Citrus Sinensis ID: 030279

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180
Protein Sequence
MENDFVDQVAISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCSNPNIRSS
Secondary Structure (PSIPRED)
cccccccccccccccccccccEEEEEEccccccccccccEEEEccEEEcccEEEEEEEcccccccccccEEEEEEEEEcccccccccEEEEEEEEEEEEcccccEEEEEEEEEEEcccccccccccEEEccccccccccEEEEcccccccccccccEEEccEEEEEEEEEcccccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHccccccccEEEEEccHHHHHHcccccEccccEEEccEEEEEEEEEccccccccccEEEEEEEEccccccccccEEEEEEEEEEEEcccccEEEEEEEEEEEcccccccEEEcccccccccccEEEEEEcccccccccEcccEEEEcccEEEEEEEEcccccccccc
Coil and Loop (DISEMBL)
MENDFVDQVAISrsishvppahFLLKIEAFSSLVENDVenykslefdaggykWKLVVypngnknenvKDHISIYLAMVDtsslglgweVYVIFRLFVLDQKKDEFLILQEVFVKETKkctgeclsmkkltsasnyKHVWKIKnfsklpdniyesevfvaGDQKWYVYFLKwcsnpnirss
Flexible Loop (DISEMBL)
MENDFVDQVAISrsishvppAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVketkkctgeclsmkkltsasnykHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWcsnpnirss
Low Complexity Region (SEG)
MENDFVDQVAISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCSNPNIRSS
Disordered region (IsUnstruct)
*******QVAISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCS*******
Disordered Region (DISOPRED)
********************AHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKW*********
Disordered Region (DISEMBL)
MENDFVDQVAISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCSNPNIRSS
Disordered Region (DISPRO)
*************SISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCS*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MENDFVDQVAISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCSNPNIRSS
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	180	2.2.26 [Sep-21-2011]
Q84WU2	1115	Ubiquitin carboxyl-termin	no	no	0.533	0.086	0.346	2e-08
Q9FPT1	1116	Ubiquitin carboxyl-termin	no	no	0.477	0.077	0.365	4e-08

>sp|Q84WU2|UBP13_ARATH Ubiquitin carboxyl-terminal hydrolase 13 OS=Arabidopsis thaliana GN=UBP13 PE=1 SV=1

 Score = 58.5 bits (140), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 36/104 (34%), Positives = 57/104 (54%), Gaps = 8/104 (7%)

Query: 9   VAISRSISHVPPA-HFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENV 67
            A+       PP+  F   I  F+ L  N  ++Y  + F  GGYKW+++++P GN   NV
Sbjct: 41  TAVENPPPEDPPSLKFTWTIPMFTRL--NTRKHYSDV-FVVGGYKWRILIFPKGN---NV 94

Query: 68  KDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEV 111
            DH+S+YL + D ++L  GW  Y  F L V++Q  + + I +E 
Sbjct: 95  -DHLSMYLDVADAANLPYGWSRYSQFSLAVVNQVNNRYSIRKET 137

Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin. Involved in the processing of poly-ubiquitin precursors as well as that of ubiquitinated proteins.
Arabidopsis thaliana (taxid: 3702)
EC: 3EC: .EC: 4EC: .EC: 1EC: 9EC: .EC: 1EC: 2

>sp|Q9FPT1|UBP12_ARATH Ubiquitin carboxyl-terminal hydrolase 12 OS=Arabidopsis thaliana GN=UBP12 PE=1 SV=2

 Score = 57.8 bits (138), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 34/93 (36%), Positives = 52/93 (55%), Gaps = 7/93 (7%)

Query: 19  PPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMV 78
           P   F   I  FS   +N  ++Y  + F  GGYKW+++++P GN   NV DH+S+YL + 
Sbjct: 53  PTLKFTWTIPNFSR--QNTRKHYSDV-FVVGGYKWRILIFPKGN---NV-DHLSMYLDVS 105

Query: 79  DTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEV 111
           D +SL  GW  Y  F L V++Q    + + +E 
Sbjct: 106 DAASLPYGWSRYAQFSLAVVNQIHTRYTVRKET 138

Recognizes and hydrolyzes the peptide bond at the C-terminal Gly of ubiquitin. Involved in the processing of poly-ubiquitin precursors as well as that of ubiquitinated proteins.

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: 1

EC: 2

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	180
297830352	309	hypothetical protein ARALYDRAFT_479214 [	0.888	0.517	0.465	5e-43
21537273	309	unknown [Arabidopsis thaliana]	0.888	0.517	0.460	2e-42
18401489	309	TRAF-like family protein [Arabidopsis th	0.888	0.517	0.455	9e-38
11994555	304	unnamed protein product [Arabidopsis tha	0.866	0.513	0.46	1e-37
224101481	292	predicted protein [Populus trichocarpa]	0.844	0.520	0.5	5e-37
449441502	316	PREDICTED: BTB/POZ and MATH domain-conta	0.888	0.506	0.438	2e-36
449522688	316	PREDICTED: BTB/POZ and MATH domain-conta	0.888	0.506	0.438	2e-36
255556544	455	nucleic acid binding protein, putative [	0.816	0.323	0.428	4e-34
357479139	311	Ubiquitin carboxyl-terminal hydrolase [M	0.861	0.498	0.420	3e-33
255636923	276	unknown [Glycine max]	0.872	0.568	0.411	5e-33

>gi|297830352|ref|XP_002883058.1| hypothetical protein ARALYDRAFT_479214 [Arabidopsis lyrata subsp. lyrata] gi|297328898|gb|EFH59317.1| hypothetical protein ARALYDRAFT_479214 [Arabidopsis lyrata subsp. lyrata]

 Score =  179 bits (454), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 95/204 (46%), Positives = 124/204 (60%), Gaps = 44/204 (21%)

Query: 7   DQVAISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNEN 66
           D   I +SIS  PP H+++KIE+FS L ++ +E Y++  F+AGGYKWKLV+YPNGNK++N
Sbjct: 6   DHDEIIKSISDAPPTHYMVKIESFSLLTKHAIERYETESFEAGGYKWKLVLYPNGNKSKN 65

Query: 67  VKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQ----------------- 109
            KDH+S+YLA+ D+SSL  GWEVY +FRL++LDQ KD +LILQ                 
Sbjct: 66  TKDHVSVYLALADSSSLSPGWEVYAVFRLYLLDQNKDNYLILQGNERRFHAVKREWGFDK 125

Query: 110 ------------------------EVFV-KETKKCTGECLSMKKLTSASNYKHVWKIKNF 144
                                   +VFV KE +   GECLSM K   A++ KHVWKI+NF
Sbjct: 126 FIPTGTFSDASNGYLMEDTCMFGADVFVSKERRSGRGECLSMIK--DATSSKHVWKIENF 183

Query: 145 SKLPDNIYESEVFVAGDQKWYVYF 168
           SKL    Y+S  F AGD+KW V F
Sbjct: 184 SKLDKESYDSNAFFAGDRKWKVRF 207

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|21537273|gb|AAM61614.1| unknown [Arabidopsis thaliana]

 Score =  177 bits (448), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 94/204 (46%), Positives = 124/204 (60%), Gaps = 44/204 (21%)

Query: 7   DQVAISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNEN 66
           D   I +SIS  PP H+++KIE+FS L ++ +E Y++  F+AGGYKWKLV+YPNGNK++N
Sbjct: 6   DYDEIIKSISDAPPTHYMVKIESFSLLTKHAIERYETESFEAGGYKWKLVLYPNGNKSKN 65

Query: 67  VKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQ----------------- 109
            KDH+S+YLA+ D+SSL  GWEVY +FRL++LDQ KD +LILQ                 
Sbjct: 66  TKDHVSVYLALADSSSLSPGWEVYAVFRLYLLDQNKDNYLILQGNERRFHSVKREWGFDK 125

Query: 110 ------------------------EVFV-KETKKCTGECLSMKKLTSASNYKHVWKIKNF 144
                                   +VFV KE +   GECLSM K   A++ KHVWKI+NF
Sbjct: 126 FIPTGTFSDSSNGYLMEDTCMFGADVFVSKERRSGRGECLSMIK--DATSSKHVWKIENF 183

Query: 145 SKLPDNIYESEVFVAGDQKWYVYF 168
           SKL    Y+S  F AGD+KW + F
Sbjct: 184 SKLDKESYDSNAFFAGDRKWKIEF 207

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18401489|ref|NP_566576.1| TRAF-like family protein [Arabidopsis thaliana] gi|332642426|gb|AEE75947.1| TRAF-like family protein [Arabidopsis thaliana]

 Score =  161 bits (408), Expect = 9e-38,   Method: Compositional matrix adjust.
 Identities = 93/204 (45%), Positives = 124/204 (60%), Gaps = 44/204 (21%)

Query: 7   DQVAISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNEN 66
           D   I +SIS  PP H+++KIE+FS L ++ +E Y++  F+AGGYKWKLV+YPNGNK++N
Sbjct: 6   DYDEIIKSISDAPPTHYMVKIESFSLLTKHAIERYETESFEAGGYKWKLVLYPNGNKSKN 65

Query: 67  VKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQ----------------- 109
            KDH+S+YL++ D+SSL  GWEVY +FRL++LDQ KD +LILQ                 
Sbjct: 66  TKDHVSVYLSLADSSSLSPGWEVYAVFRLYLLDQNKDNYLILQGNERRFHSVKREWGFDK 125

Query: 110 ------------------------EVFV-KETKKCTGECLSMKKLTSASNYKHVWKIKNF 144
                                   +VFV KE +   GECLSM K   A++ KHVWKI+NF
Sbjct: 126 FIPTGTFSDASNGYLMEDTCMFGADVFVSKERRSGRGECLSMIK--DATSSKHVWKIENF 183

Query: 145 SKLPDNIYESEVFVAGDQKWYVYF 168
           SKL    Y+S  F AGD+KW + F
Sbjct: 184 SKLDKESYDSNAFFAGDRKWKIEF 207

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|11994555|dbj|BAB02742.1| unnamed protein product [Arabidopsis thaliana]

 Score =  161 bits (407), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 92/200 (46%), Positives = 123/200 (61%), Gaps = 44/200 (22%)

Query: 11  ISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDH 70
           I +SIS  PP H+++KIE+FS L ++ +E Y++  F+AGGYKWKLV+YPNGNK++N KDH
Sbjct: 5   IIKSISDAPPTHYMVKIESFSLLTKHAIERYETESFEAGGYKWKLVLYPNGNKSKNTKDH 64

Query: 71  ISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQ--------------------- 109
           +S+YL++ D+SSL  GWEVY +FRL++LDQ KD +LILQ                     
Sbjct: 65  VSVYLSLADSSSLSPGWEVYAVFRLYLLDQNKDNYLILQGNERRFHSVKREWGFDKFIPT 124

Query: 110 --------------------EVFV-KETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLP 148
                               +VFV KE +   GECLSM K   A++ KHVWKI+NFSKL 
Sbjct: 125 GTFSDASNGYLMEDTCMFGADVFVSKERRSGRGECLSMIK--DATSSKHVWKIENFSKLD 182

Query: 149 DNIYESEVFVAGDQKWYVYF 168
              Y+S  F AGD+KW + F
Sbjct: 183 KESYDSNAFFAGDRKWKIEF 202

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224101481|ref|XP_002312298.1| predicted protein [Populus trichocarpa] gi|222852118|gb|EEE89665.1| predicted protein [Populus trichocarpa]

 Score =  159 bits (402), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 86/172 (50%), Positives = 112/172 (65%), Gaps = 20/172 (11%)

Query: 14  SISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISI 73
           SIS   P H+ +KIE FS L +N VE Y++  F+AGGY WKLV+YP+GNK+ NVKD+IS+
Sbjct: 17  SISDASPVHYTVKIELFSLLAKNAVEKYETGVFEAGGYTWKLVLYPSGNKSRNVKDYISL 76

Query: 74  YLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQ------------------EVFV-K 114
           YLA VD SSL LGWEV+VIFRLF+LDQ KD +L+                    EVFV +
Sbjct: 77  YLAKVDASSLPLGWEVHVIFRLFLLDQNKDSYLLSTFNDSRYGFLLEDTCVLGAEVFVRR 136

Query: 115 ETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYV 166
           E  +  GE LSM K  +A+ +KH WKI+NF KL +   ES+ F +  +KW +
Sbjct: 137 ERSRGKGEVLSMIKQPTAA-FKHTWKIENFLKLDEKRQESQTFSSASEKWKI 187

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449441502|ref|XP_004138521.1| PREDICTED: BTB/POZ and MATH domain-containing protein 3-like [Cucumis sativus]

 Score =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 92/210 (43%), Positives = 123/210 (58%), Gaps = 50/210 (23%)

Query: 3   NDFVDQVAISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGN 62
            D +D+  ISR +S VPPAH+ +KIE+FS L +N V+ ++S EF+AGGYKWKLV++P+G+
Sbjct: 6   GDDIDE--ISRYVSDVPPAHYTVKIESFSLLTKNSVDQFESGEFEAGGYKWKLVLHPHGD 63

Query: 63  KNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQ------------- 109
           K++N  DHIS+YL +  T SL   WEV+V++RLF+LDQ KD +L ++             
Sbjct: 64  KSKNGNDHISLYLEIAGTDSLQPSWEVFVVYRLFLLDQNKDNYLTVEDGKWKPRRFRGMK 123

Query: 110 -------------------------------EVFV-KET-KKCTGECLSMKKLTSASNYK 136
                                          EVFV KE  K   GECLSM  + S   YK
Sbjct: 124 KQWGFDKYISLKEFKESSNGYLVDDVCVFGAEVFVCKENFKGGKGECLSM--IKSPVTYK 181

Query: 137 HVWKIKNFSKLPDNIYESEVFVAGDQKWYV 166
           HVWKI NFSKL    YES++F AGD+KW +
Sbjct: 182 HVWKIDNFSKLDAESYESKIFNAGDKKWKI 211

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449522688|ref|XP_004168358.1| PREDICTED: BTB/POZ and MATH domain-containing protein 3-like [Cucumis sativus]

 Score =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 92/210 (43%), Positives = 123/210 (58%), Gaps = 50/210 (23%)

Query: 3   NDFVDQVAISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGN 62
            D +D+  ISR +S VPPAH+ +KIE+FS L +N V+ ++S EF+AGGYKWKLV++P+G+
Sbjct: 6   GDDIDE--ISRYVSDVPPAHYTVKIESFSLLTKNSVDQFESGEFEAGGYKWKLVLHPHGD 63

Query: 63  KNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQ------------- 109
           K++N  DHIS+YL +  T SL   WEV+V++RLF+LDQ KD +L ++             
Sbjct: 64  KSKNGNDHISLYLEIAGTDSLQPSWEVFVVYRLFLLDQNKDNYLTVEDGKWKPRRFRGMK 123

Query: 110 -------------------------------EVFV-KET-KKCTGECLSMKKLTSASNYK 136
                                          EVFV KE  K   GECLSM  + S   YK
Sbjct: 124 KQWGFDKYISLKEFKESSNGYLVDDVCVFGAEVFVCKENFKGGKGECLSM--IKSPVTYK 181

Query: 137 HVWKIKNFSKLPDNIYESEVFVAGDQKWYV 166
           HVWKI NFSKL    YES++F AGD+KW +
Sbjct: 182 HVWKIDNFSKLDAESYESKIFNAGDKKWKI 211

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255556544|ref|XP_002519306.1| nucleic acid binding protein, putative [Ricinus communis] gi|223541621|gb|EEF43170.1| nucleic acid binding protein, putative [Ricinus communis]

 Score =  149 bits (376), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 84/196 (42%), Positives = 117/196 (59%), Gaps = 49/196 (25%)

Query: 14  SISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISI 73
           ++S   P H+ +KI+ FS L    VE Y+S  F+AGGYKWKLV+YP GNK++NV +H+S+
Sbjct: 162 TMSDASPTHYTVKIQLFSLLA---VEKYESGSFEAGGYKWKLVLYPKGNKSKNVMEHLSL 218

Query: 74  YLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLIL------------------------- 108
           Y+AM D+S+L LGWEV+V+FRLF+LDQ +D +LIL                         
Sbjct: 219 YIAMADSSNLQLGWEVHVVFRLFLLDQIRDNYLILPGKECRFHGFRLEWGFDQLIPLATL 278

Query: 109 ----------------QEVFVKETKKCT--GECLSMKKLTSASNYKHVWKIKNFSKLPDN 150
                            EVFV++ + CT  GECLSM K  S+S  K++W+ +NFSKL   
Sbjct: 279 KDTKNGYLVEDTCVFGAEVFVRK-ESCTGKGECLSMIK--SSSTSKNLWRFENFSKLDAE 335

Query: 151 IYESEVFVAGDQKWYV 166
             +S+ FVAGDQ+W +
Sbjct: 336 CNDSKTFVAGDQRWKI 351

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357479139|ref|XP_003609855.1| Ubiquitin carboxyl-terminal hydrolase [Medicago truncatula] gi|355510910|gb|AES92052.1| Ubiquitin carboxyl-terminal hydrolase [Medicago truncatula]

 Score =  146 bits (369), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 85/202 (42%), Positives = 113/202 (55%), Gaps = 47/202 (23%)

Query: 10  AISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKD 69
            ISRSI    P H+++KI++FS L  N +E Y+S  F+AGG+KWKLV+YP+GNK++NVKD
Sbjct: 7   GISRSIVEASPVHYIMKIQSFSLLTTNSIERYESGRFEAGGHKWKLVLYPSGNKSKNVKD 66

Query: 70  HISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQ-------------------- 109
           HIS+YLA+ ++SSL  GWE+YV F+LFV DQ  D +L+LQ                    
Sbjct: 67  HISLYLALEESSSLHPGWEIYVNFKLFVYDQNNDNYLVLQDDVKKEKRFHRMKVEWGFDQ 126

Query: 110 ------------------------EVFV-KETKKCTGECLSMKKLTSASNYKHVWKIKNF 144
                                   EVFV +E     GE L M K   A  YKHVW+IK+F
Sbjct: 127 FIPLKDFNIGSKGYLLDDICAFGAEVFVCRENYTGKGESLIMMK--DALPYKHVWEIKDF 184

Query: 145 SKLPDNIYESEVFVAGDQKWYV 166
           SKL     +S+ F  G+ KW +
Sbjct: 185 SKLDSECCDSKPFNVGNYKWQI 206

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255636923|gb|ACU18794.1| unknown [Glycine max]

 Score =  145 bits (367), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 84/204 (41%), Positives = 114/204 (55%), Gaps = 47/204 (23%)

Query: 8   QVAISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENV 67
           Q AI RS    PPAH+++KI++FS L +N +E Y+S +F+AGGYKWKLV+YP+GNK++N+
Sbjct: 4   QDAIPRSTVDAPPAHYVMKIQSFSLLAKNSIERYESGKFEAGGYKWKLVLYPSGNKSKNI 63

Query: 68  KDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLI-------------------- 107
           ++HIS+YLA+ DTSSL  GWE+YV FR F+ DQ  D +L+                    
Sbjct: 64  REHISLYLALDDTSSLHHGWEIYVNFRFFLHDQTNDNYLVGPDTVRNERRFHKMKAEWGI 123

Query: 108 ------------------------LQEVFV-KETKKCTGECLSMKKLTSASNYKHVWKIK 142
                                     EVFV KE     GECL M K   A  YKH+++  
Sbjct: 124 DQFIPLRDFNLASKGYLVDDTCAFGAEVFVCKERSTGKGECLVMMK--EAILYKHLYEFD 181

Query: 143 NFSKLPDNIYESEVFVAGDQKWYV 166
           N SKL    Y+S+ F AG+ KW +
Sbjct: 182 NLSKLDLECYDSKPFNAGNFKWKI 205

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	180
TAIR|locus:2089045	309	AT3G17380 "AT3G17380" [Arabido	0.572	0.333	0.582	5.3e-47
TAIR|locus:2179699	350	AT5G26280 "AT5G26280" [Arabido	0.594	0.305	0.398	3.7e-23
TAIR|locus:2151054	349	AT5G26300 "AT5G26300" [Arabido	0.522	0.269	0.410	1.9e-20
TAIR|locus:2092344	379	AT3G20370 "AT3G20370" [Arabido	0.516	0.245	0.364	1.4e-19
TAIR|locus:2179744	351	AT5G26260 "AT5G26260" [Arabido	0.566	0.290	0.359	2.9e-19
TAIR|locus:2092329	363	AT3G20360 "AT3G20360" [Arabido	0.588	0.292	0.345	4.3e-19
TAIR|locus:2118465	297	AT4G09770 "AT4G09770" [Arabido	0.588	0.356	0.309	1.3e-18
TAIR|locus:2056008	411	AT2G04190 "AT2G04190" [Arabido	0.55	0.240	0.336	1e-17
TAIR|locus:2151049	333	AT5G26290 "AT5G26290" [Arabido	0.811	0.438	0.354	2.6e-17
TAIR|locus:2055998	420	AT2G04170 "AT2G04170" [Arabido	0.522	0.223	0.442	4.7e-17

TAIR|locus:2089045 AT3G17380 "AT3G17380" [Arabidopsis thaliana (taxid:3702)]

 Score = 351 (128.6 bits), Expect = 5.3e-47, Sum P(2) = 5.3e-47
 Identities = 60/103 (58%), Positives = 83/103 (80%)

Query:     7 DQVAISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNEN 66
             D   I +SIS  PP H+++KIE+FS L ++ +E Y++  F+AGGYKWKLV+YPNGNK++N
Sbjct:     6 DYDEIIKSISDAPPTHYMVKIESFSLLTKHAIERYETESFEAGGYKWKLVLYPNGNKSKN 65

Query:    67 VKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQ 109
              KDH+S+YL++ D+SSL  GWEVY +FRL++LDQ KD +LILQ
Sbjct:    66 TKDHVSVYLSLADSSSLSPGWEVYAVFRLYLLDQNKDNYLILQ 108

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2179699 AT5G26280 "AT5G26280" [Arabidopsis thaliana (taxid:3702)]

 Score = 216 (81.1 bits), Expect = 3.7e-23, Sum P(2) = 3.7e-23
 Identities = 43/108 (39%), Positives = 70/108 (64%)

Query:     7 DQVAISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNEN 66
             + + ++R +    P+  ++ I +FS +++   E Y+S  F+A GYKW+LV+Y NGNKN+ 
Sbjct:    46 ENLGVTRELREERPSSKIVTITSFS-VIKGRGEPYESSVFEAAGYKWRLVLYVNGNKNDG 104

Query:    67 VKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVK 114
               DHIS+Y  + +T+SL LGWEV V  +LFV + K  ++L + +  VK
Sbjct:   105 GNDHISLYARIEETNSLPLGWEVNVDLKLFVHNGKLHKYLTVTDGLVK 152

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0016020 "membrane" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

GO:0000041 "transition metal ion transport" evidence=RCA

TAIR|locus:2151054 AT5G26300 "AT5G26300" [Arabidopsis thaliana (taxid:3702)]

 Score = 196 (74.1 bits), Expect = 1.9e-20, Sum P(2) = 1.9e-20
 Identities = 39/95 (41%), Positives = 63/95 (66%)

Query:    20 PAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVD 79
             P+  +L I  FS +++  VE Y+S  F+A GYKW+LV+Y NGN N++  DHIS+Y+ + +
Sbjct:    59 PSSKILTITNFS-VIKGRVEPYESSVFEAAGYKWRLVLYVNGNPNDSGNDHISLYVRIEE 117

Query:    80 TSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVK 114
             T  L  GWEV V  +LF+ + K +++L + +  +K
Sbjct:   118 TEYLPRGWEVNVDLKLFIHNGKLNKYLAISDGTLK 152

GO:0003674 "molecular_function" evidence=ND

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0031225 "anchored to membrane" evidence=TAS

TAIR|locus:2092344 AT3G20370 "AT3G20370" [Arabidopsis thaliana (taxid:3702)]

 Score = 187 (70.9 bits), Expect = 1.4e-19, Sum P(2) = 1.4e-19
 Identities = 35/96 (36%), Positives = 63/96 (65%)

Query:    19 PPAHFLLKIEAFSSLVEND-VENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAM 77
             PP+ + LK+E+F++L+++   E Y S  F  GGY W LVV+PNGNK ++   ++S+Y+A 
Sbjct:    84 PPSSYSLKMESFNTLLKSTYTEKYVSRPFSVGGYNWTLVVFPNGNKKDSGSGYLSLYVA- 142

Query:    78 VDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFV 113
             +D S+LG   E+Y   R ++ ++ + ++  +Q+  V
Sbjct:   143 IDNSTLGQQ-EIYADLRFYIFNKNERKYFTIQDTDV 177

GO:0003674 "molecular_function" evidence=ND

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0016020 "membrane" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

TAIR|locus:2179744 AT5G26260 "AT5G26260" [Arabidopsis thaliana (taxid:3702)]

 Score = 178 (67.7 bits), Expect = 2.9e-19, Sum P(2) = 2.9e-19
 Identities = 37/103 (35%), Positives = 64/103 (62%)

Query:    12 SRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHI 71
             +R +    P+  ++ I +FS ++++  E Y+S  F+A GYKW+LV+Y  GN    + +HI
Sbjct:    52 TRELRDERPSSKIVTITSFS-VIKDRGEPYESSIFEAAGYKWRLVLYVKGNPKGGINNHI 110

Query:    72 SIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVK 114
             S+Y  + +T +L  GWEV V  +LFV ++K  ++L + +  VK
Sbjct:   111 SLYARIEETETLPRGWEVNVDLKLFVHNRKLKKYLSVTDGTVK 153

GO:0003674 "molecular_function" evidence=ND

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

TAIR|locus:2092329 AT3G20360 "AT3G20360" [Arabidopsis thaliana (taxid:3702)]

 Score = 190 (71.9 bits), Expect = 4.3e-19, Sum P(2) = 4.3e-19
 Identities = 38/110 (34%), Positives = 70/110 (63%)

Query:     8 QVAISRSISHV---PPAHFLLKIEAFSSLVEND-VENYKSLEFDAGGYKWKLVVYPNGNK 63
             +V++S ++  +   PP+ + LK+E+F++L+++   E Y+S  F  G Y W LVVYP GNK
Sbjct:    51 KVSLSSTVKGLRERPPSSYSLKMESFNTLMKSVYTERYESRPFRVGRYNWTLVVYPKGNK 110

Query:    64 NENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFV 113
             N+N   HIS+Y+ + +++      EV+V  R +V ++K+ ++  +Q+  V
Sbjct:   111 NDNGTGHISLYVVLDNSTLTSQSEEVHVDLRFYVFNKKETKYFTIQDTDV 160

GO:0003674 "molecular_function" evidence=ND

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2118465 AT4G09770 "AT4G09770" [Arabidopsis thaliana (taxid:3702)]

 Score = 167 (63.8 bits), Expect = 1.3e-18, Sum P(2) = 1.3e-18
 Identities = 34/110 (30%), Positives = 61/110 (55%)

