Citrus Sinensis ID: 046357

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------
Protein Sequence
MTLQKSETSSLPTGWEVNAIINFFFYCEKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVCEEVFVVKNTFKGERSSMMHEPPHLLPYLESCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLGVVLAKT
Secondary Structure (PSIPRED)
cEEEEEcccccccccEEEEEEEEEEEEEEcccccccccccccEEEccccccccccEEEccEEEEcEEEEEEEEEccccccEEEEEEEccccccccccccccEEEEEEccccccccEEEcEEEEEEEEEEEEEEEEcc
Secondary Structure Prediction (SSPRO)
cEEEEEccccccccEEEEEEEEEEEEccHHHHHHHHccccccEEEcHHcccccccEEEccEEEEEEEEEEEEEEEccccccEEEEcccccccccHHHHHHHHHHHHHccccccccEEccEEEEEEEEEEHEEEcccc
Coil and Loop (DISEMBL)
mtlqksetsslptgwevNAIINFFFYCEKHFRAVKTKWCITKFIDLETLSNTLNEYLINdvcvcgcvceeVFVVKNTfkgerssmmhepphllpYLESCAQLMSLaklkdpkegymvrDICIIKAEFTLLGVVLAKT
Flexible Loop (DISEMBL)
mtlqksetsslptgweVNAIINFFFYCEKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVCEEVFVVKNTFKGERSSMMHEPPHLLPYLESCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLGVVLAKT
Low Complexity Region (SEG)
MTLQKSETSSLPTGWEVNAIINFFFYCEKHFRAVKTKWCITKFIDLETLSNTLNEYLINDvcvcgcvceevfvvKNTFKGERSSMMHEPPHLLPYLESCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLGVVLAKT
Disordered region (IsUnstruct)
************TGWEVNAIINFFFYCEKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVCEEVFVVKNTFKG**********HLLPYLESCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLGVVL***
Disordered Region (DISOPRED)
MTLQ*SETSSLPTGWEVNAIINFFFYCEKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVCEEVFVVKNTFKGERSSMMHEPPHLLPYLESCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLGVVLA**
Disordered Region (DISEMBL)
***********PTGWEVNAIINFFFYCEKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVCEEVFVVKNTFKGERSSMMHEPPHLLPYLESCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLGVVLAKT
Disordered Region (DISPRO)
MTLQKSETSSLPTGWEVNAIINFFFYCEKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVCEEVFVVKNTFKGERSSMMHEPPHLLPYLESCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLGVVLAK*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MTLQKSETSSLPTGWEVNAIINFFFYCEKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVCEEVFVVKNTFKGERSSMMHEPPHLLPYLESCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLGVVLAKT
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

No hits with e-value below 0.001 by BLAST

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	137
356505546	233	PREDICTED: ubiquitin carboxyl-terminal h	0.700	0.412	0.422	5e-13
224153137	222	predicted protein [Populus trichocarpa]	0.591	0.364	0.381	6e-11
224140755	290	predicted protein [Populus trichocarpa]	0.591	0.279	0.381	6e-10
224140753	311	predicted protein [Populus trichocarpa]	0.591	0.260	0.381	8e-10
225429035	330	PREDICTED: MATH domain-containing protei	0.627	0.260	0.336	6e-08
296083026	672	unnamed protein product [Vitis vinifera]	0.627	0.127	0.336	7e-08
356503299	322	PREDICTED: uncharacterized protein LOC10	0.642	0.273	0.330	7e-08
224100297	505	predicted protein [Populus trichocarpa]	0.605	0.164	0.336	1e-07
147827577	341	hypothetical protein VITISV_024779 [Viti	0.627	0.252	0.346	4e-07
225429037	261	PREDICTED: uncharacterized protein LOC10	0.591	0.310	0.343	6e-07

>gi|356505546|ref|XP_003521551.1| PREDICTED: ubiquitin carboxyl-terminal hydrolase 12-like [Glycine max]

 Score = 79.3 bits (194), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 49/116 (42%), Positives = 65/116 (56%), Gaps = 20/116 (17%)

Query: 7   ETSSLPTGWEVNAIINFFFYC-------------EKHFRAVKTKWCITKFIDLETLSNTL 53
           ++SSLP  WEVNAI+NF  Y               + F  +KT+W + KFID++T ++  
Sbjct: 2   DSSSLPVDWEVNAIVNFSAYNFIDDEYVATQDTNVRRFHVLKTEWGVAKFIDIDTFNDPS 61

Query: 54  NEYLINDVCVCGCVCEEVFVVKNTFKGERSSMMHEPPHLLPYLESCA-QLMSLAKL 108
           N YL++D CV G    EVFVVK T KG+  SM+H P   +P   S      SLAKL
Sbjct: 62  NGYLMDDTCVFGA---EVFVVKTTTKGDCLSMIHGP---IPLSHSWKFDNFSLAKL 111

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224153137|ref|XP_002337319.1| predicted protein [Populus trichocarpa] gi|222838767|gb|EEE77118.1| predicted protein [Populus trichocarpa]

 Score = 72.4 bits (176), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 37/97 (38%), Positives = 51/97 (52%), Gaps = 16/97 (16%)

Query: 6   SETSSLPTGWEVNAIINFFFYCE-------------KHFRAVKTKWCITKFIDLETLSNT 52
           ++T+  P GWE+NAI   F Y +             + F A+K KW   + + L   +N 
Sbjct: 97  ADTTGFPAGWEINAIFKLFVYDQLQDKYLTFGDGRLRRFCAIKNKWGFPQMLPLSIFNNA 156

Query: 53  LNEYLINDVCVCGCVCEEVFVVKNTFKGERSSMMHEP 89
            N YLI D CV G    EVFV+K+  KGER SM+ +P
Sbjct: 157 SNGYLIGDSCVFGA---EVFVIKSEGKGERFSMIKDP 190

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224140755|ref|XP_002323744.1| predicted protein [Populus trichocarpa] gi|222866746|gb|EEF03877.1| predicted protein [Populus trichocarpa]

 Score = 68.9 bits (167), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 37/97 (38%), Positives = 50/97 (51%), Gaps = 16/97 (16%)

Query: 6   SETSSLPTGWEVNAIINFFFYCE-------------KHFRAVKTKWCITKFIDLETLSNT 52
           ++T+  P GWE+NAI   F Y +             + F A+  KW   + + L T +N 
Sbjct: 58  ADTTGFPAGWEINAIFKLFVYDQLQDKYLTIGDGRLRRFCAIMNKWGFPQMLPLSTFNNA 117

Query: 53  LNEYLINDVCVCGCVCEEVFVVKNTFKGERSSMMHEP 89
            N YLI D CV G    EVFVVK+  KGE  SM+ +P
Sbjct: 118 SNGYLIGDSCVFGA---EVFVVKSEGKGEHFSMIKDP 151

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224140753|ref|XP_002323743.1| predicted protein [Populus trichocarpa] gi|222866745|gb|EEF03876.1| predicted protein [Populus trichocarpa]

 Score = 68.6 bits (166), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 37/97 (38%), Positives = 50/97 (51%), Gaps = 16/97 (16%)

Query: 6   SETSSLPTGWEVNAIINFFFYCE-------------KHFRAVKTKWCITKFIDLETLSNT 52
           ++T+  P GWE+NAI   F Y +             + F A+  KW   + + L T +N 
Sbjct: 79  ADTTGFPPGWEINAIFKLFVYDQLQDKYLTIGDGRLRRFCAIMNKWGFPQMLPLSTFNNA 138

Query: 53  LNEYLINDVCVCGCVCEEVFVVKNTFKGERSSMMHEP 89
            N YLI D CV G    EVFVVK+  KGE  SM+ +P
Sbjct: 139 SNGYLIGDSCVFGA---EVFVVKSEGKGEHFSMIKDP 172

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225429035|ref|XP_002268000.1| PREDICTED: MATH domain-containing protein At5g43560-like [Vitis vinifera]

 Score = 62.4 bits (150), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 35/104 (33%), Positives = 53/104 (50%), Gaps = 18/104 (17%)

Query: 1   MTLQKSETSSLPTGWEVNAIINFFFYCE---------------KHFRAVKTKWCITKFID 45
           + L+ SE  +LP GWEV      F +                 +HF A+KT+    +F+ 
Sbjct: 87  LYLEISEAQNLPLGWEVTVNFKLFVFNHIHEKYLTVQDADGKVRHFNAMKTRCGFAQFLS 146

Query: 46  LETLSNTLNEYLINDVCVCGCVCEEVFVVKNTFKGERSSMMHEP 89
           L+ L +  N YL++D C+ G    EVFV+K + KGE  SM+ +P
Sbjct: 147 LDVLKDPRNGYLMDDSCIFGA---EVFVIKYSGKGESLSMIKDP 187

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296083026|emb|CBI22430.3| unnamed protein product [Vitis vinifera]

 Score = 62.0 bits (149), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 35/104 (33%), Positives = 53/104 (50%), Gaps = 18/104 (17%)

Query: 1   MTLQKSETSSLPTGWEVNAIINFFFYCE---------------KHFRAVKTKWCITKFID 45
           + L+ SE  +LP GWEV      F +                 +HF A+KT+    +F+ 
Sbjct: 87  LYLEISEAQNLPLGWEVTVNFKLFVFNHIHEKYLTVQDADGKVRHFNAMKTRCGFAQFLS 146

Query: 46  LETLSNTLNEYLINDVCVCGCVCEEVFVVKNTFKGERSSMMHEP 89
           L+ L +  N YL++D C+ G    EVFV+K + KGE  SM+ +P
Sbjct: 147 LDVLKDPRNGYLMDDSCIFGA---EVFVIKYSGKGESLSMIKDP 187

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356503299|ref|XP_003520448.1| PREDICTED: uncharacterized protein LOC100809118 [Glycine max]

 Score = 62.0 bits (149), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 35/106 (33%), Positives = 54/106 (50%), Gaps = 18/106 (16%)

Query: 1   MTLQKSETSSLPTGWEVNAIINFFFYCEKH---------------FRAVKTKWCITKFID 45
           + L  ++T  L +GWEV+     F + +K+               F+ +KT+W   + I 
Sbjct: 83  LYLAIADTEKLSSGWEVDVNFKLFVFNQKNNNYLTIQDADGTVRKFQEMKTEWGFEQLIS 142

Query: 46  LETLSNTLNEYLINDVCVCGCVCEEVFVVKNTFKGERSSMMHEPPH 91
           LETL ++ N Y + D C+ G    EVFV+  + K E  SM+ EPPH
Sbjct: 143 LETLLDSSNGYHVEDSCLFGA---EVFVISRSGKWESLSMVKEPPH 185

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224100297|ref|XP_002311820.1| predicted protein [Populus trichocarpa] gi|222851640|gb|EEE89187.1| predicted protein [Populus trichocarpa]

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 34/101 (33%), Positives = 49/101 (48%), Gaps = 18/101 (17%)

Query: 6   SETSSLPTGWEVNAIINFFFYCE---------------KHFRAVKTKWCITKFIDLETLS 50
           ++  ++P G+E+N     F Y                 + F  VK +   TKFI L T  
Sbjct: 98  ADPDNMPAGFEINVSFKLFVYDHFQDEYLTIQDINGRVRRFNKVKIEHGFTKFISLGTFK 157

Query: 51  NTLNEYLINDVCVCGCVCEEVFVVKNTFKGERSSMMHEPPH 91
              N YL+ND CV G    E+FV++NT KG+R  ++ EP H
Sbjct: 158 EPSNGYLLNDSCVFGA---EIFVIRNTNKGDRLLLVQEPAH 195

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|147827577|emb|CAN66220.1| hypothetical protein VITISV_024779 [Vitis vinifera]

 Score = 59.7 bits (143), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 36/104 (34%), Positives = 52/104 (50%), Gaps = 18/104 (17%)

Query: 1   MTLQKSETSSLPTGWEVNAIINFFFYCEKH---------------FRAVKTKWCITKFID 45
           + L  ++T  LP GWEVN     F +  KH               F  +KT+    +F+ 
Sbjct: 99  LYLAIADTKMLPLGWEVNVNFKLFVFNHKHDQYLTVQDAGGKLTRFNVMKTQCGFPQFLS 158

Query: 46  LETLSNTLNEYLINDVCVCGCVCEEVFVVKNTFKGERSSMMHEP 89
           L+ L++  N YL+ D C+ G    EVFV+K + KGE  SM+ EP
Sbjct: 159 LDVLNDPCNGYLMEDSCIFGA---EVFVIKYSGKGECLSMIKEP 199

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225429037|ref|XP_002265732.1| PREDICTED: uncharacterized protein LOC100258339 [Vitis vinifera]

 Score = 58.9 bits (141), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 34/99 (34%), Positives = 51/99 (51%), Gaps = 18/99 (18%)

Query: 6   SETSSLPTGWEVNAIINFFFYCE---------------KHFRAVKTKWCITKFIDLETLS 50
           S+T +LP GWEV      F +                 +HF  +KT+    +F+ L+ L+
Sbjct: 76  SDTQNLPLGWEVTVSFKLFVFNHIHEEYLTVQDTDGKVRHFNVMKTQCGFAQFLPLDVLT 135

Query: 51  NTLNEYLINDVCVCGCVCEEVFVVKNTFKGERSSMMHEP 89
           +  N YL++D C+ G    EVFV+K + KGE  SM+ EP
Sbjct: 136 DPCNGYLMDDSCIFGA---EVFVIKYSGKGECLSMIKEP 171

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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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	137
TAIR|locus:2089045	309	AT3G17380 "AT3G17380" [Arabido	0.423	0.187	0.342	3.9e-07
TAIR|locus:2179744	351	AT5G26260 "AT5G26260" [Arabido	0.591	0.230	0.268	2.7e-05

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

 Score = 89 (36.4 bits), Expect = 3.9e-07, Sum P(2) = 3.9e-07
 Identities = 24/70 (34%), Positives = 34/70 (48%)

Query:     3 LQKSETSSLPTGWEVNAIINFFF-------YC-----EKHFRAVKTKWCITKFIDLETLS 50
             L  +++SSL  GWEV A+   +        Y      E+ F +VK +W   KFI   T S
Sbjct:    74 LSLADSSSLSPGWEVYAVFRLYLLDQNKDNYLILQGNERRFHSVKREWGFDKFIPTGTFS 133

Query:    51 NTLNEYLIND 60
             +  N YL+ D
Sbjct:   134 DASNGYLMED 143

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 82 (33.9 bits), Expect = 2.7e-05, Sum P(2) = 2.7e-05
 Identities = 26/97 (26%), Positives = 36/97 (37%)

Query:     7 ETSSLPTGWEVNAIINFFFYCEK-------------HFRAVKTKWCITKFIDLETLSNTL 53
             ET +LP GWEVN  +  F +  K              +   K +W  T+ I L T  N  
Sbjct:   118 ETETLPRGWEVNVDLKLFVHNRKLKKYLSVTDGTVKRYNDAKKEWGFTQLISLPTFYNAN 177

Query:    54 NEYLINDXXXXXXXXXXXXXXKNTFKGERSSMMHEPP 90
               YL+ D                T K E+ + +  PP
Sbjct:   178 EGYLVQDTASFGAEIFIV---NPTEKQEKVTFISNPP 211

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

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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!

