Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_011884947.1 acetyl-CoA acetyltransferase
Query= SwissProt::P14611 (393 letters) >NCBI__GCF_000016205.1:WP_011884947.1 Length = 393 Score = 669 bits (1725), Expect = 0.0 Identities = 340/392 (86%), Positives = 361/392 (92%) Query: 1 MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60 MTDVVIVSAARTAVGKFGGSLAK+ APELGA VI+A LERAGV+P+QVSEVIMGQVL AG Sbjct: 1 MTDVVIVSAARTAVGKFGGSLAKVAAPELGATVIRAVLERAGVQPDQVSEVIMGQVLAAG 60 Query: 61 SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120 SGQNPARQ+ IKAGLP VP MTINKVCGSGLKAVMLAANAI AGDAEIV+AGGQENMSA Sbjct: 61 SGQNPARQSLIKAGLPTAVPGMTINKVCGSGLKAVMLAANAIAAGDAEIVIAGGQENMSA 120 Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITRE QD FA Sbjct: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREEQDAFAA 180 Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAG 240 SQNKAEAAQKAG+F +EIVPV IPQRKG+P+ F TDEFVR G T +S++GLKPAF K G Sbjct: 181 LSQNKAEAAQKAGRFADEIVPVSIPQRKGEPLQFATDEFVRHGVTAESLAGLKPAFAKDG 240 Query: 241 TVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA 300 +VTAANASGLNDGAAAV+VMSA KA+ LGLTPLA IK+YANAGVDP VMGMGPVPAS+R Sbjct: 241 SVTAANASGLNDGAAAVLVMSARKAQSLGLTPLARIKAYANAGVDPSVMGMGPVPASRRC 300 Query: 301 LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360 L RA WTP DLDLMEINEAFAAQALAVH+QMGWDTSKVNVNGGAIAIGHPIGASGCRILV Sbjct: 301 LERAGWTPGDLDLMEINEAFAAQALAVHKQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360 Query: 361 TLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392 TLLHEM +RDAK+GLASLCIGGGMGVALAVER Sbjct: 361 TLLHEMVKRDAKRGLASLCIGGGMGVALAVER 392 Lambda K H 0.315 0.131 0.369 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: 590 Number of extensions: 18 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: 393 Length of database: 393 Length adjustment: 31 Effective length of query: 362 Effective length of database: 362 Effective search space: 131044 Effective search space used: 131044 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_011884947.1 (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.3996.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6e-154 498.6 9.6 6.7e-154 498.4 9.6 1.0 1 lcl|NCBI__GCF_000016205.1:WP_011884947.1 acetyl-CoA acetyltransferase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016205.1:WP_011884947.1 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 498.4 9.6 6.7e-154 6.7e-154 1 385 [] 6 391 .. 6 391 .. 0.99 Alignments for each domain: == domain 1 score: 498.4 bits; conditional E-value: 6.7e-154 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 iv+a+Rt++gk+ggsl+++ a +L+a+vi+++lerag++p+++ evi+G+vl ag+++n+aR+ +++ag lcl|NCBI__GCF_000016205.1:WP_011884947.1 6 IVSAARTAVGKFGGSLAKVAAPELGATVIRAVLERAGVQPDQVSEVIMGQVLAAGSGQNPARQSLIKAG 74 8******************************************************************** PP TIGR01930 70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138 lp+ vp++t+n+vC+Sgl+Av+laa++i+aG+a++v+aGG E+mS +p++l+ s r+++++g+akl d lcl|NCBI__GCF_000016205.1:WP_011884947.1 75 LPTAVPGMTINKVCGSGLKAVMLAANAIAAGDAEIVIAGGQENMSAAPHVLPGS--RDGFRMGDAKLVD 141 ****************************************************98..9************ PP TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk... 201 +++ d+ v+++++mg+tAen+ak+ygi+ReeqD++a+ S++ka++A+++g+f+deivpv+++++ lcl|NCBI__GCF_000016205.1:WP_011884947.1 142 TMIVDGlwdVYNQYHMGITAENVAKEYGITREEQDAFAALSQNKAEAAQKAGRFADEIVPVSIPQRkge 210 *****9***99*****************************************************99999 PP TIGR01930 202 kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplariv 270 + ++++De +r ++t+e+La+Lkpaf++ +gs vtA+N+s+lnDGAaa+l+ms ++a++lgltplari lcl|NCBI__GCF_000016205.1:WP_011884947.1 211 PLQFATDEFVRHGVTAESLAGLKPAFAK-DGS-VTAANASGLNDGAAAVLVMSARKAQSLGLTPLARIK 277 99************************95.9*7.************************************ PP TIGR01930 271 saavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAi 339 ++a+agvdp++mg+gpvpA++++L++ag++ d+dl+EinEAFAaq+lav k++g d++kvNvnGGAi lcl|NCBI__GCF_000016205.1:WP_011884947.1 278 AYANAGVDPSVMGMGPVPASRRCLERAGWTPGDLDLMEINEAFAAQALAVHKQMG-WDTSKVNVNGGAI 345 *******************************************************.88*********** PP TIGR01930 340 AlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 A+GHP+GasG+ri++tll+e+ +r++k+Gla+lC+ggG+G+A+ +e lcl|NCBI__GCF_000016205.1:WP_011884947.1 346 AIGHPIGASGCRILVTLLHEMVKRDAKRGLASLCIGGGMGVALAVE 391 ******************************************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (393 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: 10.46 // [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