Score = 60.5 bits (145), Expect = 3e-09, Method: Composition-based stats.
Identities = 29/57 (50%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 1 MSRTIIDPVTSVQLPDGKTGELCLKGDVFL-GYRNKVEATKEMLDDDGWLHTGDLAY 56
M I+DP T LP GKTGEL L+G V + GY +A+ E +D +GWL TGDL Y
Sbjct: 385 MEAKIVDPSTGESLPPGKTGELWLRGPVIMKGYVGNEKASAETVDKEGWLKTGDLCY 441
Contributes to jasmonic acid biosynthesis by initiating the beta-oxidative chain shortening of its precursors. Converts 12-oxo-phytodienoic acid (OPDA) into OPDA-CoA.
Score = 59.7 bits (143), Expect = 5e-09, Method: Composition-based stats.
Identities = 27/62 (43%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGDVFL-GYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTH 63
++D T + LP K+GE+C++G + GY N EAT +D DGWLHTGD+ + D
Sbjct: 399 VVDTETGISLPRNKSGEICVRGHQLMKGYLNDPEATARTIDKDGWLHTGDIGFVDDDDEI 458
Query: 64 FI 65
FI
Sbjct: 459 FI 460
Produces CoA thioesters of a variety of hydroxy- and methoxy-substituted cinnamic acids, which are used to synthesize several phenylpropanoid-derived compounds, including anthocyanins, flavonoids, isoflavonoids, coumarins, lignin, suberin and wall-bound phenolics.
Acyl-CoA synthetases (ACSL) activates long-chain fatty acids for both synthesis of cellular lipids, and degradation via beta-oxidation. ACSL5 may sensitize epithelial cells to apoptosis specifically triggered by the death ligand TRAIL at the villus tip of the crypt-villus axis of the small intestine (By similarity). May have a role in the survival of glioma cells (By similarity). May activate fatty acids from exogenous sources for the synthesis of triacylglycerol destined for intracellular storage. It was suggested that it may also stimulate fatty acid oxidation. Utilizes a wide range of saturated fatty acids with a preference for C16-C18 unsaturated fatty acids.
Rattus norvegicus (taxid: 10116)
EC: 6
EC: .
EC: 2
EC: .
EC: 1
EC: .
EC: 3
Close Homologs in the Non-Redundant Database Detected by BLAST
Score = 81.1 bits (201), Expect = 4e-20
Identities = 30/62 (48%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTH 63
I+D L + GELC+KG + GY N EATKE +D+DGWLHTGD+ Y DG
Sbjct: 329 IVDEDGGKSLGPNERGELCVKGPQIMKGYLNNPEATKETIDEDGWLHTGDIGYFDEDGNF 388
Query: 64 FI 65
+I
Sbjct: 389 YI 390
This family contains two functionally unique groups of proteins; one group is insect firefly luciferases and the other is plant 4-coumarate:coenzyme A ligases. However, they share significant sequence similarity in spite of their functional diversity. Luciferase catalyzes the production of light in the presence of MgATP, molecular oxygen, and luciferin. In the first step, luciferin is activated by acylation of its carboxylate group with ATP, resulting in an enzyme-bound luciferyl adenylate. In the second step, luciferyl adenylate reacts with molecular oxygen, producing an enzyme-bound excited state product (Luc=O*) and releasing AMP. This excited-state product then decays to the ground state (Luc=O), emitting a quantum of visible light. 4-coumarate:coenzyme A ligase is a key enzyme in the phenylpropanoid metabolic pathway for monolignol and flavonoid biosynthesis. It catalyzes the synthesis of hydroxycinnamate-CoA thioesters in a two-step reaction, involving the formation of hydroxycinnamate-AMP anhydride and then the nucleophilic substitution of AMP by CoA. The phenylpropanoid pathway is one of the most important secondary metabolism pathways in plants and hydroxycinnamate-CoA thioesters are the precursors of lignin and other important phenylpropanoids. Length = 487
Score = 78.4 bits (194), Expect = 4e-19
Identities = 33/62 (53%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTH 63
I+DP T LP + GEL ++G V GY N EAT E +D DGWLHTGDL Y DG
Sbjct: 343 IVDPETGESLPPNQPGELWVRGPQVMKGYLNNPEATAETIDKDGWLHTGDLGYFDEDGYL 402
Query: 64 FI 65
FI
Sbjct: 403 FI 404
4-Coumarate:coenzyme A ligase is a key enzyme in the phenylpropanoid metabolic pathway for monolignol and flavonoid biosynthesis. It catalyzes the synthesis of hydroxycinnamate-CoA thioesters in a two-step reaction, involving the formation of hydroxycinnamate-AMP anhydride and the nucleophilic substitution of AMP by CoA. The phenylpropanoid pathway is one of the most important secondary metabolism pathways in plants and hydroxycinnamate-CoA thioesters are the precursors of lignin and other important phenylpropanoids. Length = 504
>gnl|CDD|213284 cd05917, FACL_like_2, Uncharacterized subfamily of fatty acid CoA ligase (FACL)
Score = 72.6 bits (179), Expect = 4e-17
Identities = 31/62 (50%), Positives = 39/62 (62%), Gaps = 2/62 (3%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTH 63
I+DP ++P G+ GE+C++G V GY N EAT E +D DGWLHTGDL Y DG
Sbjct: 186 IVDPDGG-EVPPGEVGEICVRGYSVMKGYYNDPEATAEAIDADGWLHTGDLGYMDEDGYL 244
Query: 64 FI 65
I
Sbjct: 245 RI 246
Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. Length = 347
Score = 69.9 bits (172), Expect = 4e-16
Identities = 28/62 (45%), Positives = 37/62 (59%), Gaps = 3/62 (4%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTH 63
I+D + LP G+ GEL ++G V GY N+ E T E+L D GWL TGD+ Y DG
Sbjct: 308 IVDDEGNE-LPPGEVGELVVRGPQVMKGYWNRPEETAEVLTD-GWLRTGDIGYMDEDGYF 365
Query: 64 FI 65
+I
Sbjct: 366 YI 367
This subfamily of the AMP-forming adenylation family contains Escherichia coli FadD and similar prokaryotic fatty acid CoA synthetases. FadD was characterized as a long-chain fatty acid CoA synthetase. The gene fadD is regulated by the fatty acid regulatory protein FadR. Fatty acid CoA synthetase catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, followed by the formation of a fatty acyl-CoA. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. Length = 468