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Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: grail3.8193000101 hypothetical protein (222 aa) (Populus trichocarpa)

Predicted Functional Partners:

Sorry, there are no predicted associations at the current settings.

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	137
cd03772	137	MATH_HAUSP Herpesvirus-associated ubiquitin-specif	99.5
cd03775	134	MATH_Ubp21p Ubiquitin-specific protease 21 (Ubp21p	99.47
cd03774	139	MATH_SPOP Speckle-type POZ protein (SPOP) family,	99.28
PF00917	119	MATH: MATH domain; InterPro: IPR002083 Although ap	99.11
cd00121	126	MATH MATH (meprin and TRAF-C homology) domain; an	98.97
cd00270	149	MATH_TRAF_C Tumor Necrosis Factor Receptor (TNFR)-	98.88
cd03773	132	MATH_TRIM37 Tripartite motif containing protein 37	98.74
cd03776	147	MATH_TRAF6 Tumor Necrosis Factor Receptor (TNFR)-A	98.54
KOG1987	297	consensus Speckle-type POZ protein SPOP and relate	98.48
cd03778	164	MATH_TRAF2 Tumor Necrosis Factor Receptor (TNFR) A	98.33
cd03779	147	MATH_TRAF1 Tumor Necrosis Factor Receptor (TNFR) A	98.28
COG5077	1089	Ubiquitin carboxyl-terminal hydrolase [Posttransla	98.23
cd03781	154	MATH_TRAF4 Tumor Necrosis Factor Receptor (TNFR)-A	98.23
cd03780	148	MATH_TRAF5 Tumor Necrosis Factor Receptor (TNFR)-A	98.18
cd03772	137	MATH_HAUSP Herpesvirus-associated ubiquitin-specif	98.03
smart00061	95	MATH meprin and TRAF homology.	97.95
cd03777	186	MATH_TRAF3 Tumor Necrosis Factor Receptor (TNFR)-A	97.91
cd03771	167	MATH_Meprin Meprin family, MATH domain; Meprins ar	97.82
cd03774	139	MATH_SPOP Speckle-type POZ protein (SPOP) family,	97.55
cd03778	164	MATH_TRAF2 Tumor Necrosis Factor Receptor (TNFR) A	97.35
KOG1863	1093	consensus Ubiquitin carboxyl-terminal hydrolase [P	97.25
PF00917	119	MATH: MATH domain; InterPro: IPR002083 Although ap	97.2
cd03775	134	MATH_Ubp21p Ubiquitin-specific protease 21 (Ubp21p	97.15
cd00270	149	MATH_TRAF_C Tumor Necrosis Factor Receptor (TNFR)-	96.64
cd03771	167	MATH_Meprin Meprin family, MATH domain; Meprins ar	95.34
cd03780	148	MATH_TRAF5 Tumor Necrosis Factor Receptor (TNFR)-A	95.18
cd03773	132	MATH_TRIM37 Tripartite motif containing protein 37	95.16
cd03776	147	MATH_TRAF6 Tumor Necrosis Factor Receptor (TNFR)-A	94.9
cd00121	126	MATH MATH (meprin and TRAF-C homology) domain; an	94.58
cd03783	167	MATH_Meprin_Alpha Meprin family, Alpha subunit, MA	94.45
cd03779	147	MATH_TRAF1 Tumor Necrosis Factor Receptor (TNFR) A	93.58
cd03781	154	MATH_TRAF4 Tumor Necrosis Factor Receptor (TNFR)-A	92.89
cd03782	167	MATH_Meprin_Beta Meprin family, Beta subunit, MATH	91.32
cd03783	167	MATH_Meprin_Alpha Meprin family, Alpha subunit, MA	89.67
cd03777	186	MATH_TRAF3 Tumor Necrosis Factor Receptor (TNFR)-A	89.64

>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=99.50  E-value=6.3e-14  Score=102.17  Aligned_cols=71  Identities=15%  Similarity=0.242  Sum_probs=61.1

Q ss_pred             CeEEecCCCCCCCCCEEEEEEEEEEEe------------CcccccccccccccceeccccccccCCceEeCCeEEEEEee
Q 046357            1 MTLQKSETSSLPTGWEVNAIINFFFYC------------EKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVC   68 (137)
Q Consensus         1 lYL~~~~~~~l~~~w~v~a~fkl~i~N------------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~~   68 (137)
                      |||++.+.. ..++|++.|+|+|+|+|            .++|+.....|||++||++++|.++++|||+||+++|+|  
T Consensus        52 vyL~~~~~~-~~~~w~i~a~~~~~l~~~~~~~~~~~~~~~~~f~~~~~~~G~~~fi~~~~L~~~~sgyl~~D~l~Ie~--  128 (137)
T cd03772          52 FFLQCNAES-DSTSWSCHAQAVLRIINYKDDEPSFSRRISHLFFSKENDWGFSNFMTWSEVTDPEKGFIEDDTITLEV--  128 (137)
T ss_pred             EEEeeCCcC-CCCCCeEEEEEEEEEEcCCCCcccEEEeeeeEEcCCCCCccchheeEHHHhcCCCCCcEECCEEEEEE--
Confidence            589987644 44599999999999999            346877778999999999999999999999999999999  


Q ss_pred             eeEEEEc
Q 046357           69 EEVFVVK   75 (137)
Q Consensus        69 ~eV~vv~   75 (137)
                       +|.|=.
T Consensus       129 -~V~~~~  134 (137)
T cd03772         129 -YVQADA  134 (137)
T ss_pred             -EEEeeC
Confidence             997643

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

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

Probab=99.47  E-value=1.1e-13  Score=100.87  Aligned_cols=68  Identities=24%  Similarity=0.392  Sum_probs=59.3

Q ss_pred             CeEEecCCCC----CCCCCEEEEEEEEEEEe------------Ccccccccccccccceecccccccc----CCceEeCC
Q 046357            1 MTLQKSETSS----LPTGWEVNAIINFFFYC------------EKHFRAVKTKWCITKFIDLETLSNT----LNEYLIND   60 (137)
Q Consensus         1 lYL~~~~~~~----l~~~w~v~a~fkl~i~N------------~~~F~~~~~~wG~~~fi~l~~l~d~----~~GyLv~D   60 (137)
                      +||++.+.+.    ++++|.++|+|+|+++|            .++|+.....|||.+||++++|.+|    .+|||+||
T Consensus        46 lyL~l~~~~~~~~~~~~~~~v~a~f~~~l~n~~~~~~~~~~~~~~~F~~~~~~wG~~~fi~~~~L~~~~~~~~~g~l~nD  125 (134)
T cd03775          46 IYLEPHPEEEEKAPLDEDWSVCAQFALVISNPGDPSIQLSNVAHHRFNAEDKDWGFTRFIELRKLAHRTPDKPSPFLENG  125 (134)
T ss_pred             EEEEecCcccccccCCCCCeEEEEEEEEEEcCCCCccceEccceeEeCCCCCCCChhHcccHHHHcccccCCCCceeECC
Confidence            5888876554    47899999999999999            4688877789999999999999965    68999999


Q ss_pred             eEEEEEeeeeE
Q 046357           61 VCVCGCVCEEV   71 (137)
Q Consensus        61 ~~v~~a~~~eV   71 (137)
                      +++|.|   +|
T Consensus       126 ~l~I~~---~~  133 (134)
T cd03775         126 ELNITV---YV  133 (134)
T ss_pred             EEEEEE---EE
Confidence            999999   76

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=99.28  E-value=7.7e-12  Score=91.23  Aligned_cols=68  Identities=28%  Similarity=0.332  Sum_probs=57.0

Q ss_pred             CeEEecCCCCCCCCCEEEEEEEEEEEe-------------CcccccccccccccceeccccccccCCceEeCCeEEEEEe
Q 046357            1 MTLQKSETSSLPTGWEVNAIINFFFYC-------------EKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCV   67 (137)
Q Consensus         1 lYL~~~~~~~l~~~w~v~a~fkl~i~N-------------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~   67 (137)
                      |||++.+.+    .+.+.|+|+|+++|             .++|+. ...|||.+||++++|.++.+|||+||+++|++ 
T Consensus        59 lyL~l~~~~----~~~v~a~f~~~l~n~~~~~~~~~~~~~~~~f~~-~~~wG~~~fi~~~~L~~~~~g~l~dD~l~I~c-  132 (139)
T cd03774          59 LYLLLVSCP----KSEVRAKFKFSILNAKGEETKAMESQRAYRFVQ-GKDWGFKKFIRRDFLLDEANGLLPDDKLTLFC-  132 (139)
T ss_pred             EEEEEccCC----CCcEEEEEEEEEEecCCCeeeeecccCcEeCCC-CCccCHHHeeeHHHhhhhhcccccCCEEEEEE-
Confidence            588876532    46899999999999             245654 46899999999999998889999999999999 


Q ss_pred             eeeEEEEcc
Q 046357           68 CEEVFVVKN   76 (137)
Q Consensus        68 ~~eV~vv~~   76 (137)
                        +|.|+++
T Consensus       133 --~I~V~~~  139 (139)
T cd03774         133 --EVSVVQD  139 (139)
T ss_pred             --EEEEEcC
Confidence              9999853

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

>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=99.11  E-value=1e-10  Score=81.20  Aligned_cols=67  Identities=21%  Similarity=0.416  Sum_probs=56.9

Q ss_pred             CeEEecCCCCCC-CCCEEEEEEEEEEEe-----------CcccccccccccccceeccccccccCCceEeCCeEEEEEee
Q 046357            1 MTLQKSETSSLP-TGWEVNAIINFFFYC-----------EKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVC   68 (137)
Q Consensus         1 lYL~~~~~~~l~-~~w~v~a~fkl~i~N-----------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~~   68 (137)
                      +||.+..++... .+|.+.|++++.++|           .+.|+.. ..|||.+||++++|.++.  |+.||+++|+|  
T Consensus        41 ~~L~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~F~~~-~~~g~~~fi~~~~l~~~~--fl~dd~l~ie~--  115 (119)
T PF00917_consen   41 VYLHCDKGENDSDLEWSIEAEFRFRLLNQNGKSISKRIKSHSFNNP-SSWGWSSFISWEDLEDPY--FLVDDSLTIEV--  115 (119)
T ss_dssp             EEEEEECSTTGGGSSSSEEEEEEEEEE-TTSCEEEEEEECEEECTT-SEEEEEEEEEHHHHTTCT--TSBTTEEEEEE--
T ss_pred             EEEEEeecccccccceeeeEEEEEEEecCCCCcceeeeeeeEEeee-cccchhheeEHHHhCccC--CeECCEEEEEE--
Confidence            589998887665 799999999999998           2567444 799999999999999765  99999999999  


Q ss_pred             eeEEE
Q 046357           69 EEVFV   73 (137)
Q Consensus        69 ~eV~v   73 (137)
                       +|.|
T Consensus       116 -~v~I  119 (119)
T PF00917_consen  116 -EVKI  119 (119)
T ss_dssp             -EEEE
T ss_pred             -EEEC
Confidence             9976

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 ....