Query:    14 SISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISI 73
             +I    P+ +L+K+  FS  V+   + Y+S +FD GG+KW+L+ YP G   E  KDH+SI
Sbjct:     3 TIREEAPSSYLMKLVGFSE-VKFSHQPYESADFDVGGHKWRLIFYPAGKLEEGGKDHVSI 61

Query:    74 YLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVKETKKCTGEC 123
             Y A ++  ++G   ++    + F+ +    ++ + Q+  +K   K   EC
Sbjct:    62 Y-ARIE--NVGASMQIDAELKFFIYNHNNKQYSVFQDGTMKHYNKEKKEC 108

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

TAIR|locus:2056008 AT2G04190 "AT2G04190" [Arabidopsis thaliana (taxid:3702)]

 Score = 174 (66.3 bits), Expect = 1.0e-17, Sum P(2) = 1.0e-17
 Identities = 34/101 (33%), Positives = 63/101 (62%)

Query:    11 ISRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAG-GYKWKLVVYPNGNKNENVKD 69
             ++R++   PP+H +L I  FS ++  + E Y+S  F+A   +KW+L++Y NGN+N+   +
Sbjct:   110 VTRTLRDEPPSHRILTITNFSEIIGRE-EPYESSVFEAYFEHKWRLILYVNGNQNDGGSN 168

Query:    70 HISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQE 110
             HIS+YL   +T  L     +  + +LFV + K+D++L + +
Sbjct:   169 HISLYLRSEETDHLTYDGSINFVLKLFVYNGKQDKYLTVTD 209

GO:0003674 "molecular_function" evidence=ND

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005739 "mitochondrion" evidence=IDA

TAIR|locus:2151049 AT5G26290 "AT5G26290" [Arabidopsis thaliana (taxid:3702)]

 Score = 213 (80.0 bits), Expect = 2.6e-17, P = 2.6e-17
 Identities = 56/158 (35%), Positives = 87/158 (55%)

Query:    20 PAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVD 79
             P+  +L I +FS ++    E Y+S  F+A GYKW+LV+Y NGN+ +  KDH+S+Y  +V+
Sbjct:    52 PSDKILSITSFS-IIRTRPEPYESSVFEAVGYKWRLVLYVNGNEKDGGKDHVSLYAKIVE 110

Query:    80 TSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVW 139
             T SL +GWEV V  +LFV + K +++LI   V VK     T E L   +L   S +    
Sbjct:   111 TESLPVGWEVNVDLKLFVYNGKLNKYLI---VTVKRYNNATKE-LGYGQLIPQSTFYD-- 164

Query:   140 KIKNFSKLPDNIYESEVFVA--GDQKWYVYFLKWCSNP 175
                 + +     + +E+++     QK  V F+   SNP
Sbjct:   165 GNDGYREQDTGTFGAEIYIVKPAQQKEKVTFI---SNP 199

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0031225 "anchored to membrane" evidence=TAS

TAIR|locus:2055998 AT2G04170 "AT2G04170" [Arabidopsis thaliana (taxid:3702)]

 Score = 215 (80.7 bits), Expect = 4.7e-17, P = 4.7e-17
 Identities = 42/95 (44%), Positives = 68/95 (71%)

Query:    20 PAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVD 79
             P++ +L I +FS +++   E Y+S  F+AGGYKW+LV+Y NGN+N+   +HIS+Y+ + +
Sbjct:   129 PSNKILTITSFS-VIKGRGEPYESSVFEAGGYKWRLVLYVNGNQNDGGNNHISLYVRIEE 187

Query:    80 TSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVK 114
             T SL  GWEV V  +LFV + K+ ++LI+++  VK
Sbjct:   188 TESLPKGWEVNVELKLFVYNGKQRKYLIVKDGIVK 222

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	180
cd00121	126	cd00121, MATH, MATH (meprin and TRAF-C homology) d	4e-16
pfam00917	116	pfam00917, MATH, MATH domain	1e-05
cd00121	126	cd00121, MATH, MATH (meprin and TRAF-C homology) d	2e-04
smart00061	95	smart00061, MATH, meprin and TRAF homology	2e-04
cd03775	134	cd03775, MATH_Ubp21p, Ubiquitin-specific protease	0.004

>gnl|CDD|238068 cd00121, MATH, MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins

 Score = 70.1 bits (172), Expect = 4e-16
 Identities = 31/100 (31%), Positives = 48/100 (48%), Gaps = 5/100 (5%)

Query: 22  HFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTS 81
               KI  FS L     E+  S  F+ GGYKW++ +YPNG+      D++S+YL +    
Sbjct: 2   KHTWKIVNFSELEG---ESIYSPPFEVGGYKWRIRIYPNGDGES--GDYLSLYLELDKGE 56

Query: 82  SLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVKETKKCTG 121
           S    W V   F L +++Q   + L      V  ++K +G
Sbjct: 57  SDLEKWSVRAEFTLKLVNQNGGKSLSKSFTHVFFSEKGSG 96

Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains. Length = 126

>gnl|CDD|216189 pfam00917, MATH, MATH domain

 Score = 42.3 bits (100), Expect = 1e-05
 Identities = 26/105 (24%), Positives = 39/105 (37%), Gaps = 11/105 (10%)

Query: 30  FSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYL-AMVDTSSLGLGWE 88
           FS + E +   Y S   +  G  W+L +Y NG         + +YL          LGW 
Sbjct: 4   FSKIKEGE-NYYTSPYEERFGIPWRLRIYRNG-------GFLGLYLHCEKGEKDELLGWS 55

Query: 89  VYVIFRLFVLDQ--KKDEFLILQEVFVKETKKCTGECLSMKKLTS 131
           +   F L ++    K         VF K T    G+ +S   L +
Sbjct: 56  IETEFTLKLVSDNGKSLTKRNKSHVFTKPTGYGWGKFISWDDLEN 100

This motif has been called the Meprin And TRAF-Homology (MATH) domain. This domain is hugely expanded in the nematode C. elegans. Length = 116

>gnl|CDD|238068 cd00121, MATH, MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins

 Score = 39.3 bits (92), Expect = 2e-04
 Identities = 14/33 (42%), Positives = 16/33 (48%)

Query: 136 KHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYF 168
           KH WKI NFS+L      S  F  G  KW +  
Sbjct: 2   KHTWKIVNFSELEGESIYSPPFEVGGYKWRIRI 34

Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains. Length = 126

>gnl|CDD|214496 smart00061, MATH, meprin and TRAF homology

 Score = 38.0 bits (89), Expect = 2e-04
 Identities = 16/75 (21%), Positives = 26/75 (34%), Gaps = 9/75 (12%)

Query: 26  KIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGL 85
             +  S L E   E+Y S   +     W+L +Y            +S+YL          
Sbjct: 5   TFKNVSRLEEG--ESYFSPSEEHFNIPWRLKIYRKN-------GFLSLYLHCEKEECDSR 55

Query: 86  GWEVYVIFRLFVLDQ 100
            W +   F L ++ Q
Sbjct: 56  KWSIEAEFTLKLVSQ 70

Length = 95

>gnl|CDD|239744 cd03775, MATH_Ubp21p, Ubiquitin-specific protease 21 (Ubp21p) family, MATH domain; composed of fungal proteins with similarity to Ubp21p of fission yeast

 Score = 35.4 bits (82), Expect = 0.004
 Identities = 12/38 (31%), Positives = 23/38 (60%), Gaps = 3/38 (7%)

Query: 39 ENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLA 76
          +   S +F  GG++W+++++P GN   +    +SIYL 
Sbjct: 15 KKVHSPKFKCGGFEWRILLFPQGN---SQTGGVSIYLE 49

Ubp21p is a deubiquitinating enzyme that may be involved in the regulation of the protein kinase Prp4p, which controls the formation of active spliceosomes. Members of this family are similar to human HAUSP (Herpesvirus-associated ubiquitin-specific protease) in that they contain an N-terminal MATH domain and a C-terminal catalytic protease (C19 family) domain. HAUSP is also an ubiquitin-specific protease that specifically catalyzes the deubiquitylation of p53 and MDM2. The MATH domain of HAUSP contains the binding site for p53 and MDM2. Similarly, the MATH domain of members in this family may be involved in substrate binding. Length = 134

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	180
cd03775	134	MATH_Ubp21p Ubiquitin-specific protease 21 (Ubp21p	99.91
cd03774	139	MATH_SPOP Speckle-type POZ protein (SPOP) family,	99.87
cd03772	137	MATH_HAUSP Herpesvirus-associated ubiquitin-specif	99.87
cd00270	149	MATH_TRAF_C Tumor Necrosis Factor Receptor (TNFR)-	99.86
cd03780	148	MATH_TRAF5 Tumor Necrosis Factor Receptor (TNFR)-A	99.86
cd03776	147	MATH_TRAF6 Tumor Necrosis Factor Receptor (TNFR)-A	99.85
cd03773	132	MATH_TRIM37 Tripartite motif containing protein 37	99.85
cd03781	154	MATH_TRAF4 Tumor Necrosis Factor Receptor (TNFR)-A	99.83
cd03771	167	MATH_Meprin Meprin family, MATH domain; Meprins ar	99.83
cd03777	186	MATH_TRAF3 Tumor Necrosis Factor Receptor (TNFR)-A	99.83
cd03779	147	MATH_TRAF1 Tumor Necrosis Factor Receptor (TNFR) A	99.8
cd03778	164	MATH_TRAF2 Tumor Necrosis Factor Receptor (TNFR) A	99.78
cd00121	126	MATH MATH (meprin and TRAF-C homology) domain; an	99.74
smart00061	95	MATH meprin and TRAF homology.	99.71
PF00917	119	MATH: MATH domain; InterPro: IPR002083 Although ap	99.53
cd03782	167	MATH_Meprin_Beta Meprin family, Beta subunit, MATH	99.52
COG5077	1089	Ubiquitin carboxyl-terminal hydrolase [Posttransla	99.5
cd03783	167	MATH_Meprin_Alpha Meprin family, Alpha subunit, MA	99.44
cd03773	132	MATH_TRIM37 Tripartite motif containing protein 37	98.9
cd03775	134	MATH_Ubp21p Ubiquitin-specific protease 21 (Ubp21p	98.88
KOG1987	297	consensus Speckle-type POZ protein SPOP and relate	98.81
cd03772	137	MATH_HAUSP Herpesvirus-associated ubiquitin-specif	98.63
cd03774	139	MATH_SPOP Speckle-type POZ protein (SPOP) family,	98.53
cd03777	186	MATH_TRAF3 Tumor Necrosis Factor Receptor (TNFR)-A	98.14
smart00061	95	MATH meprin and TRAF homology.	98.09
cd00121	126	MATH MATH (meprin and TRAF-C homology) domain; an	98.05
COG5077	1089	Ubiquitin carboxyl-terminal hydrolase [Posttransla	97.94
cd03778	164	MATH_TRAF2 Tumor Necrosis Factor Receptor (TNFR) A	97.66
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.48
PF00917	119	MATH: MATH domain; InterPro: IPR002083 Although ap	97.12
cd00270	149	MATH_TRAF_C Tumor Necrosis Factor Receptor (TNFR)-	97.04
cd03776	147	MATH_TRAF6 Tumor Necrosis Factor Receptor (TNFR)-A	96.64
cd03780	148	MATH_TRAF5 Tumor Necrosis Factor Receptor (TNFR)-A	96.61
cd03781	154	MATH_TRAF4 Tumor Necrosis Factor Receptor (TNFR)-A	96.61
KOG1863	1093	consensus Ubiquitin carboxyl-terminal hydrolase [P	96.25
cd03779	147	MATH_TRAF1 Tumor Necrosis Factor Receptor (TNFR) A	94.78

>cd03775 MATH_Ubp21p Ubiquitin-specific protease 21 (Ubp21p) family, MATH domain; composed of fungal proteins with similarity to Ubp21p of fission yeast

Probab=99.91  E-value=6.2e-24  Score=158.14  Aligned_cols=123  Identities=20%  Similarity=0.434  Sum_probs=96.4

Q ss_pred             EEEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC----CCCCcEEEEEEEEEE
Q 030279           22 HFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS----LGLGWEVYVIFRLFV   97 (180)
Q Consensus        22 ~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~----~~~~~~~~a~f~~~l   97 (180)
                      +|+|+|+|||++    ++.+.|++|.||||+|+|.+||+|+..   .+||||||++.+...    ++.+|.++|+|+|.|
T Consensus         2 ~f~w~I~~fS~~----~~~~~S~~F~vGG~~W~l~~yP~G~~~---~~~iSlyL~l~~~~~~~~~~~~~~~v~a~f~~~l   74 (134)
T cd03775           2 SFTWRIKNWSEL----EKKVHSPKFKCGGFEWRILLFPQGNSQ---TGGVSIYLEPHPEEEEKAPLDEDWSVCAQFALVI   74 (134)
T ss_pred             cEEEEECCcccC----CcceeCCCEEECCeeEEEEEeCCCCCC---CCeEEEEEEecCcccccccCCCCCeEEEEEEEEE
Confidence            699999999997    589999999999999999999999862   789999999976553    367899999999999


Q ss_pred             EeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCc----cCCCcEEeCCeEEEEEEe
Q 030279           98 LDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNI----YESEVFVAGDQKWYVYFL  169 (180)
Q Consensus        98 lnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~----~~S~~F~vg~~~w~i~~y  169 (180)
                      +||.++.....           ....      +.|......||+..|+++.++.    ....+|+++| ...|.+|
T Consensus        75 ~n~~~~~~~~~-----------~~~~------~~F~~~~~~wG~~~fi~~~~L~~~~~~~~~g~l~nD-~l~I~~~  132 (134)
T cd03775          75 SNPGDPSIQLS-----------NVAH------HRFNAEDKDWGFTRFIELRKLAHRTPDKPSPFLENG-ELNITVY  132 (134)
T ss_pred             EcCCCCccceE-----------ccce------eEeCCCCCCCChhHcccHHHHcccccCCCCceeECC-EEEEEEE
Confidence            99986543331           1111      1233345689999999987654    2356899999 6667665

Ubp21p is a deubiquitinating enzyme that may be involved in the regulation of the protein kinase Prp4p, which controls the formation of active spliceosomes. Members of this family are similar to human HAUSP (Herpesvirus-associated ubiquitin-specific protease) in that they contain an N-terminal MATH domain and a C-terminal catalytic protease (C19 family) domain. HAUSP is also an ubiquitin-specific protease that specifically catalyzes the deubiquitylation of p53 and MDM2. The MATH domain of HAUSP contains the binding site for p53 and MDM2. Similarly, the MATH domain of members in this family may be involved in substrate binding.

>cd03774 MATH_SPOP Speckle-type POZ protein (SPOP) family, MATH domain; composed of proteins with similarity to human SPOP

Probab=99.87  E-value=4.7e-22  Score=148.65  Aligned_cols=121  Identities=26%  Similarity=0.357  Sum_probs=93.1

Q ss_pred             CCcEEEEEEcCccccccCCCCeEEccceeecCe---EEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEEEEEEE
Q 030279           19 PPAHFLLKIEAFSSLVENDVENYKSLEFDAGGY---KWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRL   95 (180)
Q Consensus        19 ~~~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~---~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~   95 (180)
                      ..-+|+|+|+|||++++..++.+.|++|.+|||   +|+|.+||+|+.. +..+||||||++++..    .++++|+|+|
T Consensus         3 ~~~~~~w~I~~fS~~~~~~~~~i~S~~F~vgg~~~~~W~l~~yP~G~~~-~~~~~iSlyL~l~~~~----~~~v~a~f~~   77 (139)
T cd03774           3 VKFCYMWTISNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDE-ESKDYLSLYLLLVSCP----KSEVRAKFKF   77 (139)
T ss_pred             eEEEEEEEECCchhhhhcCCCEEECCCeecCCcCCceEEEEEeCCCCCC-CCCCeEEEEEEEccCC----CCcEEEEEEE
Confidence            456899999999998755578999999999995   9999999999863 4578999999997643    2579999999


Q ss_pred             EEEeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCC
Q 030279           96 FVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGD  161 (180)
Q Consensus        96 ~llnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~  161 (180)
                      .|+||.+++....          ......      .+.. ...||+.+|.++.++.....+|+++|
T Consensus        78 ~l~n~~~~~~~~~----------~~~~~~------~f~~-~~~wG~~~fi~~~~L~~~~~g~l~dD  126 (139)
T cd03774          78 SILNAKGEETKAM----------ESQRAY------RFVQ-GKDWGFKKFIRRDFLLDEANGLLPDD  126 (139)
T ss_pred             EEEecCCCeeeee----------cccCcE------eCCC-CCccCHHHeeeHHHhhhhhcccccCC
Confidence            9999998764331          111111      1222 35899999999887644456799988

SPOP was isolated as a novel antigen recognized by serum from a scleroderma patient, whose overexpression in COS cells results in a discrete speckled pattern in the nuclei. It contains an N-terminal MATH domain and a C-terminal BTB (also called POZ) domain. Together with Cul3, SPOP constitutes an ubiquitin E3 ligase which is able to ubiquitinate the PcG protein BMI1, the variant histone macroH2A1 and the death domain-associated protein Daxx. Therefore, SPOP may be involved in the regulation of these proteins and may play a role in transcriptional regulation, apoptosis and X-chromosome inactivation. Cul3 binds to the BTB domain of SPOP whereas Daxx and the macroH2A1 nonhistone region have been shown to bind to the MATH domain. Both MATH and BTB domains are necessary for the nuclear speckled accumulation of SPOP. There are many proteins, mostly uncharacterized, conta

>cd03772 MATH_HAUSP Herpesvirus-associated ubiquitin-specific protease (HAUSP, also known as USP7) family, N-terminal MATH (TRAF-like) domain; composed of proteins similar to human HAUSP, an enzyme that specifically catalyzes the deubiquitylation of p53 and MDM2, hence playing an important role in the p53-MDM2 pathway

Probab=99.87  E-value=1.8e-21  Score=145.31  Aligned_cols=125  Identities=19%  Similarity=0.255  Sum_probs=94.8

Q ss_pred             CcEEEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCC-CCCCcEEEEEEeecCCCCCCCcEEEEEEEEEEE
Q 030279           20 PAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNE-NVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVL   98 (180)
Q Consensus        20 ~~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~-~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~~ll   98 (180)
                      .++|+|+|.|||++    ++.+.|+.|.+|||.|+|.+||+|+... +..+||||||++.+.. ...+|.+.|+|+|.|+
T Consensus         2 ~~~~~~~I~~~S~l----~e~~~S~~f~vgG~~W~i~~~P~g~~~~~~~~~~lsvyL~~~~~~-~~~~w~i~a~~~~~l~   76 (137)
T cd03772           2 EATFSFTVERFSRL----SESVLSPPCFVRNLPWKIMVMPRNYPDRNPHQKSVGFFLQCNAES-DSTSWSCHAQAVLRII   76 (137)
T ss_pred             CcEEEEEECCcccC----CCcEECCCEEECCcceEEEEEeCCCCCCCCCCCeEEEEEeeCCcC-CCCCCeEEEEEEEEEE
Confidence            57899999999998    5789999999999999999999996531 2358999999997654 3347999999999999


Q ss_pred             eCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCCeEEEEE
Q 030279           99 DQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVY  167 (180)
Q Consensus        99 nq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~  167 (180)
                      ||.+......+          ....       .+......||+.+|++++++...+.+|+++|+ ..|.
T Consensus        77 ~~~~~~~~~~~----------~~~~-------~f~~~~~~~G~~~fi~~~~L~~~~sgyl~~D~-l~Ie  127 (137)
T cd03772          77 NYKDDEPSFSR----------RISH-------LFFSKENDWGFSNFMTWSEVTDPEKGFIEDDT-ITLE  127 (137)
T ss_pred             cCCCCcccEEE----------eeee-------EEcCCCCCccchheeEHHHhcCCCCCcEECCE-EEEE
Confidence            99854332211          0111       12223347999999999887666788999994 3443

It contains an N-terminal TRAF-like domain and a C-terminal catalytic protease (C19 family) domain. The tumor suppressor p53 protein is a transcription factor that responds to many cellular stress signals and is regulated primarily through ubiquitylation and subsequent degradation. MDM2 is a RING-finger E3 ubiquitin ligase that promotes p53 ubiquitinylation. p53 and MDM2 bind to the same site in the N-terminal TRAF-like domain of HAUSP in a mutually exclusive manner. HAUSP also interacts with the Epstein-Barr nuclear antigen 1 (EBNA1) protein of the Epstein-Barr virus (EBV), which efficiently immortalizes infected cells predisposing the host to a variety of cancers. EBNA1

>cd00270 MATH_TRAF_C Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link cell surface TNFRs and receptors of the interleukin-1/Toll-like family to downstream kinase signaling cascades which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems

Probab=99.86  E-value=1.2e-21  Score=147.81  Aligned_cols=135  Identities=21%  Similarity=0.324  Sum_probs=94.6

Q ss_pred             cEEEEEEcCcccccc----CCCCeEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEEEEEE
Q 030279           21 AHFLLKIEAFSSLVE----NDVENYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEVYVIF   93 (180)
Q Consensus        21 ~~~~w~I~~fS~l~~----~~~~~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~~a~f   93 (180)
                      |+|+|+|++||++++    ..++.++|++|.+|  ||+|+|.+||+|+.. +..+||||||++++... .+.+|++.|+|
T Consensus         1 g~~~w~I~~fs~~~~~~~~~~~~~~~S~~F~vg~~G~~w~i~~yP~G~~~-~~~~~lsl~L~l~~~~~d~~~~w~~~~~~   79 (149)
T cd00270           1 GVLIWKIKDYSRKLQEAVAGSNTVLYSPPFYTSRYGYKLCLRLYLNGDGT-GKGTHLSLFVHVMKGEYDALLEWPFRGKI   79 (149)
T ss_pred             CEEEEEECCHHHHHHHHhcCCCceEECCCcccCCCCceEEEEEEeCCCCC-CCCCEEEEEEEEeccCCCccccCCccceE
Confidence            689999999999865    24679999999999  999999999999863 35689999999987643 24679999999


Q ss_pred             EEEEEeCCCC--ceeEEeeEE-eccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCCeEEEEE
Q 030279           94 RLFVLDQKKD--EFLILQEVF-VKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVY  167 (180)
Q Consensus        94 ~~~llnq~~~--~~~~~~dvF-~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~  167 (180)
                      +|+|+||.++  .... .+.| ..+      +...|.. .......-.||+..|.++.++.  +.+|+++|+ ..|.
T Consensus        80 ~~~l~d~~~~~~~~~~-~~~~~~~~------~~~~f~~-~~~~~~~~~~G~~~fi~~~~L~--~~gfl~dD~-l~I~  145 (149)
T cd00270          80 TLTLLDQSDDSKRKHI-TETFMPDP------NSSAFQR-PPTGENNIGFGYPEFVPLEKLE--SRGYVKDDT-LFIK  145 (149)
T ss_pred             EEEEECCCCccccCce-EEEEEcCC------chHhhcC-CCcccCCCCcCcceEeEHHHhc--cCCCEeCCE-EEEE
Confidence            9999999874  1111 0011 000      0000100 0001234579999999988763  457999994 4443

There are at least six mammalian and three Drosophila proteins containing TRAF domains. The mammalian TRAFs display varying expression profiles, indicating independent and cell type-specific regulation. They display distinct, as well as overlapping functions and interactions with receptors. Most TRAFs, except TRAF1, share N-terminal homology and contain a RING domain, multiple zinc finger domains, and a TRAF domain. TRAFs form homo- and heterotrimers through its TRAF domain. The TRAF domain can be divided into a more divergent N-ter

>cd03780 MATH_TRAF5 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF5 subfamily, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses

Probab=99.86  E-value=2.3e-21  Score=146.86  Aligned_cols=131  Identities=19%  Similarity=0.276  Sum_probs=94.4

Q ss_pred             cEEEEEEcCcccccc--CCCC--eEEccce--eecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCC-CCCcEEEEEE
Q 030279           21 AHFLLKIEAFSSLVE--NDVE--NYKSLEF--DAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSL-GLGWEVYVIF   93 (180)
Q Consensus        21 ~~~~w~I~~fS~l~~--~~~~--~~~S~~F--~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~-~~~~~~~a~f   93 (180)
                      |+|+|+|++||++++  ..|+  .+.|++|  .+|||+|+|.+||||+.. +..+||||||+|+..+.- -..|++.+++
T Consensus         1 g~~vwkI~~ys~~~~~~~~g~~~~i~S~~Fyt~~~Gy~w~i~~ypnG~~~-~~~~~iSv~l~l~~g~~D~~l~wp~~~~~   79 (148)
T cd03780           1 GKLIWKVTDYKMKKKEAVDGHTVSIFSQPFYTSRCGYRLCARAYLNGDGS-GKGTHLSLYFVVMRGEFDSLLQWPFRQRV   79 (148)
T ss_pred             CEEEEEECCHHHHHHhhcCCCccEEECCCcccCCCCeeEEEEEEcCCCCC-CCCCEEEEEEEEecCccccccCcceEEEE
Confidence            689999999999974  3566  8999999  999999999999999984 467899999999975321 2469999999


Q ss_pred             EEEEEeCCCCceeEEeeEE-eccccccccceEeceecccCC-CcceEEEeccccCCCCCccCCCcEEeCCe
Q 030279           94 RLFVLDQKKDEFLILQEVF-VKETKKCTGECLSMKKLTSAS-NYKHVWKIKNFSKLPDNIYESEVFVAGDQ  162 (180)
Q Consensus        94 ~~~llnq~~~~~~~~~dvF-~~~~~~~~~e~~s~~~~~~~~-~~~~tW~i~nFs~l~~~~~~S~~F~vg~~  162 (180)
                      +|+|+||.+.+..+. +++ .++      +...|.+   +. .....||..+|+.++.+.-.+..|+.+|+
T Consensus        80 tfsLlDq~~~~~~~~-~~~~~~~------~~~~F~r---p~~~~n~~~G~~~Fi~~~~Le~s~~~ylkdD~  140 (148)
T cd03780          80 TLMLLDQSGKKNHIM-ETFKADP------NSSSFKR---PDGEMNIASGCPRFVAHSVLENAKNTYIKDDT  140 (148)
T ss_pred             EEEEECCCCCCCCcc-eeeecCC------ccccccC---CCCCCCCCcChhheeEHHHhhcccCCcCcCCE
Confidence            999999986543211 122 111      0111211   11 11346999999998877444468888884

TRAF5 was identified as an activator of nuclear factor-kappaB and a regulator of lymphotoxin-beta receptor and CD40 signaling. Its interaction with CD40 is indirect, involving hetero-oligomerization with TRAF3. In addition, TRAF5 has been shown to associate with other TNFRs including CD27, CD30, OX40 and GITR (glucocorticoid-induced TNFR). It plays a role in modulating Th2 immune responses (driven by OX40 costimulation) and T-cell activation (triggered by GITR). It is also involved in osteoclastogenesis. TRAF5 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more dive

>cd03776 MATH_TRAF6 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF6 subfamily, TRAF domain, C-terminal MATH subdomain; composed of proteins with similarity to human TRAF6, including the Drosophila protein DTRAF2

