Align acetyl-CoA acetyltransferase (EC 2.3.1.16) (characterized)
to candidate AZOBR_RS30610 AZOBR_RS30610 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-13585 (391 letters) >FitnessBrowser__azobra:AZOBR_RS30610 Length = 391 Score = 544 bits (1402), Expect = e-159 Identities = 269/390 (68%), Positives = 321/390 (82%) Query: 1 MTNVVIVSAARTAVGSFNGAFASTPAHDLGAAVIEAVVARAGIDKADVSETILGQVLTAG 60 MT VVI SAART +GSFNGA +S PAH LG I ++RA D A+V+E ILGQ+LTAG Sbjct: 1 MTEVVIASAARTPIGSFNGALSSVPAHYLGEIAIREALSRAKTDAAEVTEVILGQILTAG 60 Query: 61 QGQNPARQAHIKAGLPQESAAWSINQVCGSGLRAVALAAQHVQLGDASIVVAGGQENMSL 120 QGQNPARQA + AG+P + A+ INQ+CGSGLR+VAL Q ++ GDA ++V GGQE+MS Sbjct: 61 QGQNPARQAAVNAGIPASATAFGINQLCGSGLRSVALGYQAIRNGDAEVMVVGGQESMSQ 120 Query: 121 SPHVAHLRAGQKMGDLSFIDSMIKDGLWDAFNGYHMGQTAENVAAKWQISRDMQDEFAVA 180 +PHV HLR G KMG +D+M+KDGL DAF GYHMG TAENVA KWQ++R+ QD FA A Sbjct: 121 APHVMHLRNGVKMGAAEMLDTMLKDGLMDAFKGYHMGTTAENVAQKWQLTREEQDVFAAA 180 Query: 181 SQNKAEAAQKAGRFADEIVPFVIKTRKGDVTVDADEYIRHGATLDAMAKLRPAFIKDGTV 240 SQ KAEAAQK+GRF DEI+P IK RKGD+ V DEY +HG T +++AKLRPAF K+GTV Sbjct: 181 SQQKAEAAQKSGRFKDEIIPVTIKGRKGDIIVADDEYPKHGTTAESLAKLRPAFSKEGTV 240 Query: 241 TAANASGINDGAAAVLVMSAEEAEKRGLSPLARIASYATAGLDPSIMGVGPIHASRKALE 300 TA NASGINDGAAA+++M+AE A +RGL+PLARI S+ATAG+DP+IMG GPI ASR ALE Sbjct: 241 TAGNASGINDGAAALVLMTAENAARRGLTPLARIVSWATAGVDPAIMGTGPIPASRLALE 300 Query: 301 KAGWKVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVLNTL 360 KAGWK DLDL+EANEAFAAQA AVNKD+GWD S VNVNGGAIA+GHP+GASGARVL TL Sbjct: 301 KAGWKHDDLDLIEANEAFAAQALAVNKDLGWDTSKVNVNGGAIALGHPVGASGARVLTTL 360 Query: 361 LFEMQRRNAKKGLATLCIGGGMGVAMCLER 390 L+EMQ+R+AKKGLATLCIGGGMG+A+ +ER Sbjct: 361 LYEMQKRDAKKGLATLCIGGGMGIALTVER 390 Lambda K H 0.317 0.130 0.375 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: 461 Number of extensions: 11 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: 391 Length of database: 391 Length adjustment: 31 Effective length of query: 360 Effective length of database: 360 Effective search space: 129600 Effective search space used: 129600 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 AZOBR_RS30610 AZOBR_RS30610 (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.11678.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-148 479.2 10.3 5.1e-148 479.0 10.3 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS30610 AZOBR_RS30610 acetyl-CoA acetylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS30610 AZOBR_RS30610 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 479.0 10.3 5.1e-148 5.1e-148 1 385 [] 6 389 .. 6 389 .. 0.98 Alignments for each domain: == domain 1 score: 479.0 bits; conditional E-value: 5.1e-148 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 i +a+Rtpig+++g+l++++a+ L++ +i+e+l ra+ d++++ evilG+ l+ag+++n+aR+aa++ag lcl|FitnessBrowser__azobra:AZOBR_RS30610 6 IASAARTPIGSFNGALSSVPAHYLGEIAIREALSRAKTDAAEVTEVILGQILTAGQGQNPARQAAVNAG 74 789****************************************************************** PP TIGR01930 70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138 +p s a+ +n++C+Sgl++val++q+i+ G+a+v+v+GG EsmS++p++++ r+++k+g+a++ d lcl|FitnessBrowser__azobra:AZOBR_RS30610 75 IPASATAFGINQLCGSGLRSVALGYQAIRNGDAEVMVVGGQESMSQAPHVMHL---RNGVKMGAAEMLD 140 ************************************************98886...59*********** PP TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202 ++lkd+ + ++++mg+tAen+a+k++++ReeqD +a++S+qka++A+++g+fkdei+pv++kg+ + lcl|FitnessBrowser__azobra:AZOBR_RS30610 141 TMLKDGlmdAFKGYHMGTTAENVAQKWQLTREEQDVFAAASQQKAEAAQKSGRFKDEIIPVTIKGRkgD 209 *********999******************************************************999 PP TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271 +v++De ++ +tt+e+LakL+paf + +g tvtAgN+s++nDGAaal+lm+ e a++ gltplarivs lcl|FitnessBrowser__azobra:AZOBR_RS30610 210 IIVADDEYPKHGTTAESLAKLRPAFSK-EG-TVTAGNASGINDGAAALVLMTAENAARRGLTPLARIVS 276 999**********************95.8*.6************************************* PP TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340 +a+agvdp++mg+gp+pA++ aL+kag++ +d+dl+E nEAFAaq+lav+k+lg d++kvNvnGGAiA lcl|FitnessBrowser__azobra:AZOBR_RS30610 277 WATAGVDPAIMGTGPIPASRLALEKAGWKHDDLDLIEANEAFAAQALAVNKDLG-WDTSKVNVNGGAIA 344 ******************************************************.88************ PP TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 lGHP+GasGar+++tll+e+++r++k GlatlC+ggG+G+A+ +e lcl|FitnessBrowser__azobra:AZOBR_RS30610 345 LGHPVGASGARVLTTLLYEMQKRDAKKGLATLCIGGGMGIALTVE 389 *****************************************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (391 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: 00:00:00.01 # Mc/sec: 9.27 // [ok]
This GapMind analysis is from Sep 17 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