>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=98.97  E-value=2.5e-09  Score=73.75  Aligned_cols=66  Identities=24%  Similarity=0.402  Sum_probs=54.4

Q ss_pred             CeEEecCCCCCCCCCEEEEEEEEEEEe-----------Ccccc-cccccccccceeccccccccCCceEeCCeEEEEEee
Q 046357            1 MTLQKSETSSLPTGWEVNAIINFFFYC-----------EKHFR-AVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVC   68 (137)
Q Consensus         1 lYL~~~~~~~l~~~w~v~a~fkl~i~N-----------~~~F~-~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~~   68 (137)
                      +||.+.+....+..|.+.|+++|.|+|           ..+|. .....|||.+||++++|.++.  +++||+++|+|  
T Consensus        48 v~L~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~G~~~fi~~~~l~~~~--~~~~d~l~i~~--  123 (126)
T cd00121          48 LYLELDKGESDLEKWSVRAEFTLKLVNQNGGKSLSKSFTHVFFSEKGSGWGFPKFISWDDLEDSY--YLVDDSLTIEV--  123 (126)
T ss_pred             EEEEecCCCCCCCCCcEEEEEEEEEECCCCCccceEeccCCcCCCCCCCCChHHeeEHHHhccCC--cEECCEEEEEE--
Confidence            488887776667889999999999998           22443 556799999999999999643  39999999999  


Q ss_pred             eeE
Q 046357           69 EEV   71 (137)
Q Consensus        69 ~eV   71 (137)
                       +|
T Consensus       124 -~v  125 (126)
T cd00121         124 -EV  125 (126)
T ss_pred             -EE
Confidence             77

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

>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=98.88  E-value=3.3e-09  Score=77.79  Aligned_cols=66  Identities=17%  Similarity=0.289  Sum_probs=52.0

Q ss_pred             CeEEecCCCC-CCCCCEEEEEEEEEEEeCc-------------------ccc-----cccccccccceeccccccccCCc
Q 046357            1 MTLQKSETSS-LPTGWEVNAIINFFFYCEK-------------------HFR-----AVKTKWCITKFIDLETLSNTLNE   55 (137)
Q Consensus         1 lYL~~~~~~~-l~~~w~v~a~fkl~i~N~~-------------------~F~-----~~~~~wG~~~fi~l~~l~d~~~G   55 (137)
                      |||.+.+.+. .+.+|.+.|+|+|+|+|+.                   .|.     .....|||.+||++++|.+  .|
T Consensus        58 l~L~l~~~~~d~~~~w~~~~~~~~~l~d~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~fi~~~~L~~--~g  135 (149)
T cd00270          58 LFVHVMKGEYDALLEWPFRGKITLTLLDQSDDSKRKHITETFMPDPNSSAFQRPPTGENNIGFGYPEFVPLEKLES--RG  135 (149)
T ss_pred             EEEEEeccCCCccccCCccceEEEEEECCCCccccCceEEEEEcCCchHhhcCCCcccCCCCcCcceEeEHHHhcc--CC
Confidence            5888766543 3568999999999999921                   122     1346799999999999985  49


Q ss_pred             eEeCCeEEEEEeeeeE
Q 046357           56 YLINDVCVCGCVCEEV   71 (137)
Q Consensus        56 yLv~D~~v~~a~~~eV   71 (137)
                      ||+||+|+|++   +|
T Consensus       136 fl~dD~l~I~~---~v  148 (149)
T cd00270         136 YVKDDTLFIKV---EV  148 (149)
T ss_pred             CEeCCEEEEEE---EE
Confidence            99999999999   76

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

>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=98.74  E-value=1.9e-08  Score=72.28  Aligned_cols=62  Identities=19%  Similarity=0.260  Sum_probs=49.3

Q ss_pred             CeEEecCCCCCCCCCEEEEEEEEEEEe------------CcccccccccccccceeccccccccCCceEeC--CeEEEEE
Q 046357            1 MTLQKSETSSLPTGWEVNAIINFFFYC------------EKHFRAVKTKWCITKFIDLETLSNTLNEYLIN--DVCVCGC   66 (137)
Q Consensus         1 lYL~~~~~~~l~~~w~v~a~fkl~i~N------------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv~--D~~v~~a   66 (137)
                      +||++.+.    .+|.+.++|+|+|+|            .++|.. ...|||.+||++++|.+  +|||.|  |+++|++
T Consensus        55 l~L~l~~~----~~~~~~~~~~l~llnq~~~~~~~~~~~~~~f~~-~~~wG~~~Fi~~~~L~~--~gfl~~~~D~l~i~~  127 (132)
T cd03773          55 VFLELCSG----LGEASKYEYRVEMVHQANPTKNIKREFASDFEV-GECWGYNRFFRLDLLIN--EGYLLPENDTLILRF  127 (132)
T ss_pred             EEEEeecC----CCCceeEEEEEEEEcCCCCccceEEeccccccC-CCCcCHHHhccHHHHhh--CCCcCCCCCEEEEEE
Confidence            47776543    247789999999998            346654 46799999999999974  799999  9999999


Q ss_pred             eeeeEE
Q 046357           67 VCEEVF   72 (137)
Q Consensus        67 ~~~eV~   72 (137)
                         +|+
T Consensus       128 ---~v~  130 (132)
T cd03773         128 ---SVR  130 (132)
T ss_pred             ---EEe
Confidence               664

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

>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=98.54  E-value=1.1e-07  Score=70.03  Aligned_cols=66  Identities=15%  Similarity=0.277  Sum_probs=50.9

Q ss_pred             CeEEecCCCC-CCCCCEEEEEEEEEEEeCc-----------------cccc-----ccccccccceeccccccccCCceE
Q 046357            1 MTLQKSETSS-LPTGWEVNAIINFFFYCEK-----------------HFRA-----VKTKWCITKFIDLETLSNTLNEYL   57 (137)
Q Consensus         1 lYL~~~~~~~-l~~~w~v~a~fkl~i~N~~-----------------~F~~-----~~~~wG~~~fi~l~~l~d~~~GyL   57 (137)
                      +||.+.+... ...+|.+.|+++|++.|+.                 .|..     ....|||++||++++|..  .|||
T Consensus        58 ~~L~l~~~~~d~~l~wpv~a~~~~~lldq~~~~~~~~~~~~~~~~~~~F~~p~~~~~~~~~G~~~fi~~~~Le~--~~yl  135 (147)
T cd03776          58 LFVHLMQGENDSHLDWPFQGTITLTLLDQSEPRQNIHETMMSKPELLAFQRPTTDRNPKGFGYVEFAHIEDLLQ--RGFV  135 (147)
T ss_pred             EEEEEeccCCCcccCCcccceeEEEEECCCcccCccEEEEEcCCChHhhcCCCcCCCCCCeeEceeeEHHHhhh--CCCc
Confidence            4788765432 3457999999999999921                 2431     235799999999999974  5899


Q ss_pred             eCCeEEEEEeeeeE
Q 046357           58 INDVCVCGCVCEEV   71 (137)
Q Consensus        58 v~D~~v~~a~~~eV   71 (137)
                      .||+++|++   +|
T Consensus       136 ~dD~l~I~c---~V  146 (147)
T cd03776         136 KNDTLLIKI---EV  146 (147)
T ss_pred             cCCEEEEEE---EE
Confidence            999999999   76

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

>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=98.48  E-value=4.3e-08  Score=79.09  Aligned_cols=64  Identities=25%  Similarity=0.355  Sum_probs=49.8

Q ss_pred             CCEEEEEEEEEEEeCcc---------------cccccccccccceeccccccccCCceEeCCeEEEEEeeeeEEEEccCC
Q 046357           14 GWEVNAIINFFFYCEKH---------------FRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVCEEVFVVKNTF   78 (137)
Q Consensus        14 ~w~v~a~fkl~i~N~~~---------------F~~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~~~eV~vv~~~~   78 (137)
                      +|+++|+++|+++|+..               |+...+.||+.+++|+..+.++..||+++..+++.|   .+.|.++..
T Consensus        54 ~~~~~~~~~l~v~n~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~g~~~~~~~~~~a---~~~V~~~~~  130 (297)
T KOG1987|consen   54 GWERYAKLRLTVVNQKSEKYLSTVEEGFSWFRFNKVLKEWGFGKMLPLTLLIDCSNGFLVAHKLVLVA---RSEVFEAMG  130 (297)
T ss_pred             CcceeEEEEEEEccCCCcceeeeeeeeEEeccccccccccCcccccChHHhhcccCcEEEcCceEEEe---eecceeeec
Confidence            99999999999999321               222357899999999999999999999996666666   455666554


Q ss_pred             CC
Q 046357           79 KG   80 (137)
Q Consensus        79 ~~   80 (137)
                      +.
T Consensus       131 ~~  132 (297)
T KOG1987|consen  131 KS  132 (297)
T ss_pred             cc
Confidence            43

>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=98.33  E-value=1.6e-06  Score=66.22  Aligned_cols=65  Identities=11%  Similarity=0.204  Sum_probs=53.0

Q ss_pred             CeEEecCCCCCC-CCCEEEEEEEEEEEeCc----------------cc----ccccccccccceeccccccccCCceEeC
Q 046357            1 MTLQKSETSSLP-TGWEVNAIINFFFYCEK----------------HF----RAVKTKWCITKFIDLETLSNTLNEYLIN   59 (137)
Q Consensus         1 lYL~~~~~~~l~-~~w~v~a~fkl~i~N~~----------------~F----~~~~~~wG~~~fi~l~~l~d~~~GyLv~   59 (137)
                      +|+.+...+..+ .+|-...+++|.|.||.                .|    +.....||+++|+|+++|.++ .|||.|
T Consensus        76 ly~~l~~Ge~D~~L~WPf~~~itl~llDQ~~r~hi~~~~~pd~~~~~f~RP~~~~n~~~G~~~Fv~l~~l~~~-~~Yv~d  154 (164)
T cd03778          76 LFFVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKXEAK-NSYVRD  154 (164)
T ss_pred             EEEEEecCCcCcccCCceeeEEEEEEECCCCCCcceeEEEcCcchHhcCCCCcccccCcCcceEEEhhHcccc-CCcccC
Confidence            578888877776 89999999999999821                24    223346999999999999864 599999


Q ss_pred             CeEEEEE
Q 046357           60 DVCVCGC   66 (137)
Q Consensus        60 D~~v~~a   66 (137)
                      |++.++|
T Consensus       155 DtlfIk~  161 (164)
T cd03778         155 DAIFIKA  161 (164)
T ss_pred             CeEEEEE
Confidence            9999998

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

>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=98.28  E-value=2.5e-06  Score=63.91  Aligned_cols=68  Identities=15%  Similarity=0.253  Sum_probs=51.2

Q ss_pred             CeEEecCCCC-CCCCCEEEEEEEEEEEeC----------------cccc----cccccccccceeccccccccCCceEeC
Q 046357            1 MTLQKSETSS-LPTGWEVNAIINFFFYCE----------------KHFR----AVKTKWCITKFIDLETLSNTLNEYLIN   59 (137)
Q Consensus         1 lYL~~~~~~~-l~~~w~v~a~fkl~i~N~----------------~~F~----~~~~~wG~~~fi~l~~l~d~~~GyLv~   59 (137)
                      +||.+...+. --..|.+.|+++|.++|+                +.|+    .....||+++||++++|..+..+||.|
T Consensus        58 v~l~l~~g~~D~~l~wpv~~~~tfsLlDq~~~~~~~~~~~~~~~~~~F~rP~~~~n~~~G~~~Fi~~~~Le~s~~~ylkD  137 (147)
T cd03779          58 LFFVIMKGEYDALLPWPFRHKVTFMLLDQNNREHVIDAFRPDLSSASFQRPVSDMNVASGCPLFFPLKKLQSPKHAYCKD  137 (147)
T ss_pred             EEEEEecCCcccccCcceEEEEEEEEECCCCCCCCcEeecCCcccccccCcccCCCCCcchhheeEHHHhcccCCCcEeC
Confidence            4677764221 123689999999999981                3465    333479999999999997544599999


Q ss_pred             CeEEEEEeeeeE
Q 046357           60 DVCVCGCVCEEV   71 (137)
Q Consensus        60 D~~v~~a~~~eV   71 (137)
                      |++.|.|   +|
T Consensus       138 D~~~Irc---~V  146 (147)
T cd03779         138 DTIYIKC---VV  146 (147)
T ss_pred             CEEEEEE---EE
Confidence            9999999   76

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

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

Probab=98.23  E-value=7.9e-07  Score=81.13  Aligned_cols=74  Identities=23%  Similarity=0.287  Sum_probs=62.8

Q ss_pred             CeEEecCCC--CCC-CCCEEEEEEEEEEEe------------CcccccccccccccceeccccccccCCc---eEeCCeE
Q 046357            1 MTLQKSETS--SLP-TGWEVNAIINFFFYC------------EKHFRAVKTKWCITKFIDLETLSNTLNE---YLINDVC   62 (137)
Q Consensus         1 lYL~~~~~~--~l~-~~w~v~a~fkl~i~N------------~~~F~~~~~~wG~~~fi~l~~l~d~~~G---yLv~D~~   62 (137)
                      +||+..-.+  .+. ..|.++|+|.|.|-|            +|||+...++|||++|+.|..+..|+.|   |+.++++
T Consensus        83 VyLe~~pqe~e~~~gk~~~ccaqFaf~Is~p~~pti~~iN~sHhrFs~~~tDwGFt~f~dL~kl~~psp~~Ppfleeg~l  162 (1089)
T COG5077          83 VYLEYEPQELEETGGKYYDCCAQFAFDISNPKYPTIEYINKSHHRFSMESTDWGFTNFIDLNKLIEPSPGRPPFLEEGTL  162 (1089)
T ss_pred             EEEEeccchhhhhcCcchhhhhheeeecCCCCCCchhhhhcccccccccccccchhhhhhhhhhcCCCCCCCCcccCCeE
Confidence            366654332  222 459999999999977            7999999999999999999999998888   7899999


Q ss_pred             EEEEeeeeEEEEccC
Q 046357           63 VCGCVCEEVFVVKNT   77 (137)
Q Consensus        63 v~~a~~~eV~vv~~~   77 (137)
                      ++.|   .|.|++++
T Consensus       163 ~Itv---yVRvlkdP  174 (1089)
T COG5077         163 VITV---YVRVLKDP  174 (1089)
T ss_pred             EEEE---EEEEEeCC
Confidence            9999   99999985

>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=98.23  E-value=2.7e-06  Score=63.52  Aligned_cols=66  Identities=18%  Similarity=0.269  Sum_probs=49.9

Q ss_pred             CeEEecCCCCCC-CCCEEEEEEEEEEEeCc------------c---------cc--------cccccccccceecccccc
Q 046357            1 MTLQKSETSSLP-TGWEVNAIINFFFYCEK------------H---------FR--------AVKTKWCITKFIDLETLS   50 (137)
Q Consensus         1 lYL~~~~~~~l~-~~w~v~a~fkl~i~N~~------------~---------F~--------~~~~~wG~~~fi~l~~l~   50 (137)
                      +||.+...+.-+ ..|.+.|+++|++.|+.            .         |+        .....||+.+||++++|.
T Consensus        58 ~~l~l~~ge~d~~l~wp~~a~~~~~llDq~~~~~~~~~~~~~~~~~~~~~~~F~rp~~~~~~~~~~~~G~~~fi~~~~Le  137 (154)
T cd03781          58 VYIRVLPGEYDNLLEWPFSHRITFTLLDQSDPSLSKPQHITETFTPDPTWKNFQKPSASRLDESTLGFGYPKFISHEDLK  137 (154)
T ss_pred             EEEEEecCCcccccCCceeeEEEEEEECCCCCccccCcceEEEEEcCCchhhhcCCcccccCCCCCccchhHeeEHHHHh
Confidence            477776644333 48999999999999831            1         11        122359999999999997


