Citrus Sinensis ID: 041904

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------
Protein Sequence
MSTEGGAVLAGRNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLLDEFYESESFGCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLLTKYFLCVENQMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGLVLAET
Secondary Structure (PSIPRED)
cccccccEEEcccccccEEEEEEccccccccccccEEEEccEEEcccEEEEEEEEcccccccccccEEEEEEEccccccccccEEEEEEEEEEEEEEEEEEEEEccccEEEEEEEEEEEccccccccccEEEcccccccccccEEccEEEEEEEEEEEEcccccccccccccccccccEEEEcccccccccEEcccccEEEEEEEEcccEEEEEEEEccccccccccEEEEEEEcccccccccEEEEEEEEEEEEccccccEEEEEEEEEcccccccccccEEEccccccccccEEEccEEEEEEEEEEEEEEEEcc
Secondary Structure Prediction (SSPRO)
cccccccEEcccccccccEEEEEccHHHHHHHccccccccEEEEcccEEEEEEEEccccccccccEEEEEEEEcccccccccccEEEEEEEEEEEEEEEEcEccccccEEEEcEEEEccccccccccHHcccHHHcccccccEEEccEEEEEEEEEEEEcccccEEEEEEcccccccEEEEEEccHHccccccccccccccEEEEEcccEEEEEEEEcccccccccEEEEEEEEcccccccccEEEEEEEEEEEEcccccEEEEEcEEEEccccccccccccEEHHHHccccccEEEccEEEEEEEEEEEEEEEccc
Coil and Loop (DISEMBL)
msteggavlagrnaapshylfKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLtgsksvnvtDHISIYLELaetsslptgwevnaiTISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKfidlktfsdplngylindacvfGAEVFVVKNTfkgeclsmmhdpptyyhtwkvsnfSSLLDefyesesfgcykwyANYSMDVKILlypngngeakgnCISLFLdvsqssippntkLLTKYFLCVEnqmngknsevegeWLYTLTnraiggrqfmtlaklkdptegylvddsciiKAEVTLhglvlaet
Flexible Loop (DISEMBL)
msteggavlagrnaapsHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELaetsslptgwEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLLDEFYESESFGCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLLTKYFLCVENQMNgknsevegeWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLhglvlaet
Low Complexity Region (SEG)
MSTEGGAVLAGRNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLLDEFYESESFGCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLLTKYFLCVENQMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGLVLAET
Disordered region (IsUnstruct)
*************AAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLLDEFYESESFGCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLLTKYFLCVENQMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGLVL***
Disordered Region (DISOPRED)
******************YLFKIESFSLLSKASV*QLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLLDEFYESESFGCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLLTKYFLCVENQMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGLVLAE*
Disordered Region (DISEMBL)
********LAGRNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLLDEFYESESFGCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLLTKYFLCVENQMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGLVLAET
Disordered Region (DISPRO)
*****GAVLAGRNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLLDEFYESESFGCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLLTKYFLCVENQMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGLVL***
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSTEGGAVLAGRNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLLDEFYESESFGCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLLTKYFLCVENQMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGLVLAET
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	317	2.2.26 [Sep-21-2011]
Q9FPT1	1116	Ubiquitin carboxyl-termin	no	no	0.400	0.113	0.330	3e-12
Q84WU2	1115	Ubiquitin carboxyl-termin	no	no	0.400	0.113	0.323	6e-12

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

 Score = 73.2 bits (178), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 47/142 (33%), Positives = 76/142 (53%), Gaps = 15/142 (10%)

Query: 172 DPPTYYHTWKVSNFSSLLDEFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCIS 229
           DPPT   TW + NFS      + S+ F  G YKW        +IL++P GN     + +S
Sbjct: 51  DPPTLKFTWTIPNFSRQNTRKHYSDVFVVGGYKW--------RILIFPKGNNV---DHLS 99

Query: 230 LFLDVSQS-SIPPNTKLLTKYFLCVENQMNGKNS-EVEGEWLYTLTNRAIGGRQFMTLAK 287
           ++LDVS + S+P       ++ L V NQ++ + +   E +  +       G   FM L++
Sbjct: 100 MYLDVSDAASLPYGWSRYAQFSLAVVNQIHTRYTVRKETQHQFNARESDWGFTSFMPLSE 159

Query: 288 LKDPTEGYLVDDSCIIKAEVTL 309
           L DP+ GYLV+D+ +++AEV +
Sbjct: 160 LYDPSRGYLVNDTVLVEAEVAV 181

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

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

 Score = 71.6 bits (174), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 46/142 (32%), Positives = 77/142 (54%), Gaps = 15/142 (10%)

Query: 172 DPPTYYHTWKVSNFSSLLDEFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCIS 229
           DPP+   TW +  F+ L    + S+ F  G YKW        +IL++P GN     + +S
Sbjct: 50  DPPSLKFTWTIPMFTRLNTRKHYSDVFVVGGYKW--------RILIFPKGNNV---DHLS 98

Query: 230 LFLDVSQSS-IPPNTKLLTKYFLCVENQMNGKNS-EVEGEWLYTLTNRAIGGRQFMTLAK 287
           ++LDV+ ++ +P      +++ L V NQ+N + S   E +  +       G   FM L++
Sbjct: 99  MYLDVADAANLPYGWSRYSQFSLAVVNQVNNRYSIRKETQHQFNARESDWGFTSFMPLSE 158

Query: 288 LKDPTEGYLVDDSCIIKAEVTL 309
           L +PT GYLV+D+ +I+AEV +
Sbjct: 159 LYEPTRGYLVNDTVLIEAEVAV 180

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

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: 1

EC: 2

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	317
449441502	316	PREDICTED: BTB/POZ and MATH domain-conta	0.917	0.920	0.423	1e-57
449522688	316	PREDICTED: BTB/POZ and MATH domain-conta	0.917	0.920	0.423	2e-57
356505546	233	PREDICTED: ubiquitin carboxyl-terminal h	0.709	0.965	0.477	8e-54
297830352	309	hypothetical protein ARALYDRAFT_479214 [	0.908	0.932	0.376	2e-53
21537273	309	unknown [Arabidopsis thaliana]	0.908	0.932	0.376	5e-53
356519881	310	PREDICTED: uncharacterized protein LOC10	0.949	0.970	0.385	2e-51
296083023	389	unnamed protein product [Vitis vinifera]	0.902	0.735	0.379	2e-49
224074494	321	predicted protein [Populus trichocarpa]	0.917	0.906	0.360	2e-49
18401489	309	TRAF-like family protein [Arabidopsis th	0.908	0.932	0.376	5e-49
11994555	304	unnamed protein product [Arabidopsis tha	0.908	0.947	0.376	6e-49

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

 Score =  229 bits (584), Expect = 1e-57,   Method: Compositional matrix adjust.
 Identities = 131/309 (42%), Positives = 185/309 (59%), Gaps = 18/309 (5%)

Query: 13  NAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLE 72
           +  P+HY  KIESFSLL+K SV+Q     FEAGGYKWKL +H  G KS N  DHIS+YLE
Sbjct: 18  DVPPAHYTVKIESFSLLTKNSVDQFESGEFEAGGYKWKLVLHPHGDKSKNGNDHISLYLE 77

Query: 73  LAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFID 132
           +A T SL   WEV  +   F   + K N L   V +       + F  MK ++G  K+I 
Sbjct: 78  IAGTDSLQPSWEVFVVYRLFLLDQNKDNYLT--VEDGKWK--PRRFRGMKKQWGFDKYIS 133

Query: 133 LKTFSDPLNGYLINDACVFGAEVFVVKNTF---KGECLSMMHDPPTYYHTWKVSNFSSLL 189
           LK F +  NGYL++D CVFGAEVFV K  F   KGECLSM+  P TY H WK+ NFS L 
Sbjct: 134 LKEFKESSNGYLVDDVCVFGAEVFVCKENFKGGKGECLSMIKSPVTYKHVWKIDNFSKLD 193

Query: 190 DEFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQ-SSIPPNTKLL 246
            E YES+ F  G  KW        KI +YP G+G  +G+ +S +L+++  +++ P TK+ 
Sbjct: 194 AESYESKIFNAGDKKW--------KIRVYPKGHGSGEGSHLSPYLELADPAALHPATKIY 245

Query: 247 TKYFLCVENQMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAE 306
            +  L +++Q+  K+   +  + ++ +N  +GG +F+ L   K P  G+LV D+ I++AE
Sbjct: 246 AEVTLRLQDQIYSKHHSGKVSYWFSASNPEVGGPRFILLDNFKQPNIGFLVKDAFIVEAE 305

Query: 307 VTLHGLVLA 315
           V++ G+  A
Sbjct: 306 VSIIGVANA 314

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  228 bits (581), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 131/309 (42%), Positives = 184/309 (59%), Gaps = 18/309 (5%)

Query: 13  NAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLE 72
           +  P+HY  KIESFSLL+K SV+Q     FEAGGYKWKL +H  G KS N  DHIS+YLE
Sbjct: 18  DVPPAHYTVKIESFSLLTKNSVDQFESGEFEAGGYKWKLVLHPHGDKSKNGNDHISLYLE 77

Query: 73  LAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFID 132
           +A T SL   WEV  +   F   + K N L   V +       + F  MK ++G  K+I 
Sbjct: 78  IAGTDSLQPSWEVFVVYRLFLLDQNKDNYLT--VEDGKWK--PRRFRGMKKQWGFDKYIS 133

Query: 133 LKTFSDPLNGYLINDACVFGAEVFVVKNTF---KGECLSMMHDPPTYYHTWKVSNFSSLL 189
           LK F +  NGYL++D CVFGAEVFV K  F   KGECLSM+  P TY H WK+ NFS L 
Sbjct: 134 LKEFKESSNGYLVDDVCVFGAEVFVCKENFKGGKGECLSMIKSPVTYKHVWKIDNFSKLD 193

Query: 190 DEFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQ-SSIPPNTKLL 246
            E YES+ F  G  KW        KI +YP G+G  +G+ +S +L+++  +++ P TK+ 
Sbjct: 194 AESYESKIFNAGDKKW--------KIRVYPKGHGSGEGSHLSPYLELADPAALHPATKIY 245

Query: 247 TKYFLCVENQMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAE 306
            +  L +++Q+  K+   +  + ++ +N  +GG +F+ L   K P  G+LV D+ I++AE
Sbjct: 246 AEVTLRLQDQIYSKHHSGKVSYWFSASNPEVGGPRFILLDNFKQPNIGFLVKDAFIVEAE 305

Query: 307 VTLHGLVLA 315
           V + G+  A
Sbjct: 306 VNVIGVANA 314

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  216 bits (551), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 115/241 (47%), Positives = 161/241 (66%), Gaps = 16/241 (6%)

Query: 75  ETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLK 134
           ++SSLP  WEVNAI ++F +  F  +  V+     T +  V+ FH +K+++GVAKFID+ 
Sbjct: 2   DSSSLPVDWEVNAI-VNFSAYNFIDDEYVA-----TQDTNVRRFHVLKTEWGVAKFIDID 55

Query: 135 TFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLLDEFYE 194
           TF+DP NGYL++D CVFGAEVFVVK T KG+CLSM+H P    H+WK  NFS    + YE
Sbjct: 56  TFNDPSNGYLMDDTCVFGAEVFVVKTTTKGDCLSMIHGPIPLSHSWKFDNFSLAKLDKYE 115

Query: 195 SESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLLTKYFLC 252
           SESF  G Y+W        K++LYPNG  E KGN ISLFL +  S++PPNTKL+ +  L 
Sbjct: 116 SESFVGGNYRW--------KLILYPNGIVEGKGNSISLFLTLEVSTLPPNTKLVVECTLR 167

Query: 253 VENQMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGL 312
            + Q++G +++      ++ +N   G RQ + LAKL DP  G+LV+D+CI++AE T+ GL
Sbjct: 168 AKKQISGHHAQTGFCRKFSSSNSTWGTRQLVALAKLTDPNSGFLVNDTCILEAEFTILGL 227

Query: 313 V 313
           +
Sbjct: 228 M 228

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  215 bits (548), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 116/308 (37%), Positives = 183/308 (59%), Gaps = 20/308 (6%)

Query: 13  NAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLE 72
           +A P+HY+ KIESFSLL+K ++E+   ++FEAGGYKWKL ++  G+KS N  DH+S+YL 
Sbjct: 16  DAPPTHYMVKIESFSLLTKHAIERYETESFEAGGYKWKLVLYPNGNKSKNTKDHVSVYLA 75

Query: 73  LAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFID 132
           LA++SSL  GWEV A+   +   + K N L+ +          + FHA+K ++G  KFI 
Sbjct: 76  LADSSSLSPGWEVYAVFRLYLLDQNKDNYLILQGNE-------RRFHAVKREWGFDKFIP 128

Query: 133 LKTFSDPLNGYLINDACVFGAEVFVVK--NTFKGECLSMMHDPPTYYHTWKVSNFSSLLD 190
             TFSD  NGYL+ D C+FGA+VFV K   + +GECLSM+ D  +  H WK+ NFS L  
Sbjct: 129 TGTFSDASNGYLMEDTCMFGADVFVSKERRSGRGECLSMIKDATSSKHVWKIENFSKLDK 188

Query: 191 EFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQSSIPPNTKLLT 247
           E Y+S +F  G  KW        K+  YP G  +  G  +S++L  V   +I   TK+  
Sbjct: 189 ESYDSNAFFAGDRKW--------KVRFYPTGTKQGTGTHLSIYLTLVDPETISDGTKIFV 240

Query: 248 KYFLCVENQMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEV 307
           ++ + + +Q+ G++   +    ++ ++   G  +++++     P  G L+ D C+++A+V
Sbjct: 241 EFTIRIFDQLQGRHIAGKVTKWFSRSSSEHGWVKYVSMVYFTQPNSGLLLKDVCLVEADV 300

Query: 308 TLHGLVLA 315
            +HG+  A
Sbjct: 301 CVHGITSA 308

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  214 bits (545), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 116/308 (37%), Positives = 183/308 (59%), Gaps = 20/308 (6%)

Query: 13  NAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLE 72
           +A P+HY+ KIESFSLL+K ++E+   ++FEAGGYKWKL ++  G+KS N  DH+S+YL 
Sbjct: 16  DAPPTHYMVKIESFSLLTKHAIERYETESFEAGGYKWKLVLYPNGNKSKNTKDHVSVYLA 75

Query: 73  LAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFID 132
           LA++SSL  GWEV A+   +   + K N L+ +          + FH++K ++G  KFI 
Sbjct: 76  LADSSSLSPGWEVYAVFRLYLLDQNKDNYLILQGNE-------RRFHSVKREWGFDKFIP 128

Query: 133 LKTFSDPLNGYLINDACVFGAEVFVVK--NTFKGECLSMMHDPPTYYHTWKVSNFSSLLD 190
             TFSD  NGYL+ D C+FGA+VFV K   + +GECLSM+ D  +  H WK+ NFS L  
Sbjct: 129 TGTFSDSSNGYLMEDTCMFGADVFVSKERRSGRGECLSMIKDATSSKHVWKIENFSKLDK 188

Query: 191 EFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQSSIPPNTKLLT 247
           E Y+S +F  G  KW        KI  YP G  +  G  +S++L  V   +I   TK+  
Sbjct: 189 ESYDSNAFFAGDRKW--------KIEFYPTGTKQGTGTHLSIYLTLVDPETISDGTKIFV 240

Query: 248 KYFLCVENQMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEV 307
           ++ + + +Q+ G++   +    ++ ++   G  +++++     P  G L+ D C+++A+V
Sbjct: 241 EFTIRIFDQLQGRHIAGKVTKWFSRSSSEHGWVKYVSMVYFTQPNSGLLLKDVCLVEADV 300

Query: 308 TLHGLVLA 315
            +HG+  A
Sbjct: 301 CVHGITSA 308

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356519881|ref|XP_003528597.1| PREDICTED: uncharacterized protein LOC100779090 [Glycine max]

 Score =  208 bits (530), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 124/322 (38%), Positives = 186/322 (57%), Gaps = 21/322 (6%)

Query: 1   MSTEGGAVLAGRNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKS 60
           M ++     +  +A P+HY+ KI+SFSLL+K S+E+     FEAGGYKWKL ++ +G+KS
Sbjct: 1   MGSQDAIPRSTVDAPPAHYVMKIQSFSLLAKNSIERYESGKFEAGGYKWKLVLYPSGNKS 60

Query: 61  VNVTDHISIYLELAETSSLPTGWEVNAITISFYSIKFKTNILVSK--VRNSTINVIVKHF 118
            N+ +HIS+YL L +TSSL  GWE+      F   +   N LV    VRN       + F
Sbjct: 61  KNIREHISLYLALDDTSSLHHGWEIYVNFRFFLHDQTNDNYLVGPDTVRNE------RRF 114

Query: 119 HAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVK--NTFKGECLSMMHDPPTY 176
           H MK+++G+ +FI L+ F+    GYL++D C FGAEVFV K  +T KGECL MM +   Y
Sbjct: 115 HKMKAEWGIDQFIPLRDFNLASKGYLVDDTCAFGAEVFVCKERSTGKGECLVMMKEAILY 174

Query: 177 YHTWKVSNFSSLLDEFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDV 234
            H ++  N S L  E Y+S+ F  G +KW        KI LYP G G   GN +SL+L +
Sbjct: 175 KHLYEFDNLSKLDLECYDSKPFNAGNFKW--------KIKLYPKGKGAELGNYLSLYLAL 226

Query: 235 SQ-SSIPPNTKLLTKYFLCVENQMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTE 293
           +  S++ P +K+  +  L + +Q   K+   +  + ++ ++   G   FM +    +   
Sbjct: 227 ADPSALSPCSKIYAQITLRILDQKQAKHHFGKANYWFSASSHENGAAIFMPINNFTNQNF 286

Query: 294 GYLVDDSCIIKAEVTLHGLVLA 315
           GY+V DSC ++AEV + G+V A
Sbjct: 287 GYVVKDSCFVEAEVIILGVVDA 308

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|296083023|emb|CBI22427.3| unnamed protein product [Vitis vinifera]

 Score =  202 bits (513), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 116/306 (37%), Positives = 187/306 (61%), Gaps = 20/306 (6%)

Query: 12  RNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYL 71
           R+  P+HYLF++ES S+L   S+E+    +FE GGYKW+L ++  G+K  +   HIS+YL
Sbjct: 89  RSIQPAHYLFRVESMSVLLDTSIEKYESGSFEVGGYKWRLCLYPNGNKKSDGDGHISLYL 148

Query: 72  ELAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFI 131
            +++T +LP GWEV   T+SF    F  +I    +     +  V+HF+ MK++ G A+F+
Sbjct: 149 VISDTQNLPLGWEV---TVSFKLFVF-NHIHEEYLTVQDTDGKVRHFNVMKTQCGFAQFL 204

Query: 132 DLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLLDE 191
            L   +DP NGYL++D+C+FGAEVFV+K + KGECLSM+ +P     TW + NFS L  E
Sbjct: 205 PLDVLTDPCNGYLMDDSCIFGAEVFVIKYSGKGECLSMIKEPDDGTFTWMIENFSRLKQE 264

Query: 192 FYESESFGC--YKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVS-QSSIPPNTKLLTK 248
              SE F    +KW        K+++YP GN +AK   +SLFL+++ + ++    KL T+
Sbjct: 265 AIYSEIFTVKDFKW--------KLVVYPKGNYKAKNKSLSLFLELANRGTLHHQRKLYTE 316

Query: 249 YFLCVENQMNG---KNSEVE--GEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCII 303
           + L V+ Q NG   K S V+  G+  +  + +  G    ++L+ LKD +  ++++D+ I+
Sbjct: 317 FELLVKEQCNGGHVKPSHVKLNGQTWFCDSIKDWGFSNMISLSDLKDKSNHFILNDTLIV 376

Query: 304 KAEVTL 309
           +A++ L
Sbjct: 377 EAKIML 382

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224074494|ref|XP_002304380.1| predicted protein [Populus trichocarpa] gi|118485977|gb|ABK94833.1| unknown [Populus trichocarpa] gi|222841812|gb|EEE79359.1| predicted protein [Populus trichocarpa]

 Score =  202 bits (513), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 111/308 (36%), Positives = 177/308 (57%), Gaps = 17/308 (5%)

Query: 12  RNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYL 71
           R+  P+HY FKIE+FSLL+ A ++     +FE G YKW+L ++  G+K  N   HIS+YL
Sbjct: 25  RDLPPAHYTFKIENFSLLANAKIDNFESGDFEVGSYKWRLRLYPNGNKKNNGDGHISLYL 84

Query: 72  ELAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFI 131
             + +++LP GWEVN     F   + +   L  +         V+ FH MK++ G  + I
Sbjct: 85  AFSNSNALPFGWEVNVNFRLFVYNQIQDKYLTIQYAKGR----VRRFHGMKTELGFDQLI 140

Query: 132 DLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLLDE 191
            L  F+D   GYLI+D C+FGAE+FV+K T KGECL++++ P +   TWK+ NFS+L  E
Sbjct: 141 PLTIFNDESKGYLIDDRCIFGAEIFVIKPTGKGECLTLVNQPVSDTFTWKIQNFSALDQE 200

Query: 192 FYESE--SFGCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQ-SSIPPNTKLLTK 248
            Y+S+  SFG YKW         +L+YP GN   KG  +S++L +    ++P       +
Sbjct: 201 SYKSQVFSFGGYKW--------ALLVYPKGNSTEKGKSLSIYLKMEDFETLPCGRTTYAE 252

Query: 249 YFLCVENQMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVT 308
           Y L V++Q+ GK+ E +    ++ + +  G   FM+L  +    +G+LV+D+  +  EV 
Sbjct: 253 YMLRVKDQLFGKHIEKKAYSHFSYSIKDWGHLNFMSLDDVNALPKGFLVNDTLAV--EVQ 310

Query: 309 LHGLVLAE 316
           +H + + +
Sbjct: 311 IHVITVVK 318

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  201 bits (510), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 116/308 (37%), Positives = 183/308 (59%), Gaps = 20/308 (6%)

Query: 13  NAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLE 72
           +A P+HY+ KIESFSLL+K ++E+   ++FEAGGYKWKL ++  G+KS N  DH+S+YL 
Sbjct: 16  DAPPTHYMVKIESFSLLTKHAIERYETESFEAGGYKWKLVLYPNGNKSKNTKDHVSVYLS 75

Query: 73  LAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFID 132
           LA++SSL  GWEV A+   +   + K N L+ +          + FH++K ++G  KFI 
Sbjct: 76  LADSSSLSPGWEVYAVFRLYLLDQNKDNYLILQGNE-------RRFHSVKREWGFDKFIP 128

Query: 133 LKTFSDPLNGYLINDACVFGAEVFVVK--NTFKGECLSMMHDPPTYYHTWKVSNFSSLLD 190
             TFSD  NGYL+ D C+FGA+VFV K   + +GECLSM+ D  +  H WK+ NFS L  
Sbjct: 129 TGTFSDASNGYLMEDTCMFGADVFVSKERRSGRGECLSMIKDATSSKHVWKIENFSKLDK 188

Query: 191 EFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQSSIPPNTKLLT 247
           E Y+S +F  G  KW        KI  YP G  +  G  +S++L  V   +I   TK+  
Sbjct: 189 ESYDSNAFFAGDRKW--------KIEFYPTGTKQGTGTHLSIYLTLVDPETISDGTKIFV 240

Query: 248 KYFLCVENQMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEV 307
           ++ + + +Q+ G++   +    ++ ++   G  +++++     P  G L+ D C+++A+V
Sbjct: 241 EFTIRIFDQLQGRHIAGKVTKWFSRSSSEHGWVKYVSMVYFTQPNSGLLLKDVCLVEADV 300

Query: 308 TLHGLVLA 315
            +HG+  A
Sbjct: 301 CVHGITSA 308

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  200 bits (509), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 116/308 (37%), Positives = 183/308 (59%), Gaps = 20/308 (6%)

Query: 13  NAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLE 72
           +A P+HY+ KIESFSLL+K ++E+   ++FEAGGYKWKL ++  G+KS N  DH+S+YL 
Sbjct: 11  DAPPTHYMVKIESFSLLTKHAIERYETESFEAGGYKWKLVLYPNGNKSKNTKDHVSVYLS 70

Query: 73  LAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFID 132
           LA++SSL  GWEV A+   +   + K N L+ +          + FH++K ++G  KFI 
Sbjct: 71  LADSSSLSPGWEVYAVFRLYLLDQNKDNYLILQGNE-------RRFHSVKREWGFDKFIP 123

Query: 133 LKTFSDPLNGYLINDACVFGAEVFVVK--NTFKGECLSMMHDPPTYYHTWKVSNFSSLLD 190
             TFSD  NGYL+ D C+FGA+VFV K   + +GECLSM+ D  +  H WK+ NFS L  
Sbjct: 124 TGTFSDASNGYLMEDTCMFGADVFVSKERRSGRGECLSMIKDATSSKHVWKIENFSKLDK 183

Query: 191 EFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQSSIPPNTKLLT 247
           E Y+S +F  G  KW        KI  YP G  +  G  +S++L  V   +I   TK+  
Sbjct: 184 ESYDSNAFFAGDRKW--------KIEFYPTGTKQGTGTHLSIYLTLVDPETISDGTKIFV 235

Query: 248 KYFLCVENQMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEV 307
           ++ + + +Q+ G++   +    ++ ++   G  +++++     P  G L+ D C+++A+V
Sbjct: 236 EFTIRIFDQLQGRHIAGKVTKWFSRSSSEHGWVKYVSMVYFTQPNSGLLLKDVCLVEADV 295

Query: 308 TLHGLVLA 315
            +HG+  A
Sbjct: 296 CVHGITSA 303

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	317
TAIR|locus:2089045	309	AT3G17380 "AT3G17380" [Arabido	0.905	0.928	0.378	1e-52
TAIR|locus:2055998	420	AT2G04170 "AT2G04170" [Arabido	0.883	0.666	0.325	9.2e-36
TAIR|locus:2179744	351	AT5G26260 "AT5G26260" [Arabido	0.876	0.792	0.306	5.1e-35
TAIR|locus:2179699	350	AT5G26280 "AT5G26280" [Arabido	0.886	0.802	0.316	2e-33
TAIR|locus:2151054	349	AT5G26300 "AT5G26300" [Arabido	0.876	0.796	0.298	3e-30
TAIR|locus:2151049	333	AT5G26290 "AT5G26290" [Arabido	0.867	0.825	0.308	4.9e-30
TAIR|locus:2151064	352	AT5G26320 "AT5G26320" [Arabido	0.911	0.821	0.287	5.6e-29
TAIR|locus:2118465	297	AT4G09770 "AT4G09770" [Arabido	0.864	0.922	0.301	7.3e-27
TAIR|locus:2056008	411	AT2G04190 "AT2G04190" [Arabido	0.883	0.681	0.301	9.4e-27
TAIR|locus:2092359	375	AT3G20380 "AT3G20380" [Arabido	0.880	0.744	0.31	2.5e-26

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

 Score = 546 (197.3 bits), Expect = 1.0e-52, P = 1.0e-52
 Identities = 117/309 (37%), Positives = 185/309 (59%)

Query:    13 NAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLE 72
             +A P+HY+ KIESFSLL+K ++E+   ++FEAGGYKWKL ++  G+KS N  DH+S+YL 
Sbjct:    16 DAPPTHYMVKIESFSLLTKHAIERYETESFEAGGYKWKLVLYPNGNKSKNTKDHVSVYLS 75

Query:    73 LAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFID 132
             LA++SSL  GWEV A+   +   + K N L+ +          + FH++K ++G  KFI 
Sbjct:    76 LADSSSLSPGWEVYAVFRLYLLDQNKDNYLILQGNE-------RRFHSVKREWGFDKFIP 128

Query:   133 LKTFSDPLNGYLINDACVFGAEVFVVKN--TFKGECLSMMHDPPTYYHTWKVSNFSSLLD 190
               TFSD  NGYL+ D C+FGA+VFV K   + +GECLSM+ D  +  H WK+ NFS L  
Sbjct:   129 TGTFSDASNGYLMEDTCMFGADVFVSKERRSGRGECLSMIKDATSSKHVWKIENFSKLDK 188

Query:   191 EFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQSSIPPNTKLLT 247
             E Y+S +F  G  KW        KI  YP G  +  G  +S++L  V   +I   TK+  
Sbjct:   189 ESYDSNAFFAGDRKW--------KIEFYPTGTKQGTGTHLSIYLTLVDPETISDGTKIFV 240

Query:   248 KYFLCVENQMNGKNSEVE-GEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAE 306
             ++ + + +Q+ G++   +  +W ++ ++   G  +++++     P  G L+ D C+++A+
Sbjct:   241 EFTIRIFDQLQGRHIAGKVTKW-FSRSSSEHGWVKYVSMVYFTQPNSGLLLKDVCLVEAD 299

Query:   307 VTLHGLVLA 315
             V +HG+  A
Sbjct:   300 VCVHGITSA 308

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 386 (140.9 bits), Expect = 9.2e-36, P = 9.2e-36
 Identities = 98/301 (32%), Positives = 158/301 (52%)

Query:    12 RNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYL 71
             R+  PS+ +  I SFS++ K   E      FEAGGYKW+L +++ G+++    +HIS+Y+
Sbjct:   125 RDERPSNKILTITSFSVI-KGRGEPYESSVFEAGGYKWRLVLYVNGNQNDGGNNHISLYV 183

Query:    72 ELAETSSLPTGWEVNA-ITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKF 130
              + ET SLP GWEVN  + +  Y+ K +  ++V        + IVK ++  K ++G  K 
Sbjct:   184 RIEETESLPKGWEVNVELKLFVYNGKQRKYLIVK-------DGIVKRYNDAKKEWGYGKL 236

Query:   131 IDLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLLD 190
             I L TF D   GYL  D   FGAE+F        E ++ + +PP    TWK+ +FS+L D
Sbjct:   237 IPLTTFLDTNEGYLEQDIASFGAEIFSGTAVQVQEKVTFISNPPNNVFTWKILHFSNLED 296

Query:   191 EFYESESFGCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPN---TKLLT 247
             +FY S+ F     Y     +      P G G+ +   I +FL  +Q    PN   T    
Sbjct:   297 KFYYSDDFLVEDRYWRLGFN------PKGTGDGRSQAIPIFL-YAQGH-KPNAVATNTWG 348

Query:   248 KYFLCVENQMNGKNSEV-EGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAE 306
                L ++NQ +  ++++    W  T ++  +G    ++LA+  D ++GY V+DS I +AE
Sbjct:   349 AVNLRLKNQRSSNHAQIYSAAWYPTRSDYGVGVNTIISLAEFNDASKGYSVNDSIIFEAE 408

Query:   307 V 307
             +
Sbjct:   409 M 409

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

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

 Score = 379 (138.5 bits), Expect = 5.1e-35, P = 5.1e-35
 Identities = 93/303 (30%), Positives = 161/303 (53%)

Query:    12 RNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYL 71
             R+  PS  +  I SFS++ K   E      FEA GYKW+L +++ G+    + +HIS+Y 
Sbjct:    56 RDERPSSKIVTITSFSVI-KDRGEPYESSIFEAAGYKWRLVLYVKGNPKGGINNHISLYA 114

Query:    72 ELAETSSLPTGWEVNA-ITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKF 130
              + ET +LP GWEVN  + +  ++ K K  + V+   + T    VK ++  K ++G  + 
Sbjct:   115 RIEETETLPRGWEVNVDLKLFVHNRKLKKYLSVT---DGT----VKRYNDAKKEWGFTQL 167

Query:   131 IDLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLLD 190
             I L TF +   GYL+ D   FGAE+F+V  T K E ++ + +PP    TWK+  FS+L D
Sbjct:   168 ISLPTFYNANEGYLVQDTASFGAEIFIVNPTEKQEKVTFISNPPDNVFTWKILRFSTLED 227

Query:   191 EFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVS---QSSIPPNTKL 245
             +FY S+ F  G   W   ++        P G+G  + + + +FL       +++  NT  
Sbjct:   228 KFYYSDDFLVGDRYWRLGFN--------PKGSGGGRPHALPIFLYAQGHKANAVVTNTWG 279

