Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF4237 HP15_4177 acetyl-CoA synthetase
Query= BRENDA::D6EQU8 (658 letters) >FitnessBrowser__Marino:GFF4237 Length = 662 Score = 561 bits (1445), Expect = e-164 Identities = 283/653 (43%), Positives = 407/653 (62%), Gaps = 15/653 (2%) Query: 2 STENPQPLWQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTE 61 +T +P LW P + +R+ +F+AW E G Y AL++WS+DEL+TFW+ V + Sbjct: 5 TTPSPDILWSPSEDTLKNSRMGQFKAWL-EQQGLGPFTDYHALYQWSIDELETFWQKVWD 63 Query: 62 WFDVRFSTPYARVLGDRTMPGAQWFPGATLNYAEHALRAA-GTRPDEPALLYVDETHEPA 120 + + TP +VLG R MPGA+WFPG LN+A + LR A G D+ A++ ET Sbjct: 64 YCGLVCDTPAEKVLGKRDMPGAEWFPGMKLNFAANLLRLADGEHADQEAVVAYCETRPVL 123 Query: 121 PVTWAELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDF 180 T+A+L+ +L A LR G++ GDRV+G + N +A+V +LA ++G +W+S +PDF Sbjct: 124 RRTYAQLKADAGALEAFLRDKGIQQGDRVAGVVTNGYEALVGMLAATSMGAIWSSASPDF 183 Query: 181 GARSVLDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGTEAP 240 G ++LDRF Q+EP L V+GY YGGK R+ AEL LPTL++V+ + L E P Sbjct: 184 GIGAILDRFGQIEPAALIVVNGYGYGGKVFARQQDFAELIAGLPTLKSVVSVQQLPDEPP 243 Query: 241 -DGTL--DWETLTAADA--EPVYEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEHLK 295 G L WE + A P + +P DHP+++LYSSGTTG PK IV G+LV H K Sbjct: 244 IAGNLVTTWEDMLAYGKGNAPSFTPLPPDHPVYILYSSGTTGKPKCIVHGNAGLLVNHAK 303 Query: 296 QLGLHCDLGPGDRFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGFPATDAQWRIAERT 355 +L LH D+GP DRF ++T+ GWMMWN+ S L+TG ++ DGSPG+P+ + W Sbjct: 304 ELMLHGDVGPEDRFLYFTTCGWMMWNWQASALMTGAAVITVDGSPGYPSLNFLWDTVAEE 363 Query: 356 GATLFGTSAAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAAGGADL 415 T FGTSA ++ CRK + PA+ LD S ++ V +TGSPL P+ + W++ + G D Sbjct: 364 KVTHFGTSARFIAGCRKGELKPAKTLDQSKLRVVFSTGSPLLPEDYDWVYSD---GAPDA 420 Query: 416 WIASVSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEVGELVVTNP 475 + S++GGTD+C CF G+ P LPV GE+Q LG D ++ G P+++ GELV P Sbjct: 421 LLGSIAGGTDICGCFVGSTPLLPVRRGEIQCRFLGVDAVAYGDDGQPVSEGRGELVCRQP 480 Query: 476 MPSMPIRFWNDPDGSRYHDSYFDTYPGVWRHGDWITLTSRGSVVIHGRSDSTLNRQGVRM 535 +PSMP+ FW DP RY D+YF+T+PGVW HGD+I T G +I+GRSD+TLN GVR+ Sbjct: 481 LPSMPVSFWQDPGDERYKDAYFNTFPGVWAHGDFIEFTEHGGAIIYGRSDATLNPGGVRI 540 Query: 536 GSADIYEAVERLPEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIKRTIRVNL 595 G+A+IY VE + E+++SLV+G Q DG + L V A G + + LL ++K IR Sbjct: 541 GTAEIYRQVETVAEVKDSLVVG-RQIDGDVEVVLLVVPAAGQEITNDLLKQLKSRIREGA 599 Query: 596 SPRHVPDEVIEVPGIPHTLTGKRIEVPVKRLLQGTP----LDKAVNPGSIDNL 644 SPRHVP +++V IP+T +GK++E+ V RL+ G+ D NP ++D + Sbjct: 600 SPRHVPKRIVQVNDIPYTRSGKKVELAVARLINGSKKSDNRDALSNPEALDEI 652 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: 1418 Number of extensions: 69 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 GFF4237 HP15_4177 (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.23203.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-242 792.3 0.0 2e-242 791.9 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF4237 HP15_4177 acetyl-CoA synthetase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF4237 HP15_4177 acetyl-CoA synthetase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 791.9 0.0 2e-242 2e-242 3 642 .. 9 650 .. 7 657 .. 