Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_073036290.1 BUB04_RS01550 acetoacetate--CoA ligase
Query= BRENDA::Q9Z3R3
(650 letters)
>NCBI__GCF_900129305.1:WP_073036290.1
Length = 650
Score = 711 bits (1835), Expect = 0.0
Identities = 351/647 (54%), Positives = 451/647 (69%), Gaps = 4/647 (0%)
Query: 7 LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVI-GE 65
LW P E ++ S M F+ + ER G++F YD ++WSV+E FW W++ ++
Sbjct: 5 LWKPSEERIQNSNMYHFMQYVNERHGKAFRAYDELYEWSVTEIPTFWATFWDYSDILCSR 64
Query: 66 SGEKALVDGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
S ++ + D ++ AR+F ARLNFAENLLR AL F+GE + + +T+ +L V
Sbjct: 65 SYDQVVDDVAKLPGARWFEGARLNFAENLLRYRDDCIALSFKGEGQPTRHITYAQLYDRV 124
Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185
+RL ++LR GI GDR+A +PNM ET+ MLA SVGA+WSSCSPDFG +GVLDRFGQ
Sbjct: 125 ARLAKSLRDMGIQPGDRIAGFVPNMIETVIAMLAATSVGAVWSSCSPDFGIKGVLDRFGQ 184
Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVEGGVTL 243
I P++ DGY+YNGK D +++ + K L + V++PY D V GV L
Sbjct: 185 IEPRVLFTADGYYYNGKTFDSLARIAEILKELPSIEKVVVMPYT-DPKPDPGRVRNGVLL 243
Query: 244 ADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGLR 303
DF+A + FE++P HPLYI++SSGTTGVPKCIVH GTL+QHLKE R H L+
Sbjct: 244 EDFLAKDDGLEIEFEQVPANHPLYIMYSSGTTGVPKCIVHGVVGTLIQHLKELRLHTDLK 303
Query: 304 DGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTSA 363
+ +FYFTTCGWMMWNWL S LA+GA + LYDGSPF PD ++ A E+ +FGTSA
Sbjct: 304 RDDTIFYFTTCGWMMWNWLVSSLALGARVLLYDGSPFYPDPGAMWQMAQDEKITIFGTSA 363
Query: 364 KYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDIV 423
KY+ AV K G P T+DL+ L+ + STGSPLS E F +VY IK D+ L+SISGGTDI+
Sbjct: 364 KYLAAVEKAGVKPKETYDLTPLKAVLSTGSPLSIESFEYVYRDIKEDLCLSSISGGTDII 423
Query: 424 SCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWNDP 483
SCF LGNP+ PV+ GE+Q GLG+ V+ W+++G+PV G+KGELVCT A PSMP+ FWNDP
Sbjct: 424 SCFALGNPMGPVYAGELQCRGLGMKVEAWDEDGRPVIGQKGELVCTAAAPSMPIYFWNDP 483
Query: 484 DGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQM 543
G KYR AYF + VW HGDF E T GG++I+GRSDATLNPGGVRIGTAEIY QVE +
Sbjct: 484 HGQKYRDAYFSVYPGVWHHGDFIEITERGGVIIYGRSDATLNPGGVRIGTAEIYRQVETI 543
Query: 544 DEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIAVA 603
EV ++L +GQDW++DVRV+LFV+L G ELT+ L IK IR +PRHVPAKIIAV
Sbjct: 544 PEVLDSLVVGQDWDNDVRVILFVKLREGHELTDELINRIKKAIRENTTPRHVPAKIIAVP 603
Query: 604 DIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELKS 650
DIP T SGK VELAVR V+H + VKNK+ALANPE+LD F + EL++
Sbjct: 604 DIPYTISGKKVELAVRKVIHNQEVKNKDALANPESLDYFKDIPELQN 650
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: 1306
Number of extensions: 56
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: 650
Length adjustment: 38
Effective length of query: 612
Effective length of database: 612
Effective search space: 374544
Effective search space used: 374544
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_073036290.1 BUB04_RS01550 (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.797.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
4.1e-295 966.0 0.0 4.6e-295 965.8 0.0 1.0 1 lcl|NCBI__GCF_900129305.1:WP_073036290.1 BUB04_RS01550 acetoacetate--CoA
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900129305.1:WP_073036290.1 BUB04_RS01550 acetoacetate--CoA ligase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 965.8 0.0 4.6e-295 4.6e-295 4 651 .. 3 649 .. 1 650 [] 0.99
Alignments for each domain:
== domain 1 score: 965.8 bits; conditional E-value: 4.6e-295
TIGR01217 4 qvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvd 72