Probab=99.85  E-value=3e-21  Score=145.77  Aligned_cols=136  Identities=21%  Similarity=0.271  Sum_probs=92.5

Q ss_pred             cEEEEEEcCcccccc--CCCC--eEEccceee--cCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEEEEEE
Q 030279           21 AHFLLKIEAFSSLVE--NDVE--NYKSLEFDA--GGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEVYVIF   93 (180)
Q Consensus        21 ~~~~w~I~~fS~l~~--~~~~--~~~S~~F~v--gG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~~a~f   93 (180)
                      |+|+|+|.+||++++  ..++  .+.|++|.+  |||+|+|.+||+|... +..+|||+||+|++... ...+|++.|+|
T Consensus         1 g~h~~~I~~yS~~~~~~~~g~~~~i~S~~F~~~~gGy~W~i~~yP~G~~~-~~~~~lS~~L~l~~~~~d~~l~wpv~a~~   79 (147)
T cd03776           1 GIYVWKIKNFSNLRRSMEAGSPVVIHSPGFYTSPPGYKLCARLNLSLPEA-RCPNYISLFVHLMQGENDSHLDWPFQGTI   79 (147)
T ss_pred             CEEEEEECCHHHHHHHHhcCCCceEECCCcccCCCCceEEEEEEeCCCCC-CCCCEEEEEEEEeccCCCcccCCccccee
Confidence            689999999998654  2455  488999985  7999999999999874 46789999999987543 24579999999


Q ss_pred             EEEEEeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCCeEEEEE
Q 030279           94 RLFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVY  167 (180)
Q Consensus        94 ~~~llnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~  167 (180)
                      +|.|+||.++..... +.+.     ...+...|.+..+ ....-.||+.+|.+++.+  .+.+|+++|+ ..|.
T Consensus        80 ~~~lldq~~~~~~~~-~~~~-----~~~~~~~F~~p~~-~~~~~~~G~~~fi~~~~L--e~~~yl~dD~-l~I~  143 (147)
T cd03776          80 TLTLLDQSEPRQNIH-ETMM-----SKPELLAFQRPTT-DRNPKGFGYVEFAHIEDL--LQRGFVKNDT-LLIK  143 (147)
T ss_pred             EEEEECCCcccCccE-EEEE-----cCCChHhhcCCCc-CCCCCCeeEceeeEHHHh--hhCCCccCCE-EEEE
Confidence            999999986433211 0010     0000000111000 012346999999998766  3457999984 4443

TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF6 is the most divergent in its TRAF domain among the mammalian TRAFs. In addition to mediating TNFR family signaling, it is also an essential signaling molecule of the interleukin-1/Toll-like receptor superfamily. Whereas other TRAF molecules display similar and overlapping TNFR-binding specificities, TRAF6 binds completely different sites on receptors such as CD40 and RANK. TRAF6 serves as a molecular bridge between innate and adaptive immunity and plays a central role in osteoimmunology. DTRAF2, as an activator of nuclear factor-kapp

>cd03773 MATH_TRIM37 Tripartite motif containing protein 37 (TRIM37) family, MATH domain; TRIM37 is a peroxisomal protein and is a member of the tripartite motif (TRIM) protein subfamily, also known as the RING-B-box-coiled-coil (RBCC) subfamily of zinc-finger proteins

Probab=99.85  E-value=7e-21  Score=140.77  Aligned_cols=118  Identities=21%  Similarity=0.320  Sum_probs=89.6

Q ss_pred             CCCcEEEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEEEEEEEEE
Q 030279           18 VPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFV   97 (180)
Q Consensus        18 ~~~~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~~l   97 (180)
                      +..++++|+|.|||++++ .++++.|++|.+|||+|+|.+||+|+.. +..+||||||++.+..    ++.+.++|+|.|
T Consensus         2 ~~~~~~~~~I~~fS~~~~-~~~~~~S~~F~vgG~~W~i~~yP~G~~~-~~~~~lSl~L~l~~~~----~~~~~~~~~l~l   75 (132)
T cd03773           2 PPYDSATFTLENFSTLRQ-SADPVYSDPLNVDGLCWRLKVYPDGNGE-VRGNFLSVFLELCSGL----GEASKYEYRVEM   75 (132)
T ss_pred             CCCcccEEEECChhhhhc-CCcceeCCCeEeCCccEEEEEECCCCCC-CCCCEEEEEEEeecCC----CCceeEEEEEEE
Confidence            356789999999999864 4689999999999999999999999874 4578999999987642    367889999999


Q ss_pred             EeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeC--C
Q 030279           98 LDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAG--D  161 (180)
Q Consensus        98 lnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg--~  161 (180)
                      +||.++.....+          ...       ..+.. ...||+.+|.+++.+  ...+|+++  |
T Consensus        76 lnq~~~~~~~~~----------~~~-------~~f~~-~~~wG~~~Fi~~~~L--~~~gfl~~~~D  121 (132)
T cd03773          76 VHQANPTKNIKR----------EFA-------SDFEV-GECWGYNRFFRLDLL--INEGYLLPEND  121 (132)
T ss_pred             EcCCCCccceEE----------ecc-------ccccC-CCCcCHHHhccHHHH--hhCCCcCCCCC
Confidence            999644332211          000       01222 346999999998765  34689998  7

Mutations in the human TRIM37 gene (also known as MUL) cause Mulibrey (muscle-liver-brain-eye) nanism, a rare growth disorder of prenatal onset characterized by dysmorphic features, pericardial constriction and hepatomegaly. TRIM37, similar to other TRIMs, contains a cysteine-rich, zinc-binding RING-finger domain followed by another cysteine-rich zinc-binding domain, the B-box, and a coiled-coil domain. TRIM37 is autoubiquitinated in a RING domain-dependent manner, indicating that it functions as an ubiquitin E3 ligase. In addition to the tripartite motif, TRIM37 also contains a MATH domain C-terminal to the coiled-coil domain. The MATH domain of TRIM37 has been shown to interact with the TRAF domain of six known TRAFs i

>cd03781 MATH_TRAF4 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF4 subfamily, TRAF domain, C-terminal MATH subdomain; composed of proteins with similarity to human TRAF4, including the Drosophila protein DTRAF1

Probab=99.83  E-value=1.7e-20  Score=142.93  Aligned_cols=130  Identities=22%  Similarity=0.316  Sum_probs=92.8

Q ss_pred             cEEEEEEcCcccccc---C-CCCeEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCC-CCcEEEEEE
Q 030279           21 AHFLLKIEAFSSLVE---N-DVENYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLG-LGWEVYVIF   93 (180)
Q Consensus        21 ~~~~w~I~~fS~l~~---~-~~~~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~-~~~~~~a~f   93 (180)
                      |+|.|+|.+||++++   . .++.+.|++|.+|  ||+|+|.+||+|... +..+|||+||+|++.+... ..|++.|++
T Consensus         1 g~~~~~I~gys~~~~~~~~~~~~~i~S~~F~vg~~Gy~w~i~~yPnG~~~-~~~~~vs~~l~l~~ge~d~~l~wp~~a~~   79 (154)
T cd03781           1 GTLLWKITDYSRKLQEAKGRDNLELFSPPFYTHRYGYKLQVSAFLNGNGS-GEGSHLSVYIRVLPGEYDNLLEWPFSHRI   79 (154)
T ss_pred             CEEEEEECCHHHHHHHhhcCCCceEECCCeecCCCCEEEEEEEECCCCCC-CCCCEEEEEEEEecCCcccccCCceeeEE
Confidence            689999999999875   2 3589999999999  999999999999874 4678999999999854322 479999999


Q ss_pred             EEEEEeCCCCc--eeE-EeeEE-eccccccccceEeceecccCC-----CcceEEEeccccCCCCCccCCCcEEeCCe
Q 030279           94 RLFVLDQKKDE--FLI-LQEVF-VKETKKCTGECLSMKKLTSAS-----NYKHVWKIKNFSKLPDNIYESEVFVAGDQ  162 (180)
Q Consensus        94 ~~~llnq~~~~--~~~-~~dvF-~~~~~~~~~e~~s~~~~~~~~-----~~~~tW~i~nFs~l~~~~~~S~~F~vg~~  162 (180)
                      +|+|+||.+..  ... ..+.| ..+.      ...|.   .|.     ...-.||+..|.+++.+  .+..|+.+|+
T Consensus        80 ~~~llDq~~~~~~~~~~~~~~~~~~~~------~~~F~---rp~~~~~~~~~~~~G~~~fi~~~~L--e~~~yl~dD~  146 (154)
T cd03781          80 TFTLLDQSDPSLSKPQHITETFTPDPT------WKNFQ---KPSASRLDESTLGFGYPKFISHEDL--KKRNYIKDDA  146 (154)
T ss_pred             EEEEECCCCCccccCcceEEEEEcCCc------hhhhc---CCcccccCCCCCccchhHeeEHHHH--hhCCcccCCE
Confidence            99999998751  111 11122 1000      00011   111     12346999999998765  4457999884

TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF4 is highly expressed during embryogenesis, especially in the central and peripheral nervous system. Studies using TRAF4-deficient mice show that TRAF4 is required for neurogenesis, as well as the development of the trachea and the axial skeleton. In addition, TRAF4 augments nuclear factor-kappaB activation triggered by GITR (glucocorticoid-induced TNFR), a receptor expressed in T-cells, B-cells and macrophages. It also participates in counteracting the signaling mediated by Toll-like receptors through its association with TRAF6 and TR

>cd03771 MATH_Meprin Meprin family, MATH domain; Meprins are multidomain, highly glycosylated extracellular metalloproteases, which are either anchored to the membrane or secreted into extracellular spaces

Probab=99.83  E-value=5.8e-20  Score=141.45  Aligned_cols=137  Identities=18%  Similarity=0.276  Sum_probs=93.6

Q ss_pred             cEEEEEEcCccccc-c-CCCCeEEccce-eecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcE-EEEEEEE
Q 030279           21 AHFLLKIEAFSSLV-E-NDVENYKSLEF-DAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWE-VYVIFRL   95 (180)
Q Consensus        21 ~~~~w~I~~fS~l~-~-~~~~~~~S~~F-~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~-~~a~f~~   95 (180)
                      .+|+|+|.|||+++ + ..++.++|++| .+|||+|+|.+||+|+..  ..+||||||+|++.+. ..++|+ +.|+++|
T Consensus         2 p~hvwkI~~yS~~~~~~~~g~~i~S~~FysvgGy~w~I~~YPnG~~~--~~~~lSlyL~L~~g~~d~~L~WP~v~a~~t~   79 (167)
T cd03771           2 PEAVWRVRNFSQLLETTPKGTKIYSPRFYSPEGYAFQVGLYPNGTES--YPGYTGLYFHLCSGENDDVLEWPCPNRQATM   79 (167)
T ss_pred             CeEEEEEcCchhhhhcCCCCCEEECCCCCccCCeEEEEEEEeCCCCC--CCCcceEEEEEecCCccccccCcceeEEEEE
Confidence            57999999999996 3 35789999999 999999999999999974  5789999999987543 346799 6899999


Q ss_pred             EEEeCCCC--ceeEEeeEE-eccccccc-cceEeceec------ccC-----CCcceEEEeccccCCCCCccCCCcEEeC
Q 030279           96 FVLDQKKD--EFLILQEVF-VKETKKCT-GECLSMKKL------TSA-----SNYKHVWKIKNFSKLPDNIYESEVFVAG  160 (180)
Q Consensus        96 ~llnq~~~--~~~~~~dvF-~~~~~~~~-~e~~s~~~~------~~~-----~~~~~tW~i~nFs~l~~~~~~S~~F~vg  160 (180)
                      +|+||..+  +..-..+.| .+|..... .+.+-+.+.      ...     -...-.||...|.++.++  .+..|+.+
T Consensus        80 ~LlDQ~~~~~~r~~~~~~~~~dp~~~~~~~~~~~~~rP~~~~~~~~~~~~~~~~~~~g~G~~~Fis~~~L--~~r~ylk~  157 (167)
T cd03771          80 TLLDQDPDIQQRMSNQRSFTTDPSMTSSDNGEYFWDRPSKVGSYDTDTNGCTCYRGPGYGWSTFISHSRL--RRRDFLKG  157 (167)
T ss_pred             EEECCCCcccccCcceEEEecCCcccccccccccccCCccccccccccccccccccCccccccceeHHHh--ccCCCCcC
Confidence            99999731  111112344 33321000 000000000      000     013457999999999976  34669998


Q ss_pred             C
Q 030279          161 D  161 (180)
Q Consensus       161 ~  161 (180)
                      |
T Consensus       158 d  158 (167)
T cd03771         158 D  158 (167)
T ss_pred             C
Confidence            8

They are expressed in renal and intestinal brush border membranes, leukocytes, and cancer cells, and are capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. Meprin proteases are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. Despite their similarity, the two subunits differ in their ability to self-associate, in proteolytic processing during biosynthesis and in substrate specificity. Both subunits are synthesized as membrane spanning proteins, however, the alpha subunit is cleaved during biosynthesis and loses its transmembrane domain. Meprin beta forms homodimers or heterotetramers while meprin alpha oligomerizes into large complexes co

>cd03777 MATH_TRAF3 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses

Probab=99.83  E-value=4.4e-20  Score=144.60  Aligned_cols=133  Identities=20%  Similarity=0.256  Sum_probs=95.4

Q ss_pred             CCCcEEEEEEcCcccccc--CCCC--eEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEEE
Q 030279           18 VPPAHFLLKIEAFSSLVE--NDVE--NYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEVY   90 (180)
Q Consensus        18 ~~~~~~~w~I~~fS~l~~--~~~~--~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~~   90 (180)
                      ...|+|.|+|.+||.+++  ..|+  .+.|++|.+|  ||+|+|.+||||+.. +..+|||+||+++..+. .-..|++.
T Consensus        36 ~~~G~hvwkI~~yS~~~~~~~~g~~~~i~S~~Fyvg~~GY~w~i~~ypnG~g~-~~~~~iSvyl~L~~ge~D~~L~WP~~  114 (186)
T cd03777          36 SYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGM-GKGTHLSLFFVIMRGEYDALLPWPFK  114 (186)
T ss_pred             ccceEEEEEECChhHHHHhhccCCCcEEECCCeEeCCCCeeEEEEEEcCCCCC-CCCCEEEEEEEEecCCcccccCCcee
Confidence            347999999999999864  3455  8999999999  999999999999984 46789999999997542 12469999


Q ss_pred             EEEEEEEEeCCCCceeEEeeEE-eccccccccceEeceecccCC-CcceEEEeccccCCCCCccCCCcEEeCCeE
Q 030279           91 VIFRLFVLDQKKDEFLILQEVF-VKETKKCTGECLSMKKLTSAS-NYKHVWKIKNFSKLPDNIYESEVFVAGDQK  163 (180)
Q Consensus        91 a~f~~~llnq~~~~~~~~~dvF-~~~~~~~~~e~~s~~~~~~~~-~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~  163 (180)
                      ++++|+|+||.+..... .+.| ..|.   .   ..|.+   +. .....||...|.+++.+  .+..|+.+|+-
T Consensus       115 ~~~tfsLlDQ~~~~~~~-~~~~~p~p~---~---~~F~r---p~~~~n~~~G~~~Fi~~~~L--e~~~ylkdD~l  177 (186)
T cd03777         115 QKVTLMLMDQGSSRRHL-GDAFKPDPN---S---SSFKK---PTGEMNIASGCPVFVAQTVL--ENGTYIKDDTI  177 (186)
T ss_pred             EEEEEEEEcCCCccccc-cceeccCCc---c---ccccC---CccCCCCCCCchheeEHHHh--ccCCcEeCCEE
Confidence            99999999997532211 1223 1111   0   11221   11 11345899999988765  55678988853

TRAF3 was first described as a molecule that binds the cytoplasmic tail of CD40. However, it is not required for CD40 signaling. More recently, TRAF3 has been identified as a key regulator of type I interferon (IFN) production and the mammalian innate antiviral immunity. It mediates IFN responses in Toll-like receptor (TLR)-dependent as well as TLR-independent viral recognition pathways. It is also a key element in immunological homeostasis through its regulation of the anti-inflammatory cytokine interleukin-10. TRAF3 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal al

>cd03779 MATH_TRAF1 Tumor Necrosis Factor Receptor (TNFR) Associated Factor (TRAF) family, TRAF1 subfamily, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses

Probab=99.80  E-value=1.6e-19  Score=136.44  Aligned_cols=130  Identities=22%  Similarity=0.297  Sum_probs=91.6

Q ss_pred             cEEEEEEcCcccccc-C-C--CCeEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEEEEEE
Q 030279           21 AHFLLKIEAFSSLVE-N-D--VENYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEVYVIF   93 (180)
Q Consensus        21 ~~~~w~I~~fS~l~~-~-~--~~~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~~a~f   93 (180)
                      |+|+|+|.||+++.+ . .  ...++||+|..+  ||+|+|.+||||+.. +..+||||||+|++.+. .-+.|++.|++
T Consensus         1 g~~~W~i~~f~~~~~~a~~~~~~~~~S~~Fyt~~~Gy~w~i~~ypnG~~~-~~~~~iSv~l~l~~g~~D~~l~wpv~~~~   79 (147)
T cd03779           1 GTFLWKITDVSQKQRESSHGRDVSLCSPAFYTAKYGYKVCLRLYLNGDGA-GKGTHISLFFVIMKGEYDALLPWPFRHKV   79 (147)
T ss_pred             CeEEEEECcHHHHHHHHhcCCCceEECCCcccCCCCceEEEEEEcCCCCC-CCCCEEEEEEEEecCCcccccCcceEEEE
Confidence            689999999997654 2 2  348999999987  999999999999984 46789999999987531 12469999999


Q ss_pred             EEEEEeCCCCceeEEeeEEeccccccccceEeceecccCC-CcceEEEeccccCCCCCccCC-CcEEeCCe
Q 030279           94 RLFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSAS-NYKHVWKIKNFSKLPDNIYES-EVFVAGDQ  162 (180)
Q Consensus        94 ~~~llnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~-~~~~tW~i~nFs~l~~~~~~S-~~F~vg~~  162 (180)
                      +|+|+||.+.+....  ++ ++.    .....|.+   |. .....||..+|++++++ ..| .+|+.+|+
T Consensus        80 tfsLlDq~~~~~~~~--~~-~~~----~~~~~F~r---P~~~~n~~~G~~~Fi~~~~L-e~s~~~ylkDD~  139 (147)
T cd03779          80 TFMLLDQNNREHVID--AF-RPD----LSSASFQR---PVSDMNVASGCPLFFPLKKL-QSPKHAYCKDDT  139 (147)
T ss_pred             EEEEECCCCCCCCcE--ee-cCC----cccccccC---cccCCCCCcchhheeEHHHh-cccCCCcEeCCE
Confidence            999999986554221  11 000    00011221   11 22346999999998876 223 48888884

TRAF1 expression is the most restricted among the TRAFs. It is found exclusively in activated lymphocytes, dendritic cells and certain epithelia. TRAF1 associates, directly or indirectly through heterodimerization with TRAF2, with the TNFR family receptors TNFR-2, CD30, RANK, CD40 and LMP1, among others. It also binds the intracellular proteins TRADD, TANK, TRIP, RIP1, RIP2 and FLIP. TRAF1 is unique among the TRAFs in that it lacks a RING domain, which is critical for the activation of nuclear factor-kappaB and Jun NH2-terminal kinase. Studies on TRAF1-deficient mice suggest that TRAF1 has a negative regulatory role in TNFR-mediat

>cd03778 MATH_TRAF2 Tumor Necrosis Factor Receptor (TNFR) Associated Factor (TRAF) family, TRAF2 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses

Probab=99.78  E-value=2.8e-18  Score=131.51  Aligned_cols=132  Identities=22%  Similarity=0.343  Sum_probs=98.7

Q ss_pred             cCCCcEEEEEEcCccccccC--C--CCeEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCC-CCcEE
Q 030279           17 HVPPAHFLLKIEAFSSLVEN--D--VENYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLG-LGWEV   89 (180)
Q Consensus        17 ~~~~~~~~w~I~~fS~l~~~--~--~~~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~-~~~~~   89 (180)
                      ....|+|+|+|.||+++++.  .  ...++||+|..+  ||+|+|.+||+|++. +.+.||||||+++.++..+ ++|++
T Consensus        15 ~~~~g~fiWkI~~fs~~~~~a~~~~~~~i~Sp~Fyt~~~GYk~~l~~ylnG~g~-~~g~~LSly~~l~~Ge~D~~L~WPf   93 (164)
T cd03778          15 STYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGT-GRGTHLSLFFVVMKGPNDALLRWPF   93 (164)
T ss_pred             cccCCEEEEEECcHHHHHHHHhcCCCceEECCCcccCCCCeEEEEEEEeCCCCC-CCCCEEEEEEEEecCCcCcccCCce
Confidence            34579999999999998652  2  358999999764  899999999999985 4567999999999987655 78999


Q ss_pred             EEEEEEEEEeCCCCceeEEeeEE-eccccccccceEeceecccC-CCcceEEEeccccCCCCCccCCCcEEeCC
Q 030279           90 YVIFRLFVLDQKKDEFLILQEVF-VKETKKCTGECLSMKKLTSA-SNYKHVWKIKNFSKLPDNIYESEVFVAGD  161 (180)
Q Consensus        90 ~a~f~~~llnq~~~~~~~~~dvF-~~~~~~~~~e~~s~~~~~~~-~~~~~tW~i~nFs~l~~~~~~S~~F~vg~  161 (180)
                      ..+++|+|+||.+.++.+.  .| .++.   + .  .|.   .| ......||...|..+.++.. +.+|+.+|
T Consensus        94 ~~~itl~llDQ~~r~hi~~--~~~pd~~---~-~--~f~---RP~~~~n~~~G~~~Fv~l~~l~~-~~~Yv~dD  155 (164)
T cd03778          94 NQKVTLMLLDQNNREHVID--AFRPDVT---S-S--SFQ---RPVNDMNIASGCPLFCPVSKXEA-KNSYVRDD  155 (164)
T ss_pred             eeEEEEEEECCCCCCccee--EEEcCcc---h-H--hcC---CCCcccccCcCcceEEEhhHccc-cCCcccCC
Confidence            9999999999987555432  22 1221   0 0  111   23 22344699999999987743 36899988

TRAF2 associates with the receptors TNFR-1, TNFR-2, RANK (which mediates differentiation and maturation of osteoclasts) and CD40 (which is important for the proliferation and activation of B cells), among others. It regulates distinct pathways that lead to the activation of nuclear factor-kappaB and Jun NH2-terminal kinases. TRAF2 also indirectly associates with death receptors through its interaction with TRADD (TNFR-associated death domain protein). It is involved in regulating oxidative stress or ROS-induced cell death and in the preconditioning of cells by sublethal stress for protection from subsequent injury. TRAF2 contains a RING finger domain, five z

>cd00121 MATH MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins

Probab=99.74  E-value=3e-17  Score=118.02  Aligned_cols=117  Identities=28%  Similarity=0.442  Sum_probs=89.3

Q ss_pred             cEEEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEEEEEEEEEEeC
Q 030279           21 AHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQ  100 (180)
Q Consensus        21 ~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~~llnq  100 (180)
                      ++|+|+|.+|+..   .++.+.|+.|.++|+.|+|.+||+|...  ..+||||||++......+..|.+.|+|+|.|+||
T Consensus         1 ~~~~~~i~~~~~~---~~~~~~S~~f~~~g~~W~l~~~p~~~~~--~~~~lsv~L~~~~~~~~~~~~~~~~~~~~~l~~~   75 (126)
T cd00121           1 GKHTWKIVNFSEL---EGESIYSPPFEVGGYKWRIRIYPNGDGE--SGDYLSLYLELDKGESDLEKWSVRAEFTLKLVNQ   75 (126)
T ss_pred             CEEEEEECCCCCC---CCcEEECCCEEEcCEeEEEEEEcCCCCC--CCCEEEEEEEecCCCCCCCCCcEEEEEEEEEECC
Confidence            4799999999993   3789999999999999999999999863  5789999999987765456799999999999999


Q ss_pred             CCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCC
Q 030279          101 KKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGD  161 (180)
Q Consensus       101 ~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~  161 (180)
                      .+.+.....          ....       -+......||+.+|..++++.  .+.++++|
T Consensus        76 ~~~~~~~~~----------~~~~-------~~~~~~~~~G~~~fi~~~~l~--~~~~~~~d  117 (126)
T cd00121          76 NGGKSLSKS----------FTHV-------FFSEKGSGWGFPKFISWDDLE--DSYYLVDD  117 (126)
T ss_pred             CCCccceEe----------ccCC-------cCCCCCCCCChHHeeEHHHhc--cCCcEECC
Confidence            854443320          1111       012345789999999988663  23336666

Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH doma

>smart00061 MATH meprin and TRAF homology

Probab=99.71  E-value=1e-16  Score=110.66  Aligned_cols=74  Identities=20%  Similarity=0.335  Sum_probs=65.2

Q ss_pred             EEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEEEEEEEEEEeCCC
Q 030279           23 FLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKK  102 (180)
Q Consensus        23 ~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~~llnq~~  102 (180)
                      ++|+|.+|+.+.  .++.+.|++|.+||+.|+|.+||+       .+||||||.+.+....+.+|.+.|+|+|.|+||.+
T Consensus         2 ~~~~~~~~~~~~--~~~~~~S~~f~~~g~~W~i~~~p~-------~~~lsl~L~~~~~~~~~~~w~v~a~~~~~l~~~~~   72 (95)
T smart00061        2 LSHTFKNVSRLE--EGESYFSPSEEHFNIPWRLKIYRK-------NGFLSLYLHCEKEECDSRKWSIEAEFTLKLVSQNG   72 (95)
T ss_pred             ceeEEEchhhcc--cCceEeCChhEEcCceeEEEEEEc-------CCEEEEEEEeCCCcCCCCCeEEEEEEEEEEEeCCC
Confidence            579999999984  378999999999999999999998       36999999998776555589999999999999998


Q ss_pred             Cce
Q 030279          103 DEF  105 (180)
Q Consensus       103 ~~~  105 (180)
                      .++
T Consensus        73 ~~~   75 (95)
T smart00061       73 KSL   75 (95)
T ss_pred             CEE
Confidence            665

>PF00917 MATH: MATH domain; InterPro: IPR002083 Although apparently functionally unrelated, intracellular TRAFs and extracellular meprins share a conserved region of about 180 residues, the meprin and TRAF homology (MATH) domain []

Probab=99.53  E-value=1.8e-14  Score=103.41  Aligned_cols=112  Identities=29%  Similarity=0.477  Sum_probs=82.1

Q ss_pred             EcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCC-CCcEEEEEEEEEEEeCCCCce
Q 030279           27 IEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLG-LGWEVYVIFRLFVLDQKKDEF  105 (180)
Q Consensus        27 I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~-~~~~~~a~f~~~llnq~~~~~  105 (180)
                      |+|||+++. .+..+.|+.|.+||+.|+|.+||+|+     .+++|+||++....... .+|++.|++++.|+++.+...
T Consensus         1 i~nfs~l~~-~~~~~~s~~~~~~g~~W~l~~~~~~~-----~~~l~~~L~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~   74 (119)
T PF00917_consen    1 IKNFSKLKE-GEEYSSSFVFSHGGYPWRLKVYPKGN-----GKYLSVYLHCDKGENDSDLEWSIEAEFRFRLLNQNGKSI   74 (119)
T ss_dssp             ETTGGGHHT-SEEEEEEEESSTTSEEEEEEEETTES-----TTEEEEEEEEECSTTGGGSSSSEEEEEEEEEE-TTSCEE
T ss_pred             CcccceEeC-CCcEECCCeEEECCEEEEEEEEeCCC-----cCcEEEEEEEeecccccccceeeeEEEEEEEecCCCCcc
Confidence            789999972 24455669999999999999999986     57999999999886543 689999999999999999874


Q ss_pred             eEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCCeEEEE
Q 030279          106 LILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYV  166 (180)
Q Consensus       106 ~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i  166 (180)
                      ...            .+...|.       ....||+..|++++++..  +.|+++| +..|
T Consensus        75 ~~~------------~~~~~F~-------~~~~~g~~~fi~~~~l~~--~~fl~dd-~l~i  113 (119)
T PF00917_consen   75 SKR------------IKSHSFN-------NPSSWGWSSFISWEDLED--PYFLVDD-SLTI  113 (119)
T ss_dssp             EEE------------EECEEEC-------TTSEEEEEEEEEHHHHTT--CTTSBTT-EEEE
T ss_pred             eee------------eeeeEEe-------eecccchhheeEHHHhCc--cCCeECC-EEEE
Confidence            332            0111111       237899999999886532  3378887 4433

Meprins are mammalian tissue-specific metalloendopeptidases of the astacin family implicated in developmental, normal and pathological processes by hydrolysing a variety of proteins. Various growth factors, cytokines, and extracellular matrix proteins are substrates for meprins. They are composed of five structural domains: an N-terminal endopeptidase domain, a MAM domain (see PDOC00604 from PROSITEDOC), a MATH domain, an EGF-like domain (see PDOC00021 from PROSITEDOC) and a C-terminal transmembrane region. Meprin A and B form membrane bound homotetramer whereas homooligomers of meprin A are secreted. A proteolitic site adjacent to the MATH domain, only present in meprin A, allows the release of the protein from the membrane []. TRAF proteins were first isolated by their ability to interact with TNF receptors []. They promote cell survival by the activation of downstream protein kinases and, finally, transcription factors of the NF-kB and AP-1 family. The TRAF proteins are composed of 3 structural domains: a RING finger (see PDOC00449 from PROSITEDOC) in the N-terminal part of the protein, one to seven TRAF zinc fingers (see PDOC50145 from PROSITEDOC) in the middle and the MATH domain in the C-terminal part []. The MATH domain is necessary and sufficient for self-association and receptor interaction. From the structural analysis two consensus sequence recognised by the TRAF domain have been defined: a major one, [PSAT]x[QE]E and a minor one, PxQxxD []. The structure of the TRAF2 protein reveals a trimeric self-association of the MATH domain []. The domain forms a new, light-stranded antiparallel beta sandwich structure. A coiled-coil region adjacent to the MATH domain is also important for the trimerisation. The oligomerisation is essential for establishing appropriate connections to form signalling complexes with TNF receptor-1. The ligand binding surface of TRAF proteins is located in beta-strands 6 and 7 [].; GO: 0005515 protein binding; PDB: 1D00_E 1CZY_A 1D01_F 1CA9_A 1D0J_D 1F3V_B 1CA4_C 1D0A_A 1QSC_C 1CZZ_C ....

