Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_011765880.1 AZO_RS10865 acetoacetate--CoA ligase
Query= BRENDA::Q9Z3R3
(650 letters)
>NCBI__GCF_000061505.1:WP_011765880.1
Length = 661
Score = 823 bits (2126), Expect = 0.0
Identities = 411/658 (62%), Positives = 483/658 (73%), Gaps = 16/658 (2%)
Query: 2 QAERPLWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCK 61
Q + PLW P E + + M F R+ DY A H WSV FW +VWE
Sbjct: 7 QPDTPLWTPSAERIAAANMTAFRHTAERRWNIELPDYAALHAWSVDHPEQFWVSVWEDGD 66
Query: 62 VIGESGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDEL 121
V+G+ G + LVDGDRM A++FP+ARLNFA+NLLR+ DA++F GEDKV RLT EL
Sbjct: 67 VVGKRGVRVLVDGDRMPGAQWFPDARLNFAQNLLRRRDGDDAVVFWGEDKVRDRLTHGEL 126
Query: 122 RALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLD 181
V++ ALR QG+G GDRVAA MPNMPET+ MLA AS+GAI++S SPDFG QGVLD
Sbjct: 127 YRRVAQFSAALREQGVGKGDRVAAYMPNMPETLIAMLAAASIGAIFTSASPDFGVQGVLD 186
Query: 182 RFGQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGAP--TVIVPYAGDSAALAPTVEG 239
RFGQ PK+ + CDGY+YNGK D +K+ + L + VIVPY AL G
Sbjct: 187 RFGQTEPKVLLACDGYYYNGKMVDCLAKLGEIVPQLPSVERVVIVPYVHRDHAL-----G 241
Query: 240 GVT----LADFIAGFQAGPLV-FERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLK 294
G+ ADF+A A + FE LPF HPLY+++SSGTTGVPKCIVHSAGG LLQHLK
Sbjct: 242 GIPHARMYADFVAPHHAATEIGFEALPFSHPLYVMYSSGTTGVPKCIVHSAGGALLQHLK 301
Query: 295 EHRFHCGLRDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAE 354
EHR HC ++ G+R+FYFTTCGWMMWNWL SGLA GAT+ LYDGSPF D +LFDYA AE
Sbjct: 302 EHRLHCDVKPGDRVFYFTTCGWMMWNWLVSGLAAGATILLYDGSPFAADNRILFDYADAE 361
Query: 355 RFAVFGTSAKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLA 414
R FGTSAK+IDA K G P TH L+++R M STGSPL PEGF +VY IK D+QL+
Sbjct: 362 RMTHFGTSAKFIDAAAKFGLKPRETHSLATVRAMMSTGSPLVPEGFDYVYRDIKADLQLS 421
Query: 415 SISGGTDIVSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPS 474
SISGGTDI+SCFVLGNP+ PVWRGEIQ GLGLAVDVW+DEG+PVRGEKGELVC R FP+
Sbjct: 422 SISGGTDILSCFVLGNPVLPVWRGEIQCRGLGLAVDVWDDEGRPVRGEKGELVCARPFPA 481
Query: 475 MPVMFWNDPDGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTA 534
MPV FW D DG+KYRAAYF+RFDNVWCHGDF E T HGG++I+GRSDATLNPGGVRIGTA
Sbjct: 482 MPVGFWRDEDGSKYRAAYFERFDNVWCHGDFCEITAHGGLIIYGRSDATLNPGGVRIGTA 541
Query: 535 EIYNQVEQMDEVAEALCIGQDW----EDDVRVVLFVRLARGVELTEALTREIKNRIRSGA 590
EIY QVE++ EV E++ IGQDW +DVRVVLFV+L G+ L + L IK IR
Sbjct: 542 EIYRQVEKLHEVVESIVIGQDWPPQNPNDVRVVLFVKLRDGMTLDDTLADRIKRTIRDNT 601
Query: 591 SPRHVPAKIIAVADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEEL 648
+PRHVPAK++ VADIPRTKSGKIVELAVR+VVHGR VKN+EALANPEAL F +EL
Sbjct: 602 TPRHVPAKVLQVADIPRTKSGKIVELAVRNVVHGRAVKNQEALANPEALAHFRDRDEL 659
Lambda K H
0.322 0.139 0.441
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: 1483
Number of extensions: 59
Number of successful extensions: 3
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: 650
Length of database: 661
Length adjustment: 38
Effective length of query: 612
Effective length of database: 623
Effective search space: 381276
Effective search space used: 381276
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 (21.9 bits)
S2: 54 (25.4 bits)
Align candidate WP_011765880.1 AZO_RS10865 (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.29420.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
1.4e-297 974.1 0.0 1.7e-297 973.9 0.0 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011765880.1 AZO_RS10865 acetoacetate--CoA li
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000061505.1:WP_011765880.1 AZO_RS10865 acetoacetate--CoA ligase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 973.9 0.0 1.7e-297 1.7e-297 4 650 .. 10 659 .. 7 661 .] 0.98
