Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_057506694.1 ABB28_RS00230 acetyl-CoA acetyltransferase
Query= SwissProt::O32177 (391 letters) >NCBI__GCF_001431535.1:WP_057506694.1 Length = 402 Score = 374 bits (960), Expect = e-108 Identities = 207/397 (52%), Positives = 271/397 (68%), Gaps = 9/397 (2%) Query: 1 MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATP 59 +++A IV+ RTPVGKA KG RPDD+ A ++ + +A G + N IDD IIGCA P Sbjct: 5 IQDAYIVAATRTPVGKAPKGVFRNTRPDDMLAHVLRSVVAQAPGIDVNRIDDAIIGCAMP 64 Query: 60 EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119 EAEQG+N+AR LAGLP T+ A TVNR+CSSGLQ++A AA++I LG D +AGG ES Sbjct: 65 EAEQGMNVARIGVLLAGLPDTIAAQTVNRFCSSGLQAVAMAADQIRLGNADLMLAGGTES 124 Query: 120 MSQVPMMGH--VTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAA 177 MS VPMMG+ P++ + Y MG TAE+VA+++ VSRE+QDAFA+ SHQ A Sbjct: 125 MSMVPMMGNKIAMAPSVFDNDHVAIAY-GMGITAEKVAEEWKVSREEQDAFALASHQKAI 183 Query: 178 KALAEGKFKDEIVPVEVTVTE--IGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAF- 234 A+ G+FKDEI P +V + + + + + + + DEG R ++A+ L+ LRP F Sbjct: 184 AAIQNGEFKDEISPYDVRTRQPDLADGRRIITRDKIVDTDEGPRLDSSAEGLAKLRPVFR 243 Query: 235 --SVDGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPV 292 GTVTAGNSSQ SDGA AV+L + GL PL +F SF+V GV PEVMGIGP+ Sbjct: 244 NGQFGGTVTAGNSSQMSDGAGAVLLASEQAVKDYGLKPLARFVSFSVAGVRPEVMGIGPI 303 Query: 293 EAIPRALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCT 352 AIP+ALK AGL + ELNEAFA+Q++ VIR+ G+D KVN GGAIALGHPLG T Sbjct: 304 AAIPKALKQAGLTQDQLDWIELNEAFAAQSLAVIRDCGLDPSKVNPLGGAIALGHPLGAT 363 Query: 353 GTKLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389 G T +L+H ++RR +++G+VTMCIG GMGAAG+FE Sbjct: 364 GAIRTATLLHGLRRRQQKYGMVTMCIGTGMGAAGIFE 400 Lambda K H 0.316 0.133 0.377 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: 441 Number of extensions: 20 Number of successful extensions: 5 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: 391 Length of database: 402 Length adjustment: 31 Effective length of query: 360 Effective length of database: 371 Effective search space: 133560 Effective search space used: 133560 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 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_057506694.1 ABB28_RS00230 (acetyl-CoA acetyltransferase)
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.30589.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-146 472.5 2.5 5.7e-146 472.3 2.5 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057506694.1 ABB28_RS00230 acetyl-CoA acetylt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057506694.1 ABB28_RS00230 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 472.3 2.5 5.7e-146 5.7e-146 1 385 [] 10 400 .. 10 400 .. 0.97 Alignments for each domain: == domain 1 score: 472.3 bits; conditional E-value: 5.7e-146 TIGR01930 1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaal 66 iv+a+Rtp+g + +g++++++++d+la+v+++++++a g+d ++id++i+G++++++eq +n+aR +l lcl|NCBI__GCF_001431535.1:WP_057506694.1 10 IVAATRTPVGkAPKGVFRNTRPDDMLAHVLRSVVAQApGIDVNRIDDAIIGCAMPEAEQgMNVARIGVL 78 8*********988******************************************************** PP TIGR01930 67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkak 135 aglp++++a tvnr+C+SglqAva+aa++i+ G+ad+++aGG EsmS vp++ ++ + + ++ lcl|NCBI__GCF_001431535.1:WP_057506694.1 79 LAGLPDTIAAQTVNRFCSSGLQAVAMAADQIRLGNADLMLAGGTESMSMVPMMGNK----IAMAPSVFD 143 ***************************************************97766....467777777 PP TIGR01930 136 ledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk... 201 +++ v ++ mg+tAe++a+++++sReeqD++al+Shqka +Ai++g+fkdei p++v+++ lcl|NCBI__GCF_001431535.1:WP_057506694.1 144 NDH------VAIAYGMGITAEKVAEEWKVSREEQDAFALASHQKAIAAIQNGEFKDEISPYDVRTRqpd 206 777......5678***************************************************999** PP TIGR01930 202 ..........kkvvskDegirpnttlekLakLkpafke.kkgstvtAgNssqlnDGAaalllmseevak 259 +k+v++Deg+r ++++e LakL+p+f++ + g tvtAgNssq++DGA+a+ll+se+++k lcl|NCBI__GCF_001431535.1:WP_057506694.1 207 ladgrriitrDKIVDTDEGPRLDSSAEGLAKLRPVFRNgQFGGTVTAGNSSQMSDGAGAVLLASEQAVK 275 **********9*************************97522339************************* PP TIGR01930 260 elgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsld 328 ++gl+plar+vs++vagv pe+mg+gp+ Ai+kaLk+agl+ +++d++E+nEAFAaq lav+++ g ld lcl|NCBI__GCF_001431535.1:WP_057506694.1 276 DYGLKPLARFVSFSVAGVRPEVMGIGPIAAIPKALKQAGLTQDQLDWIELNEAFAAQSLAVIRDCG-LD 343 ******************************************************************.99 PP TIGR01930 329 lekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 ++kvN GGAiAlGHPlGa+Ga+ ++tll+ L++r++kyG++t+C+g+G+GaA i+e lcl|NCBI__GCF_001431535.1:WP_057506694.1 344 PSKVNPLGGAIALGHPLGATGAIRTATLLHGLRRRQQKYGMVTMCIGTGMGAAGIFE 400 ******************************************************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (402 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: 00:00:00.01 # Mc/sec: 12.31 // [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