Q ss_pred             ccCCceEeCCeEEEEEeeeeE
Q 046357           51 NTLNEYLINDVCVCGCVCEEV   71 (137)
Q Consensus        51 d~~~GyLv~D~~v~~a~~~eV   71 (137)
                        ++|||.||+++|++   +|
T Consensus       138 --~~~yl~dD~l~Irc---~v  153 (154)
T cd03781         138 --KRNYIKDDAIFLRA---SV  153 (154)
T ss_pred             --hCCcccCCEEEEEE---Ee
Confidence              47899999999999   76

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

>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=98.18  E-value=4.5e-06  Score=62.47  Aligned_cols=66  Identities=12%  Similarity=0.197  Sum_probs=50.2

Q ss_pred             CeEEecCCCCC-CCCCEEEEEEEEEEEeC-----------------cccccc----cccccccceeccccccccCCceEe
Q 046357            1 MTLQKSETSSL-PTGWEVNAIINFFFYCE-----------------KHFRAV----KTKWCITKFIDLETLSNTLNEYLI   58 (137)
Q Consensus         1 lYL~~~~~~~l-~~~w~v~a~fkl~i~N~-----------------~~F~~~----~~~wG~~~fi~l~~l~d~~~GyLv   58 (137)
                      +||.+...+.- -..|.+.++++|.++++                 +.|+..    ...||+++||++++|..++.+||.
T Consensus        58 v~l~l~~g~~D~~l~wp~~~~~tfsLlDq~~~~~~~~~~~~~~~~~~~F~rp~~~~n~~~G~~~Fi~~~~Le~s~~~ylk  137 (148)
T cd03780          58 LYFVVMRGEFDSLLQWPFRQRVTLMLLDQSGKKNHIMETFKADPNSSSFKRPDGEMNIASGCPRFVAHSVLENAKNTYIK  137 (148)
T ss_pred             EEEEEecCccccccCcceEEEEEEEEECCCCCCCCcceeeecCCccccccCCCCCCCCCcChhheeEHHHhhcccCCcCc
Confidence            46776643211 14699999999999881                 236443    346999999999999866679999


Q ss_pred             CCeEEEEE
Q 046357           59 NDVCVCGC   66 (137)
Q Consensus        59 ~D~~v~~a   66 (137)
                      ||++.|.|
T Consensus       138 dD~~~Ik~  145 (148)
T cd03780         138 DDTLFLKV  145 (148)
T ss_pred             CCEEEEEE
Confidence            99999998

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

>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=98.03  E-value=4.4e-06  Score=60.71  Aligned_cols=63  Identities=13%  Similarity=0.280  Sum_probs=43.3

Q ss_pred             eEEEEEeeeeEEEEccCCCCccceeeeCCCeeeeeec-----ccceeeecccccCCCCCeEEcCeEEEEEEEEEE
Q 046357           61 VCVCGCVCEEVFVVKNTFKGERSSMMHEPPHLLPYLE-----SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLL  130 (137)
Q Consensus        61 ~~v~~a~~~eV~vv~~~~~~e~~s~ik~~~~lslyL~-----d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~  130 (137)
                      ++....   ++.++........++  +...+  .|-.     +|++||++++|.++++|||+||+|+||++|+|=
T Consensus        66 ~i~a~~---~~~l~~~~~~~~~~~--~~~~~--~f~~~~~~~G~~~fi~~~~L~~~~sgyl~~D~l~Ie~~V~~~  133 (137)
T cd03772          66 SCHAQA---VLRIINYKDDEPSFS--RRISH--LFFSKENDWGFSNFMTWSEVTDPEKGFIEDDTITLEVYVQAD  133 (137)
T ss_pred             eEEEEE---EEEEEcCCCCcccEE--Eeeee--EEcCCCCCccchheeEHHHhcCCCCCcEECCEEEEEEEEEee
Confidence            466666   777776653222222  11111  2311     499999999999999999999999999999763

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

>smart00061 MATH meprin and TRAF homology

Probab=97.95  E-value=1.5e-05  Score=52.78  Aligned_cols=43  Identities=19%  Similarity=0.426  Sum_probs=35.8

Q ss_pred             CeEEecCCCCCCCCCEEEEEEEEEEEe----------Cccccccccccccccee
Q 046357            1 MTLQKSETSSLPTGWEVNAIINFFFYC----------EKHFRAVKTKWCITKFI   44 (137)
Q Consensus         1 lYL~~~~~~~l~~~w~v~a~fkl~i~N----------~~~F~~~~~~wG~~~fi   44 (137)
                      +||.+.+....+.+|.+.|+++|+|.|          .++|.. ...|||++||
T Consensus        43 l~L~~~~~~~~~~~w~v~a~~~~~l~~~~~~~~~~~~~~~F~~-~~~~G~~~fi   95 (95)
T smart00061       43 LYLHCEKEECDSRKWSIEAEFTLKLVSQNGKSLSKKDKHVFEK-PSGWGFSKFI   95 (95)
T ss_pred             EEEEeCCCcCCCCCeEEEEEEEEEEEeCCCCEEeeeeeEEEcC-CCccceeeEC
Confidence            588888877677799999999999998          356765 6789999885

>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=97.91  E-value=3.7e-05  Score=59.68  Aligned_cols=67  Identities=10%  Similarity=0.137  Sum_probs=50.5

Q ss_pred             CeEEecCCCC-CCCCCEEEEEEEEEEEeCc-----------------ccc-cc---cccccccceeccccccccCCceEe
Q 046357            1 MTLQKSETSS-LPTGWEVNAIINFFFYCEK-----------------HFR-AV---KTKWCITKFIDLETLSNTLNEYLI   58 (137)
Q Consensus         1 lYL~~~~~~~-l~~~w~v~a~fkl~i~N~~-----------------~F~-~~---~~~wG~~~fi~l~~l~d~~~GyLv   58 (137)
                      +||.+...+. --..|.+.++++|.+.++.                 .|+ ..   ...||+++||++++|.  +.+||.
T Consensus        96 vyl~L~~ge~D~~L~WP~~~~~tfsLlDQ~~~~~~~~~~~~p~p~~~~F~rp~~~~n~~~G~~~Fi~~~~Le--~~~ylk  173 (186)
T cd03777          96 LFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLE--NGTYIK  173 (186)
T ss_pred             EEEEEecCCcccccCCceeEEEEEEEEcCCCccccccceeccCCccccccCCccCCCCCCCchheeEHHHhc--cCCcEe
Confidence            4677654321 1236999999999999832                 275 22   3479999999999997  478999


Q ss_pred             CCeEEEEEeeeeEE
Q 046357           59 NDVCVCGCVCEEVF   72 (137)
Q Consensus        59 ~D~~v~~a~~~eV~   72 (137)
                      ||++.|.|   .|.
T Consensus       174 dD~l~Irv---~v~  184 (186)
T cd03777         174 DDTIFIKV---IVD  184 (186)
T ss_pred             CCEEEEEE---EEe
Confidence            99999999   664

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

>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=97.82  E-value=4.3e-05  Score=58.45  Aligned_cols=64  Identities=11%  Similarity=0.156  Sum_probs=48.0

Q ss_pred             CeEEecCCCC-CCCCCE-EEEEEEEEEEeCc----------c-----------------cccc-----------------
Q 046357            1 MTLQKSETSS-LPTGWE-VNAIINFFFYCEK----------H-----------------FRAV-----------------   34 (137)
Q Consensus         1 lYL~~~~~~~-l~~~w~-v~a~fkl~i~N~~----------~-----------------F~~~-----------------   34 (137)
                      +||.+.+.+. ....|- +.|+++|+++++.          +                 |+..                 
T Consensus        55 lyL~L~~g~~d~~L~WP~v~a~~t~~LlDQ~~~~~~r~~~~~~~~~dp~~~~~~~~~~~~~rP~~~~~~~~~~~~~~~~~  134 (167)
T cd03771          55 LYFHLCSGENDDVLEWPCPNRQATMTLLDQDPDIQQRMSNQRSFTTDPSMTSSDNGEYFWDRPSKVGSYDTDTNGCTCYR  134 (167)
T ss_pred             EEEEEecCCccccccCcceeEEEEEEEECCCCcccccCcceEEEecCCcccccccccccccCCccccccccccccccccc
Confidence            5788765433 356788 6899999999821          1                 2221                 


Q ss_pred             cccccccceeccccccccCCceEeCCeEEEEE
Q 046357           35 KTKWCITKFIDLETLSNTLNEYLINDVCVCGC   66 (137)
Q Consensus        35 ~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a   66 (137)
                      ...|||++|||++.|..  .+||.||++.|.+
T Consensus       135 ~~g~G~~~Fis~~~L~~--r~ylk~dtl~i~~  164 (167)
T cd03771         135 GPGYGWSTFISHSRLRR--RDFLKGDDLIILL  164 (167)
T ss_pred             cCccccccceeHHHhcc--CCCCcCCEEEEEE
Confidence            13699999999999985  4599999999999

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

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

Probab=97.55  E-value=4.6e-05  Score=55.33  Aligned_cols=34  Identities=15%  Similarity=0.212  Sum_probs=31.7

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLG  131 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~~  131 (137)
                      +|.+||++++|.++.+|||+||++.|+++|+|++
T Consensus       105 G~~~fi~~~~L~~~~~g~l~dD~l~I~c~I~V~~  138 (139)
T cd03774         105 GFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQ  138 (139)
T ss_pred             CHHHeeeHHHhhhhhcccccCCEEEEEEEEEEEc
Confidence            5899999999998889999999999999999975

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

>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=97.35  E-value=0.00022  Score=54.54  Aligned_cols=29  Identities=24%  Similarity=0.430  Sum_probs=26.0

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEF  127 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev  127 (137)
                      ++++|+|+++|.++ .|||++|++.|+|.|
T Consensus       135 G~~~Fv~l~~l~~~-~~Yv~dDtlfIk~~V  163 (164)
T cd03778         135 GCPLFCPVSKXEAK-NSYVRDDAIFIKAIV  163 (164)
T ss_pred             CcceEEEhhHcccc-CCcccCCeEEEEEEE
Confidence            49999999999764 699999999999987

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

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

Probab=97.25  E-value=0.00024  Score=67.62  Aligned_cols=74  Identities=19%  Similarity=0.206  Sum_probs=66.2

Q ss_pred             eEEecCCCCCCCCCEEEEEEEEEEEe------------CcccccccccccccceeccccccccCCceEeCCeEEEEEeee
Q 046357            2 TLQKSETSSLPTGWEVNAIINFFFYC------------EKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVCE   69 (137)
Q Consensus         2 YL~~~~~~~l~~~w~v~a~fkl~i~N------------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~~~   69 (137)
                      |+++..+... +.|.+++++.+.+.|            +|+|.+..++||+.+|+.++++.++..||+.+|++.+.+   
T Consensus        72 ~~~~~~~~~~-~~~s~~~~~~~~v~~~~~~~~~~~~~~~h~~~~~~~dwg~~~~~~~~~~~~~~~~~~~~~~~~~~~---  147 (1093)
T KOG1863|consen   72 KLEVMPSQSL-KSWSCGAQAVLRVKNTIDNLPDPEKAIHHVFTADERDWGFSCFSTSSDIRKPEDGYVRNGLEKLEK---  147 (1093)
T ss_pred             EeeeccCCCC-cceEecchhhhccccCCCCchhhhhhhhhcccccccchhhccchhHhhccCcccccccccceeeee---
Confidence            5666666666 559999999999988            889999999999999999999999999999999999999   


Q ss_pred             eEEEEccCCC
Q 046357           70 EVFVVKNTFK   79 (137)
Q Consensus        70 eV~vv~~~~~   79 (137)
                      +|.+-.++..
T Consensus       148 ~v~v~~~~~~  157 (1093)
T KOG1863|consen  148 RVRVEQPTSL  157 (1093)
T ss_pred             eeeeecCCcc
Confidence            9999887754

>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=97.20  E-value=0.00027  Score=48.63  Aligned_cols=30  Identities=27%  Similarity=0.515  Sum_probs=27.4

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTL  129 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i  129 (137)
                      +|.+||++++|.++.  |++||+++|||+|+|
T Consensus        90 g~~~fi~~~~l~~~~--fl~dd~l~ie~~v~I  119 (119)
T PF00917_consen   90 GWSSFISWEDLEDPY--FLVDDSLTIEVEVKI  119 (119)
T ss_dssp             EEEEEEEHHHHTTCT--TSBTTEEEEEEEEEE
T ss_pred             chhheeEHHHhCccC--CeECCEEEEEEEEEC
Confidence            489999999999875  899999999999986

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 ....

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

Probab=97.15  E-value=0.00028  Score=51.08  Aligned_cols=30  Identities=13%  Similarity=0.170  Sum_probs=27.1

Q ss_pred             ccceeeecccccCC----CCCeEEcCeEEEEEEE
Q 046357           98 SCAQLMSLAKLKDP----KEGYMVRDICIIKAEF  127 (137)
Q Consensus        98 d~~~fi~l~~l~~~----~~gylv~D~~~ieaev  127 (137)
                      +|.+||++++|.++    ..|||+||+++|+++|
T Consensus       100 G~~~fi~~~~L~~~~~~~~~g~l~nD~l~I~~~~  133 (134)
T cd03775         100 GFTRFIELRKLAHRTPDKPSPFLENGELNITVYV  133 (134)
T ss_pred             ChhHcccHHHHcccccCCCCceeECCEEEEEEEE
Confidence            48999999999955    6799999999999987

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.

