Ribonuclease H-like superfamily

SCOP classification

• Root: SCOP hierarchy in SUPERFAMILY [ 0] (11)
• Class: Alpha and beta proteins (a/b) [ 51349] (147)
• Fold: Ribonuclease H-like motif [ 53066] (7)
• Superfamily: Ribonuclease H-like [ 53098] (14)
• Families:
  • Ribonuclease H [ 53099] (4)
  • Retroviral integrase, catalytic domain [ 53107]
  • mu transposase, core domain [ 53112]
  • Transposase inhibitor (Tn5 transposase) [ 53115]
  • DnaQ-like 3'-5' exonuclease [ 53118] (15)
  • RuvC resolvase [ 53134]
  • Mitochondrial resolvase ydc2 catalytic domain [ 69533]
  • Putative Holliday junction resolvase RuvX [ 102485] (3)
  • CAF1-like ribonuclease [ 102492] (2)
  • PIWI domain [ 110640] (3)
  • TM1739-like [ 142505]
  • Hermes transposase-like [ 142508]
  • Tex RuvX-like domain-like [ 159635]
  • Prp8 beta-finger domain-like [ 159638]

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Superfamily statistics

	Genomes (3,259)	Uniprot 2018_03 genome	PDB chains (SCOP 1.75)
Domains	132,337	626,221	182
Proteins	128,491	598,729	182

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Functional annotation

• General category: Metabolism
• Detailed category: Nucleotide metabolism and transport

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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)	Exoribonucleases producing 5'-phosphomonoesters	0	1.305	--	DIRECT
Enzyme Commission (EC)	Transferring phosphorous-containing groups	0	0.2175	--	DIRECT
Enzyme Commission (EC)	Hydrolases	0	0.04271	--	DIRECT
Enzyme Commission (EC)	Endodeoxyribonucleases producing other than 5'-pho	0	2.259	--	DIRECT
Enzyme Commission (EC)	HIV-1 retropepsin	0	1.657	--	DIRECT
Enzyme Commission (EC)	Exodeoxyribonuclease I	0.0000000003654	2.56	--	DIRECT
Enzyme Commission (EC)	HIV-2 retropepsin	0.00002448	1.657	--	DIRECT
Enzyme Commission (EC)	Exodeoxyribonucleases producing 5'-phosphomonoeste	1	1.782	--	INHERITED FROM: Exodeoxyribonuclease III || Exodeoxyribonuclease I
Enzyme Commission (EC)	Transferases	1	0	--	INHERITED FROM: RNA-directed DNA polymerase || Nucleotidyltransferases || DNA-directed DNA polymerase || Transferring phosphorous-containing groups
Enzyme Commission (EC)	Nucleotidyltransferases	0	0.6105	Least Informative	DIRECT
Enzyme Commission (EC)	Acting on ester bonds	0	0.4665	Least Informative	DIRECT
Enzyme Commission (EC)	Acting on peptide bonds (peptide hydrolases)	1	0.5513	Least Informative	INHERITED FROM: Aspartic endopeptidases || HIV-2 retropepsin || HIV-1 retropepsin
Enzyme Commission (EC)	Endoribonucleases producing 5'-phosphomonoesters	0	1.238	Moderately Informative	DIRECT
Enzyme Commission (EC)	DNA-directed DNA polymerase	0	1.238	Moderately Informative	DIRECT
Enzyme Commission (EC)	Aspartic endopeptidases	0	1.56	Informative	DIRECT
Enzyme Commission (EC)	RNA-directed DNA polymerase	0	1.519	Informative	DIRECT
Enzyme Commission (EC)	Exoribonuclease H	0.0000000008901	1.56	Informative	DIRECT
Enzyme Commission (EC)	Retroviral ribonuclease H	0.000000001817	1.56	Informative	DIRECT
Enzyme Commission (EC)	Ribonuclease H	0	2.083	Highly Informative	DIRECT
Enzyme Commission (EC)	Exodeoxyribonuclease III	0.000005258	2.083	Highly Informative	DIRECT

