Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_110204929.1 DNK54_RS00015 acetyl-CoA C-acetyltransferase
Query= SwissProt::P14611 (393 letters) >NCBI__GCF_003194585.1:WP_110204929.1 Length = 395 Score = 354 bits (909), Expect = e-102 Identities = 200/392 (51%), Positives = 256/392 (65%), Gaps = 4/392 (1%) Query: 1 MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60 M+ VIV+ ART VG+ G L + A +LG V IK ALE+AG+ +QV V+MG V+ AG Sbjct: 1 MSGSVIVAGARTPVGRLLGGLKDLSAADLGGVAIKGALEKAGISGDQVDYVVMGHVIQAG 60 Query: 61 SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120 +GQ ARQAA+K G+P VP++TINKVC SG+ A+ LA I AG+ EIVVAGG E+M+ Sbjct: 61 AGQITARQAAVKGGIPMGVPSLTINKVCLSGINAIALADQLIRAGEHEIVVAGGMESMTQ 120 Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAE--NVAKEYGITREAQDEF 178 APH+LP SR+GF+ GD KLVD+M D L+D + MG E NVA +TRE QD F Sbjct: 121 APHLLPKSREGFKYGDTKLVDSMAYDALYDQFTDQAMGNLTEQCNVAGG-NLTREEQDAF 179 Query: 179 AVGSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDK 238 + S A AAQK G FD+EIVPV I R+GD V DE VR T +S+ GL+PAF K Sbjct: 180 SARSHQLAAAAQKNGVFDDEIVPVTISSRRGD-VVVSVDEGVRGDTTAESLGGLRPAFAK 238 Query: 239 AGTVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASK 298 GT+TA ++S ++DGA AVVVMS AKA+ELGL LA I + + + P A Sbjct: 239 DGTITAGSSSQISDGACAVVVMSKAKAEELGLEWLAEIGASGQVAGPDSTLQLQPARAIA 298 Query: 299 RALSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRI 358 +A+ + D+DL E+NEAFAA + +++G KVNVNGGAIAIGHP+G SG RI Sbjct: 299 KAVEKEGIAVSDIDLFELNEAFAAVGIESARELGVSEDKVNVNGGAIAIGHPVGMSGARI 358 Query: 359 LVTLLHEMKRRDAKKGLASLCIGGGMGVALAV 390 ++ L E+KRR G A+LC GGG G AL V Sbjct: 359 VLHLALELKRRGGGIGAAALCGGGGQGDALIV 390 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: 451 Number of extensions: 16 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: 393 Length of database: 395 Length adjustment: 31 Effective length of query: 362 Effective length of database: 364 Effective search space: 131768 Effective search space used: 131768 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_110204929.1 DNK54_RS00015 (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.156848.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-136 439.3 8.6 6.8e-136 439.1 8.6 1.0 1 NCBI__GCF_003194585.1:WP_110204929.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003194585.1:WP_110204929.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 439.1 8.6 6.8e-136 6.8e-136 1 384 [. 6 390 .. 6 391 .. 0.98 Alignments for each domain: == domain 1 score: 439.1 bits; conditional E-value: 6.8e-136 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 iv+++Rtp+g+l g lk+lsa+dL+ +ik++le+ag++ +++d+v++G+v+qag+++ +aR+aa++ g+p NCBI__GCF_003194585.1:WP_110204929.1 6 IVAGARTPVGRLLGGLKDLSAADLGGVAIKGALEKAGISGDQVDYVVMGHVIQAGAGQITARQAAVKGGIPMG 78 8*********99************************************************************* PP TIGR01930 74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144 vp+lt+n+vC Sg++A+ala q i+aGe ++vvaGG+Esm+++p+ll++s re++k+g++kl d++++d+ NCBI__GCF_003194585.1:WP_110204929.1 79 VPSLTINKVCLSGINAIALADQLIRAGEHEIVVAGGMESMTQAPHLLPKS--REGFKYGDTKLVDSMAYDAly 149 ************************************************98..9*****************99* PP TIGR01930 145 .vktklsmgetAenlakk.ygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirp 213 + t+ +mg+ +e++ +++ReeqD++++rShq aa+A+++g f+deivpv++ + ++vvs Deg+r NCBI__GCF_003194585.1:WP_110204929.1 150 dQFTDQAMGNLTEQCNVAgGNLTREEQDAFSARSHQLAAAAQKNGVFDDEIVPVTISSRrgDVVVSVDEGVRG 222 999**********88755268***********************************999999*********** PP TIGR01930 214 nttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgp 286 +tt+e+L++L+paf++ +g t+tAg+ssq++DGA+a+++ms+++a+elgl++la+i + ++++ + ++++l+p NCBI__GCF_003194585.1:WP_110204929.1 223 DTTAESLGGLRPAFAK-DG-TITAGSSSQISDGACAVVVMSKAKAEELGLEWLAEIGASGQVAGPDSTLQLQP 293 **************95.9*.6**************************************************** PP TIGR01930 287 vpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllke 359 + Ai ka++k+g+ +sdidl+E+nEAFAa+ + +++elg +++kvNvnGGAiA+GHP+G+sGarivl+l+ e NCBI__GCF_003194585.1:WP_110204929.1 294 ARAIAKAVEKEGIAVSDIDLFELNEAFAAVGIESARELG-VSEDKVNVNGGAIAIGHPVGMSGARIVLHLALE 365 ***************************************.77******************************* PP TIGR01930 360 LkergkkyGlatlCvggGqGaAvil 384 Lk+rg+ +G a+lC ggGqG A+i+ NCBI__GCF_003194585.1:WP_110204929.1 366 LKRRGGGIGAAALCGGGGQGDALIV 390 ***********************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (395 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: 14.56 // [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