Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate Ac3H11_4867 Acetoacetyl-CoA synthetase (EC 6.2.1.16)
Query= BRENDA::D6EQU8
(658 letters)
>FitnessBrowser__acidovorax_3H11:Ac3H11_4867
Length = 710
Score = 610 bits (1572), Expect = e-179
Identities = 324/692 (46%), Positives = 427/692 (61%), Gaps = 49/692 (7%)
Query: 8 PLWQPDAQRIAQARITRFQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTEWFDVRF 67
P P I Q R+ +Q W + G + Y AL RWS ELD FW++V ++F +
Sbjct: 21 PATGPQPPYIPQIRL--YQNWLRDERGLQWDS-YDALWRWSTTELDAFWQSVWDYFQIES 77
Query: 68 STPYARVLGDRTMPGAQWFPGATLNYAEHALRA--AGTRPDEPALLYVDETHEPAPVTWA 125
TP+ VLG TMPGAQWFPGA +NYA ALR A PA++ +E + ++W
Sbjct: 78 PTPHTAVLGKNTMPGAQWFPGAQVNYARQALRHVDAAHAAGLPAIISRNEKGQHRELSWP 137
Query: 126 ELRRQVASLAAELRALGVRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDFGARSV 185
ELRRQVASLA L+A GV PGDRV+ YLPN+P+A++A LAT ++GGVW+ CAPD G +V
Sbjct: 138 ELRRQVASLALHLKAQGVMPGDRVAAYLPNVPEAMIAFLATVSIGGVWSICAPDMGTHAV 197
Query: 186 LDRFQQVEPVVLFTVDGYRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGT-EAPDGTL 244
LDRF+Q+ P VL VDG YGG++HDRR +AELR LP+++ H LLG +A
Sbjct: 198 LDRFRQIAPKVLIGVDGVSYGGRDHDRRPVLAELREALPSVQ---HAVLLGNLDASVSIA 254
Query: 245 DWETLTAADA---------EPVYEQVPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEHLK 295
W + T A A EP++ +PFDHPLW++YSSGTTGLPK IV GG ++ L+
Sbjct: 255 GWASWTGATARSDAETTAFEPLW--LPFDHPLWIVYSSGTTGLPKPIVHGHGGTVLVALQ 312
Query: 296 QLGLHCDLGP-------GDRFFWYTSTGWMMWNFLVSGLLTGTTIVLYDGSPGF----PA 344
LH D+G G+R+ WY+STGW+MWN +SGLL+GTT V+YDG+PG P
Sbjct: 313 LKVLHNDIGCSYEPNSFGERYHWYSSTGWVMWNAQLSGLLSGTTCVIYDGNPGGSKDNPD 372
Query: 345 TDAQWRIAERTGATLFGTSAAYVMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWL 404
WR A TG T FG AA+ C KAG+ A DL+ I+ + TTGSPL P+ W
Sbjct: 373 WGVLWRFAAETGVTFFGAGAAFFANCMKAGITLADYGDLTRIRALGTTGSPLSPEVQEWG 432
Query: 405 HDEFAA-GGADLWIASVSGGTDVCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPL 463
+F A G +D+W ++SGGTD C F G +P GE+Q LG ++SWD G P+
Sbjct: 433 TAQFEALGTSDIWWNNISGGTDFCGAFIGGHREMPQVPGEMQCRMLGAAVESWDAEGRPV 492
Query: 464 TDEVGELVVTNPMPSMPIRFWNDPDGSRYHDSYFDTYPG-----------------VWRH 506
D VGELV P+PSMP+ W D DGSRY SYFD YP VWRH
Sbjct: 493 QDAVGELVCAQPIPSMPLYLWGDKDGSRYLSSYFDMYPAGHGRQPGGGDGPAAMGAVWRH 552
Query: 507 GDWITLTSRGSVVIHGRSDSTLNRQGVRMGSADIYEAVERLPEIRESLVIGIEQPDGGYW 566
GDW+ + + G VI+GRSD+T+NR G+RMG+++IY AVE LPE+ +SLV+ +E +
Sbjct: 553 GDWLKIGANGGCVIYGRSDATINRHGLRMGTSEIYSAVESLPEVLDSLVVDLEYLGRESY 612
Query: 567 MPLFVHLAPGATLDDALLDRIKRTIRVNLSPRHVPDEVIEVPGIPHTLTGKRIEVPVKRL 626
MPLFV L PG LDDAL RI +R LSPR VPD++ V +P TL+GK+ E+P+K+L
Sbjct: 613 MPLFVVLRPGYALDDALRARINGAVRTALSPRFVPDDIFAVAEVPRTLSGKKQELPIKKL 672
Query: 627 LQGTPLDKAVNPGSIDNLDLLHFYEELARKRS 658
L G P++K VN ++ N L +Y A +R+
Sbjct: 673 LLGQPIEKVVNKDAMANPGCLDWYVAFAAERA 704
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: 1701
Number of extensions: 111
Number of successful extensions: 7
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: 710
Length adjustment: 39
Effective length of query: 619
Effective length of database: 671
Effective search space: 415349
Effective search space used: 415349
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 Ac3H11_4867 (Acetoacetyl-CoA synthetase (EC 6.2.1.16))
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.10615.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.2e-208 680.2 0.0 3.2e-208 678.9 0.0 1.5 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 Acetoacetyl-CoA synthetase (EC 6
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 Acetoacetyl-CoA synthetase (EC 6.2.1.16)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 678.9 0.0 3.2e-208 3.2e-208 18 648 .. 32 700 .. 29 704 .. 0.94
Alignments for each domain:
== domain 1 score: 678.9 bits; conditional E-value: 3.2e-208
