Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate Pf6N2E2_2042 Acetoacetyl-CoA synthetase (EC 6.2.1.16)
Query= BRENDA::Q9Z3R3 (650 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 Length = 651 Score = 687 bits (1774), Expect = 0.0 Identities = 355/647 (54%), Positives = 439/647 (67%), Gaps = 7/647 (1%) Query: 7 LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKV-IGE 65 LW P E + +S M F + R DY A H WS+ +R AFW A+ + ++ + Sbjct: 5 LWQPSPERIAQSRMNAFRQFVNARHHLQLHDYPALHAWSIDQREAFWQAIVDFFEIHFHQ 64 Query: 66 SGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125 + + LV+G +M A++FP A LNFAE+LLR+ A++ E+ +LTW EL A V Sbjct: 65 APDAVLVEGAQMPSAQWFPGATLNFAEHLLRRRDDAVAVVALDENGSQEQLTWAELAAHV 124 Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185 + LQ +L+A G+ GDRVAA MPN +T+ MLAT S+GAIWS SPDFG QGV+DRFGQ Sbjct: 125 AGLQTSLKAAGVTQGDRVAACMPNTWQTLVGMLATTSLGAIWSCSSPDFGTQGVIDRFGQ 184 Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAP--TVEGGV 241 I PK+ I C GY Y GK D +KV + + L + +++PYA A + T Sbjct: 185 IEPKVLITCAGYRYAGKVIDQRTKVNEILERLPSLQQLIVLPYAQPDACVEDFKTPAAVA 244 Query: 242 TLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCG 301 DF G F +PF HPLYIL+SSGTTGVPKCIVH GG LLQH+KEH H Sbjct: 245 LWNDFYQS--GGEPAFVSVPFDHPLYILYSSGTTGVPKCIVHGTGGVLLQHVKEHGLHVD 302 Query: 302 LRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGT 361 L +RLFY+TTCGWMMWNWL S LAVG+T+ LYDGSPF P L D +R +VFGT Sbjct: 303 LGPEDRLFYYTTCGWMMWNWLVSALAVGSTVVLYDGSPFHPGPERLLDLIDQQRISVFGT 362 Query: 362 SAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTD 421 S K++ A+ G P +TH L SLR + STGS L+P + +VY IK DV LAS+SGGTD Sbjct: 363 SPKFLAALESEGLKPRQTHRLDSLRALLSTGSALAPHSYDYVYRDIKADVCLASMSGGTD 422 Query: 422 IVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWN 481 IVSCFV GNPL PV RGE+QG LG+AV VWN+ G PV GEKGELVCTR FP+MP+ WN Sbjct: 423 IVSCFVNGNPLSPVSRGEMQGKSLGMAVQVWNEAGNPVIGEKGELVCTRHFPAMPIGLWN 482 Query: 482 DPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVE 541 DP K RA+YF +F VW GD+AE PHGG +IHGRSDA LNPGGVRIGTAEIY QVE Sbjct: 483 DPRQEKLRASYFAQFPGVWAQGDYAEELPHGGFLIHGRSDAVLNPGGVRIGTAEIYRQVE 542 Query: 542 QMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIA 601 ++++V + + IGQ W+ DVRVVLFVRL GV L EAL ++I+ IR+ +PRHVPAKI+A Sbjct: 543 KVEQVLDCVAIGQRWQGDVRVVLFVRLRDGVTLNEALAQQIRQVIRANTTPRHVPAKILA 602 Query: 602 VADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEEL 648 V+DIPRT SGK+VELAVR+VVHG VKN +ALANPEAL+ F EL Sbjct: 603 VSDIPRTISGKVVELAVRNVVHGEAVKNTDALANPEALEQFRDRPEL 649 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: 1361 Number of extensions: 70 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: 651 Length adjustment: 38 Effective length of query: 612 Effective length of database: 613 Effective search space: 375156 Effective search space used: 375156 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 Pf6N2E2_2042 (Acetoacetyl-CoA synthetase (EC 6.2.1.16))
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.6891.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-271 886.9 0.0 3.8e-271 886.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 Acetoacetyl-CoA synthetase (EC 6 Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 Acetoacetyl-CoA synthetase (EC 6.2.1.16) # 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 5 650 .. 4 649 .. 