Human and mouse proteases are divided into five classes, which are subdivided into families according to the MEROPS database criteria (Tables S1–S5). We have provided the MEROPS code for all enzymes for which they are available. There are some conflicting cases in which different codes have been previously assigned to human and mouse protease genes that were shown in this work to be true orthologues. In these cases, the human code is proposed for both orthologues. The genes encoding protease-like proteins that show changes in crucial residues for proteolytic activity are indicated as ‘np’ (non-protease homologues) after the code.

The Locus link or nucleotide accession number is provided for each protease. The information for human enzymes is labelled in green and for mouse in yellow. Genes that are absent from human or mouse are labelled in red. Genes that have been inactivated by mutation in one species, but are functional in the other, are labelled in pink. Although these specific pseudogenes have been included in the Tables to emphasize the human–mouse difference, they have not been incorporated into the final counts of protease genes. Genes that have been verified experimentally, but the sequence of which is missing from the available genome sequences, are indicated in red and in parentheses. ‘Y’ indicates that the corresponding human and mouse genes are syntenic. The percentage of identities between orthologous proteases are also shown.

Aspartic proteases

These are divided into four families: A01, A02, A22 and Ax1. There are several pepsinogen A isozymogens encoded by highly related genes (>95% identities) that form part of a cluster located at 11q12. The individual pepsinogen A isozymogens result from haplotypes that contain different number of genes (ranging from 1 to 4)^1,2. In agreement with other databases, this region has been annotated as a single gene in human. According to the criteria discussed above, we have assigned mouse pepsinogen F as the orthologue of human pepsinogen A, despite notable divergence of their structure and regulation³ . Ren2 is absent in some strains of laboratory mice. The gene that encodes prochymosin has been inactivated by mutations and frameshifts in the human genome and is classified as a pseudogene, although in mouse and other species it is functional⁴ .

The genes DDI1, DDI2, DDI-RP, NRIP2 and NRIP3 are included in the family A02 that contains predicted retroviral-like aspartic proteases⁵. All of these have mouse orthologues at syntenic regions, and are not embedded in endogenous retroviral elements. The human and mouse genomes also contain several aspartic protease-related sequences derived from endogenous retrovirus, but we have not annotated these as human or mouse proteases. In this regard, it is remarkable that most of the retroviruses embedded in both genomes have suffered inactivating mutations, also affecting the putative proteases that are encoded by these viral elements. However, HERV-K113, for example, which is located at 19p13 in ~30% of the human population, has intact open-reading frames for all viral proteins, including the corresponding aspartic protease, and remains capable of reinfecting human today⁶. The catalogue of aspartic proteases also includes a new family that is derived from the protein prolactin inducible protein/gross cystic disease fluid protein-15 (PIP/GCDFP15), which has recently been characterized as a protease belonging to this class of enzymes⁷. The four PIP-related proteins lack residues proposed to be essential for PIP proteolytic activity and have been classified as non-protease homologues.

Cysteine proteases

                                                                                                                                                     

C02.002	calpain 2	CAPN2	824	1q42	Capn2	12334	1H4	y	93
C02.004	calpain 3	CAPN3	825	15q15	Capn3	12335	2F1	y	93
C02.011	calpain 5	CAPN5	726	11q13	Capn5	12337	7F1	y	92
C02.971np	calpain 6	CAPN6	827	Xq23	Capn6	12338	XF2	y	95
C02.008	calpain 7	CAPN7	23473	3p25	Capn7	12339	14B	y	95
C02.007	calpain 8	CAPN8	AA043093	(1q42)	Capn8	170725	1H4	y	72
C02.006	calpain 9	CAPN9	10753	1q42	Capn9	73647	8E2	y	85
C02.018	calpain 10	CAPN10	11132	2q37	Capn10	23830	1D	y	81
C02.013	calpain 11	CAPN11	11131	6p21	Capn11	103998	17C	y	83
C02.017	calpain 12	CAPN12	147968	19q13	Capn12	60594	7A3	y	87
C02.020	calpain 13	CAPN13	92291	2p23	Capn13	240159	17E2	y	62
C02.xxx	calpain 14	CAPN14	114773	2p23
C02.010	calpain 15/Sol protein	SOLH	6650	16p13	Solh	50817	17B1	y	89
C12.001	ubiquitin C-terminal hydrolase 1	UCHL1	7345	4p14	Uchl1	22223	5D	y	94
C12.003	ubiquitin C-terminal hydrolase 3	UCHL3	7347	13q22	Uchl3	50933	14E2	y	98
C12.004	ubiquitin C-term. hydrolase BAP1	BAP1	8314	3p21	Bap1	104416	14B	y	93
C12.005	ubiquitin C-terminal hydrolase 5	UCHL5	51377	1q31	Uchl5	56207	1F	y	96
C12.007	ubiquitin C-terminal hydrolase 4				Uchl4	93841	9D
C12.xxx	cylindromatosis protein	CYLD1	1540	16q12	Cyld1	74256	8C4	y	95
C13.004	legumain	LGMN	5641	14q32	Lgmn	19141	12F1	y	82
C13.xxx	legumain-2	LGMN2	122199	13q21
C13.005	hGPI8	PIGK	10026	1p31	Pigk	66613	3H4	y	94
C14.001	caspase-1	CASP1	834	11q22	Casp1	12362	9A1	y	62
C14.006	caspase-2	CASP2	835	7q34	Casp2	12366	6B2	y	89
C14.003	caspase-3	CASP3	836	4q35	Casp3	12367	8B2	y	87
C14.007	caspase-4/11	CASP4	837	11q22	Casp11	12363	9A1	y	60
C14.008	caspase-5	CASP5	838	11q22
C14.005	caspase-6	CASP6	839	4q25	Casp6	12368	3H1	y	90