0.97 Alignments for each domain: == domain 1 score: 791.9 bits; conditional E-value: 2e-242 TIGR01217 3 eqvlwepdaervkdarlarfraavgerfGa.algdydalyrwsvdeldafwkavwefsdvvfssaekevvddskm 76 +++lw p ++ k++r+ +f+a+ ++ G+ ++dy aly+ws+del++fw++vw+++++v++++ ++v++++ m lcl|FitnessBrowser__Marino:GFF4237 9 PDILWSPSEDTLKNSRMGQFKAWLEQQ-GLgPFTDYHALYQWSIDELETFWQKVWDYCGLVCDTPAEKVLGKRDM 82 679********************9665.6659******************************************* PP TIGR01217 77 laarffpgarlnyaenllrkkgs....edallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylp 147 ++a++fpg +ln+a nllr ++ ++a++ e++ + + t+++l++ l+a lr G+++Gdrvag++ lcl|FitnessBrowser__Marino:GFF4237 83 PGAEWFPGMKLNFAANLLRLADGehadQEAVVAYCETRPVLRRTYAQLKADAGALEAFLRDKGIQQGDRVAGVVT 157 *******************8876566556677778899999********************************** PP TIGR01217 148 nipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlrav 222 n ea++ +la++s+Gaiwss+spdfG ++ldrf+qiep l++v+gy y+Gk r++ +e+ +lp+l++v lcl|FitnessBrowser__Marino:GFF4237 158 NGYEALVGMLAATSMGAIWSSASPDFGIGAILDRFGQIEPAALIVVNGYGYGGKVFARQQDFAELIAGLPTLKSV 232 *************************************************************************** PP TIGR01217 223 vlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGvpkaivhsaGGtlvqhlkeh 297 v + + d+ +a + t+ed+la + + + f lp dhp+yil+ssGttG pk+ivh + G+lv+h ke+ lcl|FitnessBrowser__Marino:GFF4237 233 VSVQQLPDEPPIAG--NLVTTWEDMLAYGKGNAPSFTPLPPDHPVYILYSSGTTGKPKCIVHGNAGLLVNHAKEL 305 ******98888887..55679*******9********************************************** PP TIGR01217 298 vlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnvlfdlaeregitvlGtsakyvsavrk 372 lh+d+++ dr+ly+tt+Gwmmwn+ +s+l+tGa+++ dGsp+ p+ n l+d ++ e++t +Gtsa+++ +rk lcl|FitnessBrowser__Marino:GFF4237 306 MLHGDVGPEDRFLYFTTCGWMMWNWQASALMTGAAVITVDGSPGYPSLNFLWDTVAEEKVTHFGTSARFIAGCRK 380 *************************************************************************** PP TIGR01217 373 kglkparthdlsalrlvastGsplkpegfeyvyeeikadvllasisGGtdivscfvganpslpvykGeiqapglG 447 ++lkpa+t+d s lr+v stGspl pe +++vy+ ++d ll+si+GGtdi+ cfvg++p+lpv +Geiq++ lG lcl|FitnessBrowser__Marino:GFF4237 381 GELKPAKTLDQSKLRVVFSTGSPLLPEDYDWVYSDGAPDALLGSIAGGTDICGCFVGSTPLLPVRRGEIQCRFLG 455 *************************************************************************** PP TIGR01217 448 laveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkypgvwahGdyieltprGgivihGrsd 522 ++ a+ ++G+pv + +Gelv+ +plpsmpv fw d+ +y++ayf+++pgvwahGd+ie+t +Gg +i+Grsd lcl|FitnessBrowser__Marino:GFF4237 456 VDAVAYGDDGQPVSEGRGELVCRQPLPSMPVSFWQDPGDERYKDAYFNTFPGVWAHGDFIEFTEHGGAIIYGRSD 530 *************************************************************************** PP TIGR01217 523 atlnpnGvrlGsaeiynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeikdairaglsprhv 597 atlnp+Gvr+G+aeiy +ve + ev++slv+g+ q dg++ vvl+v a+G++++++l+k++k++ir g+sprhv lcl|FitnessBrowser__Marino:GFF4237 531 ATLNPGGVRIGTAEIYRQVETVAEVKDSLVVGR-QIDGDVEVVLLVVPAAGQEITNDLLKQLKSRIREGASPRHV 604 ********************************7.5799************************************* PP TIGR01217 598 pskiievagiprtlsGkkvevavkdvvaG.kpvenkgalsnpeald 642 p++i++v++ip+t sGkkve+av ++++G k +n++alsnpeald lcl|FitnessBrowser__Marino:GFF4237 605 PKRIVQVNDIPYTRSGKKVELAVARLINGsKKSDNRDALSNPEALD 650 ****************************944567***********8 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: 12.59 // [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