Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate AO353_21765 AO353_21765 acetoacetyl-CoA synthetase
Query= BRENDA::Q9Z3R3 (650 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21765 Length = 651 Score = 681 bits (1756), Expect = 0.0 Identities = 348/648 (53%), Positives = 446/648 (68%), Gaps = 9/648 (1%) Query: 7 LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKV-IGE 65 LW P E + ++ M F + +R+ + ADY A H WS+ +R FW A+ + ++ + Sbjct: 5 LWQPSAERIGKTRMDAFRRFSNQRYNLTLADYPALHQWSIDQREDFWQAIVDFFEIKFHQ 64 Query: 66 SGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125 L +G +M +A +FP A LNFAE+LLR+ + A+I E+ L++ EL V Sbjct: 65 PASTVLREGPQMPNAEWFPGATLNFAEHLLRRRDNAIAVIAIAENGQRESLSYRELAEHV 124 Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185 + LQ++LRA G+G GDRVAA MPN +T+ MLAT S+GAIWS SPDFG GV+DRFGQ Sbjct: 125 AGLQKSLRAAGVGQGDRVAACMPNTWQTLVGMLATTSLGAIWSCSSPDFGTHGVVDRFGQ 184 Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAP-TVEGGVT 242 I PK+ I C GY Y GK+ D +KV + + L + +IVPYA A + + V Sbjct: 185 IEPKVLITCAGYRYAGKKIDQTTKVNEILERLPSLQQLIIVPYARPQARVDDYKTQANVA 244 Query: 243 LAD--FIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHC 300 L D + G + G F +PF HPLYIL+SSGTTGVPKCI+HS GG LLQH+KEH H Sbjct: 245 LWDSFYRPGGEPG---FVAVPFAHPLYILYSSGTTGVPKCIIHSVGGVLLQHVKEHGLHV 301 Query: 301 GLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFG 360 L +RLFY+TTCGWMMWNWL S LAVG+++ LYDGSPF P L D +E +VFG Sbjct: 302 DLGPDDRLFYYTTCGWMMWNWLVSALAVGSSVVLYDGSPFHPGPQRLIDLIDSEAISVFG 361 Query: 361 TSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGT 420 TS KY+ + P +HDL SL+ + STGS LSP+ + +VY IK D+ L+S+SGGT Sbjct: 362 TSPKYLATLESNEIQPRLSHDLGSLKALLSTGSALSPQSYDYVYREIKSDLCLSSMSGGT 421 Query: 421 DIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFW 480 DI+SCF+ GNP+ PV RGE+Q GLG+AV+VWN+ G+PV GEKGELVCTR FP+MP+ W Sbjct: 422 DIISCFLAGNPVLPVRRGEMQCKGLGMAVEVWNEAGQPVIGEKGELVCTRHFPAMPIGLW 481 Query: 481 NDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQV 540 NDP K RA+YF +F VW GD+AE P+G +IHGRSDA LNPGGVRIGTAEIY QV Sbjct: 482 NDPQQEKLRASYFSQFPGVWAQGDYAEQRPNGSWLIHGRSDAVLNPGGVRIGTAEIYRQV 541 Query: 541 EQMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKII 600 E++ +V +++ IGQ W+DDVRVVLFVRL GV L E L +EI+ IR+ +PRHVPAKI+ Sbjct: 542 EKIHQVLDSVAIGQQWQDDVRVVLFVRLRDGVTLDEKLEQEIRQVIRANTTPRHVPAKIV 601 Query: 601 AVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEEL 648 AV DIPRT SGK+VELAVR+VVHG+PVKN +ALANPEAL+ F EL Sbjct: 602 AVTDIPRTISGKVVELAVRNVVHGQPVKNTDALANPEALEQFRDRPEL 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: 1324 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: 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 AO353_21765 AO353_21765 (acetoacetyl-CoA 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.5428.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-270 883.8 0.0 3.4e-270 883.6 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 AO353_21765 acetoacetyl-CoA synt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 AO353_21765 acetoacetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 883.6 0.0 3.4e-270 3.4e-270 4 650 .. 3 649 .. 