Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate Dsui_2297 Dsui_2297 acetoacetyl-CoA synthase
Query= BRENDA::Q9Z3R3 (650 letters) >FitnessBrowser__PS:Dsui_2297 Length = 656 Score = 797 bits (2058), Expect = 0.0 Identities = 401/650 (61%), Positives = 471/650 (72%), Gaps = 7/650 (1%) Query: 7 LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVIGES 66 LW P E V + + F+ + DYDA WSV + AFW+ +W+ C V+G+ Sbjct: 8 LWRPGPERVAAANLTRFMGAASQAAAAPLNDYDALWQWSVDQPAAFWSLLWDFCGVVGDK 67 Query: 67 GEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALVS 126 G L DGD+M AR+FP+ RLN+AENLLR +G DAL+F GEDKV L+ DELRA VS Sbjct: 68 GGTVLEDGDKMPGARWFPQGRLNYAENLLRFSGPEDALVFWGEDKVKRHLSRDELRAQVS 127 Query: 127 RLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQI 186 R QQ L G+ GDRVA +PN+PET+ MLA AS+GAIWSS SPDFG QGVLDRFGQI Sbjct: 128 RFQQFLEDAGVQPGDRVAGYLPNLPETLIAMLAAASLGAIWSSASPDFGVQGVLDRFGQI 187 Query: 187 APKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVEGGVTLA 244 PK+ + DGYWYNGK D +K A L V+VPY + + + VT Sbjct: 188 GPKVLVCVDGYWYNGKAVDCLTKNAEAAAQLPTLEKVVVVPYLAATPDIG-AIPKAVTWD 246 Query: 245 DFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGLRD 304 +A F A F RLPF HPL+I++SSGTTGVPKCIVH GG +LQHLKEH+ ++ Sbjct: 247 QALAPFSATAPAFARLPFSHPLFIMYSSGTTGVPKCIVHCHGGAVLQHLKEHQLQGDVKP 306 Query: 305 GERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTSAK 364 G+R+FYFTTCGWMMWNWL SGLA GATL LYDGSPF G VLFDYA AE FGTSAK Sbjct: 307 GDRVFYFTTCGWMMWNWLVSGLASGATLLLYDGSPFADQGKVLFDYADAEAMTHFGTSAK 366 Query: 365 YIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDIVS 424 +IDA K G P TH L +LR + STGSPLSPEGF +VY IKP++QLASISGGTDI+S Sbjct: 367 FIDAAAKMGLKPRETHKLQALRSLFSTGSPLSPEGFDYVYRDIKPELQLASISGGTDIIS 426 Query: 425 CFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWNDPD 484 CFVLG P PV+RGEIQ GLG+AVDV++D+G+PVR +KGELVCT+ FP MPV FWNDPD Sbjct: 427 CFVLGAPTLPVYRGEIQCRGLGMAVDVFDDDGQPVRRQKGELVCTKPFPVMPVGFWNDPD 486 Query: 485 GAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQMD 544 GAKY AAYF+RF NVWCHGDFAE T H G+VI+GRSDATLNPGGVRIGTAEIY QVEQ++ Sbjct: 487 GAKYHAAYFERFPNVWCHGDFAELTEHNGMVIYGRSDATLNPGGVRIGTAEIYRQVEQLE 546 Query: 545 EVAEALCIGQDWE----DDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKII 600 EV E+L IGQDW DDVRVVLFV+L G+ L +AL+ IK +IR +PRHVPAK++ Sbjct: 547 EVVESLVIGQDWPPGKYDDVRVVLFVKLRDGLTLDDALSVRIKEQIRRNTTPRHVPAKVV 606 Query: 601 AVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELKS 650 V DIPRTKSGKIVELAVR+VVH RPVKN EALANPEAL+ F EL S Sbjct: 607 QVRDIPRTKSGKIVELAVRNVVHQRPVKNVEALANPEALEEFRERPELAS 656 Lambda K H 0.322 0.139 0.441 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: 1475 Number of extensions: 59 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: 650 Length of database: 656 Length adjustment: 38 Effective length of query: 612 Effective length of database: 618 Effective search space: 378216 Effective search space used: 378216 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 54 (25.4 bits)
Align candidate Dsui_2297 Dsui_2297 (acetoacetyl-CoA synthase)
to HMM TIGR01217 (acetoacetate-CoA ligase (EC 6.2.1.16))