>cd03782 MATH_Meprin_Beta Meprin family, Beta subunit, MATH domain; Meprins are multidomain extracellular metalloproteases capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides

Probab=99.52  E-value=5.3e-14  Score=107.46  Aligned_cols=138  Identities=18%  Similarity=0.290  Sum_probs=94.6

Q ss_pred             cEEEEEEcCcccccc--CCCCeEEccceeec-CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEEE-EEEEE
Q 030279           21 AHFLLKIEAFSSLVE--NDVENYKSLEFDAG-GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEVY-VIFRL   95 (180)
Q Consensus        21 ~~~~w~I~~fS~l~~--~~~~~~~S~~F~vg-G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~~-a~f~~   95 (180)
                      ..|+|+|.||+++++  ..+..++||+|... ||+.++.+||||++. + ++|||||++++.++. .-+.|++. -+++|
T Consensus         2 p~~iWkI~~fs~~~~~~~~~~~i~Sp~FYt~~GYkl~l~~ylnG~g~-~-~~~lsl~~~lm~Ge~D~~L~WPf~~~qit~   79 (167)
T cd03782           2 PEHIWHIRNFTQLLATTPPNGKIYSPPFLSSTGYSFQVGLYLNGTDD-Y-PGNLAIYLHLTSGPNDDQLQWPCPWQQATM   79 (167)
T ss_pred             CcEEEEeCcHHHHHHhcCCCceEECCCCcCccCceeEEEEEecCCCC-C-CCEEEEEEEEeccCCCccccCCCcCCeEEE
Confidence            469999999999876  24689999999754 999999999999984 3 679999999998764 23679999 89999


Q ss_pred             EEEeCCCC--ceeEEeeEE-eccccccccceEece-ecccC-------CC-------cceEEEeccccCCCCCccCCCcE
Q 030279           96 FVLDQKKD--EFLILQEVF-VKETKKCTGECLSMK-KLTSA-------SN-------YKHVWKIKNFSKLPDNIYESEVF  157 (180)
Q Consensus        96 ~llnq~~~--~~~~~~dvF-~~~~~~~~~e~~s~~-~~~~~-------~~-------~~~tW~i~nFs~l~~~~~~S~~F  157 (180)
                      .|+||..+  +..-+.++| .+|.. ...+--++. +  +|       ..       ....||...|.++.++  .+..|
T Consensus        80 ~LlDQ~~d~~~r~~~~~~~t~~P~~-~s~~n~~f~w~--rP~kvg~~~~~~~~~~~~r~~~~G~~~Fish~~L--~~r~y  154 (167)
T cd03782          80 MLLDQHPDIRQRMSNQRSVTTDPNM-TSTDSDEYFWD--DPRKVGSEVTDTDGSTFYRGPGYGTSAFITHLRL--RSRDF  154 (167)
T ss_pred             EEEcCCCchhhccceeeeEEecCCc-ccccCccceec--CCcccCcccccccccccccccccCccceeeHHHH--hhcCc
Confidence            99999641  211123334 33310 000000010 0  11       11       1467888999998866  45778


Q ss_pred             EeCCeEEE
Q 030279          158 VAGDQKWY  165 (180)
Q Consensus       158 ~vg~~~w~  165 (180)
                      +.||.-.-
T Consensus       155 ikdD~ifi  162 (167)
T cd03782         155 IKGDDVIF  162 (167)
T ss_pred             ccCCeEEE
Confidence            88885443

They are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. The beta subunit is a type I membrane protein, which forms homodimers or heterotetramers (alpha2beta2 or alpha3beta). Meprin beta shows preference for acidic residues at the P1 and P1' sites of its substrate. Among its best substrates are growth factors and chemokines such as gastrin and osteopontin. Both alpha and beta subunits contain a catalytic astacin (M12 family) protease domain followed by the adhesion or interaction domains MAM, MATH and AM. The MATH and MAM domains provide symmetrical intersubunit disulfide bonds necessary for the dimerization of meprin subunits. The MATH domain may also be required for f

>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]

Probab=99.50  E-value=1.1e-14  Score=131.29  Aligned_cols=127  Identities=20%  Similarity=0.324  Sum_probs=96.7

Q ss_pred             CCCcEEEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC--CC-CCcEEEEEEE
Q 030279           18 VPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS--LG-LGWEVYVIFR   94 (180)
Q Consensus        18 ~~~~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~--~~-~~~~~~a~f~   94 (180)
                      ....+|+|+|.+||.+.    +++.||+|.|||+.|+|.++|+|+.+   .+ +|+||++...+.  +. ..|.+||+|.
T Consensus        36 ~~~~sftW~vk~wsel~----~k~~Sp~F~vg~~twki~lfPqG~nq---~~-~sVyLe~~pqe~e~~~gk~~~ccaqFa  107 (1089)
T COG5077          36 LLEMSFTWKVKRWSELA----KKVESPPFSVGGHTWKIILFPQGNNQ---CN-VSVYLEYEPQELEETGGKYYDCCAQFA  107 (1089)
T ss_pred             HhhcccceecCChhhhh----hhccCCcccccCeeEEEEEecccCCc---cc-cEEEEEeccchhhhhcCcchhhhhhee
Confidence            44578999999999994    68999999999999999999999974   33 999999875431  22 3499999999


Q ss_pred             EEEEeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEE--eCCeEEEEEEe
Q 030279           95 LFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFV--AGDQKWYVYFL  169 (180)
Q Consensus        95 ~~llnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~--vg~~~w~i~~y  169 (180)
                      |.|.|+..+....+          ++.       ++.|......||+.||..|++...+++++.  +.+....|.+|
T Consensus       108 f~Is~p~~pti~~i----------N~s-------HhrFs~~~tDwGFt~f~dL~kl~~psp~~Ppfleeg~l~Itvy  167 (1089)
T COG5077         108 FDISNPKYPTIEYI----------NKS-------HHRFSMESTDWGFTNFIDLNKLIEPSPGRPPFLEEGTLVITVY  167 (1089)
T ss_pred             eecCCCCCCchhhh----------hcc-------cccccccccccchhhhhhhhhhcCCCCCCCCcccCCeEEEEEE
Confidence            99999988655442          222       335777888999999999998877777654  23334444444

>cd03783 MATH_Meprin_Alpha Meprin family, Alpha subunit, MATH domain; Meprins are multidomain extracellular metalloproteases capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides

Probab=99.44  E-value=4e-13  Score=103.01  Aligned_cols=138  Identities=17%  Similarity=0.270  Sum_probs=93.5

Q ss_pred             cEEEEEEcCccccccC--CCCeEEccceeec-CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEE-EEEEEE
Q 030279           21 AHFLLKIEAFSSLVEN--DVENYKSLEFDAG-GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEV-YVIFRL   95 (180)
Q Consensus        21 ~~~~w~I~~fS~l~~~--~~~~~~S~~F~vg-G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~-~a~f~~   95 (180)
                      ..++|+|.||+++++.  .+..++||+|... ||+.+|.+||+|+...+.+.|||||++++.++. .-+.|++ .-+++|
T Consensus         2 p~~iWkI~nfs~~~~~a~~~~~i~Sp~Fyt~~GYk~~l~~~lng~~~~~~g~~lSl~~~lm~Ge~D~~L~WP~~~~~itl   81 (167)
T cd03783           2 PNAVWRVRNFSQILENTTKGDVLQSPRFYSPEGYGYGVSLYPLSNESDYSGNYTGLYFHLCSGENDAVLEWPALNRQAII   81 (167)
T ss_pred             CceeEEECcHHHHHHhCcCCCeEECCCCccCCCceEEEEEEecCCCCCCCCCEEEEEEEEecccCCCcccCCCcCCEEEE
Confidence            4689999999997652  5689999999885 999999999999874345789999999998764 2367995 569999


Q ss_pred             EEEeCCCC--ceeEEeeEE-eccccccccceE---eceecccC-----------CCcceEEEeccccCCCCCccCCCcEE
Q 030279           96 FVLDQKKD--EFLILQEVF-VKETKKCTGECL---SMKKLTSA-----------SNYKHVWKIKNFSKLPDNIYESEVFV  158 (180)
Q Consensus        96 ~llnq~~~--~~~~~~dvF-~~~~~~~~~e~~---s~~~~~~~-----------~~~~~tW~i~nFs~l~~~~~~S~~F~  158 (180)
                      +|+||..+  +..-+.+.| ..+..  ..+.+   ..-+  +|           ......+|...|.++..+  .+..|+
T Consensus        82 ~llDQ~~~~~~r~~~~~sf~~d~~~--~~~~~~~~~~f~--rP~~~~~~~~~~~~~~~~gfG~~~Fish~~L--~~r~yi  155 (167)
T cd03783          82 TVLDQDPDVRLRMSSSRSFTTDKSQ--TSSAINGTLRWD--RPSRVGTYDTSCDCFRGIDFGWSTFISHSQL--RRRSFL  155 (167)
T ss_pred             EEEcCCcchhhccccceeeecCCCc--cccccccccccc--CCcccccccccccccCCcccccccceeHHHH--hhCCcc
Confidence            99999631  111111223 22110  00000   0001  12           124557888999999876  457899


Q ss_pred             eCCeEE
Q 030279          159 AGDQKW  164 (180)
Q Consensus       159 vg~~~w  164 (180)
                      .+|.-.
T Consensus       156 kdDtlf  161 (167)
T cd03783         156 KNDDLI  161 (167)
T ss_pred             cCCeEE
Confidence            888543

They are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. The alpha subunit is synthesized as a membrane spanning protein, however, it is cleaved during biosynthesis and loses its transmembrane domain. It oligomerizes into large complexes, containing 10-100 subunits (dimers that associate noncovalently), which are secreted as latent proteases and can move through extracellular spaces in a nondestructive manner. This allows delivery of the concentrated protease to sites containing activating enzymes, such as sites of inflammation, infection or cancerous growth. Meprin alpha shows preference for small or hydrophobic residues at the P1 and P1' sites of its substrate. Both

>cd03773 MATH_TRIM37 Tripartite motif containing protein 37 (TRIM37) family, MATH domain; TRIM37 is a peroxisomal protein and is a member of the tripartite motif (TRIM) protein subfamily, also known as the RING-B-box-coiled-coil (RBCC) subfamily of zinc-finger proteins

Probab=98.90  E-value=2e-09  Score=79.23  Aligned_cols=45  Identities=13%  Similarity=0.128  Sum_probs=39.3

Q ss_pred             CCCcceEEEeccccCCC--CCccCCCcEEeCCeEEEEEEecCCCCCC
Q 030279          132 ASNYKHVWKIKNFSKLP--DNIYESEVFVAGDQKWYVYFLKWCSNPN  176 (180)
Q Consensus       132 ~~~~~~tW~i~nFs~l~--~~~~~S~~F~vg~~~w~i~~yp~g~~~~  176 (180)
                      |...+++|.|.+||.+.  ...+.|+.|.|||++|+|.+||+|+..+
T Consensus         2 ~~~~~~~~~I~~fS~~~~~~~~~~S~~F~vgG~~W~i~~yP~G~~~~   48 (132)
T cd03773           2 PPYDSATFTLENFSTLRQSADPVYSDPLNVDGLCWRLKVYPDGNGEV   48 (132)
T ss_pred             CCCcccEEEECChhhhhcCCcceeCCCeEeCCccEEEEEECCCCCCC
Confidence            45678999999999984  3578899999999999999999998653

Mutations in the human TRIM37 gene (also known as MUL) cause Mulibrey (muscle-liver-brain-eye) nanism, a rare growth disorder of prenatal onset characterized by dysmorphic features, pericardial constriction and hepatomegaly. TRIM37, similar to other TRIMs, contains a cysteine-rich, zinc-binding RING-finger domain followed by another cysteine-rich zinc-binding domain, the B-box, and a coiled-coil domain. TRIM37 is autoubiquitinated in a RING domain-dependent manner, indicating that it functions as an ubiquitin E3 ligase. In addition to the tripartite motif, TRIM37 also contains a MATH domain C-terminal to the coiled-coil domain. The MATH domain of TRIM37 has been shown to interact with the TRAF domain of six known TRAFs i

>cd03775 MATH_Ubp21p Ubiquitin-specific protease 21 (Ubp21p) family, MATH domain; composed of fungal proteins with similarity to Ubp21p of fission yeast

Probab=98.88  E-value=2.9e-09  Score=79.00  Aligned_cols=39  Identities=26%  Similarity=0.542  Sum_probs=35.4

Q ss_pred             ceEEEeccccCCCCCccCCCcEEeCCeEEEEEEecCCCCC
Q 030279          136 KHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCSNP  175 (180)
Q Consensus       136 ~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~~yp~g~~~  175 (180)
                      +|+|.|.|||++. .++.|+.|.|||++|||.+||+|+..
T Consensus         2 ~f~w~I~~fS~~~-~~~~S~~F~vGG~~W~l~~yP~G~~~   40 (134)
T cd03775           2 SFTWRIKNWSELE-KKVHSPKFKCGGFEWRILLFPQGNSQ   40 (134)
T ss_pred             cEEEEECCcccCC-cceeCCCEEECCeeEEEEEeCCCCCC
Confidence            6999999999986 46889999999999999999999864

Ubp21p is a deubiquitinating enzyme that may be involved in the regulation of the protein kinase Prp4p, which controls the formation of active spliceosomes. Members of this family are similar to human HAUSP (Herpesvirus-associated ubiquitin-specific protease) in that they contain an N-terminal MATH domain and a C-terminal catalytic protease (C19 family) domain. HAUSP is also an ubiquitin-specific protease that specifically catalyzes the deubiquitylation of p53 and MDM2. The MATH domain of HAUSP contains the binding site for p53 and MDM2. Similarly, the MATH domain of members in this family may be involved in substrate binding.

>KOG1987 consensus Speckle-type POZ protein SPOP and related proteins with TRAF, MATH and BTB/POZ domains [Cell cycle control, cell division, chromosome partitioning; General function prediction only]

Probab=98.81  E-value=2.9e-09  Score=88.49  Aligned_cols=137  Identities=23%  Similarity=0.314  Sum_probs=100.4

Q ss_pred             EEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEEEEEEEEEEeCCC
Q 030279           23 FLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKK  102 (180)
Q Consensus        23 ~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~~llnq~~  102 (180)
                      +.|.|.+|+..    +..++|..|..||+.|++.+||.|+       ++|+|+.+....    +|.++|.++|.+.||..
T Consensus         6 ~~~~~~~~~~~----~l~~ys~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~----~~~~~~~~~l~v~n~~~   70 (297)
T KOG1987|consen    6 FTWVISNFSSV----GLVIYSNGFVKGGCKWRLSAYPKGN-------YLSLTLSVSDSP----GWERYAKLRLTVVNQKS   70 (297)
T ss_pred             cceeeccCcch----hhhccccceeecCceEEEEEecCCC-------EEEEEEEeccCC----CcceeEEEEEEEccCCC
Confidence            33899999888    3789999999999999999999875       789999887653    69999999999999999


Q ss_pred             Cce-eEE-ee--EE-ec--ccccc------------------------------------ccceEecee------cccCC
Q 030279          103 DEF-LIL-QE--VF-VK--ETKKC------------------------------------TGECLSMKK------LTSAS  133 (180)
Q Consensus       103 ~~~-~~~-~d--vF-~~--~~~~~------------------------------------~~e~~s~~~------~~~~~  133 (180)
                      .++ ... .+  +| .+  ...++                                    +.+......      ..++.
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~g~~~~~~~~~~a~~~V~~~~~~~d~~~~~~~~~~~~d~~~~  150 (297)
T KOG1987|consen   71 EKYLSTVEEGFSWFRFNKVLKEWGFGKMLPLTLLIDCSNGFLVAHKLVLVARSEVFEAMGKSDVFKESSKLITLLEEKPE  150 (297)
T ss_pred             cceeeeeeeeEEeccccccccccCcccccChHHhhcccCcEEEcCceEEEeeecceeeecccccchhccccccccccchh
Confidence            876 555 23  22 11  11111                                    111111100      11233


Q ss_pred             C----cceEEEeccccCCCCC----ccCCCcEEeCCeEEEEEEecCCCC
Q 030279          134 N----YKHVWKIKNFSKLPDN----IYESEVFVAGDQKWYVYFLKWCSN  174 (180)
Q Consensus       134 ~----~~~tW~i~nFs~l~~~----~~~S~~F~vg~~~w~i~~yp~g~~  174 (180)
                      .    ..|+|.+.+|+.++..    .+.+..|.++++.||+.++|.|.+
T Consensus       151 ~~~~~~~F~~~~s~~~~~~~~~~~~~~~a~~f~~~~~~lk~~~~~~l~~  199 (297)
T KOG1987|consen  151 VLEALNGFQVLPSQVSSVERIFEKHPDLAAAFKYKNRHLKLACMPVLLS  199 (297)
T ss_pred             hHhhhceEEEeccchHHHHHhhcCChhhhhccccccHHHHHHHHHHHHH
Confidence            3    7899999999998853    556789999999999999998753

>cd03772 MATH_HAUSP Herpesvirus-associated ubiquitin-specific protease (HAUSP, also known as USP7) family, N-terminal MATH (TRAF-like) domain; composed of proteins similar to human HAUSP, an enzyme that specifically catalyzes the deubiquitylation of p53 and MDM2, hence playing an important role in the p53-MDM2 pathway

Probab=98.63  E-value=4.6e-08  Score=72.72  Aligned_cols=41  Identities=12%  Similarity=0.215  Sum_probs=36.3

Q ss_pred             CcceEEEeccccCCCCCccCCCcEEeCCeEEEEEEecCCCCC
Q 030279          134 NYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCSNP  175 (180)
Q Consensus       134 ~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~~yp~g~~~  175 (180)
                      .+.++|.|.||+.|. ..+.|+.|.|||+.|+|.+||+|...
T Consensus         2 ~~~~~~~I~~~S~l~-e~~~S~~f~vgG~~W~i~~~P~g~~~   42 (137)
T cd03772           2 EATFSFTVERFSRLS-ESVLSPPCFVRNLPWKIMVMPRNYPD   42 (137)
T ss_pred             CcEEEEEECCcccCC-CcEECCCEEECCcceEEEEEeCCCCC
Confidence            368999999999994 56889999999999999999999643

It contains an N-terminal TRAF-like domain and a C-terminal catalytic protease (C19 family) domain. The tumor suppressor p53 protein is a transcription factor that responds to many cellular stress signals and is regulated primarily through ubiquitylation and subsequent degradation. MDM2 is a RING-finger E3 ubiquitin ligase that promotes p53 ubiquitinylation. p53 and MDM2 bind to the same site in the N-terminal TRAF-like domain of HAUSP in a mutually exclusive manner. HAUSP also interacts with the Epstein-Barr nuclear antigen 1 (EBNA1) protein of the Epstein-Barr virus (EBV), which efficiently immortalizes infected cells predisposing the host to a variety of cancers. EBNA1

>cd03774 MATH_SPOP Speckle-type POZ protein (SPOP) family, MATH domain; composed of proteins with similarity to human SPOP

Probab=98.53  E-value=1.3e-07  Score=70.43  Aligned_cols=41  Identities=24%  Similarity=0.456  Sum_probs=35.5

Q ss_pred             cceEEEeccccCCC---CCccCCCcEEeCCe---EEEEEEecCCCCC
Q 030279          135 YKHVWKIKNFSKLP---DNIYESEVFVAGDQ---KWYVYFLKWCSNP  175 (180)
Q Consensus       135 ~~~tW~i~nFs~l~---~~~~~S~~F~vg~~---~w~i~~yp~g~~~  175 (180)
                      -+|+|.|.+||++.   ...+.|+.|.|||+   +|+|.+||+|...
T Consensus         5 ~~~~w~I~~fS~~~~~~~~~i~S~~F~vgg~~~~~W~l~~yP~G~~~   51 (139)
T cd03774           5 FCYMWTISNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDE   51 (139)
T ss_pred             EEEEEEECCchhhhhcCCCEEECCCeecCCcCCceEEEEEeCCCCCC
Confidence            47999999999874   45788999999995   9999999999754

SPOP was isolated as a novel antigen recognized by serum from a scleroderma patient, whose overexpression in COS cells results in a discrete speckled pattern in the nuclei. It contains an N-terminal MATH domain and a C-terminal BTB (also called POZ) domain. Together with Cul3, SPOP constitutes an ubiquitin E3 ligase which is able to ubiquitinate the PcG protein BMI1, the variant histone macroH2A1 and the death domain-associated protein Daxx. Therefore, SPOP may be involved in the regulation of these proteins and may play a role in transcriptional regulation, apoptosis and X-chromosome inactivation. Cul3 binds to the BTB domain of SPOP whereas Daxx and the macroH2A1 nonhistone region have been shown to bind to the MATH domain. Both MATH and BTB domains are necessary for the nuclear speckled accumulation of SPOP. There are many proteins, mostly uncharacterized, conta

>cd03777 MATH_TRAF3 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses

Probab=98.14  E-value=2.1e-06  Score=67.39  Aligned_cols=45  Identities=18%  Similarity=0.215  Sum_probs=38.4

Q ss_pred             CCcceEEEeccccCCCC-----C--ccCCCcEEeC--CeEEEEEEecCCCCCCC
Q 030279          133 SNYKHVWKIKNFSKLPD-----N--IYESEVFVAG--DQKWYVYFLKWCSNPNI  177 (180)
Q Consensus       133 ~~~~~tW~i~nFs~l~~-----~--~~~S~~F~vg--~~~w~i~~yp~g~~~~~  177 (180)
                      ..+.|.|+|.+|+.+.+     .  ...|+.|.+|  |++|+|.+||+|++.+.
T Consensus        37 ~~G~hvwkI~~yS~~~~~~~~g~~~~i~S~~Fyvg~~GY~w~i~~ypnG~g~~~   90 (186)
T cd03777          37 YNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGK   90 (186)
T ss_pred             cceEEEEEECChhHHHHhhccCCCcEEECCCeEeCCCCeeEEEEEEcCCCCCCC
Confidence            35889999999998752     2  5789999999  99999999999987654

TRAF3 was first described as a molecule that binds the cytoplasmic tail of CD40. However, it is not required for CD40 signaling. More recently, TRAF3 has been identified as a key regulator of type I interferon (IFN) production and the mammalian innate antiviral immunity. It mediates IFN responses in Toll-like receptor (TLR)-dependent as well as TLR-independent viral recognition pathways. It is also a key element in immunological homeostasis through its regulation of the anti-inflammatory cytokine interleukin-10. TRAF3 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal al

>smart00061 MATH meprin and TRAF homology

Probab=98.09  E-value=2.8e-06  Score=58.00  Aligned_cols=36  Identities=19%  Similarity=0.142  Sum_probs=32.3

Q ss_pred             eEEEeccccCCC-CCccCCCcEEeCCeEEEEEEecCC
Q 030279          137 HVWKIKNFSKLP-DNIYESEVFVAGDQKWYVYFLKWC  172 (180)
Q Consensus       137 ~tW~i~nFs~l~-~~~~~S~~F~vg~~~w~i~~yp~g  172 (180)
                      ++|.|+||+++. +..+.|+.|.++|+.|||.+||++
T Consensus         2 ~~~~~~~~~~~~~~~~~~S~~f~~~g~~W~i~~~p~~   38 (95)
T smart00061        2 LSHTFKNVSRLEEGESYFSPSEEHFNIPWRLKIYRKN   38 (95)
T ss_pred             ceeEEEchhhcccCceEeCChhEEcCceeEEEEEEcC
Confidence            589999999984 467889999999999999999984

