Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_054255265.1 BN2503_RS02705 acetoacetate--CoA ligase
Query= BRENDA::D6EQU8
(658 letters)
>NCBI__GCF_001298675.1:WP_054255265.1
Length = 694
Score = 598 bits (1542), Expect = e-175
Identities = 315/670 (47%), Positives = 414/670 (61%), Gaps = 37/670 (5%)
Query: 25 FQAWAAEHHGAPAEGGYAALHRWSVDELDTFWKAVTEWFDVRFSTPYARVLGDRTMPGAQ 84
+Q W + HG Y AL RWSV ELD FW++V ++F + TP+ VL MPGA+
Sbjct: 16 YQDWLRQRHGLEF-ASYDALWRWSVTELDAFWQSVWDYFAIESPTPHRAVLARNRMPGAE 74
Query: 85 WFPGATLNYAEHALR--AAGTRPDEPALLYVDETHEPAPVTWAELRRQVASLAAELRALG 142
WFPGA +NYA LR A +PAL+ +E + W ELRRQVA+LA LRA G
Sbjct: 75 WFPGAQVNYARQVLRHVAPAHAAGQPALVSRNEKGLQRELAWPELRRQVAALALHLRAQG 134
Query: 143 VRPGDRVSGYLPNIPQAVVALLATAAVGGVWTSCAPDFGARSVLDRFQQVEPVVLFTVDG 202
V+PGDRV+ YLPNIP+ VVA LAT ++G VW+ CAPD G +VLDRF+Q+ P VL DG
Sbjct: 135 VQPGDRVAAYLPNIPETVVAFLATVSLGAVWSVCAPDMGTHAVLDRFRQIAPKVLIAADG 194
Query: 203 YRYGGKEHDRRDTVAELRRELPTLRAVIHIPLLGT--EAPDGTLDWETLTAADAEPVYEQ 260
YGG++ DR D +AELR LPT++ V+ + L + DG DAE +
Sbjct: 195 VTYGGRDIDRMDVLAELRAALPTVQHVLLVNNLDASKKIADGASYASATARNDAEVAAFE 254
Query: 261 ---VPFDHPLWVLYSSGTTGLPKAIVQSQGGILVEHLKQLGLHCDLGP-------GDRFF 310
+PFDHPLW++YSSGTTGLPK IV GG+++ L+ LH D+G G+R+
Sbjct: 255 PLWLPFDHPLWIVYSSGTTGLPKPIVHGHGGMILVALQLKSLHNDVGASYAPNSFGERYH 314
Query: 311 WYTSTGWMMWNFLVSGLLTGTTIVLYDGSPG----FPATDAQWRIAERTGATLFGTSAAY 366
WY+STGW+MWN V+GLL GTT V+YDG+PG P WR A TG T FG AA+
Sbjct: 315 WYSSTGWVMWNAQVAGLLGGTTCVIYDGNPGGSKEHPDWGVLWRFAAETGVTCFGAGAAF 374
Query: 367 VMACRKAGVHPARDLDLSAIQCVATTGSPLPPDGFRWLHDEFAA-GGADLWIASVSGGTD 425
C KAG+ A DL ++ + +TGSPL P+ W +FA G D+W ++SGGTD
Sbjct: 375 YANCMKAGLQLADCGDLGRVRWLGSTGSPLAPEVQAWGTAQFATLGTPDIWWNNLSGGTD 434
Query: 426 VCSCFAGAVPTLPVHIGELQAPGLGTDLQSWDPSGDPLTDEVGELVVTNPMPSMPIRFWN 485
C F G LP+ GE+Q LG ++SWD G P+ D VGELV T P+PSMP+ W
Sbjct: 435 FCGAFIGGHRELPMVPGEMQCRMLGAAVESWDEQGRPVHDAVGELVCTQPIPSMPLYLWG 494
Query: 486 DPDGSRYHDSYFDTYP-----------------GVWRHGDWITLTSRGSVVIHGRSDSTL 528
D DGSRY SYFD YP VWRHGDW+ + ++G I+GRSD+T+
Sbjct: 495 DTDGSRYLASYFDMYPPGHGRQPGGGDGPAEMGAVWRHGDWLKIGTQGGCTIYGRSDATI 554
Query: 529 NRQGVRMGSADIYEAVERLPEIRESLVIGIEQPDGGYWMPLFVHLAPGATLDDALLDRIK 588
NR G+RMG+++IY AVE LPE+ +SLV+ +E +MPLFV L PG DDAL RI
Sbjct: 555 NRHGLRMGTSEIYSAVEGLPEVLDSLVVDLEYLGRESYMPLFVVLRPGVLFDDALRARIA 614
Query: 589 RTIRVNLSPRHVPDEVIEVPGIPHTLTGKRIEVPVKRLLQGTPLDKAVNPGSIDNLDLLH 648
IR LSPR VPD++++VP +P TL+GK+ E+P+K+LL G PL+K VN ++ N L
Sbjct: 615 SAIRTALSPRFVPDDILQVPEVPRTLSGKKQELPIKKLLLGQPLEKVVNRDAMANPGCLP 674
Query: 649 FYEELARKRS 658
+Y + A +R+
Sbjct: 675 WYVDFAARRA 684
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: 1681
Number of extensions: 92
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: 694
Length adjustment: 39
Effective length of query: 619
Effective length of database: 655
Effective search space: 405445
Effective search space used: 405445
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_054255265.1 BN2503_RS02705 (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.1316185.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-209 683.6 0.0 2.8e-209 682.3 0.0 1.5 1 NCBI__GCF_001298675.1:WP_054255265.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001298675.1:WP_054255265.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 682.3 0.0 2.8e-209 2.8e-209 19 650 .. 13 682 .. 9 684 .. 0.94
Alignments for each domain:
== domain 1 score: 682.3 bits; conditional E-value: 2.8e-209
TIGR01217 19 larfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvddskmlaarffpgarlnyae 91
