtaaaqakGffa 201 r+ kledttiGwrf+np +ka+yGvd+mp+ta+nva++++vsr+dqdafalrsqqrtaaaqa+Gffa FitnessBrowser__pseudo5_N2C3_1:AO356_04930 136 RNMKLEDTTIGWRFINPLMKAQYGVDAMPQTADNVADDYAVSRADQDAFALRSQQRTAAAQAAGFFA 202 ******************************************************************* PP TIGR02430 202 eeivpveikqkkGeetvvdkdehlraettlealaklkavvredgtvtaGnasGvndGaaalllasee 268 eeivpv+i++kkG etvv++deh+ra+ttle+l+klk+v+ +d+tvtaGnasGvndGaaal+las+e FitnessBrowser__pseudo5_N2C3_1:AO356_04930 203 EEIVPVRIAHKKG-ETVVEQDEHPRADTTLETLSKLKPVNGPDKTVTAGNASGVNDGAAALILASAE 268 *************.899************************************************** PP TIGR02430 269 avkrhgltprarilaaasaGveprvmGlgpvpavkkllaraglsledldvielneafaaqalavlre 335 avk+hgltpr+++l++asaGv+prvmG+gpvpav+kl +r+gl+++d+dvielneafa+q+lavlr+ FitnessBrowser__pseudo5_N2C3_1:AO356_04930 269 AVKKHGLTPRGKVLGMASAGVAPRVMGIGPVPAVRKLTERLGLAVADFDVIELNEAFASQGLAVLRD 335 ******************************************************************* PP TIGR02430 336 lgladddarvnpnGGaialGhplGasGarlvltalkqleksggryalatlciGvGqGialvierv 400 lgladd+ +vnpnGGaialGhplG+sGarlv+tal++lek+gg+ +lat+c+GvGqG+al+ierv FitnessBrowser__pseudo5_N2C3_1:AO356_04930 336 LGLADDAPQVNPNGGAIALGHPLGMSGARLVMTALHHLEKTGGKKGLATMCVGVGQGLALAIERV 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: 22.53 // [ok]
This GapMind analysis is from Apr 09 2024. 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