>cd00121 MATH MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins

Probab=98.05  E-value=9.5e-06  Score=57.64  Aligned_cols=40  Identities=35%  Similarity=0.539  Sum_probs=35.9

Q ss_pred             ceEEEeccccCCCCCccCCCcEEeCCeEEEEEEecCCCCC
Q 030279          136 KHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCSNP  175 (180)
Q Consensus       136 ~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~~yp~g~~~  175 (180)
                      .++|.|.+|+......+.|+.|.++|..|||.+||+|...
T Consensus         2 ~~~~~i~~~~~~~~~~~~S~~f~~~g~~W~l~~~p~~~~~   41 (126)
T cd00121           2 KHTWKIVNFSELEGESIYSPPFEVGGYKWRIRIYPNGDGE   41 (126)
T ss_pred             EEEEEECCCCCCCCcEEECCCEEEcCEeEEEEEEcCCCCC
Confidence            5899999999966667889999999999999999999854

Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH doma

>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]

Probab=97.94  E-value=5.1e-06  Score=76.22  Aligned_cols=43  Identities=26%  Similarity=0.502  Sum_probs=38.7

Q ss_pred             CCcceEEEeccccCCCCCccCCCcEEeCCeEEEEEEecCCCCCC
Q 030279          133 SNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCSNPN  176 (180)
Q Consensus       133 ~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~~yp~g~~~~  176 (180)
                      ...+|+|.|++|++|.+ ++.||.|.|||+.|+|.+||+|+++-
T Consensus        37 ~~~sftW~vk~wsel~~-k~~Sp~F~vg~~twki~lfPqG~nq~   79 (1089)
T COG5077          37 LEMSFTWKVKRWSELAK-KVESPPFSVGGHTWKIILFPQGNNQC   79 (1089)
T ss_pred             hhcccceecCChhhhhh-hccCCcccccCeeEEEEEecccCCcc
Confidence            44689999999999997 58899999999999999999998764

>cd03778 MATH_TRAF2 Tumor Necrosis Factor Receptor (TNFR) Associated Factor (TRAF) family, TRAF2 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses

Probab=97.66  E-value=2.3e-05  Score=60.27  Aligned_cols=45  Identities=16%  Similarity=0.199  Sum_probs=36.2

Q ss_pred             CCcceEEEeccccCCCCC-------ccCCCcEEeC--CeEEEEEEecCCCCCCC
Q 030279          133 SNYKHVWKIKNFSKLPDN-------IYESEVFVAG--DQKWYVYFLKWCSNPNI  177 (180)
Q Consensus       133 ~~~~~tW~i~nFs~l~~~-------~~~S~~F~vg--~~~w~i~~yp~g~~~~~  177 (180)
                      .++.|.|+|+||+.+.+.       ...|+.|..+  |++|+|.+||+|++.+.
T Consensus        17 ~~g~fiWkI~~fs~~~~~a~~~~~~~i~Sp~Fyt~~~GYk~~l~~ylnG~g~~~   70 (164)
T cd03778          17 YDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGR   70 (164)
T ss_pred             cCCEEEEEECcHHHHHHHHhcCCCceEECCCcccCCCCeEEEEEEEeCCCCCCC
Confidence            468999999999986532       4567888764  89999999999987654

TRAF2 associates with the receptors TNFR-1, TNFR-2, RANK (which mediates differentiation and maturation of osteoclasts) and CD40 (which is important for the proliferation and activation of B cells), among others. It regulates distinct pathways that lead to the activation of nuclear factor-kappaB and Jun NH2-terminal kinases. TRAF2 also indirectly associates with death receptors through its interaction with TRADD (TNFR-associated death domain protein). It is involved in regulating oxidative stress or ROS-induced cell death and in the preconditioning of cells by sublethal stress for protection from subsequent injury. TRAF2 contains a RING finger domain, five z

>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]

Probab=97.48  E-value=7.6e-05  Score=64.93  Aligned_cols=81  Identities=23%  Similarity=0.329  Sum_probs=67.8

Q ss_pred             CCcEEEEEEcCcccccc----CCCCeEEccceee--cCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCC-CCCcEEEE
Q 030279           19 PPAHFLLKIEAFSSLVE----NDVENYKSLEFDA--GGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSL-GLGWEVYV   91 (180)
Q Consensus        19 ~~~~~~w~I~~fS~l~~----~~~~~~~S~~F~v--gG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~-~~~~~~~a   91 (180)
                      ..|..+|+|.+|...+.    +....++|+.|..  .||+.+..+|-+|+.. +.+.++|+|+.++..+.. .+.|+.+-
T Consensus       278 ~~g~~iwki~~~~~~~~e~~~~~~~~~~S~~f~t~~~Gyk~~~~~~lng~g~-~~~~~~s~~~~~~~ge~d~~l~wpf~~  356 (391)
T KOG0297|consen  278 YDGTLIWKIPDYGRKKQEAVAGATLSLFSPAFYTSKYGYKLCARIYLNGDGT-GKGTHLSLYFVVMRGEYDALLPWPFRQ  356 (391)
T ss_pred             cCCEEEEEecchhhhhHHHHhccCccccccccccccccHHHHhHhhhcCCCC-CCcceeeeeeeecccCcccccccCCCC
Confidence            46899999999965543    3568999999986  5999999999999985 467799999999987643 35799999


Q ss_pred             EEEEEEEeC
Q 030279           92 IFRLFVLDQ  100 (180)
Q Consensus        92 ~f~~~llnq  100 (180)
                      +.+|.+++|
T Consensus       357 ~v~~~l~dq  365 (391)
T KOG0297|consen  357 KVTLMLLDQ  365 (391)
T ss_pred             ceEEEEecc
Confidence            999999999

>PF00917 MATH: MATH domain; InterPro: IPR002083 Although apparently functionally unrelated, intracellular TRAFs and extracellular meprins share a conserved region of about 180 residues, the meprin and TRAF homology (MATH) domain []

Probab=97.12  E-value=6.4e-05  Score=53.36  Aligned_cols=33  Identities=36%  Similarity=0.469  Sum_probs=27.9

Q ss_pred             eccccCCC--CCccCCCcEEeCCeEEEEEEecCCC
Q 030279          141 IKNFSKLP--DNIYESEVFVAGDQKWYVYFLKWCS  173 (180)
Q Consensus       141 i~nFs~l~--~~~~~S~~F~vg~~~w~i~~yp~g~  173 (180)
                      |+||++|+  +..+.|+.|.++|+.|+|.+||+|+
T Consensus         1 i~nfs~l~~~~~~~~s~~~~~~g~~W~l~~~~~~~   35 (119)
T PF00917_consen    1 IKNFSKLKEGEEYSSSFVFSHGGYPWRLKVYPKGN   35 (119)
T ss_dssp             ETTGGGHHTSEEEEEEEESSTTSEEEEEEEETTES
T ss_pred             CcccceEeCCCcEECCCeEEECCEEEEEEEEeCCC
Confidence            68999997  3345558889999999999999998

Meprins are mammalian tissue-specific metalloendopeptidases of the astacin family implicated in developmental, normal and pathological processes by hydrolysing a variety of proteins. Various growth factors, cytokines, and extracellular matrix proteins are substrates for meprins. They are composed of five structural domains: an N-terminal endopeptidase domain, a MAM domain (see PDOC00604 from PROSITEDOC), a MATH domain, an EGF-like domain (see PDOC00021 from PROSITEDOC) and a C-terminal transmembrane region. Meprin A and B form membrane bound homotetramer whereas homooligomers of meprin A are secreted. A proteolitic site adjacent to the MATH domain, only present in meprin A, allows the release of the protein from the membrane []. TRAF proteins were first isolated by their ability to interact with TNF receptors []. They promote cell survival by the activation of downstream protein kinases and, finally, transcription factors of the NF-kB and AP-1 family. The TRAF proteins are composed of 3 structural domains: a RING finger (see PDOC00449 from PROSITEDOC) in the N-terminal part of the protein, one to seven TRAF zinc fingers (see PDOC50145 from PROSITEDOC) in the middle and the MATH domain in the C-terminal part []. The MATH domain is necessary and sufficient for self-association and receptor interaction. From the structural analysis two consensus sequence recognised by the TRAF domain have been defined: a major one, [PSAT]x[QE]E and a minor one, PxQxxD []. The structure of the TRAF2 protein reveals a trimeric self-association of the MATH domain []. The domain forms a new, light-stranded antiparallel beta sandwich structure. A coiled-coil region adjacent to the MATH domain is also important for the trimerisation. The oligomerisation is essential for establishing appropriate connections to form signalling complexes with TNF receptor-1. The ligand binding surface of TRAF proteins is located in beta-strands 6 and 7 [].; GO: 0005515 protein binding; PDB: 1D00_E 1CZY_A 1D01_F 1CA9_A 1D0J_D 1F3V_B 1CA4_C 1D0A_A 1QSC_C 1CZZ_C ....

>cd00270 MATH_TRAF_C Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link cell surface TNFRs and receptors of the interleukin-1/Toll-like family to downstream kinase signaling cascades which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems

Probab=97.04  E-value=0.00058  Score=51.04  Aligned_cols=27  Identities=11%  Similarity=0.049  Sum_probs=23.5

Q ss_pred             CccCCCcEEeC--CeEEEEEEecCCCCCC
Q 030279          150 NIYESEVFVAG--DQKWYVYFLKWCSNPN  176 (180)
Q Consensus       150 ~~~~S~~F~vg--~~~w~i~~yp~g~~~~  176 (180)
                      ..+.|+.|.||  |++|+|.+||+|...+
T Consensus        23 ~~~~S~~F~vg~~G~~w~i~~yP~G~~~~   51 (149)
T cd00270          23 TVLYSPPFYTSRYGYKLCLRLYLNGDGTG   51 (149)
T ss_pred             ceEECCCcccCCCCceEEEEEEeCCCCCC
Confidence            45789999999  9999999999998543

There are at least six mammalian and three Drosophila proteins containing TRAF domains. The mammalian TRAFs display varying expression profiles, indicating independent and cell type-specific regulation. They display distinct, as well as overlapping functions and interactions with receptors. Most TRAFs, except TRAF1, share N-terminal homology and contain a RING domain, multiple zinc finger domains, and a TRAF domain. TRAFs form homo- and heterotrimers through its TRAF domain. The TRAF domain can be divided into a more divergent N-ter

>cd03776 MATH_TRAF6 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF6 subfamily, TRAF domain, C-terminal MATH subdomain; composed of proteins with similarity to human TRAF6, including the Drosophila protein DTRAF2

Probab=96.64  E-value=0.0016  Score=48.75  Aligned_cols=26  Identities=12%  Similarity=-0.067  Sum_probs=22.2

Q ss_pred             cCCCcEEe--CCeEEEEEEecCCCCCCC
Q 030279          152 YESEVFVA--GDQKWYVYFLKWCSNPNI  177 (180)
Q Consensus       152 ~~S~~F~v--g~~~w~i~~yp~g~~~~~  177 (180)
                      +.|+.|.+  ||++|+|.+||+|...+.
T Consensus        25 i~S~~F~~~~gGy~W~i~~yP~G~~~~~   52 (147)
T cd03776          25 IHSPGFYTSPPGYKLCARLNLSLPEARC   52 (147)
T ss_pred             EECCCcccCCCCceEEEEEEeCCCCCCC
Confidence            56899985  799999999999987654

TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF6 is the most divergent in its TRAF domain among the mammalian TRAFs. In addition to mediating TNFR family signaling, it is also an essential signaling molecule of the interleukin-1/Toll-like receptor superfamily. Whereas other TRAF molecules display similar and overlapping TNFR-binding specificities, TRAF6 binds completely different sites on receptors such as CD40 and RANK. TRAF6 serves as a molecular bridge between innate and adaptive immunity and plays a central role in osteoimmunology. DTRAF2, as an activator of nuclear factor-kapp

>cd03780 MATH_TRAF5 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF5 subfamily, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses

Probab=96.61  E-value=0.0018  Score=49.06  Aligned_cols=27  Identities=7%  Similarity=-0.159  Sum_probs=23.8

Q ss_pred             ccCCCcE--EeCCeEEEEEEecCCCCCCC
Q 030279          151 IYESEVF--VAGDQKWYVYFLKWCSNPNI  177 (180)
Q Consensus       151 ~~~S~~F--~vg~~~w~i~~yp~g~~~~~  177 (180)
                      ...|+.|  .++|++|+|.+||+|.+.+.
T Consensus        24 ~i~S~~Fyt~~~Gy~w~i~~ypnG~~~~~   52 (148)
T cd03780          24 SIFSQPFYTSRCGYRLCARAYLNGDGSGK   52 (148)
T ss_pred             EEECCCcccCCCCeeEEEEEEcCCCCCCC
Confidence            4679999  99999999999999997654

TRAF5 was identified as an activator of nuclear factor-kappaB and a regulator of lymphotoxin-beta receptor and CD40 signaling. Its interaction with CD40 is indirect, involving hetero-oligomerization with TRAF3. In addition, TRAF5 has been shown to associate with other TNFRs including CD27, CD30, OX40 and GITR (glucocorticoid-induced TNFR). It plays a role in modulating Th2 immune responses (driven by OX40 costimulation) and T-cell activation (triggered by GITR). It is also involved in osteoclastogenesis. TRAF5 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more dive

>cd03781 MATH_TRAF4 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF4 subfamily, TRAF domain, C-terminal MATH subdomain; composed of proteins with similarity to human TRAF4, including the Drosophila protein DTRAF1

Probab=96.61  E-value=0.0023  Score=48.51  Aligned_cols=27  Identities=15%  Similarity=-0.114  Sum_probs=23.4

Q ss_pred             ccCCCcEEeC--CeEEEEEEecCCCCCCC
Q 030279          151 IYESEVFVAG--DQKWYVYFLKWCSNPNI  177 (180)
Q Consensus       151 ~~~S~~F~vg--~~~w~i~~yp~g~~~~~  177 (180)
                      ...|+.|.||  |++|+|.+||+|...+.
T Consensus        24 ~i~S~~F~vg~~Gy~w~i~~yPnG~~~~~   52 (154)
T cd03781          24 ELFSPPFYTHRYGYKLQVSAFLNGNGSGE   52 (154)
T ss_pred             eEECCCeecCCCCEEEEEEEECCCCCCCC
Confidence            4678999999  99999999999976543

TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF4 is highly expressed during embryogenesis, especially in the central and peripheral nervous system. Studies using TRAF4-deficient mice show that TRAF4 is required for neurogenesis, as well as the development of the trachea and the axial skeleton. In addition, TRAF4 augments nuclear factor-kappaB activation triggered by GITR (glucocorticoid-induced TNFR), a receptor expressed in T-cells, B-cells and macrophages. It also participates in counteracting the signaling mediated by Toll-like receptors through its association with TRAF6 and TR

>KOG1863 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]

Probab=96.25  E-value=0.0037  Score=60.99  Aligned_cols=115  Identities=19%  Similarity=0.158  Sum_probs=84.9

Q ss_pred             cEEEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEEEEEEEEEEeC
Q 030279           21 AHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQ  100 (180)
Q Consensus        21 ~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~~llnq  100 (180)
                      ..++|.+.+...+.    ....|+.|..|+..|++.+.|+|+.    ...+++|+........ ..|.+++++.+.+.|.
T Consensus        27 ~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~-~~~s~~~~~~~~v~~~   97 (1093)
T KOG1863|consen   27 QSTTIDGIDDKSLL----YRALSSNFGAGATKWKILIAPKVNS----LQSTRKKLEVMPSQSL-KSWSCGAQAVLRVKNT   97 (1093)
T ss_pred             ccccccCcCcchhh----hHhcCccccccccceeeeeccccCc----ccceeEEeeeccCCCC-cceEecchhhhccccC
Confidence            44556665555543    3788999999999999999999984    4679999998877665 4499999999999993


Q ss_pred             CCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCC
Q 030279          101 KKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGD  161 (180)
Q Consensus       101 ~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~  161 (180)
                      .++.....           +..      .+-+......|+..+|+.+.+.+.+..+|...|
T Consensus        98 ~~~~~~~~-----------~~~------~h~~~~~~~dwg~~~~~~~~~~~~~~~~~~~~~  141 (1093)
T KOG1863|consen   98 IDNLPDPE-----------KAI------HHVFTADERDWGFSCFSTSSDIRKPEDGYVRNG  141 (1093)
T ss_pred             CCCchhhh-----------hhh------hhcccccccchhhccchhHhhccCccccccccc
Confidence            33332221           111      113456678899889998888777778888877

>cd03779 MATH_TRAF1 Tumor Necrosis Factor Receptor (TNFR) Associated Factor (TRAF) family, TRAF1 subfamily, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses

Probab=94.78  E-value=0.029  Score=42.41  Aligned_cols=26  Identities=12%  Similarity=-0.022  Sum_probs=22.0

Q ss_pred             cCCCcEEeC--CeEEEEEEecCCCCCCC
Q 030279          152 YESEVFVAG--DQKWYVYFLKWCSNPNI  177 (180)
Q Consensus       152 ~~S~~F~vg--~~~w~i~~yp~g~~~~~  177 (180)
                      ..|+.|..+  |++|+|.+||+|.+.+.
T Consensus        25 ~~S~~Fyt~~~Gy~w~i~~ypnG~~~~~   52 (147)
T cd03779          25 LCSPAFYTAKYGYKVCLRLYLNGDGAGK   52 (147)
T ss_pred             EECCCcccCCCCceEEEEEEcCCCCCCC
Confidence            568888876  99999999999987653

TRAF1 expression is the most restricted among the TRAFs. It is found exclusively in activated lymphocytes, dendritic cells and certain epithelia. TRAF1 associates, directly or indirectly through heterodimerization with TRAF2, with the TNFR family receptors TNFR-2, CD30, RANK, CD40 and LMP1, among others. It also binds the intracellular proteins TRADD, TANK, TRIP, RIP1, RIP2 and FLIP. TRAF1 is unique among the TRAFs in that it lacks a RING domain, which is critical for the activation of nuclear factor-kappaB and Jun NH2-terminal kinase. Studies on TRAF1-deficient mice suggest that TRAF1 has a negative regulatory role in TNFR-mediat

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	180
2foj_A	155	Ubiquitin carboxyl-terminal hydrolase 7; MATH doma	2e-17
2foj_A	155	Ubiquitin carboxyl-terminal hydrolase 7; MATH doma	3e-05
3ivv_A	145	Speckle-type POZ protein; protein binding, nucleus	3e-14
1lb6_A	160	TNF receptor-associated factor 6; TRAF6-CD40 compl	1e-12
3hqi_A	312	Speckle-type POZ protein; SPOP, ubiquitin, puckere	5e-12
1ca9_A	192	TRAF2, protein (TNF receptor associated factor 2);	4e-09
1d00_A	168	Tumor necrosis factor receptor associated protein	7e-09
2f1z_A	522	Ubiquitin carboxyl-terminal hydrolase 7; hausp, US	7e-09
2gkw_A	192	TNF receptor-associated factor 3; CD40, NF-KB sign	6e-08
1flk_A	228	TNF receptor associated factor 3; TNF signaling, T	1e-07

>2foj_A Ubiquitin carboxyl-terminal hydrolase 7; MATH domain, hydrolase; 1.60A {Homo sapiens} PDB: 1yze_A 1yy6_A 2foo_A 2fop_A 3mqr_A 3mqs_C 2f1w_A 2f1x_A 2f1y_A 2xxn_A Length = 155

 Score = 74.1 bits (182), Expect = 2e-17
 Identities = 19/103 (18%), Positives = 35/103 (33%), Gaps = 5/103 (4%)

Query: 19  PPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMV 78
             A F   +E FS L E+      S         WK++V P    +   +  +  +L   
Sbjct: 17  SEATFQFTVERFSRLSES----VLSPPCFVRNLPWKIMVMPRFYPDRPHQKSVGFFLQC- 71

Query: 79  DTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVKETKKCTG 121
           +  S    W  +    L +++ + DE    + +      K   
Sbjct: 72  NAESDSTSWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKEND 114

>2foj_A Ubiquitin carboxyl-terminal hydrolase 7; MATH domain, hydrolase; 1.60A {Homo sapiens} PDB: 1yze_A 1yy6_A 2foo_A 2fop_A 3mqr_A 3mqs_C 2f1w_A 2f1x_A 2f1y_A 2xxn_A Length = 155

 Score = 41.4 bits (97), Expect = 3e-05
 Identities = 5/33 (15%), Positives = 14/33 (42%), Gaps = 1/33 (3%)

Query: 136 KHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYF 168
              + ++ FS+L +++  S      +  W +  
Sbjct: 20  TFQFTVERFSRLSESVL-SPPCFVRNLPWKIMV 51

>3ivv_A Speckle-type POZ protein; protein binding, nucleus, UBL conjugation pathway, ligase; 1.25A {Homo sapiens} PDB: 3ivq_A 3ivb_A 3hsv_A 3hqh_A 3hqm_A 3hql_A 2cr2_A Length = 145

 Score = 65.7 bits (160), Expect = 3e-14
 Identities = 30/105 (28%), Positives = 44/105 (41%), Gaps = 8/105 (7%)

Query: 12  SRSISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGG---YKWKLVVYPNGNKNENVK 68
           S     V    ++  I  FS   E   E  KS  F +G     KW L V P G  +E  K
Sbjct: 2   SGGSGKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGL-DEESK 60

Query: 69  DHISIYLAMVDTSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFV 113
           D++S+YL +V         EV   F+  +L+ K +E   ++    
Sbjct: 61  DYLSLYLLLVSCP----KSEVRAKFKFSILNAKGEETKAMESQRA 101

>1lb6_A TNF receptor-associated factor 6; TRAF6-CD40 complex, signaling protein; 1.80A {Homo sapiens} SCOP: b.8.1.1 PDB: 1lb5_A 1lb4_A Length = 160

 Score = 61.5 bits (149), Expect = 1e-12
 Identities = 18/90 (20%), Positives = 34/90 (37%), Gaps = 7/90 (7%)

Query: 22  HFLLKIEAFSSLVENDVENY----KSLEF--DAGGYKWKLVVYPNGNKNENVKDHISIYL 75
            ++ KI  F   ++   E       S  F     GYK  + ++      +   ++IS+++
Sbjct: 6   IYIWKIGNFGMHLKCQEEEKPVVIHSPGFYTGKPGYKLCMRLHLQLPTAQRCANYISLFV 65

Query: 76  AMVDTSSLG-LGWEVYVIFRLFVLDQKKDE 104
             +       L W      RL +LDQ +  
Sbjct: 66  HTMQGEYDSHLPWPFQGTIRLTILDQSEAP 95

>3hqi_A Speckle-type POZ protein; SPOP, ubiquitin, puckered, nucleus, UBL conjugation pathway, protein binding, ligase; 2.62A {Homo sapiens} PDB: 3hu6_A Length = 312

 Score = 61.8 bits (150), Expect = 5e-12
 Identities = 27/83 (32%), Positives = 38/83 (45%), Gaps = 8/83 (9%)

Query: 22  HFLLKIEAFSSLVENDVENYKSLEFDAGG---YKWKLVVYPNGNKNENVKDHISIYLAMV 78
            ++  I  FS   E   E  KS  F +G     KW L V P G   E+ KD++S+YL +V
Sbjct: 8   SYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEES-KDYLSLYLLLV 66

Query: 79  DTSSLGLGWEVYVIFRLFVLDQK 101
                    EV   F+  +L+ K
Sbjct: 67  SCPK----SEVRAKFKFSILNAK 85

>1ca9_A TRAF2, protein (TNF receptor associated factor 2); TNF signaling, TRAF, adapter protein, cell surviVal; 2.30A {Homo sapiens} SCOP: b.8.1.1 h.1.2.1 PDB: 1qsc_A 1czz_A Length = 192

 Score = 52.7 bits (126), Expect = 4e-09
 Identities = 23/90 (25%), Positives = 35/90 (38%), Gaps = 8/90 (8%)

Query: 22  HFLLKIEAFSSLVENDVEN----YKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYL 75
            F+ KI  F+   +  V        S  F     GYK  L +Y NG+       H+S++ 
Sbjct: 44  VFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGD-GTGRGTHLSLFF 102

Query: 76  AMVDTSS-LGLGWEVYVIFRLFVLDQKKDE 104
            ++   +   L W       L +LDQ   E
Sbjct: 103 VVMKGPNDALLRWPFNQKVTLMLLDQNNRE 132

>1d00_A Tumor necrosis factor receptor associated protein 2; B-sandwich, protein-peptide complex, apoptosis; 2.00A {Homo sapiens} SCOP: b.8.1.1 h.1.2.1 PDB: 1ca4_A 1d0j_A 1f3v_B 1czy_A 1d01_A 1d0a_A Length = 168

 Score = 51.5 bits (123), Expect = 7e-09
 Identities = 23/90 (25%), Positives = 35/90 (38%), Gaps = 8/90 (8%)

Query: 22  HFLLKIEAFSSLVENDVEN----YKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYL 75
            F+ KI  F+   +  V        S  F     GYK  L +Y NG+       H+S++ 
Sbjct: 20  VFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGD-GTGRGTHLSLFF 78

Query: 76  AMVDTSS-LGLGWEVYVIFRLFVLDQKKDE 104
            ++   +   L W       L +LDQ   E
Sbjct: 79  VVMKGPNDALLRWPFNQKVTLMLLDQNNRE 108

>2f1z_A Ubiquitin carboxyl-terminal hydrolase 7; hausp, USP7, UBP, deubiquitinating enzyme, substrate recognition; 3.20A {Homo sapiens} Length = 522

 Score = 53.1 bits (127), Expect = 7e-09
 Identities = 18/92 (19%), Positives = 33/92 (35%), Gaps = 5/92 (5%)

Query: 19  PPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMV 78
             A F   +E FS L E+      S         WK++V P    +   +  +  +L   
Sbjct: 29  SEATFQFTVERFSRLSES----VLSPPCFVRNLPWKIMVMPRFYPDRPHQKSVGFFL-QC 83

Query: 79  DTSSLGLGWEVYVIFRLFVLDQKKDEFLILQE 110
           +  S    W  +    L +++ + DE    + 
Sbjct: 84  NAESDSTSWSCHAQAVLKIINYRDDEKSFSRR 115

>2gkw_A TNF receptor-associated factor 3; CD40, NF-KB signaling, BAFF receptor, TRAF3, apoptosis; 2.70A {Homo sapiens} PDB: 1kzz_A 1l0a_A 1zms_A 1rf3_A Length = 192

 Score = 49.2 bits (117), Expect = 6e-08
 Identities = 19/90 (21%), Positives = 30/90 (33%), Gaps = 8/90 (8%)

Query: 22  HFLLKIEAFSSLVENDVEN----YKSLEF--DAGGYKWKLVVYPNGNKNENVKDHISIYL 75
             + KI  +    +  V        S  F     GYK    VY NG+       H+S++ 
Sbjct: 41  VLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGD-GMGKGTHLSLFF 99

Query: 76  AMVDTSS-LGLGWEVYVIFRLFVLDQKKDE 104
            ++       L W       L ++DQ    
Sbjct: 100 VIMRGEYDALLPWPFKQKVTLMLMDQGSSR 129