>gnl|CDD|223395 COG0318, CaiC, Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Score = 65.7 bits (161), Expect = 1e-14
Identities = 25/62 (40%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTH 63
I+D L G+ GE+ ++G VF Y NK EAT E +DGW TGD+ DG +
Sbjct: 271 IVDEDGGEPLAAGEVGEIQVRGPNVFSEYWNKPEATAEAFTEDGWFKTGDVGVVDEDGYY 330
Query: 64 FI 65
I
Sbjct: 331 RI 332
MCS catalyzes the formation of malonyl-CoA in a two-step reaction consisting of the adenylation of malonate with ATP, followed by malonyl transfer from malonyl-AMP to CoA. Malonic acid and its derivatives are the building blocks of polyketides and malonyl-CoA serves as the substrate of polyketide synthases. Malonyl-CoA synthetase has broad substrate tolerance and can activate a variety of malonyl acid derivatives. MCS may play an important role in biosynthesis of polyketides, the important secondary metabolites with therapeutic and agrochemical utility. Length = 430
This family includes long-chain fatty acid (C12-C20) CoA synthetases and Bubblegum-like very long-chain (>C20) fatty acid CoA synthetases. FACS catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, and the formation of a fatty acyl-CoA. Eukaryotes generally have multiple isoforms of LC-FACS genes with multiple splice variants. For example, nine genes are found in Arabidopsis and six genes are expressed in mammalian cells. Drosophila melanogaster mutant bubblegum (BGM) have elevated levels of very-long-chain fatty acids (VLCFA) caused by a defective gene later named bubblegum. The human homolog (hsBG) of bubblegum has been characterized as a very long chain fatty acid CoA synthetase that functions specifically in the brain; hsBG may play a central role in brain VLCFA metabolism and myelinogenesis. Free fatty acids must be "activated" to their CoA thioesters before participating in most catabolic and anabolic reactions. Length = 456
The members of this family are putative long-chain fatty acyl-CoA synthetases, which catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. Fatty acyl-CoA synthetases are responsible for fatty acid degradation as well as physiological regulation of cellular functions via the production of fatty acyl-CoA esters. Length = 430
Score = 63.1 bits (153), Expect = 1e-13
Identities = 30/61 (49%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 6 IDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTHF 64
IDP T LP GELC++ V GY N E T +D+DGWLHTGD+ Y DG F
Sbjct: 375 IDPDTGRSLPKNTPGELCVRSQCVMQGYYNNKEETDRTIDEDGWLHTGDIGYIDDDGDIF 434
Query: 65 I 65
I
Sbjct: 435 I 435
The members of this family are eukaryotic fatty acid CoA synthetases that activate fatty acids with chain lengths of 12 to 20. LC-FACS catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, and the formation of a fatty acyl-CoA. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. Organisms tend to have multiple isoforms of LC-FACS genes with multiple splice variants. For example, nine genes are found in Arabidopsis and six genes are expressed in mammalian cells. Length = 539
The members of this family are bacterial long-chain fatty acid CoA synthetase. Marinobacter hydrocarbonoclasticus isoprenoid Coenzyme A synthetase in this family is involved in the synthesis of isoprenoid wax ester storage compounds when grown on phytol as the sole carbon source. LC-FACS catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, and the formation of a fatty acyl-CoA. Free fatty acids must be "activated" to their CoA thioesters before participating in most catabolic and anabolic reactions. Length = 504
Score = 59.0 bits (144), Expect = 3e-12
Identities = 27/49 (55%), Positives = 32/49 (65%), Gaps = 2/49 (4%)
Query: 14 LPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDG 61
LP G+ GE+ ++G V GY N+ EAT E L D GWLHTGDL Y DG
Sbjct: 190 LPPGEVGEIVVRGPAVMAGYWNRPEATAEALRD-GWLHTGDLGYLDEDG 237
Bile acid-Coenzyme A ligase catalyzes the formation of bile acid-CoA conjugates in a two-step reaction: the formation of a bile acid-AMP molecule as an intermediate, followed by the formation of a bile acid-CoA. This ligase requires a bile acid with a free carboxyl group, ATP, Mg2+, and CoA for synthesis of the final bile acid-CoA conjugate. The bile acid-CoA ligation is believed to be the initial step in the bile acid 7alpha-dehydroxylation pathway in the intestinal bacterium Eubacterium sp. Length = 342
>gnl|CDD|213299 cd05933, ACSBG_like, Bubblegum-like very long-chain fatty acid CoA synthetase (VL-FACS)
This family of very long-chain fatty acid CoA synthetase is named bubblegum because Drosophila melanogaster mutant bubblegum (BGM) has elevated levels of very-long-chain fatty acids (VLCFA) caused by a defective gene of this family. The human homolog (hsBG) has been characterized as a very long chain fatty acid CoA synthetase that functions specifically in the brain; hsBG may play a central role in brain VLCFA metabolism and myelinogenesis. VL-FACS is involved in the first reaction step of very long chain fatty acid degradation. It catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, and the formation of a fatty acyl-CoA. Free fatty acids must be "activated" to their CoA thioesters before participating in most catabolic and anabolic reactions. Length = 594
