Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_007155469.1 MDG893_RS19030 acetoacetate--CoA ligase
Query= BRENDA::D6EQU8 (658 letters) >NCBI__GCF_000170835.1:WP_007155469.1 Length = 663 Score = 560 bits (1444), Expect = e-164 Identities = 286/652 (43%), Positives = 404/652 (61%), Gaps = 13/652 (1%) Query: 2 STENPQPLWQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTE 61 +TE +W P + + +FQ W E G Y ALHRWS++ L+TFW+ V + Sbjct: 3 NTEQSPVVWSPSQDTLKHCLMGQFQGWL-EQQGFGPFADYHALHRWSIENLETFWQKVWD 61 Query: 62 WFDVRFSTPYARVLGDRTMPGAQWFPGATLNYAEHALRAA-GTRPDEPALLYVDETHEPA 120 + + TP VLG R MPGA+WFPG LN+A + LR A G + A++ ET Sbjct: 62 YCGLVCDTPADAVLGKRDMPGAEWFPGMKLNFAANLLRLAEGDHAEREAVVAYCETRPVL 121 Query: 121 PVTWAELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDF 180 T+AEL+ +L A LR G+R GDRV+G + N +A+V +LA ++G VW+S +PDF Sbjct: 122 RRTYAELKADTGALEAFLRKKGIRQGDRVAGVVTNGYEALVGMLAATSLGAVWSSASPDF 181 Query: 181 GARSVLDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGTE-- 238 G ++LDRF Q+EP L V+GY YGGK +R+D A L LP+LR V+ I L E Sbjct: 182 GVGAILDRFGQIEPAALIVVNGYGYGGKVFNRQDDFAGLIDGLPSLRCVVSIEQLPGEPA 241 Query: 239 -APDGTLDWETLTAADA--EPVYEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEHLK 295 A D W+ A P + +P +HP+++LYSSGTTG PK IV G+LV H K Sbjct: 242 VAGDKVTHWDEALAEGQGQAPSFTPLPPEHPVYILYSSGTTGKPKCIVHGNAGLLVNHAK 301 Query: 296 QLGLHCDLGPGDRFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGFPATDAQWRIAERT 355 +L LH D+GP DRF ++T+ GWMMWN+ S LLTG ++ DGSPG+P + W++ Sbjct: 302 ELMLHGDVGPDDRFLYFTTCGWMMWNWQASALLTGAAVITVDGSPGYPDLNYLWQVVADE 361 Query: 356 GATLFGTSAAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAAGGADL 415 T +GTSA ++ CRKA + PA++LDL+A++ V +TGSPL P+ + W++ + G D+ Sbjct: 362 KVTHYGTSARFIAGCRKAELTPAKNLDLTALRVVFSTGSPLLPEDYDWIYSD---GAPDV 418 Query: 416 WIASVSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEVGELVVTNP 475 + S++GGTD+C CF G+ P LPV GE+Q LG D ++ G P++ GELV P Sbjct: 419 LLGSIAGGTDICGCFVGSTPLLPVRRGEIQCRFLGVDAVAYGDDGQPVSGGRGELVCRQP 478 Query: 476 MPSMPIRFWNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLNRQGVRM 535 +PSMP+ FW+DP RY D+YF+T+P VW HGD+I T G VI+GRSD+TLN GVR+ Sbjct: 479 LPSMPVAFWDDPGNERYKDAYFNTFPDVWAHGDFIEFTEHGGAVIYGRSDATLNPGGVRI 538 Query: 536 GSADIYEAVERLPEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIKRTIRVNL 595 G+A+IY VE + E+++SLV+G Q +G + L V A G L D L +K IR Sbjct: 539 GTAEIYRQVETVAEVKDSLVVG-RQIEGDVEVVLLVVPAEGQALTDDLQKNLKTRIRQGA 597 Query: 596 SPRHVPDEVIEVPGIPHTLTGKRIEVPVKRLLQGTPLDKAVNPGSIDNLDLL 647 SPRHVP +I+VP IP+T +GK++E+ V RL+ G+ +KA N ++ N + L Sbjct: 598 SPRHVPKHIIQVPDIPYTRSGKKVELAVARLINGS--NKADNRDALGNPEAL 647 Lambda K H 0.320 0.138 0.442 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: 1463 Number of extensions: 80 Number of successful extensions: 6 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: 658 Length of database: 663 Length adjustment: 38 Effective length of query: 620 Effective length of database: 625 Effective search space: 387500 Effective search space used: 387500 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 (21.8 bits) S2: 54 (25.4 bits)
