Align Steroid 3-ketoacyl-CoA thiolase; Acetyl-CoA acetyltransferase FadA5; Beta-ketoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate WP_026606471.1 METAC_RS0106930 acetyl-CoA acetyltransferase
Query= SwissProt::I6XHI4 (391 letters) >NCBI__GCF_000427445.1:WP_026606471.1 Length = 402 Score = 259 bits (661), Expect = 1e-73 Identities = 171/417 (41%), Positives = 240/417 (57%), Gaps = 43/417 (10%) Query: 1 MGYPVIVEATRSPIG--KRNGWLSGLHATELLGAVQKAVVDKAGIQSGLHAGDVEQVIGG 58 M I + R+P G K +G L + + L V +AV D+ G+ + L V+ VI G Sbjct: 1 MAEAFIYDHVRTPRGRGKPDGALHEVSSLGLASGVLRAVKDRNGLDTKL----VDDVILG 56 Query: 59 CVTQFGEQSNNISRVAWLTAGLPEHVGATTVDCQCGSGQQANHLIAGLIAAGAIDVGIAC 118 CV GE +I+R + LTA +HV ++ C SG A + A + AG D+ I Sbjct: 57 CVDPVGEAGGDIARASALTADYGDHVPGVQINRFCASGLDAVNFAAAQVMAGQHDLTIGG 116 Query: 119 GIEAMSRVGLGANAG--PDRSLIRAQSWDIDLPNQFEAAERIAKRRGITREDVDVFGLES 176 G+E+MSRVGLGA+ G P I +S+ + Q +A+ IA + G +R+DVD++ + S Sbjct: 117 GVESMSRVGLGASGGAWPVDPAIAIKSYFMP---QGVSADLIATKYGFSRDDVDLYAVRS 173 Query: 177 QRRAQRAWAEGRFDREISPIQAPVLDEQNQPTGERRLVFRDQGLRETT-MAGLGELKPVL 235 Q+RA AW +GRFD I+P++ + N T L+ +D+ +R +T M L LKP Sbjct: 174 QQRAASAWEQGRFDLAIAPVR-----DVNGLT----LLAKDEHMRPSTDMQSLAGLKPSF 224 Query: 236 -----EGG-----------------IHTAGTSSQISDGAAAVLWMDEAVARAHGLTPRAR 273 +GG +H AG SS I DGAAAVL RA GL PRA+ Sbjct: 225 VMLAEQGGFDAVAIDAHPEIEKIVHVHHAGNSSGIVDGAAAVLLGSAEAGRAAGLKPRAK 284 Query: 274 IVAQALVGAEPYYHLDGPVQSTAKVLEKAGMKIGDIDIVEINEAFASVVLSWARVHEPDM 333 I A A +G+EP L GPV T KVL +A M + DID+ EINEAFA+VVL + + + D+ Sbjct: 285 IRAFANIGSEPAMMLTGPVDVTKKVLARAKMTLADIDLFEINEAFAAVVLRYLQAFDLDV 344 Query: 334 DRVNVNGGAIALGHPVGCTGSRLITTALHELERTDQSLALITMCAGGALSTGTIIER 390 ++VNVNGGAIA+GHP+G TG+ L+ TAL ELER+ ++ AL+T+C G + T TIIER Sbjct: 345 EKVNVNGGAIAMGHPLGATGAILLGTALDELERSGKATALVTLCIGAGMGTATIIER 401 Lambda K H 0.318 0.134 0.396 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: 427 Number of extensions: 20 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: 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_026606471.1 METAC_RS0106930 (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.14672.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-124 400.0 1.7 6.1e-124 399.8 1.7 1.0 1 lcl|NCBI__GCF_000427445.1:WP_026606471.1 METAC_RS0106930 acetyl-CoA acety Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000427445.1:WP_026606471.1 METAC_RS0106930 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 399.8 1.7 6.1e-124 6.1e-124 1 385 [] 6 400 .. 6 400 .. 0.95 Alignments for each domain: == domain 1 score: 399.8 bits; conditional E-value: 6.1e-124 TIGR01930 1 ivdavRtpig..klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaal 66 i+d vRtp g k g+l+e+s+ L++ v++++ +r+gld + +d+vilG+v + ge +iaR al lcl|NCBI__GCF_000427445.1:WP_026606471.1 6 IYDHVRTPRGrgKPDGALHEVSSLGLASGVLRAVKDRNGLDTKLVDDVILGCVDPVGEAgGDIARASAL 74 7899********99*********************************************9********* PP TIGR01930 67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkak 135 +a+ +++vp++++nr+CaSgl+Av+ aa++++aG+ d+ + GGvEsmSrv ++ + ++ +++ a lcl|NCBI__GCF_000427445.1:WP_026606471.1 75 TADYGDHVPGVQINRFCASGLDAVNFAAAQVMAGQHDLTIGGGVESMSRVGLGASGG--AWPVDPAIAI 141 **************************************************9988886..8999994444 PP TIGR01930 136 ledqllkdlvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgkkkv 204 ++ +++g++A+ +a+kyg+sR+++D ya+rS+q+aa+A+e+g+f+ i pv+ + + lcl|NCBI__GCF_000427445.1:WP_026606471.1 142 KS---------YFMPQGVSADLIATKYGFSRDDVDLYAVRSQQRAASAWEQGRFDLAIAPVRDVNGLTL 201 44.........4799**********************************************99988999 PP TIGR01930 205 vskDegirpnttlekLakLkpafke...kkgs.................tvtAgNssqlnDGAaalllm 253 ++kDe++rp t +++La+Lkp f + g +++AgNss++ DGAaa+ll lcl|NCBI__GCF_000427445.1:WP_026606471.1 202 LAKDEHMRPSTDMQSLAGLKPSFVMlaeQ-GGfdavaidahpeiekivhVHHAGNSSGIVDGAAAVLLG 269 9**********************987751.33566667777788888889******************* PP TIGR01930 254 seevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavek 322 s e+ ++ gl+p a+i+++a++g++p+ m++gpv ++k+L++a++++ didl+EinEAFAa+vl + lcl|NCBI__GCF_000427445.1:WP_026606471.1 270 SAEAGRAAGLKPRAKIRAFANIGSEPAMMLTGPVDVTKKVLARAKMTLADIDLFEINEAFAAVVLRYLQ 338 ********************************************************************* PP TIGR01930 323 elgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 +++ ld ekvNvnGGAiA+GHPlGa+Ga+++ t l+eL++ gk +l+tlC+g G+G+A+i+e lcl|NCBI__GCF_000427445.1:WP_026606471.1 339 AFD-LDVEKVNVNGGAIAMGHPLGATGAILLGTALDELERSGKATALVTLCIGAGMGTATIIE 400 ***.88*******************************************************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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 # Mc/sec: 7.05 // [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