FAAL belongs to the class I adenylate forming enzyme family and is homologous to fatty acyl-coenzyme A (CoA) ligases (FACLs). However, FAALs produce only the acyl adenylate and are unable to perform the thioester-forming reaction, while FACLs perform a two-step catalytic reaction; AMP ligation followed by CoA ligation using ATP and CoA as cofactors. FAALs have insertion motifs between the N-terminal and C-terminal subdomains that distinguish them from the FACLs. This insertion motif precludes the binding of CoA, thus preventing CoA ligation. It has been suggested that the acyl adenylates serve as substrates for multifunctional polyketide synthases to permit synthesis of complex lipids such as phthiocerol dimycocerosate, sulfolipids, mycolic acids, and mycobactin. Length = 547
Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. Members of this family include DitJ from Pseudomonas and similar proteins. Length = 421
FACL catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, followed by the formation of a fatty acyl-CoA. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. Fum10p is a fatty acid CoA ligase involved in the synthesis of fumonisin, a polyketide mycotoxin, in Gibberella moniliformis. Length = 345
>gnl|CDD|213270 cd04433, AFD_class_I, Adenylate forming domain, Class I
Score = 56.1 bits (136), Expect = 3e-11
Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 2/62 (3%)
Query: 5 IIDPVTSVQLPDGKTGELCLKG-DVFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTH 63
++D LP G+ GEL ++G V GY N T +DGW TGDL Y +G
Sbjct: 182 VVDEEGKP-LPPGEVGELVVRGPWVMKGYWNNPPETTAAATEDGWYRTGDLGYLDEEGYL 240
Query: 64 FI 65
+I
Sbjct: 241 YI 242
This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain. Length = 338
Score = 55.7 bits (135), Expect = 4e-11
Identities = 28/61 (45%), Positives = 37/61 (60%), Gaps = 4/61 (6%)
Query: 4 TIIDPVTSVQLP-DGKT-GELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPD 60
++DP T +P DGKT GE+ ++G+ V GY EAT+E GW H+GDLA PD
Sbjct: 356 DVVDPETMKDVPRDGKTIGEIVMRGNTVMKGYYKNPEATEEAFAG-GWFHSGDLAVVHPD 414
Query: 61 G 61
G
Sbjct: 415 G 415
This family includes fatty acyl-CoA synthetases that can activate medium to long-chain fatty acids. These enzymes catalyze the ATP-dependent acylation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. Fatty acyl-CoA synthetases are responsible for fatty acid degradation as well as physiological regulation of cellular functions via the production of fatty acyl-CoA esters. The fatty acyl-CoA synthetase from Thermus thermophiles in this family has been shown to catalyze the long-chain fatty acid, myristoyl acid. Also included in this family are acyl activating enzymes from Arabidopsis, which contains a large number of proteins from this family with up to 63 different genes, many of which are uncharacterized. Length = 520
2,3-dihydroxybenzoate-AMP ligase activates 2,3-dihydroxybenzoate (DHB) by ligation of AMP from ATP with the release of pyrophosphate. However, it can also catalyze the ATP-PPi exchange for 2,3-DHB analogs, such as salicyclic acid (o-hydrobenzoate), as well as 2,4-DHB and 2,5-DHB, but with less efficiency. Proteins in this family are the stand-alone adenylation components of non-ribosomal peptide synthases (NRPSs) involved in the biosynthesis of siderophores, which are low molecular weight iron-chelating compounds synthesized by many bacteria to aid in the acquisition of this vital trace elements. In Escherichia coli, the 2,3-dihydroxybenzoate-AMP ligase is called EntE, the adenylation component of the enterobactin NRPS system. Length = 483
>gnl|CDD|213271 cd05903, CHC_CoA_lg, Cyclohexanecarboxylate-CoA ligase (also called cyclohex-1-ene-1-carboxylate:CoA ligase)
Cyclohexanecarboxylate-CoA ligase activates the aliphatic ring compound, cyclohexanecarboxylate, for degradation. It catalyzes the synthesis of cyclohexanecarboxylate-CoA thioesters in a two-step reaction involving the formation of cyclohexanecarboxylate-AMP anhydride, followed by the nucleophilic substitution of AMP by CoA. Length = 437
>gnl|CDD|213277 cd05909, AAS_C, C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas)
Score = 50.7 bits (122), Expect = 2e-09
Identities = 25/64 (39%), Positives = 35/64 (54%), Gaps = 4/64 (6%)
Query: 5 IIDPVTSVQLPDGKTGELCLKG-DVFLGYRNKVEATKEM-LDDDGWLHTGDLAYRLPDGT 62
I+ P T +LP G+ G L ++G +V GY N E T E+ + DGW TGD+ DG
Sbjct: 324 IVSPETHEELPIGEGGLLLVRGPNVMSGYLNNEEKTSEVEVLGDGWYDTGDIGKIDEDG- 382
Query: 63 HFIW 66
F+
Sbjct: 383 -FLT 385
Acyl-acyl carrier protein synthase (Aas) is a membrane protein responsible for a minor pathway of incorporating exogenous fatty acids into membrane phospholipids. Its in vitro activity is characterized by the ligation of free fatty acids between 8 and 18 carbons in length to the acyl carrier protein sulfydryl group (ACP-SH) in the presence of ATP and Mg2+. However, its in vivo function is as a 2-acylglycerophosphoethanolamine (2-acyl-GPE) acyltransferase. The reaction occurs in two steps: the acyl chain is first esterified to acyl carrier protein (ACP) via a thioester bond, followed by a second step where the acyl chain is transferred to a 2-acyllysophospholipid, thus completing the transacylation reaction. This model represents the C-terminal domain of the enzyme, which belongs to the class I adenylate-forming enzyme family, including acyl-CoA synthetases. Length = 489
Score = 50.8 bits (122), Expect = 2e-09
Identities = 24/52 (46%), Positives = 32/52 (61%), Gaps = 2/52 (3%)
Query: 15 PDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTHFI 65
G+ GE+C++G V GY N+ E T E D GWLHTGD+A DG ++I
Sbjct: 361 AQGEVGEICVRGPLVMDGYWNRPEETAEAFRD-GWLHTGDVAREDEDGFYYI 411
Length = 524
>gnl|CDD|213274 cd05906, A_NRPS_TubE_like, The adenylation domain (A domain) of a family of nonribosomal peptide synthetases (NRPSs) synthesizing toxins and antitumor agents
Score = 50.0 bits (120), Expect = 5e-09
