Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_085123734.1 B9O00_RS16180 acetoacetate--CoA ligase
Query= BRENDA::Q9Z3R3 (650 letters) >NCBI__GCF_900177295.1:WP_085123734.1 Length = 652 Score = 860 bits (2221), Expect = 0.0 Identities = 420/653 (64%), Positives = 495/653 (75%), Gaps = 4/653 (0%) Query: 1 MQAERPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHC 60 M +PLW P E V + + F+ ER G +F YDA +DWS+ + FW A+W+ C Sbjct: 1 MTETQPLWTPSPERVADANLTRFMQALSERSGLAFGGYDALYDWSIRDVEGFWRAIWDWC 60 Query: 61 KVIGESG-EKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWD 119 VIGE L+DGDRM ARFFPE LNFAENLLR+ +A++FR EDK RLTW Sbjct: 61 GVIGEGPLTPGLLDGDRMPGARFFPEVTLNFAENLLRRNDGSEAIVFRSEDKAERRLTWA 120 Query: 120 ELRALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGV 179 EL VSR QAL A+G+G GDRVAA +PNMPET+ MLATA++GA++SSCSPDFGEQGV Sbjct: 121 ELTTAVSRTAQALAAEGVGPGDRVAAYLPNMPETVIAMLATAALGAVFSSCSPDFGEQGV 180 Query: 180 LDRFGQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTV 237 LDRFGQI PK+ CDGY+Y GK D+ +KVRAVA L + V+ P GD +A P V Sbjct: 181 LDRFGQIEPKVLFACDGYFYAGKTLDIRAKVRAVAAELPSVGKVVLCPLIGDGSA-EPGV 239 Query: 238 EGGVTLADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHR 297 GV LADF+A F+AGP+ + R F PLYI+FSSGTTG PKCIVH GGTLLQHLKEHR Sbjct: 240 PKGVWLADFLAPFEAGPIAYLRQGFNAPLYIMFSSGTTGKPKCIVHGVGGTLLQHLKEHR 299 Query: 298 FHCGLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFA 357 ++ G+R+FYFTTCGWMMWNWL SGLA ATL LYDGSPF P +V++DY AE+ + Sbjct: 300 LQSDVKPGDRIFYFTTCGWMMWNWLVSGLASEATLLLYDGSPFHPTRDVVYDYLQAEKAS 359 Query: 358 VFGTSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASIS 417 +FGTSAKYIDA K G P THDLSS+R++ STGSPL PE F +VY +K DV L+SIS Sbjct: 360 LFGTSAKYIDACAKAGLKPIETHDLSSVRVICSTGSPLVPESFDYVYRDVKKDVCLSSIS 419 Query: 418 GGTDIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPV 477 GGTDIVSCFVLGNP+ PVWRGEIQ GLG+AV+VWNDEG+PV GE+GELVC R FPSMP+ Sbjct: 420 GGTDIVSCFVLGNPIGPVWRGEIQARGLGMAVEVWNDEGQPVVGEQGELVCVRPFPSMPL 479 Query: 478 MFWNDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIY 537 FWNDPDG +YRAAYF+RF VWCHGDF E T HGGIVI+GRSDA LNPGGVRIGTAEIY Sbjct: 480 CFWNDPDGERYRAAYFERFPGVWCHGDFVELTTHGGIVIYGRSDAVLNPGGVRIGTAEIY 539 Query: 538 NQVEQMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPA 597 QVE++ EV E++ IGQ+W+ DVRVVLFV+LA G L + L I+ IR GASPRHVPA Sbjct: 540 RQVEKLPEVLESIVIGQNWDGDVRVVLFVKLAEGKTLDDELVARIRKTIREGASPRHVPA 599 Query: 598 KIIAVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELKS 650 KI+AV DIPRT+SGKIVELAVRDVVHGRP+KN+EALANPEALD + ELK+ Sbjct: 600 KILAVPDIPRTRSGKIVELAVRDVVHGRPIKNQEALANPEALDHYRDRSELKA 652 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: 1530 Number of extensions: 56 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: 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_085123734.1 B9O00_RS16180 (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.3119149.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-303 993.9 0.0 1.7e-303 993.7 0.0 1.0 1 NCBI__GCF_900177295.1:WP_085123734.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900177295.1:WP_085123734.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 993.7 0.0 1.7e-303 1.7e-303 3 651 .. 4 651 .. 2 652 .] 