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.15081.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: 0.07u 0.01s 00:00:00.08 Elapsed: 00:00:00.08
# Mc/sec: 5.68
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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