Identities = 19/44 (43%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 14 LPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAY 56
LP+G+ G L ++G V GY EA E +DGW TGDL +
Sbjct: 395 LPEGEVGRLQVRGPTVTSGYYRNPEANAEAFTEDGWFRTGDLGF 438
The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino)-acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. This family includes NRPSs that synthesize toxins and antitumor agents; for example, TubE for Tubulysine, CrpA for cryptophycin, TdiA for terrequinone A, KtzG for kutzneride, and Vlm1/Vlm2 for Valinomycin. Nonribosomal peptide synthetases are large multifunctional enzymes which synthesize many therapeutically useful peptides. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and, in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. Length = 560
Score = 49.1 bits (118), Expect = 9e-09
Identities = 20/55 (36%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 14 LPDGKTGELCLKGD-VFLGYRNKVEATKE---MLDDDGWLHTGDLAYRLPDGTHF 64
+P G+ GEL + G V GY N E T + + W TGDL Y DG
Sbjct: 293 VPPGEEGELVIAGPQVSPGYLNNPEKTAKAFFQDEGQRWYRTGDLVYLEDDGLLV 347
DltA belongs to the class I AMP-forming adenylation domain superfamily, which also includes acetyl-CoA synthetase, luciferase, and the adenylation domains of non-ribosomal synthetases. It catalyzes the two-step activation reaction of D-alanine: the formation of a substrate-AMP molecule as an intermediate, and then the transfer of the amino acid adenylate to teichoic acid in the biosynthesis of lipoteichoic acid (LTA) and wall teichoic acid (WTA) in gram-positive bacteria. Length = 447
>gnl|CDD|223951 COG1020, EntF, Non-ribosomal peptide synthetase modules and related proteins [Secondary metabolites biosynthesis, transport, and catabolism]
O-succinylbenzoic acid-CoA synthase catalyzes the coenzyme A (CoA)- and ATP-dependent conversion of o-succinylbenzoic acid to o-succinylbenzoyl-CoA. The reaction is the fourth step of the biosynthesis pathway of menaquinone (vitamin K2). In certain bacteria, menaquinone is used during fumarate reduction in anaerobic respiration. In cyanobacteria, the product of the menaquinone pathway is phylloquinone (2-methyl-3-phytyl-1,4-naphthoquinone), a molecule used exclusively as an electron transfer cofactor in Photosystem 1. In green sulfur bacteria and heliobacteria, menaquinones are used as loosely bound secondary electron acceptors in the photosynthetic reaction center. Length = 407
>gnl|CDD|213276 cd05908, A_NRPS_MycA_like, The adenylation domain of nonribosomal peptide synthetases (NRPS) similar to mycosubtilin synthase subunit A (MycA)
The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as (amino)-acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. This family includes NRPS similar to mycosubtilin synthase subunit A (MycA). Mycosubtilin, which is characterized by a beta-amino fatty acid moiety linked to the circular heptapeptide Asn-Tyr-Asn-Gln-Pro-Ser-Asn, belongs to the iturin family of lipopeptide antibiotics. The mycosubtilin synthase subunit A (MycA) combines functional domains derived from peptide synthetases, amino transferases, and fatty acid synthases. Nonribosomal peptide synthetases are large multifunction enzymes that synthesize many therapeutically useful peptides. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and, in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. Length = 499
>gnl|CDD|180393 PRK06087, PRK06087, short chain acyl-CoA synthetase; Reviewed
Score = 48.3 bits (116), Expect = 2e-08
Identities = 25/61 (40%), Positives = 30/61 (49%), Gaps = 8/61 (13%)
Query: 13 QLPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDD----G--WLHTGDLAYRLPDGT-HF 64
+P G GEL + GD + LGY N+ E T E D G TGDLA PDG F
Sbjct: 317 PVPIGVPGELYVGGDGLALGYLNRPELTAERFVPDPFGPGERLYRTGDLARWRPDGNIEF 376
Query: 65 I 65
+
Sbjct: 377 L 377
The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and, in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. This family includes the adenylation domain of the Bacillus subtilis termination module (Surfactin domain, SrfA-C) which recognizes a specific amino acid building block, which is then activated and transferred to the terminal thiol of the 4'-phosphopantetheine (Ppan) arm of the downstream peptidyl carrier protein (PCP) domain. Length = 474
>gnl|CDD|213286 cd05919, BCL_like, Benzoate CoA ligase (BCL) and similar adenylate forming enzymes
Score = 47.0 bits (112), Expect = 5e-08
Identities = 21/50 (42%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 14 LPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGT 62
+P G G+L ++G + GY N E T+ L D GWL TGD R DG
Sbjct: 281 VPAGTVGDLWVRGPSLAPGYWNLPEKTQRTLRD-GWLRTGDRFSRDADGW 329
This family contains benzoate CoA ligase (BCL) and related ligases that catalyze the acylation of benzoate derivatives, 2-aminobenzoate and 4-hydroxybenzoate. Aromatic compounds represent the second most abundant class of organic carbon compounds after carbohydrates. Xenobiotic aromatic compounds are also a major class of man-made pollutants. Some bacteria use benzoate as the sole source of carbon and energy through benzoate degradation. Benzoate degradation starts with its activation to benzoyl-CoA by benzoate CoA ligase. The reaction catalyzed by benzoate CoA ligase proceeds via a two-step process; the first ATP-dependent step forms an acyl-AMP intermediate, and the second step forms the acyl-CoA ester with release of the AMP. Length = 436
Score = 46.5 bits (111), Expect = 6e-08
Identities = 22/59 (37%), Positives = 26/59 (44%), Gaps = 9/59 (15%)
Query: 13 QLPDGKTGELCLKGD-VFLGYRNKVEATKE-MLDDDGWL-------HTGDLAYRLPDGT 62
