Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_004299880.1 C665_RS03170 3-oxoadipyl-CoA thiolase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_000310185.1:WP_004299880.1 Length = 401 Score = 561 bits (1446), Expect = e-164 Identities = 284/401 (70%), Positives = 326/401 (81%), Gaps = 1/401 (0%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M FICDAIRTPIGR+GG LA VRADDL AVPLKAL+ NP V W V+++ +GCANQA Sbjct: 1 MTQAFICDAIRTPIGRYGGTLASVRADDLGAVPLKALMTRNPQVDWTAVEDIIYGCANQA 60 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GEDNRNVARM+ LLAGLP +PG T+NRLC SGMDAIG A R+I SGE EL IAGGVESM Sbjct: 61 GEDNRNVARMSGLLAGLPIEVPGTTVNRLCGSGMDAIGLAARSIKSGETELMIAGGVESM 120 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 SRAPFVMGKAES +SR+ + DTTIGWRFINPLMK Y SMP+TADNVA D+ +SRAD Sbjct: 121 SRAPFVMGKAESAFSRSAAIYDTTIGWRFINPLMKKLYETHSMPQTADNVAADFDISRAD 180 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIV-ERDEHLRPETTLEALTKLKP 239 QDAFALRSQQ+ AAA AAG F +E+VPV I KKG+ IV + DEH RPETTLE L KLK Sbjct: 181 QDAFALRSQQRWAAAHAAGRFKDELVPVVIPRKKGDPIVFDTDEHPRPETTLEMLAKLKG 240 Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299 VNGP+ +VTAGNASGVNDGA AL+LAS A KHGLTPRARV+ MA+ GVAPR+MG GP Sbjct: 241 VNGPELSVTAGNASGVNDGACALLLASDAAAAKHGLTPRARVVAMATAGVAPRIMGFGPA 300 Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359 PAVRK+ + G+ + DVIELNEAFA+QGLAVLR+LG+ADD +VNPNGGAIALGHPLG Sbjct: 301 PAVRKVLAKAGLTLDQMDVIELNEAFAAQGLAVLRDLGLADDEERVNPNGGAIALGHPLG 360 Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 MSGARLV TA ++L++ GR L TMC+GVGQG+A+ IERV Sbjct: 361 MSGARLVTTAAYELQRRNGRYALCTMCIGVGQGIAMIIERV 401 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: 515 Number of extensions: 17 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: 400 Length of database: 401 Length adjustment: 31 Effective length of query: 369 Effective length of database: 370 Effective search space: 136530 Effective search space used: 136530 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_004299880.1 C665_RS03170 (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.18650.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-142 459.3 0.8 5.5e-142 459.2 0.8 1.0 1 lcl|NCBI__GCF_000310185.1:WP_004299880.1 C665_RS03170 3-oxoadipyl-CoA thi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000310185.1:WP_004299880.1 C665_RS03170 3-oxoadipyl-CoA thiolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 459.2 0.8 5.5e-142 5.5e-142 1 385 [] 6 399 .. 6 399 .. 0.95 Alignments for each domain: == domain 1 score: 459.2 bits; conditional E-value: 5.5e-142 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaala 67 i da+Rtpig++gg+l++++a+dL+a +k+l+ r+ ++d +++++i+G++ qage+ n+aR+ l lcl|NCBI__GCF_000310185.1:WP_004299880.1 6 ICDAIRTPIGRYGGTLASVRADDLGAVPLKALMTRNpQVDWTAVEDIIYGCANQAGEDnRNVARMSGLL 74 789*******99**********************************************9********** PP TIGR01930 68 aglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakl 136 aglp +vp++tvnr+C+Sg++A+ laa++ik+Ge ++++aGGvEsmSr+p+++ ++ es+ ++a lcl|NCBI__GCF_000310185.1:WP_004299880.1 75 AGLPIEVPGTTVNRLCGSGMDAIGLAARSIKSGETELMIAGGVESMSRAPFVMGKA---ESAFSRSAAI 140 ***************************************************99997...4444445555 PP TIGR01930 137 edqllkdl..........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivp 195 +d+++ + ++ sm +tA+n+a++++isR +qD++alrS+q+ a+A+++g+fkde+vp lcl|NCBI__GCF_000310185.1:WP_004299880.1 141 YDTTI--GwrfinplmkkLYETHSMPQTADNVAADFDISRADQDAFALRSQQRWAAAHAAGRFKDELVP 207 55333..1346788899988999********************************************** PP TIGR01930 196 vevkgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakel 261 v++++k + v+++De++rp+ttle LakLk + + + s vtAgN+s++nDGA+alll+s+++a+++ lcl|NCBI__GCF_000310185.1:WP_004299880.1 208 VVIPRKkgdPIVFDTDEHPRPETTLEMLAKLKGVNGP-ELS-VTAGNASGVNDGACALLLASDAAAAKH 274 ***9999999*************************95.897.*************************** PP TIGR01930 262 gltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.l 329 gltp ar+v++a+agv p++mg+gp+pA++k+L+kagl+++++d++E+nEAFAaq lav ++lg+ d + lcl|NCBI__GCF_000310185.1:WP_004299880.1 275 GLTPRARVVAMATAGVAPRIMGFGPAPAVRKVLAKAGLTLDQMDVIELNEAFAAQGLAVLRDLGLADdE 343 ****************************************************************8667* PP TIGR01930 330 ekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 e+vN nGGAiAlGHPlG+sGar+v+t ++eL++r+++y+l t+C+g GqG+A+i+e lcl|NCBI__GCF_000310185.1:WP_004299880.1 344 ERVNPNGGAIALGHPLGMSGARLVTTAAYELQRRNGRYALCTMCIGVGQGIAMIIE 399 ******************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (401 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 0.00s 00:00:00.01 Elapsed: 00:00:00.05 # Mc/sec: 3.05 // [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