TIGR01217 18 rlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddskmlaa 79
++ ++++ ++ G+ ydal+rws +eldafw++vw+++++ +++ +v+++++m++a
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 32 QIRLYQNWLRDERGLQWDSYDALWRWSTTELDAFWQSVWDYFQIESPTPHTAVLGKNTMPGA 93
577799******************************************************** PP
TIGR01217 80 rffpgarlnyaenllrkkgs.....edallyvdeekesakvtfeelrrqvaslaaalralGv 136
++fpga++nya ++lr+ ++ +a++ ++e+ + ++++ elrrqvasla l+a+Gv
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 94 QWFPGAQVNYARQALRHVDAahaagLPAIISRNEKGQHRELSWPELRRQVASLALHLKAQGV 155
*****************998655555678999999999************************ PP
TIGR01217 137 kkGdrvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvy 198
+Gdrva+ylpn+pea+ a+lat s+G++ws c+pd+G+++vldrf qi+pk+l+ vdg+ y
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 156 MPGDRVAAYLPNVPEAMIAFLATVSIGGVWSICAPDMGTHAVLDRFRQIAPKVLIGVDGVSY 217
************************************************************** PP
TIGR01217 199 nGkehdrrekvrevakelpdlravvlipyvgdreklapkvegaltledllaaaqaaelvfeq 260
+G++hdrr ++e++ lp++++ vl+ + ++ + g + +a +a fe
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 218 GGRDHDRRPVLAELREALPSVQHAVLLGNLD----ASVSIAGWASWTGATARSDAETTAFEP 275
*******************999999988777....3445688999******9999999**96 PP
TIGR01217 261 ..lpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhcdltd.......gdrllyyt 313
lpfdhpl+i++ssGttG+pk ivh GGt++ l+ +vlh d++ g+r+ +y+
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 276 lwLPFDHPLWIVYSSGTTGLPKPIVHGHGGTVLVALQLKVLHNDIGCsyepnsfGERYHWYS 337
337***************************************99974223334479****** PP
TIGR01217 314 tvGwmmwnflvsglatGatlvlydGspl....vpatnvlfdlaeregitvlGtsakyvsavr 371
++Gw+mwn sgl+ G+t v+ydG p+ p+ vl+++a+ +g+t +G++a++ +
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 338 STGWVMWNAQLSGLLSGTTCVIYDGNPGgskdNPDWGVLWRFAAETGVTFFGAGAAFFANCM 399
*************************997333358888************************* PP
TIGR01217 372 kkglkparthdlsalrlvastGsplkpegfeyvyeeika....dvllasisGGtdivscfvg 429
k+g++ a dl+ +r++ +tGspl+pe e+ +++a d++ isGGtd + f+g
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 400 KAGITLADYGDLTRIRALGTTGSPLSPEVQEWGTAQFEAlgtsDIWWNNISGGTDFCGAFIG 461
********************************99999888888******************* PP
TIGR01217 430 anpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrk 491
+ +p Ge+q++ lG ave+wd eG+pv++++Gelv+++p+psmp+ +w d+dGs+y +
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 462 GHREMPQVPGEMQCRMLGAAVESWDAEGRPVQDAVGELVCAQPIPSMPLYLWGDKDGSRYLS 523
************************************************************** PP
TIGR01217 492 ayfdkyp.......g..........vwahGdyieltprGgivihGrsdatlnpnGvrlGsae 536
+yfd yp g vw+hGd+ ++ ++Gg vi+Grsdat+n++G+r+G++e
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 524 SYFDMYPaghgrqpGggdgpaamgaVWRHGDWLKIGANGGCVIYGRSDATINRHGLRMGTSE 585
******8555444404455555556************************************* PP
TIGR01217 537 iynaverldeveeslvigqeqedgeervvlfvklasGatldealvkeikdairaglsprhvp 598
iy ave l+ev +slv+ e e +++lfv l +G ld+al +i+ a+r++lspr vp
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 586 IYSAVESLPEVLDSLVVDLEYLGRESYMPLFVVLRPGYALDDALRARINGAVRTALSPRFVP 647
************************************************************** PP
TIGR01217 599 skiievagiprtlsGkkvevavkdvvaGkpve...nkgalsnpealdlyeele 648
+ i +va++prtlsGkk e+++k+++ G+p+e nk+a++np ld y ++
lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_4867 648 DDIFAVAEVPRTLSGKKQELPIKKLLLGQPIEkvvNKDAMANPGCLDWYVAFA 700
*******************************9999**************8766 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (652 nodes)
Target sequences: 1 (710 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: 0.11u 0.02s 00:00:00.13 Elapsed: 00:00:00.11
# Mc/sec: 3.95
//
[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