Query:   246 LTKYFLCVENQMNGKNSEV-EGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIK 304
                  L ++NQ +  + ++    W    ++  +G    + +++LKD ++GY+V+D+ I +
Sbjct:   280 AVN--LRLKNQRSSNHKQLYSAAWYPIRSDYGVGVNNIILMSELKDASKGYMVNDAIIFE 337

Query:   305 AEV 307
             AE+
Sbjct:   338 AEM 340

GO:0003674 "molecular_function" evidence=ND

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

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

 Score = 364 (133.2 bits), Expect = 2.0e-33, P = 2.0e-33
 Identities = 95/300 (31%), Positives = 153/300 (51%)

Query:    12 RNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYL 71
             R   PS  +  I SFS++ K   E      FEA GYKW+L +++ G+K+    DHIS+Y 
Sbjct:    55 REERPSSKIVTITSFSVI-KGRGEPYESSVFEAAGYKWRLVLYVNGNKNDGGNDHISLYA 113

Query:    72 ELAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFI 131
              + ET+SLP GWEVN + +      F  N  + K    T + +VK ++  K ++G  + I
Sbjct:   114 RIEETNSLPLGWEVN-VDLKL----FVHNGKLHKYLTVT-DGLVKRYNNAKKEWGFGQLI 167

Query:   132 DLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLLDE 191
                TF +   GYL  D   FGAE+F+VK   + E ++ + +PP    TWK+  FS+L D+
Sbjct:   168 PRSTFYNANEGYLDQDTGSFGAEIFIVKPAQQQEKVTFISNPPNNVFTWKILRFSTLEDK 227

Query:   192 FYESESFGCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVS---QSSIPPNTKLLTK 248
             FY S+ F     Y     +      P G+G  + + + +FL       +++  NT     
Sbjct:   228 FYYSDDFLVEDRYWRLGFN------PKGDGGGRPHALPIFLFAQGHKANAVATNTWGAVN 281

Query:   249 YFLCVENQMNGKNSEV-EGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEV 307
               L ++NQ +  + ++    W    +   +G    + LA L D ++GYLV+D+ I +AE+
Sbjct:   282 --LRLKNQRSTNHRQIYSAAWYPIGSGYGVGVNNIILLADLNDASKGYLVNDAIIFEAEM 339

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0009507 "chloroplast" evidence=ISM

GO:0016020 "membrane" evidence=IDA

GO:0009506 "plasmodesma" evidence=IDA

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

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

 Score = 334 (122.6 bits), Expect = 3.0e-30, P = 3.0e-30
 Identities = 89/298 (29%), Positives = 153/298 (51%)

Query:    12 RNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYL 71
             R+  PS  +  I +FS++ K  VE      FEA GYKW+L +++ G+ + +  DHIS+Y+
Sbjct:    55 RDERPSSKILTITNFSVI-KGRVEPYESSVFEAAGYKWRLVLYVNGNPNDSGNDHISLYV 113

Query:    72 ELAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFI 131
              + ET  LP GWEVN + +  +    K N  ++ + + T+    K ++  K ++G  + I
Sbjct:   114 RIEETEYLPRGWEVN-VDLKLFIHNGKLNKYLA-ISDGTL----KLYNDAKREWGFGQLI 167

Query:   132 DLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLLDE 191
                TF +   GY+  D   FGAE+F+VK   + E ++ + +PPT   TWK+ +FS L D+
Sbjct:   168 PHVTFYNTY-GYIEQDIGSFGAEIFIVKPAQQQEKVTFISNPPTNVFTWKILHFSILEDK 226

Query:   192 FYESESFGCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVS---QSSIPPNTKLLTK 248
             FY S+ F     Y     +      P G+G  +   + +FL       +++  NT     
Sbjct:   227 FYYSDDFLVEDRYWRLGFN------PKGDGGGRPYALPIFLFAQGHKANAVATNTWGAAN 280

Query:   249 YFLCVENQMNGKNSEV-EGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKA 305
               L ++NQ +  + ++    W    +   +G    + LA L D ++GYLV+++ I +A
Sbjct:   281 --LRLKNQRSTNHRQIYTAAWYPIGSGYGVGVNNIILLADLNDASQGYLVNNAIIFEA 336

GO:0003674 "molecular_function" evidence=ND

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0031225 "anchored to membrane" evidence=TAS

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

 Score = 332 (121.9 bits), Expect = 4.9e-30, P = 4.9e-30
 Identities = 95/308 (30%), Positives = 154/308 (50%)

Query:     6 GAVLAGRNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTD 65
             G     R+  PS  +  I SFS++ +   E      FEA GYKW+L +++ G++     D
Sbjct:    42 GVTRVWRDDRPSDKILSITSFSII-RTRPEPYESSVFEAVGYKWRLVLYVNGNEKDGGKD 100

Query:    66 HISIYLELAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKY 125
             H+S+Y ++ ET SLP GWEVN        +  K  +   K+ N  + V VK ++    + 
Sbjct:   101 HVSLYAKIVETESLPVGWEVN--------VDLKLFVYNGKL-NKYLIVTVKRYNNATKEL 151

Query:   126 GVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNF 185
             G  + I   TF D  +GY   D   FGAE+++VK   + E ++ + +PP    TWK+ +F
Sbjct:   152 GYGQLIPQSTFYDGNDGYREQDTGTFGAEIYIVKPAQQKEKVTFISNPPDNVFTWKILHF 211

Query:   186 SSLLDEFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNT 243
             S+L D+ Y+S  F  G   W        K+ L P      KG  + +FL  +Q     N 
Sbjct:   212 STLEDKVYQSNEFLVGDRYW--------KLGLNP------KGGLVPIFL-YAQG-FKANA 255

Query:   244 KLLTKYF---LCVENQMNGKNSEVEGEWLYTLTNRAIG-GRQFMTLAKLKDPTEGYLVDD 299
              + T Y    L ++NQ +  +      + Y + +  +G G   + L+ +KD ++GY+V+D
Sbjct:   256 VVTTTYAATNLRLKNQRSSNHVTTYTAYWYLIPS-GLGLGVNTIPLSDVKDASKGYVVND 314

Query:   300 SCIIKAEV 307
             S II+ E+
Sbjct:   315 SIIIEVEM 322

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

GO:0031225 "anchored to membrane" evidence=TAS

TAIR|locus:2151064 AT5G26320 "AT5G26320" [Arabidopsis thaliana (taxid:3702)]

 Score = 322 (118.4 bits), Expect = 5.6e-29, P = 5.6e-29
 Identities = 91/316 (28%), Positives = 153/316 (48%)

Query:     1 MSTEGGAVLAGRNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKS 60
             + T  G     R   PS  +  I SFS++ K   E      FEA GYKW+  + + G+++
Sbjct:    44 LKTNLGLTRVLREERPSSKIVTITSFSVI-KGRSEAFESSTFEAAGYKWRFMLFVNGNQN 102

Query:    61 VNVTDH--ISIYLELAETSSLPTGWEVNA-ITISFYSIKFKTNILVSKVRNSTINVIVKH 117
                  H  +++Y+ + ET S P GWEVN  + +  ++ K    + VS   + T    VK 
Sbjct:   103 DPDGGHENMALYVGIKETESFPRGWEVNVDLKLFVHNEKLHKYLTVS---DGT----VKR 155

Query:   118 FHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYY 177
             + A K+ +G    I   T  DP  GY+++D   FGAE+ +V    K E ++ + +PP   
Sbjct:   156 YEAAKTYWGFGNLIPRTTLLDPNEGYILHDTLSFGAEISIVNPAEKQEKITFISNPPDNV 215

Query:   178 HTWKVSNFSSLLDEFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFL--- 232
              TWK+  FS+L ++FY S+ F  G   W   ++        P G    +   +S+FL   
Sbjct:   216 FTWKILRFSTLENKFYYSDEFLVGDRYWRLGFN--------PKGYQGERPRALSIFLYAQ 267

Query:   233 DVSQSSIPPNTKLLTKYFLCVENQMNGKNSEVEGE-WLYTLTNRAIGGRQFMTLAKLKDP 291
                 +++  NT       L ++NQ +  + ++  E W    +   I G   + L  L++ 
Sbjct:   268 GYKANAVITNT--WGSVNLQLKNQRSSNHIQLYSEAWCAIRSGYGIEGNSIILLEDLQNS 325

Query:   292 TEGYLVDDSCIIKAEV 307
             ++GYLV+D+ I +AE+
Sbjct:   326 SKGYLVNDAIIFEAEL 341

GO:0003674 "molecular_function" evidence=ND

GO:0008150 "biological_process" evidence=ND

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

 Score = 302 (111.4 bits), Expect = 7.3e-27, P = 7.3e-27
 Identities = 92/305 (30%), Positives = 151/305 (49%)

Query:    12 RNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYL 71
             R  APS YL K+  FS + K S +     +F+ GG+KW+L  +  G       DH+SIY 
Sbjct:     5 REEAPSSYLMKLVGFSEV-KFSHQPYESADFDVGGHKWRLIFYPAGKLEEGGKDHVSIY- 62

Query:    72 ELAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFI 131
               A   ++    +++A  + F+ I    N   S  ++ T+    KH++  K + G A+ +
Sbjct:    63 --ARIENVGASMQIDA-ELKFF-IYNHNNKQYSVFQDGTM----KHYNKEKKECGFAQML 114

Query:   132 DLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLLDE 191
                 F+DP NGY+  +AC+ G E+FV+K   K E +    +PP    TWK+S+FS + D+
Sbjct:   115 LFSKFNDPKNGYIDGNACIVGVEIFVIKPIEKVERVVFTQNPPENKFTWKISHFSYIGDK 174

Query:   192 -FYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLLTK 248
              +Y S+ F  G  KW        ++ + P G  + K   +S++  V   +  PN    + 
Sbjct:   175 RYYYSDEFVVGDRKW--------RLKISPKG--DKKVRALSVY--VQAMAYLPNAVASST 222

Query:   249 YF---LCVENQMNGKNSEVEGEWLYTLTNRAIGG-RQFMTLAKLKDPTEGYLVDDSCIIK 304
             Y    L + NQ N  + E      Y+  N    G  + +++  L D ++GYLV+DS ++ 
Sbjct:   223 YAKLRLRLLNQKNSNHIEKRVFHFYSRENGDGSGISELISVEDLNDESKGYLVEDSIVL- 281

Query:   305 AEVTL 309
              E TL
Sbjct:   282 -ETTL 285

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0008150 "biological_process" evidence=ND

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

 Score = 301 (111.0 bits), Expect = 9.4e-27, P = 9.4e-27
 Identities = 91/302 (30%), Positives = 149/302 (49%)

Query:    12 RNAAPSHYLFKIESFSLLSKASVEQLILDNFEAG-GYKWKLSIHLTGSKSVNVTDHISIY 70
             R+  PSH +  I +FS +     E      FEA   +KW+L +++ G+++   ++HIS+Y
Sbjct:   115 RDEPPSHRILTITNFSEIIGRE-EPYESSVFEAYFEHKWRLILYVNGNQNDGGSNHISLY 173

Query:    71 LELAETSSLPTGWEVNAITISF-YSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAK 129
             L   ET  L     +N +   F Y+ K    + V+       + I K ++    ++G  K
Sbjct:   174 LRSEETDHLTYDGSINFVLKLFVYNGKQDKYLTVT-------DGIQKRYNYKNKEWGYGK 226

Query:   130 FIDLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSLL 189
              I L TF D   GYL  D   FGAE+F+       E ++ + +PP    TWK+ +FS+L 
Sbjct:   227 LIPLSTFLDTSQGYLEQDTASFGAEIFLCPPIQVQEKVTFISNPPNNVFTWKILHFSTLE 286

Query:   190 DEFYESESFGCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLLTKY 249
             D  Y S+ F     Y  + + V     P G G+ +   I +FL  +Q    PN  + + +
Sbjct:   287 DIVYYSDDFLVEDRY--WRLGVN----PKGTGDGRSQAIKIFL-YAQGH-KPNAVVSSTW 338

Query:   250 F---LCVENQMNGKNSEVEGEWLYTLTNR-AIGGRQFMTLAKLKDPTEGYLVDDSCIIKA 305
                 L V+NQ +  +S++    LY + N   +G    ++LA+L D  + YLV+DS I +A
Sbjct:   339 GAVNLRVKNQRSSNHSQIYSAALYPIRNDYGVGVNTVLSLAELNDAVKEYLVNDSIIFEA 398

Query:   306 EV 307
             E+
Sbjct:   399 EM 400

GO:0003674 "molecular_function" evidence=ND

GO:0005737 "cytoplasm" evidence=ISM

GO:0008150 "biological_process" evidence=ND

GO:0005739 "mitochondrion" evidence=IDA

TAIR|locus:2092359 AT3G20380 "AT3G20380" [Arabidopsis thaliana (taxid:3702)]

 Score = 297 (109.6 bits), Expect = 2.5e-26, P = 2.5e-26
 Identities = 93/300 (31%), Positives = 145/300 (48%)

Query:    16 PSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAE 75
             PS Y FKIES++   K          F AGGY W L +H  G      + ++S+Y+ L E
Sbjct:    86 PSSYSFKIESYNSFLKIPYLGFESRPFAAGGYNWVLKVHPNGLTWDGTSGYVSLYVLLHE 145

Query:    76 TSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKT 135
             ++ + T  +V    + FY   F  N    K   +  +  V  F A K   G  K +    
Sbjct:   146 STPI-TADQVVYADLRFYI--FNNN---EKKYFTVQDTNVWKFTAPKRLLGFPKVMSADQ 199

Query:   136 FSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMMH--DPPTYYHTWKVSNFSSLLDEFY 193
             F D  NGY+ ++ C FG +V V  +  K E L +    D P +  T+ +  FS+LL E Y
Sbjct:   200 FEDLRNGYIYDNHCEFGVDVTVASHYQKSESLFVTEKFDNPIF--TYALLRFSTLLKESY 257

Query:   194 ESESFGCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLLTKYFLCV 253
             +S+ F         SM +++  +PNG   +KG  +SL+L+++     P   +  +  L V
Sbjct:   258 QSDVFSI----GGRSMYLQV--FPNGRNLSKGKAMSLYLNINDK-FKPFEMIYVRAKLRV 310

Query:   254 ENQMNGKNSEVE-GEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGL 312
              NQ    N E++   W YT      G  Q + LA L+D ++G++V+D  ++K EV L G+
Sbjct:   311 LNQRKLNNVEIQVSNW-YTSWFYYSGDFQIIPLADLRDSSKGFVVND--MLKVEVQLEGI 367

GO:0003674 "molecular_function" evidence=ND

GO:0005576 "extracellular region" evidence=ISM

GO:0008150 "biological_process" evidence=ND

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input: fgenesh2_kg.3__1915__AT3G17380.1 annotation not avaliable (309 aa) (Arabidopsis lyrata)

Predicted Functional Partners:

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

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	317
cd00121	126	cd00121, MATH, MATH (meprin and TRAF-C homology) d	3e-19
cd00121	126	cd00121, MATH, MATH (meprin and TRAF-C homology) d	4e-16
cd00270	149	cd00270, MATH_TRAF_C, Tumor Necrosis Factor Recept	5e-05
pfam00917	116	pfam00917, MATH, MATH domain	8e-05
cd03775	134	cd03775, MATH_Ubp21p, Ubiquitin-specific protease	1e-04
cd03773	132	cd03773, MATH_TRIM37, Tripartite motif containing	3e-04
smart00061	95	smart00061, MATH, meprin and TRAF homology	0.003

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

 Score = 81.7 bits (202), Expect = 3e-19
 Identities = 44/136 (32%), Positives = 64/136 (47%), Gaps = 15/136 (11%)

Query: 177 YHTWKVSNFSSLLDEFYESESFGC--YKWYANYSMDVKILLYPNGNGEAKGNCISLFLDV 234
            HTWK+ NFS L  E   S  F    YKW         I +YPNG+GE  G+ +SL+L++
Sbjct: 2   KHTWKIVNFSELEGESIYSPPFEVGGYKWR--------IRIYPNGDGE-SGDYLSLYLEL 52

Query: 235 -SQSSIPPNTKLLTKYFLCVENQMNGKNSEVEGE-WLYTLTNRAIGGRQFMTLAKLKDPT 292
               S      +  ++ L + NQ  GK+         ++      G  +F++   L+D  
Sbjct: 53  DKGESDLEKWSVRAEFTLKLVNQNGGKSLSKSFTHVFFSEKGSGWGFPKFISWDDLEDS- 111

Query: 293 EGYLVDDSCIIKAEVT 308
             YLVDDS  I+ EV 
Sbjct: 112 -YYLVDDSLTIEVEVK 126

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

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

 Score = 73.2 bits (180), Expect = 4e-16
 Identities = 39/139 (28%), Positives = 58/139 (41%), Gaps = 16/139 (11%)

Query: 18  HYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETS 77
            + +KI +FS L   S+       FE GGYKW++ I+  G       D++S+YLEL +  
Sbjct: 2   KHTWKIVNFSELEGESIYS---PPFEVGGYKWRIRIYPNGDGESG--DYLSLYLELDKGE 56

Query: 78  SLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSK-YGVAKFIDLKTF 136
           S    W V A        +F   ++      S        F + K   +G  KFI     
Sbjct: 57  SDLEKWSVRA--------EFTLKLVNQNGGKSLSKSFTHVFFSEKGSGWGFPKFISWDDL 108

Query: 137 SDPLNGYLINDACVFGAEV 155
            D    YL++D+     EV
Sbjct: 109 EDS--YYLVDDSLTIEVEV 125

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

>gnl|CDD|238168 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

 Score = 42.6 bits (101), Expect = 5e-05
 Identities = 41/161 (25%), Positives = 59/161 (36%), Gaps = 44/161 (27%)

Query: 177 YHTWKVSNFSSLLDE-------------FYESESFGCYKWYANYSMDVKILLYPNGNGEA 223
              WK+ ++S  L E             FY S  +G YK        + + LY NG+G  
Sbjct: 2   VLIWKIKDYSRKLQEAVAGSNTVLYSPPFYTS-RYG-YK--------LCLRLYLNGDGTG 51

Query: 224 KGNCISLFLDVSQSS-----------------IPPNTKLLTKYFLCVENQMNGKNSEVEG 266
           KG  +SLF+ V +                   +  +     K+    E  M   NS    
Sbjct: 52  KGTHLSLFVHVMKGEYDALLEWPFRGKITLTLLDQSDDSKRKHI--TETFMPDPNSSAFQ 109

Query: 267 EWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEV 307
                  N   G  +F+ L KL+    GY+ DD+  IK EV
Sbjct: 110 RPPTGENNIGFGYPEFVPLEKLESR--GYVKDDTLFIKVEV 148

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-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors. Length = 149

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

 Score = 41.1 bits (97), Expect = 8e-05
 Identities = 25/119 (21%), Positives = 43/119 (36%), Gaps = 20/119 (16%)

Query: 40  DNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPT-GWEVNAITISFYSIKFK 98
              E  G  W+L I+  G         + +YL   +       GW +          +F 
Sbjct: 17  PYEERFGIPWRLRIYRNG-------GFLGLYLHCEKGEKDELLGWSIET--------EFT 61

Query: 99  TNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFV 157
             ++    ++ T       F      YG  KFI   ++ D  N Y+++D  +  AEV +
Sbjct: 62  LKLVSDNGKSLTKRNKSHVFTKPTG-YGWGKFI---SWDDLENDYVVDDTIIIEAEVKI 116

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

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

 Score = 41.2 bits (97), Expect = 1e-04
 Identities = 31/124 (25%), Positives = 59/124 (47%), Gaps = 24/124 (19%)

Query: 18  HYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLE----L 73
            + ++I+++S L K          F+ GG++W++ +   G+   + T  +SIYLE     
Sbjct: 2   SFTWRIKNWSELEKKVHS----PKFKCGGFEWRILLFPQGN---SQTGGVSIYLEPHPEE 54

Query: 74  AETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVI-VKH--FHAMKSKYGVAKF 130
            E + L   W V A        +F   +++S   + +I +  V H  F+A    +G  +F
Sbjct: 55  EEKAPLDEDWSVCA--------QFA--LVISNPGDPSIQLSNVAHHRFNAEDKDWGFTRF 104

Query: 131 IDLK 134
           I+L+
Sbjct: 105 IELR 108

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

>gnl|CDD|239742 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

 Score = 39.7 bits (93), Expect = 3e-04
 Identities = 31/101 (30%), Positives = 50/101 (49%), Gaps = 13/101 (12%)

Query: 212 KILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLLTKYFLCVE--NQMN-GKNSEVEGEW 268
           ++ +YP+GNGE +GN +S+FL++       +     KY   VE  +Q N  KN + E   
Sbjct: 37  RLKVYPDGNGEVRGNFLSVFLELCSGLGEAS-----KYEYRVEMVHQANPTKNIKREFAS 91

Query: 269 LYTLTNRAIGGRQFMTLAKLKDPTEGYLVD--DSCIIKAEV 307
            +       G  +F  L  L +  EGYL+   D+ I++  V
Sbjct: 92  DFE-VGECWGYNRFFRLDLLIN--EGYLLPENDTLILRFSV 129

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 in vitro, however, it is unclear whether this is physiologically relevant. Eleven TRIM37 mutations have been associated with Mulibrey nanism so far. One mutation, Gly322Val, is located in the MATH domain and is the only mutation that does not affect the length of the protein. It results in the incorrect subcellular localization of TRIM37. Length = 132

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

 Score = 36.1 bits (84), Expect = 0.003
 Identities = 23/112 (20%), Positives = 36/112 (32%), Gaps = 18/112 (16%)

Query: 21  FKIESFSLLSKASV-EQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSL 79
               +F  +S+    E     + E     W+L I+            +S+YL   +    
Sbjct: 1   VLSHTFKNVSRLEEGESYFSPSEEHFNIPWRLKIYRKN-------GFLSLYLHCEKEECD 53

Query: 80  PTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFI 131
              W + A          K   LVS+   S        F    S +G +KFI
Sbjct: 54  SRKWSIEA------EFTLK---LVSQNGKSLSKKDKHVFEK-PSGWGFSKFI 95

Length = 95

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	317
cd03772	137	MATH_HAUSP Herpesvirus-associated ubiquitin-specif	99.95
cd03775	134	MATH_Ubp21p Ubiquitin-specific protease 21 (Ubp21p	99.94
cd03774	139	MATH_SPOP Speckle-type POZ protein (SPOP) family,	99.94
cd03772	137	MATH_HAUSP Herpesvirus-associated ubiquitin-specif	99.94
cd03780	148	MATH_TRAF5 Tumor Necrosis Factor Receptor (TNFR)-A	99.93
cd03779	147	MATH_TRAF1 Tumor Necrosis Factor Receptor (TNFR) A	99.93
cd03777	186	MATH_TRAF3 Tumor Necrosis Factor Receptor (TNFR)-A	99.93
cd00270	149	MATH_TRAF_C Tumor Necrosis Factor Receptor (TNFR)-	99.92
cd03778	164	MATH_TRAF2 Tumor Necrosis Factor Receptor (TNFR) A	99.92
cd03776	147	MATH_TRAF6 Tumor Necrosis Factor Receptor (TNFR)-A	99.92
cd03773	132	MATH_TRIM37 Tripartite motif containing protein 37	99.92
cd03781	154	MATH_TRAF4 Tumor Necrosis Factor Receptor (TNFR)-A	99.92
cd03775	134	MATH_Ubp21p Ubiquitin-specific protease 21 (Ubp21p	99.91
cd03771	167	MATH_Meprin Meprin family, MATH domain; Meprins ar	99.91
cd03774	139	MATH_SPOP Speckle-type POZ protein (SPOP) family,	99.9
cd03773	132	MATH_TRIM37 Tripartite motif containing protein 37	99.88
cd03779	147	MATH_TRAF1 Tumor Necrosis Factor Receptor (TNFR) A	99.87
cd03778	164	MATH_TRAF2 Tumor Necrosis Factor Receptor (TNFR) A	99.87
cd03780	148	MATH_TRAF5 Tumor Necrosis Factor Receptor (TNFR)-A	99.87
cd00270	149	MATH_TRAF_C Tumor Necrosis Factor Receptor (TNFR)-	99.86
cd00121	126	MATH MATH (meprin and TRAF-C homology) domain; an	99.86
cd03776	147	MATH_TRAF6 Tumor Necrosis Factor Receptor (TNFR)-A	99.85
cd03783	167	MATH_Meprin_Alpha Meprin family, Alpha subunit, MA	99.85
cd03781	154	MATH_TRAF4 Tumor Necrosis Factor Receptor (TNFR)-A	99.85
cd03777	186	MATH_TRAF3 Tumor Necrosis Factor Receptor (TNFR)-A	99.85
cd03782	167	MATH_Meprin_Beta Meprin family, Beta subunit, MATH	99.84
cd00121	126	MATH MATH (meprin and TRAF-C homology) domain; an	99.83
PF00917	119	MATH: MATH domain; InterPro: IPR002083 Although ap	99.82
cd03771	167	MATH_Meprin Meprin family, MATH domain; Meprins ar	99.82
PF00917	119	MATH: MATH domain; InterPro: IPR002083 Although ap	99.79
smart00061	95	MATH meprin and TRAF homology.	99.71
cd03782	167	MATH_Meprin_Beta Meprin family, Beta subunit, MATH	99.65
cd03783	167	MATH_Meprin_Alpha Meprin family, Alpha subunit, MA	99.64
COG5077	1089	Ubiquitin carboxyl-terminal hydrolase [Posttransla	99.57
smart00061	95	MATH meprin and TRAF homology.	99.56
COG5077	1089	Ubiquitin carboxyl-terminal hydrolase [Posttransla	99.36
KOG1987	297	consensus Speckle-type POZ protein SPOP and relate	99.08
KOG1987	297	consensus Speckle-type POZ protein SPOP and relate	98.31
KOG1863	1093	consensus Ubiquitin carboxyl-terminal hydrolase [P	98.16
KOG1863	1093	consensus Ubiquitin carboxyl-terminal hydrolase [P	97.84
KOG0297	391	consensus TNF receptor-associated factor [Signal t	97.67
KOG0297	391	consensus TNF receptor-associated factor [Signal t	96.06

>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=99.95  E-value=1.6e-26  Score=185.42  Aligned_cols=132  Identities=17%  Similarity=0.291  Sum_probs=110.0

Q ss_pred             CcEEEEEEcCcccccccccceEEcccEEeCCeEEEEEEEecCCCCC-CCCCcEEEEEEeccCCCCCCCCEEEEEEEEEEE
Q 041904           16 PSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSV-NVTDHISIYLELAETSSLPTGWEVNAITISFYS   94 (317)
Q Consensus        16 ~~~~~w~I~~fs~~~~~~~~~~~S~~F~~gG~~W~l~~~p~G~~~~-~~~~~lSvyL~~~~~~~~~~~w~v~~~f~~~l~   94 (317)
                      .++|+|+|+|||.+    ++.++||.|.+||++|+|.+||+|.... +..+||||||.|.+.. ....|++.|+|+|.|+
T Consensus         2 ~~~~~~~I~~~S~l----~e~~~S~~f~vgG~~W~i~~~P~g~~~~~~~~~~lsvyL~~~~~~-~~~~w~i~a~~~~~l~   76 (137)
T cd03772           2 EATFSFTVERFSRL----SESVLSPPCFVRNLPWKIMVMPRNYPDRNPHQKSVGFFLQCNAES-DSTSWSCHAQAVLRII   76 (137)
T ss_pred             CcEEEEEECCcccC----CCcEECCCEEECCcceEEEEEeCCCCCCCCCCCeEEEEEeeCCcC-CCCCCeEEEEEEEEEE
Confidence            68999999999998    4689999999999999999999996532 2358999999997653 3347999999999999


Q ss_pred             ecCCCcEEEEEeeecccceeeeecccccccccccceeecccccCCCCceEeCCEEEEEEEEEEEe
Q 041904           95 IKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVK  159 (317)
Q Consensus        95 n~~~~~~~~~~~~~~~~~~~~~~F~~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v~~  159 (317)
                      |+.+......+.       ..+.|......|||++||++++|.++.+|||.||+|+|+|+|+|-.
T Consensus        77 ~~~~~~~~~~~~-------~~~~f~~~~~~~G~~~fi~~~~L~~~~sgyl~~D~l~Ie~~V~~~~  134 (137)
T cd03772          77 NYKDDEPSFSRR-------ISHLFFSKENDWGFSNFMTWSEVTDPEKGFIEDDTITLEVYVQADA  134 (137)
T ss_pred             cCCCCcccEEEe-------eeeEEcCCCCCccchheeEHHHhcCCCCCcEECCEEEEEEEEEeeC
Confidence            998543333222       4467876667999999999999987789999999999999998765

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=99.94  E-value=2.4e-26  Score=183.55  Aligned_cols=125  Identities=25%  Similarity=0.439  Sum_probs=105.7

Q ss_pred             EEEEEEcCcccccccccceEEcccEEeCCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC----CCCCCEEEEEEEEEE
Q 041904           18 HYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSS----LPTGWEVNAITISFY   93 (317)
Q Consensus        18 ~~~w~I~~fs~~~~~~~~~~~S~~F~~gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~----~~~~w~v~~~f~~~l   93 (317)
                      +|+|+|+|||.+    ++.+.|++|.+|||+|+|.+||+|+..   .+|+|+||++.....    .+.+|++.|+|+|.|
T Consensus         2 ~f~w~I~~fS~~----~~~~~S~~F~vGG~~W~l~~yP~G~~~---~~~iSlyL~l~~~~~~~~~~~~~~~v~a~f~~~l   74 (134)
T cd03775           2 SFTWRIKNWSEL----EKKVHSPKFKCGGFEWRILLFPQGNSQ---TGGVSIYLEPHPEEEEKAPLDEDWSVCAQFALVI   74 (134)
T ss_pred             cEEEEECCcccC----CcceeCCCEEECCeeEEEEEeCCCCCC---CCeEEEEEEecCcccccccCCCCCeEEEEEEEEE
Confidence            599999999997    468999999999999999999999753   689999999976443    256899999999999


Q ss_pred             EecCCCcEEEEEeeecccceeeeecccccccccccceeecccccCC----CCceEeCCEEEEEEEEE
Q 041904           94 SIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDP----LNGYLINDACVFGAEVF  156 (317)
Q Consensus        94 ~n~~~~~~~~~~~~~~~~~~~~~~F~~~~~~~G~~~fi~~~~l~~~----~~~yl~~d~l~i~~~v~  156 (317)
                      +||.++.....+.       ..+.|+....+|||.+||++++|++|    ++|||+||+|+|+|.|+
T Consensus        75 ~n~~~~~~~~~~~-------~~~~F~~~~~~wG~~~fi~~~~L~~~~~~~~~g~l~nD~l~I~~~~~  134 (134)
T cd03775          75 SNPGDPSIQLSNV-------AHHRFNAEDKDWGFTRFIELRKLAHRTPDKPSPFLENGELNITVYVR  134 (134)
T ss_pred             EcCCCCccceEcc-------ceeEeCCCCCCCChhHcccHHHHcccccCCCCceeECCEEEEEEEEC
Confidence            9997655443322       56789877789999999999999854    57999999999999874

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=99.94  E-value=7.1e-26  Score=182.10  Aligned_cols=134  Identities=25%  Similarity=0.291  Sum_probs=109.9

Q ss_pred             cCCcEEEEEEcCcccccccccceEEcccEEeCC---eEEEEEEEecCCCCCCCCCcEEEEEEeccCCCCCCCCEEEEEEE
Q 041904           14 AAPSHYLFKIESFSLLSKASVEQLILDNFEAGG---YKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAITI   90 (317)
Q Consensus        14 ~~~~~~~w~I~~fs~~~~~~~~~~~S~~F~~gG---~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~~~~w~v~~~f~   90 (317)
                      ....+|+|+|+|||.+++..++.+.|++|.+||   ++|+|.+||+|...+ +.+|+|+||++.+..    .+++.|+|+
T Consensus         2 ~~~~~~~w~I~~fS~~~~~~~~~i~S~~F~vgg~~~~~W~l~~yP~G~~~~-~~~~iSlyL~l~~~~----~~~v~a~f~   76 (139)
T cd03774           2 VVKFCYMWTISNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEE-SKDYLSLYLLLVSCP----KSEVRAKFK   76 (139)
T ss_pred             ceEEEEEEEECCchhhhhcCCCEEECCCeecCCcCCceEEEEEeCCCCCCC-CCCeEEEEEEEccCC----CCcEEEEEE
Confidence            346789999999999865457899999999998   499999999998643 578999999997532    357999999