Alignments for each domain:
== domain 1 score: 973.9 bits; conditional E-value: 1.7e-297
TIGR01217 4 qvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvd 72
+lw+p aer++ a+++ fr + r+ l dy+al+ wsvd+ ++fw +vwe dvv+++++ +vd
lcl|NCBI__GCF_000061505.1:WP_011765880.1 10 TPLWTPSAERIAAANMTAFRHTAERRWNIELPDYAALHAWSVDHPEQFWVSVWEDGDVVGKRGVRVLVD 78
58******************************************************************* PP
TIGR01217 73 dskmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGdr 141
+++m++a++fp+arln+a+nllr+++ +da+++ +e+k+ ++t+ el r+va+++aalr++Gv+kGdr
lcl|NCBI__GCF_000061505.1:WP_011765880.1 79 GDRMPGAQWFPDARLNFAQNLLRRRDGDDAVVFWGEDKVRDRLTHGELYRRVAQFSAALREQGVGKGDR 147
********************************************************************* PP
TIGR01217 142 vagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekvr 210
va+y+pn+pe++ a+la+as+Gai++s+spdfG++gvldrf+q epk+l+++dgy+ynGk d k+
lcl|NCBI__GCF_000061505.1:WP_011765880.1 148 VAAYMPNMPETLIAMLAAASIGAIFTSASPDFGVQGVLDRFGQTEPKVLLACDGYYYNGKMVDCLAKLG 216
********************************************************************* PP
TIGR01217 211 evakelpdlravvlipyvgdreklapkvegaltledllaa.aqaaelvfeqlpfdhplyilfssGttGv 278
e++ +lp++++vv++pyv ++l ++ a +++d++a a+e+ fe lpf+hply+++ssGttGv
lcl|NCBI__GCF_000061505.1:WP_011765880.1 217 EIVPQLPSVERVVIVPYVHRDHALGG-IPHARMYADFVAPhHAATEIGFEALPFSHPLYVMYSSGTTGV 284
*******************6666655.************945567899********************* PP
TIGR01217 279 pkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnv 347
pk+ivhsaGG l+qhlkeh+lhcd+++gdr++y+tt+Gwmmwn+lvsgla+Gat+ lydGsp+ ++ +
lcl|NCBI__GCF_000061505.1:WP_011765880.1 285 PKCIVHSAGGALLQHLKEHRLHCDVKPGDRVFYFTTCGWMMWNWLVSGLAAGATILLYDGSPFAADNRI 353
********************************************************************* PP
TIGR01217 348 lfdlaeregitvlGtsakyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllas 416
lfd+a++e++t +Gtsak+++a k glkp +th l ++r+++stGspl pegf+yvy+ ikad++l+s
lcl|NCBI__GCF_000061505.1:WP_011765880.1 354 LFDYADAERMTHFGTSAKFIDAAAKFGLKPRETHSLATVRAMMSTGSPLVPEGFDYVYRDIKADLQLSS 422
********************************************************************* PP
TIGR01217 417 isGGtdivscfvganpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwnded 485
isGGtdi+scfv++np+lpv++Geiq++glGlav++wd+eG+pv+gekGelv+++p+p+mpv fw ded
lcl|NCBI__GCF_000061505.1:WP_011765880.1 423 ISGGTDILSCFVLGNPVLPVWRGEIQCRGLGLAVDVWDDEGRPVRGEKGELVCARPFPAMPVGFWRDED 491
********************************************************************* PP
TIGR01217 486 GskyrkayfdkypgvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvig 554
Gskyr+ayf+++++vw+hGd++e+t++Gg++i+Grsdatlnp+Gvr+G+aeiy +ve+l ev es+vig
lcl|NCBI__GCF_000061505.1:WP_011765880.1 492 GSKYRAAYFERFDNVWCHGDFCEITAHGGLIIYGRSDATLNPGGVRIGTAEIYRQVEKLHEVVESIVIG 560
********************************************************************* PP
TIGR01217 555 qeqe...dgeervvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtlsGkkvevav 620
q+++ ++rvvlfvkl G+tld+ l ++ik++ir + +prhvp+k+++va+iprt+sGk+ve+av
lcl|NCBI__GCF_000061505.1:WP_011765880.1 561 QDWPpqnPNDVRVVLFVKLRDGMTLDDTLADRIKRTIRDNTTPRHVPAKVLQVADIPRTKSGKIVELAV 629
**96222469*********************************************************** PP
TIGR01217 621 kdvvaGkpvenkgalsnpealdlyeeleel 650
++vv+G++v+n++al+npeal +++ +el
lcl|NCBI__GCF_000061505.1:WP_011765880.1 630 RNVVHGRAVKNQEALANPEALAHFRDRDEL 659
************************997775 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (652 nodes)
Target sequences: 1 (661 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 0.02s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 10.23
//
[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