Hedgehog/DD-peptidase superfamily

SCOP classification

• Root: SCOP hierarchy in SUPERFAMILY [ 0] (11)
• Class: Alpha and beta proteins (a+b) [ 53931] (376)
• Fold: Hedgehog/DD-peptidase [ 55165]
• Superfamily: Hedgehog/DD-peptidase [ 55166] (5)
• Families:
  • Muramoyl-pentapeptide carboxypeptidase [ 55167]
  • MepA-like [ 111019]
  • VanX-like [ 111022]
  • Hedgehog (development protein), N-terminal signaling domain [ 55170] (2)
  • VanY-like [ 160436]

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Superfamily statistics

	Genomes (1,838)	Uniprot 2018_03 genome	PDB chains (SCOP 1.75)
Domains	4,406	40,374	7
Proteins	4,399	40,335	7

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Functional annotation

• General category: Processes_EC
• Detailed category: Cell adhesion

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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)	D-Ala-D-Ala dipeptidase	0	2.56	--	DIRECT
Enzyme Commission (EC)	Hydrolases	0	0.04271	--	DIRECT
Enzyme Commission (EC)	Acting on peptide bonds (peptide hydrolases)	0	0.5513	Least Informative	DIRECT
Enzyme Commission (EC)	Dipeptidases	0.00000002089	1.782	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 the foot	0	1.106	--	DIRECT
Phenotypic Abnormality (PA)	Abnormality of limbs	0	0.6431	Least Informative	DIRECT
Phenotypic Abnormality (PA)	Abnormality of the lower limb	0	0.9152	Moderately Informative	DIRECT

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Mouse Phenotype (MP)

Highlighted in gray are those with FDR_all>0.001

	MP term	FDR (all)	IC level	SDMP level	Annotation (direct or inherited)
Mammalian Phenotype (MP)	abnormal nervous system morphology	0	0.627	--	DIRECT
Mammalian Phenotype (MP)	endocrine/exocrine gland phenotype	0	0.8003	--	DIRECT
Mammalian Phenotype (MP)	digestive/alimentary phenotype	0	0.9281	--	DIRECT
Mammalian Phenotype (MP)	nervous system phenotype	0	0.5166	Least Informative	DIRECT
Mammalian Phenotype (MP)	cellular phenotype	0	0.5301	Least Informative	DIRECT
Mammalian Phenotype (MP)	abnormal digestive system morphology	0	1.031	Moderately Informative	DIRECT
Mammalian Phenotype (MP)	abnormal gland morphology	0	0.8644	Moderately Informative	DIRECT