Q ss_pred             EEEEecCCCcEEEEEeeecccceeeeecccccccccccceeecccccCCCCceEeCCEEEEEEEEEEEe
Q 041904           91 SFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVK  159 (317)
Q Consensus        91 ~~l~n~~~~~~~~~~~~~~~~~~~~~~F~~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v~~  159 (317)
                      |.|+||.+.+.......      ..+.|.. ..+|||.+|+++++|.++.+|||.||+|+|+|+|+|++
T Consensus        77 ~~l~n~~~~~~~~~~~~------~~~~f~~-~~~wG~~~fi~~~~L~~~~~g~l~dD~l~I~c~I~V~~  138 (139)
T cd03774          77 FSILNAKGEETKAMESQ------RAYRFVQ-GKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQ  138 (139)
T ss_pred             EEEEecCCCeeeeeccc------CcEeCCC-CCccCHHHeeeHHHhhhhhcccccCCEEEEEEEEEEEc
Confidence            99999987654332221      3466764 47899999999999987778999999999999999975

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

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

Probab=99.94  E-value=2.4e-25  Score=178.54  Aligned_cols=128  Identities=20%  Similarity=0.314  Sum_probs=107.9

Q ss_pred             CceEEEEEecccccccceeecccc--cceEeeeccCCceEEEEecCCCCC--CCCCeEEEEEEccCCCCCCCCeEEEEEE
Q 041904          175 TYYHTWKVSNFSSLLDEFYESESF--GCYKWYANYSMDVKILLYPNGNGE--AKGNCISLFLDVSQSSIPPNTKLLTKYF  250 (317)
Q Consensus       175 ~~~~~~~i~nfs~~~~~~~~S~~f--~g~~W~~~~~~~~~i~~yp~g~~~--~~~~~lS~yL~~~~~~~~~~~~~~~~~~  250 (317)
                      .++++|+|+|||.+ ++.+.|+.|  ||++|        +|.+||+|+..  +..++|||||.|........|++.|+|+
T Consensus         2 ~~~~~~~I~~~S~l-~e~~~S~~f~vgG~~W--------~i~~~P~g~~~~~~~~~~lsvyL~~~~~~~~~~w~i~a~~~   72 (137)
T cd03772           2 EATFSFTVERFSRL-SESVLSPPCFVRNLPW--------KIMVMPRNYPDRNPHQKSVGFFLQCNAESDSTSWSCHAQAV   72 (137)
T ss_pred             CcEEEEEECCcccC-CCcEECCCEEECCcce--------EEEEEeCCCCCCCCCCCeEEEEEeeCCcCCCCCCeEEEEEE
Confidence            47899999999998 678999999  99999        99999999654  2358999999965444445899999999


Q ss_pred             EEEEECCCCC-ceeeeeeEEeeCCCCCccccccccccccCCCCCCceeCCEEEEEEEEEEEe
Q 041904          251 LCVENQMNGK-NSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHG  311 (317)
Q Consensus       251 l~l~n~~~~~-~~~~~~~~~F~~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v~~  311 (317)
                      |+|+||.+.. .......+.|.....+|||++||+|++|+++++|||+||+|+|||+|+|-.
T Consensus        73 ~~l~~~~~~~~~~~~~~~~~f~~~~~~~G~~~fi~~~~L~~~~sgyl~~D~l~Ie~~V~~~~  134 (137)
T cd03772          73 LRIINYKDDEPSFSRRISHLFFSKENDWGFSNFMTWSEVTDPEKGFIEDDTITLEVYVQADA  134 (137)
T ss_pred             EEEEcCCCCcccEEEeeeeEEcCCCCCccchheeEHHHhcCCCCCcEECCEEEEEEEEEeeC
Confidence            9999998533 334455678976668999999999999987778999999999999998864

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

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

Probab=99.93  E-value=1.1e-25  Score=181.29  Aligned_cols=136  Identities=14%  Similarity=0.222  Sum_probs=107.2

Q ss_pred             cEEEEEEcCcccccc--cccc--eEEcccE--EeCCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC-CCCCCEEEEEE
Q 041904           17 SHYLFKIESFSLLSK--ASVE--QLILDNF--EAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSS-LPTGWEVNAIT   89 (317)
Q Consensus        17 ~~~~w~I~~fs~~~~--~~~~--~~~S~~F--~~gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~-~~~~w~v~~~f   89 (317)
                      |+|.|+|++|+++++  +.|.  .++||+|  .++||+|+|++||||...+ .++||||||+++++.. ..++|++.+++
T Consensus         1 g~~vwkI~~ys~~~~~~~~g~~~~i~S~~Fyt~~~Gy~w~i~~ypnG~~~~-~~~~iSv~l~l~~g~~D~~l~wp~~~~~   79 (148)
T cd03780           1 GKLIWKVTDYKMKKKEAVDGHTVSIFSQPFYTSRCGYRLCARAYLNGDGSG-KGTHLSLYFVVMRGEFDSLLQWPFRQRV   79 (148)
T ss_pred             CEEEEEECCHHHHHHhhcCCCccEEECCCcccCCCCeeEEEEEEcCCCCCC-CCCEEEEEEEEecCccccccCcceEEEE
Confidence            689999999999975  3556  8999999  7899999999999998763 6789999999998755 35789999999


Q ss_pred             EEEEEecCCCcEEEEEeeecccceeeeecccc----cccccccceeecccccCCCCceEeCCEEEEEEEE
Q 041904           90 ISFYSIKFKTNILVSKVRNSTINVIVKHFHAM----KSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEV  155 (317)
Q Consensus        90 ~~~l~n~~~~~~~~~~~~~~~~~~~~~~F~~~----~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v  155 (317)
                      +|.|+||.+.+.... .+.. .++..+.|+..    +..||+++||++++|+..+++||+||+|+|+|.|
T Consensus        80 tfsLlDq~~~~~~~~-~~~~-~~~~~~~F~rp~~~~n~~~G~~~Fi~~~~Le~s~~~ylkdD~~~Ik~~v  147 (148)
T cd03780          80 TLMLLDQSGKKNHIM-ETFK-ADPNSSSFKRPDGEMNIASGCPRFVAHSVLENAKNTYIKDDTLFLKVAV  147 (148)
T ss_pred             EEEEECCCCCCCCcc-eeee-cCCccccccCCCCCCCCCcChhheeEHHHhhcccCCcCcCCEEEEEEEE
Confidence            999999975443211 1000 00123557543    5579999999999998444599999999999987

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

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

Probab=99.93  E-value=2.6e-25  Score=178.24  Aligned_cols=136  Identities=20%  Similarity=0.289  Sum_probs=105.5

Q ss_pred             cEEEEEEcCcccccc-c---ccceEEcccEEeC--CeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC-CCCCCEEEEEE
Q 041904           17 SHYLFKIESFSLLSK-A---SVEQLILDNFEAG--GYKWKLSIHLTGSKSVNVTDHISIYLELAETSS-LPTGWEVNAIT   89 (317)
Q Consensus        17 ~~~~w~I~~fs~~~~-~---~~~~~~S~~F~~g--G~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~-~~~~w~v~~~f   89 (317)
                      |+|.|+|+||+++++ .   ....++||+|+.+  ||+|+|.+||||.+.+ .++|+|+||+++++.. ..++|++.+++
T Consensus         1 g~~~W~i~~f~~~~~~a~~~~~~~~~S~~Fyt~~~Gy~w~i~~ypnG~~~~-~~~~iSv~l~l~~g~~D~~l~wpv~~~~   79 (147)
T cd03779           1 GTFLWKITDVSQKQRESSHGRDVSLCSPAFYTAKYGYKVCLRLYLNGDGAG-KGTHISLFFVIMKGEYDALLPWPFRHKV   79 (147)
T ss_pred             CeEEEEECcHHHHHHHHhcCCCceEECCCcccCCCCceEEEEEEcCCCCCC-CCCEEEEEEEEecCCcccccCcceEEEE
Confidence            689999999998766 2   2347999999986  9999999999998864 6789999999998643 35689999999


Q ss_pred             EEEEEecCCCcEEEEEeeecccceeeeecc----cccccccccceeecccccCCCCceEeCCEEEEEEEEE
Q 041904           90 ISFYSIKFKTNILVSKVRNSTINVIVKHFH----AMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVF  156 (317)
Q Consensus        90 ~~~l~n~~~~~~~~~~~~~~~~~~~~~~F~----~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~  156 (317)
                      +|.|+||.+.+.......  + +...+.|+    ..+..||+++||++++|+...++||+||+++|+|+|.
T Consensus        80 tfsLlDq~~~~~~~~~~~--~-~~~~~~F~rP~~~~n~~~G~~~Fi~~~~Le~s~~~ylkDD~~~Irc~V~  147 (147)
T cd03779          80 TFMLLDQNNREHVIDAFR--P-DLSSASFQRPVSDMNVASGCPLFFPLKKLQSPKHAYCKDDTIYIKCVVD  147 (147)
T ss_pred             EEEEECCCCCCCCcEeec--C-CcccccccCcccCCCCCcchhheeEHHHhcccCCCcEeCCEEEEEEEEC
Confidence            999999975443211000  0 00135686    4456799999999999983224999999999999973

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

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

Probab=99.93  E-value=5.6e-25  Score=183.33  Aligned_cols=139  Identities=14%  Similarity=0.157  Sum_probs=109.2

Q ss_pred             ccCCcEEEEEEcCcccccc--cccc--eEEcccEEeC--CeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC-CCCCCEE
Q 041904           13 NAAPSHYLFKIESFSLLSK--ASVE--QLILDNFEAG--GYKWKLSIHLTGSKSVNVTDHISIYLELAETSS-LPTGWEV   85 (317)
Q Consensus        13 ~~~~~~~~w~I~~fs~~~~--~~~~--~~~S~~F~~g--G~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~-~~~~w~v   85 (317)
                      ....|+|.|+|+|||.+++  +.|+  .++||+|++|  ||+|+|.+||||.+.+ .++|||+||+++++.. ..++|++
T Consensus        35 ~~~~G~hvwkI~~yS~~~~~~~~g~~~~i~S~~Fyvg~~GY~w~i~~ypnG~g~~-~~~~iSvyl~L~~ge~D~~L~WP~  113 (186)
T cd03777          35 ASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMG-KGTHLSLFFVIMRGEYDALLPWPF  113 (186)
T ss_pred             cccceEEEEEECChhHHHHhhccCCCcEEECCCeEeCCCCeeEEEEEEcCCCCCC-CCCEEEEEEEEecCCcccccCCce
Confidence            4457999999999999875  3445  7999999999  9999999999998763 6789999999998754 3668999


Q ss_pred             EEEEEEEEEecCCCcEEEEEeeecccceeeeecc-cc---cccccccceeecccccCCCCceEeCCEEEEEEEEE
Q 041904           86 NAITISFYSIKFKTNILVSKVRNSTINVIVKHFH-AM---KSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVF  156 (317)
Q Consensus        86 ~~~f~~~l~n~~~~~~~~~~~~~~~~~~~~~~F~-~~---~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~  156 (317)
                      .++|+|.|+||.+...... +...+. +....|+ ..   +.+||+++||++++|+  .++||+||+|+|+|.|.
T Consensus       114 ~~~~tfsLlDQ~~~~~~~~-~~~~p~-p~~~~F~rp~~~~n~~~G~~~Fi~~~~Le--~~~ylkdD~l~Irv~v~  184 (186)
T cd03777         114 KQKVTLMLMDQGSSRRHLG-DAFKPD-PNSSSFKKPTGEMNIASGCPVFVAQTVLE--NGTYIKDDTIFIKVIVD  184 (186)
T ss_pred             eEEEEEEEEcCCCcccccc-ceeccC-CccccccCCccCCCCCCCchheeEHHHhc--cCCcEeCCEEEEEEEEe
Confidence            9999999999975322221 100000 1224575 22   4579999999999998  68899999999999886

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

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

Probab=99.92  E-value=1.1e-24  Score=177.24  Aligned_cols=135  Identities=18%  Similarity=0.261  Sum_probs=104.7

Q ss_pred             cEEEEEEcCcccccc----cccceEEcccEEeC--CeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC-CCCCCEEEEEE
Q 041904           17 SHYLFKIESFSLLSK----ASVEQLILDNFEAG--GYKWKLSIHLTGSKSVNVTDHISIYLELAETSS-LPTGWEVNAIT   89 (317)
Q Consensus        17 ~~~~w~I~~fs~~~~----~~~~~~~S~~F~~g--G~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~-~~~~w~v~~~f   89 (317)
                      |+|+|+|++||.+++    ..++.++||+|++|  ||+|+|.+||+|...+ .++||||||++.+... ..++|++.++|
T Consensus         1 g~~~w~I~~fs~~~~~~~~~~~~~~~S~~F~vg~~G~~w~i~~yP~G~~~~-~~~~lsl~L~l~~~~~d~~~~w~~~~~~   79 (149)
T cd00270           1 GVLIWKIKDYSRKLQEAVAGSNTVLYSPPFYTSRYGYKLCLRLYLNGDGTG-KGTHLSLFVHVMKGEYDALLEWPFRGKI   79 (149)
T ss_pred             CEEEEEECCHHHHHHHHhcCCCceEECCCcccCCCCceEEEEEEeCCCCCC-CCCEEEEEEEEeccCCCccccCCccceE
Confidence            689999999999865    24679999999999  9999999999998653 5689999999988654 35789999999


Q ss_pred             EEEEEecCCC--cEEEEEeeecccceeeeecc-----cccccccccceeecccccCCCCceEeCCEEEEEEEEE
Q 041904           90 ISFYSIKFKT--NILVSKVRNSTINVIVKHFH-----AMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVF  156 (317)
Q Consensus        90 ~~~l~n~~~~--~~~~~~~~~~~~~~~~~~F~-----~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~  156 (317)
                      +|.|+||.++  ..+.....  ........|.     ....+|||.+|+++++|+  +.|||+||+|+|+|+|.
T Consensus        80 ~~~l~d~~~~~~~~~~~~~~--~~~~~~~~f~~~~~~~~~~~~G~~~fi~~~~L~--~~gfl~dD~l~I~~~v~  149 (149)
T cd00270          80 TLTLLDQSDDSKRKHITETF--MPDPNSSAFQRPPTGENNIGFGYPEFVPLEKLE--SRGYVKDDTLFIKVEVD  149 (149)
T ss_pred             EEEEECCCCccccCceEEEE--EcCCchHhhcCCCcccCCCCcCcceEeEHHHhc--cCCCEeCCEEEEEEEEC
Confidence            9999999874  22211110  0000123454     145789999999999998  46899999999999973

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

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

Probab=99.92  E-value=1.8e-24  Score=175.12  Aligned_cols=145  Identities=18%  Similarity=0.257  Sum_probs=110.7

Q ss_pred             CceeeccccCCcEEEEEEcCcccccc--c--ccceEEcccEEe--CCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCCC
Q 041904            6 GAVLAGRNAAPSHYLFKIESFSLLSK--A--SVEQLILDNFEA--GGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSL   79 (317)
Q Consensus         6 ~~~~~~~~~~~~~~~w~I~~fs~~~~--~--~~~~~~S~~F~~--gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~   79 (317)
                      .+.+-......|+|.|+|.||+++++  .  ....++||+|+.  +||+|+|++||||++. +.+.|||+||+++++..+
T Consensus         8 ~~~~l~~~~~~g~fiWkI~~fs~~~~~a~~~~~~~i~Sp~Fyt~~~GYk~~l~~ylnG~g~-~~g~~LSly~~l~~Ge~D   86 (164)
T cd03778           8 KVLEXEASTYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGT-GRGTHLSLFFVVMKGPND   86 (164)
T ss_pred             HhhhccccccCCEEEEEECcHHHHHHHHhcCCCceEECCCcccCCCCeEEEEEEEeCCCCC-CCCCEEEEEEEEecCCcC
Confidence            33333334568999999999999876  1  234899999997  4999999999999876 367899999999999886


Q ss_pred             C-CCCEEEEEEEEEEEecCCCcEEEEEeeecccceeeeec----ccccccccccceeecccccCCCCceEeCCEEEEEEE
Q 041904           80 P-TGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHF----HAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAE  154 (317)
Q Consensus        80 ~-~~w~v~~~f~~~l~n~~~~~~~~~~~~~~~~~~~~~~F----~~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~  154 (317)
                      . ++|++..+++|.|+||++.....  ++..++ .....|    +..+.+||++.|+++++|..+ ++||+||+|.|+|.
T Consensus        87 ~~L~WPf~~~itl~llDQ~~r~hi~--~~~~pd-~~~~~f~RP~~~~n~~~G~~~Fv~l~~l~~~-~~Yv~dDtlfIk~~  162 (164)
T cd03778          87 ALLRWPFNQKVTLMLLDQNNREHVI--DAFRPD-VTSSSFQRPVNDMNIASGCPLFCPVSKXEAK-NSYVRDDAIFIKAI  162 (164)
T ss_pred             cccCCceeeEEEEEEECCCCCCcce--eEEEcC-cchHhcCCCCcccccCcCcceEEEhhHcccc-CCcccCCeEEEEEE
Confidence            4 89999999999999997533222  110000 011235    234567999999999999742 69999999999998


Q ss_pred             E
Q 041904          155 V  155 (317)
Q Consensus       155 v  155 (317)
                      |
T Consensus       163 V  163 (164)
T cd03778         163 V  163 (164)
T ss_pred             E
Confidence            7

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

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

Probab=99.92  E-value=1e-24  Score=176.91  Aligned_cols=135  Identities=17%  Similarity=0.269  Sum_probs=104.1

Q ss_pred             cEEEEEEcCcccccc--cccc--eEEcccEEe--CCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC-CCCCCEEEEEE
Q 041904           17 SHYLFKIESFSLLSK--ASVE--QLILDNFEA--GGYKWKLSIHLTGSKSVNVTDHISIYLELAETSS-LPTGWEVNAIT   89 (317)
Q Consensus        17 ~~~~w~I~~fs~~~~--~~~~--~~~S~~F~~--gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~-~~~~w~v~~~f   89 (317)
                      |+|.|+|.+||.+++  ..++  .++||+|++  |||+|+|.+||+|...+ ..+|||+||++++... ..++|++.++|
T Consensus         1 g~h~~~I~~yS~~~~~~~~g~~~~i~S~~F~~~~gGy~W~i~~yP~G~~~~-~~~~lS~~L~l~~~~~d~~l~wpv~a~~   79 (147)
T cd03776           1 GIYVWKIKNFSNLRRSMEAGSPVVIHSPGFYTSPPGYKLCARLNLSLPEAR-CPNYISLFVHLMQGENDSHLDWPFQGTI   79 (147)
T ss_pred             CEEEEEECCHHHHHHHHhcCCCceEECCCcccCCCCceEEEEEEeCCCCCC-CCCEEEEEEEEeccCCCcccCCccccee
Confidence            689999999998654  3455  488999996  79999999999998763 5789999999988654 35689999999


Q ss_pred             EEEEEecCCCcEEEEEeeecccceeeeeccc-----ccccccccceeecccccCCCCceEeCCEEEEEEEEE
Q 041904           90 ISFYSIKFKTNILVSKVRNSTINVIVKHFHA-----MKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVF  156 (317)
Q Consensus        90 ~~~l~n~~~~~~~~~~~~~~~~~~~~~~F~~-----~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~  156 (317)
                      +|.|+||.++........ . .......|..     ...+|||.+||++++|+  +.+||+||+|+|+|+|.
T Consensus        80 ~~~lldq~~~~~~~~~~~-~-~~~~~~~F~~p~~~~~~~~~G~~~fi~~~~Le--~~~yl~dD~l~I~c~V~  147 (147)
T cd03776          80 TLTLLDQSEPRQNIHETM-M-SKPELLAFQRPTTDRNPKGFGYVEFAHIEDLL--QRGFVKNDTLLIKIEVN  147 (147)
T ss_pred             EEEEECCCcccCccEEEE-E-cCCChHhhcCCCcCCCCCCeeEceeeEHHHhh--hCCCccCCEEEEEEEEC
Confidence            999999986433221110 0 0012245652     34679999999999998  56899999999999984

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

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

Probab=99.92  E-value=2.3e-24  Score=171.84  Aligned_cols=127  Identities=20%  Similarity=0.329  Sum_probs=104.1

Q ss_pred             cCCcEEEEEEcCcccccccccceEEcccEEeCCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCCCCCCCEEEEEEEEEE
Q 041904           14 AAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAITISFY   93 (317)
Q Consensus        14 ~~~~~~~w~I~~fs~~~~~~~~~~~S~~F~~gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~~~~w~v~~~f~~~l   93 (317)
                      ++.++++|+|.|||.+++ .++.++|++|.+|||+|+|.+||+|...+ .++|||+||++...    ..|.+.++|+|.|
T Consensus         2 ~~~~~~~~~I~~fS~~~~-~~~~~~S~~F~vgG~~W~i~~yP~G~~~~-~~~~lSl~L~l~~~----~~~~~~~~~~l~l   75 (132)
T cd03773           2 PPYDSATFTLENFSTLRQ-SADPVYSDPLNVDGLCWRLKVYPDGNGEV-RGNFLSVFLELCSG----LGEASKYEYRVEM   75 (132)
T ss_pred             CCCcccEEEECChhhhhc-CCcceeCCCeEeCCccEEEEEECCCCCCC-CCCEEEEEEEeecC----CCCceeEEEEEEE
Confidence            567889999999999864 46899999999999999999999998653 56899999998763    2367888999999


Q ss_pred             EecCCCcEEEEEeeecccceeeeecccccccccccceeecccccCCCCceEeC--CEEEEEEEEE
Q 041904           94 SIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLIN--DACVFGAEVF  156 (317)
Q Consensus        94 ~n~~~~~~~~~~~~~~~~~~~~~~F~~~~~~~G~~~fi~~~~l~~~~~~yl~~--d~l~i~~~v~  156 (317)
                      +||.++.......       ..+.|.. ..+|||.+|+++++|.  ++|||.|  |+|+|+|.|+
T Consensus        76 lnq~~~~~~~~~~-------~~~~f~~-~~~wG~~~Fi~~~~L~--~~gfl~~~~D~l~i~~~v~  130 (132)
T cd03773          76 VHQANPTKNIKRE-------FASDFEV-GECWGYNRFFRLDLLI--NEGYLLPENDTLILRFSVR  130 (132)
T ss_pred             EcCCCCccceEEe-------ccccccC-CCCcCHHHhccHHHHh--hCCCcCCCCCEEEEEEEEe
Confidence            9995433333222       4566764 4679999999999997  5899999  9999999986

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

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

Probab=99.92  E-value=2.3e-24  Score=175.89  Aligned_cols=136  Identities=21%  Similarity=0.247  Sum_probs=105.3

Q ss_pred             cEEEEEEcCcccccc---c-ccceEEcccEEeC--CeEEEEEEEecCCCCCCCCCcEEEEEEeccCCCC-CCCCEEEEEE
Q 041904           17 SHYLFKIESFSLLSK---A-SVEQLILDNFEAG--GYKWKLSIHLTGSKSVNVTDHISIYLELAETSSL-PTGWEVNAIT   89 (317)
Q Consensus        17 ~~~~w~I~~fs~~~~---~-~~~~~~S~~F~~g--G~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~-~~~w~v~~~f   89 (317)
                      |+|.|+|.+||.+++   . .++.+.|++|++|  ||+|+|.+||||...+ .++|||+||+++++... .++|++.++|
T Consensus         1 g~~~~~I~gys~~~~~~~~~~~~~i~S~~F~vg~~Gy~w~i~~yPnG~~~~-~~~~vs~~l~l~~ge~d~~l~wp~~a~~   79 (154)
T cd03781           1 GTLLWKITDYSRKLQEAKGRDNLELFSPPFYTHRYGYKLQVSAFLNGNGSG-EGSHLSVYIRVLPGEYDNLLEWPFSHRI   79 (154)
T ss_pred             CEEEEEECCHHHHHHHhhcCCCceEECCCeecCCCCEEEEEEEECCCCCCC-CCCEEEEEEEEecCCcccccCCceeeEE
Confidence            689999999999875   2 3578999999999  9999999999998764 67899999999986543 3689999999


Q ss_pred             EEEEEecCCC--cEE-EEEeeecccceeeeecc--------cccccccccceeecccccCCCCceEeCCEEEEEEEEE
Q 041904           90 ISFYSIKFKT--NIL-VSKVRNSTINVIVKHFH--------AMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVF  156 (317)
Q Consensus        90 ~~~l~n~~~~--~~~-~~~~~~~~~~~~~~~F~--------~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~  156 (317)
                      +|+|+||.+.  ... ...... ..+.....|+        ..+.+||+..||++++|+  +.+||+||+|+|+|+|.
T Consensus        80 ~~~llDq~~~~~~~~~~~~~~~-~~~~~~~~F~rp~~~~~~~~~~~~G~~~fi~~~~Le--~~~yl~dD~l~Irc~v~  154 (154)
T cd03781          80 TFTLLDQSDPSLSKPQHITETF-TPDPTWKNFQKPSASRLDESTLGFGYPKFISHEDLK--KRNYIKDDAIFLRASVE  154 (154)
T ss_pred             EEEEECCCCCccccCcceEEEE-EcCCchhhhcCCcccccCCCCCccchhHeeEHHHHh--hCCcccCCEEEEEEEeC
Confidence            9999999764  111 110100 0001234455        234579999999999998  67899999999999873

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

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

Probab=99.91  E-value=6.5e-24  Score=169.47  Aligned_cols=121  Identities=22%  Similarity=0.461  Sum_probs=102.5

Q ss_pred             eEEEEEecccccccceeecccc--cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccCCC----CCCCCeEEEEE
Q 041904          177 YHTWKVSNFSSLLDEFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQSS----IPPNTKLLTKY  249 (317)
Q Consensus       177 ~~~~~i~nfs~~~~~~~~S~~f--~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~~~----~~~~~~~~~~~  249 (317)
                      +++|+|.|||.+ ++.+.|+.|  |||+|        +|.+||+|+..  .+|+|+||. .+...    .+..|.+.|+|
T Consensus         2 ~f~w~I~~fS~~-~~~~~S~~F~vGG~~W--------~l~~yP~G~~~--~~~iSlyL~l~~~~~~~~~~~~~~~v~a~f   70 (134)
T cd03775           2 SFTWRIKNWSEL-EKKVHSPKFKCGGFEW--------RILLFPQGNSQ--TGGVSIYLEPHPEEEEKAPLDEDWSVCAQF   70 (134)
T ss_pred             cEEEEECCcccC-CcceeCCCEEECCeeE--------EEEEeCCCCCC--CCeEEEEEEecCcccccccCCCCCeEEEEE
Confidence            589999999996 578999999  99999        99999999865  689999999 44433    25789999999


Q ss_pred             EEEEEECCCCCc-eeeeeeEEeeCCCCCccccccccccccCCC----CCCceeCCEEEEEEEEE
Q 041904          250 FLCVENQMNGKN-SEVEGEWLYTLTNRAIGGRQFMTLAKLKDP----TEGYLVDDSCIIKAEVT  308 (317)
Q Consensus       250 ~l~l~n~~~~~~-~~~~~~~~F~~~~~~~G~~~fi~~~~L~~~----~~gyl~dd~l~i~~~V~  308 (317)
                      +|.|+||.++.. ......+.|+....+|||.+||++++|++|    ++|||+||+|+|+|.|.
T Consensus        71 ~~~l~n~~~~~~~~~~~~~~~F~~~~~~wG~~~fi~~~~L~~~~~~~~~g~l~nD~l~I~~~~~  134 (134)
T cd03775          71 ALVISNPGDPSIQLSNVAHHRFNAEDKDWGFTRFIELRKLAHRTPDKPSPFLENGELNITVYVR  134 (134)
T ss_pred             EEEEEcCCCCccceEccceeEeCCCCCCCChhHcccHHHHcccccCCCCceeECCEEEEEEEEC
Confidence            999999976542 334557899877789999999999999954    57999999999999873

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.