>1flk_A TNF receptor associated factor 3; TNF signaling, TRAF3, CD40-binding protein, apoptosis; 2.80A {Homo sapiens} SCOP: b.8.1.1 h.1.2.1 PDB: 1fll_A Length = 228

 Score = 48.9 bits (116), Expect = 1e-07
 Identities = 19/105 (18%), Positives = 31/105 (29%), Gaps = 8/105 (7%)

Query: 22  HFLLKIEAFSSLVENDVEN----YKSLEF--DAGGYKWKLVVYPNGNKNENVKDHISIYL 75
             + KI  +    +  V        S  F     GYK    VY NG+       H+S++ 
Sbjct: 77  VLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGD-GMGKGTHLSLFF 135

Query: 76  AMVDTSS-LGLGWEVYVIFRLFVLDQKKDEFLILQEVFVKETKKC 119
            ++       L W       L ++DQ      +            
Sbjct: 136 VIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSS 180

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	180
3ivv_A	145	Speckle-type POZ protein; protein binding, nucleus	99.92
2foj_A	155	Ubiquitin carboxyl-terminal hydrolase 7; MATH doma	99.9
1lb6_A	160	TNF receptor-associated factor 6; TRAF6-CD40 compl	99.89
4gjh_A	178	TNF receptor-associated factor 5; TRAF domain, imm	99.88
1ca9_A	192	TRAF2, protein (TNF receptor associated factor 2);	99.87
4ghu_A	198	TNF receptor-associated factor 3; alpha/beta, inna	99.87
1d00_A	168	Tumor necrosis factor receptor associated protein	99.87
2gkw_A	192	TNF receptor-associated factor 3; CD40, NF-KB sign	99.86
1flk_A	228	TNF receptor associated factor 3; TNF signaling, T	99.85
2f1z_A	522	Ubiquitin carboxyl-terminal hydrolase 7; hausp, US	99.84
3hqi_A	312	Speckle-type POZ protein; SPOP, ubiquitin, puckere	99.83
3ivv_A	145	Speckle-type POZ protein; protein binding, nucleus	98.71
2foj_A	155	Ubiquitin carboxyl-terminal hydrolase 7; MATH doma	98.68
4gwm_A	592	Meprin A subunit beta; mulidomain structure, hydro	98.63
4gjh_A	178	TNF receptor-associated factor 5; TRAF domain, imm	98.62
4ghu_A	198	TNF receptor-associated factor 3; alpha/beta, inna	98.62
1ca9_A	192	TRAF2, protein (TNF receptor associated factor 2);	98.58
2gkw_A	192	TNF receptor-associated factor 3; CD40, NF-KB sign	98.53
2f1z_A	522	Ubiquitin carboxyl-terminal hydrolase 7; hausp, US	98.47
1d00_A	168	Tumor necrosis factor receptor associated protein	98.45
1flk_A	228	TNF receptor associated factor 3; TNF signaling, T	98.44
1lb6_A	160	TNF receptor-associated factor 6; TRAF6-CD40 compl	97.16
4gwm_A	592	Meprin A subunit beta; mulidomain structure, hydro	93.84

>3ivv_A Speckle-type POZ protein; protein binding, nucleus, UBL conjugation pathway, ligase; 1.25A {Homo sapiens} SCOP: b.8.1.1 PDB: 3ivq_A 3ivb_A 3hsv_A 3hqh_A 3hqm_A 3hql_A 2cr2_A

Probab=99.92  E-value=6.6e-25  Score=163.86  Aligned_cols=126  Identities=26%  Similarity=0.363  Sum_probs=100.6

Q ss_pred             EEecCCCcEEEEEEcCccccccCCCCeEEccceeecCe---EEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEE
Q 030279           14 SISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGY---KWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVY   90 (180)
Q Consensus        14 ~~~~~~~~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~---~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~   90 (180)
                      .+.+...++|+|+|+|||.+++..++.++|++|.+|||   +|+|.+||+|+.. +..+||||||++.+.    ++|+++
T Consensus         4 ~m~~~~~~~~~w~I~~fs~~~~~~g~~~~S~~F~~gg~~g~~W~i~~yP~G~~~-~~~~~lSlyL~l~~~----~~w~v~   78 (145)
T 3ivv_A            4 GSGKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDE-ESKDYLSLYLLLVSC----PKSEVR   78 (145)
T ss_dssp             -CCCCCEEEEEEEESSGGGCCCCTTCCEECCCEEESGGGCEEEEEEEETTCSSG-GGTTEEEEEEEEEEC----SSSEEE
T ss_pred             CCCcEEEEEEEEEEcCchHHhhcCCCEEECCCcCCCCcCCceEEEEEEcCCCCC-CCCCeEEEEEEEcCC----CCCcEE
Confidence            45677889999999999999755578999999999996   9999999999874 457899999999875    359999


Q ss_pred             EEEEEEEEeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCC
Q 030279           91 VIFRLFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGD  161 (180)
Q Consensus        91 a~f~~~llnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~  161 (180)
                      |+|+|.|+||.++++....          ......|.       ....||+.+|+.++++...+.+|+++|
T Consensus        79 a~f~l~llnq~~~~~~~~~----------~~~~~~F~-------~~~~wG~~~Fi~~~~L~~~~~~yl~dD  132 (145)
T 3ivv_A           79 AKFKFSILNAKGEETKAME----------SQRAYRFV-------QGKDWGFKKFIRRDFLLDEANGLLPDD  132 (145)
T ss_dssp             EEEEEEEECTTSCEEEEEE----------CSSCEEEE-------TTCEEEEEEEEEHHHHHCGGGCSSGGG
T ss_pred             EEEEEEEEecCCCceeeec----------ccceEEec-------CCCCcCHHHeEEhhhhccccCCcEeCC
Confidence            9999999999988765421          11111121       246899999999987755667899988

>2foj_A Ubiquitin carboxyl-terminal hydrolase 7; MATH domain, hydrolase; 1.60A {Homo sapiens} PDB: 1yze_A 1yy6_A 2foo_A 2fop_A 3mqr_A 3mqs_C 2f1w_A 2f1x_A 2f1y_A 2xxn_A

Probab=99.90  E-value=1.7e-23  Score=157.72  Aligned_cols=123  Identities=19%  Similarity=0.255  Sum_probs=93.7

Q ss_pred             CCCcEEEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEEEEEEEEE
Q 030279           18 VPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLFV   97 (180)
Q Consensus        18 ~~~~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~~l   97 (180)
                      .+.++|+|+|+|||.++    +.++|++|.+|||+|||.+||+|+..++..+||||||++... ..+.+|.++|+|+|.|
T Consensus        16 ~~~~~~~w~I~nfS~~~----~~~~S~~f~~gg~~W~i~~yP~G~~~~~~~~~lSlyL~~~~~-~~~~~w~v~a~~~l~l   90 (155)
T 2foj_A           16 RSEATFQFTVERFSRLS----ESVLSPPCFVRNLPWKIMVMPRFYPDRPHQKSVGFFLQCNAE-SDSTSWSCHAQAVLKI   90 (155)
T ss_dssp             CSEEEEEEEESSGGGCC----SCEECCCEEETTEEEEEEEEEEC------CBEEEEEEEESTT-CCCSSCEEEEEEEEEE
T ss_pred             CCCcEEEEEECChhhcC----CceEcCCEEECCccEEEEEEECCCCCCCCCCEEEEEEEeCCC-CCCCCCEEEEEEEEEE
Confidence            45799999999999994    789999999999999999999998631257899999998544 4567899999999999


Q ss_pred             EeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCCe
Q 030279           98 LDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQ  162 (180)
Q Consensus        98 lnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~  162 (180)
                      +||.+++.+..+.          . ..      .|......||+.+|+.++++...+.+|+++|+
T Consensus        91 ~~~~~~~~~~~~~----------~-~~------~F~~~~~~wG~~~Fi~~~~L~~~~~~yl~dD~  138 (155)
T 2foj_A           91 INYRDDEKSFSRR----------I-SH------LFFHKENDWGFSNFMAWSEVTDPEKGFIDDDK  138 (155)
T ss_dssp             CCSSCGGGCEEEE----------E-EE------EEETTBCEEEEEEEEEHHHHTCTTTSSCBTTB
T ss_pred             EcCCCCcceEEec----------c-EE------EeCCCCCCEeECCeEEHHHhcCcCCCceECCE
Confidence            9999876333210          0 11      12223558999999999877666788999984

>1lb6_A TNF receptor-associated factor 6; TRAF6-CD40 complex, signaling protein; 1.80A {Homo sapiens} SCOP: b.8.1.1 PDB: 1lb5_A 1lb4_A

Probab=99.89  E-value=2.9e-23  Score=157.41  Aligned_cols=134  Identities=19%  Similarity=0.254  Sum_probs=96.5

Q ss_pred             CCCcEEEEEEcCcccccc--CCCC--eEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCC-CCCcEEE
Q 030279           18 VPPAHFLLKIEAFSSLVE--NDVE--NYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSL-GLGWEVY   90 (180)
Q Consensus        18 ~~~~~~~w~I~~fS~l~~--~~~~--~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~-~~~~~~~   90 (180)
                      ...|+|+|+|+|||.+++  +.++  .++|++|.+|  ||+|+|++||+|+..+...+||||||++++.+.. +.+|+++
T Consensus         2 ~~~g~~~w~I~~fS~~~~~~~~g~~~~i~S~~F~vg~~Gy~w~i~~yP~G~~~~~~~~~lSlyL~l~~~~~d~~l~wp~~   81 (160)
T 1lb6_A            2 QCNGIYIWKIGNFGMHLKCQEEEKPVVIHSPGFYTGKPGYKLCMRLHLQLPTAQRCANYISLFVHTMQGEYDSHLPWPFQ   81 (160)
T ss_dssp             CCCEEEEEEECCHHHHHHHHHTTCCEEEECCCEESSSSCCEEEEEEEECCTTCTTTTTEEEEEEEEECCTTGGGSCSSCC
T ss_pred             ccCcEEEEEECCHHHHHHhhhcCCCeEEECcCeecCCCCeeEEEEEEecCCCCCCCCCEEEEEEEEeecCCCccCCCcee
Confidence            457899999999999875  2466  8999999999  9999999999998642237899999999876542 4579999


Q ss_pred             EEEEEEEEeCCCCcee-EEeeEE-eccccccccceEeceecccCCC--cceEEEeccccCCCCCccCCCcEEeCCe
Q 030279           91 VIFRLFVLDQKKDEFL-ILQEVF-VKETKKCTGECLSMKKLTSASN--YKHVWKIKNFSKLPDNIYESEVFVAGDQ  162 (180)
Q Consensus        91 a~f~~~llnq~~~~~~-~~~dvF-~~~~~~~~~e~~s~~~~~~~~~--~~~tW~i~nFs~l~~~~~~S~~F~vg~~  162 (180)
                      |+|+|+|+||.+.... ...+.| .++.      ...+.   .+..  ..-.||+..|+.+.++.  +.+|+++|+
T Consensus        82 a~~~l~lldq~~~~~~~~~~~~~~~~~~------~~~f~---~p~~~~~~~~~G~~~Fi~~~~L~--~~~yl~dD~  146 (160)
T 1lb6_A           82 GTIRLTILDQSEAPVRQNHEEIMDAKPE------LLAFQ---RPTIPRNPKGFGYVTFMHLEALR--QRTFIKDDT  146 (160)
T ss_dssp             SEEEEEECCCSCTTSCCCEEEEEECCTT------SGGGS---CCSSSBCSEEEEEEEEEEGGGGG--TSCCCBTTB
T ss_pred             eeEEEEEEcCCCccccccceEEeecCCc------chhcc---CCcccCCCCCcCEeeEeEHHHhh--hCCCccCCE
Confidence            9999999999875311 111122 1111      00011   1211  23479999999999763  578999884

>4gjh_A TNF receptor-associated factor 5; TRAF domain, immune system; 2.81A {Mus musculus}

Probab=99.88  E-value=1e-23  Score=162.91  Aligned_cols=135  Identities=17%  Similarity=0.256  Sum_probs=99.8

Q ss_pred             cCCCcEEEEEEcCcccccc---C-CCCeEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEE
Q 030279           17 HVPPAHFLLKIEAFSSLVE---N-DVENYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEV   89 (180)
Q Consensus        17 ~~~~~~~~w~I~~fS~l~~---~-~~~~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~   89 (180)
                      ....|+|+|+|+|||.+++   . .+..++|++|.+|  ||+|+|.+||+|+.. +..+||||||++++.+. ...+|++
T Consensus        20 ~~~~g~~~w~I~~fS~~~~~~~~g~~~~i~S~~F~~g~~G~~W~i~~yP~G~~~-~~~~~lSlyL~l~~~~~d~~l~W~v   98 (178)
T 4gjh_A           20 ACYSGKLIWKVTDYRVKKREAVEGHTVSVFSQPFYTSRCGYRLCARAYLNGDGS-GKGTHLSLYFVVMRGEFDSLLQWPF   98 (178)
T ss_dssp             CCSSSEEEEEECCHHHHHHHHHTTSCCCEECCCEESSTTSCEEEEEEETTCCGG-GTTTEEEEEEEEBCCTTGGGSCSSC
T ss_pred             cccceEEEEEECCHHHHHhhhhcCCCcEEECCCeEeCCCCeEEEEEEEECCCCC-CCCCEEEEEEEEecCCCCcccCCce
Confidence            4678999999999999875   1 2348999999999  999999999999874 35689999999976542 2357999


Q ss_pred             EEEEEEEEEeCCCCceeEEeeEE-eccccccccceEeceecccCC-CcceEEEeccccCCCCCccCCCcEEeCCe
Q 030279           90 YVIFRLFVLDQKKDEFLILQEVF-VKETKKCTGECLSMKKLTSAS-NYKHVWKIKNFSKLPDNIYESEVFVAGDQ  162 (180)
Q Consensus        90 ~a~f~~~llnq~~~~~~~~~dvF-~~~~~~~~~e~~s~~~~~~~~-~~~~tW~i~nFs~l~~~~~~S~~F~vg~~  162 (180)
                      +|+|+|.|+||.++.....+ .| .++.      ...|.   .+. .....||+..|+.+.++..++.+|+++|+
T Consensus        99 ~a~~~l~Lldq~~~~~~~~~-~~~~~~~------~~~F~---~p~~~~~~~wG~~~Fi~~~~L~~~~~~yL~dD~  163 (178)
T 4gjh_A           99 RQRVTLMLLDQSGKKNHIVE-TFKADPN------SSSFK---RPDGEMNIASGCPRFVSHSTLENSKNTYIKDDT  163 (178)
T ss_dssp             CCEEEEEECCTTSSCCCEEE-EEECCTT------CGGGS---CCSSSBCCCEEEEEEEEHHHHHCTTCCSSBTTB
T ss_pred             EEEEEEEEEcCCCCcceeEE-eeccCCc------ccccc---CCcccccCCcChhheeEHHHhhccccCcCcCCE
Confidence            99999999999987544321 11 0100      00111   111 23457999999999877555678999983

>1ca9_A TRAF2, protein (TNF receptor associated factor 2); TNF signaling, TRAF, adapter protein, cell surviVal; 2.30A {Homo sapiens} SCOP: b.8.1.1 h.1.2.1 PDB: 1qsc_A 1czz_A

Probab=99.87  E-value=6.7e-23  Score=159.92  Aligned_cols=132  Identities=21%  Similarity=0.284  Sum_probs=98.7

Q ss_pred             CCCcEEEEEEcCcccccc--CCCC--eEEccceee--cCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCC-CCcEEE
Q 030279           18 VPPAHFLLKIEAFSSLVE--NDVE--NYKSLEFDA--GGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLG-LGWEVY   90 (180)
Q Consensus        18 ~~~~~~~w~I~~fS~l~~--~~~~--~~~S~~F~v--gG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~-~~~~~~   90 (180)
                      ...++|+|+|+|||.+++  +.|+  .++|++|.+  |||+|+|.+||+|+.. +..+||||||++++....+ .+|+++
T Consensus        40 ~~~g~~~w~I~nfS~~~~~~~~g~~~~i~S~~F~v~~gG~~W~i~~yP~G~~~-~~~~~lSlyL~l~~~~~~~~~~W~~~  118 (192)
T 1ca9_A           40 TYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGT-GRGTHLSLFFVVMKGPNDALLRWPFN  118 (192)
T ss_dssp             CSSSEEEEEEESHHHHHHHHHTTSSCCEECCCEESSTTSCEEEEEEETTCCGG-GTTTEEEEEEEEECCTTGGGSCSSCC
T ss_pred             ccCceEEEEECCHHHHHHHhhcCCCceEECceEEeCCCCeEEEEEEEeCCCCC-CCCCEEEEEEEEccCCCCCcCCCceE
Confidence            578999999999999874  2444  699999999  9999999999999874 3578999999998876544 679999


Q ss_pred             EEEEEEEEeCCCCceeEEeeEE-eccccccccceEeceecccCC-CcceEEEeccccCCCCCccCCCcEEeCCe
Q 030279           91 VIFRLFVLDQKKDEFLILQEVF-VKETKKCTGECLSMKKLTSAS-NYKHVWKIKNFSKLPDNIYESEVFVAGDQ  162 (180)
Q Consensus        91 a~f~~~llnq~~~~~~~~~dvF-~~~~~~~~~e~~s~~~~~~~~-~~~~tW~i~nFs~l~~~~~~S~~F~vg~~  162 (180)
                      |+|+|.|+||.+.++...  .+ .++      ....+.   .|. .....||+..|+.+.++.. +.+|+++|+
T Consensus       119 a~~~l~lldq~~~~~~~~--~~~~~~------~~~~f~---rp~~~~~~~wG~~~Fi~~~~L~~-~~gyl~dD~  180 (192)
T 1ca9_A          119 QKVTLMLLDQNNREHVID--AFRPDV------TSSSFQ---RPVNDMNIASGCPLFCPVSKMEA-KNSYVRDDA  180 (192)
T ss_dssp             CCEEEEECCTTSSCCEEE--EECCCT------TSGGGS---CCSSSBCCCEEEEEEEETHHHHS-SCSSCBTTE
T ss_pred             EEEEEEEECCCCCceeeE--eeccCC------chhhhc---CCccCCCCCcChhheeEHHHhhh-ccCCEeCCE
Confidence            999999999998855321  01 000      000011   121 2345799999999987643 568999984

>4ghu_A TNF receptor-associated factor 3; alpha/beta, innate immunity, IFN pathway, immune system; 2.20A {Mus musculus} PDB: 2gkw_A 1kzz_A 1l0a_A 1zms_A 1rf3_A

Probab=99.87  E-value=4.2e-23  Score=162.18  Aligned_cols=137  Identities=18%  Similarity=0.245  Sum_probs=100.1

Q ss_pred             CCCcEEEEEEcCcccccc----CCCCeEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEEE
Q 030279           18 VPPAHFLLKIEAFSSLVE----NDVENYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEVY   90 (180)
Q Consensus        18 ~~~~~~~w~I~~fS~l~~----~~~~~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~~   90 (180)
                      ...|+|+|+|+|||.+++    +.++.++|++|.+|  ||+|+|.+||+|+.. +..+||||||.+++.+. ...+|+++
T Consensus        37 ~~~g~~~w~I~nfS~~~~~~~~~~g~~i~S~~F~vg~~Gy~W~i~~yPnG~~~-~~~~~lSlyL~l~~g~~D~~l~wp~~  115 (198)
T 4ghu_A           37 SYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGM-GKGTHLSLFFVIMRGEYDALLPWPFK  115 (198)
T ss_dssp             CSSSEEEEEECCHHHHHHHHHTTSSCCEECCCEESSTTSCEEEEEEETTCCGG-GTTTEEEEEEEEECCTTGGGSCSSCC
T ss_pred             ccccEEEEEECCHHHHHhhhccCCCcEEECCCeEECCCCcEEEEEEEeCCCCC-CCCCeEEEEEEecCCccCCCCCceEE
Confidence            567999999999999875    24689999999999  999999999999874 45789999999987643 23579999


Q ss_pred             EEEEEEEEeCCCCceeEEeeEE-eccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCCeEEEEE
Q 030279           91 VIFRLFVLDQKKDEFLILQEVF-VKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVY  167 (180)
Q Consensus        91 a~f~~~llnq~~~~~~~~~dvF-~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~  167 (180)
                      |+|+|+|+||.+......+ .| .++.      ...+.+  .+......||+..|+.+.++.  +.+|+++| ...|.
T Consensus       116 a~~~l~Lldq~~~~~~~~~-~~~~~~~------~~~f~r--p~~~~~~~wG~~~Fi~~~~L~--~~gyL~dD-~l~I~  181 (198)
T 4ghu_A          116 QKVTLMLMDQGSSRRHLGD-AFKPDPN------SSSFKK--PTGEMNIASGCPVFVAQTVLE--NGTYIKDD-TIFIK  181 (198)
T ss_dssp             CCEEEEECCCSTTCCCEEE-EECCCTT------SGGGSC--CSSSBCCCEEEEEEEEHHHHH--HTTSCBTT-BEEEE
T ss_pred             EEEEEEEEcCCCCccceEE-EeecCcc------cceecC--CcccCcCCcCchhEeEHHHhh--hcCCeeCC-EEEEE
Confidence            9999999999976544321 11 1110      000111  122334589999999988763  46799988 34333

>1d00_A Tumor necrosis factor receptor associated protein 2; B-sandwich, protein-peptide complex, apoptosis; 2.00A {Homo sapiens} SCOP: b.8.1.1 h.1.2.1 PDB: 1ca4_A 1d0j_A 1f3v_B 1czy_A 1d01_A 1d0a_A

Probab=99.87  E-value=2.5e-22  Score=153.15  Aligned_cols=133  Identities=21%  Similarity=0.284  Sum_probs=97.2

Q ss_pred             CCCcEEEEEEcCcccccc--CCCC--eEEcccee--ecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCC-CCcEEE
Q 030279           18 VPPAHFLLKIEAFSSLVE--NDVE--NYKSLEFD--AGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLG-LGWEVY   90 (180)
Q Consensus        18 ~~~~~~~w~I~~fS~l~~--~~~~--~~~S~~F~--vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~-~~~~~~   90 (180)
                      ...++|+|+|+|||.+++  ..++  .++|++|.  +|||+|+|.+||+|+.. +..+||||||++++.+..+ .+|+++
T Consensus        16 ~~~g~~~w~I~nfS~~~~~~~~g~~~~i~S~~F~~~~gG~~W~i~~yP~G~~~-~~~~~lSlyL~l~~~~~~~~~~w~~~   94 (168)
T 1d00_A           16 TYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGT-GRGTHLSLFFVVMKGPNDALLRWPFN   94 (168)
T ss_dssp             CSSSEEEEEEESHHHHHHHHHTTSSCCEECCCEESSTTSCEEEEEEETTCCGG-GTTTEEEEEEEEECCTTGGGSCSSCC
T ss_pred             ccCCEEEEEECCHHHHHHHhhcCCCeEEECCCeecCCCCEEEEEEEEeCCCCC-CCCcEEEEEEEEecCCCCccCCCceE
Confidence            468999999999999975  2455  49999995  89999999999999874 3568999999998865443 689999


Q ss_pred             EEEEEEEEeCCCCceeEEeeEEeccccccccceEeceecccCC-CcceEEEeccccCCCCCccCCCcEEeCCe
Q 030279           91 VIFRLFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSAS-NYKHVWKIKNFSKLPDNIYESEVFVAGDQ  162 (180)
Q Consensus        91 a~f~~~llnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~-~~~~tW~i~nFs~l~~~~~~S~~F~vg~~  162 (180)
                      |+|+|.|+||.+.++....  + .+.    .....+.   .+. .....||+.+|+.+.++.. +.+|+++|+
T Consensus        95 ~~~~l~ll~q~~~~~~~~~--~-~~~----~~~~~f~---~p~~~~~~~~G~~~Fi~~~~L~~-~~gyl~dD~  156 (168)
T 1d00_A           95 QKVTLMLLDQNNREHVIDA--F-RPD----VTSSSFQ---RPVNDMNIASGCPLFCPVSKMEA-KNSYVRDDA  156 (168)
T ss_dssp             CCEEEEECCTTSSCCEEEE--E-CCC----TTSGGGS---CCSSSBCCCEEEEEEEETTTTTS-SSSSSBTTE
T ss_pred             EEEEEEEECCCCCccceec--c-ccC----cchhhcc---CCCcCCCCCcCcceEeEHHHhcc-cCCceeCCE
Confidence            9999999999987644310  0 000    0000011   111 2345799999999998743 238999984

>2gkw_A TNF receptor-associated factor 3; CD40, NF-KB signaling, BAFF receptor, TRAF3, apoptosis; 2.70A {Homo sapiens} PDB: 1kzz_A 1l0a_A 1zms_A 1rf3_A

Probab=99.86  E-value=7.1e-23  Score=160.02  Aligned_cols=131  Identities=19%  Similarity=0.225  Sum_probs=96.5

Q ss_pred             CCcEEEEEEcCcccccc--CCCC--eEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCC-CCCcEEEE
Q 030279           19 PPAHFLLKIEAFSSLVE--NDVE--NYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSL-GLGWEVYV   91 (180)
Q Consensus        19 ~~~~~~w~I~~fS~l~~--~~~~--~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~-~~~~~~~a   91 (180)
                      ..|+|+|+|+|||.+++  +.++  .++|++|.+|  ||+|+|.+||+|+.. +..+||||||++++.+.. ..+|+++|
T Consensus        38 ~~g~~~w~I~~fS~~~~~~~~g~~~~i~S~~F~vg~~Gykw~i~~yPnG~~~-~~~~~lSlyL~l~~~~~d~~l~wp~~a  116 (192)
T 2gkw_A           38 YNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGM-GKGTHLSLFFVIMRGEYDALLPWPFKQ  116 (192)
T ss_dssp             CSSEEEEEEECHHHHHHHHHHTSCSCEECCCEESSTTSCEEEEEEETTCCGG-GTTTEEEEEEEEECCTTGGGSCSSCCC
T ss_pred             cCcEEEEEECCHHHHHHHhhcCCCceEEcccEEECCCCcEEEEEEEeCCCCC-CCCCEEEEEEEEecCCCCccCCCcEEE
Confidence            68999999999999974  2355  6999999999  999999999999874 457899999999876543 35799999


Q ss_pred             EEEEEEEeCCCCceeEEeeEE-eccccccccceEeceecccC-CCcceEEEeccccCCCCCccCCCcEEeCCe
Q 030279           92 IFRLFVLDQKKDEFLILQEVF-VKETKKCTGECLSMKKLTSA-SNYKHVWKIKNFSKLPDNIYESEVFVAGDQ  162 (180)
Q Consensus        92 ~f~~~llnq~~~~~~~~~dvF-~~~~~~~~~e~~s~~~~~~~-~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~  162 (180)
                      +|+|+|+||.+++....+ .| ..+.      ...|.+   + ......||+..|+.+.++.  +.+|+++|+
T Consensus       117 ~~~l~lldq~~~~~~~~~-~~~~~~~------~~~F~~---~~~~~~~~wG~~~Fi~~~~L~--~~gyl~dD~  177 (192)
T 2gkw_A          117 KVTLMLMDQGSSRRHLGD-AFKPDPN------SSSFKK---PTGEMNIASGCPVFVAQTVLE--NGTYIKDDT  177 (192)
T ss_dssp             CEEEEECCCSTTCCCEEE-EECCCTT------CTTSSC---CSSSBCCCEEEEEEEEHHHHH--HTTSCBTTE
T ss_pred             EEEEEEECCCCCccceEE-EEecCCC------cccccC---CCCCCcCCCChHHEeEHHHhC--cCCCeeCCE
Confidence            999999999987554321 11 0000      000111   1 1123479999999998763  347999984

