Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate PP_3071 PP_3071 acetoacetyl-coenzyme A synthetase
Query= BRENDA::Q9Z3R3 (650 letters) >FitnessBrowser__Putida:PP_3071 Length = 650 Score = 694 bits (1791), Expect = 0.0 Identities = 366/648 (56%), Positives = 440/648 (67%), Gaps = 6/648 (0%) Query: 7 LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVIGES 66 LW P +E S M F R+ DY A H WS+ +R AFW + E+ +V + Sbjct: 5 LWRPSTTQIEASRMDAFRRRVNLRYNLQLNDYQALHGWSIEQRPAFWQTLAEYFQVHWHT 64 Query: 67 G-EKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125 + L +G +M DA++F A LNFAE+LLR+ A++ ED T EL A V Sbjct: 65 PPSQVLSEGPQMPDAQWFANATLNFAEHLLRRRDDRPAVVAVREDGQREVFTHAELAAQV 124 Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185 + LQ A +A GI GDRVAA+MPN +T+ MLA S+GA+WS+ SP+FG G++DRFGQ Sbjct: 125 AGLQTAFKAVGIVPGDRVAAIMPNTWQTLVAMLACTSLGAVWSTSSPEFGVHGIIDRFGQ 184 Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVEGGVTL 243 I PKL IVC GY Y GK D +KV V L ++VP+ V+L Sbjct: 185 IEPKLLIVCAGYQYAGKAIDQVTKVNQVCAQLPGLEHLIVVPHTRKGTRADEFQAANVSL 244 Query: 244 -ADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGL 302 DF G F LPF HPLYIL+SSGTTGVPKCIVH AGG LLQHLKEH H L Sbjct: 245 WNDFFQ--PGGEPRFTPLPFDHPLYILYSSGTTGVPKCIVHRAGGVLLQHLKEHGLHNDL 302 Query: 303 RDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTS 362 + + LFY+TTCGWMMWNWLASGLAVGATL LYDGSPF P L D AE FGTS Sbjct: 303 KADDVLFYYTTCGWMMWNWLASGLAVGATLVLYDGSPFHPGPERLLDLIEAEGIHAFGTS 362 Query: 363 AKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDI 422 AKY+ A+ + G PA +H L+SLRL+ STGSPLSP + +VY+ IK D+ L S+SGGTDI Sbjct: 363 AKYLAALEQAGLEPANSHCLTSLRLLLSTGSPLSPHSYDYVYDKIKADLWLVSMSGGTDI 422 Query: 423 VSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWND 482 VSCFVLGNP PV RGEIQ GLG+AV+VWN++G+PV EKGELVCTR FPSMP+ FWND Sbjct: 423 VSCFVLGNPTLPVRRGEIQCKGLGMAVEVWNEQGQPVVDEKGELVCTRNFPSMPLGFWND 482 Query: 483 PDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQ 542 PDG +Y AYF +F VW GD+AE GG+VIHGRSDA LNPGGVRIGTAEIY QVE+ Sbjct: 483 PDGRRYHDAYFSQFPGVWAQGDYAEQRASGGMVIHGRSDAVLNPGGVRIGTAEIYRQVEK 542 Query: 543 MDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIAV 602 +++V E++ IGQDW DVRVVLFVRL G++L EAL + I+ IR +PRHVPA I V Sbjct: 543 VEQVVESVAIGQDWNGDVRVVLFVRLQDGLQLDEALRQHIRQVIRQYTTPRHVPAVIAQV 602 Query: 603 ADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELKS 650 +DIPRT SGK+VELA+RDVVHGRPVKN +ALANPEAL+ F ELKS Sbjct: 603 SDIPRTISGKLVELAIRDVVHGRPVKNTDALANPEALEQFRDRAELKS 650 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: 1340 Number of extensions: 60 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: 650 Length adjustment: 38 Effective length of query: 612 Effective length of database: 612 Effective search space: 374544 Effective search space used: 374544 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 PP_3071 PP_3071 (acetoacetyl-coenzyme A synthetase)