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

Probab=99.91  E-value=7.5e-24  Score=172.87  Aligned_cols=136  Identities=14%  Similarity=0.193  Sum_probs=103.2

Q ss_pred             CcEEEEEEcCcccccc--cccceEEcccE-EeCCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC-CCCCCE-EEEEEE
Q 041904           16 PSHYLFKIESFSLLSK--ASVEQLILDNF-EAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSS-LPTGWE-VNAITI   90 (317)
Q Consensus        16 ~~~~~w~I~~fs~~~~--~~~~~~~S~~F-~~gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~-~~~~w~-v~~~f~   90 (317)
                      |+.|.|+|.|||.+++  +.++.++||+| .+|||+|+|++||+|...  .++||||||+++++.. ..++|+ +.++++
T Consensus         1 cp~hvwkI~~yS~~~~~~~~g~~i~S~~FysvgGy~w~I~~YPnG~~~--~~~~lSlyL~L~~g~~d~~L~WP~v~a~~t   78 (167)
T cd03771           1 CPEAVWRVRNFSQLLETTPKGTKIYSPRFYSPEGYAFQVGLYPNGTES--YPGYTGLYFHLCSGENDDVLEWPCPNRQAT   78 (167)
T ss_pred             CCeEEEEEcCchhhhhcCCCCCEEECCCCCccCCeEEEEEEEeCCCCC--CCCcceEEEEEecCCccccccCcceeEEEE
Confidence            6789999999999963  45789999999 889999999999999875  4689999999988654 478899 589999


Q ss_pred             EEEEecCCC---cEEEEEeeecccc------eeeeecc----------c-------ccccccccceeecccccCCCCceE
Q 041904           91 SFYSIKFKT---NILVSKVRNSTIN------VIVKHFH----------A-------MKSKYGVAKFIDLKTFSDPLNGYL  144 (317)
Q Consensus        91 ~~l~n~~~~---~~~~~~~~~~~~~------~~~~~F~----------~-------~~~~~G~~~fi~~~~l~~~~~~yl  144 (317)
                      |.|+||...   ..+.... ..++.      .....|+          .       .+.+|||+.||++++|.  .++||
T Consensus        79 ~~LlDQ~~~~~~r~~~~~~-~~~dp~~~~~~~~~~~~~rP~~~~~~~~~~~~~~~~~~~g~G~~~Fis~~~L~--~r~yl  155 (167)
T cd03771          79 MTLLDQDPDIQQRMSNQRS-FTTDPSMTSSDNGEYFWDRPSKVGSYDTDTNGCTCYRGPGYGWSTFISHSRLR--RRDFL  155 (167)
T ss_pred             EEEECCCCcccccCcceEE-EecCCcccccccccccccCCccccccccccccccccccCccccccceeHHHhc--cCCCC
Confidence            999999731   1122110 00000      0111122          1       34589999999999998  57799


Q ss_pred             eCCEEEEEEEEE
Q 041904          145 INDACVFGAEVF  156 (317)
Q Consensus       145 ~~d~l~i~~~v~  156 (317)
                      +||+|.|++++.
T Consensus       156 k~dtl~i~~~~~  167 (167)
T cd03771         156 KGDDLIILLDFE  167 (167)
T ss_pred             cCCEEEEEEEeC
Confidence            999999999873

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=99.90  E-value=3.8e-23  Score=166.23  Aligned_cols=126  Identities=24%  Similarity=0.436  Sum_probs=103.4

Q ss_pred             CCceEEEEEecccccc---cceeecccc--cc---eEeeeccCCceEEEEecCCCCCCCCCeEEEEEEccCCCCCCCCeE
Q 041904          174 PTYYHTWKVSNFSSLL---DEFYESESF--GC---YKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKL  245 (317)
Q Consensus       174 ~~~~~~~~i~nfs~~~---~~~~~S~~f--~g---~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~~~~~~~~~~~~~  245 (317)
                      ...+|+|+|+|||.++   ++.+.|+.|  ||   ++|        +|.+||+|...+..+|+||||++...   ..+++
T Consensus         3 ~~~~~~w~I~~fS~~~~~~~~~i~S~~F~vgg~~~~~W--------~l~~yP~G~~~~~~~~iSlyL~l~~~---~~~~v   71 (139)
T cd03774           3 VKFCYMWTISNFSFCREEMGEVIKSSTFSSGANDKLKW--------CLRVNPKGLDEESKDYLSLYLLLVSC---PKSEV   71 (139)
T ss_pred             eEEEEEEEECCchhhhhcCCCEEECCCeecCCcCCceE--------EEEEeCCCCCCCCCCeEEEEEEEccC---CCCcE
Confidence            4578999999999874   678999999  77   599        99999999876667899999994221   24579


Q ss_pred             EEEEEEEEEECCCCCcee--eeeeEEeeCCCCCccccccccccccCCCCCCceeCCEEEEEEEEEEEe
Q 041904          246 LTKYFLCVENQMNGKNSE--VEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHG  311 (317)
Q Consensus       246 ~~~~~l~l~n~~~~~~~~--~~~~~~F~~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v~~  311 (317)
                      .|+|+|.|+||.++....  ....+.|.. ..+|||.+||++++|+++.+|||+||+|+|+|+|+|++
T Consensus        72 ~a~f~~~l~n~~~~~~~~~~~~~~~~f~~-~~~wG~~~fi~~~~L~~~~~g~l~dD~l~I~c~I~V~~  138 (139)
T cd03774          72 RAKFKFSILNAKGEETKAMESQRAYRFVQ-GKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQ  138 (139)
T ss_pred             EEEEEEEEEecCCCeeeeecccCcEeCCC-CCccCHHHeeeHHHhhhhhcccccCCEEEEEEEEEEEc
Confidence            999999999998765321  123466764 57899999999999987668999999999999999986

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

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

Probab=99.88  E-value=3.4e-22  Score=159.29  Aligned_cols=121  Identities=31%  Similarity=0.492  Sum_probs=100.5

Q ss_pred             CCCceEEEEEecccccc--cceeecccc--cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccCCCCCCCCeEEE
Q 041904          173 PPTYYHTWKVSNFSSLL--DEFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQSSIPPNTKLLT  247 (317)
Q Consensus       173 ~~~~~~~~~i~nfs~~~--~~~~~S~~f--~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~~~~~~~~~~~~  247 (317)
                      |+..+++|+|.|||.++  ++.+.|+.|  ||++|        +|.+||+|+..+.++|||+||. ++.    ..|.+.+
T Consensus         2 ~~~~~~~~~I~~fS~~~~~~~~~~S~~F~vgG~~W--------~i~~yP~G~~~~~~~~lSl~L~l~~~----~~~~~~~   69 (132)
T cd03773           2 PPYDSATFTLENFSTLRQSADPVYSDPLNVDGLCW--------RLKVYPDGNGEVRGNFLSVFLELCSG----LGEASKY   69 (132)
T ss_pred             CCCcccEEEECChhhhhcCCcceeCCCeEeCCccE--------EEEEECCCCCCCCCCEEEEEEEeecC----CCCceeE
Confidence            45677999999999985  578999999  99999        9999999988766789999999 442    2466888


Q ss_pred             EEEEEEEECCCCC-ceeeeeeEEeeCCCCCccccccccccccCCCCCCceeC--CEEEEEEEEE
Q 041904          248 KYFLCVENQMNGK-NSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVD--DSCIIKAEVT  308 (317)
Q Consensus       248 ~~~l~l~n~~~~~-~~~~~~~~~F~~~~~~~G~~~fi~~~~L~~~~~gyl~d--d~l~i~~~V~  308 (317)
                      +|+|+|+||.++. +......+.|.. ..+|||.+|+++++|++  +|||+|  |+|+|+|.|+
T Consensus        70 ~~~l~llnq~~~~~~~~~~~~~~f~~-~~~wG~~~Fi~~~~L~~--~gfl~~~~D~l~i~~~v~  130 (132)
T cd03773          70 EYRVEMVHQANPTKNIKREFASDFEV-GECWGYNRFFRLDLLIN--EGYLLPENDTLILRFSVR  130 (132)
T ss_pred             EEEEEEEcCCCCccceEEeccccccC-CCCcCHHHhccHHHHhh--CCCcCCCCCEEEEEEEEe
Confidence            9999999995433 444455677865 46899999999999985  799999  9999999985

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

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

Probab=99.87  E-value=7.9e-22  Score=158.12  Aligned_cols=125  Identities=28%  Similarity=0.312  Sum_probs=99.5

Q ss_pred             ceEEEEEecccccc-----c--ceeecccc----cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccC-CCCCCC
Q 041904          176 YYHTWKVSNFSSLL-----D--EFYESESF----GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQ-SSIPPN  242 (317)
Q Consensus       176 ~~~~~~i~nfs~~~-----~--~~~~S~~f----~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~-~~~~~~  242 (317)
                      +.+.|+|+||+.+.     +  ..++||.|    .||+|        +|++||||...++++|||+||+ +.. -+.-..
T Consensus         1 g~~~W~i~~f~~~~~~a~~~~~~~~~S~~Fyt~~~Gy~w--------~i~~ypnG~~~~~~~~iSv~l~l~~g~~D~~l~   72 (147)
T cd03779           1 GTFLWKITDVSQKQRESSHGRDVSLCSPAFYTAKYGYKV--------CLRLYLNGDGAGKGTHISLFFVIMKGEYDALLP   72 (147)
T ss_pred             CeEEEEECcHHHHHHHHhcCCCceEECCCcccCCCCceE--------EEEEEcCCCCCCCCCEEEEEEEEecCCcccccC
Confidence            46899999999765     2  36899999    79999        9999999998877899999999 532 222358


Q ss_pred             CeEEEEEEEEEEECCCCCcee--eee---eEEee----CCCCCccccccccccccCCCCCCceeCCEEEEEEEEE
Q 041904          243 TKLLTKYFLCVENQMNGKNSE--VEG---EWLYT----LTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVT  308 (317)
Q Consensus       243 ~~~~~~~~l~l~n~~~~~~~~--~~~---~~~F~----~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~  308 (317)
                      |++.++++|.|++|.++....  ...   .+.|+    ..+.+||+++||++++|+....+||.||+++|+|+|.
T Consensus        73 wpv~~~~tfsLlDq~~~~~~~~~~~~~~~~~~F~rP~~~~n~~~G~~~Fi~~~~Le~s~~~ylkDD~~~Irc~V~  147 (147)
T cd03779          73 WPFRHKVTFMLLDQNNREHVIDAFRPDLSSASFQRPVSDMNVASGCPLFFPLKKLQSPKHAYCKDDTIYIKCVVD  147 (147)
T ss_pred             cceEEEEEEEEECCCCCCCCcEeecCCcccccccCcccCCCCCcchhheeEHHHhcccCCCcEeCCEEEEEEEEC
Confidence            999999999999998654321  111   25686    3446899999999999986334899999999999983

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

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

Probab=99.87  E-value=1.8e-21  Score=157.65  Aligned_cols=127  Identities=25%  Similarity=0.281  Sum_probs=103.6

Q ss_pred             CCCceEEEEEeccccccc-------ceeecccc----cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccCCCC-
Q 041904          173 PPTYYHTWKVSNFSSLLD-------EFYESESF----GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQSSI-  239 (317)
Q Consensus       173 ~~~~~~~~~i~nfs~~~~-------~~~~S~~f----~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~~~~-  239 (317)
                      ...++++|+|+||+.+..       ..++||.|    +||+|        +|++||+|++.+++.|||+||+ +..... 
T Consensus        16 ~~~g~fiWkI~~fs~~~~~a~~~~~~~i~Sp~Fyt~~~GYk~--------~l~~ylnG~g~~~g~~LSly~~l~~Ge~D~   87 (164)
T cd03778          16 TYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKM--------CLRIYLNGDGTGRGTHLSLFFVVMKGPNDA   87 (164)
T ss_pred             ccCCEEEEEECcHHHHHHHHhcCCCceEECCCcccCCCCeEE--------EEEEEeCCCCCCCCCEEEEEEEEecCCcCc
Confidence            346899999999998762       37899999    79999        9999999999888899999999 654333 


Q ss_pred             CCCCeEEEEEEEEEEECCCCCceeeeee-----EEeeC----CCCCccccccccccccCCCCCCceeCCEEEEEEEEE
Q 041904          240 PPNTKLLTKYFLCVENQMNGKNSEVEGE-----WLYTL----TNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVT  308 (317)
Q Consensus       240 ~~~~~~~~~~~l~l~n~~~~~~~~~~~~-----~~F~~----~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~  308 (317)
                      -..|++..+++|.|+||.++++......     ..|..    .+.+||++.|+++++|+.. +|||+||+|.|+|.|.
T Consensus        88 ~L~WPf~~~itl~llDQ~~r~hi~~~~~pd~~~~~f~RP~~~~n~~~G~~~Fv~l~~l~~~-~~Yv~dDtlfIk~~Vd  164 (164)
T cd03778          88 LLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKXEAK-NSYVRDDAIFIKAIVD  164 (164)
T ss_pred             ccCCceeeEEEEEEECCCCCCcceeEEEcCcchHhcCCCCcccccCcCcceEEEhhHcccc-CCcccCCeEEEEEEEC
Confidence            3899999999999999987666543221     13532    3467999999999999863 6999999999999873

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

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

Probab=99.87  E-value=2.5e-21  Score=155.97  Aligned_cols=125  Identities=22%  Similarity=0.299  Sum_probs=100.6

Q ss_pred             ceEEEEEecccccc-----cc--eeecccc----cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccC-CCCCCC
Q 041904          176 YYHTWKVSNFSSLL-----DE--FYESESF----GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQ-SSIPPN  242 (317)
Q Consensus       176 ~~~~~~i~nfs~~~-----~~--~~~S~~f----~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~-~~~~~~  242 (317)
                      +.+.|+|.+|+.++     ++  .+.|+.|    +||+|        +|++||||...++++|||+||+ +.. -+.-..
T Consensus         1 g~~vwkI~~ys~~~~~~~~g~~~~i~S~~Fyt~~~Gy~w--------~i~~ypnG~~~~~~~~iSv~l~l~~g~~D~~l~   72 (148)
T cd03780           1 GKLIWKVTDYKMKKKEAVDGHTVSIFSQPFYTSRCGYRL--------CARAYLNGDGSGKGTHLSLYFVVMRGEFDSLLQ   72 (148)
T ss_pred             CEEEEEECCHHHHHHhhcCCCccEEECCCcccCCCCeeE--------EEEEEcCCCCCCCCCEEEEEEEEecCccccccC
Confidence            46899999999986     34  7999999    99999        9999999998878899999999 531 122368


Q ss_pred             CeEEEEEEEEEEECCCCC-c-e-eeee---eEEeeCC----CCCccccccccccccCCCCCCceeCCEEEEEEEEE
Q 041904          243 TKLLTKYFLCVENQMNGK-N-S-EVEG---EWLYTLT----NRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVT  308 (317)
Q Consensus       243 ~~~~~~~~l~l~n~~~~~-~-~-~~~~---~~~F~~~----~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~  308 (317)
                      |++.++++|.|++|.+.. + . ....   ...|+..    +..||+++||++++|+....+||.||+++|+|.|.
T Consensus        73 wp~~~~~tfsLlDq~~~~~~~~~~~~~~~~~~~F~rp~~~~n~~~G~~~Fi~~~~Le~s~~~ylkdD~~~Ik~~v~  148 (148)
T cd03780          73 WPFRQRVTLMLLDQSGKKNHIMETFKADPNSSSFKRPDGEMNIASGCPRFVAHSVLENAKNTYIKDDTLFLKVAVD  148 (148)
T ss_pred             cceEEEEEEEEECCCCCCCCcceeeecCCccccccCCCCCCCCCcChhheeEHHHhhcccCCcCcCCEEEEEEEEC
Confidence            999999999999997543 2 1 1111   3568655    56799999999999986445899999999999873

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

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

Probab=99.86  E-value=1.7e-21  Score=158.51  Aligned_cols=123  Identities=29%  Similarity=0.442  Sum_probs=98.3

Q ss_pred             ceEEEEEecccccc-------cceeecccc--c--ceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccCC-CCCCC
Q 041904          176 YYHTWKVSNFSSLL-------DEFYESESF--G--CYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQS-SIPPN  242 (317)
Q Consensus       176 ~~~~~~i~nfs~~~-------~~~~~S~~f--~--g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~~-~~~~~  242 (317)
                      ++|+|+|.+||.++       ++.+.|+.|  |  ||+|        +|++||+|...+.++||||||+ ++.. +....
T Consensus         1 g~~~w~I~~fs~~~~~~~~~~~~~~~S~~F~vg~~G~~w--------~i~~yP~G~~~~~~~~lsl~L~l~~~~~d~~~~   72 (149)
T cd00270           1 GVLIWKIKDYSRKLQEAVAGSNTVLYSPPFYTSRYGYKL--------CLRLYLNGDGTGKGTHLSLFVHVMKGEYDALLE   72 (149)
T ss_pred             CEEEEEECCHHHHHHHHhcCCCceEECCCcccCCCCceE--------EEEEEeCCCCCCCCCEEEEEEEEeccCCCcccc
Confidence            47999999999975       358999999  8  9999        9999999987666789999999 5432 23467


Q ss_pred             CeEEEEEEEEEEECCCC---Cceeee-----eeEEee-----CCCCCccccccccccccCCCCCCceeCCEEEEEEEEE
Q 041904          243 TKLLTKYFLCVENQMNG---KNSEVE-----GEWLYT-----LTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVT  308 (317)
Q Consensus       243 ~~~~~~~~l~l~n~~~~---~~~~~~-----~~~~F~-----~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~  308 (317)
                      |++.++|+|.|+||.++   .+....     ..+.|.     ....+|||.+||++++|++  .|||+||+|+|+|+|.
T Consensus        73 w~~~~~~~~~l~d~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~G~~~fi~~~~L~~--~gfl~dD~l~I~~~v~  149 (149)
T cd00270          73 WPFRGKITLTLLDQSDDSKRKHITETFMPDPNSSAFQRPPTGENNIGFGYPEFVPLEKLES--RGYVKDDTLFIKVEVD  149 (149)
T ss_pred             CCccceEEEEEECCCCccccCceEEEEEcCCchHhhcCCCcccCCCCcCcceEeEHHHhcc--CCCEeCCEEEEEEEEC
Confidence            99999999999999874   222111     123454     1357899999999999996  5899999999999983

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

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

Probab=99.86  E-value=7.4e-21  Score=149.26  Aligned_cols=125  Identities=30%  Similarity=0.435  Sum_probs=101.1

Q ss_pred             cEEEEEEcCcccccccccceEEcccEEeCCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCCCCCCCEEEEEEEEEEEec
Q 041904           17 SHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAITISFYSIK   96 (317)
Q Consensus        17 ~~~~w~I~~fs~~~~~~~~~~~S~~F~~gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~~~~w~v~~~f~~~l~n~   96 (317)
                      ++|+|+|.+|+..   .++.++||.|.++|+.|+|.+||+|...  +.+||||||+|.+.......|++.++|+|.|+|+
T Consensus         1 ~~~~~~i~~~~~~---~~~~~~S~~f~~~g~~W~l~~~p~~~~~--~~~~lsv~L~~~~~~~~~~~~~~~~~~~~~l~~~   75 (126)
T cd00121           1 GKHTWKIVNFSEL---EGESIYSPPFEVGGYKWRIRIYPNGDGE--SGDYLSLYLELDKGESDLEKWSVRAEFTLKLVNQ   75 (126)
T ss_pred             CEEEEEECCCCCC---CCcEEECCCEEEcCEeEEEEEEcCCCCC--CCCEEEEEEEecCCCCCCCCCcEEEEEEEEEECC
Confidence            4799999999992   3679999999999999999999999764  4689999999988664456799999999999999


Q ss_pred             CCCcEEEEEeeecccceeeeecc-cccccccccceeecccccCCCCceEeCCEEEEEEEEE
Q 041904           97 FKTNILVSKVRNSTINVIVKHFH-AMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVF  156 (317)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~F~-~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~  156 (317)
                      ++.+.... .       ....|. ....+|||.+|+++++|.+  ..++.||+|+|+|+|.
T Consensus        76 ~~~~~~~~-~-------~~~~~~~~~~~~~G~~~fi~~~~l~~--~~~~~~d~l~i~~~v~  126 (126)
T cd00121          76 NGGKSLSK-S-------FTHVFFSEKGSGWGFPKFISWDDLED--SYYLVDDSLTIEVEVK  126 (126)
T ss_pred             CCCccceE-e-------ccCCcCCCCCCCCChHHeeEHHHhcc--CCcEECCEEEEEEEEC
Confidence            84333221 2       233443 4568999999999999983  3349999999999973

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

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

Probab=99.85  E-value=4.3e-21  Score=155.66  Aligned_cols=123  Identities=23%  Similarity=0.282  Sum_probs=97.3

Q ss_pred             ceEEEEEecccccc-----cc--eeecccc----cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccC-CCCCCC
Q 041904          176 YYHTWKVSNFSSLL-----DE--FYESESF----GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQ-SSIPPN  242 (317)
Q Consensus       176 ~~~~~~i~nfs~~~-----~~--~~~S~~f----~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~-~~~~~~  242 (317)
                      +.|.|+|.+||.++     ++  .+.|+.|    |||+|        +|++||+|...+..+|||+||+ ++. .+....
T Consensus         1 g~h~~~I~~yS~~~~~~~~g~~~~i~S~~F~~~~gGy~W--------~i~~yP~G~~~~~~~~lS~~L~l~~~~~d~~l~   72 (147)
T cd03776           1 GIYVWKIKNFSNLRRSMEAGSPVVIHSPGFYTSPPGYKL--------CARLNLSLPEARCPNYISLFVHLMQGENDSHLD   72 (147)
T ss_pred             CEEEEEECCHHHHHHHHhcCCCceEECCCcccCCCCceE--------EEEEEeCCCCCCCCCEEEEEEEEeccCCCcccC
Confidence            47999999999764     33  4889999    69999        9999999998777789999999 442 223467


Q ss_pred             CeEEEEEEEEEEECCCCC-ceee-----eeeEEeeC-----CCCCccccccccccccCCCCCCceeCCEEEEEEEEE
Q 041904          243 TKLLTKYFLCVENQMNGK-NSEV-----EGEWLYTL-----TNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVT  308 (317)
Q Consensus       243 ~~~~~~~~l~l~n~~~~~-~~~~-----~~~~~F~~-----~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~  308 (317)
                      |++.++++|.|++|.++. +...     .....|..     .+.+|||++||++++|+.  .+||+||+|+|+|+|.
T Consensus        73 wpv~a~~~~~lldq~~~~~~~~~~~~~~~~~~~F~~p~~~~~~~~~G~~~fi~~~~Le~--~~yl~dD~l~I~c~V~  147 (147)
T cd03776          73 WPFQGTITLTLLDQSEPRQNIHETMMSKPELLAFQRPTTDRNPKGFGYVEFAHIEDLLQ--RGFVKNDTLLIKIEVN  147 (147)
T ss_pred             CcccceeEEEEECCCcccCccEEEEEcCCChHhhcCCCcCCCCCCeeEceeeEHHHhhh--CCCccCCEEEEEEEEC
Confidence            999999999999998643 2111     11245653     236799999999999986  6899999999999984

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

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

Probab=99.85  E-value=5.5e-21  Score=154.08  Aligned_cols=137  Identities=15%  Similarity=0.199  Sum_probs=104.8

Q ss_pred             CcEEEEEEcCcccccc--cccceEEcccEEeC-CeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC-CCCCCEE-EEEEE
Q 041904           16 PSHYLFKIESFSLLSK--ASVEQLILDNFEAG-GYKWKLSIHLTGSKSVNVTDHISIYLELAETSS-LPTGWEV-NAITI   90 (317)
Q Consensus        16 ~~~~~w~I~~fs~~~~--~~~~~~~S~~F~~g-G~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~-~~~~w~v-~~~f~   90 (317)
                      |+.+.|+|.||+++++  ..+..++||+|+.. ||+.+|++||+|....+.+.|||||+++++++. ..++||+ .-+++
T Consensus         1 cp~~iWkI~nfs~~~~~a~~~~~i~Sp~Fyt~~GYk~~l~~~lng~~~~~~g~~lSl~~~lm~Ge~D~~L~WP~~~~~it   80 (167)
T cd03783           1 CPNAVWRVRNFSQILENTTKGDVLQSPRFYSPEGYGYGVSLYPLSNESDYSGNYTGLYFHLCSGENDAVLEWPALNRQAI   80 (167)
T ss_pred             CCceeEEECcHHHHHHhCcCCCeEECCCCccCCCceEEEEEEecCCCCCCCCCEEEEEEEEecccCCCcccCCCcCCEEE
Confidence            5779999999999876  25678999999985 999999999999875446789999999999877 4789995 56899


Q ss_pred             EEEEecCC---CcEEEEEeeecccc-e------eeeeccc--------------ccccccccceeecccccCCCCceEeC
Q 041904           91 SFYSIKFK---TNILVSKVRNSTIN-V------IVKHFHA--------------MKSKYGVAKFIDLKTFSDPLNGYLIN  146 (317)
Q Consensus        91 ~~l~n~~~---~~~~~~~~~~~~~~-~------~~~~F~~--------------~~~~~G~~~fi~~~~l~~~~~~yl~~  146 (317)
                      |.|+||+.   ...+..... .++. +      ....|+.              .+.++||+.|+++++|.  .++||+|
T Consensus        81 l~llDQ~~~~~~r~~~~~sf-~~d~~~~~~~~~~~~~f~rP~~~~~~~~~~~~~~~~gfG~~~Fish~~L~--~r~yikd  157 (167)
T cd03783          81 ITVLDQDPDVRLRMSSSRSF-TTDKSQTSSAINGTLRWDRPSRVGTYDTSCDCFRGIDFGWSTFISHSQLR--RRSFLKN  157 (167)
T ss_pred             EEEEcCCcchhhccccceee-ecCCCcccccccccccccCCcccccccccccccCCcccccccceeHHHHh--hCCcccC
Confidence            99999964   222211000 0000 0      1112431              35689999999999998  6899999


Q ss_pred             CEEEEEEEE
Q 041904          147 DACVFGAEV  155 (317)
Q Consensus       147 d~l~i~~~v  155 (317)
                      |+|.|.+++
T Consensus       158 DtlfI~~~~  166 (167)
T cd03783         158 DDLIIFVDF  166 (167)
T ss_pred             CeEEEEEec
Confidence            999999886

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

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

Probab=99.85  E-value=1.4e-20  Score=153.61  Aligned_cols=123  Identities=20%  Similarity=0.310  Sum_probs=97.5

Q ss_pred             ceEEEEEecccccc-------cceeecccc--c--ceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccCCC-CCCC
Q 041904          176 YYHTWKVSNFSSLL-------DEFYESESF--G--CYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQSS-IPPN  242 (317)
Q Consensus       176 ~~~~~~i~nfs~~~-------~~~~~S~~f--~--g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~~~-~~~~  242 (317)
                      +.|.|+|.+||.++       +..+.|+.|  |  ||+|        +|++||+|...+.++|||+||+ +.... ....
T Consensus         1 g~~~~~I~gys~~~~~~~~~~~~~i~S~~F~vg~~Gy~w--------~i~~yPnG~~~~~~~~vs~~l~l~~ge~d~~l~   72 (154)
T cd03781           1 GTLLWKITDYSRKLQEAKGRDNLELFSPPFYTHRYGYKL--------QVSAFLNGNGSGEGSHLSVYIRVLPGEYDNLLE   72 (154)
T ss_pred             CEEEEEECCHHHHHHHhhcCCCceEECCCeecCCCCEEE--------EEEEECCCCCCCCCCEEEEEEEEecCCcccccC
Confidence            47899999999875       258999999  8  9999        9999999988877899999999 54222 2258


Q ss_pred             CeEEEEEEEEEEECCCC--C---ceeee-----eeEEeeC--------CCCCccccccccccccCCCCCCceeCCEEEEE
Q 041904          243 TKLLTKYFLCVENQMNG--K---NSEVE-----GEWLYTL--------TNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIK  304 (317)
Q Consensus       243 ~~~~~~~~l~l~n~~~~--~---~~~~~-----~~~~F~~--------~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~  304 (317)
                      |++.++++|.|++|.+.  .   +....     ....|+.        .+.+||+.+||++++|+.  ++||+||+|+|+
T Consensus        73 wp~~a~~~~~llDq~~~~~~~~~~~~~~~~~~~~~~~F~rp~~~~~~~~~~~~G~~~fi~~~~Le~--~~yl~dD~l~Ir  150 (154)
T cd03781          73 WPFSHRITFTLLDQSDPSLSKPQHITETFTPDPTWKNFQKPSASRLDESTLGFGYPKFISHEDLKK--RNYIKDDAIFLR  150 (154)
T ss_pred             CceeeEEEEEEECCCCCccccCcceEEEEEcCCchhhhcCCcccccCCCCCccchhHeeEHHHHhh--CCcccCCEEEEE
Confidence            99999999999999864  1   11111     1234542        345799999999999996  789999999999


Q ss_pred             EEEE
Q 041904          305 AEVT  308 (317)
Q Consensus       305 ~~V~  308 (317)
                      |.|.
T Consensus       151 c~v~  154 (154)
T cd03781         151 ASVE  154 (154)
T ss_pred             EEeC
Confidence            9883

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

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

Probab=99.85  E-value=1.5e-20  Score=156.76  Aligned_cols=127  Identities=24%  Similarity=0.299  Sum_probs=101.5

Q ss_pred             CCCceEEEEEecccccc-----cc--eeecccc--c--ceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccC-CCC
Q 041904          173 PPTYYHTWKVSNFSSLL-----DE--FYESESF--G--CYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQ-SSI  239 (317)
Q Consensus       173 ~~~~~~~~~i~nfs~~~-----~~--~~~S~~f--~--g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~-~~~  239 (317)
                      ...+.|.|+|.+|+.++     ++  .+.|+.|  +  ||+|        +|++||||.+.++++|||+||+ +.. -+.
T Consensus        36 ~~~G~hvwkI~~yS~~~~~~~~g~~~~i~S~~Fyvg~~GY~w--------~i~~ypnG~g~~~~~~iSvyl~L~~ge~D~  107 (186)
T cd03777          36 SYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKM--------CARVYLNGDGMGKGTHLSLFFVIMRGEYDA  107 (186)
T ss_pred             ccceEEEEEECChhHHHHhhccCCCcEEECCCeEeCCCCeeE--------EEEEEcCCCCCCCCCEEEEEEEEecCCccc
Confidence            34699999999999875     34  7999999  7  9999        9999999998878899999999 542 222


Q ss_pred             CCCCeEEEEEEEEEEECCCC-Cceee-----eeeEEee-CC---CCCccccccccccccCCCCCCceeCCEEEEEEEEEE
Q 041904          240 PPNTKLLTKYFLCVENQMNG-KNSEV-----EGEWLYT-LT---NRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTL  309 (317)
Q Consensus       240 ~~~~~~~~~~~l~l~n~~~~-~~~~~-----~~~~~F~-~~---~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v  309 (317)
                      -..|++.++++|.|++|.+. .+...     .....|. ..   +.+||+++||++++|+.  ++||.||+++|+|.|..
T Consensus       108 ~L~WP~~~~~tfsLlDQ~~~~~~~~~~~~p~p~~~~F~rp~~~~n~~~G~~~Fi~~~~Le~--~~ylkdD~l~Irv~v~~  185 (186)
T cd03777         108 LLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLEN--GTYIKDDTIFIKVIVDT  185 (186)
T ss_pred             ccCCceeEEEEEEEEcCCCccccccceeccCCccccccCCccCCCCCCCchheeEHHHhcc--CCcEeCCEEEEEEEEec
Confidence            35899999999999999742 12111     1224576 32   45799999999999986  78999999999999863

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

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

Probab=99.84  E-value=1.7e-20  Score=150.42  Aligned_cols=136  Identities=14%  Similarity=0.280  Sum_probs=104.9

Q ss_pred             CcEEEEEEcCcccccc--cccceEEcccEEe-CCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC-CCCCCEEE-EEEE
Q 041904           16 PSHYLFKIESFSLLSK--ASVEQLILDNFEA-GGYKWKLSIHLTGSKSVNVTDHISIYLELAETSS-LPTGWEVN-AITI   90 (317)
Q Consensus        16 ~~~~~w~I~~fs~~~~--~~~~~~~S~~F~~-gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~-~~~~w~v~-~~f~   90 (317)
                      |+.|.|+|.||+++++  ..+..++||+|+. .||+.+|.+||||.+.  +++|||||+++++++. ..++||+. .+++
T Consensus         1 cp~~iWkI~~fs~~~~~~~~~~~i~Sp~FYt~~GYkl~l~~ylnG~g~--~~~~lsl~~~lm~Ge~D~~L~WPf~~~qit   78 (167)
T cd03782           1 CPEHIWHIRNFTQLLATTPPNGKIYSPPFLSSTGYSFQVGLYLNGTDD--YPGNLAIYLHLTSGPNDDQLQWPCPWQQAT   78 (167)
T ss_pred             CCcEEEEeCcHHHHHHhcCCCceEECCCCcCccCceeEEEEEecCCCC--CCCEEEEEEEEeccCCCccccCCCcCCeEE
Confidence            5789999999999876  3567899999987 5999999999999986  3679999999999877 47899999 8999


Q ss_pred             EEEEecCC---CcEEEEEe-eecccc-ee-eeec--c----------c-------ccccccccceeecccccCCCCceEe
Q 041904           91 SFYSIKFK---TNILVSKV-RNSTIN-VI-VKHF--H----------A-------MKSKYGVAKFIDLKTFSDPLNGYLI  145 (317)
Q Consensus        91 ~~l~n~~~---~~~~~~~~-~~~~~~-~~-~~~F--~----------~-------~~~~~G~~~fi~~~~l~~~~~~yl~  145 (317)
                      |.|+||+.   .+.+.... +..+.. .. ...|  +          .       .+.++||+.|+++++|+  .+.||+
T Consensus        79 ~~LlDQ~~d~~~r~~~~~~~t~~P~~~s~~n~~f~w~rP~kvg~~~~~~~~~~~~r~~~~G~~~Fish~~L~--~r~yik  156 (167)
T cd03782          79 MMLLDQHPDIRQRMSNQRSVTTDPNMTSTDSDEYFWDDPRKVGSEVTDTDGSTFYRGPGYGTSAFITHLRLR--SRDFIK  156 (167)
T ss_pred             EEEEcCCCchhhccceeeeEEecCCcccccCccceecCCcccCcccccccccccccccccCccceeeHHHHh--hcCccc
Confidence            99999974   22232210 000000 00 1123  2          1       15789999999999998  689999


Q ss_pred             CCEEEEEEEE
Q 041904          146 NDACVFGAEV  155 (317)
Q Consensus       146 ~d~l~i~~~v  155 (317)
                      ||++.|-+++
T Consensus       157 dD~ifi~~~~  166 (167)
T cd03782         157 GDDVIFLLTM  166 (167)
T ss_pred             CCeEEEEEec
Confidence            9999998876

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

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

Probab=99.83  E-value=1.1e-19  Score=142.62  Aligned_cols=121  Identities=37%  Similarity=0.590  Sum_probs=100.0

Q ss_pred             eEEEEEecccccccceeecccc--cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEEcc-CCCCCCCCeEEEEEEEEE
Q 041904          177 YHTWKVSNFSSLLDEFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVS-QSSIPPNTKLLTKYFLCV  253 (317)
Q Consensus       177 ~~~~~i~nfs~~~~~~~~S~~f--~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~~~-~~~~~~~~~~~~~~~l~l  253 (317)
                      +++|+|.+|+...++.+.|+.|  +|+.|        +|.+||+|... +.++||+||+|. .......|.+.++|+|.|
T Consensus         2 ~~~~~i~~~~~~~~~~~~S~~f~~~g~~W--------~l~~~p~~~~~-~~~~lsv~L~~~~~~~~~~~~~~~~~~~~~l   72 (126)
T cd00121           2 KHTWKIVNFSELEGESIYSPPFEVGGYKW--------RIRIYPNGDGE-SGDYLSLYLELDKGESDLEKWSVRAEFTLKL   72 (126)
T ss_pred             EEEEEECCCCCCCCcEEECCCEEEcCEeE--------EEEEEcCCCCC-CCCEEEEEEEecCCCCCCCCCcEEEEEEEEE
Confidence            6899999999966789999999  99999        99999999766 468999999954 332346799999999999


Q ss_pred             EECCCCCceeeeeeEEee-CCCCCccccccccccccCCCCCCceeCCEEEEEEEEE
Q 041904          254 ENQMNGKNSEVEGEWLYT-LTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVT  308 (317)
Q Consensus       254 ~n~~~~~~~~~~~~~~F~-~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~  308 (317)
                      +++++++.......+.|. ....+|||++||++++|++  .++++||+|+|+|+|.
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~G~~~fi~~~~l~~--~~~~~~d~l~i~~~v~  126 (126)
T cd00121          73 VNQNGGKSLSKSFTHVFFSEKGSGWGFPKFISWDDLED--SYYLVDDSLTIEVEVK  126 (126)
T ss_pred             ECCCCCccceEeccCCcCCCCCCCCChHHeeEHHHhcc--CCcEECCEEEEEEEEC
Confidence            999855555555555553 4568999999999999997  3449999999999984

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

>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=99.82  E-value=4.5e-20  Score=143.92  Aligned_cols=118  Identities=25%  Similarity=0.376  Sum_probs=95.4

Q ss_pred             EcCcccccccccceEEcccEEeCCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCCCC-CCCEEEEEEEEEEEecCCCcE
Q 041904           23 IESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLP-TGWEVNAITISFYSIKFKTNI  101 (317)
Q Consensus        23 I~~fs~~~~~~~~~~~S~~F~~gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~~-~~w~v~~~f~~~l~n~~~~~~  101 (317)
                      |+|||++.. .+..+.|+.|.++|++|+|.+||+|+     .++||+||+|....... .+|++.+++++.|+++.++..
T Consensus         1 i~nfs~l~~-~~~~~~s~~~~~~g~~W~l~~~~~~~-----~~~l~~~L~~~~~~~~~~~~w~~~~~~~~~~~~~~~~~~   74 (119)
T PF00917_consen    1 IKNFSKLKE-GEEYSSSFVFSHGGYPWRLKVYPKGN-----GKYLSVYLHCDKGENDSDLEWSIEAEFRFRLLNQNGKSI   74 (119)
T ss_dssp             ETTGGGHHT-SEEEEEEEESSTTSEEEEEEEETTES-----TTEEEEEEEEECSTTGGGSSSSEEEEEEEEEE-TTSCEE
T ss_pred             CcccceEeC-CCcEECCCeEEECCEEEEEEEEeCCC-----cCcEEEEEEEeecccccccceeeeEEEEEEEecCCCCcc
Confidence            789999973 23445558888999999999999986     47999999999876543 689999999999999988774


Q ss_pred             EEEEeeecccceeeeecccccccccccceeecccccCCCCceEeCCEEEEEEEEEE
Q 041904          102 LVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFV  157 (317)
Q Consensus       102 ~~~~~~~~~~~~~~~~F~~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v  157 (317)
                      ...  .      ..+.|... .+|||.+|+++++|.++  .|+.||+|+|+|+|+|
T Consensus        75 ~~~--~------~~~~F~~~-~~~g~~~fi~~~~l~~~--~fl~dd~l~ie~~v~I  119 (119)
T PF00917_consen   75 SKR--I------KSHSFNNP-SSWGWSSFISWEDLEDP--YFLVDDSLTIEVEVKI  119 (119)
T ss_dssp             EEE--E------ECEEECTT-SEEEEEEEEEHHHHTTC--TTSBTTEEEEEEEEEE
T ss_pred             eee--e------eeeEEeee-cccchhheeEHHHhCcc--CCeECCEEEEEEEEEC
Confidence            332  1      23677643 78999999999999843  3899999999999986

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 ....