                                                                                                                                                                                                                                                                    

C19.055	USP47	USP47	55031	11p15	Usp47	320745	7F2	y	94
C19.068	USP48	USP48	84196	1p36	Usp48	170707	4D3	y	95
C19.073np	USP49	USP49	25862	6p21	Usp49	224836	17C	y	80
C19.058np	USP50	USP50	AI990110	15q21	Usp50	75083	2F2	y	75
C19.065	USP51	USP51	BF741256	Xp11
C19.xxxnp	USP52	USP52	9924	12q13	Usp52	103135	10D3	y	97
C19.031	DUB-1				Dub1	13531	7F2
C19.032	DUB-2				Dub2	13532	7F1
C19.xxx	DUB2a				Dub3	AF393638	7F1
C19.xxx	DUB2a-like				Dub4	AF393637	7F1
C19.xxx	DUB2a-like2				Dub5	BAC40791	7F1
C19.xxx	DUB6				Dub6	BN000117	7F1
C26.001	γ-glutamyl hydrolase	GGH	8836	8q12	Ggh	14590	4A3	y	69
C44.001	Gln-PRPP amidotransferase	PPAT	5471	4q12	Ppat	231327	5E1	y	93
C44.971np	Gln-fructose-6-P transamidase 1	GFPT1	2673	2p13	Gfpt1	14583	6D2	y	99
C44.972np	Gln-fructose-6-P transamidase 2	GFPT2	9945	5q35	Gfpt2	14584	11B1	y	98
C44.973np	Gln-fructose-6-P transamidase 3	GFPT3	203431	Xq21	#Gfpt3		XC3	y
C46.002	sonic hedgehog protein	SHH	6469	7q36	Shh	20423	5A3	y	92
C46.003	indian hedgehog protein	IHH	3549	2q35	Ihh	16147	1C3	y	95
C46.004	desert hedgehog protein	DHH	50846	12q13	Dhh	13363	15F2	y	97
C48.002	sentrin/SUMO protease 1	SENP1	29843	12q13	Senp1	223870	15F2	y	88
C48.007	sentrin/SUMO protease 2	SENP2	59343	3q27	Senp2	75826	16B1	y	71
C48.003	sentrin/SUMO protease 3	SENP3	26168	17p13	Senp3	80886	11B4	y	95
C48.008	sentrin/SUMO protease 5	SENP5	205564	3q29	Senp5	AK043171	16B2	y	71
C48.004	sentrin/SUMO protease 6	SENP6	26054	6q14	Senp6	215351	9E2	y	81
C48.009	sentrin/SUMO protease 7	SENP7	57337	3q12	Senp7	72869	16B1	y	87

                                            

Cx1.xxx	CGI-77	CGI77	51633	8q21	Cgi77	72201	4A2	y	87
Cx1.xxxnp	CGI-77b				Cgi77b	236778	XA3
Cx2.xxxnp	HetF-like	HETFL	23331	22q12	Hetfl	209683	5F	y	85

The cysteine proteases belong to 16 different families, and include proteins such as hedgehog family members, the protease function of which is only used for the autolytic processing of their respective precursors⁸. The C01 family is largely expanded in the mouse as a result of the presence of placental cathepsins and testins. We have annotated two further mouse testins, including testin-3, which was the first member of this subfamily predicted to be a functional protease. There are two functional human cathepsin L-like genes (CTSL and CTSL2) at 9q21, and a single gene in the mouse, which is more closely related to CTSL2. The cylindromatosis protein contains an ubiquitin C-terminal hydrolase domain and has been included in the C12 family. The genes for calpain 14, caspase 5 and caspase 10 are absent in mice, and the human gene for caspase 12 has been inactivated and is therefore classified as a pseudogene. We have annotated a second human legumain-like gene that is absent in mouse.

