Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_106711729.1 CU102_RS14130 acetyl-CoA C-acetyltransferase
Query= SwissProt::O32177 (391 letters) >NCBI__GCF_003010955.1:WP_106711729.1 Length = 402 Score = 256 bits (653), Expect = 1e-72 Identities = 154/411 (37%), Positives = 223/411 (54%), Gaps = 33/411 (8%) Query: 1 MKEAVIVSGARTPVGKAKK-GSLATVRPDDLGAICVKETLKRAGGYEGNIDDLIIGCATP 59 M EA I RTP G+ KK GSL V LGA ++ R G G +DD+I GC P Sbjct: 1 MTEAYIYDHVRTPRGRGKKDGSLHEVPAVRLGAHVLEALRDRNGLDTGLVDDIIYGCVDP 60 Query: 60 EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119 E G + R+ AG + P + ++R+C+SGL ++ +AA KI+ GA D IAGG ES Sbjct: 61 VGEAGAVIPRSSAFEAGYDFKAPGMQISRFCASGLDAVNFAAAKIVQGADDIVIAGGVES 120 Query: 120 MSQVPMMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAKA 179 MS+V M + + P Y+M G +A+ +A KYG SR+D DA+AV S + A +A Sbjct: 121 MSRVGMGMSGGAWYMDPSVGLPGYFMPQGVSADLIATKYGFSRDDVDAYAVESQKRAGEA 180 Query: 180 LAEGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDGT 239 +G FK+ ++ + K + DE +RP T L++L P+F + G Sbjct: 181 WKKGYFKNSVLEI-----------KDQNGLTILDHDEHMRPTTDMQALASLNPSFVMPGE 229 Query: 240 VT---------------------AGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFA 278 + AGNSS DGAA V+L + A+G P + R+FA Sbjct: 230 MGGFNAVGIQAHPEVETINHVHHAGNSSGIVDGAAGVLLGSKSAGKAIGTKPRARIRAFA 289 Query: 279 VGGVPPEVMGIGPVEAIPRALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNV 338 G P +M GPV+ + LK A +++ DI LFELNEAFA+ ++ ++ I +K+NV Sbjct: 290 NIGSDPALMLTGPVDVTEKLLKRAKMKISDIDLFELNEAFAAVVLRYMQAFDIPRDKINV 349 Query: 339 NGGAIALGHPLGCTGTKLTLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFE 389 NGGAIA+GHPLG TG + +++ E++RR+ +VT+CIG GMG A + E Sbjct: 350 NGGAIAMGHPLGATGAMILGTVLDELERRDLNVALVTLCIGAGMGTATIIE 400 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: 428 Number of extensions: 15 Number of successful extensions: 4 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: 402 Length adjustment: 31 Effective length of query: 360 Effective length of database: 371 Effective search space: 133560 Effective search space used: 133560 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_106711729.1 CU102_RS14130 (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.3458480.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-124 401.7 0.1 2e-124 401.4 0.1 1.1 1 NCBI__GCF_003010955.1:WP_106711729.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010955.1:WP_106711729.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 401.4 0.1 2e-124 2e-124 1 385 [] 6 400 .. 6 400 .. 0.95 Alignments for each domain: == domain 1 score: 401.4 bits; conditional E-value: 2e-124 TIGR01930 1 ivdavRtpig..klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaagl 70 i+d vRtp g k gsl+e++a+ L+a+v+++l +r+gld +d++i+G+v + ge a i R a++ag NCBI__GCF_003010955.1:WP_106711729.1 6 IYDHVRTPRGrgKKDGSLHEVPAVRLGAHVLEALRDRNGLDTGLVDDIIYGCVDPVGEAgAVIPRSSAFEAGY 78 7899*******988*********************************************************** PP TIGR01930 71 pesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkd 143 + + p+++++r+CaSgl+Av+ aa+ki G+ d+v+aGGvEsmSrv ++++ ++ +++ NCBI__GCF_003010955.1:WP_106711729.1 79 DFKAPGMQISRFCASGLDAVNFAAAKIVQGADDIVIAGGVESMSRVGMGMSGG--AWYMDPS--VG------- 140 ************************************************99997..6777772..22....... PP TIGR01930 144 lvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgkkkvvskDegirpntt 216 l+ +++g++A+ +a+kyg+sR+++D+ya++S+++a +A+++g+fk++++ ++ ++ +++++De++rp+t NCBI__GCF_003010955.1:WP_106711729.1 141 LPGYFMPQGVSADLIATKYGFSRDDVDAYAVESQKRAGEAWKKGYFKNSVLEIKDQNGLTILDHDEHMRPTTD 213 245689**********************************************99998899************* PP TIGR01930 217 lekLakLkpafkekkgs....................tvtAgNssqlnDGAaalllmseevakelgltplari 269 +++La+L+p f g+ +++AgNss++ DGAa +ll s+++ k++g +p ari NCBI__GCF_003010955.1:WP_106711729.1 214 MQALASLNPSFVM-PGEmggfnavgiqahpevetinhVHHAGNSSGIVDGAAGVLLGSKSAGKAIGTKPRARI 285 ***********98.244455666667777788888889*********************************** PP TIGR01930 270 vsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlG 342 +++a++g+dp+ m++gpv +ek+Lk+a+++isdidl+E+nEAFAa+vl +++++ + ++k+NvnGGAiA+G NCBI__GCF_003010955.1:WP_106711729.1 286 RAFANIGSDPALMLTGPVDVTEKLLKRAKMKISDIDLFELNEAFAAVVLRYMQAFD-IPRDKINVNGGAIAMG 357 ********************************************************.88************** PP TIGR01930 343 HPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 HPlGa+Ga+i+ t+l+eL++r+ +++l+tlC+g G+G+A+i+e NCBI__GCF_003010955.1:WP_106711729.1 358 HPLGATGAMILGTVLDELERRDLNVALVTLCIGAGMGTATIIE 400 *****************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (402 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: 25.35 // [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