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

Probab=99.82  E-value=1.2e-19  Score=148.13  Aligned_cols=122  Identities=22%  Similarity=0.355  Sum_probs=94.9

Q ss_pred             ceEEEEEecccccc-----cceeecccc---cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-cc-CCCCCCCCeE
Q 041904          176 YYHTWKVSNFSSLL-----DEFYESESF---GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VS-QSSIPPNTKL  245 (317)
Q Consensus       176 ~~~~~~i~nfs~~~-----~~~~~S~~f---~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~-~~~~~~~~~~  245 (317)
                      .+|.|+|.|||.++     ++.+.|+.|   |||+|        +|++||+|+.. +++||||||+ +. ..+...+|++
T Consensus         2 p~hvwkI~~yS~~~~~~~~g~~i~S~~FysvgGy~w--------~I~~YPnG~~~-~~~~lSlyL~L~~g~~d~~L~WP~   72 (167)
T cd03771           2 PEAVWRVRNFSQLLETTPKGTKIYSPRFYSPEGYAF--------QVGLYPNGTES-YPGYTGLYFHLCSGENDDVLEWPC   72 (167)
T ss_pred             CeEEEEEcCchhhhhcCCCCCEEECCCCCccCCeEE--------EEEEEeCCCCC-CCCcceEEEEEecCCccccccCcc
Confidence            57999999999985     348999997   99999        99999999987 7899999999 43 2334578995


Q ss_pred             -EEEEEEEEEECCCC----Cceee--e----------eeEEeeCC-----------------CCCccccccccccccCCC
Q 041904          246 -LTKYFLCVENQMNG----KNSEV--E----------GEWLYTLT-----------------NRAIGGRQFMTLAKLKDP  291 (317)
Q Consensus       246 -~~~~~l~l~n~~~~----~~~~~--~----------~~~~F~~~-----------------~~~~G~~~fi~~~~L~~~  291 (317)
                       .++++|.|++|...    .+...  .          ....|+..                 +.+|||++||++++|+. 
T Consensus        73 v~a~~t~~LlDQ~~~~~~r~~~~~~~~~dp~~~~~~~~~~~~~rP~~~~~~~~~~~~~~~~~~~g~G~~~Fis~~~L~~-  151 (167)
T cd03771          73 PNRQATMTLLDQDPDIQQRMSNQRSFTTDPSMTSSDNGEYFWDRPSKVGSYDTDTNGCTCYRGPGYGWSTFISHSRLRR-  151 (167)
T ss_pred             eeEEEEEEEECCCCcccccCcceEEEecCCcccccccccccccCCccccccccccccccccccCccccccceeHHHhcc-
Confidence             89999999999731    11111  0          01113322                 24799999999999997 


Q ss_pred             CCCceeCCEEEEEEEEE
Q 041904          292 TEGYLVDDSCIIKAEVT  308 (317)
Q Consensus       292 ~~gyl~dd~l~i~~~V~  308 (317)
                       .+||+||+|.|+++++
T Consensus       152 -r~ylk~dtl~i~~~~~  167 (167)
T cd03771         152 -RDFLKGDDLIILLDFE  167 (167)
T ss_pred             -CCCCcCCEEEEEEEeC
Confidence             6799999999999873

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

>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=99.79  E-value=7.1e-19  Score=137.13  Aligned_cols=113  Identities=29%  Similarity=0.497  Sum_probs=91.0

Q ss_pred             Eecccccc-c-ceeecccc--cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEEccCCCCC--CCCeEEEEEEEEEEE
Q 041904          182 VSNFSSLL-D-EFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIP--PNTKLLTKYFLCVEN  255 (317)
Q Consensus       182 i~nfs~~~-~-~~~~S~~f--~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~~~~~~~~--~~~~~~~~~~l~l~n  255 (317)
                      |+|||.++ + ..+.|+.+  +|++|        +|.+||+|+    ++++++||+|......  ..|++.+++++++++
T Consensus         1 i~nfs~l~~~~~~~~s~~~~~~g~~W--------~l~~~~~~~----~~~l~~~L~~~~~~~~~~~~w~~~~~~~~~~~~   68 (119)
T PF00917_consen    1 IKNFSKLKEGEEYSSSFVFSHGGYPW--------RLKVYPKGN----GKYLSVYLHCDKGENDSDLEWSIEAEFRFRLLN   68 (119)
T ss_dssp             ETTGGGHHTSEEEEEEEESSTTSEEE--------EEEEETTES----TTEEEEEEEEECSTTGGGSSSSEEEEEEEEEE-
T ss_pred             CcccceEeCCCcEECCCeEEECCEEE--------EEEEEeCCC----cCcEEEEEEEeecccccccceeeeEEEEEEEec
Confidence            78999998 3 34455777  99999        999999987    4799999996544332  599999999999999


Q ss_pred             CCCCCceeeeeeEEeeCCCCCccccccccccccCCCCCCceeCCEEEEEEEEEE
Q 041904          256 QMNGKNSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTL  309 (317)
Q Consensus       256 ~~~~~~~~~~~~~~F~~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v  309 (317)
                      +.++........+.|.. ..+|||.+||++++|.++  .|++||+|+|+|+|+|
T Consensus        69 ~~~~~~~~~~~~~~F~~-~~~~g~~~fi~~~~l~~~--~fl~dd~l~ie~~v~I  119 (119)
T PF00917_consen   69 QNGKSISKRIKSHSFNN-PSSWGWSSFISWEDLEDP--YFLVDDSLTIEVEVKI  119 (119)
T ss_dssp             TTSCEEEEEEECEEECT-TSEEEEEEEEEHHHHTTC--TTSBTTEEEEEEEEEE
T ss_pred             CCCCcceeeeeeeEEee-ecccchhheeEHHHhCcc--CCeECCEEEEEEEEEC
Confidence            98876332222588875 478999999999999974  3899999999999987

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 ....

>smart00061 MATH meprin and TRAF homology

Probab=99.71  E-value=1.1e-16  Score=119.40  Aligned_cols=94  Identities=19%  Similarity=0.230  Sum_probs=78.7

Q ss_pred             EEEEEcCcccccccccceEEcccEEeCCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCCCCCCCEEEEEEEEEEEecCC
Q 041904           19 YLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAITISFYSIKFK   98 (317)
Q Consensus        19 ~~w~I~~fs~~~~~~~~~~~S~~F~~gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~~~~w~v~~~f~~~l~n~~~   98 (317)
                      ++|+|.+|+.+..  ++.++||+|.++|++|+|.+||+       .+|||+||.|.+....+..|++.|+|++.|+|+++
T Consensus         2 ~~~~~~~~~~~~~--~~~~~S~~f~~~g~~W~i~~~p~-------~~~lsl~L~~~~~~~~~~~w~v~a~~~~~l~~~~~   72 (95)
T smart00061        2 LSHTFKNVSRLEE--GESYFSPSEEHFNIPWRLKIYRK-------NGFLSLYLHCEKEECDSRKWSIEAEFTLKLVSQNG   72 (95)
T ss_pred             ceeEEEchhhccc--CceEeCChhEEcCceeEEEEEEc-------CCEEEEEEEeCCCcCCCCCeEEEEEEEEEEEeCCC
Confidence            5799999999853  78999999999999999999998       37999999998765545589999999999999987


Q ss_pred             CcEEEEEeeecccceeeeeccccccccccccee
Q 041904           99 TNILVSKVRNSTINVIVKHFHAMKSKYGVAKFI  131 (317)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~F~~~~~~~G~~~fi  131 (317)
                      +....  .       ..+.|.. ..+|||.+||
T Consensus        73 ~~~~~--~-------~~~~F~~-~~~~G~~~fi   95 (95)
T smart00061       73 KSLSK--K-------DKHVFEK-PSGWGFSKFI   95 (95)
T ss_pred             CEEee--e-------eeEEEcC-CCccceeeEC
Confidence            65422  2       5677875 6789999885

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

Probab=99.65  E-value=8.1e-16  Score=123.49  Aligned_cols=121  Identities=19%  Similarity=0.297  Sum_probs=95.4

Q ss_pred             ceEEEEEecccccc-----cceeecccc---cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-cc-CCCCCCCCeE
Q 041904          176 YYHTWKVSNFSSLL-----DEFYESESF---GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VS-QSSIPPNTKL  245 (317)
Q Consensus       176 ~~~~~~i~nfs~~~-----~~~~~S~~f---~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~-~~~~~~~~~~  245 (317)
                      ..+.|+|+||+.+.     ...++||.|   .||+.        ++.+||||++.+ ++|||+|++ +. ..+.-.+|++
T Consensus         2 p~~iWkI~~fs~~~~~~~~~~~i~Sp~FYt~~GYkl--------~l~~ylnG~g~~-~~~lsl~~~lm~Ge~D~~L~WPf   72 (167)
T cd03782           2 PEHIWHIRNFTQLLATTPPNGKIYSPPFLSSTGYSF--------QVGLYLNGTDDY-PGNLAIYLHLTSGPNDDQLQWPC   72 (167)
T ss_pred             CcEEEEeCcHHHHHHhcCCCceEECCCCcCccCcee--------EEEEEecCCCCC-CCEEEEEEEEeccCCCccccCCC
Confidence            46899999999976     347899998   99999        999999999876 689999999 53 3344589999


Q ss_pred             E-EEEEEEEEECCC---C-Cceee--ee------e--EEe--eCC-----------------CCCccccccccccccCCC
Q 041904          246 L-TKYFLCVENQMN---G-KNSEV--EG------E--WLY--TLT-----------------NRAIGGRQFMTLAKLKDP  291 (317)
Q Consensus       246 ~-~~~~l~l~n~~~---~-~~~~~--~~------~--~~F--~~~-----------------~~~~G~~~fi~~~~L~~~  291 (317)
                      . .+++|.|++|+.   . .+...  ..      .  ..|  ...                 +.++|++.||++++|+. 
T Consensus        73 ~~~qit~~LlDQ~~d~~~r~~~~~~~t~~P~~~s~~n~~f~w~rP~kvg~~~~~~~~~~~~r~~~~G~~~Fish~~L~~-  151 (167)
T cd03782          73 PWQQATMMLLDQHPDIRQRMSNQRSVTTDPNMTSTDSDEYFWDDPRKVGSEVTDTDGSTFYRGPGYGTSAFITHLRLRS-  151 (167)
T ss_pred             cCCeEEEEEEcCCCchhhccceeeeEEecCCcccccCccceecCCcccCcccccccccccccccccCccceeeHHHHhh-
Confidence            9 999999999974   1 22211  10      0  124  322                 57899999999999996 


Q ss_pred             CCCceeCCEEEEEEEE
Q 041904          292 TEGYLVDDSCIIKAEV  307 (317)
Q Consensus       292 ~~gyl~dd~l~i~~~V  307 (317)
                       +.||.||++.|-+++
T Consensus       152 -r~yikdD~ifi~~~~  166 (167)
T cd03782         152 -RDFIKGDDVIFLLTM  166 (167)
T ss_pred             -cCcccCCeEEEEEec
Confidence             789999999998775

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=99.64  E-value=1e-15  Score=123.64  Aligned_cols=122  Identities=23%  Similarity=0.387  Sum_probs=94.1

Q ss_pred             ceEEEEEecccccc-----cceeecccc---cceEeeeccCCceEEEEecCCCCC-CCCCeEEEEEE-cc-CCCCCCCCe
Q 041904          176 YYHTWKVSNFSSLL-----DEFYESESF---GCYKWYANYSMDVKILLYPNGNGE-AKGNCISLFLD-VS-QSSIPPNTK  244 (317)
Q Consensus       176 ~~~~~~i~nfs~~~-----~~~~~S~~f---~g~~W~~~~~~~~~i~~yp~g~~~-~~~~~lS~yL~-~~-~~~~~~~~~  244 (317)
                      ..+.|+|+||+.+.     ...++||.|   .||+.        +|++||+|+.. ++++|+|||++ +. ..+.-.+|+
T Consensus         2 p~~iWkI~nfs~~~~~a~~~~~i~Sp~Fyt~~GYk~--------~l~~~lng~~~~~~g~~lSl~~~lm~Ge~D~~L~WP   73 (167)
T cd03783           2 PNAVWRVRNFSQILENTTKGDVLQSPRFYSPEGYGY--------GVSLYPLSNESDYSGNYTGLYFHLCSGENDAVLEWP   73 (167)
T ss_pred             CceeEEECcHHHHHHhCcCCCeEECCCCccCCCceE--------EEEEEecCCCCCCCCCEEEEEEEEecccCCCcccCC
Confidence            45899999999876     347999999   59999        99999999874 56889999999 53 333458999


Q ss_pred             E-EEEEEEEEEECCCC----Cceee----e---------eeEEeeCC--------------CCCccccccccccccCCCC
Q 041904          245 L-LTKYFLCVENQMNG----KNSEV----E---------GEWLYTLT--------------NRAIGGRQFMTLAKLKDPT  292 (317)
Q Consensus       245 ~-~~~~~l~l~n~~~~----~~~~~----~---------~~~~F~~~--------------~~~~G~~~fi~~~~L~~~~  292 (317)
                      + .-+++|.|++|+..    .+...    .         ....|+..              +.++||+.|+++++|+.  
T Consensus        74 ~~~~~itl~llDQ~~~~~~r~~~~~sf~~d~~~~~~~~~~~~~f~rP~~~~~~~~~~~~~~~~gfG~~~Fish~~L~~--  151 (167)
T cd03783          74 ALNRQAIITVLDQDPDVRLRMSSSRSFTTDKSQTSSAINGTLRWDRPSRVGTYDTSCDCFRGIDFGWSTFISHSQLRR--  151 (167)
T ss_pred             CcCCEEEEEEEcCCcchhhccccceeeecCCCcccccccccccccCCcccccccccccccCCcccccccceeHHHHhh--
Confidence            5 56999999999641    11110    0         01125433              35899999999999996  


Q ss_pred             CCceeCCEEEEEEEE
Q 041904          293 EGYLVDDSCIIKAEV  307 (317)
Q Consensus       293 ~gyl~dd~l~i~~~V  307 (317)
                      ++||.||+|.|.+++
T Consensus       152 r~yikdDtlfI~~~~  166 (167)
T cd03783         152 RSFLKNDDLIIFVDF  166 (167)
T ss_pred             CCcccCCeEEEEEec
Confidence            789999999999876

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

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

Probab=99.57  E-value=2.3e-15  Score=143.40  Aligned_cols=137  Identities=23%  Similarity=0.336  Sum_probs=113.7

Q ss_pred             eccccCCcEEEEEEcCcccccccccceEEcccEEeCCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC--C-CCCCEEE
Q 041904           10 AGRNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSS--L-PTGWEVN   86 (317)
Q Consensus        10 ~~~~~~~~~~~w~I~~fs~~~~~~~~~~~S~~F~~gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~--~-~~~w~v~   86 (317)
                      ++.+...-.|+|+|++|+.+.+    +.+||+|.+||+.|+|.++|+|+..    ..+||||+......  . ...|.|+
T Consensus        32 d~Ee~~~~sftW~vk~wsel~~----k~~Sp~F~vg~~twki~lfPqG~nq----~~~sVyLe~~pqe~e~~~gk~~~cc  103 (1089)
T COG5077          32 DVEELLEMSFTWKVKRWSELAK----KVESPPFSVGGHTWKIILFPQGNNQ----CNVSVYLEYEPQELEETGGKYYDCC  103 (1089)
T ss_pred             cHHHHhhcccceecCChhhhhh----hccCCcccccCeeEEEEEecccCCc----cccEEEEEeccchhhhhcCcchhhh
Confidence            4556677889999999999954    8999999999999999999999864    23999999876532  1 2359999


Q ss_pred             EEEEEEEEecCCCcEEEEEeeecccceeeeecccccccccccceeecccccCCCCc---eEeCCEEEEEEEEEEEeec
Q 041904           87 AITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNG---YLINDACVFGAEVFVVKNT  161 (317)
Q Consensus        87 ~~f~~~l~n~~~~~~~~~~~~~~~~~~~~~~F~~~~~~~G~~~fi~~~~l~~~~~~---yl~~d~l~i~~~v~v~~~~  161 (317)
                      |+|.|.|-|...+....       +|.+.|+|+....+||+.+|+.+..|..|+.|   |+.+|++.|+|.|+|.+.+
T Consensus       104 aqFaf~Is~p~~pti~~-------iN~sHhrFs~~~tDwGFt~f~dL~kl~~psp~~Ppfleeg~l~ItvyVRvlkdP  174 (1089)
T COG5077         104 AQFAFDISNPKYPTIEY-------INKSHHRFSMESTDWGFTNFIDLNKLIEPSPGRPPFLEEGTLVITVYVRVLKDP  174 (1089)
T ss_pred             hheeeecCCCCCCchhh-------hhcccccccccccccchhhhhhhhhhcCCCCCCCCcccCCeEEEEEEEEEEeCC
Confidence            99999999987654332       22377899999999999999999999876655   8999999999999999884

>smart00061 MATH meprin and TRAF homology

Probab=99.56  E-value=4.3e-14  Score=105.34  Aligned_cols=90  Identities=18%  Similarity=0.234  Sum_probs=74.8

Q ss_pred             EEEEEecccccc-cceeecccc--cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEEccCC-CCCCCCeEEEEEEEEE
Q 041904          178 HTWKVSNFSSLL-DEFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQS-SIPPNTKLLTKYFLCV  253 (317)
Q Consensus       178 ~~~~i~nfs~~~-~~~~~S~~f--~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~~~~~-~~~~~~~~~~~~~l~l  253 (317)
                      ++|+|+||+.+. ++.+.|+.|  +|++|        +|.+||+      ++|||+||.|... ..+..|++.|+++|.|
T Consensus         2 ~~~~~~~~~~~~~~~~~~S~~f~~~g~~W--------~i~~~p~------~~~lsl~L~~~~~~~~~~~w~v~a~~~~~l   67 (95)
T smart00061        2 LSHTFKNVSRLEEGESYFSPSEEHFNIPW--------RLKIYRK------NGFLSLYLHCEKEECDSRKWSIEAEFTLKL   67 (95)
T ss_pred             ceeEEEchhhcccCceEeCChhEEcCcee--------EEEEEEc------CCEEEEEEEeCCCcCCCCCeEEEEEEEEEE
Confidence            579999999985 678999999  99999        9999999      4799999995433 3334899999999999


Q ss_pred             EECCCCCceeeeeeEEeeCCCCCccccccc
Q 041904          254 ENQMNGKNSEVEGEWLYTLTNRAIGGRQFM  283 (317)
Q Consensus       254 ~n~~~~~~~~~~~~~~F~~~~~~~G~~~fi  283 (317)
                      ++++++.. .....+.|.. ..+|||++||
T Consensus        68 ~~~~~~~~-~~~~~~~F~~-~~~~G~~~fi   95 (95)
T smart00061       68 VSQNGKSL-SKKDKHVFEK-PSGWGFSKFI   95 (95)
T ss_pred             EeCCCCEE-eeeeeEEEcC-CCccceeeEC
Confidence            99987654 3455788986 6889999986

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

Probab=99.36  E-value=1e-12  Score=125.65  Aligned_cols=127  Identities=24%  Similarity=0.420  Sum_probs=104.9

Q ss_pred             CCceEEEEEecccccccceeecccc--cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEEccCCC---CC-CCCeEEE
Q 041904          174 PTYYHTWKVSNFSSLLDEFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSS---IP-PNTKLLT  247 (317)
Q Consensus       174 ~~~~~~~~i~nfs~~~~~~~~S~~f--~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~~~~~~---~~-~~~~~~~  247 (317)
                      ..-.++|+|++++.+.. ...||.|  |++.|        +|.++|.|+...   .+|+||...++.   .. ..|.|++
T Consensus        37 ~~~sftW~vk~wsel~~-k~~Sp~F~vg~~tw--------ki~lfPqG~nq~---~~sVyLe~~pqe~e~~~gk~~~cca  104 (1089)
T COG5077          37 LEMSFTWKVKRWSELAK-KVESPPFSVGGHTW--------KIILFPQGNNQC---NVSVYLEYEPQELEETGGKYYDCCA  104 (1089)
T ss_pred             hhcccceecCChhhhhh-hccCCcccccCeeE--------EEEEecccCCcc---ccEEEEEeccchhhhhcCcchhhhh
Confidence            34578999999999975 6789999  99999        999999998653   289999943322   12 3599999


Q ss_pred             EEEEEEEECCCCC-ceeeeeeEEeeCCCCCccccccccccccCCCCCC---ceeCCEEEEEEEEEEEee
Q 041904          248 KYFLCVENQMNGK-NSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEG---YLVDDSCIIKAEVTLHGL  312 (317)
Q Consensus       248 ~~~l~l~n~~~~~-~~~~~~~~~F~~~~~~~G~~~fi~~~~L~~~~~g---yl~dd~l~i~~~V~v~~~  312 (317)
                      +|.|.|-|+..+. ....+..|+|+....+|||.+|+.+..|..|+.|   |+.++++.|.|.|.|++.
T Consensus       105 qFaf~Is~p~~pti~~iN~sHhrFs~~~tDwGFt~f~dL~kl~~psp~~Ppfleeg~l~ItvyVRvlkd  173 (1089)
T COG5077         105 QFAFDISNPKYPTIEYINKSHHRFSMESTDWGFTNFIDLNKLIEPSPGRPPFLEEGTLVITVYVRVLKD  173 (1089)
T ss_pred             heeeecCCCCCCchhhhhcccccccccccccchhhhhhhhhhcCCCCCCCCcccCCeEEEEEEEEEEeC
Confidence            9999998877644 2245678899988899999999999999887766   688999999999999987

>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=99.08  E-value=1.3e-10  Score=105.21  Aligned_cols=261  Identities=19%  Similarity=0.193  Sum_probs=173.7

Q ss_pred             EEEEcCcccccccccceEEcccEEeCCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCCCCCCCEEEEEEEEEEEecCCC
Q 041904           20 LFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAITISFYSIKFKT   99 (317)
Q Consensus        20 ~w~I~~fs~~~~~~~~~~~S~~F~~gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~~~~w~v~~~f~~~l~n~~~~   99 (317)
                      .|.|.+++...    ..+||..|..+|..|++.+||.|+       ++|.|+.+....    +|.+.+.+++.+.|+...
T Consensus         7 ~~~~~~~~~~~----l~~ys~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~----~~~~~~~~~l~v~n~~~~   71 (297)
T KOG1987|consen    7 TWVISNFSSVG----LVIYSNGFVKGGCKWRLSAYPKGN-------YLSLTLSVSDSP----GWERYAKLRLTVVNQKSE   71 (297)
T ss_pred             ceeeccCcchh----hhccccceeecCceEEEEEecCCC-------EEEEEEEeccCC----CcceeEEEEEEEccCCCc
Confidence            39999998884    689999999999999999999973       688998887643    699999999999999887


Q ss_pred             cE-EEE-EeeecccceeeeecccccccccccceeecccccCCCCceEeCCEEEEEEEEEEEeecCccccccc--------
Q 041904          100 NI-LVS-KVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSM--------  169 (317)
Q Consensus       100 ~~-~~~-~~~~~~~~~~~~~F~~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v~~~~~~~~~~~~--------  169 (317)
                      .. ... ...      ....|..-...||+...++...+.++..||+.++.+++-+.+.|.+..+..+....        
T Consensus        72 ~~~~~~~~~~------~~~~~~~~~~~~g~~~~~~~~~~~~~~~g~~~~~~~~~~a~~~V~~~~~~~d~~~~~~~~~~~~  145 (297)
T KOG1987|consen   72 KYLSTVEEGF------SWFRFNKVLKEWGFGKMLPLTLLIDCSNGFLVAHKLVLVARSEVFEAMGKSDVFKESSKLITLL  145 (297)
T ss_pred             ceeeeeeeeE------EeccccccccccCcccccChHHhhcccCcEEEcCceEEEeeecceeeecccccchhcccccccc
Confidence            55 332 111      22233333678999999999999988899999999999999888888887776433        


Q ss_pred             ccCCCC----ceEEEEEeccccccc----ceeecccc--cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccCCC
Q 041904          170 MHDPPT----YYHTWKVSNFSSLLD----EFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQSS  238 (317)
Q Consensus       170 ~~~~~~----~~~~~~i~nfs~~~~----~~~~S~~f--~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~~~  238 (317)
                      ...+..    ..|+|.+.+++....    ..+.+..|  ++-.|        ++.++|.+....+..+++.+|. .+...
T Consensus       146 d~~~~~~~~~~~F~~~~s~~~~~~~~~~~~~~~a~~f~~~~~~l--------k~~~~~~l~~~~~~~~~~~~l~~~~~~~  217 (297)
T KOG1987|consen  146 EEKPEVLEALNGFQVLPSQVSSVERIFEKHPDLAAAFKYKNRHL--------KLACMPVLLSLIETLNVSQSLQEASNYD  217 (297)
T ss_pred             ccchhhHhhhceEEEeccchHHHHHhhcCChhhhhccccccHHH--------HHHHHHHHHHHHHhhhhcccHHHhchhH
Confidence            222334    789999999998873    24555667  99999        9999999977655667788887 43211


Q ss_pred             C--CCCCeEEEEEEEEEEECCCCC--c-eeee-eeEEeeCCCCCccccccccccccCCCCCCceeCCEEEEEEEEEEE
Q 041904          239 I--PPNTKLLTKYFLCVENQMNGK--N-SEVE-GEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLH  310 (317)
Q Consensus       239 ~--~~~~~~~~~~~l~l~n~~~~~--~-~~~~-~~~~F~~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v~  310 (317)
                      .  ...-.+.+......+|+...+  + ..+. ...+.......+ ..++.++.++.....+++.++++.+++....+
T Consensus       218 ~~~~~~~~~~~~~~~~~ld~l~~~~~~~~~k~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  294 (297)
T KOG1987|consen  218 LKEAKSALTYVIAAGFKLDWLEKKLNEVKEKKKKDLWYEIRLQEL-EEELKSLKDKCSDLEGLLVKDKAEVEAESEPL  294 (297)
T ss_pred             HHHHHHHHHHHHhccchHhHHHHHHHHHHHhhhHHHHHHHHHHHH-HHHHHhhhhhhhhHHHHHHhhhhhhhcccCCc
Confidence            1  011112222222234443321  1 1111 001111000111 34455555554444567777777777765544

>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=98.31  E-value=6.7e-06  Score=74.40  Aligned_cols=118  Identities=35%  Similarity=0.498  Sum_probs=93.5

Q ss_pred             EEEEEecccccccceeecccc--cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEEccCCCCCCCCeEEEEEEEEEEE
Q 041904          178 HTWKVSNFSSLLDEFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLLTKYFLCVEN  255 (317)
Q Consensus       178 ~~~~i~nfs~~~~~~~~S~~f--~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~~~~~~~~~~~~~~~~~~l~l~n  255 (317)
                      +.|.+.+++... ..++|..|  +++.|        ++.+||.|+      +++.|+.+...   ..|.+.+.++|.+.|
T Consensus         6 ~~~~~~~~~~~~-l~~ys~~~~~~~~~~--------~~~~~~~~~------~~~~~~~~~~~---~~~~~~~~~~l~v~n   67 (297)
T KOG1987|consen    6 FTWVISNFSSVG-LVIYSNGFVKGGCKW--------RLSAYPKGN------YLSLTLSVSDS---PGWERYAKLRLTVVN   67 (297)
T ss_pred             cceeeccCcchh-hhccccceeecCceE--------EEEEecCCC------EEEEEEEeccC---CCcceeEEEEEEEcc
Confidence            448889988877 67788888  99999        999999974      78999884311   189999999999999


Q ss_pred             CCCCCc-eee-eeeEEeeCC--CCCccccccccccccCCCCCCceeCCEEEEEEEEEEEeee
Q 041904          256 QMNGKN-SEV-EGEWLYTLT--NRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGLV  313 (317)
Q Consensus       256 ~~~~~~-~~~-~~~~~F~~~--~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v~~~~  313 (317)
                      +...++ ... .....|...  ...||+...++...+.+.+.||++++.+++-+.+.|.+..
T Consensus        68 ~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~g~~~~~~~~~~a~~~V~~~~  129 (297)
T KOG1987|consen   68 QKSEKYLSTVEEGFSWFRFNKVLKEWGFGKMLPLTLLIDCSNGFLVAHKLVLVARSEVFEAM  129 (297)
T ss_pred             CCCcceeeeeeeeEEeccccccccccCcccccChHHhhcccCcEEEcCceEEEeeecceeee
Confidence            988754 444 344454443  4789999999999999888999999888888887776654