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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)
Phenotypic Abnormality (PA)	Abnormality of male external genitalia	0.0000476	1.293	--	DIRECT
Phenotypic Abnormality (PA)	Demyelinating peripheral neuropathy	0.00005167	2.407	--	DIRECT
Phenotypic Abnormality (PA)	Abnormal external genitalia	0.00006654	1.23	--	DIRECT
Phenotypic Abnormality (PA)	Abnormality of the male genitalia	0.00007008	1.26	--	DIRECT
Phenotypic Abnormality (PA)	Glucose intolerance	0.00007283	1.804	--	DIRECT
Phenotypic Abnormality (PA)	Abnormality of the genital system	0.0001516	0.8625	--	DIRECT
Phenotypic Abnormality (PA)	Hypogonadism	0.0005868	1.628	--	DIRECT
Phenotypic Abnormality (PA)	Progressive microcephaly	0.0007265	2.407	--	DIRECT
Phenotypic Abnormality (PA)	Abnormal glucose homeostasis	0.01045	1.365	--	INHERITED FROM: Glucose intolerance
Phenotypic Abnormality (PA)	Abnormal adipose tissue morphology	0.01159	1.708	--	INHERITED FROM: Lipodystrophy
Phenotypic Abnormality (PA)	Abnormal axial skeleton morphology	0.01203	0.7344	--	INHERITED FROM: Progressive microcephaly
Phenotypic Abnormality (PA)	Abnormality of head or neck	0.0158	0.472	--	INHERITED FROM: Progressive microcephaly
Phenotypic Abnormality (PA)	Neoplasm of the breast	0.01732	2.106	--	INHERITED FROM: Breast carcinoma
Phenotypic Abnormality (PA)	Abnormality of the breast	0.01778	1.708	--	INHERITED FROM: Breast carcinoma
Phenotypic Abnormality (PA)	Decreased head circumference	0.02005	1.561	--	INHERITED FROM: Progressive microcephaly
Phenotypic Abnormality (PA)	Neoplasm by anatomical site	0.03135	1.151	--	INHERITED FROM: Breast carcinoma
Phenotypic Abnormality (PA)	Aplasia/Hypoplasia of the cerebrum	0.04568	1.293	--	INHERITED FROM: Progressive microcephaly
Phenotypic Abnormality (PA)	Abnormal homeostasis	0.06162	0.7631	--	INHERITED FROM: Glucose intolerance
Phenotypic Abnormality (PA)	Abnormality of the skeletal system	0.06173	0.4621	--	INHERITED FROM: Progressive microcephaly
Phenotypic Abnormality (PA)	Abnormality of the nervous system	0.09278	0.2543	--	INHERITED FROM: Demyelinating peripheral neuropathy || Progressive microcephaly
Phenotypic Abnormality (PA)	Abnormality of the cerebrum	0.1371	1.009	--	INHERITED FROM: Progressive microcephaly
Phenotypic Abnormality (PA)	Abnormal peripheral nervous system morphology	0.2601	1.26	--	INHERITED FROM: Demyelinating peripheral neuropathy
Phenotypic Abnormality (PA)	Abnormality of skull size	0.2976	1.26	--	INHERITED FROM: Progressive microcephaly
Phenotypic Abnormality (PA)	Puberty and gonadal disorders	0.4185	1.23	--	INHERITED FROM: Hypogonadism
Phenotypic Abnormality (PA)	Morphological abnormality of the central nervous system	0.5164	0.6284	--	INHERITED FROM: Progressive microcephaly
Phenotypic Abnormality (PA)	Abnormality of brain morphology	0.5313	0.7731	--	INHERITED FROM: Progressive microcephaly
Phenotypic Abnormality (PA)	Abnormality of the genitourinary system	0.01283	0.5432	Least Informative	INHERITED FROM: Abnormality of the male genitalia || Abnormal external genitalia || Abnormality of the genital system || Hypogonadism || Abnormality of male external genitalia
Phenotypic Abnormality (PA)	Abnormality of the head	0.01466	0.4771	Least Informative	INHERITED FROM: Progressive microcephaly
Phenotypic Abnormality (PA)	Abnormality of skeletal morphology	0.04756	0.472	Least Informative	INHERITED FROM: Progressive microcephaly
Phenotypic Abnormality (PA)	Abnormality of metabolism/homeostasis	0.1183	0.5315	Least Informative	INHERITED FROM: Glucose intolerance
Phenotypic Abnormality (PA)	Abnormality of nervous system morphology	0.1231	0.5677	Least Informative	INHERITED FROM: Demyelinating peripheral neuropathy || Progressive microcephaly
Phenotypic Abnormality (PA)	Abnormality of the endocrine system	0.000462	0.9594	Moderately Informative	DIRECT
Phenotypic Abnormality (PA)	Neoplasm	0.03793	1.106	Moderately Informative	INHERITED FROM: Breast carcinoma
Phenotypic Abnormality (PA)	Abnormality of connective tissue	0.05586	1.128	Moderately Informative	INHERITED FROM: Lipodystrophy
Phenotypic Abnormality (PA)	Abnormal skull morphology	0.3171	1.009	Moderately Informative	INHERITED FROM: Progressive microcephaly
Phenotypic Abnormality (PA)	Aplasia/Hypoplasia involving the central nervous system	0.337	1.128	Moderately Informative	INHERITED FROM: Progressive microcephaly
Phenotypic Abnormality (PA)	Abnormal reproductive system morphology	0.467	0.9594	Moderately Informative	INHERITED FROM: Abnormality of male external genitalia || Abnormality of the male genitalia || Abnormal external genitalia
Phenotypic Abnormality (PA)	Abnormality of forebrain morphology	0.4741	0.9916	Moderately Informative	INHERITED FROM: Progressive microcephaly
Phenotypic Abnormality (PA)	Abnormality of the voice	0.00009786	1.628	Informative	DIRECT
Phenotypic Abnormality (PA)	Lipodystrophy	0.0002335	1.708	Informative	DIRECT
Phenotypic Abnormality (PA)	Abnormal breast morphology	0.01738	1.708	Informative	INHERITED FROM: Breast carcinoma
Phenotypic Abnormality (PA)	Microcephaly	0.01942	1.561	Informative	INHERITED FROM: Progressive microcephaly
Phenotypic Abnormality (PA)	Abnormality of reproductive system physiology	0.2267	1.452	Informative	INHERITED FROM: Hypogonadism
Phenotypic Abnormality (PA)	Peripheral neuropathy	0.3142	1.561	Informative	INHERITED FROM: Demyelinating peripheral neuropathy
Phenotypic Abnormality (PA)	Breast carcinoma	0.0008246	2.106	Highly Informative	DIRECT
Phenotypic Abnormality (PA)	Postnatal microcephaly	0.04838	2.106	Highly Informative	INHERITED FROM: Progressive microcephaly
Phenotypic Abnormality (PA)	Abnormal myelination	0.2295	1.929	Highly Informative	INHERITED FROM: Demyelinating peripheral neuropathy