The C19 family of ubiquitin specific proteases (USPs) is large and complex. We have annotated 21 human members (USP30, 31, 34–52) and assigned their corresponding mouse orthologues. We have not found mouse orthologues for human USP6, -13, -34, -37, -42 and -51. USP17is located within the RS447 human megasatellite at 4p15⁹. This region is highly polymorphic in the human genome, containing a variable number of USP17-related intronless tandemlyrepeated sequences (>95% identical), which have probably been generated by retrotransposition. Forty-four distinct alleles in 74 unrelated chromosomes containing 20–103 copies of the RS477 unit have been identified¹⁰. We have also identified several USP17-related sequences in a cluster located at 8p25. This cluster would contain at least seven USP17-like (USP17L) intronless genes (three of these are classified as non-protease homologues) and pseudogenes. The proteins encoded by these polymorphic and variable regions have been annotated as two single proteases (USP17 and USP17L) in this table. The closest relatives of USP17 genes in the mouse genome are those that code for proteins called DUBs (deubiquitinating enzymes). DUB1, DUB2, and DUB2A have been extensively characterized as members of a novel group of cytokine-inducible deubiquitylating enzymes that are produced by lymphocytes^11–13. We have annotated three further members of this subfamily of haematopoietic proteases. The classification of mouse DUBs as orthologues of human USP17 genes is doubtful because, despite sequence similarities, their syntenic relationship is unclear. Accordingly, we have tentatively classified them as paralogous genes.

We have annotated six members of the C48 family of SUMO-1 proteases in the mouse genome, which are absent in the human genome. We have also included a family of recently described cysteine proteases with deubiquitylating activity containing the OTU-protease domain and tentatively called otubains^14,15. This family should comprise 14 orthologues and one specific member in both human and mouse. All of them contain characteristic features of active proteases with the exception of TRABID and murine Cgi77b. The last protease included in our list of cysteine proteases is called HetF-like and forms part of the superfamily of caspase-haemoglobinase fold proteases¹⁶. Human and mouse HetF-like have a serine residue instead of the active-site cysteine present in cysteine proteases, and have been classified as non-protease homologues.

Metalloproteases

Table S3 | Metalloproteases

Code M01.003 M01.014 M01.023 M01.001 M01.018 M01.004 M01.008 M01.010 M01.011 M01.022 M01.028 M01.027 M01.972np M02.001 M02.006 M02.971np M03.001 M03.002 M03.006 M08.003 M10.034 M10.001 M10.003 M10.005 M10.008	Peptidase aminopeptidase A aminopeptidase B aminopeptidase MAMS aminopeptidase N aminopeptidase PILS leukotriene A4 hydrolase pyroglutamyl-peptidase II cytosol alanyl aminopeptidase leucyl-cystinyl aminopeptidase aminopeptidase B-like 1 aminopeptidase O aminopeptidase Q TBP-associated factor 2 angiotensin-converting enzyme 1 angiotensin-converting enzyme 2 angiotensin-converting enzyme 3 thimet oligopeptidase neurolysin mitochondrial intermediate peptidase leishmanolysin-2 collagenase-like B collagenase 1 gelatinase A stromelysin 1 matrilysin	Human Gene LocusLink ENPEP 2028 RNPEP 6051 AMPEP 64167 ANPEP 290 ARTS1 51752 LTA4H 4048 TRHDE 29953 NPEPPS 9520 LNPEP 4012 RNPEPL1 57140 AOPEP 84909 AQPEP BG623101 TAF2 6873 ACE 1636 ACE2 59272 #ACE3 THOP1 7064 NLN 57486 MIPEP 4285 LMLN 89782 MMP1 4312 MMP2 4313 MMP3 4314 MMP7 4316	Locus 4q26 1q32 5q15 15q25 5q21 12q23 12q21 17q21 5q15 2q37 9q22 5q23 8q24 17q23 Xp21 17q23 19p13 5q13 13q12 3q29 11q22 16q22 11q22 11q22	Mouse Gene LocusLink Enpep 13809 Rnpep 215615 Anpep 16790 Arts1 80898 Lta4h 16993 Trhde 237553 Psa 19155 Lnpep 266720 Rnpepl1 98480 Aopep BAC31943 Aqpep 74574 Taf2 319944 Ace 11421 Ace2 70008 Ace3 217246 Thop1 50492 Nln 75805 Mipep 70478 Lmln 239833 Mcolb 83996 Mcola 83995 Mmp2 17390 Mmp3 17392 Mmp7 17393	Locus 3H1 1F 7D2 13C1 10C2 10D1 11D 13C1 1D 13B3 18C 15D 11E1 XF5 11E1 10C1 13D1 14C3 16B2 9A1 9A1 8C5 9A1 9A1	Syntenic yyyyyyyyyyyyyyy yyyyyyyy	Identity 77 86 76 85 92 94 97 88 95 72 68 99 83 82 89 90 84 73 59 95 76 70

                                                                                                                                         