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

Probab=98.16  E-value=1.7e-06  Score=90.62  Aligned_cols=131  Identities=21%  Similarity=0.193  Sum_probs=104.6

Q ss_pred             cEEEEEEcCcccccccccceEEcccEEeCCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCCCCCCCEEEEEEEEEEEec
Q 041904           17 SHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAITISFYSIK   96 (317)
Q Consensus        17 ~~~~w~I~~fs~~~~~~~~~~~S~~F~~gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~~~~w~v~~~f~~~l~n~   96 (317)
                      ...+|.+.+.....    ....||.|..|+.+|++.+.|+++.    ...+++|+.+...... ..|.+.+++.+.+.|.
T Consensus        27 ~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~-~~~s~~~~~~~~v~~~   97 (1093)
T KOG1863|consen   27 QSTTIDGIDDKSLL----YRALSSNFGAGATKWKILIAPKVNS----LQSTRKKLEVMPSQSL-KSWSCGAQAVLRVKNT   97 (1093)
T ss_pred             ccccccCcCcchhh----hHhcCccccccccceeeeeccccCc----ccceeEEeeeccCCCC-cceEecchhhhccccC
Confidence            34446554444443    2778999999999999999999984    4679999999887655 5599999999999993


Q ss_pred             CCCcEEEEEeeecccceeeeecccccccccccceeecccccCCCCceEeCCEEEEEEEEEEEeecCc
Q 041904           97 FKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKNTFK  163 (317)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~F~~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v~~~~~~  163 (317)
                      .++..... .      +..|.|.....+||+..|+.++++.++..+|+.+|++.++++|.+...++.
T Consensus        98 ~~~~~~~~-~------~~~h~~~~~~~dwg~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~~~~~  157 (1093)
T KOG1863|consen   98 IDNLPDPE-K------AIHHVFTADERDWGFSCFSTSSDIRKPEDGYVRNGLEKLEKRVRVEQPTSL  157 (1093)
T ss_pred             CCCchhhh-h------hhhhcccccccchhhccchhHhhccCcccccccccceeeeeeeeeecCCcc
Confidence            33322222 1      277889988899999999999999999999999999999999999877654

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

Probab=97.84  E-value=1.4e-05  Score=83.82  Aligned_cols=125  Identities=24%  Similarity=0.253  Sum_probs=99.8

Q ss_pred             EEEEecccccccceeecccc--cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEEccCCCCCCCCeEEEEEEEEEEEC
Q 041904          179 TWKVSNFSSLLDEFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLLTKYFLCVENQ  256 (317)
Q Consensus       179 ~~~i~nfs~~~~~~~~S~~f--~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~~~~~~~~~~~~~~~~~~l~l~n~  256 (317)
                      +|...+...+.. ...|+.|  ++.+|        +|.+.|+++.   ...+++|+.+.+......|.+.+++.+.+.|.
T Consensus        30 ~~~~~~~~~~~~-~~~~~~~~~~~~~~--------~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~s~~~~~~~~v~~~   97 (1093)
T KOG1863|consen   30 TIDGIDDKSLLY-RALSSNFGAGATKW--------KILIAPKVNS---LQSTRKKLEVMPSQSLKSWSCGAQAVLRVKNT   97 (1093)
T ss_pred             cccCcCcchhhh-HhcCccccccccce--------eeeeccccCc---ccceeEEeeeccCCCCcceEecchhhhccccC
Confidence            355555555444 6778888  89999        9999999883   46799999954433225599999999999993


Q ss_pred             CCCC-ceeeeeeEEeeCCCCCccccccccccccCCCCCCceeCCEEEEEEEEEEEeeecc
Q 041904          257 MNGK-NSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGLVLA  315 (317)
Q Consensus       257 ~~~~-~~~~~~~~~F~~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v~~~~~~  315 (317)
                      .+.. .......|.|.....+||+.+|+.+.++.+++.||+.+|++.++++|.+...++.
T Consensus        98 ~~~~~~~~~~~~h~~~~~~~dwg~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~v~~~~~~  157 (1093)
T KOG1863|consen   98 IDNLPDPEKAIHHVFTADERDWGFSCFSTSSDIRKPEDGYVRNGLEKLEKRVRVEQPTSL  157 (1093)
T ss_pred             CCCchhhhhhhhhcccccccchhhccchhHhhccCcccccccccceeeeeeeeeecCCcc
Confidence            3333 3355678899988899999999999999999999999999999999999877654

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

Probab=97.67  E-value=2.6e-05  Score=73.07  Aligned_cols=83  Identities=17%  Similarity=0.247  Sum_probs=70.8

Q ss_pred             ccCCcEEEEEEcCcccccc----cccceEEcccEEe--CCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC-CCCCCEE
Q 041904           13 NAAPSHYLFKIESFSLLSK----ASVEQLILDNFEA--GGYKWKLSIHLTGSKSVNVTDHISIYLELAETSS-LPTGWEV   85 (317)
Q Consensus        13 ~~~~~~~~w~I~~fs~~~~----~~~~~~~S~~F~~--gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~-~~~~w~v   85 (317)
                      ....|++.|+|.+|...+.    ..+..++|+.|+.  .||+.+..+|.+|+.. +.+.++|+|+.++++.. ..+.|++
T Consensus       276 ~~~~g~~iwki~~~~~~~~e~~~~~~~~~~S~~f~t~~~Gyk~~~~~~lng~g~-~~~~~~s~~~~~~~ge~d~~l~wpf  354 (391)
T KOG0297|consen  276 RSYDGTLIWKIPDYGRKKQEAVAGATLSLFSPAFYTSKYGYKLCARIYLNGDGT-GKGTHLSLYFVVMRGEYDALLPWPF  354 (391)
T ss_pred             hccCCEEEEEecchhhhhHHHHhccCccccccccccccccHHHHhHhhhcCCCC-CCcceeeeeeeecccCcccccccCC
Confidence            3457999999999965554    2467899999997  6999999999999876 37789999999999876 3678999


Q ss_pred             EEEEEEEEEec
Q 041904           86 NAITISFYSIK   96 (317)
Q Consensus        86 ~~~f~~~l~n~   96 (317)
                      .-.+++.+++|
T Consensus       355 ~~~v~~~l~dq  365 (391)
T KOG0297|consen  355 RQKVTLMLLDQ  365 (391)
T ss_pred             CCceEEEEecc
Confidence            99999999999

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

Probab=96.06  E-value=0.0043  Score=58.23  Aligned_cols=75  Identities=23%  Similarity=0.266  Sum_probs=63.5

Q ss_pred             CCceEEEEEecccccc-------cceeecccc----cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-cc-CCCCC
Q 041904          174 PTYYHTWKVSNFSSLL-------DEFYESESF----GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VS-QSSIP  240 (317)
Q Consensus       174 ~~~~~~~~i~nfs~~~-------~~~~~S~~f----~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~-~~~~~  240 (317)
                      ..++..|+|.++...+       ...+.|+.|    +||+.        +..+|-+|++.+++.++|+|+. +. ..+.-
T Consensus       278 ~~g~~iwki~~~~~~~~e~~~~~~~~~~S~~f~t~~~Gyk~--------~~~~~lng~g~~~~~~~s~~~~~~~ge~d~~  349 (391)
T KOG0297|consen  278 YDGTLIWKIPDYGRKKQEAVAGATLSLFSPAFYTSKYGYKL--------CARIYLNGDGTGKGTHLSLYFVVMRGEYDAL  349 (391)
T ss_pred             cCCEEEEEecchhhhhHHHHhccCccccccccccccccHHH--------HhHhhhcCCCCCCcceeeeeeeecccCcccc
Confidence            4688999999996554       347788888    99999        9999999999988999999998 53 33445


Q ss_pred             CCCeEEEEEEEEEEEC
Q 041904          241 PNTKLLTKYFLCVENQ  256 (317)
Q Consensus       241 ~~~~~~~~~~l~l~n~  256 (317)
                      ..|++.-.+++.+++|
T Consensus       350 l~wpf~~~v~~~l~dq  365 (391)
T KOG0297|consen  350 LPWPFRQKVTLMLLDQ  365 (391)
T ss_pred             cccCCCCceEEEEecc
Confidence            7899999999999999

---

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	317
2foj_A	155	Ubiquitin carboxyl-terminal hydrolase 7; MATH doma	4e-24
2foj_A	155	Ubiquitin carboxyl-terminal hydrolase 7; MATH doma	8e-21
3ivv_A	145	Speckle-type POZ protein; protein binding, nucleus	3e-23
3ivv_A	145	Speckle-type POZ protein; protein binding, nucleus	8e-16
1flk_A	228	TNF receptor associated factor 3; TNF signaling, T	8e-15
1flk_A	228	TNF receptor associated factor 3; TNF signaling, T	1e-07
2gkw_A	192	TNF receptor-associated factor 3; CD40, NF-KB sign	1e-14
2gkw_A	192	TNF receptor-associated factor 3; CD40, NF-KB sign	1e-07
1ca9_A	192	TRAF2, protein (TNF receptor associated factor 2);	3e-14
1ca9_A	192	TRAF2, protein (TNF receptor associated factor 2);	2e-08
1d00_A	168	Tumor necrosis factor receptor associated protein	2e-13
1d00_A	168	Tumor necrosis factor receptor associated protein	9e-08
2f1z_A	522	Ubiquitin carboxyl-terminal hydrolase 7; hausp, US	9e-13
2f1z_A	522	Ubiquitin carboxyl-terminal hydrolase 7; hausp, US	1e-10
1lb6_A	160	TNF receptor-associated factor 6; TRAF6-CD40 compl	1e-12
1lb6_A	160	TNF receptor-associated factor 6; TRAF6-CD40 compl	5e-11
3hqi_A	312	Speckle-type POZ protein; SPOP, ubiquitin, puckere	5e-12
3hqi_A	312	Speckle-type POZ protein; SPOP, ubiquitin, puckere	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	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 = 95.3 bits (237), Expect = 4e-24
 Identities = 26/136 (19%), Positives = 45/136 (33%), Gaps = 13/136 (9%)

Query: 177 YHTWKVSNFSSLLDEFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGN-CISLFLD 233
              + V  FS L  E   S         W        KI++ P    +      +  FL 
Sbjct: 20  TFQFTVERFSRL-SESVLSPPCFVRNLPW--------KIMVMPRFYPDRPHQKSVGFFLQ 70

Query: 234 VSQSSIPPNTKLLTKYFLCVENQMNGKNSEV-EGEWLYTLTNRAIGGRQFMTLAKLKDPT 292
            +  S   +     +  L + N  + + S       L+       G   FM  +++ DP 
Sbjct: 71  CNAESDSTSWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPE 130

Query: 293 EGYLVDDSCIIKAEVT 308
           +G++ DD    +  V 
Sbjct: 131 KGFIDDDKVTFEVFVQ 146

>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 = 86.0 bits (213), Expect = 8e-21
 Identities = 25/148 (16%), Positives = 49/148 (33%), Gaps = 14/148 (9%)

Query: 15  APSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELA 74
           + + + F +E FS LS    E ++          WK+ +             +  +L+  
Sbjct: 17  SEATFQFTVERFSRLS----ESVLSPPCFVRNLPWKIMVMPRFYPDRPHQKSVGFFLQC- 71

Query: 75  ETSSLPTGWEVNA-ITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDL 133
              S  T W  +A   +   + +            S    I   F   ++ +G + F+  
Sbjct: 72  NAESDSTSWSCHAQAVLKIINYRDD--------EKSFSRRISHLFFHKENDWGFSNFMAW 123

Query: 134 KTFSDPLNGYLINDACVFGAEVFVVKNT 161
              +DP  G++ +D   F   V      
Sbjct: 124 SEVTDPEKGFIDDDKVTFEVFVQADAPH 151

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

 Score = 92.3 bits (229), Expect = 3e-23
 Identities = 29/135 (21%), Positives = 56/135 (41%), Gaps = 4/135 (2%)

Query: 175 TYYHTWKVSNFSSLLDEFYESESFGCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDV 234
            + + W ++NFS   +E  E      +   AN  +   + + P G  E   + +SL+L +
Sbjct: 10  KFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEESKDYLSLYLLL 69

Query: 235 SQSSIPPNTKLLTKYFLCVENQMNGKNSEVEGEWLYTLT-NRAIGGRQFMTLAKLKDPTE 293
                 P +++  K+   + N    +   +E +  Y     +  G ++F+    L D   
Sbjct: 70  VS---CPKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEAN 126

Query: 294 GYLVDDSCIIKAEVT 308
           G L DD   +  EV+
Sbjct: 127 GLLPDDKLTLFCEVS 141

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

 Score = 72.3 bits (177), Expect = 8e-16
 Identities = 34/146 (23%), Positives = 53/146 (36%), Gaps = 15/146 (10%)

Query: 18  HYLFKIESFSLLSKASVEQLILDNFEAGG---YKWKLSIHLTGSKSVNVTDHISIYLELA 74
            Y++ I +FS   +   E +    F +G     KW L ++  G    +  D++S+YL L 
Sbjct: 12  SYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEES-KDYLSLYLLLV 70

Query: 75  ETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLK 134
                    EV A    F  +  K            +     +       +G  KFI   
Sbjct: 71  S----CPKSEVRA-KFKFSILNAKGE------ETKAMESQRAYRFVQGKDWGFKKFIRRD 119

Query: 135 TFSDPLNGYLINDACVFGAEVFVVKN 160
              D  NG L +D      EV VV++
Sbjct: 120 FLLDEANGLLPDDKLTLFCEVSVVQD 145

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

 Score = 71.7 bits (175), Expect = 8e-15
 Identities = 33/162 (20%), Positives = 51/162 (31%), Gaps = 39/162 (24%)

Query: 178 HTWKVSNFSSLLDEFYE-------SESF----GCYKWYANYSMDVKILLYPNGNGEAKGN 226
             WK+ ++     E          S+ F      YK            +Y NG+G  KG 
Sbjct: 78  LIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMC--------ARVYLNGDGMGKGT 129

Query: 227 CISLFLDVSQSSIPPNTKLLT-----KYFLCVENQMNGKNSEVEGEWL----------YT 271
            +SLF  + +        LL      K  L + +Q + +    +                
Sbjct: 130 HLSLFFVIMRG---EYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTG 186

Query: 272 LTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGLV 313
             N A G   F+    L+     Y+ DD+  IK  V    L 
Sbjct: 187 EMNIASGCPVFVAQTVLE--NGTYIKDDTIFIKVIVDTSDLP 226

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

 Score = 50.5 bits (120), Expect = 1e-07
 Identities = 22/148 (14%), Positives = 48/148 (32%), Gaps = 12/148 (8%)

Query: 17  SHYLFKIESFSLLSKASVEQLIL----DNFEAG--GYKWKLSIHLTGSKSVNVTDHISIY 70
              ++KI  +    + +V    L      F  G  GYK    ++L G   +    H+S++
Sbjct: 76  GVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNG-DGMGKGTHLSLF 134

Query: 71  LELAET---SSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGV 127
             +      + LP  ++     +       + ++  +   +   +   K    M    G 
Sbjct: 135 FVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGC 194

Query: 128 AKFIDLKTFSDPLNGYLINDACVFGAEV 155
             F+      +    Y+ +D       V
Sbjct: 195 PVFVAQTVLEN--GTYIKDDTIFIKVIV 220

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

 Score = 70.4 bits (172), Expect = 1e-14
 Identities = 33/165 (20%), Positives = 50/165 (30%), Gaps = 43/165 (26%)

Query: 177 YHTWKVSNFSSLLDE-------------FYESESFGCYKWYANYSMDVKILLYPNGNGEA 223
              WK+ ++     E             FY       YK            +Y NG+G  
Sbjct: 41  VLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGY--FGYKMC--------ARVYLNGDGMG 90

Query: 224 KGNCISLFLDVSQSSIPPNTKLLT-----KYFLCVENQMNGKNSEVEGEWL--------- 269
           KG  +SLF  + +        LL      K  L + +Q + +    +             
Sbjct: 91  KGTHLSLFFVIMRG---EYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKK 147

Query: 270 -YTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGLV 313
                N A G   F+    L+     Y+ DD+  IK  V    L 
Sbjct: 148 PTGEMNIASGCPVFVAQTVLE--NGTYIKDDTIFIKVIVDTSDLP 190

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

 Score = 50.0 bits (119), Expect = 1e-07
 Identities = 22/148 (14%), Positives = 48/148 (32%), Gaps = 12/148 (8%)

Query: 17  SHYLFKIESFSLLSKASVEQLIL----DNFEAG--GYKWKLSIHLTGSKSVNVTDHISIY 70
              ++KI  +    + +V    L      F  G  GYK    ++L G   +    H+S++
Sbjct: 40  GVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNG-DGMGKGTHLSLF 98

Query: 71  LELAET---SSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGV 127
             +      + LP  ++     +       + ++  +   +   +   K    M    G 
Sbjct: 99  FVIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGC 158

Query: 128 AKFIDLKTFSDPLNGYLINDACVFGAEV 155
             F+      +    Y+ +D       V
Sbjct: 159 PVFVAQTVLEN--GTYIKDDTIFIKVIV 184

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

 Score = 68.9 bits (168), Expect = 3e-14
 Identities = 43/166 (25%), Positives = 63/166 (37%), Gaps = 41/166 (24%)

Query: 174 PTYYHTWKVSNFSSLLDE-------------FYESESFGCYKWYANYSMDVKILLYPNGN 220
                 WK+S+F+    E             FY S     YK          + +Y NG+
Sbjct: 41  YDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSR--YGYKMC--------LRIYLNGD 90

Query: 221 GEAKGNCISLFLDVSQSSIPPNTKLLT-----KYFLCVENQMNGKNSEVEGEWLYTLT-- 273
           G  +G  +SLF  V +    PN  LL      K  L + +Q N ++         T +  
Sbjct: 91  GTGRGTHLSLFFVVMKG---PNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSF 147

Query: 274 -------NRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGL 312
                  N A G   F  ++K++     Y+ DD+  IKA V L GL
Sbjct: 148 QRPVNDMNIASGCPLFCPVSKME-AKNSYVRDDAIFIKAIVDLTGL 192

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

 Score = 52.3 bits (125), Expect = 2e-08
 Identities = 28/147 (19%), Positives = 56/147 (38%), Gaps = 10/147 (6%)

Query: 17  SHYLFKIESFSLLSKASVEQLIL----DNFEAG--GYKWKLSIHLTGSKSVNVTDHISIY 70
             +++KI  F+   + +V   I       F     GYK  L I+L G        H+S++
Sbjct: 43  GVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNG-DGTGRGTHLSLF 101

Query: 71  LELAETSSLPT-GWEVNA-ITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVA 128
             + +  +     W  N  +T+       + +++ +   + T +   +  + M    G  
Sbjct: 102 FVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCP 161

Query: 129 KFIDLKTFSDPLNGYLINDACVFGAEV 155
            F  +    +  N Y+ +DA    A V
Sbjct: 162 LFCPVSKM-EAKNSYVRDDAIFIKAIV 187

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

 Score = 66.2 bits (161), Expect = 2e-13
 Identities = 42/164 (25%), Positives = 63/164 (38%), Gaps = 37/164 (22%)

Query: 174 PTYYHTWKVSNFSSLLDE-------FYESESF----GCYKWYANYSMDVKILLYPNGNGE 222
                 WK+S+F+    E          S +F      YK          + +Y NG+G 
Sbjct: 17  YDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMC--------LRIYLNGDGT 68

Query: 223 AKGNCISLFLDVSQSSIPPNTKLLT-----KYFLCVENQMNGKNSEVEGEWLYTLT---- 273
            +G  +SLF  V +    PN  LL      K  L + +Q N ++         T +    
Sbjct: 69  GRGTHLSLFFVVMKG---PNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQR 125

Query: 274 -----NRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGL 312
                N A G   F  ++K+ +    Y+ DD+  IKA V L GL
Sbjct: 126 PVNDMNIASGCPLFCPVSKM-EAKNSYVRDDAIFIKAIVDLTGL 168

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

 Score = 50.0 bits (119), Expect = 9e-08
 Identities = 28/146 (19%), Positives = 56/146 (38%), Gaps = 10/146 (6%)

Query: 18  HYLFKIESFSLLSKASVEQLIL----DNFEAG--GYKWKLSIHLTGSKSVNVTDHISIYL 71
            +++KI  F+   + +V   I       F     GYK  L I+L G        H+S++ 
Sbjct: 20  VFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNG-DGTGRGTHLSLFF 78

Query: 72  ELAETSSLPT-GWEVNA-ITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAK 129
            + +  +     W  N  +T+       + +++ +   + T +   +  + M    G   
Sbjct: 79  VVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPL 138

Query: 130 FIDLKTFSDPLNGYLINDACVFGAEV 155
           F  +    +  N Y+ +DA    A V
Sbjct: 139 FCPVSKM-EAKNSYVRDDAIFIKAIV 163

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

 Score = 67.7 bits (165), Expect = 9e-13
 Identities = 25/135 (18%), Positives = 45/135 (33%), Gaps = 13/135 (9%)

Query: 177 YHTWKVSNFSSLLDEFYESESF--GCYKWYANYSMDVKILLYPNGNGEAKGN-CISLFLD 233
              + V  FS L +    S         W        KI++ P    +      +  FL 
Sbjct: 32  TFQFTVERFSRLSESVL-SPPCFVRNLPW--------KIMVMPRFYPDRPHQKSVGFFLQ 82

Query: 234 VSQSSIPPNTKLLTKYFLCVENQMNGKNSEV-EGEWLYTLTNRAIGGRQFMTLAKLKDPT 292
            +  S   +     +  L + N  + + S       L+       G   FM  +++ DP 
Sbjct: 83  CNAESDSTSWSCHAQAVLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPE 142

Query: 293 EGYLVDDSCIIKAEV 307
           +G++ DD    +  V
Sbjct: 143 KGFIDDDKVTFEVFV 157

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

 Score = 60.8 bits (147), Expect = 1e-10
 Identities = 24/149 (16%), Positives = 49/149 (32%), Gaps = 18/149 (12%)

Query: 17  SHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAET 76
           + + F +E FS LS+     ++          WK+ +             +  +L+    
Sbjct: 31  ATFQFTVERFSRLSE----SVLSPPCFVRNLPWKIMVMPRFYPDRPHQKSVGFFLQ-CNA 85

Query: 77  SSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINV---IVKHFHAMKSKYGVAKFIDL 133
            S  T W  +A             + +   R+   +    I   F   ++ +G + F+  
Sbjct: 86  ESDSTSWSCHA---QAV-------LKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAW 135

Query: 134 KTFSDPLNGYLINDACVFGAEVFVVKNTF 162
              +DP  G++ +D   F   V       
Sbjct: 136 SEVTDPEKGFIDDDKVTFEVFVQADAPHG 164

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

 Score = 63.8 bits (155), Expect = 1e-12
 Identities = 30/167 (17%), Positives = 49/167 (29%), Gaps = 47/167 (28%)

Query: 177 YHTWKVSNFSSLLDE-------------FYESESFGCYKWYANYSMDVKILLYPNGNGEA 223
            + WK+ NF   L               FY  +  G YK          + L+       
Sbjct: 6   IYIWKIGNFGMHLKCQEEEKPVVIHSPGFYTGK-PG-YKLC--------MRLHLQLPTAQ 55

Query: 224 K-GNCISLFLDVSQSSIPPNTKLLT-----KYFLCVENQMNGKNSEVEGEWLYTLTNRAI 277
           +  N ISLF+   Q         L         L + +Q      +   E +        
Sbjct: 56  RCANYISLFVHTMQG---EYDSHLPWPFQGTIRLTILDQSEAPVRQNHEEIMDAKPELLA 112

Query: 278 -------------GGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHG 311
                        G   FM L  L+     ++ DD+ +++ EV+   
Sbjct: 113 FQRPTIPRNPKGFGYVTFMHLEALRQ--RTFIKDDTLLVRCEVSTRF 157

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

 Score = 59.2 bits (143), Expect = 5e-11
 Identities = 24/155 (15%), Positives = 50/155 (32%), Gaps = 14/155 (9%)

Query: 18  HYLFKIESFSLLSKASVEQLIL----DNFEAG--GYKWKLSIHLTGSKSVNVTDHISIYL 71
            Y++KI +F +  K   E+  +      F  G  GYK  + +HL    +    ++IS+++
Sbjct: 6   IYIWKIGNFGMHLKCQEEEKPVVIHSPGFYTGKPGYKLCMRLHLQLPTAQRCANYISLFV 65

Query: 72  ELAETSSLPT-GWEVNAITISF----YSIKFKTNILVSKVRNSTINVIVKHFHAMKSK-Y 125
              +        W                  + N          +    +       K +
Sbjct: 66  HTMQGEYDSHLPWPFQGTIRLTILDQSEAPVRQNHEEIMDAKPELLAFQRPTIPRNPKGF 125

Query: 126 GVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKN 160
           G   F+ L+        ++ +D  +   EV    +
Sbjct: 126 GYVTFMHLEALRQ--RTFIKDDTLLVRCEVSTRFD 158

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

 Score = 64.5 bits (157), Expect = 5e-12
 Identities = 30/145 (20%), Positives = 58/145 (40%), Gaps = 20/145 (13%)

Query: 175 TYYHTWKVSNFSSLLD---EFYESESF-----GCYKWYANYSMDVKILLYPNGNGEAKGN 226
            + + W ++NFS   +   E  +S +F        KW         + + P G  E   +
Sbjct: 6   KFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWC--------LRVNPKGLDEESKD 57

Query: 227 CISLFLDVSQSSIPPNTKLLTKYFLCVENQMNGKNSEVEGEWLYTLT-NRAIGGRQFMTL 285
            +SL+L +      P +++  K+   + N    +   +E +  Y     +  G ++F+  
Sbjct: 58  YLSLYLLLVSC---PKSEVRAKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRR 114

Query: 286 AKLKDPTEGYLVDDSCIIKAEVTLH 310
             L D   G L DD   +  EV++ 
Sbjct: 115 GFLLDEANGLLPDDKLTLFCEVSVV 139

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

 Score = 53.7 bits (129), Expect = 2e-08
 Identities = 40/189 (21%), Positives = 64/189 (33%), Gaps = 26/189 (13%)

Query: 17  SHYLFKIESFSLLSKASVEQLILDNFEAGG---YKWKLSIHLTGSKSVNVTDHISIYLEL 73
             Y++ I +FS   +   E +    F +G     KW L ++  G    +  D++S+YL L
Sbjct: 7   FSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEES-KDYLSLYLLL 65

Query: 74  AETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDL 133
                     EV A    F SI          + +        +       +G  KFI  
Sbjct: 66  VSCPK----SEVRAK-FKF-SILNAKGEETKAMESQRA-----YRFVQGKDWGFKKFIRR 114

Query: 134 KTFSDPLNGYLINDACVFGAEVFVVKNTFKGECLSMM---HDPPTYYHTWKVSNFSSLLD 190
               D  NG L +D      EV VV+++      + M     P            +  L 
Sbjct: 115 GFLLDEANGLLPDDKLTLFCEVSVVQDSVNISGQNTMNMVKVPE--------CRLADELG 166

Query: 191 EFYESESFG 199
             +E+  F 
Sbjct: 167 GLWENSRFT 175

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 41.8 bits (97), Expect = 2e-04
 Identities = 52/349 (14%), Positives = 95/349 (27%), Gaps = 88/349 (25%)

Query: 1   MSTEGGAVLAGRNAAPSHYL-----FKIESFSL-LSKASVEQLILDNFEAGGYKWKLSIH 54
           +   G   +A  +   S+ +     FKI  F L L   +  + +L+  +   Y+   +  
Sbjct: 158 VLGSGKTWVAL-DVCLSYKVQCKMDFKI--FWLNLKNCNSPETVLEMLQKLLYQIDPNWT 214

Query: 55  LTGSKSVNVTDHI-SIYLELAE---TSSLPTG-------WEVNAITISFYSIKFKTNILV 103
                S N+   I SI  EL     +                 A   +F        IL+
Sbjct: 215 SRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWN-AF---NLSCKILL 270

Query: 104 ----SKVRNSTINVIVKHFHAMKSKYG---------VAKFIDLKTFSDPLNGYLIN--DA 148
                +V +        H                  + K++D +    P      N    
Sbjct: 271 TTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRL 330

Query: 149 CVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWKVSNFSSL-------LDEFYESESFGCY 201
            +                   + D    +  WK  N   L       L+    +E    +
Sbjct: 331 SIIAE---------------SIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMF 375

Query: 202 KWYANYSMDVKI---LLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLLTKYFLCVENQMN 258
              + +     I   LL            + ++ DV +S +      L KY L  +    
Sbjct: 376 DRLSVFPPSAHIPTILL-----------SL-IWFDVIKSDVMVVVNKLHKYSLVEKQPKE 423

Query: 259 GKNS--------EVEGEWLYTLTNRAIG----GRQFMTLAKLKDPTEGY 295
              S        +V+ E  Y L    +      + F +   +    + Y
Sbjct: 424 STISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQY 472

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	317
2foj_A	155	Ubiquitin carboxyl-terminal hydrolase 7; MATH doma	99.96
3ivv_A	145	Speckle-type POZ protein; protein binding, nucleus	99.96
2foj_A	155	Ubiquitin carboxyl-terminal hydrolase 7; MATH doma	99.96
4gjh_A	178	TNF receptor-associated factor 5; TRAF domain, imm	99.95
1lb6_A	160	TNF receptor-associated factor 6; TRAF6-CD40 compl	99.94
4ghu_A	198	TNF receptor-associated factor 3; alpha/beta, inna	99.94
3ivv_A	145	Speckle-type POZ protein; protein binding, nucleus	99.94
1d00_A	168	Tumor necrosis factor receptor associated protein	99.93
1ca9_A	192	TRAF2, protein (TNF receptor associated factor 2);	99.93
2gkw_A	192	TNF receptor-associated factor 3; CD40, NF-KB sign	99.93
1flk_A	228	TNF receptor associated factor 3; TNF signaling, T	99.92
4gjh_A	178	TNF receptor-associated factor 5; TRAF domain, imm	99.92
3hqi_A	312	Speckle-type POZ protein; SPOP, ubiquitin, puckere	99.91
2f1z_A	522	Ubiquitin carboxyl-terminal hydrolase 7; hausp, US	99.9
1d00_A	168	Tumor necrosis factor receptor associated protein	99.9
1ca9_A	192	TRAF2, protein (TNF receptor associated factor 2);	99.9
1lb6_A	160	TNF receptor-associated factor 6; TRAF6-CD40 compl	99.9
4ghu_A	198	TNF receptor-associated factor 3; alpha/beta, inna	99.89
2gkw_A	192	TNF receptor-associated factor 3; CD40, NF-KB sign	99.89
3hqi_A	312	Speckle-type POZ protein; SPOP, ubiquitin, puckere	99.88
1flk_A	228	TNF receptor associated factor 3; TNF signaling, T	99.88
2f1z_A	522	Ubiquitin carboxyl-terminal hydrolase 7; hausp, US	99.87
4gwm_A	592	Meprin A subunit beta; mulidomain structure, hydro	99.55
4gwm_A	592	Meprin A subunit beta; mulidomain structure, hydro	99.2

>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=99.96  E-value=1.1e-29  Score=207.00  Aligned_cols=141  Identities=18%  Similarity=0.242  Sum_probs=116.3

Q ss_pred             ccccCCcEEEEEEcCcccccccccceEEcccEEeCCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCCCCCCCEEEEEEE
Q 041904           11 GRNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAITI   90 (317)
Q Consensus        11 ~~~~~~~~~~w~I~~fs~~~~~~~~~~~S~~F~~gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~~~~w~v~~~f~   90 (317)
                      ..-.+.++|+|+|+|||.++    +.++||+|.+||++|+|.+||+|+..++..+||||||+|... ..+.+|++.|+|+
T Consensus        13 ~~~~~~~~~~w~I~nfS~~~----~~~~S~~f~~gg~~W~i~~yP~G~~~~~~~~~lSlyL~~~~~-~~~~~w~v~a~~~   87 (155)
T 2foj_A           13 TSWRSEATFQFTVERFSRLS----ESVLSPPCFVRNLPWKIMVMPRFYPDRPHQKSVGFFLQCNAE-SDSTSWSCHAQAV   87 (155)
T ss_dssp             CTTCSEEEEEEEESSGGGCC----SCEECCCEEETTEEEEEEEEEEC------CBEEEEEEEESTT-CCCSSCEEEEEEE
T ss_pred             CCcCCCcEEEEEECChhhcC----CceEcCCEEECCccEEEEEEECCCCCCCCCCEEEEEEEeCCC-CCCCCCEEEEEEE
Confidence            44467799999999999994    589999999999999999999997531246899999999654 3466799999999


