Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_101589711.1 BJEO58_RS11990 acetyl-CoA C-acetyltransferase
Query= BRENDA::P45359 (392 letters) >NCBI__GCF_900169175.1:WP_101589711.1 Length = 398 Score = 358 bits (918), Expect = e-103 Identities = 191/394 (48%), Positives = 261/394 (66%), Gaps = 6/394 (1%) Query: 1 MKEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAG 60 M E VI + RT G +L + AVDLGA AI A+ +AG+ P+ V VI+G VLQAG Sbjct: 1 MTEAVIVAGSRTPFGKMSGALGSLSAVDLGAEAISGALSRAGVSPDQVQHVIMGQVLQAG 60 Query: 61 LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSR 120 GQ PARQA+ KAG+P+ + A+TINK+C SG+ ++ AA +++AG+ DV++AGG E+M+ Sbjct: 61 CGQGPARQAAVKAGIPMSVNAITINKLCLSGINAITQAAMLVRAGEYDVVVAGGQESMTN 120 Query: 121 APYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAE----RWNISREEQD 176 AP++ +R GY+ G + D M DGLWDAF D MG E + + + +RE+QD Sbjct: 121 APHMLEKSRAGYKFGTVQVRDHMDYDGLWDAFTDEAMGGLTEAANDDDDPKRSFTREQQD 180 Query: 177 EFALASQKKAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPRFGSTIEGLAKLKPAFK 236 EFA S ++A A SG+ +EI PV +K R+GE V+ DE R ST E + KL+PAF+ Sbjct: 181 EFAATSHQRAAAAQDSGRLAEEITPVTLKSRRGEVTVELDEGVRADSTGESMGKLRPAFR 240 Query: 237 KDGTVTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYG-SAGVDPAIMGYGPFYA 295 KDGT+TAGNAS ++D A +V+MS KA+ELG+ LA+I ++ +AG D ++ + P + Sbjct: 241 KDGTITAGNASQISDGAVAVVVMSKAKAEELGLPILAEIGAHAWTAGPDSSLQ-HQPSQS 299 Query: 296 TKAAIEKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGA 355 +AA E+AG D DL E NEAFAA LA DL D KVNVNGGAIALGHPIGASGA Sbjct: 300 IRAAAERAGVAADSFDLYEINEAFAAVGLASTADLGVDAEKVNVNGGAIALGHPIGASGA 359 Query: 356 RILVTLVHAMQKRDAKKGLATLCIGGGQGTAILL 389 RI + L +++R G+A LC GGGQG A+++ Sbjct: 360 RITLDLALELKRRGGGTGVAALCGGGGQGDALII 393 Lambda K H 0.315 0.132 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: 445 Number of extensions: 15 Number of successful extensions: 2 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: 392 Length of database: 398 Length adjustment: 31 Effective length of query: 361 Effective length of database: 367 Effective search space: 132487 Effective search space used: 132487 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_101589711.1 BJEO58_RS11990 (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.3409209.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-134 434.0 9.9 2.7e-134 433.9 9.9 1.0 1 NCBI__GCF_900169175.1:WP_101589711.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900169175.1:WP_101589711.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 433.9 9.9 2.7e-134 2.7e-134 1 384 [. 6 393 .. 6 394 .. 0.97 Alignments for each domain: == domain 1 score: 433.9 bits; conditional E-value: 2.7e-134 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 iv++ Rtp+gk+ g+l +lsa+dL+a++i+++l rag++p+++ +vi+G+vlqag+++ +aR+aa++ag+p s NCBI__GCF_900169175.1:WP_101589711.1 6 IVAGSRTPFGKMSGALGSLSAVDLGAEAISGALSRAGVSPDQVQHVIMGQVLQAGCGQGPARQAAVKAGIPMS 78 8************************************************************************ PP TIGR01930 74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144 v+a+t+n++C Sg++A+++aa+ ++aGe+dvvvaGG Esm+++p++l++s r+++k+g+ +++d++ +d+ NCBI__GCF_900169175.1:WP_101589711.1 79 VNAITINKLCLSGINAITQAAMLVRAGEYDVVVAGGQESMTNAPHMLEKS--RAGYKFGTVQVRDHMDYDGlw 149 ************************************************98..89****************9** PP TIGR01930 145 .vktklsmgetAenlak....kygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDeg 210 + t+ +mg +e + k +++Re+qDe+a+ Shq+aa+A+++g++++ei+pv++k + +++v+ Deg NCBI__GCF_900169175.1:WP_101589711.1 150 dAFTDEAMGGLTEAANDdddpKRSFTREQQDEFAATSHQRAAAAQDSGRLAEEITPVTLKSRrgEVTVELDEG 222 *88999999888766652233679************************************99*********** PP TIGR01930 211 irpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemg 283 +r+++t e+++kL+paf++ +g t+tAgN+sq++DGA+a+++ms+++a+elgl +la+i ++a+++ + + ++ NCBI__GCF_900169175.1:WP_101589711.1 223 VRADSTGESMGKLRPAFRK-DG-TITAGNASQISDGAVAVVVMSKAKAEELGLPILAEIGAHAWTAGPDSSLQ 293 *****************95.9*.6************************************************* PP TIGR01930 284 lgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltl 356 +p ++i++a ++ag+ ++++dl+EinEAFAa+ la++ +lg d ekvNvnGGAiAlGHP+GasGari+l l NCBI__GCF_900169175.1:WP_101589711.1 294 HQPSQSIRAAAERAGVAADSFDLYEINEAFAAVGLASTADLG-VDAEKVNVNGGAIALGHPIGASGARITLDL 365 ******************************************.88**************************** PP TIGR01930 357 lkeLkergkkyGlatlCvggGqGaAvil 384 + eLk+rg+ G+a+lC ggGqG A+i+ NCBI__GCF_900169175.1:WP_101589711.1 366 ALELKRRGGGTGVAALCGGGGQGDALII 393 **************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (398 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: 25.94 // [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