+ lw+p +er++++++ +f ++v er+G+a+ yd+ly+wsv+e +fw+ +w++sd+++s+++++vvd
lcl|NCBI__GCF_900129305.1:WP_073036290.1 3 KLLWKPSEERIQNSNMYHFMQYVNERHGKAFRAYDELYEWSVTEIPTFWATFWDYSDILCSRSYDQVVD 71
579*****************************************************************9 PP
TIGR01217 73 d.skmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGd 140
d k ++ar+f garln+aenllr ++ al +++e + + ++t+++l +va+la++lr +G+++Gd
lcl|NCBI__GCF_900129305.1:WP_073036290.1 72 DvAKLPGARWFEGARLNFAENLLRYRDDCIALSFKGEGQPTRHITYAQLYDRVARLAKSLRDMGIQPGD 140
8457899************************************************************** PP
TIGR01217 141 rvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekv 209
r+ag++pn+ e+v a+la++svGa+wsscspdfG +gvldrf+qiep++lf+ dgy+ynGk d ++
lcl|NCBI__GCF_900129305.1:WP_073036290.1 141 RIAGFVPNMIETVIAMLAATSVGAVWSSCSPDFGIKGVLDRFGQIEPRVLFTADGYYYNGKTFDSLARI 209
********************************************************************* PP
TIGR01217 210 revakelpdlravvlipyvgdreklap.kvegaltledllaaaqaaelvfeqlpfdhplyilfssGttG 277
+e+ kelp++++vv++py ++ +p +v +++ led+la + e++feq+p +hplyi++ssGttG
lcl|NCBI__GCF_900129305.1:WP_073036290.1 210 AEILKELPSIEKVVVMPYTDPK--PDPgRVRNGVLLEDFLAKDDGLEIEFEQVPANHPLYIMYSSGTTG 276
******************9965..56668*************9999*********************** PP
TIGR01217 278 vpkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatn 346
vpk+ivh Gtl+qhlke++lh+dl+ d ++y+tt+Gwmmwn+lvs+la Ga + lydGsp+ p++
lcl|NCBI__GCF_900129305.1:WP_073036290.1 277 VPKCIVHGVVGTLIQHLKELRLHTDLKRDDTIFYFTTCGWMMWNWLVSSLALGARVLLYDGSPFYPDPG 345
********************************************************************* PP
TIGR01217 347 vlfdlaeregitvlGtsakyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvlla 415
+++++a+ e+it++Gtsaky+ av+k+g+kp +t+dl+ l++v+stGspl+ e+feyvy+ ik d+ l+
lcl|NCBI__GCF_900129305.1:WP_073036290.1 346 AMWQMAQDEKITIFGTSAKYLAAVEKAGVKPKETYDLTPLKAVLSTGSPLSIESFEYVYRDIKEDLCLS 414
********************************************************************* PP
TIGR01217 416 sisGGtdivscfvganpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwnde 484
sisGGtdi+scf+++np+ pvy Ge+q++glG++veawde+G+pv g+kGelv+t + psmp+ fwnd+
lcl|NCBI__GCF_900129305.1:WP_073036290.1 415 SISGGTDIISCFALGNPMGPVYAGELQCRGLGMKVEAWDEDGRPVIGQKGELVCTAAAPSMPIYFWNDP 483
********************************************************************* PP
TIGR01217 485 dGskyrkayfdkypgvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvi 553
+G kyr+ayf+ ypgvw hGd+ie+t rGg++i+Grsdatlnp+Gvr+G+aeiy +ve ++ev +slv+
lcl|NCBI__GCF_900129305.1:WP_073036290.1 484 HGQKYRDAYFSVYPGVWHHGDFIEITERGGVIIYGRSDATLNPGGVRIGTAEIYRQVETIPEVLDSLVV 552
********************************************************************* PP
TIGR01217 554 gqeqedgeervvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtlsGkkvevavkd 622
gq++++ ++rv+lfvkl +G++l+++l+++ik+air + +prhvp+kii+v++ip+t+sGkkve+av++
lcl|NCBI__GCF_900129305.1:WP_073036290.1 553 GQDWDN-DVRVILFVKLREGHELTDELINRIKKAIRENTTPRHVPAKIIAVPDIPYTISGKKVELAVRK 620
****87.************************************************************** PP
TIGR01217 623 vvaGkpvenkgalsnpealdlyeeleelk 651
v++ + v+nk+al+npe+ld++++++el+
lcl|NCBI__GCF_900129305.1:WP_073036290.1 621 VIHNQEVKNKDALANPESLDYFKDIPELQ 649
***************************98 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (652 nodes)
Target sequences: 1 (650 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: 12.03
//
[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