Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases family

SCOP classification

• Root: SCOP hierarchy in SUPERFAMILY [ 0] (11)
• Class: All alpha proteins [ 46456] (284)
• Fold: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [ 47322]
• Superfamily: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [ 47323]
• Family: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases [ 47324] (6)

---

Family statistics

	Genomes (3,030)	Uniprot 2018_03 genome	PDB chains (SCOP 1.75)
Domains	6,863	53,223	14
Proteins	6,863	53,219	14

---

Enzyme Commission (EC)

Highlighted in gray are those with FDR_all>0.001

	EC term	FDR (all)	IC level	SDEO level	Annotation (direct or inherited)
Enzyme Commission (EC)	Cysteine--tRNA ligase	0	2.44	--	DIRECT
Enzyme Commission (EC)	Isoleucine--tRNA ligase	0	2.264	--	DIRECT
Enzyme Commission (EC)	Leucine--tRNA ligase	0	2.264	--	DIRECT
Enzyme Commission (EC)	Forming carbon-oxygen bonds	0	1.25	--	DIRECT
Enzyme Commission (EC)	Arginine--tRNA ligase	0	2.264	--	DIRECT
Enzyme Commission (EC)	ligase	0.000239	2.44	--	DIRECT
Enzyme Commission (EC)	Ligases	0	0.7455	Least Informative	DIRECT
Enzyme Commission (EC)	Ligases forming aminoacyl-tRNA and related compoun	0	1.25	Moderately Informative	DIRECT
Enzyme Commission (EC)	Forming carbon-nitrogen bonds	1	0.993	Moderately Informative	INHERITED FROM: ligase
Enzyme Commission (EC)	Valine--tRNA ligase	0	2.139	Highly Informative	DIRECT
Enzyme Commission (EC)	Methionine--tRNA ligase	0	2.139	Highly Informative	DIRECT
Enzyme Commission (EC)	Acid--ammonia (or amide) ligases (amide synthases)	0.9667	1.963	Highly Informative	INHERITED FROM: ligase

---

Human Phenotype (HP)

Highlighted in gray are those with FDR_all>0.001

	HP term	FDR (all)	IC level	SDHP level	Annotation (direct or inherited)
	Variable expressivity	0	0.04347	--	DIRECT
	Phenotypic variability	1	0	--	INHERITED FROM: Variable expressivity
Mode of Inheritance (MI)	Autosomal recessive inheritance	0	0.2218	--	DIRECT
Phenotypic Abnormality (PA)	Abnormality of the nervous system	0	0.2371	--	DIRECT
Phenotypic Abnormality (PA)	Global developmental delay	0.0001341	1.232	--	DIRECT
Phenotypic Abnormality (PA)	Abnormality of acid-base homeostasis	0.0004212	1.258	--	DIRECT
Phenotypic Abnormality (PA)	Abnormal muscle tone	0.0006793	0.8942	--	DIRECT
Phenotypic Abnormality (PA)	Storage in hepatocytes	0.001056	1.86	--	INHERITED FROM: Hepatic steatosis
Phenotypic Abnormality (PA)	Abnormal muscle physiology	0.003644	0.6915	--	INHERITED FROM: Abnormal muscle tone
Phenotypic Abnormality (PA)	Abnormality of hepatobiliary system physiology	0.006531	2.161	--	INHERITED FROM: Decreased liver function
Phenotypic Abnormality (PA)	Neurodevelopmental abnormality	0.1034	0.7381	--	INHERITED FROM: Global developmental delay || Neurodevelopmental delay
Phenotypic Abnormality (PA)	Abnormality of the liver	0.2627	1.383	--	INHERITED FROM: Hepatic steatosis
Phenotypic Abnormality (PA)	Lipid accumulation in hepatocytes	1	1.86	--	INHERITED FROM: Hepatic steatosis
Phenotypic Abnormality (PA)	Abnormality of nervous system physiology	0	0.3869	Least Informative	DIRECT
Phenotypic Abnormality (PA)	Abnormality of the musculature	0.0115	0.5433	Least Informative	INHERITED FROM: Abnormal muscle tone
Phenotypic Abnormality (PA)	Abnormality of the digestive system	0.01288	0.5759	Least Informative	INHERITED FROM: Hepatic steatosis || Decreased liver function
Phenotypic Abnormality (PA)	Abnormality of metabolism/homeostasis	0.4811	0.5486	Least Informative	INHERITED FROM: Acidosis || Abnormality of acid-base homeostasis
Phenotypic Abnormality (PA)	Neurodevelopmental delay	0.0007929	0.9853	Moderately Informative	DIRECT
Phenotypic Abnormality (PA)	Abnormality of digestive system physiology	0.001015	0.9572	Moderately Informative	INHERITED FROM: Decreased liver function
Phenotypic Abnormality (PA)	Abnormal homeostasis	0.1263	0.7903	Moderately Informative	INHERITED FROM: Acidosis || Abnormality of acid-base homeostasis
Phenotypic Abnormality (PA)	Abnormality of the abdominal organs	0.7568	1.031	Moderately Informative	INHERITED FROM: Hepatic steatosis
Phenotypic Abnormality (PA)	Acidosis	0.0002599	1.383	Informative	DIRECT
Phenotypic Abnormality (PA)	Abnormal liver morphology	0.166	1.508	Informative	INHERITED FROM: Hepatic steatosis
Phenotypic Abnormality (PA)	Decreased liver function	0.0002528	2.161	Highly Informative	DIRECT
Phenotypic Abnormality (PA)	Hepatic steatosis	0.0008564	1.86	Highly Informative	DIRECT