M13.091	PHEX endopeptidase	PHEX	5251	Xp22	Phex	18675	XF4	y	96
M14.001	carboxypeptidase A1	CPA1	1357	7q32	Cpa1	109697	6A3	y	74
M14.002	carboxypeptidase A2	CPA2	1358	7q32	Cpa2	232680	6A3	y	86
M14.010	carboxypeptidase A3	CPA3	1359	3q24	Cpa3	12873	3A3	y	81
M14.017	carboxypeptidase A4	CPA4	51200	7q32	Cpa4	215225	6A3	y	84
M14.020	carboxypeptidase A5	CPA5	93979	7q32	Cpa5	76649	1A3	y	84
M14.018	carboxypeptidase A6	CPA6	57094	8q13	Cpa6	329093	1A3	y	86
M14.003	carboxypeptidase B	CPB1	1360	3q25	Cpb1	76703	3A3	y	72
M14.009	carboxypeptidase U	CPB2	1361	13q14	Cpb2	56373	14D2	y	82
M14.021	carboxypeptidase O	CPO	130749	2q33	#Cpo	269201	1C2	y
M14.005	carboxypeptidase E	CPE	1363	4q32	Cpe	12876	8B3	y	97
M14.004	carboxypeptidase N	CPN	1369	10q25	Cpn	93721	19D1	y	66
M14.006	carboxypeptidase M	CPM	1368	12q15	Cpm	70574	10D2	y	79
M14.011	carboxypeptidase D	CPD	1362	17q11	Cpd	12874	11B4	y	93
M14.012	carboxypeptidase Z	CPZ	8532	4p16	Cpz	242939	5B1	y	82
M14.015np	carboxypeptidase X1	CPX1	56265	20p13	Cpx1	56264	2F3	y	86
M14.019np	carboxypeptidase X2	CPX2	119587	10q26	Cpx2	55987	7F4	y	89
M14.951np	adipocyte-enhancer binding prot. 1	AEBP1	165	7p13	Aebp1	11568	11A1	y	90
M16.002	insulysin	IDE	3416	10q24	Ide	15925	19C3	y	97
M16.003	mitochondrial processing pept. β-sub	PMPCB	9512	7q22	Pmpcb	73078	5A3	y	90
M16.005	nardilysin	NRD1	4898	1p32	Nrd1	230598	4C7	y	93
M16.009	pitrilysin metalloprotease 1	PITRM1	10531	10p15	Pitrm1	69617	13A1	y	86
M16.971np	mitochondrial processing protease	INPP5E	23203	9q34	Inpp5e	66865	2A3	y	91
M16.973np	UCR1	UQCRC1	7384	3p21	Uqcrc1	22273	9F2	y	88
M16.974np	UCR2	UQCRC2	7385	16p12	Uqcrc2	67003	7F3	y	85
M16.976np	mitoch. processing protease-like	AMPP	133083	4q22
M17.001	leucyl aminopeptidase	LAP3	51056	4p15	Lap3	66988	5B3	y	90

                                                                                                                                                                                                  

M17.006	aminopeptidase-like 1	NPEPL1	79716	20q13
M18.002	aspartyl aminopeptidase	DNPEP	23549	2q36	Dnpep	13437	1C3	y	90
M19.001	membrane dipeptidase	DPEP1	1800	16q24	Dpep1	13479	8E2	y	73
M19.002	membrane dipeptidase 2	DPEP2	64174	16q22	Dpep2	244632	8D2	y	70
M19.004	membrane dipeptidase 3	DPEP3	64180	16q22	Dpep3	71854	8D2	y	73
M20.005	glu-carboxypeptidase-like 1	CPGL	55748	18q22	Cpgl	66054	18E3	y	91
M20.006	glu-carboxypeptidase-like 2	CPGL2	84735	18q22	Cpgl2	240478	18E3	y	73
M20.971np	HmrA-like protease	HMRALP	135293	6q15	Hmralp	242377	4A5	y	83
M20.973np	aminoacylase	ACY1	95	3p21	Acy1	109652	9F1	y	85
M22.003	O-sialoglycoprotein endopeptidase	OSGEP	55644	14q11	Osgep	66246	14C1	y	93
M22.004	O-sialoglycoprotein endopeptidase 2	OSGEP2	64172	2q32	Osgep2	72085	1C1	y	84
M24.001	methionyl aminopeptidase I	METAP1	23173	4q24	Metap1	75624	3H2	y	92
M24.002	methionyl aminopeptidase II	METAP2	10988	12q23	Metap2	56307	10C3	y	88
M24.028	methionyl aminopeptidase-like 1	METAPL1	254042	2q31	Metapl1	66559	2C3	y	95
M24.005	X-prolyl aminopeptidase 2	XPNPEP2	7512	Xq26	Xpnpep2	170745	XA3	y	81
M24.007	X-Pro dipeptidase	PEPD	5184	19q13	Pepd	18624	7B1	y	90
M24.009	aminopeptidase P1	XPNPEPL	7511	10q25	Xpnpep1	170750	19D2	y	81
M24.026	aminopeptidase P homologue	PEPP	63929	22q13	Pepp	321003	15E3	y	93
M24.973np	proliferation-association protein 1	PA2G4	5036	12q13	Pa2g4	18813	10D3	y	98
M24.974np	suppressor of Ty 16 homologue	SUPT16H	11198	14q11	Supt16h	114741	14C1	y	98
M28.010	glutamate carboxypeptidase II	FOLH1	2346	11p11	Folh1	53320	7E1	y	85
M28.011	NAALADASE L peptidase	NAALADL	10004	11q13	NAALADL	BN000129	19A	y	80
M28.012	NAALADASE II	NAALAD2	10003	11q14	Naalad2	72560	9A3	y	89
M28.975np	NAALADASE III	NAALAD3	254827	3q26	Naalad3	229149	3A3	y	63
M28.014	plasma Glu-carboxypeptidase	PGCP	10404	8q22	Pgcp	54381	15B3	y	93