+P G GEL + G V GY N+ E T E + D TGDL LPDG
Sbjct: 313 PVPVGVVGELYIGGPGVARGYLNRPELTAERFVPDPFAGGDGARLYRTGDLVRYLPDGN 371
This model represents a domain responsible for the specific recognition of amino acids and activation as adenylyl amino acids. The reaction catalyzed is aa + ATP -> aa-AMP + PPi. These domains are usually found as components of multi-domain non-ribosomal peptide synthetases and are usually called "A-domains" in that context (for a review, see ). A-domains are almost invariably followed by "T-domains" (thiolation domains, pfam00550) to which the amino acid adenylate is transferred as a thiol-ester to a bound pantetheine cofactor with the release of AMP (these are also called peptide carrier proteins, or PCPs. When the A-domain does not represent the first module (corresponding to the first amino acid in the product molecule) it is usually preceded by a "C-domain" (condensation domain, pfam00668) which catalyzes the ligation of two amino acid thiol-esters from neighboring modules. This domain is a subset of the AMP-binding domain found in Pfam (pfam00501) which also hits substrate--CoA ligases and luciferases. Sequences scoring in between trusted and noise for this model may be ambiguous as to whether they activate amino acids or other molecules lacking an alpha amino group. Length = 409
MACS catalyzes the two-step activation of medium chain fatty acids (containing 4-12 carbons). The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. MACS enzymes are localized to mitochondria. Length = 439
Score = 44.1 bits (105), Expect = 5e-07
Identities = 27/60 (45%), Positives = 33/60 (55%), Gaps = 5/60 (8%)
Query: 5 IIDPVTSVQLP-DGKT-GELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDG 61
I+D +LP DGKT GEL ++G V Y E T+E L DGW TGD+A DG
Sbjct: 354 IVDDEG-NELPWDGKTVGELVVRGPWVTGSYYKDPEKTEE-LTRDGWFRTGDVAVIDEDG 411
This family includes fatty acyl-CoA synthetases that can activate medium-chain to long-chain fatty acids. They catalyze the ATP-dependent acylation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. The fatty acyl-CoA synthetases are responsible for fatty acid degradation as well as physiological regulation of cellular functions via the production of fatty acyl-CoA esters. The fatty acyl-CoA synthetase from Thermus thermophiles in this family was shown catalyzing the long-chain fatty acid, myristoyl acid, while another member in this family, the AlkK protein identified from Pseudomonas oleovorans, targets medium chain fatty acids. This family also includes uncharacterized FACS proteins. Length = 517
Score = 43.4 bits (103), Expect = 1e-06
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 8/55 (14%)
Query: 15 PDGKTGELCLKGDV---FLGYRNKVEATKEMLDD-----DGWLHTGDLAYRLPDG 61
P G+ G L + F GY + K++L D D + +TGDL R G
Sbjct: 278 PPGEVGLLLGEITDRNPFDGYTDDEATEKKILRDVFKKGDAYFNTGDLVRRDGFG 332
Fatty acid transport protein (FATP) transports long-chain or very-long-chain fatty acids across the plasma membrane. FATPs also have fatty acid CoA synthetase activity, thus playing dual roles as fatty acid transporters and its activation enzymes. At least five copies of FATPs are identified in mammalian cells. This family also includes prokaryotic FATPs. FATPs are the key players in the trafficking of exogenous fatty acids into the cell and in intracellular fatty acid homeostasis. Length = 444
Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. Length = 359
Score = 42.0 bits (100), Expect = 3e-06
Identities = 23/57 (40%), Positives = 27/57 (47%), Gaps = 8/57 (14%)
Query: 14 LPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLH-------TGDLAYRLPDGT 62
+P G GEL + G V GY N+ E T E D + TGDLA LPDG
Sbjct: 286 VPVGVPGELYIGGAGVARGYLNRPELTAERFVPDPFGGPGERLYRTGDLARWLPDGN 342
The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester bond to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. Length = 445
Benzoate CoA ligase and 4-hydroxybenzoate-coenzyme A ligase catalyze the first activating step for benzoate and 4-hydroxybenzoate catabolic pathways, respectively. Although these two enzymes share very high sequence homology, they have their own substrate preference. The reaction proceeds via a two-step process; the first ATP-dependent step forms the substrate-AMP intermediate, while the second step forms the acyl-CoA ester, releasing the AMP. Aromatic compounds represent the second most abundant class of organic carbon compounds after carbohydrates. Some bacteria can use benzoic acid or benzenoid compounds as the sole source of carbon and energy through degradation. Benzoate CoA ligase and 4-hydroxybenzoate-Coenzyme A ligase are key enzymes of this process. Length = 506
Score = 41.8 bits (99), Expect = 4e-06
Identities = 20/51 (39%), Positives = 25/51 (49%), Gaps = 6/51 (11%)
Query: 17 GKTGELCLKGD-VFLGYRNKVEATKEMLD-----DDGWLHTGDLAYRLPDG 61
G+ GEL +G V GY N EAT E L + L+TGDL +G
Sbjct: 195 GEVGELVHRGANVMKGYWNDPEATAERLRPGPLPGEIVLYTGDLVRMDEEG 245
Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. Length = 350
>gnl|CDD|213322 cd12114, A_NRPS_TlmIV_like, The adenylation domain of nonribosomal peptide synthetases (NRPS), including Streptoalloteichus tallysomycin biosynthesis genes
Score = 41.4 bits (98), Expect = 4e-06
Identities = 22/53 (41%), Positives = 24/53 (45%), Gaps = 5/53 (9%)
Query: 15 PDGKTGELCLKGD-VFLGYRNKVEATKE--MLDDDG--WLHTGDLAYRLPDGT 62
PD GEL + G V LGY E T E + G TGDL PDGT
Sbjct: 322 PDWVPGELYIGGVGVALGYWGDPELTAERFITHRTGERLYRTGDLGRYRPDGT 374