---

Worm Phenotype (WP)

Highlighted in gray are those with FDR_all>0.001

	WP term	FDR (all)	IC level	SDWP level	Annotation (direct or inherited)
Worm Phenotype (WP)	growth variant	0	0.3438	--	DIRECT
Worm Phenotype (WP)	embryonic lethal	0	0.046	--	DIRECT
Worm Phenotype (WP)	lethal	0	0.00521	--	DIRECT
Worm Phenotype (WP)	fertility variant	0	0.05937	--	DIRECT
Worm Phenotype (WP)	development variant	0	0.001482	--	DIRECT
Worm Phenotype (WP)	organism development variant	0	0.00297	--	DIRECT
Worm Phenotype (WP)	organ system physiology variant	0	0.04518	--	DIRECT
Worm Phenotype (WP)	organism physiology variant	0	0.1342	--	DIRECT
Worm Phenotype (WP)	organism homeostasis metabolism variant	0	0.1444	--	DIRECT
Worm Phenotype (WP)	reproductive system physiology variant	0	0.05515	--	DIRECT
Worm Phenotype (WP)	embryonic development variant	0	0.04518	--	DIRECT
Worm Phenotype (WP)	fertility reduced	0	0.06449	--	DIRECT
Worm Phenotype (WP)	hypoxia resistant	0	2.07	--	DIRECT
Worm Phenotype (WP)	oxygen response variant	0.000000001962	1.99	--	DIRECT
Worm Phenotype (WP)	other abnormality early emb	0.00001974	1.99	--	DIRECT
Worm Phenotype (WP)	pachytene region organization variant	0.0001608	1.727	--	DIRECT
Worm Phenotype (WP)	receptor mediated endocytosis defective	0.0003246	1.689	--	DIRECT
Worm Phenotype (WP)	oocyte physiology variant	0.0003831	1.593	--	DIRECT
Worm Phenotype (WP)	meiotic progression prophase variant	0.0008356	1.407	--	DIRECT
Worm Phenotype (WP)	sexually dimorphic physiology variant	0.0008402	1.426	--	DIRECT
Worm Phenotype (WP)	endocytic transport variant	0.001455	1.354	--	INHERITED FROM: receptor mediated endocytosis defective
Worm Phenotype (WP)	meiotic progression during oogenesis variant	0.001461	1.321	--	INHERITED FROM: pachytene progression during oogenesis variant || meiotic progression prophase variant || diplotene progression during oogenesis variant || pachytene region organization variant
Worm Phenotype (WP)	germ cell compartment morphology variant	0.001895	1.354	--	INHERITED FROM: germ cell compartment expansion variant
Worm Phenotype (WP)	meiosis variant	0.007103	1.263	--	INHERITED FROM: pachytene progression during oogenesis variant || meiotic progression prophase variant || pachytene region organization variant || diplotene progression during oogenesis variant
Worm Phenotype (WP)	gonad morphology variant	0.00806	1.306	--	INHERITED FROM: pachytene region organization variant || rachis morphology variant
Worm Phenotype (WP)	gene expression variant	0.01318	0.6256	--	INHERITED FROM: transgene expression increased || level of transgene expression variant || protein expression reduced
Worm Phenotype (WP)	cell morphology variant	0.02356	0.7558	--	INHERITED FROM: oocyte number decreased || germ cell compartment expansion variant
Worm Phenotype (WP)	germ cell morphology variant	0.02418	1.156	--	INHERITED FROM: oocyte number decreased || germ cell compartment expansion variant
Worm Phenotype (WP)	vesicle trafficking variant	0.0376	1.354	--	INHERITED FROM: receptor mediated endocytosis defective