l ++++ +r+G+ ++ ydal+rwsv+eldafw++vw+++ + +++ +v+ ++m++a++fpga++nya
NCBI__GCF_001298675.1:WP_054255265.1 13 LRLYQDWLRQRHGLEFASYDALWRWSVTELDAFWQSVWDYFAIESPTPHRAVLARNRMPGAEWFPGAQVNYAR 85
6679********************************************************************* PP
TIGR01217 92 nllrkkgs.....edallyvdeekesakvtfeelrrqvaslaaalralGvkkGdrvagylpnipeavaallat 159
++lr+ ++al+ ++e+ + ++++ elrrqva la lra+Gv++Gdrva+ylpnipe+v+a+lat
NCBI__GCF_001298675.1:WP_054255265.1 86 QVLRHVAPahaagQPALVSRNEKGLQRELAWPELRRQVAALALHLRAQGVQPGDRVAAYLPNIPETVVAFLAT 158
****976556666899999999999************************************************ PP
TIGR01217 160 asvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvrevakelpdlravvlipyvgdre 232
s+Ga+ws c+pd+G+++vldrf qi+pk+l++ dg++y+G++ dr + ++e++ lp++++v+l+ + ++
NCBI__GCF_001298675.1:WP_054255265.1 159 VSLGAVWSVCAPDMGTHAVLDRFRQIAPKVLIAADGVTYGGRDIDRMDVLAELRAALPTVQHVLLVNNLDASK 231
*****************************************************************99998665 PP
TIGR01217 233 klapkvegaltledllaaaqaaelvfeq..lpfdhplyilfssGttGvpkaivhsaGGtlvqhlkehvlhcdl 303
k+a ++ ++ +a +a fe lpfdhpl+i++ssGttG+pk ivh GG+++ l+ ++lh d+
NCBI__GCF_001298675.1:WP_054255265.1 232 KIA----DGASYASATARNDAEVAAFEPlwLPFDHPLWIVYSSGTTGLPKPIVHGHGGMILVALQLKSLHNDV 300
555....588899999998888888996337*****************************************9 PP
TIGR01217 304 td.......gdrllyyttvGwmmwnflvsglatGatlvlydGspl....vpatnvlfdlaeregitvlGtsak 365
+ g+r+ +y+++Gw+mwn v+gl+ G+t v+ydG p+ p+ vl+++a+ +g+t +G++a+
NCBI__GCF_001298675.1:WP_054255265.1 301 GAsyapnsfGERYHWYSSTGWVMWNAQVAGLLGGTTCVIYDGNPGgskeHPDWGVLWRFAAETGVTCFGAGAA 373
86333344469******************************9986444479999******************* PP
TIGR01217 366 yvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeika....dvllasisGGtdivscfvganpsl 434
+ + k+gl+ a dl +r + stGspl pe + ++++ d++ +sGGtd + f+g+ l
NCBI__GCF_001298675.1:WP_054255265.1 374 FYANCMKAGLQLADCGDLGRVRWLGSTGSPLAPEVQAWGTAQFATlgtpDIWWNNLSGGTDFCGAFIGGHREL 446
***************************************9999988888************************ PP
TIGR01217 435 pvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwndedGskyrkayfdkyp......... 498
p+ Ge+q++ lG ave+wde+G+pv++++Gelv+t+p+psmp+ +w d dGs+y ++yfd yp
NCBI__GCF_001298675.1:WP_054255265.1 447 PMVPGEMQCRMLGAAVESWDEQGRPVHDAVGELVCTQPIPSMPLYLWGDTDGSRYLASYFDMYPpghgrqpgg 519
***************************************************************7666555555 PP
TIGR01217 499 ........gvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvigqeqedgeer 563
+vw+hGd+ ++ ++Gg i+Grsdat+n++G+r+G++eiy ave l+ev +slv+ e e +
NCBI__GCF_001298675.1:WP_054255265.1 520 gdgpaemgAVWRHGDWLKIGTQGGCTIYGRSDATINRHGLRMGTSEIYSAVEGLPEVLDSLVVDLEYLGRESY 592
554444445**************************************************************** PP
TIGR01217 564 vvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtlsGkkvevavkdvvaGkpve...nkg 633
++lfv l +G+ +d+al +i +air++lspr vp+ i++v+++prtlsGkk e+++k+++ G+p+e n++
NCBI__GCF_001298675.1:WP_054255265.1 593 MPLFVVLRPGVLFDDALRARIASAIRTALSPRFVPDDILQVPEVPRTLSGKKQELPIKKLLLGQPLEkvvNRD 665
******************************************************************9999*** PP
TIGR01217 634 alsnpealdlyeeleel 650
a++np l y +++ +
NCBI__GCF_001298675.1:WP_054255265.1 666 AMANPGCLPWYVDFAAR 682
***********998876 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (652 nodes)
Target sequences: 1 (694 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: 00:00:00.02
# Mc/sec: 21.18
//
[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