The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. This family includes the TLM biosynthetic gene cluster from Streptoalloteichus that consists of nine NRPS genes; the N-terminal module of TlmVI (NRPS-5) and the starter module of BlmVI (NRPS-5) are comprised of the acyl CoA ligase (AL) and acyl carrier protein (ACP)-like domains, which are thought to be involved in the biosynthesis of the beta-aminoalaninamide moiety. Length = 476
MACS catalyzes the two-step activation of medium chain fatty acids (containing 4-12 carbons). The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. The acyl-CoA is a key intermediate in many important biosynthetic and catabolic processes. Length = 430
Score = 40.7 bits (96), Expect = 9e-06
Identities = 26/68 (38%), Positives = 33/68 (48%), Gaps = 10/68 (14%)
Query: 5 IIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKE-MLDDDGWL--------HTGDL 54
++DP +P G GELC+ G V GY N+ E T E + D WL TGDL
Sbjct: 271 VLDPDLEPLVPIGAVGELCIGGPGVARGYLNRPELTAEKFIPDPFWLNNPGGRIYRTGDL 330
Query: 55 AYRLPDGT 62
L DG+
Sbjct: 331 VRYLEDGS 338
The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. This family of siderophore-synthesizing NRPS includes the third adenylation domain of SidN from the endophytic fungus Neotyphodium lolii, ferrichrome siderophore synthetase, HC-toxin synthetase, and enniatin synthase. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. Length = 447
>gnl|CDD|213324 cd12116, A_NRPS_Ta1_like, The adenylation domain of nonribosomal peptide synthetases (NRPS), including salinosporamide A polyketide synthase
Score = 40.2 bits (95), Expect = 1e-05
Identities = 23/58 (39%), Positives = 26/58 (44%), Gaps = 8/58 (13%)
Query: 13 QLPDGKTGELCLKGD-VFLGYRNKVEATKEML-----DDDG--WLHTGDLAYRLPDGT 62
+P G GEL + GD V GY + E T E DD G TGDL PDG
Sbjct: 278 PVPPGVPGELYIGGDGVARGYLGRPELTAERFVPDPFDDPGGRLYRTGDLVRWRPDGR 335
The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. This family includes the myxovirescin (TA) antibiotic biosynthetic gene in Myxococcus xanthus; TA production plays a role in predation. It also includes the salinosporamide A polyketide synthase which is involved in the biosynthesis of salinosporamide A, a marine microbial metabolite whose chlorine atom is crucial for potent proteasome inhibition and anticancer activity. Length = 438
Score = 39.9 bits (94), Expect = 2e-05
Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 3/55 (5%)
Query: 8 PVTSVQL-PDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPD 60
P T ++L P+G E+ +KG V GY E T E D++G+ GD A R D
Sbjct: 354 PGTELKLVPNGGKLEVRVKGPNVTPGYWRDPELTAEAFDEEGFYRIGD-AVRFVD 407
Feruloyl-CoA synthetase is an essential enzyme in the feruloyl acid degradation pathway and enables some proteobacteria to grow on media containing feruloyl acid as the sole carbon source. It catalyzes the transfer of CoA to the carboxyl group of ferulic acid, which then forms feruloyl-CoA in the presence of ATP and Mg2. The resulting feruloyl-CoA is further degraded to vanillin and acetyl-CoA. Feruloyl-CoA synthetase (FCS) is a subfamily of the adenylate-forming enzymes superfamily. Length = 559
Score = 39.6 bits (92), Expect = 2e-05
Identities = 24/60 (40%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 7 DPVTSVQLPDGKTGELCLKGDV-FLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGTHFI 65
P P G L +K LGY N E T E+L D GW++TGDL R DG +I
Sbjct: 362 GPTAPGAGPSASFGTLWIKSPANMLGYWNNPERTAEVLID-GWVNTGDLLERREDGFFYI 420
Score = 39.5 bits (92), Expect = 2e-05
Identities = 23/54 (42%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 11 SVQLPDGKTGELCLKGD--VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDGT 62
LP+G+ GEL + F GY N+ +AT E L D GW T D+A P GT
Sbjct: 339 DEALPNGEEGELVVAAADATFTGYLNQPQATAEKLQD-GWYRTSDVAVVDPSGT 391
CBAL catalyzes the conversion of 4-chlorobenzoate (4-CB) to 4-chlorobenzoyl-coenzyme A (4-CB-CoA) by the two-step adenylation and thioester-forming reactions. 4-Chlorobenzoate (4-CBA) is an environmental pollutant derived from microbial breakdown of aromatic pollutants, such as polychlorinated biphenyls (PCBs), DDT, and certain herbicides. The 4-CBA degrading pathway converts 4-CBA to the metabolite 4-hydroxybezoate (4-HBA), allowing some soil-dwelling microbes to utilize 4-CBA as an alternate carbon source. This pathway consists of three chemical steps catalyzed by 4-CBA-CoA ligase, 4-CBA-CoA dehalogenase, and 4HBA-CoA thioesterase in sequential reactions. Length = 495
>gnl|CDD|213323 cd12115, A_NRPS_Sfm_like, The adenylation domain of nonribosomal peptide synthetases (NRPS), including Saframycin A gene cluster from Streptomyces lavendulae
Score = 38.8 bits (91), Expect = 4e-05
Identities = 19/57 (33%), Positives = 24/57 (42%), Gaps = 9/57 (15%)
Query: 14 LPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLH--------TGDLAYRLPDG 61
+P G GEL + G V GY + E T E + + TGDL R DG
Sbjct: 289 VPVGVPGELYIGGAGVARGYLGRPELTAERFLPNPFAGSPGERLYRTGDLVRRRADG 345
The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. This family includes the saframycin A gene cluster from Streptomyces lavendulae which implicates the NRPS system for assembling the unusual tetrapeptidyl skeleton in an iterative manner. It also includes saframycin Mx1 produced by Myxococcus xanthus NRPS. Length = 449
Score = 38.7 bits (91), Expect = 4e-05
Identities = 22/56 (39%), Positives = 29/56 (51%), Gaps = 5/56 (8%)
Query: 8 PVTSVQL-P-DGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPD 60
P V+L P GK E+ +KG V GY E T E D++G+ +GD A R D
Sbjct: 399 PGCEVKLVPVGGKL-EVRVKGPNVTPGYWRAPELTAEAFDEEGYYRSGD-AVRFVD 452