Worm Phenotype (WP)	oogenesis variant	0.07565	1.237	--	INHERITED FROM: pachytene progression during oogenesis variant || pachytene region organization variant || oocyte number decreased || meiotic progression prophase variant || diplotene progression during oogenesis variant
Worm Phenotype (WP)	organ system morphology variant	0.2502	0.7516	--	INHERITED FROM: rachis morphology variant || pachytene region organization variant
Worm Phenotype (WP)	gametogenesis variant	0.4879	1.013	--	INHERITED FROM: pachytene progression during oogenesis variant || meiotic progression prophase variant || pachytene region organization variant || diplotene progression during oogenesis variant || oocyte number decreased
Worm Phenotype (WP)	transgene expression variant	0.4962	0.773	--	INHERITED FROM: transgene expression increased || level of transgene expression variant
Worm Phenotype (WP)	physiology variant	1	0	--	INHERITED FROM: hypoxia response variant || hypoxia resistant || reproductive system physiology variant || pleiotropic defects severe early emb || diplotene progression during oogenesis variant || organism homeostasis metabolism variant || oocyte number decreased || lethal || organism physiology variant || oocyte physiology variant || sexually dimorphic physiology variant || organism stress response variant || cell differentiation variant || development variant || organism environmental stimulus response variant || growth variant || embryonic development variant || embryonic lethal || fertility variant || protein expression reduced || other abnormality early emb || pachytene progression during oogenesis variant || meiotic progression prophase variant || organ system physiology variant || oxygen response variant || organism development variant || level of transgene expression variant || hermaphrodite physiology variant || receptor mediated endocytosis defective || fertility reduced || transgene expression increased || pachytene region organization variant || cell development variant
Worm Phenotype (WP)	morphology variant	1	0.046	--	INHERITED FROM: rachis morphology variant || pachytene region organization variant || oocyte number decreased || germ cell compartment expansion variant
Worm Phenotype (WP)	cell development variant	0.00006127	0.6752	Least Informative	DIRECT
Worm Phenotype (WP)	organism environmental stimulus response variant	0.0005805	0.6614	Least Informative	DIRECT
Worm Phenotype (WP)	cell physiology variant	0.00312	0.5955	Least Informative	INHERITED FROM: oocyte physiology variant || diplotene progression during oogenesis variant || pachytene progression during oogenesis variant || meiotic progression prophase variant || pachytene region organization variant || receptor mediated endocytosis defective
Worm Phenotype (WP)	organism metabolism processing variant	0.06724	0.4899	Least Informative	INHERITED FROM: transgene expression increased || protein expression reduced || level of transgene expression variant
Worm Phenotype (WP)	organism stress response variant	0.000002817	0.9693	Moderately Informative	DIRECT
Worm Phenotype (WP)	level of transgene expression variant	0.0008629	1.125	Moderately Informative	DIRECT