                                                                                                                                                                                                                                                     

M28.018	Ojeda peptidase	OJP	79956	9p24	Ojp	BAC38286	19C2	y	87
M28.972np	transferrin receptor protein	TFRC	7037	3q29	Trfr	22042	16B3	y	77
M28.973np	transferrin receptor 2 protein	TFR2	7036	7q22	Trfr2	50765	5G1	y	84
M28.974np	glutaminyl cyclase	QPCT	25797	2p22	Qpct	70536	17E3	y	81
M28.016	glutaminyl cyclase 2	QPCT2	54814	19q13	Qpct2	67369	7A2	y	84
M38.972np	dihydroorotase	CAD	790	2p23	Cad	69719	5B1	y	94
M38.973np	dihydropyrimidinase	DPYS	1807	8q22	Dpys	64705	15C	y	88
M38.xxxnp	dihydropyrimidinase-related prot. 1	CRMP1	1400	4p16	Crmp1	12933	5B2	y	96
M38.xxxnp	dihydropyrimidinase-related prot. 2	DPYSL2	1808	8p21	Dpysl2	12934	14D1	y	98
M38.xxxnp	dihydropyrimidinase-related prot. 3	DPYSL3	1809	5q32	Dpysl3	22240	18B3	y	98
M38.xxxnp	dihydropyrimidinase-related prot. 4	DPYSL4	10570	10q26	Dpysl4	26757	7F5	y	93
M38.xxxnp	dihydropyrimidinase-related prot. 5	DPYSL5	56896	2p23	Dpysl5	65254	5B1	y	98
M41.004	i-AAA protease	YME1L1	10730	10p12	Yme1l1	27377	2A3	y	95
M41.006	paraplegin	SPG7	6687	16q24	Spg7	234847	8E2	y	89
M41.010	Afg3-like protein 1	#AFG3L1	172	16q24	Afg3l1	114896	8E2	y
M41.007	Afg3-like protein 2	AFG3L2	10939	18p11	Afg3l2	69597	18E1	y	94
M43.004	pappalysin-1	PAPPA	5069	9q32	Pappa	18491	4C1	y	93
M43.005	pappalysin-2	PLAC3	60676	1q25	Plac3	240848	1H1	y	78
M47.001	procol. III N-endopeptidase	PCOLN3	5119	16q24	#Pcoln3	BI690732	8E2	y
M48.003	FACE-1/ZMPSTE24	FACE1	10269	1p34	Face1	230709	4D1	y	91
M48.017	VVML	VVML	115209	1p32	Vvml	67013	4C6	y	71
M49.001	dipeptidyl-peptidase III	DPP3	10072	11q13	Dpp3	75221	19A	y	92
M50.001	S2P protease	MBTPS2	51360	Xp22	Mbtps2	270669	XF4	y	97

These belong to 26 distinct families. The M01 family contains 13 members in human and 12 in mouse, which lacks aminopeptidase MAMS. We propose the names aminopeptidases O and Q for the M01 proteases previously annotated as human hypothetical proteins FLJ14675 and BG623101. We have also identified orthologues for these genes located at mouse chromosomes 13B3 and 18C. In the M02 family, we have tentatively annotated a mouse gene for a third angiotensin-converting enzyme-like (Ace3), which is located at chromosome 11E1. We have classified Ace3 as a non-protease homologue because it contains the HQMGH sequence instead of the consensus Zn-binding HExxH motif. No expressed sequence tags (ESTs) have been found for mouse Ace3, which could be an inactive pseudogene, although the locus is apparently complete and conserved in the rat. The corresponding human gene is a pseudogene as a result of the accumulation of stop codons and frameshifts.

