Align Beta-ketothiolase BktB; Acetyl-CoA acetyltransferase; Acetyl-CoA acyltransferase; EC 2.3.1.16; EC 2.3.1.9 (characterized)
to candidate WP_110804635.1 C8J30_RS05090 acetyl-CoA C-acyltransferase family protein
Query= SwissProt::Q0KBP1 (394 letters) >NCBI__GCF_003217355.1:WP_110804635.1 Length = 391 Score = 455 bits (1170), Expect = e-132 Identities = 228/390 (58%), Positives = 288/390 (73%), Gaps = 2/390 (0%) Query: 5 VVVVSGVRTAIGTFGGSLKDVAPAELGALVVREALARAQVSGDDVGHVVFGNVIQTEPRD 64 +V++SG RTAIG FGGSL AP +LG + R AL R+ ++ + + VV G+++ TEPRD Sbjct: 4 IVILSGARTAIGAFGGSLAGFAPVDLGTIAARAALERSGIAPEQINQVVMGHILNTEPRD 63 Query: 65 MYLGRVAAVNGGVTINAPALTVNRLCGSGLQAIVSAAQTILLGDTDVAIGGGAESMSRAP 124 MY+ RVAA+ G+ + PA+ VNRLCGSG+QAIVSAAQ ++LG+ D A+ GG + MSRAP Sbjct: 64 MYVSRVAAIQAGIPVETPAMNVNRLCGSGVQAIVSAAQALMLGEGDFALAGGVDVMSRAP 123 Query: 125 YLAPAARWGARMGDAGLVDMMLGALHDPFHRIHMGVTAENVAKEYDISRAQQDEAALESH 184 Y+ PAAR+G +MGDA ++DMM+GAL PF HMGVTAENVA E ISR QD ALES Sbjct: 124 YILPAARFGQKMGDASVIDMMVGALSCPFGTGHMGVTAENVATECAISREDQDTFALESQ 183 Query: 185 RRASAAIKAGYFKDQIVPVVSKGRKGDVTFDTDEHVRHDATIDDMTKLRPVFVKENGTVT 244 RA+AAI AG FKD+IVPV RKG V FDTDEH + T+D + L+P F+K G+VT Sbjct: 184 TRAAAAIAAGAFKDEIVPVEIASRKGTVIFDTDEHPK-ATTLDKLAALKPAFLK-GGSVT 241 Query: 245 AGNASGLNDAAAAVVMMERAEAERRGLKPLARLVSYGHAGVDPKAMGIGPVPATKIALER 304 AGNASG+ND A A+V+ A GLKPLAR+ + AGV P+ MG+GP+PA ++ E+ Sbjct: 242 AGNASGINDGAGALVIAREDAAVATGLKPLARIRGFAIAGVRPEVMGLGPIPAVRLLCEK 301 Query: 305 AGLQVSDLDVIEANEAFAAQACAVTKALGLDPAKVNPNGSGISLGHPIGATGALITVKAL 364 GL+VSD DVIE+NEAFAAQA AV++AL LDP KVNPNG I+LGHP+GATGA++TVK L Sbjct: 302 TGLKVSDFDVIESNEAFAAQALAVSRALDLDPTKVNPNGGAIALGHPVGATGAILTVKTL 361 Query: 365 HELNRVQGRYALVTMCIGGGQGIAAIFERI 394 + L R GR L+TMCIGGGQGIA ER+ Sbjct: 362 YHLRRTGGRLGLITMCIGGGQGIALAIERL 391 Lambda K H 0.318 0.134 0.381 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: 512 Number of extensions: 19 Number of successful extensions: 3 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: 394 Length of database: 391 Length adjustment: 31 Effective length of query: 363 Effective length of database: 360 Effective search space: 130680 Effective search space used: 130680 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 WP_110804635.1 C8J30_RS05090 (acetyl-CoA C-acyltransferase family protein)
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.2325385.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-136 441.5 6.6 1.4e-136 441.4 6.6 1.0 1 NCBI__GCF_003217355.1:WP_110804635.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003217355.1:WP_110804635.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 441.4 6.6 1.4e-136 1.4e-136 1 385 [] 6 389 .. 6 389 .. 0.98 Alignments for each domain: == domain 1 score: 441.4 bits; conditional E-value: 1.4e-136 TIGR01930 1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglpe 72 i++++Rt+ig++ggsl+ + ++dL++ + +++ler+g+ pe+i++v++G+ l++ + + R aa++ag+p NCBI__GCF_003217355.1:WP_110804635.1 6 ILSGARTAIGAFGGSLAGFAPVDLGTIAARAALERSGIAPEQINQVVMGHILNTEPRdMYVSRVAAIQAGIPV 78 899**************************************************99988*************** PP TIGR01930 73 svpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl. 144 ++pa++vnr+C+Sg+qA+ +aaq+++ Ge d ++aGGv+ mSr+p++l+a+ r + k+g+a++ d+++ l NCBI__GCF_003217355.1:WP_110804635.1 79 ETPAMNVNRLCGSGVQAIVSAAQALMLGEGDFALAGGVDVMSRAPYILPAA--RFGQKMGDASVIDMMVGALs 149 *************************************************98..89***********9998889 PP TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214 + +mg+tAen+a++ +isRe+qD +al+S+++aa+Ai++g fkdeivpve+ + ++++++De+++ NCBI__GCF_003217355.1:WP_110804635.1 150 cPFGTGHMGVTAENVATECAISREDQDTFALESQTRAAAAIAAGAFKDEIVPVEIASRkgTVIFDTDEHPK-A 221 9999***************************************************999999999*****99.8 PP TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287 ttl+kLa Lkpaf + gs vtAgN+s++nDGA+al+++ e++a + gl+plari+++a+agv pe+mglgp+ NCBI__GCF_003217355.1:WP_110804635.1 222 TTLDKLAALKPAFLK-GGS-VTAGNASGINDGAGALVIAREDAAVATGLKPLARIRGFAIAGVRPEVMGLGPI 292 9************95.796.***************************************************** PP TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360 pA++ + +k+gl++sd+d++E nEAFAaq+lav ++l+ ld+ kvN nGGAiAlGHP+Ga+Ga++++++l++L NCBI__GCF_003217355.1:WP_110804635.1 293 PAVRLLCEKTGLKVSDFDVIESNEAFAAQALAVSRALD-LDPTKVNPNGGAIALGHPVGATGAILTVKTLYHL 364 **************************************.89******************************** PP TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385 ++ g+++Gl+t+C+ggGqG+A+ +e NCBI__GCF_003217355.1:WP_110804635.1 365 RRTGGRLGLITMCIGGGQGIALAIE 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 12.65 // [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