Worm Phenotype (WP)	germ cell differentiation variant	0.001192	1.167	Moderately Informative	INHERITED FROM: meiotic progression prophase variant || oocyte number decreased || diplotene progression during oogenesis variant || pachytene progression during oogenesis variant || pachytene region organization variant
Worm Phenotype (WP)	early embryonic lethal	0.01498	1.178	Moderately Informative	INHERITED FROM: pleiotropic defects severe early emb || other abnormality early emb
Worm Phenotype (WP)	reproductive system morphology variant	0.06482	1.078	Moderately Informative	INHERITED FROM: pachytene region organization variant || rachis morphology variant
Worm Phenotype (WP)	cell cycle variant	0.1401	1.225	Moderately Informative	INHERITED FROM: diplotene progression during oogenesis variant || pachytene region organization variant || meiotic progression prophase variant || pachytene progression during oogenesis variant
Worm Phenotype (WP)	protein expression variant	0.156	1.125	Moderately Informative	INHERITED FROM: protein expression reduced
Worm Phenotype (WP)	cell division variant	0.3667	1.036	Moderately Informative	INHERITED FROM: meiotic progression prophase variant || pachytene progression during oogenesis variant || pachytene region organization variant || diplotene progression during oogenesis variant
Worm Phenotype (WP)	cell type morphology variant	0.7911	0.8878	Moderately Informative	INHERITED FROM: germ cell compartment expansion variant || oocyte number decreased
Worm Phenotype (WP)	germ cell development variant	1	1.013	Moderately Informative	INHERITED FROM: pachytene region organization variant || oocyte number decreased || diplotene progression during oogenesis variant || pachytene progression during oogenesis variant || meiotic progression prophase variant
Worm Phenotype (WP)	transgene expression increased	0.00002743	1.426	Informative	DIRECT
Worm Phenotype (WP)	pachytene progression during oogenesis variant	0.0002637	1.565	Informative	DIRECT
Worm Phenotype (WP)	diplotene progression during oogenesis variant	0.0002637	1.655	Informative	DIRECT
Worm Phenotype (WP)	hermaphrodite physiology variant	0.000483	1.446	Informative	DIRECT
Worm Phenotype (WP)	germ cell compartment expansion variant	0.0008591	1.468	Informative	DIRECT
Worm Phenotype (WP)	rachis morphology variant	0.0009067	1.623	Informative	DIRECT
Worm Phenotype (WP)	germ cell physiology variant	0.001067	1.49	Informative	INHERITED FROM: oocyte physiology variant || receptor mediated endocytosis defective
Worm Phenotype (WP)	endocytic transport defect	0.001334	1.407	Informative	INHERITED FROM: receptor mediated endocytosis defective
Worm Phenotype (WP)	level of protein expression variant	0.001411	1.689	Informative	INHERITED FROM: protein expression reduced
Worm Phenotype (WP)	oocyte morphology variant	0.003817	1.292	Informative	INHERITED FROM: oocyte number decreased
Worm Phenotype (WP)	cell differentiation variant	0.0000000007219	1.99	Highly Informative	DIRECT
Worm Phenotype (WP)	hypoxia response variant	0.00000002962	1.99	Highly Informative	DIRECT
Worm Phenotype (WP)	pleiotropic defects severe early emb	0.00001247	1.99	Highly Informative	DIRECT
Worm Phenotype (WP)	oocyte number decreased	0.0002587	1.924	Highly Informative	DIRECT
Worm Phenotype (WP)	protein expression reduced	0.0005635	1.814	Highly Informative	DIRECT