Align candidate WP_007155469.1 MDG893_RS19030 (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.3452309.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-242 792.4 0.0 1.8e-242 792.0 0.0 1.0 1 NCBI__GCF_000170835.1:WP_007155469.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000170835.1:WP_007155469.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 792.0 0.0 1.8e-242 1.8e-242 3 646 .. 7 652 .. 5 657 .. 0.97 Alignments for each domain: == domain 1 score: 792.0 bits; conditional E-value: 1.8e-242 TIGR01217 3 eqvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddsk 75 v+w p ++ k++ + +f+ + ++ ++dy al+rws+++l++fw++vw+++++v++++ ++v++++ NCBI__GCF_000170835.1:WP_007155469.1 7 SPVVWSPSQDTLKHCLMGQFQGWLEQQGFGPFADYHALHRWSIENLETFWQKVWDYCGLVCDTPADAVLGKRD 79 5689*******************97776569****************************************** PP TIGR01217 76 mlaarffpgarlnyaenllrkkgs....edallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvag 144 m++a++fpg +ln+a nllr ++ +a++ e++ + + t++el++ l+a lr+ G+++Gdrvag NCBI__GCF_000170835.1:WP_007155469.1 80 MPGAEWFPGMKLNFAANLLRLAEGdhaeREAVVAYCETRPVLRRTYAELKADTGALEAFLRKKGIRQGDRVAG 152 ********************99875554345666678899999****************************** PP TIGR01217 145 ylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelp 217 ++ n ea++ +la++s+Ga+wss+spdfG+ ++ldrf+qiep l++v+gy y+Gk +r++ + + +lp NCBI__GCF_000170835.1:WP_007155469.1 153 VVTNGYEALVGMLAATSLGAVWSSASPDFGVGAILDRFGQIEPAALIVVNGYGYGGKVFNRQDDFAGLIDGLP 225 ************************************************************************* PP TIGR01217 218 dlravvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtl 290 +lr vv i + + ++a + ++++ la q + f lp +hp+yil+ssGttG pk+ivh + G+l NCBI__GCF_000170835.1:WP_007155469.1 226 SLRCVVSIEQLPGEPAVAG--DKVTHWDEALAEGQGQAPSFTPLPPEHPVYILYSSGTTGKPKCIVHGNAGLL 296 *********9997777777..9999************************************************ PP TIGR01217 291 vqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGts 363 v+h ke+ lh+d+++ dr+ly+tt+Gwmmwn+ +s+l+tGa+++ dGsp+ p+ n l+++++ e++t +Gts NCBI__GCF_000170835.1:WP_007155469.1 297 VNHAKELMLHGDVGPDDRFLYFTTCGWMMWNWQASALLTGAAVITVDGSPGYPDLNYLWQVVADEKVTHYGTS 369 ************************************************************************* PP TIGR01217 364 akyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpv 436 a+++ +rk++l+pa+++dl+alr+v stGspl pe ++++y+ ++dvll+si+GGtdi+ cfvg++p+lpv NCBI__GCF_000170835.1:WP_007155469.1 370 ARFIAGCRKAELTPAKNLDLTALRVVFSTGSPLLPEDYDWIYSDGAPDVLLGSIAGGTDICGCFVGSTPLLPV 442 ************************************************************************* PP TIGR01217 437 ykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyiel 509 +Geiq++ lG++ a+ ++G+pv g +Gelv+ +plpsmpv fw+d+ +y++ayf+++p+vwahGd+ie+ NCBI__GCF_000170835.1:WP_007155469.1 443 RRGEIQCRFLGVDAVAYGDDGQPVSGGRGELVCRQPLPSMPVAFWDDPGNERYKDAYFNTFPDVWAHGDFIEF 515 ************************************************************************* PP TIGR01217 510 tprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvk 582 t +Gg vi+Grsdatlnp+Gvr+G+aeiy +ve + ev++slv+g++ e g++ vvl+v a+G+ l+++l k NCBI__GCF_000170835.1:WP_007155469.1 516 TEHGGAVIYGRSDATLNPGGVRIGTAEIYRQVETVAEVKDSLVVGRQIE-GDVEVVLLVVPAEGQALTDDLQK 587 *********************************************8765.7********************** PP TIGR01217 583 eikdairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkp.venkgalsnpealdlyee 646 ++k +ir g+sprhvp++ii+v++ip+t sGkkve+av ++++G +n++al npeald +e NCBI__GCF_000170835.1:WP_007155469.1 588 NLKTRIRQGASPRHVPKHIIQVPDIPYTRSGKKVELAVARLINGSNkADNRDALGNPEALDRIRE 652 ********************************************76267***********98776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (652 nodes) Target sequences: 1 (663 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 23.29 // [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