Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_011383023.1 AMB_RS03000 acetoacetate--CoA ligase
Query= BRENDA::Q9Z3R3 (650 letters) >NCBI__GCF_000009985.1:WP_011383023.1 Length = 652 Score = 811 bits (2096), Expect = 0.0 Identities = 406/648 (62%), Positives = 487/648 (75%), Gaps = 6/648 (0%) Query: 7 LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVIGES 66 LW P +E E S +A F+ RF DY WSV FW+ VW+ +IG+ Sbjct: 5 LWQPSKERAEASALARFMRRADARFQVGATDYAGLWRWSVDRPDQFWSLVWDEVGIIGDR 64 Query: 67 GEKALV--DGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRAL 124 + +V D RM AR+FPEARLNFAENLLR+ GDAL+F GEDKV RL++ ELRAL Sbjct: 65 PDGGVVVDDAGRMPGARWFPEARLNFAENLLRRDDGGDALVFWGEDKVKRRLSFAELRAL 124 Query: 125 VSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFG 184 VSRLQQAL A G+G GDRVA MPNMPE++A MLA AS+GAIWSS SPDFG QGVLDRFG Sbjct: 125 VSRLQQALSAAGVGKGDRVAGYMPNMPESVAFMLAVASLGAIWSSASPDFGVQGVLDRFG 184 Query: 185 QIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVEGGVT 242 QIAPK+ + +GY+Y+GK D K+ A+ + + V+VPY ++A L+ V+ V Sbjct: 185 QIAPKVLVAAEGYFYSGKAHDCLEKLAAIVPGIPSLERVVVVPYTREAADLSG-VDKAVH 243 Query: 243 LADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGL 302 L DF+A F A + F RLPF HPLYI++SSGTTG PKCIVHSAGG+L+Q LKEHR HC + Sbjct: 244 LGDFLAPFPAKAVEFLRLPFDHPLYIMYSSGTTGAPKCIVHSAGGSLIQQLKEHRLHCDV 303 Query: 303 RDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTS 362 R +R+FYFTTCGWMMWNWL +GL ATL LYDG+P GN+LFD+A AE +FGTS Sbjct: 304 RKDDRVFYFTTCGWMMWNWLVAGLGAEATLLLYDGNPSHLGGNILFDFADAEGMTLFGTS 363 Query: 363 AKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDI 422 AK+IDA+ K G P +TH L+++R + STGS L+PEGF +VY +K DVQLASISGGTDI Sbjct: 364 AKWIDAIAKSGLEPIKTHSLATVRTICSTGSVLAPEGFDYVYAKVKADVQLASISGGTDI 423 Query: 423 VSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWND 482 +SCF+LGNPL PV+RGEIQ GLG+ V+V+++ G+ + G KGELVCTRAFPSMPV FWND Sbjct: 424 ISCFMLGNPLVPVYRGEIQCRGLGMKVEVFDENGQSLAGSKGELVCTRAFPSMPVGFWND 483 Query: 483 PDGAKYRAAYFDRFDNVWCHGDFAEWTPH-GGIVIHGRSDATLNPGGVRIGTAEIYNQVE 541 DGAKYRAAYF++F +W HGD+ E P GGI++ GRSDATLNPGGVRIGTAEIY QVE Sbjct: 484 DDGAKYRAAYFEKFPGIWTHGDWVELNPETGGIIVFGRSDATLNPGGVRIGTAEIYRQVE 543 Query: 542 QMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIA 601 Q+D+V E+L IGQDW+ DVRVVLFVRL GV L+ L IK RIR +PRHVPAK++ Sbjct: 544 QIDDVLESLVIGQDWQADVRVVLFVRLRDGVTLSPELETRIKKRIRDNTTPRHVPAKVVQ 603 Query: 602 VADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELK 649 VADIPRTKSGKIVELAVRDVVHGR VKNKEALANPEALDLFAG EL+ Sbjct: 604 VADIPRTKSGKIVELAVRDVVHGRAVKNKEALANPEALDLFAGRAELE 651 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: 1441 Number of extensions: 65 Number of successful extensions: 4 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: 652 Length adjustment: 38 Effective length of query: 612 Effective length of database: 614 Effective search space: 375768 Effective search space used: 375768 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 WP_011383023.1 AMB_RS03000 (acetoacetate--CoA ligase)
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.2075582.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-292 955.7 0.0 6.5e-292 955.4 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011383023.1 AMB_RS03000 acetoacetate--CoA li Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011383023.1 AMB_RS03000 acetoacetate--CoA ligase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 955.4 0.0 6.5e-292 6.5e-292 5 650 .. 4 650 .. 2 652 .] 