---

Yeast Phenotype (YP)

Highlighted in gray are those with FDR_all>0.001

	YP term	FDR (all)	IC level	SDYP level	Annotation (direct or inherited)
Yeast Phenotype (YP)	cellular processes	0	0.09186	--	DIRECT
Yeast Phenotype (YP)	stress resistance	0	0.1452	--	DIRECT
Yeast Phenotype (YP)	competitive fitness	0	0.1116	--	DIRECT
Yeast Phenotype (YP)	fitness	0	0.1096	--	DIRECT
Yeast Phenotype (YP)	resistance to chemicals	0	0.3202	Least Informative	DIRECT

---

Fly Anatomy (FA)

Highlighted in gray are those with FDR_all>0.001

	FA term	FDR (all)	IC level	SDFA level	Annotation (direct or inherited)
Fly Anatomy (FA)	organism	0	0.06695	--	DIRECT
Fly Anatomy (FA)	multicellular structure	0	0.008955	--	DIRECT
Fly Anatomy (FA)	anatomical structure	1	0	--	INHERITED FROM: organism || larva || multicellular structure
Fly Anatomy (FA)	material anatomical entity	1	0	--	INHERITED FROM: multicellular structure || larva || organism
Fly Anatomy (FA)	larva	0	0.3763	Least Informative	DIRECT

---

Zebrafish Anatomy (ZA)

Highlighted in gray are those with FDR_all>0.001

	ZA term	FDR (all)	IC level	SDZA level	Annotation (direct or inherited)
Zebrafish Anatomy (ZA)	compound organ	0	0.4299	--	DIRECT
Zebrafish Anatomy (ZA)	whole organism	0	0.00147	--	DIRECT
Zebrafish Anatomy (ZA)	anatomical system	0	0.1857	--	DIRECT
Zebrafish Anatomy (ZA)	anatomical group	0	0.1532	--	DIRECT
Zebrafish Anatomy (ZA)	anatomical structure	1	0	--	INHERITED FROM: anatomical system || anatomical group || whole organism || compound organ || cavitated compound organ || nervous system
Zebrafish Anatomy (ZA)	nervous system	0	0.7079	Least Informative	DIRECT
Zebrafish Anatomy (ZA)	cavitated compound organ	0	0.5123	Least Informative	DIRECT

---

Xenopus Anatomy (XA)

Highlighted in gray are those with FDR_all>0.001

	XA term	FDR (all)	IC level	SDXA level	Annotation (direct or inherited)
Xenopus ANatomical entity (XAN)	genital system	0	0.5751	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical structure	0	0	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical group	0	0.1408	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical system	1	0.283	--	INHERITED FROM: urogenital system || genital system
Xenopus ANatomical entity (XAN)	whole organism	1	0.0884	--	INHERITED FROM: urogenital system || genital system || anatomical group
Xenopus ANatomical entity (XAN)	urogenital system	0	0.4777	Least Informative	DIRECT
Xenopus DEvelopment stage (XDE)	NF stage	0	0.01895	--	DIRECT

---

Arabidopsis Plant Ontology (AP)