This family is most similar to acetyl-CoA synthetase. Acetyl-CoA synthetase (ACS) catalyzes the formation of acetyl-CoA from acetate, CoA, and ATP. Synthesis of acetyl-CoA is carried out in a two-step reaction. In the first step, the enzyme catalyzes the synthesis of acetyl-AMP intermediate from acetate and ATP. In the second step, acetyl-AMP reacts with CoA to produce acetyl-CoA. This enzyme is only present in bacteria. Length = 443
MACS catalyzes the two-step activation of medium chain fatty acids (containing 4-12 carbons). The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This family of MACS enzymes is found in archaea and bacteria. It is represented by the acyl-adenylating enzyme from Methanosarcina acetivorans (AAE_MA). AAE_MA is most active with propionate, butyrate, and the branched analogs: 2-methyl-propionate, butyrate, and pentanoate. The specific activity is weaker for smaller or larger acids. Length = 537
>gnl|CDD|213278 cd05910, FACL_like_1, Uncharacterized subfamily of fatty acid CoA ligase (FACL)
Score = 37.4 bits (87), Expect = 1e-04
Identities = 19/52 (36%), Positives = 24/52 (46%), Gaps = 4/52 (7%)
Query: 14 LPDGKTGELCLKGD-VFLGYRNKVEAT---KEMLDDDGWLHTGDLAYRLPDG 61
LP G+ GE+ + G V Y N+ EAT K + W GDL Y G
Sbjct: 293 LPPGEVGEIIVSGPHVTREYYNRPEATKLAKISDGNRIWHRMGDLGYFDDQG 344
Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. Length = 455
Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. Length = 448
Score = 36.0 bits (84), Expect = 3e-04
Identities = 26/68 (38%), Positives = 31/68 (45%), Gaps = 5/68 (7%)
Query: 2 SRTIIDPVTSVQLPDGKTGELCLKGD-VFLGYRNKVEATKE---MLDDDGWLHTGDLAYR 57
S +I +LPDG+ GE+ + G V GY N E T E D HTGD Y
Sbjct: 327 SPLLIIDEEGTKLPDGEQGEIVISGPSVSKGYLNNPEKTAEAFFTFDGQPAYHTGDAGY- 385
Query: 58 LPDGTHFI 65
L DG F
Sbjct: 386 LEDGLLFY 393
This model represents an enzyme, O-succinylbenzoate-CoA ligase, which is involved in the fourth step of the menaquinone biosynthesis pathway. O-succinylbenzoate-CoA ligase, together with menB - naphtoate synthase, take 2-succinylbenzoate and convert it into 1,4-di-hydroxy-2- naphtoate [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone]. Length = 436
MACS catalyzes the two-step activation of medium chain fatty acids (containing 4-12 carbons). The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. MACS enzymes are localized to mitochondria. Length = 433
Score = 34.9 bits (80), Expect = 0.001
Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 7/51 (13%)
Query: 14 LPDGKTGELCLKG-DVFLGY--RNKVEATKEMLDDDGWLHTGDLAYRLPDG 61
L G+TG L ++G F GY R + +T D +GW TGDLA++ +G
Sbjct: 385 LSQGETGRLLVRGCSNFGGYLKRPHLNST----DAEGWFDTGDLAFQDAEG 431
Members of this protein family are cyclohexanecarboxylate-CoA ligase. This enzyme prepares the aliphatic ring compound, cyclohexanecarboxylate, for dehydrogenation and then degradation by a pathway also used in benzoyl-CoA degradation in Rhodopseudomonas palustris. Length = 538
Score = 33.6 bits (77), Expect = 0.003
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 14 LPDGKTGELCLKGD-VFLGYRNKVEATKEMLDDDGWLHTGDLAYRLPDG 61
+ G+TG L +G F GY E D +G+ +TGDL P+G
Sbjct: 373 VAPGETGMLLTRGPYTFRGYYKAPEHNAAAFDAEGFYYTGDLVRLTPEG 421
Proteins in this family belong to the AMP-binding enzyme family (pfam00501). Members activate 2,3-dihydroxybenzoate (DHB) by ligation of AMP from ATP with the release of pyrophosphate; many are involved in synthesis of siderophores such as enterobactin, vibriobactin, vulnibactin, etc. The most closely related proteine believed to differ in function activates salicylate rather than DHB [Transport and binding proteins, Cations and iron carrying compounds]. Length = 526
>PF00501 AMP-binding: AMP-binding enzyme; InterPro: IPR000873 A number of prokaryotic and eukaryotic enzymes, which appear to act via an ATP-dependent covalent binding of AMP to their substrate, share a region of sequence similarity [, , ]
This region is a Ser/Thr/Gly-rich domain that is further characterised by a conserved Pro-Lys-Gly triplet. The family of enzymes includes luciferase, long chain fatty acid Co-A ligase, acetyl-CoA synthetase and various other closely-related synthetases.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 2V7B_A 2Y4O_B 2VSQ_A 3L8C_B 1RY2_A 3KXW_A 3LNV_A 3ETC_B 3A9U_A 3A9V_A ....
>COG0318 CaiC Acyl-CoA synthetases (AMP-forming)/AMP-acid ligases II [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Proteins in this family belong to the AMP-binding enzyme family (pfam00501). Members activate 2,3-dihydroxybenzoate (DHB) by ligation of AMP from ATP with the release of pyrophosphate; many are involved in synthesis of siderophores such as enterobactin, vibriobactin, vulnibactin, etc. The most closely related proteine believed to differ in function activates salicylate rather than DHB.
Members of this protein family are L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31), product of the LYS2 gene. It is also called alpha-aminoadipate reductase. In fungi, lysine is synthesized via aminoadipate. Currently, all members of this family are fungal.
This model describes acetate-CoA ligase (EC 6.2.1.1), also called acetyl-CoA synthetase and acetyl-activating enzyme. It catalyzes the reaction ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA and belongs to the family of AMP-binding enzymes described by Pfam model pfam00501.
This family contains one of three readily separable clades of proteins in the group of acetate and propionate--CoA ligases. Characterized members of this family act on propionate. From propionyl-CoA, there is a cyclic degradation pathway: it is ligated by PrpC to the TCA cycle intermediate oxaloacetate, acted upon further by PrpD and an aconitase, then cleaved by PrpB to pyruvate and the TCA cycle intermediate succinate.
