Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF3858 HP15_3799 acetyl-CoA synthetase
Query= BRENDA::D6EQU8 (658 letters) >FitnessBrowser__Marino:GFF3858 Length = 662 Score = 579 bits (1492), Expect = e-169 Identities = 296/662 (44%), Positives = 414/662 (62%), Gaps = 15/662 (2%) Query: 1 MSTENPQPL-WQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAV 59 MS E P+ W P +A +R+ +F+AW E G Y ALH+WS+DEL+TFW+ V Sbjct: 1 MSNEEQSPVVWSPSEDTLANSRMGQFKAWL-EQQGFGPFADYHALHQWSIDELETFWQKV 59 Query: 60 TEWFDVRFSTPYARVLGDRTMPGAQWFPGATLNYAEHALRAA-GTRPDEPALLYVDETHE 118 ++ + TP +VLG MPGA+WFPG LN+A + LR A G D A++ ET Sbjct: 60 WDYCGLVCDTPAEKVLGKHEMPGAEWFPGMKLNFAANLLRLADGEHRDREAVVAYCETRP 119 Query: 119 PAPVTWAELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAP 178 T+AEL+ +L A LR+ G++ GDRV+G + N +A+V +LA ++G +W+S +P Sbjct: 120 VLRRTYAELKADAGALEAFLRSKGIKQGDRVAGVVTNGYEALVGMLAATSLGAIWSSASP 179 Query: 179 DFGARSVLDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGTE 238 DFG ++LDRF Q+EP L V+GY YGGK R+ AEL LPTL+AV+ + L E Sbjct: 180 DFGIGAILDRFGQIEPSALIVVNGYGYGGKVFARQQDFAELIAGLPTLKAVVSVQQLPDE 239 Query: 239 AP---DGTLDWETLTAAD--AEPVYEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEH 293 AP D WE AA P + +P DHP+++LYSSGTTG PK IV G+LV H Sbjct: 240 APISGDLVTTWENALAAGEGTAPSFTPLPPDHPVYILYSSGTTGKPKCIVHGNAGLLVNH 299 Query: 294 LKQLGLHCDLGPGDRFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGFPATDAQWRIAE 353 K+L LH D+GP DRF ++T+ GWMMWN+ S L+TG ++ DGSPG+P+ + W Sbjct: 300 AKELMLHGDVGPEDRFLYFTTCGWMMWNWQASALMTGAAVITVDGSPGYPSLNFLWDTVA 359 Query: 354 RTGATLFGTSAAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAAGGA 413 T FGTSA ++ CRK + PA+ LD S ++ V +TGSPL P+ + W++ + G Sbjct: 360 EEKVTHFGTSARFIAGCRKGELKPAKTLDQSKLRVVFSTGSPLLPEDYDWVYSD---GAP 416 Query: 414 DLWIASVSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEVGELVVT 473 D + S++GGTD+C CF G+ P LPV GE+Q LG D ++ G P+++ GELV Sbjct: 417 DALLGSIAGGTDICGCFVGSTPLLPVRRGEIQCRFLGVDAVAYGDDGQPVSEGRGELVCR 476 Query: 474 NPMPSMPIRFWNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLNRQGV 533 P+PSMP+ FW DPDG RY D+YF+T+PGVW HGD+I T G +I+GRSD+TLN GV Sbjct: 477 QPLPSMPVSFWQDPDGERYRDAYFNTFPGVWAHGDFIEFTEHGGAIIYGRSDATLNPGGV 536 Query: 534 RMGSADIYEAVERLPEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIKRTIRV 593 R+G+A+IY VE + E+++SLV+G Q DG + L V A G + D LL ++K IR Sbjct: 537 RIGTAEIYRQVETVAEVKDSLVVG-RQIDGDVEVVLLVVPADGQEITDDLLKQLKSRIRE 595 Query: 594 NLSPRHVPDEVIEVPGIPHTLTGKRIEVPVKRLLQGTPLDKAVNPGSIDNLDLL-HFYEE 652 SPRHVP ++EV IP+T +GK++E+ V RL+ G+ KA N ++ N + L H E Sbjct: 596 GASPRHVPKHIVEVNDIPYTRSGKKVELAVARLINGS--KKADNRDALGNPEALDHIRER 653 Query: 653 LA 654 L+ Sbjct: 654 LS 655 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: 1456 Number of extensions: 82 Number of successful extensions: 5 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: 662 Length adjustment: 38 Effective length of query: 620 Effective length of database: 624 Effective search space: 386880 Effective search space used: 386880 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 GFF3858 HP15_3799 (acetyl-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.28877.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-246 804.8 0.0 3.2e-246 804.4 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF3858 HP15_3799 acetyl-CoA synthetase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF3858 HP15_3799 acetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 804.4 0.0 3.2e-246 3.2e-246 3 646 .. 