Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_028315561.1 G491_RS0117905 acetoacetate--CoA ligase
Query= BRENDA::Q9Z3R3
(650 letters)
>NCBI__GCF_000429905.1:WP_028315561.1
Length = 650
Score = 656 bits (1693), Expect = 0.0
Identities = 321/645 (49%), Positives = 434/645 (67%), Gaps = 4/645 (0%)
Query: 7 LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVIGES 66
LW P +E +E++ M F+ +RFG++F Y H WSV FWT +W+ V +
Sbjct: 5 LWTPSKERIEQTNMFRFMGEINQRFGKNFQTYPELHQWSVDNIADFWTVLWDFVGVKAST 64
Query: 67 GEKALVDGD-RMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRALV 125
++D +M A++F A+LNFAEN+L+ A++F+GE R+T+ +L V
Sbjct: 65 SYTQVIDDPTKMPGAKWFEGAKLNFAENMLKYRDDQLAIVFQGEGAEPVRITYAQLYDQV 124
Query: 126 SRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFGQ 185
+RL ++LR G+ GDRVA MPNMP+T+ MLA AS+GAIWSSCSPDFG +GVLDRFGQ
Sbjct: 125 ARLAKSLRDMGVKTGDRVAGFMPNMPQTVMAMLAAASIGAIWSSCSPDFGIKGVLDRFGQ 184
Query: 186 IAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVEGGVTL 243
I PK+ +GY + GK D K+ V L + V+VPY + A ++ + +
Sbjct: 185 IKPKVLFTANGYRFKGKDLDSLEKISGVVNQLPSLEKLVVVPYTQERADIS-ALPNAIHF 243
Query: 244 ADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGLR 303
DFI+ + FE+LPF HPLYI++SSGTTG+PKC+V S GG L+ HLKE H L+
Sbjct: 244 QDFISREDGLEIEFEQLPFDHPLYIMYSSGTTGLPKCMVQSTGGILVHHLKELVLHTDLK 303
Query: 304 DGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTSA 363
+ +FYFTTCGWMMWNWL S L VGAT+ YDG PF PD VL+ A E+ VFG SA
Sbjct: 304 REDNIFYFTTCGWMMWNWLTSSLGVGATIIQYDGQPFHPDAEVLWKMAQDEKVTVFGASA 363
Query: 364 KYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDIV 423
YI A+ P + +DLSS+R + STGSPLS EGF +VY +K D+QLASI+GGTD+
Sbjct: 364 GYIAALMDQEGQPGKHYDLSSVRAVLSTGSPLSIEGFEWVYREVKEDLQLASIAGGTDLN 423
Query: 424 SCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWNDP 483
CF LGNP+ PV+ GE+Q GL + V +++ G+PV ++ ELVC + FPSMP+ FW DP
Sbjct: 424 GCFALGNPMGPVYAGELQCRGLAMDVAAFDENGQPVINQQAELVCCKPFPSMPIYFWEDP 483
Query: 484 DGAKYRAAYFDRFDNVWCHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQM 543
DG KY AYFD++ VW HGDF T GG+V++GRSDATLNPGGVRIGTAEIY VE
Sbjct: 484 DGKKYHKAYFDKYPGVWHHGDFITVTERGGVVMYGRSDATLNPGGVRIGTAEIYRVVENF 543
Query: 544 DEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIAVA 603
+E+A+++ +GQ+W++DVRV+LFV++A G LT+ + +++ IR ASPRHVPAK+I V
Sbjct: 544 EEIADSVVVGQNWDNDVRVILFVKMAEGQALTDDVINKLRAGIRQNASPRHVPAKVIEVP 603
Query: 604 DIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEEL 648
D+P T + K VELAV+ V+ +PV+N +ALANP+ALD + + EL
Sbjct: 604 DVPYTLNMKKVELAVKKVIENKPVENTDALANPQALDFYKDIPEL 648
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: 1303
Number of extensions: 75
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_028315561.1 G491_RS0117905 (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.6934.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
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
5.2e-287 939.2 0.0 5.7e-287 939.1 0.0 1.0 1 lcl|NCBI__GCF_000429905.1:WP_028315561.1 G491_RS0117905 acetoacetate--CoA
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000429905.1:WP_028315561.1 G491_RS0117905 acetoacetate--CoA ligase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 939.1 0.0 5.7e-287 5.7e-287 4 650 .. 3 648 .. 1 650 [] 0.99
Alignments for each domain:
== domain 1 score: 939.1 bits; conditional E-value: 5.7e-287
TIGR01217 4 qvlwepdaervkdarlarfraavgerfGaalgdydalyrwsvdeldafwkavwefsdvvfssaekevvd 72