0.99 Alignments for each domain: == domain 1 score: 993.7 bits; conditional E-value: 1.7e-303 TIGR01217 3 eqvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaek.evvdds 74 q+lw+p erv+da+l+rf +a +er G+a+g+ydaly+ws+++ + fw+a+w++++v+++ + ++d++ NCBI__GCF_900177295.1:WP_085123734.1 4 TQPLWTPSPERVADANLTRFMQALSERSGLAFGGYDALYDWSIRDVEGFWRAIWDWCGVIGEGPLTpGLLDGD 76 59************************************************************9875379**** PP TIGR01217 75 kmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylp 147 +m++arffp+ +ln+aenllr+++ +a+++++e+k ++t++el v++ a+al a Gv++Gdrva+ylp NCBI__GCF_900177295.1:WP_085123734.1 77 RMPGARFFPEVTLNFAENLLRRNDGSEAIVFRSEDKAERRLTWAELTTAVSRTAQALAAEGVGPGDRVAAYLP 149 ************************************************************************* PP TIGR01217 148 nipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlr 220 n+pe+v a+lata++Ga++sscspdfG++gvldrf+qiepk+lf++dgy y Gk d r kvr+va elp++ NCBI__GCF_900177295.1:WP_085123734.1 150 NMPETVIAMLATAALGAVFSSCSPDFGEQGVLDRFGQIEPKVLFACDGYFYAGKTLDIRAKVRAVAAELPSVG 222 ************************************************************************* PP TIGR01217 221 avvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqh 293 +vvl p++gd ++ +p v+ ++ l+d+la ++a+++ + + f+ plyi+fssGttG pk+ivh GGtl+qh NCBI__GCF_900177295.1:WP_085123734.1 223 KVVLCPLIGDGSA-EPGVPKGVWLADFLAPFEAGPIAYLRQGFNAPLYIMFSSGTTGKPKCIVHGVGGTLLQH 294 *********7665.577******************************************************** PP TIGR01217 294 lkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsaky 366 lkeh+l +d+++gdr++y+tt+Gwmmwn+lvsgla atl lydGsp+ p+ +v +d+ ++e+++++Gtsaky NCBI__GCF_900177295.1:WP_085123734.1 295 LKEHRLQSDVKPGDRIFYFTTCGWMMWNWLVSGLASEATLLLYDGSPFHPTRDVVYDYLQAEKASLFGTSAKY 367 ************************************************************************* PP TIGR01217 367 vsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykG 439 ++a+ k+glkp++thdls++r++ stGspl pe+f+yvy+ +k dv l+sisGGtdivscfv++np pv++G NCBI__GCF_900177295.1:WP_085123734.1 368 IDACAKAGLKPIETHDLSSVRVICSTGSPLVPESFDYVYRDVKKDVCLSSISGGTDIVSCFVLGNPIGPVWRG 440 ************************************************************************* PP TIGR01217 440 eiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltpr 512 eiqa+glG+ave+w++eG+pv ge+Gelv+ +p+psmp+ fwnd+dG +yr+ayf+++pgvw+hGd++elt++ NCBI__GCF_900177295.1:WP_085123734.1 441 EIQARGLGMAVEVWNDEGQPVVGEQGELVCVRPFPSMPLCFWNDPDGERYRAAYFERFPGVWCHGDFVELTTH 513 ************************************************************************* PP TIGR01217 513 GgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeik 585 Ggivi+Grsda lnp+Gvr+G+aeiy +ve+l+ev es+vigq++ dg++rvvlfvkla+G+tld++lv +i+ NCBI__GCF_900177295.1:WP_085123734.1 514 GGIVIYGRSDAVLNPGGVRIGTAEIYRQVEKLPEVLESIVIGQNW-DGDVRVVLFVKLAEGKTLDDELVARIR 585 *******************************************98.89************************* PP TIGR01217 586 dairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpvenkgalsnpealdlyeeleelk 651 ++ir g+sprhvp+ki++v++iprt sGk+ve+av+dvv+G+p++n++al+npeald y++ +elk NCBI__GCF_900177295.1:WP_085123734.1 586 KTIREGASPRHVPAKILAVPDIPRTRSGKIVELAVRDVVHGRPIKNQEALANPEALDHYRDRSELK 651 *************************************************************99887 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: 35.39 // [ok]
This GapMind analysis is from Sep 24 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