7 652 .. 4 655 .. 0.97 Alignments for each domain: == domain 1 score: 804.4 bits; conditional E-value: 3.2e-246 TIGR01217 3 eqvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddskml 77 v+w p ++ +++r+ +f+a+ ++ ++dy al++ws+del++fw++vw+++++v++++ ++v+++++m+ lcl|FitnessBrowser__Marino:GFF3858 7 SPVVWSPSEDTLANSRMGQFKAWLEQQGFGPFADYHALHQWSIDELETFWQKVWDYCGLVCDTPAEKVLGKHEMP 81 4589*******************97776569******************************************** PP TIGR01217 78 aarffpgarlnyaenllrkkgs....edallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpn 148 +a++fpg +ln+a nllr ++ +a++ e++ + + t++el++ l+a lr+ G+k+Gdrvag++ n lcl|FitnessBrowser__Marino:GFF3858 82 GAEWFPGMKLNFAANLLRLADGehrdREAVVAYCETRPVLRRTYAELKADAGALEAFLRSKGIKQGDRVAGVVTN 156 ******************8876566545666667889999*********************************** PP TIGR01217 149 ipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlravv 223 ea++ +la++s+Gaiwss+spdfG ++ldrf+qiep l++v+gy y+Gk r++ +e+ +lp+l+avv lcl|FitnessBrowser__Marino:GFF3858 157 GYEALVGMLAATSLGAIWSSASPDFGIGAILDRFGQIEPSALIVVNGYGYGGKVFARQQDFAELIAGLPTLKAVV 231 *************************************************************************** PP TIGR01217 224 lipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehv 298 + + d++ ++ + t+e+ laa + + + f lp dhp+yil+ssGttG pk+ivh + G+lv+h ke+ lcl|FitnessBrowser__Marino:GFF3858 232 SVQQLPDEAPISG--DLVTTWENALAAGEGTAPSFTPLPPDHPVYILYSSGTTGKPKCIVHGNAGLLVNHAKELM 304 *****98777777..77889*******9*********************************************** PP TIGR01217 299 lhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrkk 373 lh+d+++ dr+ly+tt+Gwmmwn+ +s+l+tGa+++ dGsp+ p+ n l+d ++ e++t +Gtsa+++ +rk+ lcl|FitnessBrowser__Marino:GFF3858 305 LHGDVGPEDRFLYFTTCGWMMWNWQASALMTGAAVITVDGSPGYPSLNFLWDTVAEEKVTHFGTSARFIAGCRKG 379 *************************************************************************** PP TIGR01217 374 glkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglGl 448 +lkpa+t+d s lr+v stGspl pe +++vy+ ++d ll+si+GGtdi+ cfvg++p+lpv +Geiq++ lG+ lcl|FitnessBrowser__Marino:GFF3858 380 ELKPAKTLDQSKLRVVFSTGSPLLPEDYDWVYSDGAPDALLGSIAGGTDICGCFVGSTPLLPVRRGEIQCRFLGV 454 *************************************************************************** PP TIGR01217 449 aveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprGgivihGrsda 523 + a+ ++G+pv + +Gelv+ +plpsmpv fw d+dG +yr+ayf+++pgvwahGd+ie+t +Gg +i+Grsda lcl|FitnessBrowser__Marino:GFF3858 455 DAVAYGDDGQPVSEGRGELVCRQPLPSMPVSFWQDPDGERYRDAYFNTFPGVWAHGDFIEFTEHGGAIIYGRSDA 529 *************************************************************************** PP TIGR01217 524 tlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeikdairaglsprhvp 598 tlnp+Gvr+G+aeiy +ve + ev++slv+g+ q dg++ vvl+v a G++++++l+k++k++ir g+sprhvp lcl|FitnessBrowser__Marino:GFF3858 530 TLNPGGVRIGTAEIYRQVETVAEVKDSLVVGR-QIDGDVEVVLLVVPADGQEITDDLLKQLKSRIREGASPRHVP 603 *******************************7.5799************************************** PP TIGR01217 599 skiievagiprtlsGkkvevavkdvvaG.kpvenkgalsnpealdlyee 646 ++i+ev++ip+t sGkkve+av ++++G k +n++al npeald +e lcl|FitnessBrowser__Marino:GFF3858 604 KHIVEVNDIPYTRSGKKVELAVARLINGsKKADNRDALGNPEALDHIRE 652 ***************************945678***********98765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (652 nodes) Target sequences: 1 (662 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 11.37 // [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