There are some differences between human and mouse members of the M10 family of matrix metalloproteases (MMPs). Mouse McolB, a diverging counterpart of human MMP1 is absent in human, whereas human matrilysin-2 (MMP26) is absent from mouse, although there are some gaps in the mouse genome region which could contain this missing gene. MMP23 has been recently duplicated in the human genome¹⁷, generating two closely related genes MMP23A and MMP23B. This region is artefactually collapsed in the available public and private genome sequences owing to the high sequence identity between both genes, and is erroneously considered as containing a single gene. Apparently, there is a single mouse MMP23gene, although the possibility that this region is duplicated in the mouse genome and has also been computer-collapsed can not be ruled out. In the family M12, we have annotated a new member within the meprin/tolloid subfamily¹⁸ .

The ADAM (a disintegrin and metalloprotease) subfamily of M12 metalloproteases¹⁹ shows important differences between both organisms. The genes for ADAM-1, -3, -4, -5, -6 and -25 are pseudogenes in the human but active genes in the mouse. ADAM-1 and -6 are duplicated in mouse, whereas ADAM-20 is duplicated in human (ADAM-20 and ADAM-21). Also, testases — a subgroup of ADAMs located at 8B1 — are mouse specific. We have annotated five further members of this family (testases 5–9), although they are intronless and their functional relevance remains to be shown. The group of ADAMTSs (ADAMs with thrombospondin domains) is completed with the inclusion of human and mouse ADAMTS-20. In the M14 family of carboxypeptidases, we have found that mouse carboxypeptidase O has been specifically inactivated by mutation and is annotated as a pseudogene²⁰. Dihydroorotase and several dihydropyrimidinases have been included as non-protease homologues of bacterial isoaspartyl dipeptidases. The gene that encodes procollagen III N-endopeptidase is inactivated in mouse, thereby representing an interesting difference between both human and mouse degradomes, as there are no other functional members in the M47 family that could compensate this specific loss in mouse. We have annotated 14 human and 13 mouse proteins in the recently described M67 family of metalloisopeptidases^21,22. All of them contain the JAMM motif, although some lack conserved residues that are predicted to be essential for proteolytic activity, and have therefore been classified as non-protease homologues.

There are doubts about the ascription of the FACE-2/RCE1 prenyl endopeptidase to the cysteine or metalloprotease classes of enzymes²³; however, in agreement with recent structural comparisons²⁴, we have included it as the only human and mouse representative of a new family of membrane-bound metalloproteases. Finally, we have included three aminoacylases in our catalogue of metalloproteases. These enzymes are not, strictly speaking, proteases because they cleave peptide bonds that connect an acyl derivative with an amino acid²⁵. However, the structure of ACY1 clearly allows its inclusion in the M20 family of metalloproteases, whereas those of ACY2 and ACY3 have also been proposed to be part of a superfamily of metalloproteases that contains members of the M14 family of carboxypeptidases²⁶.

Serine proteases

                                                                                                                                                                                                                          

S01.192	complement component C1ra	C1R	715	12p13	C1ra	50909	6F2	y	81
S01.xxx	complement component C1rb				C1rb	AF459018	(6F2)
S01.193	complement component C1sa	C1S	716	12p13	C1sa	50908	6F2	y	74
S01.xxx	complement component C1sb				C1sb	317677	6F2
S01.191	complement factor D	DF	1675	19p13	Df	11537	10C1	y	67
S01.xxx	complement factor D-like	DF2	199783	19p13	Df2	270746	10C1	y	79
S01.199	complement factor I	IF	3426	4q25	If	12630	3H1	y	69
S01.198	MASP1/3	MASP1/3	5648	3q29	Masp1/3	17174	16B1	y	86
S01.229	MASP2	MASP2	10747	1p36	Masp2	17175	4E1	y	81
S01.237	neurotrypsin	PRSS12	8492	4q28	Prss12	19142	3G3	y	82
S01.231	u-plasminogen activator	PLAU	5328	10q22	Plau	18792	14B	y	69
S01.232	t-plasminogen activator	PLAT	5327	8p11	Plat	18791	8A3	y	80
S01.233	plasminogen	PLG	5340	6q26	Plg	18815	17A2	y	79
S01.976np	hepatocyte growth factor	HGF	3082	7q21	Hgf	15234	5A3	y	91
S01.975np	macrophage-stimulating protein	MSP	4485	3p21	Msp	15235	9F2	y	80
S01.999np	apolipoprotein	LPA	4018	6q26
S01.223	acrosin	ACR	49	22q13	Acr	11434	15F1	y	68
S01.972np	haptoglobin-1	HP	3240	16q22	Hp	15439	8D3	y	79
S01.974np	haptoglobin-related protein	HPR	3250	16q22
S01.277	osteoblast serine protease	HTRA1	5654	10q26	Htra1	56213	7F4	y	91
S01.278	HTRA2	HTRA2	27429	2p12	Htra2	64704	6D1	y	84
S01.284	HTRA3	HTRA3	94031	4p16	Htra3	78558	5B1	y	86
S01.285	HTRA4	HTRA4	203100	8p11	Htra4	66943	8A3	y	66
S01.309	umbilical vein protease	SPUVE	11098	11q14	Spuve	76453	7E1	y	90
S01.994np	similar to SPUVE	SPUVE2	167681	6q14	Spuve2	244954	9E3	y	77
S01.104	plasma-kallikrein-like 1	KLKBL1	XP_116753	8p23	Klkbl1	74215	(14C3)		66
S01.415	plasma-kallikrein-like 2	KLKBL2	203074	8p23	Klkbl2	71037	14C3	y	71
S01.419	plasma-kallikrein-like 3	#KLKBL3		8p23	Klkbl3	73382	14C3	y