>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=96.64  E-value=0.0015  Score=47.60  Aligned_cols=29  Identities=31%  Similarity=0.535  Sum_probs=25.8

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFT  128 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~  128 (137)
                      +|.+||++++|.++  |||+||+|+|+++|.
T Consensus       121 G~~~fi~~~~L~~~--gfl~dD~l~I~~~v~  149 (149)
T cd00270         121 GYPEFVPLEKLESR--GYVKDDTLFIKVEVD  149 (149)
T ss_pred             CcceEeEHHHhccC--CCEeCCEEEEEEEEC
Confidence            59999999999754  999999999999873

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

>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=95.34  E-value=0.0098  Score=45.52  Aligned_cols=29  Identities=21%  Similarity=0.402  Sum_probs=26.0

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFT  128 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~  128 (137)
                      +|++||++++|+.  ++||++|+++|+++++
T Consensus       139 G~~~Fis~~~L~~--r~ylk~dtl~i~~~~~  167 (167)
T cd03771         139 GWSTFISHSRLRR--RDFLKGDDLIILLDFE  167 (167)
T ss_pred             ccccceeHHHhcc--CCCCcCCEEEEEEEeC
Confidence            4999999999986  5699999999999974

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

>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=95.18  E-value=0.014  Score=43.62  Aligned_cols=30  Identities=20%  Similarity=0.497  Sum_probs=27.3

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEF  127 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev  127 (137)
                      ++++||+.++|..++.|||.+|++.|+|+|
T Consensus       118 G~~~Fi~~~~Le~s~~~ylkdD~~~Ik~~v  147 (148)
T cd03780         118 GCPRFVAHSVLENAKNTYIKDDTLFLKVAV  147 (148)
T ss_pred             ChhheeEHHHhhcccCCcCcCCEEEEEEEE
Confidence            589999999997777899999999999976

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

>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=95.16  E-value=0.0091  Score=42.51  Aligned_cols=29  Identities=24%  Similarity=0.481  Sum_probs=25.7

Q ss_pred             ccceeeecccccCCCCCeEEc--CeEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVR--DICIIKAEFT  128 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~--D~~~ieaev~  128 (137)
                      +|.+||++++|.+  +|||+|  |++.||+.|.
T Consensus       100 G~~~Fi~~~~L~~--~gfl~~~~D~l~i~~~v~  130 (132)
T cd03773         100 GYNRFFRLDLLIN--EGYLLPENDTLILRFSVR  130 (132)
T ss_pred             CHHHhccHHHHhh--CCCcCCCCCEEEEEEEEe
Confidence            5999999999964  699999  9999999874

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

>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=94.90  E-value=0.019  Score=42.06  Aligned_cols=28  Identities=21%  Similarity=0.438  Sum_probs=25.1

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEF  127 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev  127 (137)
                      +|++||+.++|..  .|||+||++.|+++|
T Consensus       119 G~~~fi~~~~Le~--~~yl~dD~l~I~c~V  146 (147)
T cd03776         119 GYVEFAHIEDLLQ--RGFVKNDTLLIKIEV  146 (147)
T ss_pred             eEceeeEHHHhhh--CCCccCCEEEEEEEE
Confidence            4899999999965  489999999999987

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

>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=94.58  E-value=0.03  Score=38.00  Aligned_cols=29  Identities=28%  Similarity=0.432  Sum_probs=25.0

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFT  128 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~  128 (137)
                      +|++||++++|.++  +++++|++.|+++|.
T Consensus        98 G~~~fi~~~~l~~~--~~~~~d~l~i~~~v~  126 (126)
T cd00121          98 GFPKFISWDDLEDS--YYLVDDSLTIEVEVK  126 (126)
T ss_pred             ChHHeeEHHHhccC--CcEECCEEEEEEEEC
Confidence            58999999999886  239999999999983

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

>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=94.45  E-value=0.023  Score=43.62  Aligned_cols=29  Identities=21%  Similarity=0.273  Sum_probs=26.5

Q ss_pred             ccccccceeccccccccCCceEeCCeEEEEE
Q 046357           36 TKWCITKFIDLETLSNTLNEYLINDVCVCGC   66 (137)
Q Consensus        36 ~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a   66 (137)
                      ..+||+.|||++.|..  .+||.||++.|-+
T Consensus       136 ~gfG~~~Fish~~L~~--r~yikdDtlfI~~  164 (167)
T cd03783         136 IDFGWSTFISHSQLRR--RSFLKNDDLIIFV  164 (167)
T ss_pred             cccccccceeHHHHhh--CCcccCCeEEEEE
Confidence            3799999999999984  7899999999988

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

>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=93.58  E-value=0.064  Score=40.12  Aligned_cols=30  Identities=33%  Similarity=0.580  Sum_probs=26.3

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEF  127 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev  127 (137)
                      ++++||+.++|..+..|||.+|++.|+++|
T Consensus       117 G~~~Fi~~~~Le~s~~~ylkDD~~~Irc~V  146 (147)
T cd03779         117 GCPLFFPLKKLQSPKHAYCKDDTIYIKCVV  146 (147)
T ss_pred             chhheeEHHHhcccCCCcEeCCEEEEEEEE
Confidence            589999999996544799999999999987

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

>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=92.89  E-value=0.067  Score=39.74  Aligned_cols=28  Identities=21%  Similarity=0.427  Sum_probs=24.8

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEF  127 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev  127 (137)
                      ++.+||+.++|..  .|||+||+++|+++|
T Consensus       126 G~~~fi~~~~Le~--~~yl~dD~l~Irc~v  153 (154)
T cd03781         126 GYPKFISHEDLKK--RNYIKDDAIFLRASV  153 (154)
T ss_pred             chhHeeEHHHHhh--CCcccCCEEEEEEEe
Confidence            4899999999953  689999999999987

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

>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=91.32  E-value=0.13  Score=39.58  Aligned_cols=30  Identities=13%  Similarity=0.210  Sum_probs=26.7

Q ss_pred             cccccccceeccccccccCCceEeCCeEEEEE
Q 046357           35 KTKWCITKFIDLETLSNTLNEYLINDVCVCGC   66 (137)
Q Consensus        35 ~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a   66 (137)
                      ...+|++.|||++.|..  ..||.||.+.|-+
T Consensus       135 ~~~~G~~~Fish~~L~~--r~yikdD~ifi~~  164 (167)
T cd03782         135 GPGYGTSAFITHLRLRS--RDFIKGDDVIFLL  164 (167)
T ss_pred             ccccCccceeeHHHHhh--cCcccCCeEEEEE
Confidence            36799999999999985  7799999999877

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

>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=89.67  E-value=0.18  Score=38.81  Aligned_cols=29  Identities=21%  Similarity=0.408  Sum_probs=25.7

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFT  128 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~  128 (137)
                      +|++||+++.|+.  ++||.+|+++|-++++
T Consensus       139 G~~~Fish~~L~~--r~yikdDtlfI~~~~~  167 (167)
T cd03783         139 GWSTFISHSQLRR--RSFLKNDDLIIFVDFE  167 (167)
T ss_pred             ccccceeHHHHhh--CCcccCCeEEEEEecC
Confidence            3999999999975  8999999999988763

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

>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=89.64  E-value=0.34  Score=37.54  Aligned_cols=29  Identities=21%  Similarity=0.406  Sum_probs=25.8

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFT  128 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~  128 (137)
                      ++++||+.++|..  .+||.+|++.|+++|.
T Consensus       156 G~~~Fi~~~~Le~--~~ylkdD~l~Irv~v~  184 (186)
T cd03777         156 GCPVFVAQTVLEN--GTYIKDDTIFIKVIVD  184 (186)
T ss_pred             CchheeEHHHhcc--CCcEeCCEEEEEEEEe
Confidence            4899999999953  6999999999999885

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

---

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	137
2foj_A	155	Ubiquitin carboxyl-terminal hydrolase 7; MATH doma	2e-04

>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 = 37.9 bits (88), Expect = 2e-04
 Identities = 8/83 (9%), Positives = 20/83 (24%), Gaps = 15/83 (18%)

Query: 7   ETSSLPTGWEVNAIINFFFYCEKHFRAVKTK------------WCITKFIDLETLSNTLN 54
              S  T W  +A         +      ++            W  + F+    +++   
Sbjct: 72  NAESDSTSWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEK 131

Query: 55  EYLINDVCVCGCVCEEVFVVKNT 77
            ++ +D          V      
Sbjct: 132 GFIDDDKVTFEV---FVQADAPH 151

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	137
2foj_A	155	Ubiquitin carboxyl-terminal hydrolase 7; MATH doma	99.59
3ivv_A	145	Speckle-type POZ protein; protein binding, nucleus	99.52
2f1z_A	522	Ubiquitin carboxyl-terminal hydrolase 7; hausp, US	99.33
4gjh_A	178	TNF receptor-associated factor 5; TRAF domain, imm	99.24
1ca9_A	192	TRAF2, protein (TNF receptor associated factor 2);	99.18
3hqi_A	312	Speckle-type POZ protein; SPOP, ubiquitin, puckere	99.17
1d00_A	168	Tumor necrosis factor receptor associated protein	99.17
1lb6_A	160	TNF receptor-associated factor 6; TRAF6-CD40 compl	99.07
4ghu_A	198	TNF receptor-associated factor 3; alpha/beta, inna	98.99
2gkw_A	192	TNF receptor-associated factor 3; CD40, NF-KB sign	98.97
1flk_A	228	TNF receptor associated factor 3; TNF signaling, T	98.95
2foj_A	155	Ubiquitin carboxyl-terminal hydrolase 7; MATH doma	98.6
3ivv_A	145	Speckle-type POZ protein; protein binding, nucleus	98.13
3hqi_A	312	Speckle-type POZ protein; SPOP, ubiquitin, puckere	97.84
4gjh_A	178	TNF receptor-associated factor 5; TRAF domain, imm	97.73
1d00_A	168	Tumor necrosis factor receptor associated protein	97.49
1lb6_A	160	TNF receptor-associated factor 6; TRAF6-CD40 compl	97.49
1ca9_A	192	TRAF2, protein (TNF receptor associated factor 2);	97.44
2f1z_A	522	Ubiquitin carboxyl-terminal hydrolase 7; hausp, US	97.43
4ghu_A	198	TNF receptor-associated factor 3; alpha/beta, inna	96.76
2gkw_A	192	TNF receptor-associated factor 3; CD40, NF-KB sign	96.75
1flk_A	228	TNF receptor associated factor 3; TNF signaling, T	96.65
4gwm_A	592	Meprin A subunit beta; mulidomain structure, hydro	90.11

>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=99.59  E-value=1.3e-15  Score=111.42  Aligned_cols=74  Identities=15%  Similarity=0.184  Sum_probs=64.8

Q ss_pred             CeEEecCCCCCCCCCEEEEEEEEEEEe------------CcccccccccccccceeccccccccCCceEeCCeEEEEEee
Q 046357            1 MTLQKSETSSLPTGWEVNAIINFFFYC------------EKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVC   68 (137)
Q Consensus         1 lYL~~~~~~~l~~~w~v~a~fkl~i~N------------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~~   68 (137)
                      +||+++. +..+++|.++|+|+|+|+|            .++|+.....|||++||++++|.|+.+|||+||+++|+|  
T Consensus        67 lyL~~~~-~~~~~~w~v~a~~~l~l~~~~~~~~~~~~~~~~~F~~~~~~wG~~~Fi~~~~L~~~~~~yl~dD~l~Ie~--  143 (155)
T 2foj_A           67 FFLQCNA-ESDSTSWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDDKVTFEV--  143 (155)
T ss_dssp             EEEEEST-TCCCSSCEEEEEEEEEECCSSCGGGCEEEEEEEEEETTBCEEEEEEEEEHHHHTCTTTSSCBTTBEEEEE--
T ss_pred             EEEEeCC-CCCCCCCEEEEEEEEEEEcCCCCcceEEeccEEEeCCCCCCEeECCeEEHHHhcCcCCCceECCEEEEEE--
Confidence            5898854 4578899999999999998            346877678999999999999999999999999999999  


Q ss_pred             eeEEEEccCC
Q 046357           69 EEVFVVKNTF   78 (137)
Q Consensus        69 ~eV~vv~~~~   78 (137)
                       +|.|.++++
T Consensus       144 -~V~V~~~tG  152 (155)
T 2foj_A          144 -FVQADAPHG  152 (155)
T ss_dssp             -EEEECCCBS
T ss_pred             -EEEEeCccc
Confidence             999977654

>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=99.52  E-value=4.4e-15  Score=107.64  Aligned_cols=68  Identities=28%  Similarity=0.324  Sum_probs=59.0

Q ss_pred             CeEEecCCCCCCCCCEEEEEEEEEEEe-------------CcccccccccccccceeccccccccCCceEeCCeEEEEEe
Q 046357            1 MTLQKSETSSLPTGWEVNAIINFFFYC-------------EKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCV   67 (137)
Q Consensus         1 lYL~~~~~~~l~~~w~v~a~fkl~i~N-------------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~   67 (137)
                      +||++.+.    ++|.++|+|+|+|+|             .++|+ ....|||++||++++|+++++|||+||+++|+| 
T Consensus        65 lyL~l~~~----~~w~v~a~f~l~llnq~~~~~~~~~~~~~~~F~-~~~~wG~~~Fi~~~~L~~~~~~yl~dD~l~I~~-  138 (145)
T 3ivv_A           65 LYLLLVSC----PKSEVRAKFKFSILNAKGEETKAMESQRAYRFV-QGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFC-  138 (145)
T ss_dssp             EEEEEEEC----SSSEEEEEEEEEEECTTSCEEEEEECSSCEEEE-TTCEEEEEEEEEHHHHHCGGGCSSGGGCEEEEE-
T ss_pred             EEEEEcCC----CCCcEEEEEEEEEEecCCCceeeecccceEEec-CCCCcCHHHeEEhhhhccccCCcEeCCEEEEEE-
Confidence            58888764    579999999999998             24575 357899999999999999999999999999999 