Members of this protein family are cyclohexanecarboxylate-CoA ligase. This enzyme prepares the aliphatic ring compound, cyclohexanecarboxylate, for dehydrogenation and then degradation by a pathway also used in benzoyl-CoA degradation in Rhodopseudomonas palustris.
This domain is a subset of the AMP-binding domain found in Pfam (pfam00501) which also hits substrate--CoA ligases and luciferases. Sequences scoring in between trusted and noise for this model may be ambiguous as to whether they activate amino acids or other molecules lacking an alpha amino group.
This model represents the enzyme (also called D-alanine-D-alanyl carrier protein ligase) which activates D-alanine as an adenylate via the reaction D-ala + ATP - D-ala-AMP + PPi, and further catalyzes the condensation of the amino acid adenylate with the D-alanyl carrier protein (D-ala-ACP). The D-alanine is then further transferred to teichoic acid in the biosynthesis of lipoteichoic acid (LTA) and wall teichoic acid (WTA) in gram positive bacteria, both polysacchatides.
Characterized members of this protein family include benzoate-CoA ligase, 4-hydroxybenzoate-CoA ligase, 2-aminobenzoate-CoA ligase, etc. Members are related to fatty acid and acetate CoA ligases.
This enzyme catalyzes the first step of the mevalonate pathway of IPP biosynthesis. Most bacteria do not use this pathway, but rather the deoxyxylulose pathway.
PimA, a member of a large family of acyl-CoA ligases, is found in a characteristic operon pimFABCDE for the metabolism of pimelate and related compounds. It is found, so far, in Bradyrhizobium japonicum and several strains of Rhodopseudomonas palustris. PimA from R. palustris was shown to be active as a CoA ligase for C(7) to C(14) dicarboxylates and fatty acids.
This group of proteins contains an AMP-binding domain (pfam00501) associated with acyl CoA-ligases. These proteins are generally found in genomes containing the exosortase/PEP-CTERM protein expoert system, specifically the type 1 variant of this system described by the Genome Property GenProp0652. When found in this context they are invariably present next to a decarboxylase enzyme. A number of sequences from Burkholderia species also hit this model, but the genomic context is obviously different. The hypothesis of a constant substrate for this family is only strong where the exosortase context is present.
This model represents an enzyme, O-succinylbenzoate-CoA ligase, which is involved in the fourth step of the menaquinone biosynthesis pathway. O-succinylbenzoate-CoA ligase, together with menB - naphtoate synthase, take 2-succinylbenzoate and convert it into 1,4-di-hydroxy-2- naphtoate.
Phenylacetate-CoA ligase (PA-CoA ligase) catalyzes the first step in aromatic catabolism of phenylacetic acid (PA) into phenylacetyl-CoA (PA-CoA). Often located in a conserved gene cluster with enzymes involved in phenylacetic acid activation (paaG/H/I/J), phenylacetate-CoA ligase has been found among the proteobacteria as well as in gram positive prokaryotes. In the B-subclass proteobacterium Azoarcus evansii, phenylacetate-CoA ligase has been shown to be induced under aerobic and anaerobic growth conditions. It remains unclear however, whether this induction is due to the same enzyme or to another isoenzyme restricted to specific anaerobic growth conditions.
>PRK09188 serine/threonine protein kinase; Provisional
This enzyme, characterized in Methanobacterium thermoautotrophicum and found in several other methanogens, modifies coenzyme F420 by ligation of AMP (or GMP) from ATP (or GTP). On F420, it activates an aromatic hydroxyl group, which is unusual chemistry for an adenylyltransferase. This enzyme name has been attached to numbers of uncharacterized genes likely to instead act as phenylacetate CoA ligase, based on proximity to predicted indolepyruvate ferredoxin oxidoreductase (1.2.7.8) genes. The enzyme acts during transient exposure of the organism to oxygen.
Ectothiorhodospira halophila. This enzyme is designated 6.2.1.12 and therefore joins a number of plant enzymes linked to lignin biosynthesis and given similar names.
>PF04443 LuxE: Acyl-protein synthetase, LuxE; InterPro: IPR007534 LuxE is an acyl-protein synthetase found in bioluminescent bacteria
LuxE catalyses the formation of an acyl-protein thiolester from a fatty acid and a protein. This is the second step in the bioluminescent fatty acid reduction system, which converts tetradecanoic acid to the aldehyde substrate of the luciferase-catalysed bioluminescence reaction []. A conserved cysteine found at position 364 in Photobacterium phosphoreum LuxE (Q52100 from SWISSPROT) is thought to be acylated during the transfer of the acyl group from the synthetase subunit to the reductase. The C-terminal of the synthetase is though to act as a flexible arm to transfer acyl groups between the sites of activation and reduction []. A LuxE domain is also found in the Vibrio cholerae RBFN protein (Q06961 from SWISSPROT), which is involved in the biosynthesis of the O-antigen component 3-deoxy-L-glycero-tetronic acid. This entry represents the LuxE domain, which is found in archaeal and bacterial proteins.; GO: 0047474 long-chain fatty acid luciferin component ligase activity, 0008218 bioluminescence
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats
These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
>pdb|2D1T|A Chain A, Crystal Structure Of The Thermostable Japanese Firefly Luciferase Red-Color Emission S286n Mutant Complexed With High-Energy Intermediate Analogue Length = 548
>pdb|3O82|A Chain A, Structure Of Base N-Terminal Domain From Acinetobacter Baumannii Bound To 5'-O-[n-(2,3-Dihydroxybenzoyl)sulfamoyl] Adenosine Length = 544
Score = 40.2 bits (95), Expect = 7e-06
Identities = 18/53 (33%), Positives = 22/53 (41%), Gaps = 4/53 (7%)
Query: 14 LPDGKTGELCLKGD-VFLGYRNKVEATKEM-LDDDG-WL-HTGDLAYRLPDGT 62
L G+ GE+ + G V GY N E T E G HTGD+ D
Sbjct: 343 LSSGEQGEIIVTGPAVSKGYLNNPEKTAEAFFTFKGQPAYHTGDIGSLTEDNI 395
