Align acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_078428644.1 BK574_RS11035 acetyl-CoA C-acetyltransferase
Query= BRENDA::P42765 (397 letters) >NCBI__GCF_002019605.1:WP_078428644.1 Length = 394 Score = 385 bits (989), Expect = e-111 Identities = 200/392 (51%), Positives = 271/392 (69%), Gaps = 3/392 (0%) Query: 7 VFVVAAKRTPFGAYGGLLKDFTATDLSEFAAKAALSAGKVSPETVDSVIMGNVLQSSSDA 66 V++V RTP GA+G L + T+L A+ A+ +D+VI GNV+ +S++A Sbjct: 4 VYIVEGARTPIGAFGKSLSQVSTTELGRLTAEEAIKRSNCEATDIDNVIYGNVIHTSTNA 63 Query: 67 IYLARHVGLRVGIPKETPALTINRLCGSGFQSIVNGCQEICVKEAEVVLCGGTESMSQAP 126 Y+ARH+ L G+P ETP+L +NRLCGSG Q+I++ Q I + E+ + L GG E+MS AP Sbjct: 64 SYVARHIALHSGVPIETPSLLVNRLCGSGLQAIISAAQSIKLGESRLALAGGVENMSMAP 123 Query: 127 YCVRNVRF-GTKLGSDIKLEDSLWVSLTDQHVQLPMAMTAENLAVKHKISREECDKYALQ 185 + RF GTK G+ + ED L +L D++ M +TAENL+ K++ISRE+ D +AL Sbjct: 124 HSNFTSRFNGTKYGA-LAFEDMLLRTLADEYTGCGMGITAENLSEKYEISREDQDAFALL 182 Query: 186 SQQRWKAANDAGYFNDEMAPIEVKTKKGKQTMQVDEHARPQTTLEQLQKLPPVFKKDGTV 245 SQQR A + G F +E+ P+E+KT+KG + DEH R TT E L KL P FKKDGTV Sbjct: 183 SQQRAMKAVETGVFKEEIVPVELKTRKGSTFVTADEHIRKDTTTENLSKLVPAFKKDGTV 242 Query: 246 TAGNASGVADGAGAVIIASEDAVKKHNFTPLARIVGYFVSGCDPSIMGIGPVPAISGALK 305 T+GNASG+ DGA ++I+ASE+ + LA+I + V G DP+IMGIGPVPAI AL+ Sbjct: 243 TSGNASGINDGAASLILASEEKLHS-GMKALAKIRSWAVVGVDPNIMGIGPVPAIKLALQ 301 Query: 306 KAGLSLKDMDLVEVNEAFAPQYLAVERSLDLDISKTNVNGGAIALGHPLGGSGSRITAHL 365 +A L+L+DMD +EVNEAFA QYLAVE+ L+L KTNV GGAIALGHP+G SG+RIT L Sbjct: 302 RANLTLEDMDRIEVNEAFAAQYLAVEKELELPREKTNVYGGAIALGHPVGMSGARITLSL 361 Query: 366 VHELRRRGGKYAVGSACIGGGQGIAVIIQSTA 397 +ELRR+G +Y + S CIGGGQGIA++I++ A Sbjct: 362 AYELRRKGLRYGIASLCIGGGQGIAIVIENEA 393 Lambda K H 0.317 0.133 0.383 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: 370 Number of extensions: 10 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: 397 Length of database: 394 Length adjustment: 31 Effective length of query: 366 Effective length of database: 363 Effective search space: 132858 Effective search space used: 132858 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_078428644.1 BK574_RS11035 (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.30764.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-146 472.7 1.9 4.9e-146 472.5 1.9 1.0 1 lcl|NCBI__GCF_002019605.1:WP_078428644.1 BK574_RS11035 acetyl-CoA C-acety Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_078428644.1 BK574_RS11035 acetyl-CoA C-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 472.5 1.9 4.9e-146 4.9e-146 1 385 [] 6 390 .. 6 390 .. 0.98 Alignments for each domain: == domain 1 score: 472.5 bits; conditional E-value: 4.9e-146 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaa 68 iv+++Rtpig++g+sl+++s +L++ + +e+++r++ ++ +id+vi+Gnv++++++ + +aR++al + lcl|NCBI__GCF_002019605.1:WP_078428644.1 6 IVEGARTPIGAFGKSLSQVSTTELGRLTAEEAIKRSNCEATDIDNVIYGNVIHTSTNaSYVARHIALHS 74 8********************************************************9*********** PP TIGR01930 69 glpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakle 137 g+p ++p+l vnr+C+SglqA+++aaq+ik Ge ++++aGGvE+mS +p+++ s r ++ k+g+ e lcl|NCBI__GCF_002019605.1:WP_078428644.1 75 GVPIETPSLLVNRLCGSGLQAIISAAQSIKLGESRLALAGGVENMSMAPHSNFTS-RFNGTKYGALAFE 142 **************************************************99998.89*********** PP TIGR01930 138 dqllkdl..vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202 d+ll++l ++t+ mg+tAenl++ky+isRe+qD++al S+q+a kA+e g fk+eivpve+k++ + lcl|NCBI__GCF_002019605.1:WP_078428644.1 143 DMLLRTLadEYTGCGMGITAENLSEKYEISREDQDAFALLSQQRAMKAVETGVFKEEIVPVELKTRkgS 211 **999999999*****************************************************99999 PP TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271 + v+ De+ir++tt e+L+kL pafk+ +g tvt gN+s++nDGAa l+l+see+++ g++ la+i+s lcl|NCBI__GCF_002019605.1:WP_078428644.1 212 TFVTADEHIRKDTTTENLSKLVPAFKK-DG-TVTSGNASGINDGAASLILASEEKLH-SGMKALAKIRS 277 999**********************95.9*.6***********************97.589******** PP TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340 +av+gvdp++mg+gpvpAi+ aL++a+l+++d+d +E+nEAFAaq+lavekel+ l +ek Nv+GGAiA lcl|NCBI__GCF_002019605.1:WP_078428644.1 278 WAVVGVDPNIMGIGPVPAIKLALQRANLTLEDMDRIEVNEAFAAQYLAVEKELE-LPREKTNVYGGAIA 345 ******************************************************.88************ PP TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385 lGHP+G+sGari+l+l++eL+++g +yG+a+lC+ggGqG+A+++e lcl|NCBI__GCF_002019605.1:WP_078428644.1 346 LGHPVGMSGARITLSLAYELRRKGLRYGIASLCIGGGQGIAIVIE 390 *******************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (394 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: 7.63 // [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