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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)	lethal	0	0.01121	--	DIRECT
Worm Phenotype (WP)	development variant	0	0.001706	--	DIRECT
Worm Phenotype (WP)	organism development variant	0	0.004279	--	DIRECT
Worm Phenotype (WP)	21U RNA expression variant	0.000000000001218	2.407	--	DIRECT
Worm Phenotype (WP)	siRNA expression variant	0.00000003158	2.407	--	DIRECT
Worm Phenotype (WP)	somatic transgene silencing variant	0.00001235	2.407	--	DIRECT
Worm Phenotype (WP)	RNAi enhanced	0.0002058	2.407	--	DIRECT
Worm Phenotype (WP)	gene expression variant	0.5967	0.6038	--	INHERITED FROM: siRNA expression variant || 21U RNA expression variant || RNA expression variant
Worm Phenotype (WP)	organism physiology variant	0.8165	0.1405	--	INHERITED FROM: RNAi enhanced || siRNA expression variant || 21U RNA expression variant || somatic transgene silencing variant || RNA expression variant || maintenance of gene silencing variant || RNAi response variant
Worm Phenotype (WP)	organism homeostasis metabolism variant	0.8829	0.1501	--	INHERITED FROM: siRNA expression variant || RNAi enhanced || maintenance of gene silencing variant || RNA expression variant || 21U RNA expression variant || somatic transgene silencing variant || RNAi response variant
Worm Phenotype (WP)	physiology variant	1	0	--	INHERITED FROM: RNAi response variant || RNAi enhanced || siRNA expression variant || RNA expression variant || maintenance of gene silencing variant || lethal || 21U RNA expression variant || development variant || somatic transgene silencing variant || organism development variant
Worm Phenotype (WP)	organism metabolism processing variant	0.8533	0.4572	Least Informative	INHERITED FROM: siRNA expression variant || RNA expression variant || 21U RNA expression variant
Worm Phenotype (WP)	RNA expression variant	0.000000002584	1.407	Informative	DIRECT
Worm Phenotype (WP)	maintenance of gene silencing variant	0.00000008421	1.666	Informative	DIRECT
Worm Phenotype (WP)	RNAi response variant	0.00000000008595	1.804	Highly Informative	DIRECT
Worm Phenotype (WP)	transgene silencing variant	0.5247	2.106	Highly Informative	INHERITED FROM: somatic transgene silencing variant