>1flk_A TNF receptor associated factor 3; TNF signaling, TRAF3, CD40-binding protein, apoptosis; 2.80A {Homo sapiens} SCOP: b.8.1.1 h.1.2.1 PDB: 1fll_A

Probab=99.85  E-value=2.8e-22  Score=160.56  Aligned_cols=132  Identities=18%  Similarity=0.203  Sum_probs=97.4

Q ss_pred             CCCcEEEEEEcCcccccc--CCC--CeEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCC-CCCcEEE
Q 030279           18 VPPAHFLLKIEAFSSLVE--NDV--ENYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSL-GLGWEVY   90 (180)
Q Consensus        18 ~~~~~~~w~I~~fS~l~~--~~~--~~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~-~~~~~~~   90 (180)
                      ...|+|+|+|+|||.+++  +.+  ..++|++|.+|  ||+|+|.+||+|+.. +..+||||||++++.+.. ..+|++.
T Consensus        73 ~~~g~~~wkI~nfS~~~~~~~~g~~~~i~S~~F~vg~~Gy~w~i~~yPnG~~~-~~~~~lSlyL~l~~~~~d~~l~Wp~~  151 (228)
T 1flk_A           73 SYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGM-GKGTHLSLFFVIMRGEYDALLPWPFK  151 (228)
T ss_dssp             CSSSEEEEEEECHHHHHHHHHTTSCCCEECCCEESSTTSCEECEEEETTCCGG-GTTTEEEEEECCBCCTTTTSSCSSCC
T ss_pred             CcCcEEEEEECCHHHHHHHhhcCCCeeEECceEEeCCCCcEEEEEEEcCCCCC-CCCCEEEEEEEEecCCccccCCCcEE
Confidence            468999999999999874  233  48999999999  999999999999874 467899999999876543 4579999


Q ss_pred             EEEEEEEEeCCCCceeEEeeEE-eccccccccceEeceecccC-CCcceEEEeccccCCCCCccCCCcEEeCCe
Q 030279           91 VIFRLFVLDQKKDEFLILQEVF-VKETKKCTGECLSMKKLTSA-SNYKHVWKIKNFSKLPDNIYESEVFVAGDQ  162 (180)
Q Consensus        91 a~f~~~llnq~~~~~~~~~dvF-~~~~~~~~~e~~s~~~~~~~-~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~  162 (180)
                      |+|+|+|+||.+++....+ .| .++.      ...|.   .+ ....-.||+..|..+.++.  +.+|+++|+
T Consensus       152 a~~~l~lldq~~~~~~~~~-~~~~~~~------~~~F~---rp~~~~~~~wG~~~Fi~~~~L~--~~gyL~dD~  213 (228)
T 1flk_A          152 QKVTLMLMDQGSSRRHLGD-AFKPDPN------SSSFK---KPTGEMNIASGCPVFVAQTVLE--NGTYIKDDT  213 (228)
T ss_dssp             CCEEEEECCCSSSCCCEEE-EECCCTT------CTTSS---SCSSSBCCCCSEEEEEEHHHHS--SSTTCCSSE
T ss_pred             EEEEEEEEcCCCCccceee-eecCCCc------ccccc---CCccCCCCCcCHHHeeEHHHHc--cCCCccCCE
Confidence            9999999999988654321 11 0000      00011   11 1223479999999988653  467999884

>2f1z_A Ubiquitin carboxyl-terminal hydrolase 7; hausp, USP7, UBP, deubiquitinating enzyme, substrate recognition; 3.20A {Homo sapiens}

Probab=99.84  E-value=3.7e-21  Score=170.00  Aligned_cols=129  Identities=18%  Similarity=0.224  Sum_probs=96.2

Q ss_pred             cCCCcEEEEEEcCccccccCCCCeEEccceeecCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEEEEEEEE
Q 030279           17 HVPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLF   96 (180)
Q Consensus        17 ~~~~~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~~   96 (180)
                      ..+.++|+|+|+|||.++    +.++|++|.+|||+|||++||+|+..++..+||||||++.+. ..+.+|.++|+|+|.
T Consensus        27 ~~~~~~~~w~I~nfS~~~----~~~~S~~F~vgg~~W~i~~yP~G~~~~~~~~~lSlyL~~~~~-~~~~~w~v~a~f~l~  101 (522)
T 2f1z_A           27 WRSEATFQFTVERFSRLS----ESVLSPPCFVRNLPWKIMVMPRFYPDRPHQKSVGFFLQCNAE-SDSTSWSCHAQAVLK  101 (522)
T ss_dssp             CCSEEEEEEEESSCTTCC----SCEECCCEEETTEEEEEEECBC--------CBBCEEEEESTT-CCCSSCBEEEEEEEE
T ss_pred             ccCCcEEEEEECChhhcC----CceeCCCEEECCEeeEEEEEeCCCCCCCCCCeEEEEEEecCC-CCCCCceEEEEEEEE
Confidence            356799999999999996    389999999999999999999997633357899999999877 457789999999999


Q ss_pred             EEeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCCeEEEEEE
Q 030279           97 VLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYF  168 (180)
Q Consensus        97 llnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~~  168 (180)
                      |+||.+.+.+..+           ....      .|......||+.+|+.+.++...+.+|+++|+ ..|.+
T Consensus       102 l~n~~~~~~~~~~-----------~~~~------~F~~~~~~wG~~~Fi~~~~L~~~~~g~L~nD~-l~i~~  155 (522)
T 2f1z_A          102 IINYRDDEKSFSR-----------RISH------LFFHKENDWGFSNFMAWSEVTDPEKGFIDDDK-VTFEV  155 (522)
T ss_dssp             ECCTTCGGGCEEE-----------ECCE------EECGGGCEEEESSSSBHHHHSCGGGSSCBTTB-EEEEE
T ss_pred             EEcCCCCccceec-----------ccee------EecCCCCCcchhheeEhhHhcCcccCcccCCc-EEEEE
Confidence            9999986554321           1111      23334568999999998876556678988884 44444

>3hqi_A Speckle-type POZ protein; SPOP, ubiquitin, puckered, nucleus, UBL conjugation pathway, protein binding, ligase; 2.62A {Homo sapiens} PDB: 3hu6_A

Probab=99.83  E-value=5.3e-21  Score=158.52  Aligned_cols=123  Identities=27%  Similarity=0.390  Sum_probs=92.9

Q ss_pred             CCCcEEEEEEcCccccccCCCCeEEccceeecCe---EEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEEEEEE
Q 030279           18 VPPAHFLLKIEAFSSLVENDVENYKSLEFDAGGY---KWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFR   94 (180)
Q Consensus        18 ~~~~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~---~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~a~f~   94 (180)
                      ...++|+|+|.|||.++...++.+.|++|.+|||   +|+|.+||+|+.. +..+|||+||++.+..    +|+++|+|+
T Consensus         4 ~~~~~~~w~I~nfs~~~~~~~~~i~S~~F~~gg~~~~~W~i~~yP~G~~~-~~~~~lslyL~~~~~~----~~~v~a~~~   78 (312)
T 3hqi_A            4 VVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDE-ESKDYLSLYLLLVSCP----KSEVRAKFK   78 (312)
T ss_dssp             EEEEEEEEEETTGGGCCCCTTCCEECCCBCC--CCCCEEEEEEETTCCC---CTTEEEEEEEEEECC----C-CEEEEEE
T ss_pred             eEEEEEEEEEcCcchhhhcCCCeEeeCCcccCCCCCceEEEEEECCCCCc-cCCCcEEEEEEEcCCC----CCcEEEEEE
Confidence            3468999999999999755589999999999996   9999999999874 4678999999998654    589999999


Q ss_pred             EEEEeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCCe
Q 030279           95 LFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQ  162 (180)
Q Consensus        95 ~~llnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~  162 (180)
                      |.|+||.+++....+          ......|      .. ...||+.+|..++++...+.+|+++|+
T Consensus        79 ~~l~~~~~~~~~~~~----------~~~~~~F------~~-~~~wG~~~Fi~~~~L~~~~~~yl~dD~  129 (312)
T 3hqi_A           79 FSILNAKGEETKAME----------SQRAYRF------VQ-GKDWGFKKFIRRGFLLDEANGLLPDDK  129 (312)
T ss_dssp             EEEECTTSCEEEEEE----------CSSCEEE------CT-TCEEEEEEEEEHHHHTCGGGCCCGGGC
T ss_pred             EEEEeCCCCcccccc----------cCCceeC------CC-CCCcCHHHhccHHHhhccccCeecCCE
Confidence            999999987765421          1111112      22 238999999998876555667888873

>3ivv_A Speckle-type POZ protein; protein binding, nucleus, UBL conjugation pathway, ligase; 1.25A {Homo sapiens} SCOP: b.8.1.1 PDB: 3ivq_A 3ivb_A 3hsv_A 3hqh_A 3hqm_A 3hql_A 2cr2_A

Probab=98.71  E-value=1e-08  Score=75.62  Aligned_cols=44  Identities=23%  Similarity=0.471  Sum_probs=38.2

Q ss_pred             CCCcceEEEeccccCCCC---CccCCCcEEeCCe---EEEEEEecCCCCC
Q 030279          132 ASNYKHVWKIKNFSKLPD---NIYESEVFVAGDQ---KWYVYFLKWCSNP  175 (180)
Q Consensus       132 ~~~~~~tW~i~nFs~l~~---~~~~S~~F~vg~~---~w~i~~yp~g~~~  175 (180)
                      ...+.|+|.|.||+.+++   ..+.|+.|.+||+   +|+|.+||+|++.
T Consensus         8 ~~~~~~~w~I~~fs~~~~~~g~~~~S~~F~~gg~~g~~W~i~~yP~G~~~   57 (145)
T 3ivv_A            8 VVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDE   57 (145)
T ss_dssp             CCEEEEEEEESSGGGCCCCTTCCEECCCEEESGGGCEEEEEEEETTCSSG
T ss_pred             EEEEEEEEEEcCchHHhhcCCCEEECCCcCCCCcCCceEEEEEEcCCCCC
Confidence            345789999999999873   5688999999995   9999999999865

>2foj_A Ubiquitin carboxyl-terminal hydrolase 7; MATH domain, hydrolase; 1.60A {Homo sapiens} PDB: 1yze_A 1yy6_A 2foo_A 2fop_A 3mqr_A 3mqs_C 2f1w_A 2f1x_A 2f1y_A 2xxn_A

Probab=98.68  E-value=1.2e-08  Score=76.08  Aligned_cols=42  Identities=14%  Similarity=0.231  Sum_probs=35.5

Q ss_pred             CCcceEEEeccccCCCCCccCCCcEEeCCeEEEEEEecCCCCC
Q 030279          133 SNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCSNP  175 (180)
Q Consensus       133 ~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~~yp~g~~~  175 (180)
                      ..+.|+|.|.||+.++ ..+.|+.|.+||++|||.+||+|++.
T Consensus        17 ~~~~~~w~I~nfS~~~-~~~~S~~f~~gg~~W~i~~yP~G~~~   58 (155)
T 2foj_A           17 SEATFQFTVERFSRLS-ESVLSPPCFVRNLPWKIMVMPRFYPD   58 (155)
T ss_dssp             SEEEEEEEESSGGGCC-SCEECCCEEETTEEEEEEEEEEC---
T ss_pred             CCcEEEEEECChhhcC-CceEcCCEEECCccEEEEEEECCCCC
Confidence            4568999999999996 56779999999999999999999754

>4gwm_A Meprin A subunit beta; mulidomain structure, hydrolase; HET: NAG BMA FUC MAN; 1.85A {Homo sapiens} PDB: 4gwn_A*

Probab=98.63  E-value=9.6e-08  Score=85.50  Aligned_cols=142  Identities=16%  Similarity=0.233  Sum_probs=93.2

Q ss_pred             EecCCCcEEEEEEcCccccccCCCCeEEccceee-cCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEE-EE
Q 030279           15 ISHVPPAHFLLKIEAFSSLVENDVENYKSLEFDA-GGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEV-YV   91 (180)
Q Consensus        15 ~~~~~~~~~~w~I~~fS~l~~~~~~~~~S~~F~v-gG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~-~a   91 (180)
                      +.+..+..+.|+|.||+++....+..++||+|.. .||+++|.+||+|      ..|+|||++|+..+. .-+.|++ .-
T Consensus       400 ~t~G~CP~~vw~i~nfs~~l~~~~~~~~Sp~Fys~~GY~~~v~l~~~~------~~~~~~~~~l~sG~~D~~L~WP~~~~  473 (592)
T 4gwm_A          400 LSETRCPHHIWHIRNFTQFIGSPNGTLYSPPFYSSKGYAFQIYLNLAH------VTNAGIYFHLISGANDDQLQWPCPWQ  473 (592)
T ss_dssp             EESSCCCSEEEEECSCGGGTTCTTCEEECCCEECTTSCEEEEEEECCS------SSEEEEEEEEECCTTGGGSCSSCCSE
T ss_pred             EeeCCCCCCceeecCHHHhhcCCCCceeCCCccCCCCeEEEEEEecCC------CceEEEEEEEecCCCCCCccCCCCCC
Confidence            3566778899999999999864567999999975 5999999999864      458999999998653 2367999 47


Q ss_pred             EEEEEEEeCCCCce--eEEeeEE-ecccc--------ccc----cceEeceecccCCCcceEEEeccccCCCCCccCCCc
Q 030279           92 IFRLFVLDQKKDEF--LILQEVF-VKETK--------KCT----GECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEV  156 (180)
Q Consensus        92 ~f~~~llnq~~~~~--~~~~dvF-~~~~~--------~~~----~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~  156 (180)
                      ++++.|+||..+-.  ...+..| ..+..        |.+    +...++.. .......-.||..+|+++..+  .+..
T Consensus       474 q~t~~llDQ~pd~~~rms~~~s~ttdp~~~~~~~~~~w~~P~~~g~~~~~~~-~~~~~r~~~~G~~~fish~~l--~~r~  550 (592)
T 4gwm_A          474 QATMTLLDQNPDIRQRMSNQRSITTDPFMTTDNGNYFWDRPSKVGTVALFSN-GTQFRRGGGYGTSAFITHERL--KSRD  550 (592)
T ss_dssp             EEEEEECCCCSSGGGCCCEEEEEECCTTCBCTTSCBTTSCHHHHCEEEECTT-CCEEEEEEEEEEEEEEEHHHH--TSTT
T ss_pred             EEEEEEeCCCCChHhcCceeEEEEcCCcccCcccccccCCcccccccccccC-CcceeecCCcCccccccHHHH--hhcC
Confidence            89999999974421  1122344 22210        000    00000100 000112356899999998754  3566


Q ss_pred             EEeCCeEEE
Q 030279          157 FVAGDQKWY  165 (180)
Q Consensus       157 F~vg~~~w~  165 (180)
                      |+.+|.---
T Consensus       551 fiK~d~~~i  559 (592)
T 4gwm_A          551 FIKGDDVYI  559 (592)
T ss_dssp             SSBTTBEEE
T ss_pred             cccCCeEEE
Confidence            888875443

>4gjh_A TNF receptor-associated factor 5; TRAF domain, immune system; 2.81A {Mus musculus}

Probab=98.62  E-value=6.5e-09  Score=79.59  Aligned_cols=45  Identities=11%  Similarity=0.120  Sum_probs=39.0

Q ss_pred             CCCcceEEEeccccCCCCC-------ccCCCcEEeC--CeEEEEEEecCCCCCC
Q 030279          132 ASNYKHVWKIKNFSKLPDN-------IYESEVFVAG--DQKWYVYFLKWCSNPN  176 (180)
Q Consensus       132 ~~~~~~tW~i~nFs~l~~~-------~~~S~~F~vg--~~~w~i~~yp~g~~~~  176 (180)
                      ...+.|+|.|.||+.+++.       .+.|+.|.+|  |++|+|.+||+|++.+
T Consensus        21 ~~~g~~~w~I~~fS~~~~~~~~g~~~~i~S~~F~~g~~G~~W~i~~yP~G~~~~   74 (178)
T 4gjh_A           21 CYSGKLIWKVTDYRVKKREAVEGHTVSVFSQPFYTSRCGYRLCARAYLNGDGSG   74 (178)
T ss_dssp             CSSSEEEEEECCHHHHHHHHHTTSCCCEECCCEESSTTSCEEEEEEETTCCGGG
T ss_pred             ccceEEEEEECCHHHHHhhhhcCCCcEEECCCeEeCCCCeEEEEEEEECCCCCC
Confidence            4568999999999998642       6789999999  9999999999998654

>4ghu_A TNF receptor-associated factor 3; alpha/beta, innate immunity, IFN pathway, immune system; 2.20A {Mus musculus} PDB: 2gkw_A 1kzz_A 1l0a_A 1zms_A 1rf3_A

Probab=98.62  E-value=8.4e-09  Score=80.48  Aligned_cols=45  Identities=18%  Similarity=0.211  Sum_probs=39.2

Q ss_pred             CCCcceEEEeccccCCCC-------CccCCCcEEeC--CeEEEEEEecCCCCCC
Q 030279          132 ASNYKHVWKIKNFSKLPD-------NIYESEVFVAG--DQKWYVYFLKWCSNPN  176 (180)
Q Consensus       132 ~~~~~~tW~i~nFs~l~~-------~~~~S~~F~vg--~~~w~i~~yp~g~~~~  176 (180)
                      ...+.|+|.|.|||.+++       ..+.|+.|.+|  |++|+|.+||+|++.+
T Consensus        37 ~~~g~~~w~I~nfS~~~~~~~~~~g~~i~S~~F~vg~~Gy~W~i~~yPnG~~~~   90 (198)
T 4ghu_A           37 SYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMG   90 (198)
T ss_dssp             CSSSEEEEEECCHHHHHHHHHTTSSCCEECCCEESSTTSCEEEEEEETTCCGGG
T ss_pred             ccccEEEEEECCHHHHHhhhccCCCcEEECCCeEECCCCcEEEEEEEeCCCCCC
Confidence            356899999999999864       46889999999  9999999999998653

>1ca9_A TRAF2, protein (TNF receptor associated factor 2); TNF signaling, TRAF, adapter protein, cell surviVal; 2.30A {Homo sapiens} SCOP: b.8.1.1 h.1.2.1 PDB: 1qsc_A 1czz_A

Probab=98.58  E-value=8.6e-09  Score=79.71  Aligned_cols=45  Identities=16%  Similarity=0.189  Sum_probs=38.8

Q ss_pred             CCCcceEEEeccccCCCCC-------ccCCCcEEe--CCeEEEEEEecCCCCCC
Q 030279          132 ASNYKHVWKIKNFSKLPDN-------IYESEVFVA--GDQKWYVYFLKWCSNPN  176 (180)
Q Consensus       132 ~~~~~~tW~i~nFs~l~~~-------~~~S~~F~v--g~~~w~i~~yp~g~~~~  176 (180)
                      ...+.|+|.|.||+.+++.       .+.|+.|.+  ||++|+|.+||+|++.+
T Consensus        40 ~~~g~~~w~I~nfS~~~~~~~~g~~~~i~S~~F~v~~gG~~W~i~~yP~G~~~~   93 (192)
T 1ca9_A           40 TYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTG   93 (192)
T ss_dssp             CSSSEEEEEEESHHHHHHHHHTTSSCCEECCCEESSTTSCEEEEEEETTCCGGG
T ss_pred             ccCceEEEEECCHHHHHHHhhcCCCceEECceEEeCCCCeEEEEEEEeCCCCCC
Confidence            4678999999999998743       378999999  99999999999997643

>2gkw_A TNF receptor-associated factor 3; CD40, NF-KB signaling, BAFF receptor, TRAF3, apoptosis; 2.70A {Homo sapiens} PDB: 1kzz_A 1l0a_A 1zms_A 1rf3_A

Probab=98.53  E-value=1.5e-08  Score=78.59  Aligned_cols=44  Identities=18%  Similarity=0.237  Sum_probs=37.9

Q ss_pred             CCcceEEEeccccCCCCC-------ccCCCcEEeC--CeEEEEEEecCCCCCC
Q 030279          133 SNYKHVWKIKNFSKLPDN-------IYESEVFVAG--DQKWYVYFLKWCSNPN  176 (180)
Q Consensus       133 ~~~~~tW~i~nFs~l~~~-------~~~S~~F~vg--~~~w~i~~yp~g~~~~  176 (180)
                      ..+.|+|.|.|||.+++.       .+.|+.|.+|  |++|+|.+||+|++.+
T Consensus        38 ~~g~~~w~I~~fS~~~~~~~~g~~~~i~S~~F~vg~~Gykw~i~~yPnG~~~~   90 (192)
T 2gkw_A           38 YNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMG   90 (192)
T ss_dssp             CSSEEEEEEECHHHHHHHHHHTSCSCEECCCEESSTTSCEEEEEEETTCCGGG
T ss_pred             cCcEEEEEECCHHHHHHHhhcCCCceEEcccEEECCCCcEEEEEEEeCCCCCC
Confidence            567899999999998631       4779999999  9999999999998643

>2f1z_A Ubiquitin carboxyl-terminal hydrolase 7; hausp, USP7, UBP, deubiquitinating enzyme, substrate recognition; 3.20A {Homo sapiens}

Probab=98.47  E-value=1.1e-07  Score=83.75  Aligned_cols=41  Identities=15%  Similarity=0.257  Sum_probs=35.1

Q ss_pred             CCcceEEEeccccCCCCCccCCCcEEeCCeEEEEEEecCCCC
Q 030279          133 SNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVYFLKWCSN  174 (180)
Q Consensus       133 ~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~~yp~g~~  174 (180)
                      ..+.|+|.|.|||.+++ .+.|+.|.|||++|||.+||+|+.
T Consensus        29 ~~~~~~w~I~nfS~~~~-~~~S~~F~vgg~~W~i~~yP~G~~   69 (522)
T 2f1z_A           29 SEATFQFTVERFSRLSE-SVLSPPCFVRNLPWKIMVMPRFYP   69 (522)
T ss_dssp             SEEEEEEEESSCTTCCS-CEECCCEEETTEEEEEEECBC---
T ss_pred             CCcEEEEEECChhhcCC-ceeCCCEEECCEeeEEEEEeCCCC
Confidence            45689999999999987 678999999999999999999964

>1d00_A Tumor necrosis factor receptor associated protein 2; B-sandwich, protein-peptide complex, apoptosis; 2.00A {Homo sapiens} SCOP: b.8.1.1 h.1.2.1 PDB: 1ca4_A 1d0j_A 1f3v_B 1czy_A 1d01_A 1d0a_A

Probab=98.45  E-value=3e-08  Score=74.80  Aligned_cols=44  Identities=16%  Similarity=0.181  Sum_probs=37.0

Q ss_pred             CCCcceEEEeccccCCCCC-------ccCCCcEE--eCCeEEEEEEecCCCCC
Q 030279          132 ASNYKHVWKIKNFSKLPDN-------IYESEVFV--AGDQKWYVYFLKWCSNP  175 (180)
Q Consensus       132 ~~~~~~tW~i~nFs~l~~~-------~~~S~~F~--vg~~~w~i~~yp~g~~~  175 (180)
                      ...+.|+|.|.||+.+++.       ...|+.|.  +||++|+|.+||+|++.
T Consensus        16 ~~~g~~~w~I~nfS~~~~~~~~g~~~~i~S~~F~~~~gG~~W~i~~yP~G~~~   68 (168)
T 1d00_A           16 TYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGT   68 (168)
T ss_dssp             CSSSEEEEEEESHHHHHHHHHTTSSCCEECCCEESSTTSCEEEEEEETTCCGG
T ss_pred             ccCCEEEEEECCHHHHHHHhhcCCCeEEECCCeecCCCCEEEEEEEEeCCCCC
Confidence            3568999999999998642       26799996  89999999999999764

>1flk_A TNF receptor associated factor 3; TNF signaling, TRAF3, CD40-binding protein, apoptosis; 2.80A {Homo sapiens} SCOP: b.8.1.1 h.1.2.1 PDB: 1fll_A

Probab=98.44  E-value=2.7e-08  Score=79.09  Aligned_cols=44  Identities=18%  Similarity=0.207  Sum_probs=38.2

Q ss_pred             CCcceEEEeccccCCCC-------CccCCCcEEeC--CeEEEEEEecCCCCCC
Q 030279          133 SNYKHVWKIKNFSKLPD-------NIYESEVFVAG--DQKWYVYFLKWCSNPN  176 (180)
Q Consensus       133 ~~~~~tW~i~nFs~l~~-------~~~~S~~F~vg--~~~w~i~~yp~g~~~~  176 (180)
                      ..+.|+|.|.|||.+.+       ..+.|+.|.+|  |++|+|.+||+|++.+
T Consensus        74 ~~g~~~wkI~nfS~~~~~~~~g~~~~i~S~~F~vg~~Gy~w~i~~yPnG~~~~  126 (228)
T 1flk_A           74 YNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMG  126 (228)
T ss_dssp             SSSEEEEEEECHHHHHHHHHTTSCCCEECCCEESSTTSCEECEEEETTCCGGG
T ss_pred             cCcEEEEEECCHHHHHHHhhcCCCeeEECceEEeCCCCcEEEEEEEcCCCCCC
Confidence            56789999999999863       26789999999  9999999999998653

>1lb6_A TNF receptor-associated factor 6; TRAF6-CD40 complex, signaling protein; 1.80A {Homo sapiens} SCOP: b.8.1.1 PDB: 1lb5_A 1lb4_A

Probab=97.16  E-value=0.00022  Score=52.90  Aligned_cols=26  Identities=15%  Similarity=0.133  Sum_probs=23.2

Q ss_pred             ccCCCcEEeC--CeEEEEEEecCCCCCC
Q 030279          151 IYESEVFVAG--DQKWYVYFLKWCSNPN  176 (180)
Q Consensus       151 ~~~S~~F~vg--~~~w~i~~yp~g~~~~  176 (180)
                      .+.|+.|.+|  |++|+|.+||+|++.+
T Consensus        28 ~i~S~~F~vg~~Gy~w~i~~yP~G~~~~   55 (160)
T 1lb6_A           28 VIHSPGFYTGKPGYKLCMRLHLQLPTAQ   55 (160)
T ss_dssp             EEECCCEESSSSCCEEEEEEEECCTTCT
T ss_pred             EEECcCeecCCCCeeEEEEEEecCCCCC
Confidence            5779999999  9999999999998653