                                                                                                                                                                                                                                

S01.992np	plasma-kallikrein-like 4	KLKBL4	221191	16q21	Klkbl4	BN000132	8C5	y	62
S01.286	similar to Arabidopsis Ser-prot.	SASP	219743	10q22	Sasp	71767	10B4	y	80
S01.991np	chymase-like serine protease				Clsp	75106	XC3
S08.063	site-1 protease	MBTPS1	8720	16q23	Mbtps1	56453	8E1	y	96
S08.039	proprotein convertase 9	PCSK9	255738	1p32	Pcsk9	100102	4C7	y	73
S08.090	tripeptidyl-peptidase II	TPP2	7174	13q33	Tpp2	22019	1C1	y	95
S08.072	proprotein convertase 1	PCSK1	5122	5q15	Pcsk1	18548	13C1	y	93
S08.073	proprotein convertase 2	PCSK2	5126	20p12	Pcsk2	18549	2H1	y	97
S08.071	furin	PCSK3	5045	15q26	Pcsk3	18550	7D2	y	94
S08.074	proprotein convertase 4	PCSK4	5124	19p13	Pcsk4	18551	10C1	y	82
S08.076	proprotein convertase 5	PCSK5	5125	9q21	Pcsk5	18552	19B	y	92
S08.075	PACE4 proprotein convertase	PCSK6	5046	15q26	Pcsk6	18553	7C	y	93
S08.077	proprotein convertase 7	PCSK7	9159	11q23	Pcsk7	18554	9B	y	88
S09.001	prolyl oligopeptidase	PREP	5550	6q22	Prep	19072	10B2	y	96
S09.015	prolyl-oligopeptidase 2	PREP2	9581	2p21	Prep2	213760	17E4	y	94
S09.003	dipeptidyl-peptidase 4	DPP4	1803	2q24	CD26	13482	2C3	y	85
S09.973np	dipeptidyl-peptidase 6	DPP6	1804	7q36	Dpp6	13483	5A3	y	91
S09.018	dipeptidyl-peptidase 8	DPP8	54878	15q23	Dpp8	74388	9D	y	95
S09.019	dipeptidyl-peptidase 9	DPP9	91039	19p13	Dpp9	224897	17D	y	89
S09.974np	dipeptidyl-peptidase 10	DPP10	57628	2q14	Dpp10	269109	1E2	y	88
S09.007	Seprase	FAP	2191	2q24	Fap	14089	2C3	y	90
S09.004	acylaminoacyl-peptidase	APEH	327	3p21	Apeh	235606	9F2	y	91
S09.055	CGI-67 protein	CGI-67	51104	9q21	Cgi-67	BN000127	19C1	y	98
S09.052	CGI-67-like protease-1	CGI-67L1	81926	19p13	Cgi-67l1	216169	10C1	y	93
S09.053	CGI-67-like protease-2	CGI-67L2	58489	15q25	Cgi-67l2	70178	7D3	y	97
S09.051	BEM46-like 1	BEM46L1	84945	13q33	Bem46l1	68904	8A2	y	97

                                                                                                                                                                                                                                                                             