1 651 [] 0.98 Alignments for each domain: == domain 1 score: 883.6 bits; conditional E-value: 3.4e-270 TIGR01217 4 qvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaek 68 +vlw+p aer+ ++r++ fr + +r+ ++l+dy al++ws+d++++fw+a+++f+++ f+++ + lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 3 EVLWQPSAERIGKTRMDAFRRFSNQRYNLTLADYPALHQWSIDQREDFWQAIVDFFEIKFHQPAS 67 58**************************************************************9 PP TIGR01217 69 evv.ddskmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalr 132 v+ ++ +m++a++fpga+ln+ae+llr++++ a++ ++e+ + +++ el + va l+++lr lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 68 TVLrEGPQMPNAEWFPGATLNFAEHLLRRRDNAIAVIAIAENGQRESLSYRELAEHVAGLQKSLR 132 99935689********************************************************* PP TIGR01217 133 alGvkkGdrvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyv 197 a Gv++Gdrva+ +pn+ ++++ +lat+s+Gaiws +spdfG++gv+drf+qiepk+l+++ gy+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 133 AAGVGQGDRVAACMPNTWQTLVGMLATTSLGAIWSCSSPDFGTHGVVDRFGQIEPKVLITCAGYR 197 ***************************************************************** PP TIGR01217 198 ynGkehdrrekvrevakelpdlravvlipyvgdreklap.kvegal.tledllaaaqaaelvfeq 260 y Gk+ d++ kv+e+ lp+l++ +++py+ ++++++ k ++ + ++ + +e+ f lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 198 YAGKKIDQTTKVNEILERLPSLQQLIIVPYARPQARVDDyKTQANVaLWDSFYRP--GGEPGFVA 260 ***********************************99987666555157888877..99****** PP TIGR01217 261 lpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvs 325 +pf hplyil+ssGttGvpk+i+hs GG+l+qh+keh+lh dl++ drl+yytt+Gwmmwn+lvs lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 261 VPFAHPLYILYSSGTTGVPKCIIHSVGGVLLQHVKEHGLHVDLGPDDRLFYYTTCGWMMWNWLVS 325 ***************************************************************** PP TIGR01217 326 glatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkkglkparthdlsalrlva 390 +la+G+++vlydGsp+ p ++ l dl++ e i+v+Gts ky+ +++ ++++p +hdl +l++++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 326 ALAVGSSVVLYDGSPFHPGPQRLIDLIDSEAISVFGTSPKYLATLESNEIQPRLSHDLGSLKALL 390 ***************************************************************** PP TIGR01217 391 stGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglGlaveawde 455 stGs l+p++++yvy+eik+d+ l+s+sGGtdi+scf+ +np+lpv +Ge+q++glG+ave+w+e lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 391 STGSALSPQSYDYVYREIKSDLCLSSMSGGTDIISCFLAGNPVLPVRRGEMQCKGLGMAVEVWNE 455 ***************************************************************** PP TIGR01217 456 eGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprGgivihGr 520 G+pv gekGelv+t+ +p+mp+ +wnd++ k r++yf+++pgvwa Gdy+e p+G+ +ihGr lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 456 AGQPVIGEKGELVCTRHFPAMPIGLWNDPQQEKLRASYFSQFPGVWAQGDYAEQRPNGSWLIHGR 520 ***************************************************************** PP TIGR01217 521 sdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeik 585 sda lnp+Gvr+G+aeiy +ve++ +v +s+ igq+++d ++rvvlfv+l G+tlde+l +ei+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 521 SDAVLNPGGVRIGTAEIYRQVEKIHQVLDSVAIGQQWQD-DVRVVLFVRLRDGVTLDEKLEQEIR 584 ***************************************.************************* PP TIGR01217 586 dairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpvenkgalsnpealdlyeeleel 650 + ira+ +prhvp+ki++v++iprt+sGk ve+av++vv+G+pv+n +al+npeal+ +++ +el lcl|FitnessBrowser__pseudo3_N2E3:AO353_21765 585 QVIRANTTPRHVPAKIVAVTDIPRTISGKVVELAVRNVVHGQPVKNTDALANPEALEQFRDRPEL 649 ************************************************************98876 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: 00:00:00.04 # Mc/sec: 9.78 // [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