>4gwm_A Meprin A subunit beta; mulidomain structure, hydrolase; HET: NAG BMA FUC MAN; 1.85A {Homo sapiens} PDB: 4gwn_A*

Probab=93.84  E-value=2.9  Score=37.32  Aligned_cols=137  Identities=18%  Similarity=0.302  Sum_probs=78.2

Q ss_pred             CcEEEEEEcCccccccCCCCeEEccceee--cCeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC--------------C
Q 030279           20 PAHFLLKIEAFSSLVENDVENYKSLEFDA--GGYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS--------------L   83 (180)
Q Consensus        20 ~~~~~w~I~~fS~l~~~~~~~~~S~~F~v--gG~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~--------------~   83 (180)
                      .|.|.+ |+.-+.. ....-.+.|+.|..  +.+..++.+|=.|..    .+-|.|||.......              -
T Consensus       286 ~G~Ymy-iesS~~~-~g~~ArL~Sp~~~p~~~~~CL~FwYhMyG~~----vG~L~Vyv~~~~~~~~~~~~~~lw~~sG~q  359 (592)
T 4gwm_A          286 SGFFMH-FDSSSVN-VGATAVLESRTLYPKRGFQCLQFYLYNSGSE----SDQLNIYIREYSADNVDGNLTLVEEIKEIP  359 (592)
T ss_dssp             CCCEEE-EECSSSC-TTCEEEEECCCBCCSSSCEEEEEEEEECSCT----TCEEEEEEEEEETTEEEEEEEEEEEEESCC
T ss_pred             ceEEEE-EECCCCC-CCCEEEEEcCCccCCCCCeEEEEEeEccCCC----CCEEEEEEEeccccCCCCceEEEEEEecCC
Confidence            467776 4442221 11234688998864  456666677777754    567999987533210              0


Q ss_pred             CCCcEEEEEEEEEEEeCCCCceeEEeeEE--eccccccccce----EeceecccCCCcceEEEeccccCCC---CCccCC
Q 030279           84 GLGWEVYVIFRLFVLDQKKDEFLILQEVF--VKETKKCTGEC----LSMKKLTSASNYKHVWKIKNFSKLP---DNIYES  154 (180)
Q Consensus        84 ~~~~~~~a~f~~~llnq~~~~~~~~~dvF--~~~~~~~~~e~----~s~~~~~~~~~~~~tW~i~nFs~l~---~~~~~S  154 (180)
                      ...| ..|++.|.    ...++.+   ||  .+......+..    +++.   +-.-..+.|.|+||+.|-   .....|
T Consensus       360 G~~W-~~a~V~l~----~~~~fqI---vFEgvrG~g~~~GDIAIDDIs~t---~G~CP~~vw~i~nfs~~l~~~~~~~~S  428 (592)
T 4gwm_A          360 TGSW-QLYHVTLK----VTKKFRV---VFEGRKGSGASLGGLSIDDINLS---ETRCPHHIWHIRNFTQFIGSPNGTLYS  428 (592)
T ss_dssp             BSSC-EEEEEEEC----CCSCEEE---EEEEECCSSCCSSEEEEEEEEEE---SSCCCSEEEEECSCGGGTTCTTCEEEC
T ss_pred             CCce-EEEEEEEc----CCCCEEE---EEEEEECCCCCCceEEEeeEEEe---eCCCCCCceeecCHHHhhcCCCCceeC
Confidence            1124 23444432    1223333   56  23221112221    2233   345668999999999974   235667


Q ss_pred             CcEEe-CCeEEEEEEecCCC
Q 030279          155 EVFVA-GDQKWYVYFLKWCS  173 (180)
Q Consensus       155 ~~F~v-g~~~w~i~~yp~g~  173 (180)
                      +.|.- .|++++|.+||+|.
T Consensus       429 p~Fys~~GY~~~v~l~~~~~  448 (592)
T 4gwm_A          429 PPFYSSKGYAFQIYLNLAHV  448 (592)
T ss_dssp             CCEECTTSCEEEEEEECCSS
T ss_pred             CCccCCCCeEEEEEEecCCC
Confidence            77764 59999999999773

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	180
d1lb6a_	155	b.8.1.1 (A:) TNF receptor associated factor 6 (TRA	7e-11
d1czya1	152	b.8.1.1 (A:350-501) TNF receptor associated factor	7e-09
d1l0aa1	155	b.8.1.1 (A:350-504) TNF receptor associated factor	1e-08
d2cr2a1	146	b.8.1.1 (A:8-153) Speckle-type poz protein SPOP {H	1e-07
d2cr2a1	146	b.8.1.1 (A:8-153) Speckle-type poz protein SPOP {H	5e-04

>d1lb6a_ b.8.1.1 (A:) TNF receptor associated factor 6 (TRAF6) {Human (Homo sapiens) [TaxId: 9606]} Length = 155

class: All beta proteins
fold: TRAF domain-like
superfamily: TRAF domain-like
family: MATH domain
domain: TNF receptor associated factor 6 (TRAF6)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.6 bits (133), Expect = 7e-11
 Identities = 19/90 (21%), Positives = 35/90 (38%), Gaps = 7/90 (7%)

Query: 22  HFLLKIEAFSSLVENDVEN----YKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYL 75
            ++ KI  F   ++   E       S  F  G  GYK  + ++      +   ++IS+++
Sbjct: 6   IYIWKIGNFGMHLKCQEEEKPVVIHSPGFYTGKPGYKLCMRLHLQLPTAQRCANYISLFV 65

Query: 76  AMVDTSSLG-LGWEVYVIFRLFVLDQKKDE 104
             +       L W      RL +LDQ +  
Sbjct: 66  HTMQGEYDSHLPWPFQGTIRLTILDQSEAP 95

>d1czya1 b.8.1.1 (A:350-501) TNF receptor associated factor 2 (TRAF2) {Human (Homo sapiens) [TaxId: 9606]} Length = 152

class: All beta proteins
fold: TRAF domain-like
superfamily: TRAF domain-like
family: MATH domain
domain: TNF receptor associated factor 2 (TRAF2)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 50.1 bits (119), Expect = 7e-09
 Identities = 23/90 (25%), Positives = 34/90 (37%), Gaps = 8/90 (8%)

Query: 22  HFLLKIEAFSSLVENDVEN----YKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYL 75
            F+ KI  F    +  V        S  F     GYK  L +Y NG+       H+S++ 
Sbjct: 4   VFIWKISDFPRKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGR-GTHLSLFF 62

Query: 76  AMVDTSSL-GLGWEVYVIFRLFVLDQKKDE 104
            ++   +   L W       L +LDQ   E
Sbjct: 63  VVMKGPNDALLRWPFNQKVTLMLLDQNNRE 92

>d1l0aa1 b.8.1.1 (A:350-504) TNF receptor associated factor 3 (TRAF3) {Human (Homo sapiens) [TaxId: 9606]} Length = 155

class: All beta proteins
fold: TRAF domain-like
superfamily: TRAF domain-like
family: MATH domain
domain: TNF receptor associated factor 3 (TRAF3)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 49.5 bits (117), Expect = 1e-08
 Identities = 19/113 (16%), Positives = 33/113 (29%), Gaps = 8/113 (7%)

Query: 22  HFLLKIEAFSSLVEN----DVENYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYL 75
             + KI  +    +        +  S  F  G  GYK    VY NG+       H+S++ 
Sbjct: 4   VLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGK-GTHLSLFF 62

Query: 76  AMVD-TSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVKETKKCTGECLSMK 127
            ++       L W       L ++DQ      +              +     
Sbjct: 63  VIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEM 115

>d2cr2a1 b.8.1.1 (A:8-153) Speckle-type poz protein SPOP {Human (Homo sapiens) [TaxId: 9606]} Length = 146

class: All beta proteins
fold: TRAF domain-like
superfamily: TRAF domain-like
family: MATH domain
domain: Speckle-type poz protein SPOP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.3 bits (109), Expect = 1e-07
 Identities = 28/101 (27%), Positives = 43/101 (42%), Gaps = 8/101 (7%)

Query: 23  FLLKIEAFSSLVENDVENYKSLEFDAGG---YKWKLVVYPNGNKNENVKDHISIYLAMVD 79
           ++  I  FS   E   E  KS  F +G     KW L V P G   E+ KD++S+YL +V 
Sbjct: 7   YMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEES-KDYLSLYLLLVS 65

Query: 80  TSSLGLGWEVYVIFRLFVLDQKKDEFLILQEVFVKETKKCT 120
                   EV   F+  +L+ K +E   ++        +  
Sbjct: 66  ----CPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGK 102

>d2cr2a1 b.8.1.1 (A:8-153) Speckle-type poz protein SPOP {Human (Homo sapiens) [TaxId: 9606]} Length = 146

class: All beta proteins
fold: TRAF domain-like
superfamily: TRAF domain-like
family: MATH domain
domain: Speckle-type poz protein SPOP
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 36.7 bits (84), Expect = 5e-04
 Identities = 10/50 (20%), Positives = 19/50 (38%), Gaps = 3/50 (6%)

Query: 134 NYKHVWKIKNFSKLPDNI---YESEVFVAGDQKWYVYFLKWCSNPNIRSS 180
            + ++W I NFS   + +    +S  F +G      + L+         S
Sbjct: 4   KFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEES 53

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	180
d1lb6a_	155	TNF receptor associated factor 6 (TRAF6) {Human (H	99.89
d1czya1	152	TNF receptor associated factor 2 (TRAF2) {Human (H	99.89
d1l0aa1	155	TNF receptor associated factor 3 (TRAF3) {Human (H	99.87
d2cr2a1	146	Speckle-type poz protein SPOP {Human (Homo sapiens	99.86
d2cr2a1	146	Speckle-type poz protein SPOP {Human (Homo sapiens	98.53
d1czya1	152	TNF receptor associated factor 2 (TRAF2) {Human (H	97.17
d1l0aa1	155	TNF receptor associated factor 3 (TRAF3) {Human (H	97.12
d1lb6a_	155	TNF receptor associated factor 6 (TRAF6) {Human (H	96.99

>d1lb6a_ b.8.1.1 (A:) TNF receptor associated factor 6 (TRAF6) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: TRAF domain-like
superfamily: TRAF domain-like
family: MATH domain
domain: TNF receptor associated factor 6 (TRAF6)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=2.4e-23  Score=154.48  Aligned_cols=140  Identities=18%  Similarity=0.223  Sum_probs=103.3

Q ss_pred             CCCcEEEEEEcCccccccC----CCCeEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEEE
Q 030279           18 VPPAHFLLKIEAFSSLVEN----DVENYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEVY   90 (180)
Q Consensus        18 ~~~~~~~w~I~~fS~l~~~----~~~~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~~   90 (180)
                      ...|+|+|+|+|||++++.    .++.++||+|.+|  ||+|||.+||+|+..+...+||||||++.+... .+.+|+++
T Consensus         2 ~~~G~f~W~I~nfs~~~~~~~~~~~~~i~Sp~F~~g~~Gy~wrl~~yp~g~~~~~~~~~lsvyL~l~~~~~d~~~~~~~~   81 (155)
T d1lb6a_           2 QCNGIYIWKIGNFGMHLKCQEEEKPVVIHSPGFYTGKPGYKLCMRLHLQLPTAQRCANYISLFVHTMQGEYDSHLPWPFQ   81 (155)
T ss_dssp             CCCEEEEEEECCHHHHHHHHHTTCCEEEECCCEESSSSCCEEEEEEEECCTTCTTTTTEEEEEEEEECCTTGGGSCSSCC
T ss_pred             ccccEEEEEECChHHHHHhhhcCCCcEEECcCEEeCCCCcEEEEEEEeCCCCCCCCCCEEEEEEEEecCcccccCCCcEE
Confidence            5679999999999998652    3578999999999  999999999999875445789999999987653 34679999


Q ss_pred             EEEEEEEEeCCCCceeEEe-eEE-eccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCCeEEEEE
Q 030279           91 VIFRLFVLDQKKDEFLILQ-EVF-VKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQKWYVY  167 (180)
Q Consensus        91 a~f~~~llnq~~~~~~~~~-dvF-~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~~w~i~  167 (180)
                      |+++|.|+||.+....... ..+ ..+.   ..   .+.+ ..+......||+..|+.++.+.  +.+|+++|+ ..|.
T Consensus        82 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~---~~---~~~~-~~~~~~~~~~G~~~fi~~~~L~--~~gyl~dD~-l~I~  150 (155)
T d1lb6a_          82 GTIRLTILDQSEAPVRQNHEEIMDAKPE---LL---AFQR-PTIPRNPKGFGYVTFMHLEALR--QRTFIKDDT-LLVR  150 (155)
T ss_dssp             SEEEEEECCCSCTTSCCCEEEEEECCTT---SG---GGSC-CSSSBCSEEEEEEEEEEGGGGG--TSCCCBTTB-EEEE
T ss_pred             EEEEEEEECCCCCccceeeEEeeecCCc---cc---cccC-CcccCCcCCcChHHeeEHHHhc--cCCCEECCE-EEEE
Confidence            9999999999887654321 111 1111   00   0111 1234456789999999999773  578999994 4443

>d1czya1 b.8.1.1 (A:350-501) TNF receptor associated factor 2 (TRAF2) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: TRAF domain-like
superfamily: TRAF domain-like
family: MATH domain
domain: TNF receptor associated factor 2 (TRAF2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.89  E-value=1.5e-23  Score=155.67  Aligned_cols=132  Identities=22%  Similarity=0.357  Sum_probs=98.8

Q ss_pred             CcEEEEEEcCccccccC----CCCeEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEEEEE
Q 030279           20 PAHFLLKIEAFSSLVEN----DVENYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEVYVI   92 (180)
Q Consensus        20 ~~~~~w~I~~fS~l~~~----~~~~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~~a~   92 (180)
                      .|+|+|+|+|||.+++.    .++.++||+|.+|  ||+|||.+||+|+.. +..+||||||++.+... .+..|++.|+
T Consensus         2 ~g~f~W~I~nFs~l~~~~~~~~~~~~~Sp~F~~g~~Gy~w~l~~yP~G~~~-~~~~~lSlyL~l~~~~~d~~~~~~~~~~   80 (152)
T d1czya1           2 DGVFIWKISDFPRKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGT-GRGTHLSLFFVVMKGPNDALLRWPFNQK   80 (152)
T ss_dssp             SSEEEEEECSHHHHHHHHHTTSCCCEECCCEESSTTSCEEEEEEETTCCGG-GTTTEEEEEEEEECCTTGGGSCSSCCCC
T ss_pred             CCEEEEEECCcHHHHHhhhcCCCceEECcCEEcCCCCeEEEEEEEeCCCCC-CCCCEEEEEEEEccCCcCcccccceeeE
Confidence            58999999999998752    3568999999999  999999999999874 45789999999987653 2457999999


Q ss_pred             EEEEEEeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCCe
Q 030279           93 FRLFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQ  162 (180)
Q Consensus        93 f~~~llnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~  162 (180)
                      |+|+|+||.+.+.....  +....   ...  .+.+  ........||+..|++++++ ..+.+|+++|+
T Consensus        81 ~~~~l~d~~~~~~~~~~--~~~~~---~~~--~~~r--~~~~~~~~~G~~~fi~~~~L-~~~~gfl~dD~  140 (152)
T d1czya1          81 VTLMLLDQNNREHVIDA--FRPDV---TSS--SFQR--PVNDMNIASGCPLFCPVSKM-EAKNSYVRDDA  140 (152)
T ss_dssp             EEEEECCTTSSCCEEEE--ECCCT---TSG--GGSC--CSSSBCCCEEEEEEEETCCC-CCSTTTSCSSC
T ss_pred             EEEEEEcCCCCccceee--ecccc---ccc--cccC--CCcccccccchhhEEEHHHh-cccCCcEeCCE
Confidence            99999999987665421  00000   000  0111  12344568999999999876 34568999995

>d1l0aa1 b.8.1.1 (A:350-504) TNF receptor associated factor 3 (TRAF3) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: TRAF domain-like
superfamily: TRAF domain-like
family: MATH domain
domain: TNF receptor associated factor 3 (TRAF3)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=4.1e-23  Score=153.47  Aligned_cols=132  Identities=19%  Similarity=0.255  Sum_probs=98.8

Q ss_pred             CcEEEEEEcCccccccC----CCCeEEccceeec--CeEEEEEEeeCCCcCCCCCCcEEEEEEeecCCC-CCCCcEEEEE
Q 030279           20 PAHFLLKIEAFSSLVEN----DVENYKSLEFDAG--GYKWKLVVYPNGNKNENVKDHISIYLAMVDTSS-LGLGWEVYVI   92 (180)
Q Consensus        20 ~~~~~w~I~~fS~l~~~----~~~~~~S~~F~vg--G~~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~-~~~~~~~~a~   92 (180)
                      +|+|+|+|+|||.+++.    .++.++||+|.+|  ||+|||.+||+|+.. +..+||||||++.+.+. ...+|+++|+
T Consensus         2 ~g~f~W~I~nfs~~~~~~~~~~~~~~~S~~F~~~~~Gy~w~l~~yp~G~~~-~~~~~lSlyL~l~~~~~d~~~~~~~~~~   80 (155)
T d1l0aa1           2 NGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGM-GKGTHLSLFFVIMRGEYDALLPWPFKQK   80 (155)
T ss_dssp             SSEEEEEEECHHHHHHHHHTTSCSEEECCCEESSTTSCEEEEEEETTCCGG-GTTTEEEEEEEEECCTTTTTSCSSCCCC
T ss_pred             CCEEEEEECCcHHHHHhhhcCCCcEEECcCEEeCCCCcEEEEEEEeCCCCC-CCCCEEEEEEEEccCCcCcccCCcEEEE
Confidence            68999999999998652    4568999999999  999999999999974 46789999999987653 2467999999


Q ss_pred             EEEEEEeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCCe
Q 030279           93 FRLFVLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQ  162 (180)
Q Consensus        93 f~~~llnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~  162 (180)
                      |+|.|+||.+........+-..+.   ..   .+.+  .+......||+.+|++++.+  .+.+|+++|+
T Consensus        81 ~~~~l~~q~~~~~~~~~~~~~~~~---~~---~f~~--~~~~~~~~~G~~~fi~~~~L--~~~gfl~dD~  140 (155)
T d1l0aa1          81 VTLMLMDQGSSRRHLGDAFKPDPN---SS---SFKK--PTGEMNIASGCPVFVAQTVL--ENGTYIKDDT  140 (155)
T ss_dssp             EEEEECCCSSSCCCEEEEECCCTT---ST---TSSC--CSSSBCCCEEEEEEEEHHHH--HTTTTCBTTE
T ss_pred             EEEEEecCCCCccceeEEEeeccc---cc---cccc--cccccccCcChhheeEHHHh--hhCCCEECCE
Confidence            999999999876654321001110   00   0111  12334568999999999876  3678999995

>d2cr2a1 b.8.1.1 (A:8-153) Speckle-type poz protein SPOP {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: TRAF domain-like
superfamily: TRAF domain-like
family: MATH domain
domain: Speckle-type poz protein SPOP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.86  E-value=1.4e-22  Score=149.30  Aligned_cols=121  Identities=26%  Similarity=0.371  Sum_probs=96.9

Q ss_pred             CcEEEEEEcCccccccCCCCeEEccceeecCe---EEEEEEeeCCCcCCCCCCcEEEEEEeecCCCCCCCcEEEEEEEEE
Q 030279           20 PAHFLLKIEAFSSLVENDVENYKSLEFDAGGY---KWKLVVYPNGNKNENVKDHISIYLAMVDTSSLGLGWEVYVIFRLF   96 (180)
Q Consensus        20 ~~~~~w~I~~fS~l~~~~~~~~~S~~F~vgG~---~Wrl~~yP~G~~~~~~~~~lSlyL~l~~~~~~~~~~~~~a~f~~~   96 (180)
                      ..+|+|+|+|||.+++..+++++||.|.+||+   +|+|.+||+|+.. +..+||||||.+.+..    .|.+.|+|+|.
T Consensus         4 ~~~~~W~I~nfs~~~~~~~~~~~Sp~F~~~~~~~~~W~l~lyp~G~~~-~~~~~lSv~L~~~~~~----~~~v~~~~~~~   78 (146)
T d2cr2a1           4 KFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDE-ESKDYLSLYLLLVSCP----KSEVRAKFKFS   78 (146)
T ss_dssp             EEEEEEEEETGGGCCCCSSCCEECCCBCSSSCCSCCBEEEECTTCSSS-SSSSBCCEEEECCCCS----SSEEEEECEEE
T ss_pred             EEEEEEEECCchHHhhcCCCEEECCCEEeCCcCCeEEEEEEEECCCCC-CCCCEEEEEEEeccCC----CceEEEEEEEE
Confidence            46899999999998776678999999999985   8999999999884 5678999999998754    48999999999


Q ss_pred             EEeCCCCceeEEeeEEeccccccccceEeceecccCCCcceEEEeccccCCCCCccCCCcEEeCCe
Q 030279           97 VLDQKKDEFLILQEVFVKETKKCTGECLSMKKLTSASNYKHVWKIKNFSKLPDNIYESEVFVAGDQ  162 (180)
Q Consensus        97 llnq~~~~~~~~~dvF~~~~~~~~~e~~s~~~~~~~~~~~~tW~i~nFs~l~~~~~~S~~F~vg~~  162 (180)
                      |+||.+++....+          +....       +......||+.+|..+..+.....+|+++|+
T Consensus        79 l~n~~~~~~~~~~----------~~~~~-------~~~~~~~~G~~~fi~~~~l~~~~~g~l~~d~  127 (146)
T d2cr2a1          79 ILNAKGEETKAME----------SQRAY-------RFVQGKDWGFKKFIRRDFLLDEANGLLPDDK  127 (146)
T ss_dssp             EECTTSCEEEEEE----------CSCCE-------EEETTCEEEESCCSBHHHHSCTTTTSCTTSE
T ss_pred             EEcCCCCcccceE----------ecceE-------eCCCCCeeeccEEEEHHHhcCcccCceeCCE
Confidence            9999988766542          11111       1123457999999998876666778999883

>d2cr2a1 b.8.1.1 (A:8-153) Speckle-type poz protein SPOP {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: TRAF domain-like
superfamily: TRAF domain-like
family: MATH domain
domain: Speckle-type poz protein SPOP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.53  E-value=1.9e-08  Score=72.35  Aligned_cols=44  Identities=23%  Similarity=0.486  Sum_probs=37.1

Q ss_pred             cceEEEeccccCCCC---CccCCCcEEeCCe---EEEEEEecCCCCCCCC
Q 030279          135 YKHVWKIKNFSKLPD---NIYESEVFVAGDQ---KWYVYFLKWCSNPNIR  178 (180)
Q Consensus       135 ~~~tW~i~nFs~l~~---~~~~S~~F~vg~~---~w~i~~yp~g~~~~~~  178 (180)
                      -+|+|.|+||+.+++   ..+.|+.|.+||+   +|+|.+||+|.+.+..
T Consensus         5 ~~~~W~I~nfs~~~~~~~~~~~Sp~F~~~~~~~~~W~l~lyp~G~~~~~~   54 (146)
T d2cr2a1           5 FSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESK   54 (146)
T ss_dssp             EEEEEEEETGGGCCCCSSCCEECCCBCSSSCCSCCBEEEECTTCSSSSSS
T ss_pred             EEEEEEECCchHHhhcCCCEEECCCEEeCCcCCeEEEEEEEECCCCCCCC
Confidence            369999999999875   3678999999885   8999999999876554

>d1czya1 b.8.1.1 (A:350-501) TNF receptor associated factor 2 (TRAF2) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: TRAF domain-like
superfamily: TRAF domain-like
family: MATH domain
domain: TNF receptor associated factor 2 (TRAF2)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.17  E-value=9.8e-05  Score=52.48  Aligned_cols=27  Identities=11%  Similarity=-0.050  Sum_probs=23.3

Q ss_pred             ccCCCcEEeC--CeEEEEEEecCCCCCCC
Q 030279          151 IYESEVFVAG--DQKWYVYFLKWCSNPNI  177 (180)
Q Consensus       151 ~~~S~~F~vg--~~~w~i~~yp~g~~~~~  177 (180)
                      ...|+.|.+|  |++|||.+||+|++.+.
T Consensus        26 ~~~Sp~F~~g~~Gy~w~l~~yP~G~~~~~   54 (152)
T d1czya1          26 AIFSPAFYTSRYGYKMCLRIYLNGDGTGR   54 (152)
T ss_dssp             CEECCCEESSTTSCEEEEEEETTCCGGGT
T ss_pred             eEECcCEEcCCCCeEEEEEEEeCCCCCCC
Confidence            4679999999  99999999999986543

>d1l0aa1 b.8.1.1 (A:350-504) TNF receptor associated factor 3 (TRAF3) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: TRAF domain-like
superfamily: TRAF domain-like
family: MATH domain
domain: TNF receptor associated factor 3 (TRAF3)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.12  E-value=0.00012  Score=52.05  Aligned_cols=28  Identities=14%  Similarity=-0.053  Sum_probs=24.0

Q ss_pred             CccCCCcEEeC--CeEEEEEEecCCCCCCC
Q 030279          150 NIYESEVFVAG--DQKWYVYFLKWCSNPNI  177 (180)
Q Consensus       150 ~~~~S~~F~vg--~~~w~i~~yp~g~~~~~  177 (180)
                      ..+.|+.|.+|  |++|||.+||+|++.+.
T Consensus        25 ~~~~S~~F~~~~~Gy~w~l~~yp~G~~~~~   54 (155)
T d1l0aa1          25 LSLYSQPFYTGYFGYKMCARVYLNGDGMGK   54 (155)
T ss_dssp             SEEECCCEESSTTSCEEEEEEETTCCGGGT
T ss_pred             cEEECcCEEeCCCCcEEEEEEEeCCCCCCC
Confidence            45679999999  89999999999986554

>d1lb6a_ b.8.1.1 (A:) TNF receptor associated factor 6 (TRAF6) {Human (Homo sapiens) [TaxId: 9606]}

class: All beta proteins
fold: TRAF domain-like
superfamily: TRAF domain-like
family: MATH domain
domain: TNF receptor associated factor 6 (TRAF6)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.99  E-value=0.00024  Score=50.26  Aligned_cols=27  Identities=15%  Similarity=0.101  Sum_probs=23.5

Q ss_pred             CccCCCcEEeC--CeEEEEEEecCCCCCC
Q 030279          150 NIYESEVFVAG--DQKWYVYFLKWCSNPN  176 (180)
Q Consensus       150 ~~~~S~~F~vg--~~~w~i~~yp~g~~~~  176 (180)
                      ..+.|+.|.+|  |++|||.+||+|.+.+
T Consensus        27 ~~i~Sp~F~~g~~Gy~wrl~~yp~g~~~~   55 (155)
T d1lb6a_          27 VVIHSPGFYTGKPGYKLCMRLHLQLPTAQ   55 (155)
T ss_dssp             EEEECCCEESSSSCCEEEEEEEECCTTCT
T ss_pred             cEEECcCEEeCCCCcEEEEEEEeCCCCCC
Confidence            45789999999  9999999999997654