Highlighted in gray are those with FDR_all>0.001

	AP term	FDR (all)	IC level	SDAP level	Annotation (direct or inherited)
Plant ANatomical entity (PAN)	whole plant	0	0.3507	--	DIRECT
Plant ANatomical entity (PAN)	guard cell	0	0.2279	--	DIRECT
Plant ANatomical entity (PAN)	stomatal complex	0	0.2279	--	DIRECT
Plant ANatomical entity (PAN)	epidermal cell	0	0.2152	--	DIRECT
Plant ANatomical entity (PAN)	epidermis	0	0.2046	--	DIRECT
Plant ANatomical entity (PAN)	phyllome	0	0.3234	--	DIRECT
Plant ANatomical entity (PAN)	shoot epidermis	0	0.2224	--	DIRECT
Plant ANatomical entity (PAN)	plant cell	0	0.1228	--	DIRECT
Plant ANatomical entity (PAN)	shoot system	0	0.05272	--	DIRECT
Plant ANatomical entity (PAN)	portion of plant tissue	0	0.1621	--	DIRECT
Plant ANatomical entity (PAN)	plant organ	0	0.2391	--	DIRECT
Plant ANatomical entity (PAN)	sporophyll	0	0.3985	--	DIRECT
Plant ANatomical entity (PAN)	shoot epidermal cell	0	0.227	--	DIRECT
Plant ANatomical entity (PAN)	multi-tissue plant structure	0	0.2335	--	DIRECT
Plant ANatomical entity (PAN)	collective plant structure	0	0.01555	--	DIRECT
Plant ANatomical entity (PAN)	plant structure	1	0	--	INHERITED FROM: sporophyll || collective plant structure || phyllome || multi-tissue plant structure || guard cell || shoot system || portion of plant tissue || stomatal complex || plant organ || whole plant || epidermis || epidermal cell || shoot epidermal cell || plant cell || shoot epidermis
Plant ANatomical entity (PAN)	collective plant organ structure	1	0.03998	--	INHERITED FROM: sporophyll || phyllome || guard cell || shoot epidermal cell || stomatal complex || shoot system || shoot epidermis
Plant structure DEvelopment stage (PDE)	floral organ differentiation stage	0	0.07163	--	DIRECT
Plant structure DEvelopment stage (PDE)	collective plant organ structure development stage	0	0.0282	--	DIRECT
Plant structure DEvelopment stage (PDE)	plant organ development stage	0	0.06127	--	DIRECT
Plant structure DEvelopment stage (PDE)	reproductive shoot system development stage	0	0.0371	--	DIRECT
Plant structure DEvelopment stage (PDE)	collective phyllome structure development stage	0	0.07163	--	DIRECT
Plant structure DEvelopment stage (PDE)	floral organ formation stage	0	0.07163	--	DIRECT
Plant structure DEvelopment stage (PDE)	sporophyte vegetative stage	0.4841	0.1593	--	INHERITED FROM: 0 seed germination stage
Plant structure DEvelopment stage (PDE)	whole plant development stage	0.4876	0.1547	--	INHERITED FROM: 0 seed germination stage
Plant structure DEvelopment stage (PDE)	flower development stage	1	0.05402	--	INHERITED FROM: floral organ differentiation stage || floral organ formation stage
Plant structure DEvelopment stage (PDE)	life of whole plant stage	1	0.1584	--	INHERITED FROM: 0 seed germination stage
Plant structure DEvelopment stage (PDE)	shoot system development stage	1	0.02956	--	INHERITED FROM: reproductive shoot system development stage || floral organ formation stage || floral organ differentiation stage || plant organ development stage
Plant structure DEvelopment stage (PDE)	sporophyte development stage	1	0.1584	--	INHERITED FROM: 0 seed germination stage
Plant structure DEvelopment stage (PDE)	0 seed germination stage	0.000006253	1.689	Informative	DIRECT

---

Enzyme Commission (EC)

Highlighted in gray are those with FDR_all>0.001

	EC term	FDR (all)	IC level	SDEC level	Annotation (direct or inherited)
Enzyme Commission (EC)	Methionine--tRNA ligase	0	2.628	--	DIRECT
Enzyme Commission (EC)	Cysteine--tRNA ligase	0	2.929	--	DIRECT
Enzyme Commission (EC)	Arginine--tRNA ligase	0	2.753	--	DIRECT
Enzyme Commission (EC)	Leucine--tRNA ligase	0	2.753	--	DIRECT
Enzyme Commission (EC)	Isoleucine--tRNA ligase	0	2.753	--	DIRECT
Enzyme Commission (EC)	Valine--tRNA ligase	0	2.628	--	DIRECT
Enzyme Commission (EC)	ligase	0.0001392	2.929	--	DIRECT
Enzyme Commission (EC)	Ligases	0	1.14	Moderately Informative	DIRECT
Enzyme Commission (EC)	Forming carbon-oxygen bonds	0	1.738	Informative	DIRECT
Enzyme Commission (EC)	Forming carbon-nitrogen bonds	1	1.338	Informative	INHERITED FROM: ligase
Enzyme Commission (EC)	Ligases forming aminoacyl-tRNA and related compounds	0	1.753	Highly Informative	DIRECT
Enzyme Commission (EC)	Acid--ammonia (or amine) ligases (amide synthases)	0.9868	2.188	Highly Informative	INHERITED FROM: ligase

---