1 651 [] 0.98 Alignments for each domain: == domain 1 score: 886.8 bits; conditional E-value: 3.8e-271 TIGR01217 5 vlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaek 68 +lw+p er++++r++ fr++v r+ + l dy al+ ws+d+++afw+a+++f+++ f++a + lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 4 ILWQPSPERIAQSRMNAFRQFVNARHHLQLHDYPALHAWSIDQREAFWQAIVDFFEIHFHQAPD 67 79********************************************************998777 PP TIGR01217 69 ev.vddskmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaal 131 +v v++ +m++a++fpga+ln+ae+llr+++ a++ de+ + ++t++el + va l+++l lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 68 AVlVEGAQMPSAQWFPGATLNFAEHLLRRRDDAVAVVALDENGSQEQLTWAELAAHVAGLQTSL 131 652899********************************************************** PP TIGR01217 132 ralGvkkGdrvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdg 195 +a Gv +Gdrva+ +pn+ ++++ +lat+s+Gaiws +spdfG++gv+drf+qiepk+l+++ g lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 132 KAAGVTQGDRVAACMPNTWQTLVGMLATTSLGAIWSCSSPDFGTQGVIDRFGQIEPKVLITCAG 195 **************************************************************** PP TIGR01217 196 yvynGkehdrrekvrevakelpdlravvlipyvgdreklap.kvegalt.ledllaaaqaaelv 257 y+y Gk d+r kv+e+ lp+l++ +++py+ + + ++ k ++a+ ++d+ + +e+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 196 YRYAGKVIDQRTKVNEILERLPSLQQLIVLPYAQPDACVEDfKTPAAVAlWNDFYQS--GGEPA 257 **********************************998766559999986489**999..99*** PP TIGR01217 258 feqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwn 321 f +pfdhplyil+ssGttGvpk+ivh +GG+l+qh+keh+lh dl++ drl+yytt+Gwmmwn lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 258 FVSVPFDHPLYILYSSGTTGVPKCIVHGTGGVLLQHVKEHGLHVDLGPEDRLFYYTTCGWMMWN 321 **************************************************************** PP TIGR01217 322 flvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkkglkparthdlsa 385 +lvs+la+G+t+vlydGsp+ p ++ l dl+++++i+v+Gts k++ a++ +glkp +th l++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 322 WLVSALAVGSTVVLYDGSPFHPGPERLLDLIDQQRISVFGTSPKFLAALESEGLKPRQTHRLDS 385 **************************************************************** PP TIGR01217 386 lrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglGla 449 lr+++stGs l p++++yvy+ ikadv las+sGGtdivscfv +np+ pv +Ge+q+++lG+a lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 386 LRALLSTGSALAPHSYDYVYRDIKADVCLASMSGGTDIVSCFVNGNPLSPVSRGEMQGKSLGMA 449 **************************************************************** PP TIGR01217 450 veawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprG 513 v++w+e G+pv gekGelv+t+ +p+mp+ +wnd+ k r++yf ++pgvwa Gdy+e p+G lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 450 VQVWNEAGNPVIGEKGELVCTRHFPAMPIGLWNDPRQEKLRASYFAQFPGVWAQGDYAEELPHG 513 **************************************************************** PP TIGR01217 514 givihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatld 577 g +ihGrsda lnp+Gvr+G+aeiy +ve++++v +++ igq ++ g++rvvlfv+l G+tl+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 514 GFLIHGRSDAVLNPGGVRIGTAEIYRQVEKVEQVLDCVAIGQRWQ-GDVRVVLFVRLRDGVTLN 576 *******************************************98.5***************** PP TIGR01217 578 ealvkeikdairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpvenkgalsnpeal 641 eal ++i++ ira+ +prhvp+ki++v++iprt+sGk ve+av++vv+G++v+n +al+npeal lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 577 EALAQQIRQVIRANTTPRHVPAKILAVSDIPRTISGKVVELAVRNVVHGEAVKNTDALANPEAL 640 **************************************************************** PP TIGR01217 642 dlyeeleel 650 + +++ +el lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2042 641 EQFRDRPEL 649 ****98887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (652 nodes) Target sequences: 1 (651 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 0.01s 00:00:00.05 Elapsed: 00:00:00.05 # Mc/sec: 7.89 // [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