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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	0.1328	--	DIRECT

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Fly Phenotype (FP)

Highlighted in gray are those with FDR_all>0.001

	FP term	FDR (all)	IC level	SDFP level	Annotation (direct or inherited)
Fly Phenotype (FP)	melanotic mass phenotype	0.0001318	2.303	--	DIRECT
Fly Phenotype (FP)	phenotype	0.5939	0.05522	--	INHERITED FROM: melanotic mass phenotype

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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	0.07918	--	DIRECT
Fly Anatomy (FA)	multicellular structure	0	0.009143	--	DIRECT
Fly Anatomy (FA)	anatomical structure	1	0	--	INHERITED FROM: organism || multicellular structure
Fly Anatomy (FA)	material anatomical entity	1	0	--	INHERITED FROM: multicellular structure || organism

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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)	whole organism	0	0.004764	--	DIRECT
Zebrafish Anatomy (ZA)	anatomical structure	1	0	--	INHERITED FROM: whole organism

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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)	anatomical structure	0	0	--	DIRECT
Xenopus ANatomical entity (XAN)	male organism	0.000002222	0.8318	--	DIRECT
Xenopus ANatomical entity (XAN)	gonad	0.0000163	0.8318	--	DIRECT
Xenopus ANatomical entity (XAN)	genital system	0.00006878	0.5909	--	DIRECT
Xenopus ANatomical entity (XAN)	trunk region	0.0004476	0.4287	--	DIRECT
Xenopus ANatomical entity (XAN)	male genitalia	0.008966	0.8318	--	INHERITED FROM: testis
Xenopus ANatomical entity (XAN)	compound organ	0.06815	0.24	--	INHERITED FROM: gonad || testis
Xenopus ANatomical entity (XAN)	anatomical region	0.1416	0.193	--	INHERITED FROM: trunk region || trunk || gonad || testis
Xenopus ANatomical entity (XAN)	organism subdivision	0.1913	0.1871	--	INHERITED FROM: trunk || gonad || testis
Xenopus ANatomical entity (XAN)	anatomical group	0.2431	0.1442	--	INHERITED FROM: testis || urogenital system || genital system
Xenopus ANatomical entity (XAN)	multicellular anatomical structure	0.3903	0.1217	--	INHERITED FROM: testis || gonad || trunk
Xenopus ANatomical entity (XAN)	anatomical system	1	0.3094	--	INHERITED FROM: testis || urogenital system || genital system
Xenopus ANatomical entity (XAN)	whole organism	1	0.09747	--	INHERITED FROM: urogenital system || genital system || testis || gonad || trunk || trunk region || male organism
Xenopus ANatomical entity (XAN)	trunk	0.0004384	0.4308	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	urogenital system	0.0007411	0.5011	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	cavitated compound organ	0.02408	0.3033	Least Informative	INHERITED FROM: gonad || testis
Xenopus ANatomical entity (XAN)	testis	0.000002165	0.8318	Moderately Informative	DIRECT
Xenopus DEvelopment stage (XDE)	NF stage	0	0.02327	--	DIRECT