# 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/TIGR01217.hmm # target sequence database: /tmp/gapView.21047.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01217 [M=652] Accession: TIGR01217 Description: ac_ac_CoA_syn: acetoacetate-CoA ligase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-291 953.6 0.0 2.6e-291 953.4 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_2297 Dsui_2297 acetoacetyl-CoA syntha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_2297 Dsui_2297 acetoacetyl-CoA synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 953.4 0.0 2.6e-291 2.6e-291 5 650 .. 7 654 .. 3 656 .] 0.98 Alignments for each domain: == domain 1 score: 953.4 bits; conditional E-value: 2.6e-291 TIGR01217 5 vlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddskmlaarf 81 lw+p erv+ a+l+rf a++++ a l dydal++wsvd+ afw+ +w+f++vv++++ + d++km++ar+ lcl|FitnessBrowser__PS:Dsui_2297 7 LLWRPGPERVAAANLTRFMGAASQAAAAPLNDYDALWQWSVDQPAAFWSLLWDFCGVVGDKGGTVLEDGDKMPGARW 83 79*************************************************************************** PP TIGR01217 82 fpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpnipeavaalla 158 fp+ rlnyaenllr +g edal++ +e+k++ +++ +elr+qv+++++ l Gv++Gdrvagylpn+pe++ a+la lcl|FitnessBrowser__PS:Dsui_2297 84 FPQGRLNYAENLLRFSGPEDALVFWGEDKVKRHLSRDELRAQVSRFQQFLEDAGVQPGDRVAGYLPNLPETLIAMLA 160 ***************************************************************************** PP TIGR01217 159 tasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlravvlipyvgdrekla 235 +as+Gaiwss+spdfG++gvldrf+qi pk+l++vdgy+ynGk d k +e a +lp+l++vv++py+ + + lcl|FitnessBrowser__PS:Dsui_2297 161 AASLGAIWSSASPDFGVQGVLDRFGQIGPKVLVCVDGYWYNGKAVDCLTKNAEAAAQLPTLEKVVVVPYLAAT--PD 235 ***********************************************************************55..55 PP TIGR01217 236 p.kvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhcdltdgdrlly 311 + ++ a+t+++ la + a+ + f +lpf+hpl+i++ssGttGvpk+ivh GG ++qhlkeh+l +d+++gdr++y lcl|FitnessBrowser__PS:Dsui_2297 236 IgAIPKAVTWDQALAPFSATAPAFARLPFSHPLFIMYSSGTTGVPKCIVHCHGGAVLQHLKEHQLQGDVKPGDRVFY 312 556************************************************************************** PP TIGR01217 312 yttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkkglkparthdlsalrl 388 +tt+Gwmmwn+lvsgla Gatl lydGsp+ +++vlfd+a++e +t +Gtsak+++a k glkp +th+l+alr lcl|FitnessBrowser__PS:Dsui_2297 313 FTTCGWMMWNWLVSGLASGATLLLYDGSPFADQGKVLFDYADAEAMTHFGTSAKFIDAAAKMGLKPRETHKLQALRS 389 ***************************************************************************** PP TIGR01217 389 vastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglGlaveawdeeGkpvtgekG 465 + stGspl+pegf+yvy+ ik++++lasisGGtdi+scfv++ p+lpvy+Geiq++glG+av+++d++G+pv+ +kG lcl|FitnessBrowser__PS:Dsui_2297 390 LFSTGSPLSPEGFDYVYRDIKPELQLASISGGTDIISCFVLGAPTLPVYRGEIQCRGLGMAVDVFDDDGQPVRRQKG 466 ***************************************************************************** PP TIGR01217 466 elvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynave 542 elv+tkp+p mpv fwnd+dG+ky++ayf+++p+vw+hGd++elt + g+vi+Grsdatlnp+Gvr+G+aeiy +ve lcl|FitnessBrowser__PS:Dsui_2297 467 ELVCTKPFPVMPVGFWNDPDGAKYHAAYFERFPNVWCHGDFAELTEHNGMVIYGRSDATLNPGGVRIGTAEIYRQVE 543 ***************************************************************************** PP TIGR01217 543 rldeveeslvigqeqedg...eervvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtlsGkkv 616 +l+ev eslvigq+++ g ++rvvlfvkl G tld+al +ik++ir + +prhvp+k+++v++iprt+sGk+v lcl|FitnessBrowser__PS:Dsui_2297 544 QLEEVVESLVIGQDWPPGkydDVRVVLFVKLRDGLTLDDALSVRIKEQIRRNTTPRHVPAKVVQVRDIPRTKSGKIV 620 ***************98744468****************************************************** PP TIGR01217 617 evavkdvvaGkpvenkgalsnpealdlyeeleel 650 e+av++vv+ +pv+n +al+npeal+ ++e +el lcl|FitnessBrowser__PS:Dsui_2297 621 ELAVRNVVHQRPVKNVEALANPEALEEFRERPEL 654 *****************************98887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (652 nodes) Target sequences: 1 (656 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 10.95 // [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