Q ss_pred             EEEEecCCCcEEEEEeeecccceeeeecccccccccccceeecccccCCCCceEeCCEEEEEEEEEEEeecCc
Q 041904           91 SFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKNTFK  163 (317)
Q Consensus        91 ~~l~n~~~~~~~~~~~~~~~~~~~~~~F~~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v~~~~~~  163 (317)
                      |.|+||+++.....+.       ..+.|.....+|||++||++++|++++++||+||+|+|+|+|+|.+++|.
T Consensus        88 l~l~~~~~~~~~~~~~-------~~~~F~~~~~~wG~~~Fi~~~~L~~~~~~yl~dD~l~Ie~~V~V~~~tG~  153 (155)
T 2foj_A           88 LKIINYRDDEKSFSRR-------ISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDDKVTFEVFVQADAPHGV  153 (155)
T ss_dssp             EEECCSSCGGGCEEEE-------EEEEEETTBCEEEEEEEEEHHHHTCTTTSSCBTTBEEEEEEEEECCCBSS
T ss_pred             EEEEcCCCCcceEEec-------cEEEeCCCCCCEeECCeEEHHHhcCcCCCceECCEEEEEEEEEEeCcccc
Confidence            9999998875333323       56788866788999999999999888899999999999999999877664

>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=99.96  E-value=6e-30  Score=206.23  Aligned_cols=139  Identities=24%  Similarity=0.285  Sum_probs=117.5

Q ss_pred             eccccCCcEEEEEEcCcccccccccceEEcccEEeCCe---EEEEEEEecCCCCCCCCCcEEEEEEeccCCCCCCCCEEE
Q 041904           10 AGRNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGY---KWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVN   86 (317)
Q Consensus        10 ~~~~~~~~~~~w~I~~fs~~~~~~~~~~~S~~F~~gG~---~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~~~~w~v~   86 (317)
                      .+.+...++|+|+|+|||.++++.++.++||+|.+|||   +|+|.+||+|+..+ +.+|||+||+|.+.    ..|++.
T Consensus         4 ~m~~~~~~~~~w~I~~fs~~~~~~g~~~~S~~F~~gg~~g~~W~i~~yP~G~~~~-~~~~lSlyL~l~~~----~~w~v~   78 (145)
T 3ivv_A            4 GSGKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEE-SKDYLSLYLLLVSC----PKSEVR   78 (145)
T ss_dssp             -CCCCCEEEEEEEESSGGGCCCCTTCCEECCCEEESGGGCEEEEEEEETTCSSGG-GTTEEEEEEEEEEC----SSSEEE
T ss_pred             CCCcEEEEEEEEEEcCchHHhhcCCCEEECCCcCCCCcCCceEEEEEEcCCCCCC-CCCeEEEEEEEcCC----CCCcEE
Confidence            46678899999999999998754578999999999985   99999999998753 56899999999875    369999


Q ss_pred             EEEEEEEEecCCCcEEEEEeeecccceeeeecccccccccccceeecccccCCCCceEeCCEEEEEEEEEEEee
Q 041904           87 AITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKN  160 (317)
Q Consensus        87 ~~f~~~l~n~~~~~~~~~~~~~~~~~~~~~~F~~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v~~~  160 (317)
                      |+|+|.|+||.++........      ..+.|+ ...+|||++||++++|.+++++||+||+|+|+|+|+|+++
T Consensus        79 a~f~l~llnq~~~~~~~~~~~------~~~~F~-~~~~wG~~~Fi~~~~L~~~~~~yl~dD~l~I~~~V~V~~d  145 (145)
T 3ivv_A           79 AKFKFSILNAKGEETKAMESQ------RAYRFV-QGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQD  145 (145)
T ss_dssp             EEEEEEEECTTSCEEEEEECS------SCEEEE-TTCEEEEEEEEEHHHHHCGGGCSSGGGCEEEEEEEEECC-
T ss_pred             EEEEEEEEecCCCceeeeccc------ceEEec-CCCCcCHHHeEEhhhhccccCCcEeCCEEEEEEEEEEEeC
Confidence            999999999988765543222      457786 4578999999999999877899999999999999999853

>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=99.96  E-value=5.9e-29  Score=202.67  Aligned_cols=134  Identities=19%  Similarity=0.236  Sum_probs=115.1

Q ss_pred             CCCceEEEEEecccccccceeecccc--cceEeeeccCCceEEEEecCCCCC-CCCCeEEEEEEccCCCCCCCCeEEEEE
Q 041904          173 PPTYYHTWKVSNFSSLLDEFYESESF--GCYKWYANYSMDVKILLYPNGNGE-AKGNCISLFLDVSQSSIPPNTKLLTKY  249 (317)
Q Consensus       173 ~~~~~~~~~i~nfs~~~~~~~~S~~f--~g~~W~~~~~~~~~i~~yp~g~~~-~~~~~lS~yL~~~~~~~~~~~~~~~~~  249 (317)
                      .+.++|+|+|+|||.++ +.++|+.|  ||++|        +|++||+|+.. ++++||||||+|+....+..|++.|+|
T Consensus        16 ~~~~~~~w~I~nfS~~~-~~~~S~~f~~gg~~W--------~i~~yP~G~~~~~~~~~lSlyL~~~~~~~~~~w~v~a~~   86 (155)
T 2foj_A           16 RSEATFQFTVERFSRLS-ESVLSPPCFVRNLPW--------KIMVMPRFYPDRPHQKSVGFFLQCNAESDSTSWSCHAQA   86 (155)
T ss_dssp             CSEEEEEEEESSGGGCC-SCEECCCEEETTEEE--------EEEEEEEC------CBEEEEEEEESTTCCCSSCEEEEEE
T ss_pred             CCCcEEEEEECChhhcC-CceEcCCEEECCccE--------EEEEEECCCCCCCCCCEEEEEEEeCCCCCCCCCEEEEEE
Confidence            45689999999999995 78899999  99999        99999999765 357899999997555556789999999


Q ss_pred             EEEEEECCCCC-ceeeeeeEEeeCCCCCccccccccccccCCCCCCceeCCEEEEEEEEEEEeeecc
Q 041904          250 FLCVENQMNGK-NSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGLVLA  315 (317)
Q Consensus       250 ~l~l~n~~~~~-~~~~~~~~~F~~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v~~~~~~  315 (317)
                      +|.|+||.++. +......+.|.....+|||++||++++|+++++|||+||+|+|+|+|+|.+++|+
T Consensus        87 ~l~l~~~~~~~~~~~~~~~~~F~~~~~~wG~~~Fi~~~~L~~~~~~yl~dD~l~Ie~~V~V~~~tG~  153 (155)
T 2foj_A           87 VLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDDKVTFEVFVQADAPHGV  153 (155)
T ss_dssp             EEEECCSSCGGGCEEEEEEEEEETTBCEEEEEEEEEHHHHTCTTTSSCBTTBEEEEEEEEECCCBSS
T ss_pred             EEEEEcCCCCcceEEeccEEEeCCCCCCEeECCeEEHHHhcCcCCCceECCEEEEEEEEEEeCcccc
Confidence            99999998865 4456678899876789999999999999987799999999999999999999987

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

Probab=99.95  E-value=9.5e-29  Score=205.78  Aligned_cols=148  Identities=14%  Similarity=0.214  Sum_probs=116.7

Q ss_pred             eeccccCCcEEEEEEcCcccccc--cc--cceEEcccEEeC--CeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC-CCC
Q 041904            9 LAGRNAAPSHYLFKIESFSLLSK--AS--VEQLILDNFEAG--GYKWKLSIHLTGSKSVNVTDHISIYLELAETSS-LPT   81 (317)
Q Consensus         9 ~~~~~~~~~~~~w~I~~fs~~~~--~~--~~~~~S~~F~~g--G~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~-~~~   81 (317)
                      +....+..|+|+|+|+|||.+++  +.  +..++||+|++|  ||+|+|.+||+|+..+ .++|||+||+|.++.. ..+
T Consensus        16 ~~~~~~~~g~~~w~I~~fS~~~~~~~~g~~~~i~S~~F~~g~~G~~W~i~~yP~G~~~~-~~~~lSlyL~l~~~~~d~~l   94 (178)
T 4gjh_A           16 QLEGACYSGKLIWKVTDYRVKKREAVEGHTVSVFSQPFYTSRCGYRLCARAYLNGDGSG-KGTHLSLYFVVMRGEFDSLL   94 (178)
T ss_dssp             HHHHCCSSSEEEEEECCHHHHHHHHHTTSCCCEECCCEESSTTSCEEEEEEETTCCGGG-TTTEEEEEEEEBCCTTGGGS
T ss_pred             HhcCcccceEEEEEECCHHHHHhhhhcCCCcEEECCCeEeCCCCeEEEEEEEECCCCCC-CCCEEEEEEEEecCCCCccc
Confidence            33446788999999999999875  12  348999999999  9999999999998753 5689999999987653 346


Q ss_pred             CCEEEEEEEEEEEecCCCcEEEEEeeecccceeeeecc----cccccccccceeecccccCCCCceEeCCEEEEEEEEEE
Q 041904           82 GWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKHFH----AMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFV  157 (317)
Q Consensus        82 ~w~v~~~f~~~l~n~~~~~~~~~~~~~~~~~~~~~~F~----~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v  157 (317)
                      +|++.++|+|.|+||.++..+..+..  +.+...+.|+    ....+|||.+||++++|+++.++||+||+|+|+|+|.|
T Consensus        95 ~W~v~a~~~l~Lldq~~~~~~~~~~~--~~~~~~~~F~~p~~~~~~~wG~~~Fi~~~~L~~~~~~yL~dD~l~I~~~V~i  172 (178)
T 4gjh_A           95 QWPFRQRVTLMLLDQSGKKNHIVETF--KADPNSSSFKRPDGEMNIASGCPRFVSHSTLENSKNTYIKDDTLFLKVAVDL  172 (178)
T ss_dssp             CSSCCCEEEEEECCTTSSCCCEEEEE--ECCTTCGGGSCCSSSBCCCEEEEEEEEHHHHHCTTCCSSBTTBEEEEEEECC
T ss_pred             CCceEEEEEEEEEcCCCCcceeEEee--ccCCccccccCCcccccCCcChhheeEHHHhhccccCcCcCCEEEEEEEEEe
Confidence            89999999999999987654332110  0001235676    23568999999999999977799999999999999976


Q ss_pred             Ee
Q 041904          158 VK  159 (317)
Q Consensus       158 ~~  159 (317)
                      .+
T Consensus       173 ~~  174 (178)
T 4gjh_A          173 TD  174 (178)
T ss_dssp             TT
T ss_pred             cC
Confidence            54

>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=99.94  E-value=2.2e-27  Score=194.30  Aligned_cols=143  Identities=15%  Similarity=0.260  Sum_probs=108.3

Q ss_pred             cCCcEEEEEEcCcccccc--cccc--eEEcccEEeC--CeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC-CCCCCEEE
Q 041904           14 AAPSHYLFKIESFSLLSK--ASVE--QLILDNFEAG--GYKWKLSIHLTGSKSVNVTDHISIYLELAETSS-LPTGWEVN   86 (317)
Q Consensus        14 ~~~~~~~w~I~~fs~~~~--~~~~--~~~S~~F~~g--G~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~-~~~~w~v~   86 (317)
                      ...|+|+|+|+|||.+++  +.++  .++||+|++|  ||+|+|.+||+|+..+.+++|||+||+++++.. ..++|++.
T Consensus         2 ~~~g~~~w~I~~fS~~~~~~~~g~~~~i~S~~F~vg~~Gy~w~i~~yP~G~~~~~~~~~lSlyL~l~~~~~d~~l~wp~~   81 (160)
T 1lb6_A            2 QCNGIYIWKIGNFGMHLKCQEEEKPVVIHSPGFYTGKPGYKLCMRLHLQLPTAQRCANYISLFVHTMQGEYDSHLPWPFQ   81 (160)
T ss_dssp             CCCEEEEEEECCHHHHHHHHHTTCCEEEECCCEESSSSCCEEEEEEEECCTTCTTTTTEEEEEEEEECCTTGGGSCSSCC
T ss_pred             ccCcEEEEEECCHHHHHHhhhcCCCeEEECcCeecCCCCeeEEEEEEecCCCCCCCCCEEEEEEEEeecCCCccCCCcee
Confidence            467999999999999875  2455  8999999999  999999999999764323689999999987654 35679999


Q ss_pred             EEEEEEEEecCCCcE--EEEEeeecccceeeeeccc-----ccccccccceeecccccCCCCceEeCCEEEEEEEEEEEe
Q 041904           87 AITISFYSIKFKTNI--LVSKVRNSTINVIVKHFHA-----MKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVK  159 (317)
Q Consensus        87 ~~f~~~l~n~~~~~~--~~~~~~~~~~~~~~~~F~~-----~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v~~  159 (317)
                      ++|+|.|+||.+...  ...+.. .+ ......|..     ...+|||.+||++++|+  +++||+||+|+|+|+|.|+.
T Consensus        82 a~~~l~lldq~~~~~~~~~~~~~-~~-~~~~~~f~~p~~~~~~~~~G~~~Fi~~~~L~--~~~yl~dD~l~I~~~V~v~~  157 (160)
T 1lb6_A           82 GTIRLTILDQSEAPVRQNHEEIM-DA-KPELLAFQRPTIPRNPKGFGYVTFMHLEALR--QRTFIKDDTLLVRCEVSTRF  157 (160)
T ss_dssp             SEEEEEECCCSCTTSCCCEEEEE-EC-CTTSGGGSCCSSSBCSEEEEEEEEEEGGGGG--TSCCCBTTBEEEEEEEEC--
T ss_pred             eeEEEEEEcCCCccccccceEEe-ec-CCcchhccCCcccCCCCCcCEeeEeEHHHhh--hCCCccCCEEEEEEEEEEee
Confidence            999999999986521  111010 00 001234542     12479999999999998  68999999999999999875


Q ss_pred             e
Q 041904          160 N  160 (317)
Q Consensus       160 ~  160 (317)
                      +
T Consensus       158 ~  158 (160)
T 1lb6_A          158 D  158 (160)
T ss_dssp             -
T ss_pred             c
Confidence            4

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

Probab=99.94  E-value=4.6e-28  Score=204.39  Aligned_cols=144  Identities=14%  Similarity=0.152  Sum_probs=113.8

Q ss_pred             ccCCcEEEEEEcCcccccc----cccceEEcccEEeC--CeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC-CCCCCEE
Q 041904           13 NAAPSHYLFKIESFSLLSK----ASVEQLILDNFEAG--GYKWKLSIHLTGSKSVNVTDHISIYLELAETSS-LPTGWEV   85 (317)
Q Consensus        13 ~~~~~~~~w~I~~fs~~~~----~~~~~~~S~~F~~g--G~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~-~~~~w~v   85 (317)
                      ....|+|.|+|+|||.+++    +.++.++||+|++|  ||+|+|.+||+|+..+ .++|||+||++.++.. ..++|++
T Consensus        36 ~~~~g~~~w~I~nfS~~~~~~~~~~g~~i~S~~F~vg~~Gy~W~i~~yPnG~~~~-~~~~lSlyL~l~~g~~D~~l~wp~  114 (198)
T 4ghu_A           36 ASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMG-KGTHLSLFFVIMRGEYDALLPWPF  114 (198)
T ss_dssp             CCSSSEEEEEECCHHHHHHHHHTTSSCCEECCCEESSTTSCEEEEEEETTCCGGG-TTTEEEEEEEEECCTTGGGSCSSC
T ss_pred             cccccEEEEEECCHHHHHhhhccCCCcEEECCCeEECCCCcEEEEEEEeCCCCCC-CCCeEEEEEEecCCccCCCCCceE
Confidence            4678999999999999875    23579999999999  9999999999998753 5789999999987654 2468999


Q ss_pred             EEEEEEEEEecCCCcEEEEEeeecccc---eeeeecccccccccccceeecccccCCCCceEeCCEEEEEEEEEEEee
Q 041904           86 NAITISFYSIKFKTNILVSKVRNSTIN---VIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKN  160 (317)
Q Consensus        86 ~~~f~~~l~n~~~~~~~~~~~~~~~~~---~~~~~F~~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v~~~  160 (317)
                      .++|+|.|+||.+...+..+.. .+..   ...+.|...+.+|||.+||++++|+  ++|||+||+|+|+|+|.|+..
T Consensus       115 ~a~~~l~Lldq~~~~~~~~~~~-~~~~~~~~f~rp~~~~~~~wG~~~Fi~~~~L~--~~gyL~dD~l~I~~~V~v~~~  189 (198)
T 4ghu_A          115 KQKVTLMLMDQGSSRRHLGDAF-KPDPNSSSFKKPTGEMNIASGCPVFVAQTVLE--NGTYIKDDTIFIKVIVDTSDL  189 (198)
T ss_dssp             CCCEEEEECCCSTTCCCEEEEE-CCCTTSGGGSCCSSSBCCCEEEEEEEEHHHHH--HTTSCBTTBEEEEEEECCTTC
T ss_pred             EEEEEEEEEcCCCCccceEEEe-ecCcccceecCCcccCcCCcCchhEeEHHHhh--hcCCeeCCEEEEEEEEEeccC
Confidence            9999999999987654432210 0000   0112244456789999999999998  589999999999999987654

>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=99.94  E-value=6.8e-27  Score=188.27  Aligned_cols=130  Identities=22%  Similarity=0.402  Sum_probs=109.7

Q ss_pred             cCCCCceEEEEEecccccc---cceeecccc--cc---eEeeeccCCceEEEEecCCCCCCCCCeEEEEEEccCCCCCCC
Q 041904          171 HDPPTYYHTWKVSNFSSLL---DEFYESESF--GC---YKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPN  242 (317)
Q Consensus       171 ~~~~~~~~~~~i~nfs~~~---~~~~~S~~f--~g---~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~~~~~~~~~~  242 (317)
                      .+...++|+|+|+|||.++   ++.+.|+.|  ||   ++|        +|++||+|+..++++|||+||++...   ..
T Consensus         6 ~~~~~~~~~w~I~~fs~~~~~~g~~~~S~~F~~gg~~g~~W--------~i~~yP~G~~~~~~~~lSlyL~l~~~---~~   74 (145)
T 3ivv_A            6 GKVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKW--------CLRVNPKGLDEESKDYLSLYLLLVSC---PK   74 (145)
T ss_dssp             CCCCEEEEEEEESSGGGCCCCTTCCEECCCEEESGGGCEEE--------EEEEETTCSSGGGTTEEEEEEEEEEC---SS
T ss_pred             CcEEEEEEEEEEcCchHHhhcCCCEEECCCcCCCCcCCceE--------EEEEEcCCCCCCCCCeEEEEEEEcCC---CC
Confidence            4456789999999999987   478999999  77   599        99999999877667899999995322   47


Q ss_pred             CeEEEEEEEEEEECCCCCcee--eeeeEEeeCCCCCccccccccccccCCCCCCceeCCEEEEEEEEEEEee
Q 041904          243 TKLLTKYFLCVENQMNGKNSE--VEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGL  312 (317)
Q Consensus       243 ~~~~~~~~l~l~n~~~~~~~~--~~~~~~F~~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v~~~  312 (317)
                      |++.|+|+|.|+||.++....  ....+.|. ...+|||++||++++|+++++|||+||+|+|+|+|+|++.
T Consensus        75 w~v~a~f~l~llnq~~~~~~~~~~~~~~~F~-~~~~wG~~~Fi~~~~L~~~~~~yl~dD~l~I~~~V~V~~d  145 (145)
T 3ivv_A           75 SEVRAKFKFSILNAKGEETKAMESQRAYRFV-QGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQD  145 (145)
T ss_dssp             SEEEEEEEEEEECTTSCEEEEEECSSCEEEE-TTCEEEEEEEEEHHHHHCGGGCSSGGGCEEEEEEEEECC-
T ss_pred             CcEEEEEEEEEEecCCCceeeecccceEEec-CCCCcCHHHeEEhhhhccccCCcEeCCEEEEEEEEEEEeC
Confidence            999999999999999876442  23467887 4689999999999999766689999999999999999863

>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=99.93  E-value=3.9e-27  Score=194.41  Aligned_cols=141  Identities=18%  Similarity=0.271  Sum_probs=109.9

Q ss_pred             ccCCcEEEEEEcCcccccc--cccc--eEEcccEE--eCCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCCCC-CCCEE
Q 041904           13 NAAPSHYLFKIESFSLLSK--ASVE--QLILDNFE--AGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLP-TGWEV   85 (317)
Q Consensus        13 ~~~~~~~~w~I~~fs~~~~--~~~~--~~~S~~F~--~gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~~-~~w~v   85 (317)
                      ....|+|+|+|+|||.+++  ..++  .++||+|+  +|||+|+|.+||+|+..+ .++|||+||++.++...+ ++|++
T Consensus        15 ~~~~g~~~w~I~nfS~~~~~~~~g~~~~i~S~~F~~~~gG~~W~i~~yP~G~~~~-~~~~lSlyL~l~~~~~~~~~~w~~   93 (168)
T 1d00_A           15 STYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTG-RGTHLSLFFVVMKGPNDALLRWPF   93 (168)
T ss_dssp             CCSSSEEEEEEESHHHHHHHHHTTSSCCEECCCEESSTTSCEEEEEEETTCCGGG-TTTEEEEEEEEECCTTGGGSCSSC
T ss_pred             cccCCEEEEEECCHHHHHHHhhcCCCeEEECCCeecCCCCEEEEEEEEeCCCCCC-CCcEEEEEEEEecCCCCccCCCce
Confidence            3578999999999999976  2344  49999997  789999999999998653 568999999998865543 68999


Q ss_pred             EEEEEEEEEecCCCcEEEEEeeecccceeeeeccc----ccccccccceeecccccCCCCceEeCCEEEEEEEEEEE
Q 041904           86 NAITISFYSIKFKTNILVSKVRNSTINVIVKHFHA----MKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVV  158 (317)
Q Consensus        86 ~~~f~~~l~n~~~~~~~~~~~~~~~~~~~~~~F~~----~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v~  158 (317)
                      .++|+|.|+||++.+.... .. .+ +...+.|..    .+.+|||.+||++++|+++ +|||+||+|+|+|+|.|.
T Consensus        94 ~~~~~l~ll~q~~~~~~~~-~~-~~-~~~~~~f~~p~~~~~~~~G~~~Fi~~~~L~~~-~gyl~dD~l~I~~~V~v~  166 (168)
T 1d00_A           94 NQKVTLMLLDQNNREHVID-AF-RP-DVTSSSFQRPVNDMNIASGCPLFCPVSKMEAK-NSYVRDDAIFIKAIVDLT  166 (168)
T ss_dssp             CCCEEEEECCTTSSCCEEE-EE-CC-CTTSGGGSCCSSSBCCCEEEEEEEETTTTTSS-SSSSBTTEEEEEEEECCT
T ss_pred             EEEEEEEEECCCCCcccee-cc-cc-CcchhhccCCCcCCCCCcCcceEeEHHHhccc-CCceeCCEEEEEEEEEec
Confidence            9999999999988653321 10 00 001235652    3578999999999999843 499999999999999864

>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=99.93  E-value=7.8e-27  Score=196.64  Aligned_cols=140  Identities=19%  Similarity=0.265  Sum_probs=111.0

Q ss_pred             cCCcEEEEEEcCcccccc--cccc--eEEcccEEe--CCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCCCC-CCCEEE
Q 041904           14 AAPSHYLFKIESFSLLSK--ASVE--QLILDNFEA--GGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLP-TGWEVN   86 (317)
Q Consensus        14 ~~~~~~~w~I~~fs~~~~--~~~~--~~~S~~F~~--gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~~-~~w~v~   86 (317)
                      ...|+|+|+|+|||.+++  +.|+  .++||+|++  |||+|+|.+||+|+..+ .++|||+||++.++...+ ++|++.
T Consensus        40 ~~~g~~~w~I~nfS~~~~~~~~g~~~~i~S~~F~v~~gG~~W~i~~yP~G~~~~-~~~~lSlyL~l~~~~~~~~~~W~~~  118 (192)
T 1ca9_A           40 TYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTG-RGTHLSLFFVVMKGPNDALLRWPFN  118 (192)
T ss_dssp             CSSSEEEEEEESHHHHHHHHHTTSSCCEECCCEESSTTSCEEEEEEETTCCGGG-TTTEEEEEEEEECCTTGGGSCSSCC
T ss_pred             ccCceEEEEECCHHHHHHHhhcCCCceEECceEEeCCCCeEEEEEEEeCCCCCC-CCCEEEEEEEEccCCCCCcCCCceE
Confidence            578999999999999875  2344  699999999  99999999999998653 568999999998875443 789999


Q ss_pred             EEEEEEEEecCCCcEEEEEeeecccceeeeecc----cccccccccceeecccccCCCCceEeCCEEEEEEEEEEE
Q 041904           87 AITISFYSIKFKTNILVSKVRNSTINVIVKHFH----AMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVV  158 (317)
Q Consensus        87 ~~f~~~l~n~~~~~~~~~~~~~~~~~~~~~~F~----~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v~  158 (317)
                      ++|+|.|+||++++.... ..  .-+.....|.    ....+|||.+||++++|.+ ++|||+||+|+|+|+|.|.
T Consensus       119 a~~~l~lldq~~~~~~~~-~~--~~~~~~~~f~rp~~~~~~~wG~~~Fi~~~~L~~-~~gyl~dD~l~I~~~V~V~  190 (192)
T 1ca9_A          119 QKVTLMLLDQNNREHVID-AF--RPDVTSSSFQRPVNDMNIASGCPLFCPVSKMEA-KNSYVRDDAIFIKAIVDLT  190 (192)
T ss_dssp             CCEEEEECCTTSSCCEEE-EE--CCCTTSGGGSCCSSSBCCCEEEEEEEETHHHHS-SCSSCBTTEEEEEEEECCT
T ss_pred             EEEEEEEECCCCCceeeE-ee--ccCCchhhhcCCccCCCCCcChhheeEHHHhhh-ccCCEeCCEEEEEEEEEec
Confidence            999999999988743221 10  0000122464    2356899999999999986 5799999999999999875

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

Probab=99.93  E-value=6.5e-27  Score=196.87  Aligned_cols=141  Identities=14%  Similarity=0.175  Sum_probs=111.4

Q ss_pred             cCCcEEEEEEcCcccccc--cccc--eEEcccEEeC--CeEEEEEEEecCCCCCCCCCcEEEEEEeccCCCC-CCCCEEE
Q 041904           14 AAPSHYLFKIESFSLLSK--ASVE--QLILDNFEAG--GYKWKLSIHLTGSKSVNVTDHISIYLELAETSSL-PTGWEVN   86 (317)
Q Consensus        14 ~~~~~~~w~I~~fs~~~~--~~~~--~~~S~~F~~g--G~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~-~~~w~v~   86 (317)
                      ...|+|.|+|+|||.+++  +.++  .++||+|++|  ||+|+|.+||+|++.+ .++|||+||+++++..+ .++|++.
T Consensus        37 ~~~g~~~w~I~~fS~~~~~~~~g~~~~i~S~~F~vg~~Gykw~i~~yPnG~~~~-~~~~lSlyL~l~~~~~d~~l~wp~~  115 (192)
T 2gkw_A           37 SYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMG-KGTHLSLFFVIMRGEYDALLPWPFK  115 (192)
T ss_dssp             CCSSEEEEEEECHHHHHHHHHHTSCSCEECCCEESSTTSCEEEEEEETTCCGGG-TTTEEEEEEEEECCTTGGGSCSSCC
T ss_pred             ccCcEEEEEECCHHHHHHHhhcCCCceEEcccEEECCCCcEEEEEEEeCCCCCC-CCCEEEEEEEEecCCCCccCCCcEE
Confidence            378999999999999974  3355  5999999999  9999999999998653 57899999999876543 4689999


Q ss_pred             EEEEEEEEecCCCcEEEEEeeecccceeeeeccc----ccccccccceeecccccCCCCceEeCCEEEEEEEEEEEe
Q 041904           87 AITISFYSIKFKTNILVSKVRNSTINVIVKHFHA----MKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVK  159 (317)
Q Consensus        87 ~~f~~~l~n~~~~~~~~~~~~~~~~~~~~~~F~~----~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v~~  159 (317)
                      ++|+|.|+||.+.+.+..+..  ..+...+.|..    .+.+|||++||++++|+  ++|||+||+|+|+|+|.|..
T Consensus       116 a~~~l~lldq~~~~~~~~~~~--~~~~~~~~F~~~~~~~~~~wG~~~Fi~~~~L~--~~gyl~dD~l~I~~~V~v~~  188 (192)
T 2gkw_A          116 QKVTLMLMDQGSSRRHLGDAF--KPDPNSSSFKKPTGEMNIASGCPVFVAQTVLE--NGTYIKDDTIFIKVIVDTSD  188 (192)
T ss_dssp             CCEEEEECCCSTTCCCEEEEE--CCCTTCTTSSCCSSSBCCCEEEEEEEEHHHHH--HTTSCBTTEEEEEEEECCTT
T ss_pred             EEEEEEEECCCCCccceEEEE--ecCCCcccccCCCCCCcCCCChHHEeEHHHhC--cCCCeeCCEEEEEEEEEcCC
Confidence            999999999988754432110  00002245753    24689999999999998  46999999999999997643

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

Probab=99.92  E-value=5.6e-26  Score=196.10  Aligned_cols=141  Identities=14%  Similarity=0.175  Sum_probs=111.7

Q ss_pred             cCCcEEEEEEcCcccccc--ccc--ceEEcccEEeC--CeEEEEEEEecCCCCCCCCCcEEEEEEeccCCCC-CCCCEEE
Q 041904           14 AAPSHYLFKIESFSLLSK--ASV--EQLILDNFEAG--GYKWKLSIHLTGSKSVNVTDHISIYLELAETSSL-PTGWEVN   86 (317)
Q Consensus        14 ~~~~~~~w~I~~fs~~~~--~~~--~~~~S~~F~~g--G~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~-~~~w~v~   86 (317)
                      ...|+|.|+|+|||.++.  +.|  ..++||+|++|  ||+|+|.+||+|++. +.++|||+||+++++... .++|++.
T Consensus        73 ~~~g~~~wkI~nfS~~~~~~~~g~~~~i~S~~F~vg~~Gy~w~i~~yPnG~~~-~~~~~lSlyL~l~~~~~d~~l~Wp~~  151 (228)
T 1flk_A           73 SYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGM-GKGTHLSLFFVIMRGEYDALLPWPFK  151 (228)
T ss_dssp             CSSSEEEEEEECHHHHHHHHHTTSCCCEECCCEESSTTSCEECEEEETTCCGG-GTTTEEEEEECCBCCTTTTSSCSSCC
T ss_pred             CcCcEEEEEECCHHHHHHHhhcCCCeeEECceEEeCCCCcEEEEEEEcCCCCC-CCCCEEEEEEEEecCCccccCCCcEE
Confidence            478999999999999875  223  38999999999  999999999999865 367899999999876543 5689999