Q ss_pred             eeeEEEEcc
Q 046357           68 CEEVFVVKN   76 (137)
Q Consensus        68 ~~eV~vv~~   76 (137)
                        +|.|+++
T Consensus       139 --~V~V~~d  145 (145)
T 3ivv_A          139 --EVSVVQD  145 (145)
T ss_dssp             --EEEECC-
T ss_pred             --EEEEEeC
Confidence              9999864

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

Probab=99.33  E-value=6.6e-13  Score=113.57  Aligned_cols=73  Identities=15%  Similarity=0.209  Sum_probs=65.7

Q ss_pred             CeEEecCCCCCCCCCEEEEEEEEEEEe------------CcccccccccccccceeccccccccCCceEeCCeEEEEEee
Q 046357            1 MTLQKSETSSLPTGWEVNAIINFFFYC------------EKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVC   68 (137)
Q Consensus         1 lYL~~~~~~~l~~~w~v~a~fkl~i~N------------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~~   68 (137)
                      +||++.+. ..+++|+++|+|+|+++|            .++|.....+|||++||++++|.++.+|||+||+++|+|  
T Consensus        79 lyL~~~~~-~~~~~w~v~a~f~l~l~n~~~~~~~~~~~~~~~F~~~~~~wG~~~Fi~~~~L~~~~~g~L~nD~l~i~~--  155 (522)
T 2f1z_A           79 FFLQCNAE-SDSTSWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDDKVTFEV--  155 (522)
T ss_dssp             EEEEESTT-CCCSSCBEEEEEEEEECCTTCGGGCEEEECCEEECGGGCEEEESSSSBHHHHSCGGGSSCBTTBEEEEE--
T ss_pred             EEEEecCC-CCCCCceEEEEEEEEEEcCCCCccceeccceeEecCCCCCcchhheeEhhHhcCcccCcccCCcEEEEE--
Confidence            59999877 578899999999999998            467877778999999999999999999999999999999  


Q ss_pred             eeEEEEccC
Q 046357           69 EEVFVVKNT   77 (137)
Q Consensus        69 ~eV~vv~~~   77 (137)
                       +|.|..+.
T Consensus       156 -~V~v~~p~  163 (522)
T 2f1z_A          156 -FVQADAPH  163 (522)
T ss_dssp             -EEEECCCB
T ss_pred             -Eeeccccc
Confidence             99997554

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

Probab=99.24  E-value=2.3e-12  Score=96.84  Aligned_cols=71  Identities=14%  Similarity=0.231  Sum_probs=58.0

Q ss_pred             CeEEecCCCC-CCCCCEEEEEEEEEEEeC-----------------ccccc----ccccccccceeccccccccCCceEe
Q 046357            1 MTLQKSETSS-LPTGWEVNAIINFFFYCE-----------------KHFRA----VKTKWCITKFIDLETLSNTLNEYLI   58 (137)
Q Consensus         1 lYL~~~~~~~-l~~~w~v~a~fkl~i~N~-----------------~~F~~----~~~~wG~~~fi~l~~l~d~~~GyLv   58 (137)
                      +||.+.+.+. ...+|.+.|+|+|+|+|+                 ++|+.    ....|||++||++++|.++++|||+
T Consensus        81 lyL~l~~~~~d~~l~W~v~a~~~l~Lldq~~~~~~~~~~~~~~~~~~~F~~p~~~~~~~wG~~~Fi~~~~L~~~~~~yL~  160 (178)
T 4gjh_A           81 LYFVVMRGEFDSLLQWPFRQRVTLMLLDQSGKKNHIVETFKADPNSSSFKRPDGEMNIASGCPRFVSHSTLENSKNTYIK  160 (178)
T ss_dssp             EEEEEBCCTTGGGSCSSCCCEEEEEECCTTSSCCCEEEEEECCTTCGGGSCCSSSBCCCEEEEEEEEHHHHHCTTCCSSB
T ss_pred             EEEEEecCCCCcccCCceEEEEEEEEEcCCCCcceeEEeeccCCccccccCCcccccCCcChhheeEHHHhhccccCcCc
Confidence            5888866542 345899999999999981                 35552    3468999999999999999999999


Q ss_pred             CCeEEEEEeeeeEEEE
Q 046357           59 NDVCVCGCVCEEVFVV   74 (137)
Q Consensus        59 ~D~~v~~a~~~eV~vv   74 (137)
                      ||+++|+|   +|.|.
T Consensus       161 dD~l~I~~---~V~i~  173 (178)
T 4gjh_A          161 DDTLFLKV---AVDLT  173 (178)
T ss_dssp             TTBEEEEE---EECCT
T ss_pred             CCEEEEEE---EEEec
Confidence            99999999   88654

>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=99.18  E-value=4.7e-12  Score=95.91  Aligned_cols=71  Identities=11%  Similarity=0.173  Sum_probs=58.4

Q ss_pred             CeEEecCCCCCC-CCCEEEEEEEEEEEe---C-------------cccc----cccccccccceeccccccccCCceEeC
Q 046357            1 MTLQKSETSSLP-TGWEVNAIINFFFYC---E-------------KHFR----AVKTKWCITKFIDLETLSNTLNEYLIN   59 (137)
Q Consensus         1 lYL~~~~~~~l~-~~w~v~a~fkl~i~N---~-------------~~F~----~~~~~wG~~~fi~l~~l~d~~~GyLv~   59 (137)
                      +||.+.+.+..+ .+|.++|+|+|+|+|   .             +.|+    .....|||++||++++|.+ ++|||+|
T Consensus       100 lyL~l~~~~~~~~~~W~~~a~~~l~lldq~~~~~~~~~~~~~~~~~~f~rp~~~~~~~wG~~~Fi~~~~L~~-~~gyl~d  178 (192)
T 1ca9_A          100 LFFVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKMEA-KNSYVRD  178 (192)
T ss_dssp             EEEEEECCTTGGGSCSSCCCCEEEEECCTTSSCCEEEEECCCTTSGGGSCCSSSBCCCEEEEEEEETHHHHS-SCSSCBT
T ss_pred             EEEEEccCCCCCcCCCceEEEEEEEEECCCCCceeeEeeccCCchhhhcCCccCCCCCcChhheeEHHHhhh-ccCCEeC
Confidence            589988876665 789999999999998   1             1254    2345899999999999997 6899999


Q ss_pred             CeEEEEEeeeeEEEEc
Q 046357           60 DVCVCGCVCEEVFVVK   75 (137)
Q Consensus        60 D~~v~~a~~~eV~vv~   75 (137)
                      |+++|+|   +|.|.+
T Consensus       179 D~l~I~~---~V~V~~  191 (192)
T 1ca9_A          179 DAIFIKA---IVDLTG  191 (192)
T ss_dssp             TEEEEEE---EECCTT
T ss_pred             CEEEEEE---EEEecC
Confidence            9999999   987753

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

Probab=99.17  E-value=1.6e-11  Score=98.10  Aligned_cols=69  Identities=28%  Similarity=0.316  Sum_probs=58.4

Q ss_pred             CeEEecCCCCCCCCCEEEEEEEEEEEe-------------CcccccccccccccceeccccccccCCceEeCCeEEEEEe
Q 046357            1 MTLQKSETSSLPTGWEVNAIINFFFYC-------------EKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCV   67 (137)
Q Consensus         1 lYL~~~~~~~l~~~w~v~a~fkl~i~N-------------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~   67 (137)
                      +||.+.++    ++|.+.|+|+|+++|             .++|+. ...|||++||++++|.++++|||+||+++|+| 
T Consensus        61 lyL~~~~~----~~~~v~a~~~~~l~~~~~~~~~~~~~~~~~~F~~-~~~wG~~~Fi~~~~L~~~~~~yl~dD~l~i~~-  134 (312)
T 3hqi_A           61 LYLLLVSC----PKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQ-GKDWGFKKFIRRGFLLDEANGLLPDDKLTLFC-  134 (312)
T ss_dssp             EEEEEEEC----CC-CEEEEEEEEEECTTSCEEEEEECSSCEEECT-TCEEEEEEEEEHHHHTCGGGCCCGGGCEEEEE-
T ss_pred             EEEEEcCC----CCCcEEEEEEEEEEeCCCCcccccccCCceeCCC-CCCcCHHHhccHHHhhccccCeecCCEEEEEE-
Confidence            57887754    379999999999998             346654 35899999999999999999999999999999 


Q ss_pred             eeeEEEEccC
Q 046357           68 CEEVFVVKNT   77 (137)
Q Consensus        68 ~~eV~vv~~~   77 (137)
                        +|.|++..
T Consensus       135 --~v~v~~~~  142 (312)
T 3hqi_A          135 --EVSVVQDS  142 (312)
T ss_dssp             --EEEEEEEC
T ss_pred             --EEEEEecc
Confidence              99999765

>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=99.17  E-value=7e-12  Score=92.53  Aligned_cols=70  Identities=11%  Similarity=0.196  Sum_probs=57.4

Q ss_pred             CeEEecCCCCCC-CCCEEEEEEEEEEEeC----------------ccccc----ccccccccceeccccccccCCceEeC
Q 046357            1 MTLQKSETSSLP-TGWEVNAIINFFFYCE----------------KHFRA----VKTKWCITKFIDLETLSNTLNEYLIN   59 (137)
Q Consensus         1 lYL~~~~~~~l~-~~w~v~a~fkl~i~N~----------------~~F~~----~~~~wG~~~fi~l~~l~d~~~GyLv~   59 (137)
                      +||.+.+.+..+ .+|.++|+|+|+|+|+                +.|..    ....|||++||++++|.++ +|||+|
T Consensus        76 lyL~l~~~~~~~~~~w~~~~~~~l~ll~q~~~~~~~~~~~~~~~~~~f~~p~~~~~~~~G~~~Fi~~~~L~~~-~gyl~d  154 (168)
T 1d00_A           76 LFFVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKMEAK-NSYVRD  154 (168)
T ss_dssp             EEEEEECCTTGGGSCSSCCCCEEEEECCTTSSCCEEEEECCCTTSGGGSCCSSSBCCCEEEEEEEETTTTTSS-SSSSBT
T ss_pred             EEEEEecCCCCccCCCceEEEEEEEEECCCCCccceeccccCcchhhccCCCcCCCCCcCcceEeEHHHhccc-CCceeC
Confidence            589988776655 7999999999999981                14542    3467999999999999875 499999


Q ss_pred             CeEEEEEeeeeEEEE
Q 046357           60 DVCVCGCVCEEVFVV   74 (137)
Q Consensus        60 D~~v~~a~~~eV~vv   74 (137)
                      |+++|+|   +|.|.
T Consensus       155 D~l~I~~---~V~v~  166 (168)
T 1d00_A          155 DAIFIKA---IVDLT  166 (168)
T ss_dssp             TEEEEEE---EECCT
T ss_pred             CEEEEEE---EEEec
Confidence            9999999   88763

>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=99.07  E-value=6.3e-11  Score=86.98  Aligned_cols=72  Identities=15%  Similarity=0.277  Sum_probs=54.8

Q ss_pred             CeEEecCCCCC-CCCCEEEEEEEEEEEeCc-------------------cccc-----ccccccccceeccccccccCCc
Q 046357            1 MTLQKSETSSL-PTGWEVNAIINFFFYCEK-------------------HFRA-----VKTKWCITKFIDLETLSNTLNE   55 (137)
Q Consensus         1 lYL~~~~~~~l-~~~w~v~a~fkl~i~N~~-------------------~F~~-----~~~~wG~~~fi~l~~l~d~~~G   55 (137)
                      |||.+.+.+.. +.+|.+.|+|+|+|+|+.                   .|+.     ....|||++||++++|.  ++|
T Consensus        63 lyL~l~~~~~d~~l~wp~~a~~~l~lldq~~~~~~~~~~~~~~~~~~~~~f~~p~~~~~~~~~G~~~Fi~~~~L~--~~~  140 (160)
T 1lb6_A           63 LFVHTMQGEYDSHLPWPFQGTIRLTILDQSEAPVRQNHEEIMDAKPELLAFQRPTIPRNPKGFGYVTFMHLEALR--QRT  140 (160)
T ss_dssp             EEEEEECCTTGGGSCSSCCSEEEEEECCCSCTTSCCCEEEEEECCTTSGGGSCCSSSBCSEEEEEEEEEEGGGGG--TSC
T ss_pred             EEEEEeecCCCccCCCceeeeEEEEEEcCCCccccccceEEeecCCcchhccCCcccCCCCCcCEeeEeEHHHhh--hCC
Confidence            58888766543 457999999999999921                   2332     12379999999999998  589


Q ss_pred             eEeCCeEEEEEeeeeEEEEccC
Q 046357           56 YLINDVCVCGCVCEEVFVVKNT   77 (137)
Q Consensus        56 yLv~D~~v~~a~~~eV~vv~~~   77 (137)
                      ||+||+++|+|   +|.|+.+.
T Consensus       141 yl~dD~l~I~~---~V~v~~~~  159 (160)
T 1lb6_A          141 FIKDDTLLVRC---EVSTRFDL  159 (160)
T ss_dssp             CCBTTBEEEEE---EEEC----
T ss_pred             CccCCEEEEEE---EEEEeecC
Confidence            99999999999   99998653

>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=98.99  E-value=7e-11  Score=90.66  Aligned_cols=72  Identities=11%  Similarity=0.119  Sum_probs=57.3