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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)	Acting on ester bonds	0	0.7559	--	DIRECT
Enzyme Commission (EC)	Endodeoxyribonucleases producing other than 5'-phosphomonoesters	0	2.475	--	DIRECT
Enzyme Commission (EC)	Ribonuclease H	0	2.475	--	DIRECT
Enzyme Commission (EC)	Aspartic endopeptidases	0	1.91	--	DIRECT
Enzyme Commission (EC)	Exodeoxyribonuclease I	0.0000000299	2.475	--	DIRECT
Enzyme Commission (EC)	Exodeoxyribonuclease III	0.00001409	2.475	--	DIRECT
Enzyme Commission (EC)	Transferases	1	0.3035	--	INHERITED FROM: DNA-directed DNA polymerase || RNA-directed DNA polymerase || Nucleotidyltransferases || Transferring phosphorus-containing groups
Enzyme Commission (EC)	Transferring phosphorus-containing groups	0	0.5453	Least Informative	DIRECT
Enzyme Commission (EC)	Hydrolases	0	0.3541	Least Informative	DIRECT
Enzyme Commission (EC)	Nucleotidyltransferases	0	0.9432	Moderately Informative	DIRECT
Enzyme Commission (EC)	Acting on peptide bonds (peptidases)	1	0.8949	Moderately Informative	INHERITED FROM: Aspartic endopeptidases || HIV-1 retropepsin || HIV-2 retropepsin
Enzyme Commission (EC)	Acting on acid anhydrides	1	0.9562	Moderately Informative	INHERITED FROM: dUTP diphosphatase
Enzyme Commission (EC)	DNA-directed DNA polymerase	0	1.59	Informative	DIRECT
Enzyme Commission (EC)	Exoribonucleases producing 5'-phosphomonoesters	0	1.673	Informative	DIRECT
Enzyme Commission (EC)	Endoribonucleases producing 5'-phosphomonoesters	0	1.572	Informative	DIRECT
Enzyme Commission (EC)	In phosphorus-containing anhydrides	1	1.28	Informative	INHERITED FROM: dUTP diphosphatase
Enzyme Commission (EC)	RNA-directed DNA polymerase	0	1.91	Highly Informative	DIRECT
Enzyme Commission (EC)	HIV-1 retropepsin	0	2.049	Highly Informative	DIRECT
Enzyme Commission (EC)	Exoribonuclease H	0.0000000035	1.952	Highly Informative	DIRECT
Enzyme Commission (EC)	Retroviral ribonuclease H	0.000000007947	1.952	Highly Informative	DIRECT
Enzyme Commission (EC)	HIV-2 retropepsin	0.0000202	2.049	Highly Informative	DIRECT
Enzyme Commission (EC)	dUTP diphosphatase	0.00003319	1.998	Highly Informative	DIRECT
Enzyme Commission (EC)	Exodeoxyribonucleases producing 5'-phosphomonoesters	1	1.91	Highly Informative	INHERITED FROM: Exodeoxyribonuclease III || Exodeoxyribonuclease I

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InterPro annotation

• Cross references: IPR012337 SSF53098 Protein matches
• Abstract:

  The catalytic domain of several polynucleotidyl transferases share a similar structure, consisting of a 3-layer alpha/beta/alpha fold that contains mixed beta sheets, suggesting that they share a similar mechanism of catalysis. Polynucleotidyl transferases containing this domain include ribonuclease H class I (RNase HI) and class II (RNase HII), HIV RNase (reverse transcriptase domain), retroviral integrase (catalytic domain), Mu transposase (core domain), transposase inhibitor Tn5 (containing additional all-alpha subdomains), DnaQ-like 3¿-5¿ exonucleases (exonuclease domains), RuvC resolvase, and mitochondrial resolvase ydc2 (catalytic domain) [15299518, 8696976, 12823554].

InterPro database

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