0.98 Alignments for each domain: == domain 1 score: 955.4 bits; conditional E-value: 6.5e-292 TIGR01217 5 vlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevv.. 71 lw+p +er + + larf + rf +dy+ l+rwsvd d+fw+ vw+ ++++++++ vv lcl|NCBI__GCF_000009985.1:WP_011383023.1 4 LLWQPSKERAEASALARFMRRADARFQVGATDYAGLWRWSVDRPDQFWSLVWDEVGIIGDRPDGGVVvd 72 59************************************************************9877633 PP TIGR01217 72 ddskmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGd 140 d +m++ar+fp+arln+aenllr+ + +dal++ +e+k++ +++f+elr++v++l++al a Gv+kGd lcl|NCBI__GCF_000009985.1:WP_011383023.1 73 DAGRMPGARWFPEARLNFAENLLRRDDGGDALVFWGEDKVKRRLSFAELRALVSRLQQALSAAGVGKGD 141 3459***************************************************************** PP TIGR01217 141 rvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekv 209 rvagy+pn+pe+va +la as+Gaiwss+spdfG++gvldrf+qi+pk+l++ +gy y+Gk hd ek+ lcl|NCBI__GCF_000009985.1:WP_011383023.1 142 RVAGYMPNMPESVAFMLAVASLGAIWSSASPDFGVQGVLDRFGQIAPKVLVAAEGYFYSGKAHDCLEKL 210 ********************************************************************* PP TIGR01217 210 revakelpdlravvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGv 278 ++++ ++p+l++vv++py +++ l+ v+ a++l d+la + a ++f +lpfdhplyi++ssGttG+ lcl|NCBI__GCF_000009985.1:WP_011383023.1 211 AAIVPGIPSLERVVVVPYTREAADLSG-VDKAVHLGDFLAPFPAKAVEFLRLPFDHPLYIMYSSGTTGA 278 *******************97777766.***************************************** PP TIGR01217 279 pkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnv 347 pk+ivhsaGG l+q lkeh+lhcd+++ dr++y+tt+Gwmmwn+lv+gl + atl lydG p +n+ lcl|NCBI__GCF_000009985.1:WP_011383023.1 279 PKCIVHSAGGSLIQQLKEHRLHCDVRKDDRVFYFTTCGWMMWNWLVAGLGAEATLLLYDGNPSHLGGNI 347 ********************************************************************* PP TIGR01217 348 lfdlaeregitvlGtsakyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllas 416 lfd+a++eg+t++Gtsak+++a+ k+gl+p++th l ++r++ stGs l pegf+yvy ++kadv+las lcl|NCBI__GCF_000009985.1:WP_011383023.1 348 LFDFADAEGMTLFGTSAKWIDAIAKSGLEPIKTHSLATVRTICSTGSVLAPEGFDYVYAKVKADVQLAS 416 ********************************************************************* PP TIGR01217 417 isGGtdivscfvganpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwnded 485 isGGtdi+scf+++np++pvy+Geiq++glG++ve++de+G+++ g kGelv+t+++psmpv fwnd+d lcl|NCBI__GCF_000009985.1:WP_011383023.1 417 ISGGTDIISCFMLGNPLVPVYRGEIQCRGLGMKVEVFDENGQSLAGSKGELVCTRAFPSMPVGFWNDDD 485 ********************************************************************* PP TIGR01217 486 GskyrkayfdkypgvwahGdyieltp.rGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvi 553 G+kyr+ayf+k+pg+w+hGd++el+p +Ggi+++Grsdatlnp+Gvr+G+aeiy +ve++d+v eslvi lcl|NCBI__GCF_000009985.1:WP_011383023.1 486 GAKYRAAYFEKFPGIWTHGDWVELNPeTGGIIVFGRSDATLNPGGVRIGTAEIYRQVEQIDDVLESLVI 554 **************************99***************************************** PP TIGR01217 554 gqeqedgeervvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtlsGkkvevavkd 622 gq+++ ++rvvlfv+l G+tl+++l +ik++ir + +prhvp+k+++va+iprt+sGk+ve+av+d lcl|NCBI__GCF_000009985.1:WP_011383023.1 555 GQDWQA-DVRVVLFVRLRDGVTLSPELETRIKKRIRDNTTPRHVPAKVVQVADIPRTKSGKIVELAVRD 622 ****98.************************************************************** PP TIGR01217 623 vvaGkpvenkgalsnpealdlyeeleel 650 vv+G++v+nk+al+npealdl+++ +el lcl|NCBI__GCF_000009985.1:WP_011383023.1 623 VVHGRAVKNKEALANPEALDLFAGRAEL 650 **********************998876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (652 nodes) Target sequences: 1 (652 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 27.65 // [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