Align acetyl-CoA C-acetyltransferase (EC 2.3.1.16) (characterized)
to candidate GFF1043 Psest_1076 acetyl-CoA acetyltransferases
Query= metacyc::MONOMER-20831 (393 letters) >FitnessBrowser__psRCH2:GFF1043 Length = 393 Score = 656 bits (1693), Expect = 0.0 Identities = 327/392 (83%), Positives = 363/392 (92%) Query: 1 MQDVVIVAATRTAVGSFQGSLASIPAPELGAAVIRRLLEQTGLDPAQVDEVILGQVLTAG 60 MQDVVIVAATRTA+GSFQGSLA++PA ELGA VIR LLE+TG++PAQVDEVILG VLTAG Sbjct: 1 MQDVVIVAATRTAIGSFQGSLANVPAVELGATVIRALLEKTGIEPAQVDEVILGHVLTAG 60 Query: 61 SGQNPARQASILAGLPHAVPSLTLNKVCGSGLKALHLGAQAIRCGDAEVIIAGGMENMSL 120 +GQN ARQASI AGLPHAVPS+TLNKVCGSGLKA+HL QAIRCGDA+VIIAGGMENMSL Sbjct: 61 AGQNTARQASIKAGLPHAVPSMTLNKVCGSGLKAVHLAVQAIRCGDADVIIAGGMENMSL 120 Query: 121 APYVLPAARTGLRMGHAKMIDSMITDGLWDAFNDYHMGITAENLVDKYGISREAQDAFAA 180 APYVLP ARTGLRMGHA+++D+MITDGLWDAFNDYHMGITAENL +KYGI R QDAFAA Sbjct: 121 APYVLPGARTGLRMGHAQIVDTMITDGLWDAFNDYHMGITAENLAEKYGIDRAQQDAFAA 180 Query: 181 ASQQKATAAIEAGRFVDEITPILIPQRKGDPVAFAVDEQPRAGTTAESLAKLKPAFKKDG 240 SQQ+A AAIE+GRF EITP++IPQRKGDP+AFA DEQPRAGTTAESL L+ AFKKDG Sbjct: 181 QSQQRAAAAIESGRFDAEITPVMIPQRKGDPLAFARDEQPRAGTTAESLGGLRAAFKKDG 240 Query: 241 SVTAGNASSLNDGAAAVLLMSADKAKALGLPVLARIASYANAGVDPAIMGIGPVSATRRC 300 VTAGNAS+LNDGAAAV+LMSA KA+ALGLPVLA+IA YANAGVDPAIMGIGPV+ATRRC Sbjct: 241 CVTAGNASTLNDGAAAVVLMSASKAEALGLPVLAKIAGYANAGVDPAIMGIGPVTATRRC 300 Query: 301 LDKAGWSLGDLDLIEANEAFAAQSLAVGKELEWDAEKVNVNGGAIAIGHPIGASGCRVLV 360 LDKAGW+L +LDLIEANEAFA Q+L+VGKEL WDA+KVNVNGGAIA+GHPIGASGCR+LV Sbjct: 301 LDKAGWTLAELDLIEANEAFAVQALSVGKELGWDADKVNVNGGAIALGHPIGASGCRILV 360 Query: 361 TLLHEMIKRDAKKGLATLCIGGGQGVALALER 392 TLLHEM +RD +KGLATLCIGGGQGVALA+ER Sbjct: 361 TLLHEMQRRDVRKGLATLCIGGGQGVALAVER 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: 537 Number of extensions: 13 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: 393 Length adjustment: 31 Effective length of query: 362 Effective length of database: 362 Effective search space: 131044 Effective search space used: 131044 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 GFF1043 Psest_1076 (acetyl-CoA acetyltransferases)
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.2368049.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-153 494.7 8.8 9.7e-153 494.6 8.8 1.0 1 FitnessBrowser__psRCH2:GFF1043 Domain annotation for each sequence (and alignments): >> FitnessBrowser__psRCH2:GFF1043 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 494.6 8.8 9.7e-153 9.7e-153 1 385 [] 6 391 .. 6 391 .. 0.99 Alignments for each domain: == domain 1 score: 494.6 bits; conditional E-value: 9.7e-153 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpesvpaltv 79 iv+a+Rt+ig+++gsl++++a++L+a+vi++lle++g++p+++devilG+vl+ag+++n+aR+a ++aglp+ vp++t+ FitnessBrowser__psRCH2:GFF1043 6 IVAATRTAIGSFQGSLANVPAVELGATVIRALLEKTGIEPAQVDEVILGHVLTAGAGQNTARQASIKAGLPHAVPSMTL 84 8****************************************************************************** PP TIGR01930 80 nrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl...vktklsmgetA 155 n+vC+Sgl+Av+la+q+i++G+adv++aGG+E+mS +p++l+ + r +l++g+a+ d+++ d+ + ++++mg+tA FitnessBrowser__psRCH2:GFF1043 85 NKVCGSGLKAVHLAVQAIRCGDADVIIAGGMENMSLAPYVLPGA--RTGLRMGHAQIVDTMITDGlwdAFNDYHMGITA 161 ******************************************98..89********************99********* PP TIGR01930 156 enlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...kkvvskDegirpnttlekLakLkpafkekk 231 enla+kygi R +qD++a++S+q+aa+Aie+g+f++ei+pv ++++ + +++De++r++tt+e+L++L++afk+ + FitnessBrowser__psRCH2:GFF1043 162 ENLAEKYGIDRAQQDAFAAQSQQRAAAAIESGRFDAEITPVMIPQRkgdPLAFARDEQPRAGTTAESLGGLRAAFKK-D 239 ********************************************9999999************************95.9 PP TIGR01930 232 gstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEin 310 g vtAgN+s lnDGAaa++lms ++a++lgl +la+i ++a+agvdp++mg+gpv A++++L+kag+++ ++dl+E n FitnessBrowser__psRCH2:GFF1043 240 G-CVTAGNASTLNDGAAAVVLMSASKAEALGLPVLAKIAGYANAGVDPAIMGIGPVTATRRCLDKAGWTLAELDLIEAN 317 *.6**************************************************************************** PP TIGR01930 311 EAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 EAFA+q+l v kelg d +kvNvnGGAiAlGHP+GasG+ri++tll+e+++r+++ GlatlC+ggGqG+A+ +e FitnessBrowser__psRCH2:GFF1043 318 EAFAVQALSVGKELG-WDADKVNVNGGAIALGHPIGASGCRILVTLLHEMQRRDVRKGLATLCIGGGQGVALAVE 391 ***************.88*****************************************************9886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (393 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: 28.05 // [ok]
This GapMind analysis is from Apr 09 2024. 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