Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_068168283.1 HTA01S_RS06660 acetyl-CoA C-acetyltransferase
Query= SwissProt::P14611 (393 letters) >NCBI__GCF_001592305.1:WP_068168283.1 Length = 392 Score = 557 bits (1435), Expect = e-163 Identities = 283/392 (72%), Positives = 325/392 (82%) Query: 1 MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60 M D+VIVSAARTAVGKFGGSLAK PA ELG++VIK L R G+ + V EVIMGQVL AG Sbjct: 1 MEDIVIVSAARTAVGKFGGSLAKTPATELGSIVIKELLARTGLPVDAVGEVIMGQVLAAG 60 Query: 61 SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120 GQNPARQA +KAG+ PA+TIN VCGSGLKAVMLAA A+ GD+EIV+AGGQENMSA Sbjct: 61 CGQNPARQAMMKAGVAKETPALTINAVCGSGLKAVMLAAQAVAWGDSEIVIAGGQENMSA 120 Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180 +PHVL GSRDG RMGD K+ DTMIVDGLWDVYNQYHMGITAENVAK GITRE QD A Sbjct: 121 SPHVLNGSRDGQRMGDWKMTDTMIVDGLWDVYNQYHMGITAENVAKAQGITREMQDALAA 180 Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAG 240 GSQ KA AAQ AGKF +EIV V IPQRKGDPV F +DEF+ T + ++GL+PAFDK+G Sbjct: 181 GSQQKAAAAQAAGKFKDEIVGVSIPQRKGDPVLFNSDEFINAKTTAEVLAGLRPAFDKSG 240 Query: 241 TVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA 300 +VTA NASG+NDGAAAV+VM+A KA LGLTPLA I ++ +G+DP +MGMGPVPAS++A Sbjct: 241 SVTAGNASGINDGAAAVMVMTAKKAAALGLTPLARIAAFGTSGLDPALMGMGPVPASQKA 300 Query: 301 LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360 L+RA W D+D+ E+NEAFAAQA AV+ + D +KVNVNGGAIAIGHPIGASGCRILV Sbjct: 301 LARAGWKASDVDVFELNEAFAAQACAVNMALDIDPAKVNVNGGAIAIGHPIGASGCRILV 360 Query: 361 TLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392 TLLHEM+RR AKKGLA+LCIGGGMGV+LAVER Sbjct: 361 TLLHEMQRRGAKKGLAALCIGGGMGVSLAVER 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: 528 Number of extensions: 16 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: 392 Length adjustment: 31 Effective length of query: 362 Effective length of database: 361 Effective search space: 130682 Effective search space used: 130682 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_068168283.1 HTA01S_RS06660 (acetyl-CoA C-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.1851374.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-144 468.1 15.0 1.2e-144 467.9 15.0 1.0 1 NCBI__GCF_001592305.1:WP_068168283.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001592305.1:WP_068168283.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 467.9 15.0 1.2e-144 1.2e-144 1 385 [] 6 391 .. 6 391 .. 0.99 Alignments for each domain: == domain 1 score: 467.9 bits; conditional E-value: 1.2e-144 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 iv+a+Rt++gk+ggsl++++a +L++ vikell+r+gl +++ evi+G+vl ag+++n+aR+a+++ag+ ++ NCBI__GCF_001592305.1:WP_068168283.1 6 IVSAARTAVGKFGGSLAKTPATELGSIVIKELLARTGLPVDAVGEVIMGQVLAAGCGQNPARQAMMKAGVAKE 78 8************************************************************************ PP TIGR01930 74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144 +palt+n vC+Sgl+Av+laaq+++ G+ ++v+aGG E+mS +p++l+ s r++ ++g+ k+ d+++ d+ NCBI__GCF_001592305.1:WP_068168283.1 79 TPALTINAVCGSGLKAVMLAAQAVAWGDSEIVIAGGQENMSASPHVLNGS--RDGQRMGDWKMTDTMIVDGlw 149 ************************************************98..8*****************9** PP TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvskDegirp 213 v+++++mg+tAen+ak gi+Re+qD++a+ S+qkaa+A+++gkfkdeiv v+++++ ++ +++De i + NCBI__GCF_001592305.1:WP_068168283.1 150 dVYNQYHMGITAENVAKAQGITREMQDALAAGSQQKAAAAQAAGKFKDEIVGVSIPQRkgdPVLFNSDEFINA 222 *99*****************************************************999*99*********** PP TIGR01930 214 nttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgp 286 +tt+e La+L+paf++ +gs vtAgN+s++nDGAaa+++m+ ++a++lgltplari +++++g+dp+ mg+gp NCBI__GCF_001592305.1:WP_068168283.1 223 KTTAEVLAGLRPAFDK-SGS-VTAGNASGINDGAAAVMVMTAKKAAALGLTPLARIAAFGTSGLDPALMGMGP 293 **************95.8*7.**************************************************** PP TIGR01930 287 vpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllke 359 vpA++kaL++ag+++sd+d++E+nEAFAaq+ av+ +l+ +d++kvNvnGGAiA+GHP+GasG+ri++tll+e NCBI__GCF_001592305.1:WP_068168283.1 294 VPASQKALARAGWKASDVDVFELNEAFAAQACAVNMALD-IDPAKVNVNGGAIAIGHPIGASGCRILVTLLHE 365 ***************************************.88******************************* PP TIGR01930 360 LkergkkyGlatlCvggGqGaAvile 385 +++rg+k Gla+lC+ggG+G+++ +e NCBI__GCF_001592305.1:WP_068168283.1 366 MQRRGAKKGLAALCIGGGMGVSLAVE 391 *********************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (392 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 19.64 // [ok]
This GapMind analysis is from Apr 09 2024. 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