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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)	primary germ layer	0	0.7237	--	DIRECT
Xenopus ANatomical entity (XAN)	trunk region	0	0.4287	--	DIRECT
Xenopus ANatomical entity (XAN)	retinal pigmented epithelium	0	2.46	--	DIRECT
Xenopus ANatomical entity (XAN)	neuroectoderm	0	1.33	--	DIRECT
Xenopus ANatomical entity (XAN)	compound organ	0	0.24	--	DIRECT
Xenopus ANatomical entity (XAN)	organism subdivision	0	0.1871	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical group	0	0.1442	--	DIRECT
Xenopus ANatomical entity (XAN)	head region	0	0.5108	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical cluster	0	0.7974	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical structure	0	0	--	DIRECT
Xenopus ANatomical entity (XAN)	pharyngeal arch	0	1.647	--	DIRECT
Xenopus ANatomical entity (XAN)	visual system	0	1.363	--	DIRECT
Xenopus ANatomical entity (XAN)	central nervous system	0	0.6506	--	DIRECT
Xenopus ANatomical entity (XAN)	multicellular anatomical structure	0	0.1217	--	DIRECT
Xenopus ANatomical entity (XAN)	anatomical region	0	0.193	--	DIRECT
Xenopus ANatomical entity (XAN)	retina	0	1.807	--	DIRECT
Xenopus ANatomical entity (XAN)	whole organism	1	0.09747	--	INHERITED FROM: neural plate || head region || brain || intestine || nervous system || retina || alimentary system || retinal pigmented epithelium || hindbrain || anatomical group || cavitated compound organ || multicellular anatomical structure || mesoderm || ectoderm || compound organ || trunk || tissue || anatomical region || marginal zone || central nervous system || epithelium || pharyngeal region || visual system || trunk region || eye || anatomical cluster || viscus || sensory system || pharyngeal arch || multi-tissue structure || neuroectoderm || organism subdivision || embryonic structure || head || primary germ layer
Xenopus ANatomical entity (XAN)	anatomical system	1	0.3094	--	INHERITED FROM: retina || alimentary system || hindbrain || retinal pigmented epithelium || intestine || nervous system || brain || sensory system || central nervous system || eye || visual system
Xenopus ANatomical entity (XAN)	embryo	0	0.6341	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	trunk	0	0.4308	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	nervous system	0	0.6341	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	cavitated compound organ	0	0.3033	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	tissue	0	0.5011	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	head	0	0.5108	Least Informative	DIRECT
Xenopus ANatomical entity (XAN)	multi-tissue structure	0	1.071	Moderately Informative	DIRECT
Xenopus ANatomical entity (XAN)	sensory system	0	1.17	Moderately Informative	DIRECT
Xenopus ANatomical entity (XAN)	brain	0	0.8635	Moderately Informative	DIRECT
Xenopus ANatomical entity (XAN)	embryonic structure	0	1.138	Moderately Informative	DIRECT
Xenopus ANatomical entity (XAN)	ectoderm	0	0.9688	Moderately Informative	DIRECT
Xenopus ANatomical entity (XAN)	alimentary system	0	0.955	Moderately Informative	DIRECT
Xenopus ANatomical entity (XAN)	viscus	0	0.9618	Moderately Informative	DIRECT
Xenopus ANatomical entity (XAN)	epithelium	0	1.615	Informative	DIRECT
Xenopus ANatomical entity (XAN)	pharyngeal region	0	1.482	Informative	DIRECT
Xenopus ANatomical entity (XAN)	eye	0	1.399	Informative	DIRECT
Xenopus ANatomical entity (XAN)	intestine	0	1.363	Informative	DIRECT
Xenopus ANatomical entity (XAN)	neural plate	0	1.482	Informative	DIRECT
Xenopus ANatomical entity (XAN)	mesoderm	0	1.314	Informative	DIRECT
Xenopus ANatomical entity (XAN)	hindbrain	0	1.761	Highly Informative	DIRECT
Xenopus ANatomical entity (XAN)	marginal zone	0	1.858	Highly Informative	DIRECT
Xenopus DEvelopment stage (XDE)	NF stage	0	0.02327	--	DIRECT
Xenopus DEvelopment stage (XDE)	gastrula stage	0	1.885	--	DIRECT
Xenopus DEvelopment stage (XDE)	embryonic stage	0	1.05	Moderately Informative	DIRECT
Xenopus DEvelopment stage (XDE)	NF stage 10	0	2.061	Highly Informative	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)	D-Ala-D-Ala dipeptidase	0	2.952	--	DIRECT
Enzyme Commission (EC)	Hydrolases	0	0.3541	Least Informative	DIRECT
Enzyme Commission (EC)	Acting on peptide bonds (peptidases)	0	0.8949	Moderately Informative	DIRECT
Enzyme Commission (EC)	Dipeptidases	0.0000000007614	2.174	Highly Informative	DIRECT

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InterPro annotation

• Cross references: IPR009045 SSF55166 Protein matches
• Abstract:

  Hedgehog is a family of secreted signal molecules required for embryonic cell differentiation. Members of this family are composed of two domains. These proteins are autocatalytically cleaved by the C-terminal domain . This entry represents the zinc-binding domain found in the N-terminal region of Hedgehog proteins, and is responsible for both local and long-range signalling activities.

  The structure of this domain is known [7477329] and reveals a tetrahedrally coordinated zinc ion that is structurally homologous to the zinc-binding motif in bacterial D-alanyl-D-alanine carboxypeptidases (DD-peptidases), but it is not necessarily found at the N-terminus in these proteins. The DD-peptidase family contains many penicillin binding proteins that remove the terminal D-alanine from peptide side chains of peptidoglycan [9841666].

InterPro database

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