Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate WP_065401082.1 BBI00_RS22490 3-oxoadipyl-CoA thiolase
Query= metacyc::MONOMER-3207 (400 letters) >NCBI__GCF_001684965.1:WP_065401082.1 Length = 401 Score = 475 bits (1222), Expect = e-138 Identities = 237/401 (59%), Positives = 307/401 (76%), Gaps = 1/401 (0%) Query: 1 MRDVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQA 60 M +V+I D +RTPI + G L+ VRADDLAA+ +K ++ NP V +++++V FGCANQA Sbjct: 1 MNNVYIIDYVRTPISKLQGGLSEVRADDLAAIVIKEVVARNPEVPVEEIEDVIFGCANQA 60 Query: 61 GEDNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESM 120 GEDNRNVARM LLLAGLP I G T+NRLCASGM A+ AFR+IASGE E+ IAGGVE M Sbjct: 61 GEDNRNVARMGLLLAGLPYKIGGETVNRLCASGMSAVANAFRSIASGEGEIYIAGGVEHM 120 Query: 121 SRAPFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRAD 180 +R+P+VM K + + R+ ++ DTT GWRFINP MK YGVD M ETA+N+AD + +SR D Sbjct: 121 TRSPYVMSKPGAAFGRDSQMFDTTFGWRFINPKMKEMYGVDGMGETAENLADMHHISRED 180 Query: 181 QDAFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGETIV-ERDEHLRPETTLEALTKLKP 239 QD FAL SQQKA AQ +G AEEIV V I +KGE ++ E+DE ++P +++E L KL+P Sbjct: 181 QDKFALWSQQKATKAQESGRLAEEIVKVEIPQRKGEPVIFEKDEFIKPGSSMEGLGKLRP 240 Query: 240 VNGPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPV 299 + TVTAGNASG+NDGAAALILAS EAVKK+GL P+AR+LG + GV PR+MGIGPV Sbjct: 241 AFRKEGTVTAGNASGMNDGAAALILASEEAVKKYGLKPKARILGSSVAGVEPRIMGIGPV 300 Query: 300 PAVRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLG 359 A +KL +RL +++ D D+IELNEAFA+Q LAV R LG+ DD ++NPNGGAIA+GHPLG Sbjct: 301 EATQKLLKRLDLSLEDMDIIELNEAFAAQALAVTRTLGLKDDDSRINPNGGAIAIGHPLG 360 Query: 360 MSGARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400 +SGAR++ +A +L+K + L T+C+GVGQG A+ IE+V Sbjct: 361 VSGARIIGSAAMELQKQNKKYALCTLCIGVGQGYAMVIEKV 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: 451 Number of extensions: 12 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_065401082.1 BBI00_RS22490 (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.1913766.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-144 466.7 0.3 3.2e-144 466.5 0.3 1.0 1 NCBI__GCF_001684965.1:WP_065401082.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001684965.1:WP_065401082.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 466.5 0.3 3.2e-144 3.2e-144 1 385 [] 6 399 .. 6 399 .. 0.94 Alignments for each domain: == domain 1 score: 466.5 bits; conditional E-value: 3.2e-144 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglp 71 i+d+vRtpi kl+g l+e++a+dL+a vike+++r+ ++ e+i++vi+G++ qage+ n+aR+ +l aglp NCBI__GCF_001684965.1:WP_065401082.1 6 IIDYVRTPISKLQGGLSEVRADDLAAIVIKEVVARNpEVPVEEIEDVIFGCANQAGEDnRNVARMGLLLAGLP 78 89********************************************************9************** PP TIGR01930 72 esvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl 144 +++ + tvnr+CaSg+ Ava+a ++i++Ge ++++aGGvE+m+r+p+++++ ++ + + +++ d+ NCBI__GCF_001684965.1:WP_065401082.1 79 YKIGGETVNRLCASGMSAVANAFRSIASGEGEIYIAGGVEHMTRSPYVMSKPGAAFGRD---SQMFDT----T 144 ***********************************************999974333333...333331....1 PP TIGR01930 145 ............vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...k 202 + mgetAenla+ ++isRe+qD++al S+qka+kA+e+g++++eiv ve++++ + NCBI__GCF_001684965.1:WP_065401082.1 145 fgwrfinpkmkeMYGVDGMGETAENLADMHHISREDQDKFALWSQQKATKAQESGRLAEEIVKVEIPQRkgeP 217 234456777787666778*************************************************999*9* PP TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaava 275 ++++kDe i+p++++e L+kL+paf++ +g tvtAgN+s++nDGAaal+l+see++k++gl+p+ari + +va NCBI__GCF_001684965.1:WP_065401082.1 218 VIFEKDEFIKPGSSMEGLGKLRPAFRK-EG-TVTAGNASGMNDGAAALILASEEAVKKYGLKPKARILGSSVA 288 *************************95.8*.6***************************************** PP TIGR01930 276 gvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld.lekvNvnGGAiAlGHPlGa 347 gv+p++mg+gpv+A++k+Lk+ +ls++d+d++E+nEAFAaq+lav++ lg++d ++++N nGGAiA+GHPlG+ NCBI__GCF_001684965.1:WP_065401082.1 289 GVEPRIMGIGPVEATQKLLKRLDLSLEDMDIIELNEAFAAQALAVTRTLGLKDdDSRINPNGGAIAIGHPLGV 361 **************************************************8667******************* PP TIGR01930 348 sGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 sGari+ + + eL++++kky+l tlC+g GqG A+++e NCBI__GCF_001684965.1:WP_065401082.1 362 SGARIIGSAAMELQKQNKKYALCTLCIGVGQGYAMVIE 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 10.32 // [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