Q ss_pred             CeEEecCCCCC-CCCCEEEEEEEEEEEeCc-----------------cc----ccccccccccceeccccccccCCceEe
Q 046357            1 MTLQKSETSSL-PTGWEVNAIINFFFYCEK-----------------HF----RAVKTKWCITKFIDLETLSNTLNEYLI   58 (137)
Q Consensus         1 lYL~~~~~~~l-~~~w~v~a~fkl~i~N~~-----------------~F----~~~~~~wG~~~fi~l~~l~d~~~GyLv   58 (137)
                      |||.+.+.+.- ..+|.+.|+|+|+|+|+.                 .|    +.....|||++||++++|.+  +|||.
T Consensus        97 lyL~l~~g~~D~~l~wp~~a~~~l~Lldq~~~~~~~~~~~~~~~~~~~f~rp~~~~~~~wG~~~Fi~~~~L~~--~gyL~  174 (198)
T 4ghu_A           97 LFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLEN--GTYIK  174 (198)
T ss_dssp             EEEEEECCTTGGGSCSSCCCCEEEEECCCSTTCCCEEEEECCCTTSGGGSCCSSSBCCCEEEEEEEEHHHHHH--TTSCB
T ss_pred             EEEEecCCccCCCCCceEEEEEEEEEEcCCCCccceEEEeecCcccceecCCcccCcCCcCchhEeEHHHhhh--cCCee
Confidence            58888765432 358999999999999921                 12    23446899999999999984  89999


Q ss_pred             CCeEEEEEeeeeEEEEccC
Q 046357           59 NDVCVCGCVCEEVFVVKNT   77 (137)
Q Consensus        59 ~D~~v~~a~~~eV~vv~~~   77 (137)
                      ||+++|+|   +|.|+..+
T Consensus       175 dD~l~I~~---~V~v~~~~  190 (198)
T 4ghu_A          175 DDTIFIKV---IVDTSDLP  190 (198)
T ss_dssp             TTBEEEEE---EECCTTCC
T ss_pred             CCEEEEEE---EEEeccCC
Confidence            99999999   99887644

>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=98.97  E-value=1.1e-10  Score=88.74  Aligned_cols=69  Identities=12%  Similarity=0.135  Sum_probs=56.0

Q ss_pred             CeEEecCCCCC-CCCCEEEEEEEEEEEe-----C------------cccccc----cccccccceeccccccccCCceEe
Q 046357            1 MTLQKSETSSL-PTGWEVNAIINFFFYC-----E------------KHFRAV----KTKWCITKFIDLETLSNTLNEYLI   58 (137)
Q Consensus         1 lYL~~~~~~~l-~~~w~v~a~fkl~i~N-----~------------~~F~~~----~~~wG~~~fi~l~~l~d~~~GyLv   58 (137)
                      +||.+.+.+.. ..+|.+.|+|+|+|+|     .            ++|...    ...|||++|||+++|.+  +|||+
T Consensus        97 lyL~l~~~~~d~~l~wp~~a~~~l~lldq~~~~~~~~~~~~~~~~~~~F~~~~~~~~~~wG~~~Fi~~~~L~~--~gyl~  174 (192)
T 2gkw_A           97 LFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLEN--GTYIK  174 (192)
T ss_dssp             EEEEEECCTTGGGSCSSCCCCEEEEECCCSTTCCCEEEEECCCTTCTTSSCCSSSBCCCEEEEEEEEHHHHHH--TTSCB
T ss_pred             EEEEEecCCCCccCCCcEEEEEEEEEECCCCCccceEEEEecCCCcccccCCCCCCcCCCChHHEeEHHHhCc--CCCee
Confidence            58988876654 4589999999999998     1            346432    35899999999999986  59999


Q ss_pred             CCeEEEEEeeeeEEEE
Q 046357           59 NDVCVCGCVCEEVFVV   74 (137)
Q Consensus        59 ~D~~v~~a~~~eV~vv   74 (137)
                      ||+++|+|   +|.|.
T Consensus       175 dD~l~I~~---~V~v~  187 (192)
T 2gkw_A          175 DDTIFIKV---IVDTS  187 (192)
T ss_dssp             TTEEEEEE---EECCT
T ss_pred             CCEEEEEE---EEEcC
Confidence            99999999   88653

>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=98.95  E-value=1.3e-10  Score=90.58  Aligned_cols=70  Identities=11%  Similarity=0.160  Sum_probs=56.1

Q ss_pred             CeEEecCCCCC-CCCCEEEEEEEEEEEeC-----------------cccc----cccccccccceeccccccccCCceEe
Q 046357            1 MTLQKSETSSL-PTGWEVNAIINFFFYCE-----------------KHFR----AVKTKWCITKFIDLETLSNTLNEYLI   58 (137)
Q Consensus         1 lYL~~~~~~~l-~~~w~v~a~fkl~i~N~-----------------~~F~----~~~~~wG~~~fi~l~~l~d~~~GyLv   58 (137)
                      +||.+.+.+.. ..+|.+.|+|+|+|+|+                 ++|.    .....|||++|||+++|.+  +|||+
T Consensus       133 lyL~l~~~~~d~~l~Wp~~a~~~l~lldq~~~~~~~~~~~~~~~~~~~F~rp~~~~~~~wG~~~Fi~~~~L~~--~gyL~  210 (228)
T 1flk_A          133 LFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLEN--GTYIK  210 (228)
T ss_dssp             EEECCBCCTTTTSSCSSCCCCEEEEECCCSSSCCCEEEEECCCTTCTTSSSCSSSBCCCCSEEEEEEHHHHSS--STTCC
T ss_pred             EEEEEecCCccccCCCcEEEEEEEEEEcCCCCccceeeeecCCCccccccCCccCCCCCcCHHHeeEHHHHcc--CCCcc
Confidence            58888766554 45899999999999981                 1354    2235799999999999985  79999


Q ss_pred             CCeEEEEEeeeeEEEEc
Q 046357           59 NDVCVCGCVCEEVFVVK   75 (137)
Q Consensus        59 ~D~~v~~a~~~eV~vv~   75 (137)
                      ||++.|+|   +|.|.+
T Consensus       211 dD~l~I~~---~V~v~~  224 (228)
T 1flk_A          211 DDTIFIKV---IVDTSD  224 (228)
T ss_dssp             SSEEEEEE---ECCCTT
T ss_pred             CCEEEEEE---EEEccc
Confidence            99999999   887754

>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=98.60  E-value=2.2e-08  Score=72.71  Aligned_cols=36  Identities=14%  Similarity=0.279  Sum_probs=33.5

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEEEEEEe
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLGVV  133 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~~~t  133 (137)
                      +|++||++++|.++++|||+||+++|||+|.|..+|
T Consensus       116 G~~~Fi~~~~L~~~~~~yl~dD~l~Ie~~V~V~~~t  151 (155)
T 2foj_A          116 GFSNFMAWSEVTDPEKGFIDDDKVTFEVFVQADAPH  151 (155)
T ss_dssp             EEEEEEEHHHHTCTTTSSCBTTBEEEEEEEEECCCB
T ss_pred             eECCeEEHHHhcCcCCCceECCEEEEEEEEEEeCcc
Confidence            499999999999999999999999999999997765

>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=98.13  E-value=4.8e-07  Score=64.93  Aligned_cols=34  Identities=15%  Similarity=0.212  Sum_probs=31.9

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLG  131 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~~  131 (137)
                      +|++||++++|+++++|||+||+++|||+|.|++
T Consensus       111 G~~~Fi~~~~L~~~~~~yl~dD~l~I~~~V~V~~  144 (145)
T 3ivv_A          111 GFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQ  144 (145)
T ss_dssp             EEEEEEEHHHHHCGGGCSSGGGCEEEEEEEEECC
T ss_pred             CHHHeEEhhhhccccCCcEeCCEEEEEEEEEEEe
Confidence            4899999999999999999999999999999874

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

Probab=97.84  E-value=8.6e-06  Score=64.67  Aligned_cols=35  Identities=14%  Similarity=0.186  Sum_probs=32.6

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLGV  132 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~~~  132 (137)
                      +|++||++++|.++++|||+||+++|+++|.|+..
T Consensus       107 G~~~Fi~~~~L~~~~~~yl~dD~l~i~~~v~v~~~  141 (312)
T 3hqi_A          107 GFKKFIRRGFLLDEANGLLPDDKLTLFCEVSVVQD  141 (312)
T ss_dssp             EEEEEEEHHHHTCGGGCCCGGGCEEEEEEEEEEEE
T ss_pred             CHHHhccHHHhhccccCeecCCEEEEEEEEEEEec
Confidence            48999999999999999999999999999999963

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

Probab=97.73  E-value=7.7e-06  Score=60.95  Aligned_cols=33  Identities=24%  Similarity=0.510  Sum_probs=30.6

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLL  130 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~  130 (137)
                      +|++||++++|.++++|||+||+++|+|+|.|.
T Consensus       141 G~~~Fi~~~~L~~~~~~yL~dD~l~I~~~V~i~  173 (178)
T 4gjh_A          141 GCPRFVSHSTLENSKNTYIKDDTLFLKVAVDLT  173 (178)
T ss_dssp             EEEEEEEHHHHHCTTCCSSBTTBEEEEEEECCT
T ss_pred             ChhheeEHHHhhccccCcCcCCEEEEEEEEEec
Confidence            499999999999999999999999999999664

>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=97.49  E-value=4.2e-05  Score=55.83  Aligned_cols=32  Identities=25%  Similarity=0.451  Sum_probs=28.5

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLL  130 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~  130 (137)
                      +|++||++++|.++ +|||+||+++|+++|.|.
T Consensus       135 G~~~Fi~~~~L~~~-~gyl~dD~l~I~~~V~v~  166 (168)
T 1d00_A          135 GCPLFCPVSKMEAK-NSYVRDDAIFIKAIVDLT  166 (168)
T ss_dssp             EEEEEEETTTTTSS-SSSSBTTEEEEEEEECCT
T ss_pred             CcceEeEHHHhccc-CCceeCCEEEEEEEEEec
Confidence            49999999999875 599999999999999763

>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=97.49  E-value=5.9e-05  Score=54.78  Aligned_cols=32  Identities=16%  Similarity=0.324  Sum_probs=28.0

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLG  131 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~~  131 (137)
                      +|++||++++|.  ++|||+||+++|+++|.|+.
T Consensus       126 G~~~Fi~~~~L~--~~~yl~dD~l~I~~~V~v~~  157 (160)
T 1lb6_A          126 GYVTFMHLEALR--QRTFIKDDTLLVRCEVSTRF  157 (160)
T ss_dssp             EEEEEEEGGGGG--TSCCCBTTBEEEEEEEEC--
T ss_pred             CEeeEeEHHHhh--hCCCccCCEEEEEEEEEEee
Confidence            599999999997  57999999999999999874

>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=97.44  E-value=3.9e-05  Score=57.56  Aligned_cols=32  Identities=28%  Similarity=0.490  Sum_probs=29.3

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLL  130 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~  130 (137)
                      +|++||++++|.+ ++|||+||+++|+++|.|.
T Consensus       159 G~~~Fi~~~~L~~-~~gyl~dD~l~I~~~V~V~  190 (192)
T 1ca9_A          159 GCPLFCPVSKMEA-KNSYVRDDAIFIKAIVDLT  190 (192)
T ss_dssp             EEEEEEETHHHHS-SCSSCBTTEEEEEEEECCT
T ss_pred             ChhheeEHHHhhh-ccCCEeCCEEEEEEEEEec
Confidence            5999999999987 6899999999999999774

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

Probab=97.43  E-value=3.9e-05  Score=65.33  Aligned_cols=35  Identities=14%  Similarity=0.306  Sum_probs=31.9

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLGV  132 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~~~  132 (137)
                      +|++||++++|.++++|||+||++.|+|+|.|...
T Consensus       128 G~~~Fi~~~~L~~~~~g~L~nD~l~i~~~V~v~~p  162 (522)
T 2f1z_A          128 GFSNFMAWSEVTDPEKGFIDDDKVTFEVFVQADAP  162 (522)
T ss_dssp             EESSSSBHHHHSCGGGSSCBTTBEEEEEEEEECCC
T ss_pred             chhheeEhhHhcCcccCcccCCcEEEEEEeecccc
Confidence            49999999999999999999999999999988543

>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=96.76  E-value=0.00022  Score=54.28  Aligned_cols=32  Identities=19%  Similarity=0.334  Sum_probs=28.8

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLG  131 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~~  131 (137)
                      +|++||++++|.+  +|||+||+++|+++|.++.
T Consensus       157 G~~~Fi~~~~L~~--~gyL~dD~l~I~~~V~v~~  188 (198)
T 4ghu_A          157 GCPVFVAQTVLEN--GTYIKDDTIFIKVIVDTSD  188 (198)
T ss_dssp             EEEEEEEHHHHHH--TTSCBTTBEEEEEEECCTT
T ss_pred             CchhEeEHHHhhh--cCCeeCCEEEEEEEEEecc
Confidence            4999999999974  8999999999999998764

>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=96.75  E-value=0.00032  Score=52.76  Aligned_cols=31  Identities=19%  Similarity=0.343  Sum_probs=27.6

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLL  130 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~  130 (137)
                      +|++||++++|.+  +|||+||+++|+++|.|.
T Consensus       157 G~~~Fi~~~~L~~--~gyl~dD~l~I~~~V~v~  187 (192)
T 2gkw_A          157 GCPVFVAQTVLEN--GTYIKDDTIFIKVIVDTS  187 (192)
T ss_dssp             EEEEEEEHHHHHH--TTSCBTTEEEEEEEECCT
T ss_pred             ChHHEeEHHHhCc--CCCeeCCEEEEEEEEEcC
Confidence            5999999999986  599999999999999653

>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=96.65  E-value=0.00043  Score=53.49  Aligned_cols=32  Identities=19%  Similarity=0.334  Sum_probs=28.7

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLG  131 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~~  131 (137)
                      +|++||++++|.+  +|||+||++.|+++|.+.+
T Consensus       193 G~~~Fi~~~~L~~--~gyL~dD~l~I~~~V~v~~  224 (228)
T 1flk_A          193 GCPVFVAQTVLEN--GTYIKDDTIFIKVIVDTSD  224 (228)
T ss_dssp             SEEEEEEHHHHSS--STTCCSSEEEEEEECCCTT
T ss_pred             CHHHeeEHHHHcc--CCCccCCEEEEEEEEEccc
Confidence            5999999999986  7999999999999997754

