Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_013257091.1 DEBA_RS01270 acetyl-CoA C-acetyltransferase
Query= SwissProt::P14611 (393 letters) >NCBI__GCF_000143965.1:WP_013257091.1 Length = 400 Score = 380 bits (975), Expect = e-110 Identities = 199/398 (50%), Positives = 271/398 (68%), Gaps = 14/398 (3%) Query: 3 DVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAGSG 62 D VIV+ RTA+G FGGSLA + A EL A+V K L++ G+ P +V+MG Sbjct: 6 DTVIVAMGRTAIGDFGGSLAGLRAHELAAIVTKNLLDKTGLDPAMFDDVLMGDCCQCPDE 65 Query: 63 QNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSAAP 122 N AR AA+KAG+P VPAMTI + C S ++A+ A I AG+AE+++AGG E+MS AP Sbjct: 66 ANTARTAALKAGIPVDVPAMTIQRQCSSAMQALAQAEVYIRAGEAEVMLAGGVESMSNAP 125 Query: 123 HVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQ---------YHMGITAENVAKEYGITRE 173 + LP +R G R+ AK+VD LW++ + Y MG TAEN+A++Y ++R+ Sbjct: 126 YTLPKARWGARLQHAKMVDA-----LWEMLHSGSTLLEPPGYIMGQTAENLARKYDVSRQ 180 Query: 174 AQDEFAVGSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLK 233 QD A+ S N AEAA KAGKF +EIVPV +PQRKG+P TDE VR G T+ + L+ Sbjct: 181 EQDIVALRSHNNAEAAIKAGKFKDEIVPVPVPQRKGEPKIVDTDEHVRMGLTMADLDKLR 240 Query: 234 PAFDKAGTVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGP 293 PAF K GTVTA NASGLNDGAA +VMS KAK+LGLTP+A I +A AG P++MG GP Sbjct: 241 PAFAKDGTVTAGNASGLNDGAALCIVMSREKAKDLGLTPIAKIVGHAAAGCPPEIMGWGP 300 Query: 294 VPASKRALSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGA 353 VP++++ + + +D++L+E+NEAFAAQ LA + +G + VNVNG I +GHP+G Sbjct: 301 VPSTQKVMKKLGMNLKDIELIELNEAFAAQYLACEKGLGLNRDIVNVNGSGIGLGHPVGC 360 Query: 354 SGCRILVTLLHEMKRRDAKKGLASLCIGGGMGVALAVE 391 +G RI+++L+ EMKRR A GLA+LC+GGGMG+++ VE Sbjct: 361 TGARIVISLIGEMKRRGATVGLATLCVGGGMGMSMVVE 398 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: 439 Number of extensions: 21 Number of successful extensions: 2 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: 400 Length adjustment: 31 Effective length of query: 362 Effective length of database: 369 Effective search space: 133578 Effective search space used: 133578 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_013257091.1 DEBA_RS01270 (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.17625.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-145 471.5 1.6 1.1e-145 471.3 1.6 1.0 1 lcl|NCBI__GCF_000143965.1:WP_013257091.1 DEBA_RS01270 acetyl-CoA C-acetyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000143965.1:WP_013257091.1 DEBA_RS01270 acetyl-CoA C-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 471.3 1.6 1.1e-145 1.1e-145 1 385 [] 9 398 .. 9 398 .. 0.98 Alignments for each domain: == domain 1 score: 471.3 bits; conditional E-value: 1.1e-145 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 iv+ Rt+ig +ggsl+ l+a++L+a v k+ll+++gldp+ d+v +G q ++an+aR+aal+ag lcl|NCBI__GCF_000143965.1:WP_013257091.1 9 IVAMGRTAIGDFGGSLAGLRAHELAAIVTKNLLDKTGLDPAMFDDVLMGDCCQCPDEANTARTAALKAG 77 8999***************************************************************** PP TIGR01930 70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138 +p +vpa+t++r+C+S++qA+a+a i+aGea+v++aGGvEsmS++p+ l+++ r++++l++ak+ d lcl|NCBI__GCF_000143965.1:WP_013257091.1 78 IPVDVPAMTIQRQCSSAMQALAQAEVYIRAGEAEVMLAGGVESMSNAPYTLPKA--RWGARLQHAKMVD 144 ****************************************************98..89*********** PP TIGR01930 139 qllkdl.......vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkg 200 +l + l + ++ mg+tAenla+ky++sR+eqD alrSh++a++Ai++gkfkdeivpv v++ lcl|NCBI__GCF_000143965.1:WP_013257091.1 145 ALWEMLhsgstllEPPGYIMGQTAENLARKYDVSRQEQDIVALRSHNNAEAAIKAGKFKDEIVPVPVPQ 213 888877999***9678****************************************************9 PP TIGR01930 201 k...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltpl 266 + +k+v++De++r ++t+++L kL+paf++ +g tvtAgN+s+lnDGAa+ ++ms+e+ak+lgltp+ lcl|NCBI__GCF_000143965.1:WP_013257091.1 214 RkgePKIVDTDEHVRMGLTMADLDKLRPAFAK-DG-TVTAGNASGLNDGAALCIVMSREKAKDLGLTPI 280 99**9*************************95.9*.6******************************** PP TIGR01930 267 arivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvn 335 a+iv++a ag++pe+mg+gpvp+++k++kk g++++di+l+E+nEAFAaq+la+ek lg l+++ vNvn lcl|NCBI__GCF_000143965.1:WP_013257091.1 281 AKIVGHAAAGCPPEIMGWGPVPSTQKVMKKLGMNLKDIELIELNEAFAAQYLACEKGLG-LNRDIVNVN 348 ***********************************************************.88******* PP TIGR01930 336 GGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 G+ i lGHP+G++Gariv++l+ e+k+rg+++GlatlCvggG+G+++++e lcl|NCBI__GCF_000143965.1:WP_013257091.1 349 GSGIGLGHPVGCTGARIVISLIGEMKRRGATVGLATLCVGGGMGMSMVVE 398 ************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (400 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 12.21 // [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