Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate AO353_01065 AO353_01065 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20831 (393 letters) >FitnessBrowser__pseudo3_N2E3:AO353_01065 Length = 392 Score = 627 bits (1617), Expect = 0.0 Identities = 314/392 (80%), Positives = 351/392 (89%) Query: 1 MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60 M +VVIVAATRTA+GSFQG+L++IPA ELGAAVIRRLLEQTG+D AQ+DEVILGQVLTAG Sbjct: 1 MNEVVIVAATRTAIGSFQGALSAIPATELGAAVIRRLLEQTGIDAAQIDEVILGQVLTAG 60 Query: 61 SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120 +GQNPARQ +I AGLPH P+LTLNKVCGSGLKA+HL QAIRCGDAE++IAGG ENMSL Sbjct: 61 AGQNPARQTAIKAGLPHTTPALTLNKVCGSGLKAVHLAVQAIRCGDAELVIAGGQENMSL 120 Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180 APYVLP ARTGLRMGHA++ DSMI DGLWDAFNDYHMGITAENL KY ISREAQD FAA Sbjct: 121 APYVLPKARTGLRMGHAQLQDSMIQDGLWDAFNDYHMGITAENLAQKYEISREAQDTFAA 180 Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240 ASQQKA AAIE GRF EITPILIPQRKG+P+ F DEQPR +TA++LAKLKPAF+KDG Sbjct: 181 ASQQKAAAAIEGGRFQSEITPILIPQRKGEPLVFDTDEQPRIDSTAQALAKLKPAFQKDG 240 Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300 SVTAGNAS+LNDGAA +LL SA KA+ALGLPVLARI +YA+AGVDP+IMGIGPV ATR Sbjct: 241 SVTAGNASTLNDGAAVLLLASAAKAQALGLPVLARIKAYASAGVDPSIMGIGPVPATRLT 300 Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360 L KAGW++ DLDLIEANEAFAAQ+LAVGKEL WD KVNVNGGAIA+GHPIGASG R+LV Sbjct: 301 LQKAGWNVEDLDLIEANEAFAAQALAVGKELGWDTSKVNVNGGAIALGHPIGASGARILV 360 Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALER 392 +L+HE+I+RD KKGLATLCIGGGQGV LA+ER Sbjct: 361 SLVHELIRRDGKKGLATLCIGGGQGVGLAIER 392 Lambda K H 0.317 0.133 0.378 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: 506 Number of extensions: 10 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: 393 Length of database: 392 Length adjustment: 31 Effective length of query: 362 Effective length of database: 361 Effective search space: 130682 Effective search space used: 130682 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 AO353_01065 AO353_01065 (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.13080.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-153 495.7 6.6 4.9e-153 495.5 6.6 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_01065 AO353_01065 acetyl-CoA acetyltra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_01065 AO353_01065 acetyl-CoA acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 495.5 6.6 4.9e-153 4.9e-153 1 385 [] 6 391 .. 6 391 .. 0.99 Alignments for each domain: == domain 1 score: 495.5 bits; conditional E-value: 4.9e-153 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaa 65 iv+a+Rt+ig+++g+l+ ++a +L+aavi++lle++g+d+++idevilG+vl+ag+++n+aR+ a lcl|FitnessBrowser__pseudo3_N2E3:AO353_01065 6 IVAATRTAIGSFQGALSAIPATELGAAVIRRLLEQTGIDAAQIDEVILGQVLTAGAGQNPARQTA 70 8**************************************************************** PP TIGR01930 66 laaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslk 130 ++aglp+++palt+n+vC+Sgl+Av+la+q+i++G+a++v+aGG E+mS +p++l+++ r +l+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_01065 71 IKAGLPHTTPALTLNKVCGSGLKAVHLAVQAIRCGDAELVIAGGQENMSLAPYVLPKA--RTGLR 133 ********************************************************98..89*** PP TIGR01930 131 lgkakledqllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkde 192 +g+a+l+d++++d+ + ++++mg+tAenla+ky+isRe qD +a++S+qkaa+Aie g+f++e lcl|FitnessBrowser__pseudo3_N2E3:AO353_01065 134 MGHAQLQDSMIQDGlwdAFNDYHMGITAENLAQKYEISREAQDTFAAASQQKAAAAIEGGRFQSE 198 *****************99********************************************** PP TIGR01930 193 ivpvevkgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllms 254 i+p+ ++++ + v+++De++r ++t+++LakLkpaf++ +gs vtAgN+s lnDGAa+lll+s lcl|FitnessBrowser__pseudo3_N2E3:AO353_01065 199 ITPILIPQRkgePLVFDTDEQPRIDSTAQALAKLKPAFQK-DGS-VTAGNASTLNDGAAVLLLAS 261 ******9999999*************************95.9*7.******************** PP TIGR01930 255 eevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvla 319 ++a++lgl +lari ++a agvdp++mg+gpvpA++ L+kag++++d+dl+E nEAFAaq+la lcl|FitnessBrowser__pseudo3_N2E3:AO353_01065 262 AAKAQALGLPVLARIKAYASAGVDPSIMGIGPVPATRLTLQKAGWNVEDLDLIEANEAFAAQALA 326 ***************************************************************** PP TIGR01930 320 vekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvil 384 v kelg d++kvNvnGGAiAlGHP+GasGari+++l++eL +r++k GlatlC+ggGqG+ + + lcl|FitnessBrowser__pseudo3_N2E3:AO353_01065 327 VGKELG-WDTSKVNVNGGAIALGHPIGASGARILVSLVHELIRRDGKKGLATLCIGGGQGVGLAI 390 ******.88***************************************************98877 PP TIGR01930 385 e 385 e lcl|FitnessBrowser__pseudo3_N2E3:AO353_01065 391 E 391 5 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (392 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.58 // [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