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

Probab=90.11  E-value=0.086  Score=46.34  Aligned_cols=35  Identities=17%  Similarity=0.190  Sum_probs=29.0

Q ss_pred             cccccceeccccccccCCceEeCCeEEEEEeeeeEEEEcc
Q 046357           37 KWCITKFIDLETLSNTLNEYLINDVCVCGCVCEEVFVVKN   76 (137)
Q Consensus        37 ~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~~~eV~vv~~   76 (137)
                      .|||+.||+++.|+  +..||.||.++|-+   +|+=+..
T Consensus       534 ~~G~~~fish~~l~--~r~fiK~d~~~i~~---~~eD~~~  568 (592)
T 4gwm_A          534 GYGTSAFITHERLK--SRDFIKGDDVYILL---TVEDISH  568 (592)
T ss_dssp             EEEEEEEEEHHHHT--STTSSBTTBEEEEE---EEEECGG
T ss_pred             CcCccccccHHHHh--hcCcccCCeEEEEE---EEEeCcc
Confidence            48999999999998  45699999999999   6654443

---

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	137
d2cr2a1	146	b.8.1.1 (A:8-153) Speckle-type poz protein SPOP {H	0.002

>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 = 34.4 bits (78), Expect = 0.002
 Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 3/50 (6%)

Query: 29  KHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVCEEVFVVKNTF 78
            +       W   KFI  + L +  N  L +D     C   EV VV+++ 
Sbjct: 95  AYRFVQGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFC---EVSVVQDSV 141

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	137
d2cr2a1	146	Speckle-type poz protein SPOP {Human (Homo sapiens	99.32
d1czya1	152	TNF receptor associated factor 2 (TRAF2) {Human (H	99.18
d1l0aa1	155	TNF receptor associated factor 3 (TRAF3) {Human (H	99.01
d1lb6a_	155	TNF receptor associated factor 6 (TRAF6) {Human (H	99.01
d2cr2a1	146	Speckle-type poz protein SPOP {Human (Homo sapiens	98.37
d1czya1	152	TNF receptor associated factor 2 (TRAF2) {Human (H	98.19
d1lb6a_	155	TNF receptor associated factor 6 (TRAF6) {Human (H	97.79
d1l0aa1	155	TNF receptor associated factor 3 (TRAF3) {Human (H	97.56

>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=99.32  E-value=6.5e-13  Score=94.18  Aligned_cols=70  Identities=26%  Similarity=0.265  Sum_probs=59.7

Q ss_pred             CeEEecCCCCCCCCCEEEEEEEEEEEe------------CcccccccccccccceeccccccccCCceEeCCeEEEEEee
Q 046357            1 MTLQKSETSSLPTGWEVNAIINFFFYC------------EKHFRAVKTKWCITKFIDLETLSNTLNEYLINDVCVCGCVC   68 (137)
Q Consensus         1 lYL~~~~~~~l~~~w~v~a~fkl~i~N------------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv~D~~v~~a~~   68 (137)
                      +||.+.+.    ++|.+.|+++|+|.|            .+++......|||++||++++|.++.+|||+||+++|++  
T Consensus        59 v~L~~~~~----~~~~v~~~~~~~l~n~~~~~~~~~~~~~~~~~~~~~~~G~~~fi~~~~l~~~~~g~l~~d~l~I~~--  132 (146)
T d2cr2a1          59 LYLLLVSC----PKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFC--  132 (146)
T ss_dssp             EEEECCCC----SSSEEEEECEEEEECTTSCEEEEEECSCCEEEETTCEEEESCCSBHHHHSCTTTTSCTTSEEEEEE--
T ss_pred             EEEEeccC----CCceEEEEEEEEEEcCCCCcccceEecceEeCCCCCeeeccEEEEHHHhcCcccCceeCCEEEEEE--
Confidence            46766543    469999999999998            334556667899999999999999999999999999999  


Q ss_pred             eeEEEEccC
Q 046357           69 EEVFVVKNT   77 (137)
Q Consensus        69 ~eV~vv~~~   77 (137)
                       +|.|++++
T Consensus       133 -~I~v~~e~  140 (146)
T d2cr2a1         133 -EVSVVQDS  140 (146)
T ss_dssp             -EEEEECCS
T ss_pred             -EEEEEeCC
Confidence             99999765

>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=99.18  E-value=2.3e-12  Score=91.87  Aligned_cols=70  Identities=10%  Similarity=0.152  Sum_probs=55.7

Q ss_pred             CeEEecCCCCC-CCCCEEEEEEEEEEEe--------------------CcccccccccccccceeccccccccCCceEeC
Q 046357            1 MTLQKSETSSL-PTGWEVNAIINFFFYC--------------------EKHFRAVKTKWCITKFIDLETLSNTLNEYLIN   59 (137)
Q Consensus         1 lYL~~~~~~~l-~~~w~v~a~fkl~i~N--------------------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv~   59 (137)
                      +||++.+.+.. +..|.+.|+|+|+|+|                    ++.+......|||++||++++| ++++|||.|
T Consensus        60 lyL~l~~~~~d~~~~~~~~~~~~~~l~d~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~G~~~fi~~~~L-~~~~gfl~d  138 (152)
T d1czya1          60 LFFVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKM-EAKNSYVRD  138 (152)
T ss_dssp             EEEEEECCTTGGGSCSSCCCCEEEEECCTTSSCCEEEEECCCTTSGGGSCCSSSBCCCEEEEEEEETCCC-CCSTTTSCS
T ss_pred             EEEEEccCCcCcccccceeeEEEEEEEcCCCCccceeeeccccccccccCCCcccccccchhhEEEHHHh-cccCCcEeC
Confidence            58888766543 5589999999999998                    1123344567999999999998 566899999


Q ss_pred             CeEEEEEeeeeEEEE
Q 046357           60 DVCVCGCVCEEVFVV   74 (137)
Q Consensus        60 D~~v~~a~~~eV~vv   74 (137)
                      |+++|+|   +|.|.
T Consensus       139 D~l~I~~---~V~v~  150 (152)
T d1czya1         139 DAIFIKA---IVDLT  150 (152)
T ss_dssp             SCEEEEE---EECCT
T ss_pred             CEEEEEE---EEEec
Confidence            9999999   88664

>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=99.01  E-value=5.1e-11  Score=84.63  Aligned_cols=68  Identities=10%  Similarity=0.092  Sum_probs=54.9

Q ss_pred             CeEEecCCCC-CCCCCEEEEEEEEEEEe---------------------CcccccccccccccceeccccccccCCceEe
Q 046357            1 MTLQKSETSS-LPTGWEVNAIINFFFYC---------------------EKHFRAVKTKWCITKFIDLETLSNTLNEYLI   58 (137)
Q Consensus         1 lYL~~~~~~~-l~~~w~v~a~fkl~i~N---------------------~~~F~~~~~~wG~~~fi~l~~l~d~~~GyLv   58 (137)
                      +||++.+.+. ...+|.+.|+|+|+|+|                     ++.+......|||++||++++|.  ++|||+
T Consensus        60 lyL~l~~~~~d~~~~~~~~~~~~~~l~~q~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~G~~~fi~~~~L~--~~gfl~  137 (155)
T d1l0aa1          60 LFFVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLE--NGTYIK  137 (155)
T ss_dssp             EEEEEECCTTTTTSCSSCCCCEEEEECCCSSSCCCEEEEECCCTTSTTSSCCSSSBCCCEEEEEEEEHHHHH--TTTTCB
T ss_pred             EEEEEccCCcCcccCCcEEEEEEEEEecCCCCccceeEEEeeccccccccccccccccCcChhheeEHHHhh--hCCCEE
Confidence            5888876653 35689999999999998                     12344455689999999999997  479999


Q ss_pred             CCeEEEEEeeeeEEE
Q 046357           59 NDVCVCGCVCEEVFV   73 (137)
Q Consensus        59 ~D~~v~~a~~~eV~v   73 (137)
                      ||+++|++   +|.+
T Consensus       138 dD~l~I~~---~V~~  149 (155)
T d1l0aa1         138 DDTIFIKV---IVDT  149 (155)
T ss_dssp             TTEEEEEE---EECC
T ss_pred             CCEEEEEE---EEEe
Confidence            99999999   8753

>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=99.01  E-value=9.2e-11  Score=83.01  Aligned_cols=67  Identities=15%  Similarity=0.279  Sum_probs=54.4

Q ss_pred             CeEEecCCCC-CCCCCEEEEEEEEEEEe------------------------CcccccccccccccceeccccccccCCc
Q 046357            1 MTLQKSETSS-LPTGWEVNAIINFFFYC------------------------EKHFRAVKTKWCITKFIDLETLSNTLNE   55 (137)
Q Consensus         1 lYL~~~~~~~-l~~~w~v~a~fkl~i~N------------------------~~~F~~~~~~wG~~~fi~l~~l~d~~~G   55 (137)
                      +||++.+.+. .+.+|.+.|+++|.|.|                        .++|......|||++||++++|.  ++|
T Consensus        63 vyL~l~~~~~d~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~fi~~~~L~--~~g  140 (155)
T d1lb6a_          63 LFVHTMQGEYDSHLPWPFQGTIRLTILDQSEAPVRQNHEEIMDAKPELLAFQRPTIPRNPKGFGYVTFMHLEALR--QRT  140 (155)
T ss_dssp             EEEEEECCTTGGGSCSSCCSEEEEEECCCSCTTSCCCEEEEEECCTTSGGGSCCSSSBCSEEEEEEEEEEGGGGG--TSC
T ss_pred             EEEEEecCcccccCCCcEEEEEEEEEECCCCCccceeeEEeeecCCccccccCCcccCCcCCcChHHeeEHHHhc--cCC
Confidence            5788776553 45689999999999988                        12345555689999999999997  479


Q ss_pred             eEeCCeEEEEEeeeeEE
Q 046357           56 YLINDVCVCGCVCEEVF   72 (137)
Q Consensus        56 yLv~D~~v~~a~~~eV~   72 (137)
                      ||+||+++|+|   +|.
T Consensus       141 yl~dD~l~I~~---~V~  154 (155)
T d1lb6a_         141 FIKDDTLLVRC---EVS  154 (155)
T ss_dssp             CCBTTBEEEEE---EEE
T ss_pred             CEECCEEEEEE---EEE
Confidence            99999999999   875

>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=98.37  E-value=6.1e-08  Score=67.83  Aligned_cols=36  Identities=14%  Similarity=0.164  Sum_probs=33.5

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEEEEEEe
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLLGVV  133 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~~~t  133 (137)
                      +|++||++++|.++.+|||++|+++|+++|+|++.+
T Consensus       105 G~~~fi~~~~l~~~~~g~l~~d~l~I~~~I~v~~e~  140 (146)
T d2cr2a1         105 GFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQDS  140 (146)
T ss_dssp             EESCCSBHHHHSCTTTTSCTTSEEEEEEEEEEECCS
T ss_pred             eccEEEEHHHhcCcccCceeCCEEEEEEEEEEEeCC
Confidence            399999999999999999999999999999998754

>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=98.19  E-value=2.1e-07  Score=65.39  Aligned_cols=32  Identities=28%  Similarity=0.512  Sum_probs=28.5

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTLL  130 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i~  130 (137)
                      +|++||++++| ++++|||+||+|+|+++|.+.
T Consensus       119 G~~~fi~~~~L-~~~~gfl~dD~l~I~~~V~v~  150 (152)
T d1czya1         119 GCPLFCPVSKM-EAKNSYVRDDAIFIKAIVDLT  150 (152)
T ss_dssp             EEEEEEETCCC-CCSTTTSCSSCEEEEEEECCT
T ss_pred             chhhEEEHHHh-cccCCcEeCCEEEEEEEEEec
Confidence            39999999999 567899999999999999764

>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=97.79  E-value=9.7e-06  Score=56.27  Aligned_cols=28  Identities=18%  Similarity=0.469  Sum_probs=25.9

Q ss_pred             cceeeecccccCCCCCeEEcCeEEEEEEEE
Q 046357           99 CAQLMSLAKLKDPKEGYMVRDICIIKAEFT  128 (137)
Q Consensus        99 ~~~fi~l~~l~~~~~gylv~D~~~ieaev~  128 (137)
                      |++||++++|.  ++|||+||++.|+++|+
T Consensus       127 ~~~fi~~~~L~--~~gyl~dD~l~I~~~V~  154 (155)
T d1lb6a_         127 YVTFMHLEALR--QRTFIKDDTLLVRCEVS  154 (155)
T ss_dssp             EEEEEEGGGGG--TSCCCBTTBEEEEEEEE
T ss_pred             hHHeeEHHHhc--cCCCEECCEEEEEEEEE
Confidence            99999999996  47999999999999985

>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=97.56  E-value=1.3e-05  Score=55.76  Aligned_cols=30  Identities=20%  Similarity=0.362  Sum_probs=26.6

Q ss_pred             ccceeeecccccCCCCCeEEcCeEEEEEEEEE
Q 046357           98 SCAQLMSLAKLKDPKEGYMVRDICIIKAEFTL  129 (137)
Q Consensus        98 d~~~fi~l~~l~~~~~gylv~D~~~ieaev~i  129 (137)
                      +|++||++++|.  ++|||+||++.|+++|.+
T Consensus       120 G~~~fi~~~~L~--~~gfl~dD~l~I~~~V~~  149 (155)
T d1l0aa1         120 GCPVFVAQTVLE--NGTYIKDDTIFIKVIVDT  149 (155)
T ss_dssp             EEEEEEEHHHHH--TTTTCBTTEEEEEEEECC
T ss_pred             ChhheeEHHHhh--hCCCEECCEEEEEEEEEe
Confidence            399999999996  479999999999999864