S09.054	BEM46-like 2	BEM46L2	26090	20p11	Bem46l2	76192	2H1	y	90
S09.xxx	BEM46-like 3	BEM46L3	BG74273	14q22	Bem46l3	278594	12C3	y	78
S10.002	lysosomal carboxypeptidase A	PPGB	5476	20q13	Ppgb	19025	2H3	y	87
S10.003	vitellogenic carboxypeptidase-L	CPVL	54504	7p15	Cpvl	71287	6B3	y	76
S10.013	serine carboxypeptidase 1	RISC	59342	17q23	Risc	74617	11C	y	82
S12.004	β-lactamase	LACTB	114294	15q22	Lactb	80907	9D	y	85
S14.003	endopeptidase Clp	CLPP	8192	19p13	Clpp	53895	17E1	y	87
S16.002	PIM1 endopeptidase	PRSS15	9361	19p13	Prss15	74142	17E1	y	88
S16.006	PIM2 endopeptidase	PIM2	83752	16q21	Pim2	66887	8C4	y	95
S26.009	signalase 18 kDa component	SPC18	23478	15q25	Spc18	56529	7D2	y	98
S26.010	signalase 21 kDa component	SPC21	90701	18q21	Spc21	66286	18E1	y	98
S26.xxx	signalase-like 1	SPCL1	158326	9p22	Spcl1	230344	4C3	y	76
S26.012	mitoc. inner membrane protease 2	IMMP2L	83943	7q31	Immp2l	93757	12B3	y	90
S26.013	mitochondrial signal peptidase	IMMP1	196294	11p13	Immp1	66541	2E3	y	95
S26.xxx	lactotransferrin	LTF	4057	3p21	Ltf	17002	9F2	y	70
S28.001	lysosomal Pro-X carboxypeptidase	PRCP	5547	11q14	Prcp	72461	7E2	y	77
S28.002	dipeptidyl-peptidase II	DPP7	29952	(9q24)	Dpp7	83768	2A3	y	80
S28.003	thymus-specific serine peptidase	PRSS16	10279	6p21	Prss16	54373	13A3	y	79
S33.009	αβ-hydrolase dom. containing 4	ABHD4	63874	14q11	Abhd4	105501	14C1	y	96
S33.971np	epoxyde hydrolase	EPHX1	2052	1q42	Ephx1	13849	1H4	y	83
S33.972np	Mesoderm specific transcript hom.	MEST	4232	7q32	Mest	17294	6A3	y	97
S33.974np	epoxyde hydrolase related protein	EPHXRP	253152	1p22	Ephxrp	243192	5E	y	87
S33.xxxnp	CGI-58	CGI-58	51099	3p21	Cgi-58	67469	9F4	y	94
S53.003	tripeptidyl-peptidase I	CLN2	1200	11p15	Cln2	12751	7F1	y	88

Most of these belong to the S01 family, but there are representatives of 13 further serine protease families in the human and mouse degradomes. All differences between human and mouse serine proteases correspond to changes in members of this densely populated family. The kallikreins are duplicated in mouse almost entirely — there are 28 members in mouse and 15 in human. The genes for mastin, implantation serine protease-2 (ISP-2), intestinal serine protease (DISP-1), and testis serine proteases TESP-2 and -3, are inactivated in human hence their classification as pseudogenes. The absence of genes for human DISP-2, ISP-1 and TESP-1, together with the finding that human DISP-1, ISP-2, TESP-2 and TESP-3 are pseudogenes, indicates that the functions performed by ISP, DISP and TESP proteases might be mouse-specific. We have also annotated several new members of the testis-specific serine protease (TESSP) subfamily, with TESSP-3, -4 and -6 being pseudogenes in human and active genes in mouse. Mast-cell proteases (Mcpt), granzymes (Gzm), trypsins and human-airway trypsin-like (HAT-like) proteases are expanded in mouse; two tryptases, an ovochymase-like protease and a form of pancreatic elastase, are only present in human. Two well-known non-protease homologues, apolipoprotein (a) (LPA) and haptoglobin-related protein, are absent in mouse. Further characteristic features of the mouse degradome include the duplication of complement factors C1r and C1s, and the presence of an extra functional member of the plasma-kallikrein like subfamily (Klkbl3), and of a non-protease homologue called Clsp (chymase-like serine protease).

We have included in the catalogue of serine proteases, a series of proteins such as lactoferrin, reelin and tumour rejection antigen (gp96), which have been recently reported to have this kind of proteolytic activity^27–29. On the basis of structural analysis, lactoferrin has been tentatively classified as a member of the S26 family of serine proteases, whereas reelin, gp96 and their close relatives have been preliminarily ascribed to two Sx families of presently unclassified serine proteases. Gene Ontology annotation of the human proteome also predicts a series of serine proteases with minimal relationship to other members of this class of enzymes. They include torsin, NSP (novel serine protease) and Ufd1L (ubiquitin fusion degradation protein 1 homologue), but owing to the absence of enough evidence to support its ascription as serine proteases, they have not been included in the present version of the human and mouse degradomes.

Threonine proteases

                             

T03.016	γ-glutamyltransferase m-3	GGTL4	91227	22q11
T03.002	γ-glutamyltransferase 5	GGTLA1	220522	22q11

The most recently identified catalytic class of proteases, the threonine proteases³⁰, are classified into three families: T01, containing the proteasome components; T02, composed of three distinct glycosylasparaginases; and T03, including diverse γ-glutamyltransferases (GGTs). All members of the T01 and T02 families are conserved between human and mouse. There are, however, some differences in the number of GGT genes clustered in a region of chromosome 22, which has undergone successive duplications³¹. As a consequence of this dynamic evolution, there are four GGT genes in this region of the human genome but only one in the corresponding region of the mouse genome (10B5). An additional GGT gene located at 20q11 is conserved in the mouse genome at an equivalent position (2H2).

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