Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate Echvi_1071 Echvi_1071 acetyl-CoA acetyltransferases
Query= SwissProt::O32177 (391 letters) >FitnessBrowser__Cola:Echvi_1071 Length = 391 Score = 411 bits (1057), Expect = e-119 Identities = 210/389 (53%), Positives = 265/389 (68%), Gaps = 2/389 (0%) Query: 3 EAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATPEA 61 +A I+ G RT VGKAKKG RPDDL +K+ + G E +DDLI+G A PEA Sbjct: 2 DAYIIKGYRTAVGKAKKGGFRFYRPDDLAVDVIKKLIADTPGLEAERVDDLIVGNAVPEA 61 Query: 62 EQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAESMS 121 EQG+ M R I +A L VP +NRYC SGL++IA A KI G D IAGG ESMS Sbjct: 62 EQGMQMGRMISLMA-LGKVVPGFIINRYCGSGLEAIALATAKIKSGMADCIIAGGTESMS 120 Query: 122 QVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKALA 181 VPMMG+ T N +A + P+YY+SMG TAE++AK Y +SRED D FAV SH+ A A+ Sbjct: 121 MVPMMGYKTALNWKIASEHPDYYLSMGLTAEELAKDYDISREDSDQFAVTSHERAISAIK 180 Query: 182 EGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDGTVT 241 EG+FK+EIVP+EV T + K + F DEG RP T D+L L+PAF G VT Sbjct: 181 EGRFKEEIVPIEVEETFVDASGKRQTRTFTVDTDEGPRPGTNMDVLGGLKPAFKQGGQVT 240 Query: 242 AGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIPRALKL 301 AGNSSQTSDGAA ++M L L P+ + S++V GV P +MGIGP EA+P+ALK Sbjct: 241 AGNSSQTSDGAAFTVVMSERMVKELNLEPVARLVSYSVAGVDPRIMGIGPKEAVPKALKQ 300 Query: 302 AGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKLTLSLI 361 AG+++ DI L ELNEAFA+QA+ VIR L +D VNVNGGA+ALGHPLGCTG KLT+ +I Sbjct: 301 AGMKMSDISLVELNEAFAAQALAVIRALDMDPNTVNVNGGAVALGHPLGCTGAKLTVQMI 360 Query: 362 HEMKRRNEQFGVVTMCIGGGMGAAGVFEL 390 +E++RRN+++G+VT C+GGG G AGV EL Sbjct: 361 NELRRRNQKYGMVTACVGGGQGVAGVVEL 389 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: 426 Number of extensions: 17 Number of successful extensions: 3 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: 391 Length adjustment: 31 Effective length of query: 360 Effective length of database: 360 Effective search space: 129600 Effective search space used: 129600 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 Echvi_1071 Echvi_1071 (acetyl-CoA acetyltransferases)
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.6122.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-140 452.2 1.4 7.9e-140 452.1 1.4 1.0 1 lcl|FitnessBrowser__Cola:Echvi_1071 Echvi_1071 acetyl-CoA acetyltran Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cola:Echvi_1071 Echvi_1071 acetyl-CoA acetyltransferases # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 452.1 1.4 7.9e-140 7.9e-140 1 385 [] 5 388 .. 5 388 .. 0.96 Alignments for each domain: == domain 1 score: 452.1 bits; conditional E-value: 7.9e-140 TIGR01930 1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaaglp 71 i++++Rt++g + +g ++ +++dL++ vik+l++ + gl++e++d++i+Gn+++++eq ++++R++ l a l+ lcl|FitnessBrowser__Cola:Echvi_1071 5 IIKGYRTAVGkAKKGGFRFYRPDDLAVDVIKKLIADTpGLEAERVDDLIVGNAVPEAEQgMQMGRMISLMA-LG 77 899*******9569*********************************************999***999976.99 PP TIGR01930 72 esvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdlv 145 + vp++ +nr+C+Sgl+A+ala +kik+G+ad+++aGG EsmS vp++ + l+ + a+ + lcl|FitnessBrowser__Cola:Echvi_1071 78 KVVPGFIINRYCGSGLEAIALATAKIKSGMADCIIAGGTESMSMVPMMGYKT----ALNWKIASEHP------- 140 99*********************************************88886....44444445555....... PP TIGR01930 146 ktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...........kkvvskD 208 + lsmg tAe+lak+y+isRe+ D++a+ Sh++a +Ai+eg+fk+eivp+ev+++ + +v++D lcl|FitnessBrowser__Cola:Echvi_1071 141 DYYLSMGLTAEELAKDYDISREDSDQFAVTSHERAISAIKEGRFKEEIVPIEVEETfvdasgkrqtrTFTVDTD 214 567***************************************************99*********99999**** PP TIGR01930 209 egirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeem 282 eg+rp+t+++ L++Lkpafk+ g+ vtAgNssq++DGAa++++mse+++kel+l+p+ar+vs++vagvdp++m lcl|FitnessBrowser__Cola:Echvi_1071 215 EGPRPGTNMDVLGGLKPAFKQ-GGQ-VTAGNSSQTSDGAAFTVVMSERMVKELNLEPVARLVSYSVAGVDPRIM 286 *******************95.797.************************************************ PP TIGR01930 283 glgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltl 356 g+gp +A++kaLk+ag+++sdi lvE+nEAFAaq+lav+++l+ +d++ vNvnGGA+AlGHPlG++Ga +++++ lcl|FitnessBrowser__Cola:Echvi_1071 287 GIGPKEAVPKALKQAGMKMSDISLVELNEAFAAQALAVIRALD-MDPNTVNVNGGAVALGHPLGCTGAKLTVQM 359 *******************************************.88**************************** PP TIGR01930 357 lkeLkergkkyGlatlCvggGqGaAvile 385 ++eL++r++kyG++t+CvggGqG+A ++e lcl|FitnessBrowser__Cola:Echvi_1071 360 INELRRRNQKYGMVTACVGGGQGVAGVVE 388 *************************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (391 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.38 // [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