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.454.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-271 887.0 0.0 3.8e-271 886.8 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_3071 PP_3071 acetoacetyl-coenzyme A s Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_3071 PP_3071 acetoacetyl-coenzyme A synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 886.8 0.0 3.8e-271 3.8e-271 4 652 .] 3 650 .] 1 650 [] 0.98 Alignments for each domain: == domain 1 score: 886.8 bits; conditional E-value: 3.8e-271 TIGR01217 4 qvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvd.dskml 77 +vlw+p + +++ +r++ fr v r+ + l dy+al+ ws++++ afw+ + e+++v +++ ++v+ + +m+ lcl|FitnessBrowser__Putida:PP_3071 3 DVLWRPSTTQIEASRMDAFRRRVNLRYNLQLNDYQALHGWSIEQRPAFWQTLAEYFQVHWHTPPSQVLSeGPQMP 77 59************************************************************99999861679** PP TIGR01217 78 aarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpnipea 152 +a++f +a+ln+ae+llr+++ +a++ v e+ + t++el +qva l++a++a+G+ +Gdrva+++pn+ ++ lcl|FitnessBrowser__Putida:PP_3071 78 DAQWFANATLNFAEHLLRRRDDRPAVVAVREDGQREVFTHAELAAQVAGLQTAFKAVGIVPGDRVAAIMPNTWQT 152 *************************************************************************** PP TIGR01217 153 vaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlravvlipy 227 ++a+la++s+Ga+ws++sp+fG++g++drf+qiepkll+++ gy+y Gk d+ kv++v +lp l++ +++p+ lcl|FitnessBrowser__Putida:PP_3071 153 LVAMLACTSLGAVWSTSSPEFGVHGIIDRFGQIEPKLLIVCAGYQYAGKAIDQVTKVNQVCAQLPGLEHLIVVPH 227 *************************************************************************** PP TIGR01217 228 vgdreklap.kvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhc 301 + + + + + ++d+ +e+ f lpfdhplyil+ssGttGvpk+ivh aGG+l+qhlkeh+lh lcl|FitnessBrowser__Putida:PP_3071 228 TRKGTRADEfQAANVSLWNDFFQP--GGEPRFTPLPFDHPLYILYSSGTTGVPKCIVHRAGGVLLQHLKEHGLHN 300 997777766577888899***988..89*********************************************** PP TIGR01217 302 dltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkkglk 376 dl+ d+l+yytt+Gwmmwn+l+sgla+GatlvlydGsp+ p ++ l dl+e+egi +Gtsaky+ a++++gl+ lcl|FitnessBrowser__Putida:PP_3071 301 DLKADDVLFYYTTCGWMMWNWLASGLAVGATLVLYDGSPFHPGPERLLDLIEAEGIHAFGTSAKYLAALEQAGLE 375 *************************************************************************** PP TIGR01217 377 parthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglGlave 451 pa++h l++lrl++stGspl+p++++yvy++ikad++l s+sGGtdivscfv++np+lpv +Geiq++glG+ave lcl|FitnessBrowser__Putida:PP_3071 376 PANSHCLTSLRLLLSTGSPLSPHSYDYVYDKIKADLWLVSMSGGTDIVSCFVLGNPTLPVRRGEIQCKGLGMAVE 450 *************************************************************************** PP TIGR01217 452 awdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprGgivihGrsdatln 526 +w+e+G+pv +ekGelv+t+ +psmp+ fwnd+dG +y++ayf+++pgvwa Gdy+e + Gg+vihGrsda ln lcl|FitnessBrowser__Putida:PP_3071 451 VWNEQGQPVVDEKGELVCTRNFPSMPLGFWNDPDGRRYHDAYFSQFPGVWAQGDYAEQRASGGMVIHGRSDAVLN 525 *************************************************************************** PP TIGR01217 527 pnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeikdairaglsprhvpski 601 p+Gvr+G+aeiy +ve++++v es+ igq+++ g++rvvlfv+l G +ldeal ++i++ ir +prhvp+ i lcl|FitnessBrowser__Putida:PP_3071 526 PGGVRIGTAEIYRQVEKVEQVVESVAIGQDWN-GDVRVVLFVRLQDGLQLDEALRQHIRQVIRQYTTPRHVPAVI 599 *******************************7.6***************************************** PP TIGR01217 602 ievagiprtlsGkkvevavkdvvaGkpvenkgalsnpealdlyeeleelks 652 +v++iprt+sGk ve+a++dvv+G+pv+n +al+npeal+ +++ +elks lcl|FitnessBrowser__Putida:PP_3071 600 AQVSDIPRTISGKLVELAIRDVVHGRPVKNTDALANPEALEQFRDRAELKS 650 *********************************************999986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (652 nodes) Target sequences: 1 (650 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 7.42 // [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