+ lw+p +er++++++ rf + +rfG+ + y +l++wsvd+ +fw+ +w+f++v +s+++ +v+d
lcl|NCBI__GCF_000429905.1:WP_028315561.1 3 KLLWTPSKERIEQTNMFRFMGEINQRFGKNFQTYPELHQWSVDNIADFWTVLWDFVGVKASTSYTQVID 71
579*****************************************************************9 PP
TIGR01217 73 d.skmlaarffpgarlnyaenllrkkgsedallyvdeekesakvtfeelrrqvaslaaalralGvkkGd 140
d +km++a++f ga+ln+aen+l+ ++ + a+++++e e+ ++t+++l qva+la++lr +Gvk+Gd
lcl|NCBI__GCF_000429905.1:WP_028315561.1 72 DpTKMPGAKWFEGAKLNFAENMLKYRDDQLAIVFQGEGAEPVRITYAQLYDQVARLAKSLRDMGVKTGD 140
84689**************************************************************** PP
TIGR01217 141 rvagylpnipeavaallatasvGaiwsscspdfGargvldrfsqiepkllfsvdgyvynGkehdrrekv 209
rvag++pn+p++v+a+la+as+GaiwsscspdfG +gvldrf+qi+pk+lf+ +gy+++Gk+ d ek+
lcl|NCBI__GCF_000429905.1:WP_028315561.1 141 RVAGFMPNMPQTVMAMLAAASIGAIWSSCSPDFGIKGVLDRFGQIKPKVLFTANGYRFKGKDLDSLEKI 209
********************************************************************* PP
TIGR01217 210 revakelpdlravvlipyvgdreklapkvegaltledllaaaqaaelvfeqlpfdhplyilfssGttGv 278
v+++lp+l++ v++py +r+ ++ +++a++++d+++ + e++feqlpfdhplyi++ssGttG+
lcl|NCBI__GCF_000429905.1:WP_028315561.1 210 SGVVNQLPSLEKLVVVPYTQERADISA-LPNAIHFQDFISREDGLEIEFEQLPFDHPLYIMYSSGTTGL 277
********************9999988.*************9999************************ PP
TIGR01217 279 pkaivhsaGGtlvqhlkehvlhcdltdgdrllyyttvGwmmwnflvsglatGatlvlydGsplvpatnv 347
pk++v+s+GG+lv+hlke+vlh+dl+ d ++y+tt+Gwmmwn+l s+l +Gat++ ydG p+ p+++v
lcl|NCBI__GCF_000429905.1:WP_028315561.1 278 PKCMVQSTGGILVHHLKELVLHTDLKREDNIFYFTTCGWMMWNWLTSSLGVGATIIQYDGQPFHPDAEV 346
********************************************************************* PP
TIGR01217 348 lfdlaeregitvlGtsakyvsavrkkglkparthdlsalrlvastGsplkpegfeyvyeeikadvllas 416
l+++a+ e++tv+G+sa y+ a+ +++ +p + +dls++r+v+stGspl+ egfe+vy+e+k d++las
lcl|NCBI__GCF_000429905.1:WP_028315561.1 347 LWKMAQDEKVTVFGASAGYIAALMDQEGQPGKHYDLSSVRAVLSTGSPLSIEGFEWVYREVKEDLQLAS 415
********************************************************************* PP
TIGR01217 417 isGGtdivscfvganpslpvykGeiqapglGlaveawdeeGkpvtgekGelvvtkplpsmpvrfwnded 485
i+GGtd+ cf+++np+ pvy Ge+q++gl ++v a+de+G+pv +++ elv+ kp+psmp+ fw+d+d
lcl|NCBI__GCF_000429905.1:WP_028315561.1 416 IAGGTDLNGCFALGNPMGPVYAGELQCRGLAMDVAAFDENGQPVINQQAELVCCKPFPSMPIYFWEDPD 484
********************************************************************* PP
TIGR01217 486 GskyrkayfdkypgvwahGdyieltprGgivihGrsdatlnpnGvrlGsaeiynaverldeveeslvig 554
G ky+kayfdkypgvw hGd+i++t rGg+v++Grsdatlnp+Gvr+G+aeiy +ve+++e+++s+v+g
lcl|NCBI__GCF_000429905.1:WP_028315561.1 485 GKKYHKAYFDKYPGVWHHGDFITVTERGGVVMYGRSDATLNPGGVRIGTAEIYRVVENFEEIADSVVVG 553
********************************************************************* PP
TIGR01217 555 qeqedgeervvlfvklasGatldealvkeikdairaglsprhvpskiievagiprtlsGkkvevavkdv 623
q++++ ++rv+lfvk+a+G+ l+++++++++ ir ++sprhvp+k+iev+++p+tl+ kkve+avk+v
lcl|NCBI__GCF_000429905.1:WP_028315561.1 554 QNWDN-DVRVILFVKMAEGQALTDDVINKLRAGIRQNASPRHVPAKVIEVPDVPYTLNMKKVELAVKKV 621
**987.*************************************************************** PP
TIGR01217 624 vaGkpvenkgalsnpealdlyeeleel 650
++ kpven +al+np+ald+y++++el
lcl|NCBI__GCF_000429905.1:WP_028315561.1 622 IENKPVENTDALANPQALDFYKDIPEL 648
************************997 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: 00:00:00.04
# Mc/sec: 8.73
//
[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