Q ss_pred             EEEEEEEEecCCCcEEEEEeeecccceeeeecc----cccccccccceeecccccCCCCceEeCCEEEEEEEEEEEe
Q 041904           87 AITISFYSIKFKTNILVSKVRNSTINVIVKHFH----AMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVK  159 (317)
Q Consensus        87 ~~f~~~l~n~~~~~~~~~~~~~~~~~~~~~~F~----~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v~~  159 (317)
                      ++|+|.|+||.+.+.+..+..  +-+...+.|.    ..+.+|||++||++++|+  ++|||+||+|+|+|+|.|.+
T Consensus       152 a~~~l~lldq~~~~~~~~~~~--~~~~~~~~F~rp~~~~~~~wG~~~Fi~~~~L~--~~gyL~dD~l~I~~~V~v~~  224 (228)
T 1flk_A          152 QKVTLMLMDQGSSRRHLGDAF--KPDPNSSSFKKPTGEMNIASGCPVFVAQTVLE--NGTYIKDDTIFIKVIVDTSD  224 (228)
T ss_dssp             CCEEEEECCCSSSCCCEEEEE--CCCTTCTTSSSCSSSBCCCCSEEEEEEHHHHS--SSTTCCSSEEEEEEECCCTT
T ss_pred             EEEEEEEEcCCCCccceeeee--cCCCccccccCCccCCCCCcCHHHeeEHHHHc--cCCCccCCEEEEEEEEEccc
Confidence            999999999987754332110  0001223464    235689999999999998  48999999999999998754

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

Probab=99.92  E-value=6.6e-26  Score=188.56  Aligned_cols=133  Identities=23%  Similarity=0.304  Sum_probs=108.8

Q ss_pred             CCCCceEEEEEecccccccc-------eeecccc--c--ceEeeeccCCceEEEEecCCCCCCCCCeEEEEEEc-cCC-C
Q 041904          172 DPPTYYHTWKVSNFSSLLDE-------FYESESF--G--CYKWYANYSMDVKILLYPNGNGEAKGNCISLFLDV-SQS-S  238 (317)
Q Consensus       172 ~~~~~~~~~~i~nfs~~~~~-------~~~S~~f--~--g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~~-~~~-~  238 (317)
                      ....++|+|+|+|||.++++       .+.|+.|  |  ||+|        +|.+||+|+..++++|||+||++ +.. +
T Consensus        20 ~~~~g~~~w~I~~fS~~~~~~~~g~~~~i~S~~F~~g~~G~~W--------~i~~yP~G~~~~~~~~lSlyL~l~~~~~d   91 (178)
T 4gjh_A           20 ACYSGKLIWKVTDYRVKKREAVEGHTVSVFSQPFYTSRCGYRL--------CARAYLNGDGSGKGTHLSLYFVVMRGEFD   91 (178)
T ss_dssp             CCSSSEEEEEECCHHHHHHHHHTTSCCCEECCCEESSTTSCEE--------EEEEETTCCGGGTTTEEEEEEEEBCCTTG
T ss_pred             cccceEEEEEECCHHHHHhhhhcCCCcEEECCCeEeCCCCeEE--------EEEEEECCCCCCCCCEEEEEEEEecCCCC
Confidence            45679999999999998742       7999999  8  9999        99999999887777999999994 432 2


Q ss_pred             CCCCCeEEEEEEEEEEECCCCC-ceeee-----eeEEeeC----CCCCccccccccccccCCCCCCceeCCEEEEEEEEE
Q 041904          239 IPPNTKLLTKYFLCVENQMNGK-NSEVE-----GEWLYTL----TNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVT  308 (317)
Q Consensus       239 ~~~~~~~~~~~~l~l~n~~~~~-~~~~~-----~~~~F~~----~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~  308 (317)
                      ....|++.++|+|.|+||.++. +....     ..+.|..    .+.+|||++||++++|+++.+|||+||+|+|+|+|+
T Consensus        92 ~~l~W~v~a~~~l~Lldq~~~~~~~~~~~~~~~~~~~F~~p~~~~~~~wG~~~Fi~~~~L~~~~~~yL~dD~l~I~~~V~  171 (178)
T 4gjh_A           92 SLLQWPFRQRVTLMLLDQSGKKNHIVETFKADPNSSSFKRPDGEMNIASGCPRFVSHSTLENSKNTYIKDDTLFLKVAVD  171 (178)
T ss_dssp             GGSCSSCCCEEEEEECCTTSSCCCEEEEEECCTTCGGGSCCSSSBCCCEEEEEEEEHHHHHCTTCCSSBTTBEEEEEEEC
T ss_pred             cccCCceEEEEEEEEEcCCCCcceeEEeeccCCccccccCCcccccCCcChhheeEHHHhhccccCcCcCCEEEEEEEEE
Confidence            2357999999999999998754 32221     2356763    246899999999999998778999999999999998


Q ss_pred             EEee
Q 041904          309 LHGL  312 (317)
Q Consensus       309 v~~~  312 (317)
                      |.++
T Consensus       172 i~~~  175 (178)
T 4gjh_A          172 LTDL  175 (178)
T ss_dssp             CTTC
T ss_pred             ecCC
Confidence            7654

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

Probab=99.91  E-value=8.4e-25  Score=197.98  Aligned_cols=137  Identities=24%  Similarity=0.292  Sum_probs=112.4

Q ss_pred             ccCCcEEEEEEcCcccccccccceEEcccEEeCCe---EEEEEEEecCCCCCCCCCcEEEEEEeccCCCCCCCCEEEEEE
Q 041904           13 NAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGY---KWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAIT   89 (317)
Q Consensus        13 ~~~~~~~~w~I~~fs~~~~~~~~~~~S~~F~~gG~---~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~~~~w~v~~~f   89 (317)
                      +...++|+|+|.|||.++.+.++.++||+|.+||+   +|+|.+||+|.... +++|||+||+|.+..    .|++.|+|
T Consensus         3 ~~~~~~~~w~I~nfs~~~~~~~~~i~S~~F~~gg~~~~~W~i~~yP~G~~~~-~~~~lslyL~~~~~~----~~~v~a~~   77 (312)
T 3hqi_A            3 KVVKFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEE-SKDYLSLYLLLVSCP----KSEVRAKF   77 (312)
T ss_dssp             EEEEEEEEEEETTGGGCCCCTTCCEECCCBCC--CCCCEEEEEEETTCCC---CTTEEEEEEEEEECC----C-CEEEEE
T ss_pred             ceEEEEEEEEEcCcchhhhcCCCeEeeCCcccCCCCCceEEEEEECCCCCcc-CCCcEEEEEEEcCCC----CCcEEEEE
Confidence            34568999999999999754578999999999985   99999999998653 578999999998653    58999999


Q ss_pred             EEEEEecCCCcEEEEEeeecccceeeeecccccccccccceeecccccCCCCceEeCCEEEEEEEEEEEeec
Q 041904           90 ISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKNT  161 (317)
Q Consensus        90 ~~~l~n~~~~~~~~~~~~~~~~~~~~~~F~~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v~~~~  161 (317)
                      +|.|+||+++........      ..+.|.. ..+|||++||++++|+++.+|||+||+|+|+|+|.|+...
T Consensus        78 ~~~l~~~~~~~~~~~~~~------~~~~F~~-~~~wG~~~Fi~~~~L~~~~~~yl~dD~l~i~~~v~v~~~~  142 (312)
T 3hqi_A           78 KFSILNAKGEETKAMESQ------RAYRFVQ-GKDWGFKKFIRRGFLLDEANGLLPDDKLTLFCEVSVVQDS  142 (312)
T ss_dssp             EEEEECTTSCEEEEEECS------SCEEECT-TCEEEEEEEEEHHHHTCGGGCCCGGGCEEEEEEEEEEEEC
T ss_pred             EEEEEeCCCCcccccccC------CceeCCC-CCCcCHHHhccHHHhhccccCeecCCEEEEEEEEEEEecc
Confidence            999999998765554322      5567874 4589999999999998777899999999999999999764

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

Probab=99.90  E-value=2.5e-24  Score=207.94  Aligned_cols=141  Identities=17%  Similarity=0.239  Sum_probs=113.7

Q ss_pred             eccccCCcEEEEEEcCcccccccccceEEcccEEeCCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCCCCCCCEEEEEE
Q 041904           10 AGRNAAPSHYLFKIESFSLLSKASVEQLILDNFEAGGYKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAIT   89 (317)
Q Consensus        10 ~~~~~~~~~~~w~I~~fs~~~~~~~~~~~S~~F~~gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~~~~w~v~~~f   89 (317)
                      +....+.++|+|+|+|||.+++    .++|++|.+||++|+|.+||+|+..+++.+|||+||.|.+.. .+..|.+.|+|
T Consensus        24 ~~~~~~~~~~~w~I~nfS~~~~----~~~S~~F~vgg~~W~i~~yP~G~~~~~~~~~lSlyL~~~~~~-~~~~w~v~a~f   98 (522)
T 2f1z_A           24 DTSWRSEATFQFTVERFSRLSE----SVLSPPCFVRNLPWKIMVMPRFYPDRPHQKSVGFFLQCNAES-DSTSWSCHAQA   98 (522)
T ss_dssp             --CCCSEEEEEEEESSCTTCCS----CEECCCEEETTEEEEEEECBC--------CBBCEEEEESTTC-CCSSCBEEEEE
T ss_pred             cccccCCcEEEEEECChhhcCC----ceeCCCEEECCEeeEEEEEeCCCCCCCCCCeEEEEEEecCCC-CCCCceEEEEE
Confidence            3334678999999999999963    899999999999999999999975422568999999998763 56789999999


Q ss_pred             EEEEEecCCCcEEEEEeeecccceeeeecccccccccccceeecccccCCCCceEeCCEEEEEEEEEEEeecC
Q 041904           90 ISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKNTF  162 (317)
Q Consensus        90 ~~~l~n~~~~~~~~~~~~~~~~~~~~~~F~~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v~~~~~  162 (317)
                      +|.|+|+.++.....+.       ..+.|.....+|||.+||++++|.++++|||.||+++|+|.|+|..+++
T Consensus        99 ~l~l~n~~~~~~~~~~~-------~~~~F~~~~~~wG~~~Fi~~~~L~~~~~g~L~nD~l~i~~~V~v~~p~g  164 (522)
T 2f1z_A           99 VLKIINYRDDEKSFSRR-------ISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDDKVTFEVFVQADAPHG  164 (522)
T ss_dssp             EEEECCTTCGGGCEEEE-------CCEEECGGGCEEEESSSSBHHHHSCGGGSSCBTTBEEEEEEEEECCCBS
T ss_pred             EEEEEcCCCCccceecc-------ceeEecCCCCCcchhheeEhhHhcCcccCcccCCcEEEEEEeecccccc
Confidence            99999998765544333       6678887778899999999999987789999999999999999975543

>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=99.90  E-value=9.5e-25  Score=180.08  Aligned_cols=130  Identities=26%  Similarity=0.317  Sum_probs=105.0

Q ss_pred             CCCceEEEEEeccccccc-----c--eeecccc----cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccCCCCC
Q 041904          173 PPTYYHTWKVSNFSSLLD-----E--FYESESF----GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQSSIP  240 (317)
Q Consensus       173 ~~~~~~~~~i~nfs~~~~-----~--~~~S~~f----~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~~~~~  240 (317)
                      ...++|+|+|+|||.+++     +  .+.|+.|    |||+|        +|++||+|+..++++|||+||+ ++....+
T Consensus        16 ~~~g~~~w~I~nfS~~~~~~~~g~~~~i~S~~F~~~~gG~~W--------~i~~yP~G~~~~~~~~lSlyL~l~~~~~~~   87 (168)
T 1d00_A           16 TYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKM--------CLRIYLNGDGTGRGTHLSLFFVVMKGPNDA   87 (168)
T ss_dssp             CSSSEEEEEEESHHHHHHHHHTTSSCCEECCCEESSTTSCEE--------EEEEETTCCGGGTTTEEEEEEEEECCTTGG
T ss_pred             ccCCEEEEEECCHHHHHHHhhcCCCeEEECCCeecCCCCEEE--------EEEEEeCCCCCCCCcEEEEEEEEecCCCCc
Confidence            467899999999999873     2  3889998    79999        9999999987766799999999 4533332


Q ss_pred             -CCCeEEEEEEEEEEECCCCCceeeee-----eEEeeC----CCCCccccccccccccCCCCCCceeCCEEEEEEEEEEE
Q 041904          241 -PNTKLLTKYFLCVENQMNGKNSEVEG-----EWLYTL----TNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLH  310 (317)
Q Consensus       241 -~~~~~~~~~~l~l~n~~~~~~~~~~~-----~~~F~~----~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v~  310 (317)
                       ..|++.++|+|.|+||.++++.....     .+.|..    .+.+|||++||++++|+++ +|||+||+|+|+|+|+|.
T Consensus        88 ~~~w~~~~~~~l~ll~q~~~~~~~~~~~~~~~~~~f~~p~~~~~~~~G~~~Fi~~~~L~~~-~gyl~dD~l~I~~~V~v~  166 (168)
T 1d00_A           88 LLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKMEAK-NSYVRDDAIFIKAIVDLT  166 (168)
T ss_dssp             GSCSSCCCCEEEEECCTTSSCCEEEEECCCTTSGGGSCCSSSBCCCEEEEEEEETTTTTSS-SSSSBTTEEEEEEEECCT
T ss_pred             cCCCceEEEEEEEEECCCCCccceeccccCcchhhccCCCcCCCCCcCcceEeEHHHhccc-CCceeCCEEEEEEEEEec
Confidence             68999999999999999866443321     124642    3578999999999999973 499999999999999875


Q ss_pred             e
Q 041904          311 G  311 (317)
Q Consensus       311 ~  311 (317)
                      +
T Consensus       167 ~  167 (168)
T 1d00_A          167 G  167 (168)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=99.90  E-value=1.3e-24  Score=183.12  Aligned_cols=130  Identities=27%  Similarity=0.327  Sum_probs=105.5

Q ss_pred             CCCceEEEEEecccccccc-------eeecccc----cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccCCCCC
Q 041904          173 PPTYYHTWKVSNFSSLLDE-------FYESESF----GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQSSIP  240 (317)
Q Consensus       173 ~~~~~~~~~i~nfs~~~~~-------~~~S~~f----~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~~~~~  240 (317)
                      ...++|+|+|+|||.+++.       .++|+.|    |||+|        +|.+||+|+..++++|||+||+ ++....+
T Consensus        40 ~~~g~~~w~I~nfS~~~~~~~~g~~~~i~S~~F~v~~gG~~W--------~i~~yP~G~~~~~~~~lSlyL~l~~~~~~~  111 (192)
T 1ca9_A           40 TYDGVFIWKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKM--------CLRIYLNGDGTGRGTHLSLFFVVMKGPNDA  111 (192)
T ss_dssp             CSSSEEEEEEESHHHHHHHHHTTSSCCEECCCEESSTTSCEE--------EEEEETTCCGGGTTTEEEEEEEEECCTTGG
T ss_pred             ccCceEEEEECCHHHHHHHhhcCCCceEECceEEeCCCCeEE--------EEEEEeCCCCCCCCCEEEEEEEEccCCCCC
Confidence            4678999999999998732       5899999    79999        9999999987766789999999 5543333


Q ss_pred             -CCCeEEEEEEEEEEECCCCCceeeee-----eEEeeC----CCCCccccccccccccCCCCCCceeCCEEEEEEEEEEE
Q 041904          241 -PNTKLLTKYFLCVENQMNGKNSEVEG-----EWLYTL----TNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLH  310 (317)
Q Consensus       241 -~~~~~~~~~~l~l~n~~~~~~~~~~~-----~~~F~~----~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v~  310 (317)
                       ..|++.++|+|.|+||.++++.....     .+.|..    .+.+|||++||++++|++ .+|||+||+|+|+|+|+|.
T Consensus       112 ~~~W~~~a~~~l~lldq~~~~~~~~~~~~~~~~~~f~rp~~~~~~~wG~~~Fi~~~~L~~-~~gyl~dD~l~I~~~V~V~  190 (192)
T 1ca9_A          112 LLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKMEA-KNSYVRDDAIFIKAIVDLT  190 (192)
T ss_dssp             GSCSSCCCCEEEEECCTTSSCCEEEEECCCTTSGGGSCCSSSBCCCEEEEEEEETHHHHS-SCSSCBTTEEEEEEEECCT
T ss_pred             cCCCceEEEEEEEEECCCCCceeeEeeccCCchhhhcCCccCCCCCcChhheeEHHHhhh-ccCCEeCCEEEEEEEEEec
Confidence             68999999999999999875443221     123542    246899999999999995 3799999999999999885


Q ss_pred             e
Q 041904          311 G  311 (317)
Q Consensus       311 ~  311 (317)
                      +
T Consensus       191 ~  191 (192)
T 1ca9_A          191 G  191 (192)
T ss_dssp             T
T ss_pred             C
Confidence            4

>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=99.90  E-value=7.2e-24  Score=173.35  Aligned_cols=129  Identities=22%  Similarity=0.246  Sum_probs=99.1

Q ss_pred             CCceEEEEEeccccccc-----c--eeecccc--c--ceEeeeccCCceEEEEecCCCCCC-CCCeEEEEEE-ccCC-CC
Q 041904          174 PTYYHTWKVSNFSSLLD-----E--FYESESF--G--CYKWYANYSMDVKILLYPNGNGEA-KGNCISLFLD-VSQS-SI  239 (317)
Q Consensus       174 ~~~~~~~~i~nfs~~~~-----~--~~~S~~f--~--g~~W~~~~~~~~~i~~yp~g~~~~-~~~~lS~yL~-~~~~-~~  239 (317)
                      ..++|+|+|+|||.+++     +  .+.|+.|  |  ||+|        +|++||+|+..+ +++|||+||+ ++.. +.
T Consensus         3 ~~g~~~w~I~~fS~~~~~~~~g~~~~i~S~~F~vg~~Gy~w--------~i~~yP~G~~~~~~~~~lSlyL~l~~~~~d~   74 (160)
T 1lb6_A            3 CNGIYIWKIGNFGMHLKCQEEEKPVVIHSPGFYTGKPGYKL--------CMRLHLQLPTAQRCANYISLFVHTMQGEYDS   74 (160)
T ss_dssp             CCEEEEEEECCHHHHHHHHHTTCCEEEECCCEESSSSCCEE--------EEEEEECCTTCTTTTTEEEEEEEEECCTTGG
T ss_pred             cCcEEEEEECCHHHHHHhhhcCCCeEEECcCeecCCCCeeE--------EEEEEecCCCCCCCCCEEEEEEEEeecCCCc
Confidence            46789999999999863     3  8999999  8  9999        999999998765 3789999999 5432 22


Q ss_pred             CCCCeEEEEEEEEEEECCCCCc---eeeee-----eEEeeCC-----CCCccccccccccccCCCCCCceeCCEEEEEEE
Q 041904          240 PPNTKLLTKYFLCVENQMNGKN---SEVEG-----EWLYTLT-----NRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAE  306 (317)
Q Consensus       240 ~~~~~~~~~~~l~l~n~~~~~~---~~~~~-----~~~F~~~-----~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~  306 (317)
                      ...|++.++|+|.|+||.+...   .....     ...|...     ..+|||++||++++|+.  +|||+||+|+|+|+
T Consensus        75 ~l~wp~~a~~~l~lldq~~~~~~~~~~~~~~~~~~~~~f~~p~~~~~~~~~G~~~Fi~~~~L~~--~~yl~dD~l~I~~~  152 (160)
T 1lb6_A           75 HLPWPFQGTIRLTILDQSEAPVRQNHEEIMDAKPELLAFQRPTIPRNPKGFGYVTFMHLEALRQ--RTFIKDDTLLVRCE  152 (160)
T ss_dssp             GSCSSCCSEEEEEECCCSCTTSCCCEEEEEECCTTSGGGSCCSSSBCSEEEEEEEEEEGGGGGT--SCCCBTTBEEEEEE
T ss_pred             cCCCceeeeEEEEEEcCCCccccccceEEeecCCcchhccCCcccCCCCCcCEeeEeEHHHhhh--CCCccCCEEEEEEE
Confidence            4579999999999999986521   11111     0124321     23799999999999995  79999999999999


Q ss_pred             EEEEee
Q 041904          307 VTLHGL  312 (317)
Q Consensus       307 V~v~~~  312 (317)
                      |.|+..
T Consensus       153 V~v~~~  158 (160)
T 1lb6_A          153 VSTRFD  158 (160)
T ss_dssp             EEC---
T ss_pred             EEEeec
Confidence            999864

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

Probab=99.89  E-value=1.9e-24  Score=182.23  Aligned_cols=132  Identities=23%  Similarity=0.264  Sum_probs=106.2

Q ss_pred             CCCCceEEEEEeccccccc-------ceeecccc--c--ceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccCC-C
Q 041904          172 DPPTYYHTWKVSNFSSLLD-------EFYESESF--G--CYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQS-S  238 (317)
Q Consensus       172 ~~~~~~~~~~i~nfs~~~~-------~~~~S~~f--~--g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~~-~  238 (317)
                      ....++|+|+|+|||.+++       +.+.|+.|  |  ||+|        +|.+||+|+..++++|||+||+ ++.. +
T Consensus        36 ~~~~g~~~w~I~nfS~~~~~~~~~~g~~i~S~~F~vg~~Gy~W--------~i~~yPnG~~~~~~~~lSlyL~l~~g~~D  107 (198)
T 4ghu_A           36 ASYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKM--------CARVYLNGDGMGKGTHLSLFFVIMRGEYD  107 (198)
T ss_dssp             CCSSSEEEEEECCHHHHHHHHHTTSSCCEECCCEESSTTSCEE--------EEEEETTCCGGGTTTEEEEEEEEECCTTG
T ss_pred             cccccEEEEEECCHHHHHhhhccCCCcEEECCCeEECCCCcEE--------EEEEEeCCCCCCCCCeEEEEEEecCCccC
Confidence            3567899999999999874       58999999  8  9999        9999999998777899999999 5432 2


Q ss_pred             CCCCCeEEEEEEEEEEECCCCC-ceeeee-----eEEe----eCCCCCccccccccccccCCCCCCceeCCEEEEEEEEE
Q 041904          239 IPPNTKLLTKYFLCVENQMNGK-NSEVEG-----EWLY----TLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVT  308 (317)
Q Consensus       239 ~~~~~~~~~~~~l~l~n~~~~~-~~~~~~-----~~~F----~~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~  308 (317)
                      ....|++.++|+|.|+||.++. +.....     ...|    ...+.+|||++||++++|++  +|||+||+|+|+|+|.
T Consensus       108 ~~l~wp~~a~~~l~Lldq~~~~~~~~~~~~~~~~~~~f~rp~~~~~~~wG~~~Fi~~~~L~~--~gyL~dD~l~I~~~V~  185 (198)
T 4ghu_A          108 ALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLEN--GTYIKDDTIFIKVIVD  185 (198)
T ss_dssp             GGSCSSCCCCEEEEECCCSTTCCCEEEEECCCTTSGGGSCCSSSBCCCEEEEEEEEHHHHHH--TTSCBTTBEEEEEEEC
T ss_pred             CCCCceEEEEEEEEEEcCCCCccceEEEeecCcccceecCCcccCcCCcCchhEeEHHHhhh--cCCeeCCEEEEEEEEE
Confidence            2358999999999999998653 322211     1123    23457899999999999995  7999999999999999


Q ss_pred             EEeee
Q 041904          309 LHGLV  313 (317)
Q Consensus       309 v~~~~  313 (317)
                      |+..+
T Consensus       186 v~~~~  190 (198)
T 4ghu_A          186 TSDLP  190 (198)
T ss_dssp             CTTCC
T ss_pred             eccCC
Confidence            98654

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

Probab=99.89  E-value=2.8e-24  Score=180.74  Aligned_cols=129  Identities=24%  Similarity=0.290  Sum_probs=104.7

Q ss_pred             CCceEEEEEecccccc-----cc--eeecccc--c--ceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccCC-CCC
Q 041904          174 PTYYHTWKVSNFSSLL-----DE--FYESESF--G--CYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQS-SIP  240 (317)
Q Consensus       174 ~~~~~~~~i~nfs~~~-----~~--~~~S~~f--~--g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~~-~~~  240 (317)
                      ..++|+|+|+|||.++     ++  .+.|++|  |  ||+|        +|.+||+|++.++++|||+||+ ++.. +..
T Consensus        38 ~~g~~~w~I~~fS~~~~~~~~g~~~~i~S~~F~vg~~Gykw--------~i~~yPnG~~~~~~~~lSlyL~l~~~~~d~~  109 (192)
T 2gkw_A           38 YNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKM--------CARVYLNGDGMGKGTHLSLFFVIMRGEYDAL  109 (192)
T ss_dssp             CSSEEEEEEECHHHHHHHHHHTSCSCEECCCEESSTTSCEE--------EEEEETTCCGGGTTTEEEEEEEEECCTTGGG
T ss_pred             cCcEEEEEECCHHHHHHHhhcCCCceEEcccEEECCCCcEE--------EEEEEeCCCCCCCCCEEEEEEEEecCCCCcc
Confidence            6789999999999987     23  5899999  7  9999        9999999987777899999999 5433 223


Q ss_pred             CCCeEEEEEEEEEEECCCCC-ceeeee-----eEEeeCC----CCCccccccccccccCCCCCCceeCCEEEEEEEEEEE
Q 041904          241 PNTKLLTKYFLCVENQMNGK-NSEVEG-----EWLYTLT----NRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLH  310 (317)
Q Consensus       241 ~~~~~~~~~~l~l~n~~~~~-~~~~~~-----~~~F~~~----~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v~  310 (317)
                      ..|++.++|+|.|+||.++. +.....     .+.|...    +.+|||++||++++|++  +|||+||+|+|+|+|.|.
T Consensus       110 l~wp~~a~~~l~lldq~~~~~~~~~~~~~~~~~~~F~~~~~~~~~~wG~~~Fi~~~~L~~--~gyl~dD~l~I~~~V~v~  187 (192)
T 2gkw_A          110 LPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLEN--GTYIKDDTIFIKVIVDTS  187 (192)
T ss_dssp             SCSSCCCCEEEEECCCSTTCCCEEEEECCCTTCTTSSCCSSSBCCCEEEEEEEEHHHHHH--TTSCBTTEEEEEEEECCT
T ss_pred             CCCcEEEEEEEEEECCCCCccceEEEEecCCCcccccCCCCCCcCCCChHHEeEHHHhCc--CCCeeCCEEEEEEEEEcC
Confidence            57999999999999998864 332221     1457542    46899999999999996  699999999999999875


Q ss_pred             ee
Q 041904          311 GL  312 (317)
Q Consensus       311 ~~  312 (317)
                      +.
T Consensus       188 ~~  189 (192)
T 2gkw_A          188 DL  189 (192)
T ss_dssp             TS
T ss_pred             CC
Confidence            43

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

Probab=99.88  E-value=1.8e-22  Score=182.63  Aligned_cols=126  Identities=23%  Similarity=0.423  Sum_probs=103.9

Q ss_pred             CceEEEEEecccccc---cceeecccc--cc---eEeeeccCCceEEEEecCCCCCCCCCeEEEEEEccCCCCCCCCeEE
Q 041904          175 TYYHTWKVSNFSSLL---DEFYESESF--GC---YKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLL  246 (317)
Q Consensus       175 ~~~~~~~i~nfs~~~---~~~~~S~~f--~g---~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~~~~~~~~~~~~~~  246 (317)
                      .++|+|+|+|||.++   ++.+.|+.|  ||   ++|        +|.+||+|+...+++|+|+||++..   ...|++.
T Consensus         6 ~~~~~w~I~nfs~~~~~~~~~i~S~~F~~gg~~~~~W--------~i~~yP~G~~~~~~~~lslyL~~~~---~~~~~v~   74 (312)
T 3hqi_A            6 KFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKW--------CLRVNPKGLDEESKDYLSLYLLLVS---CPKSEVR   74 (312)
T ss_dssp             EEEEEEEETTGGGCCCCTTCCEECCCBCC--CCCCEE--------EEEEETTCCC--CTTEEEEEEEEEE---CCC-CEE
T ss_pred             EEEEEEEEcCcchhhhcCCCeEeeCCcccCCCCCceE--------EEEEECCCCCccCCCcEEEEEEEcC---CCCCcEE
Confidence            468999999999997   678999999  77   599        9999999987767799999999542   2478999


Q ss_pred             EEEEEEEEECCCCCceee--eeeEEeeCCCCCccccccccccccCCCCCCceeCCEEEEEEEEEEEee
Q 041904          247 TKYFLCVENQMNGKNSEV--EGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGL  312 (317)
Q Consensus       247 ~~~~l~l~n~~~~~~~~~--~~~~~F~~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v~~~  312 (317)
                      ++|+|.|+||+++.....  ...+.|.. +.+|||++||+|++|+++.+|||+||+++|+|+|+|++.
T Consensus        75 a~~~~~l~~~~~~~~~~~~~~~~~~F~~-~~~wG~~~Fi~~~~L~~~~~~yl~dD~l~i~~~v~v~~~  141 (312)
T 3hqi_A           75 AKFKFSILNAKGEETKAMESQRAYRFVQ-GKDWGFKKFIRRGFLLDEANGLLPDDKLTLFCEVSVVQD  141 (312)
T ss_dssp             EEEEEEEECTTSCEEEEEECSSCEEECT-TCEEEEEEEEEHHHHTCGGGCCCGGGCEEEEEEEEEEEE
T ss_pred             EEEEEEEEeCCCCcccccccCCceeCCC-CCCcCHHHhccHHHhhccccCeecCCEEEEEEEEEEEec
Confidence            999999999988664432  35678874 468999999999999887789999999999999999953

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

Probab=99.88  E-value=2.6e-23  Score=179.33  Aligned_cols=131  Identities=24%  Similarity=0.286  Sum_probs=106.2

Q ss_pred             CCCceEEEEEeccccccc-------ceeecccc--c--ceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccCC-CC
Q 041904          173 PPTYYHTWKVSNFSSLLD-------EFYESESF--G--CYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQS-SI  239 (317)
Q Consensus       173 ~~~~~~~~~i~nfs~~~~-------~~~~S~~f--~--g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~~-~~  239 (317)
                      ...++|+|+|+|||.+++       ..+.|++|  |  ||+|        +|.+||+|+..++++|||+||+ ++.. +.
T Consensus        73 ~~~g~~~wkI~nfS~~~~~~~~g~~~~i~S~~F~vg~~Gy~w--------~i~~yPnG~~~~~~~~lSlyL~l~~~~~d~  144 (228)
T 1flk_A           73 SYNGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKM--------CARVYLNGDGMGKGTHLSLFFVIMRGEYDA  144 (228)
T ss_dssp             CSSSEEEEEEECHHHHHHHHHTTSCCCEECCCEESSTTSCEE--------CEEEETTCCGGGTTTEEEEEECCBCCTTTT
T ss_pred             CcCcEEEEEECCHHHHHHHhhcCCCeeEECceEEeCCCCcEE--------EEEEEcCCCCCCCCCEEEEEEEEecCCccc
Confidence            367899999999999863       27899999  7  9999        9999999988777899999999 5433 33


Q ss_pred             CCCCeEEEEEEEEEEECCCCC-ceeee-----eeEEeeC----CCCCccccccccccccCCCCCCceeCCEEEEEEEEEE
Q 041904          240 PPNTKLLTKYFLCVENQMNGK-NSEVE-----GEWLYTL----TNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTL  309 (317)
Q Consensus       240 ~~~~~~~~~~~l~l~n~~~~~-~~~~~-----~~~~F~~----~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v  309 (317)
                      ...|++.++|+|.|+||.++. +....     ..+.|..    .+.+|||++||++++|++  +|||+||+|+|+|+|.|
T Consensus       145 ~l~Wp~~a~~~l~lldq~~~~~~~~~~~~~~~~~~~F~rp~~~~~~~wG~~~Fi~~~~L~~--~gyL~dD~l~I~~~V~v  222 (228)
T 1flk_A          145 LLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLEN--GTYIKDDTIFIKVIVDT  222 (228)
T ss_dssp             SSCSSCCCCEEEEECCCSSSCCCEEEEECCCTTCTTSSSCSSSBCCCCSEEEEEEHHHHSS--STTCCSSEEEEEEECCC
T ss_pred             cCCCcEEEEEEEEEEcCCCCccceeeeecCCCccccccCCccCCCCCcCHHHeeEHHHHcc--CCCccCCEEEEEEEEEc
Confidence            458999999999999998765 33221     1224642    246899999999999996  79999999999999998


Q ss_pred             Eeee
Q 041904          310 HGLV  313 (317)
Q Consensus       310 ~~~~  313 (317)
                      .+..
T Consensus       223 ~~~~  226 (228)
T 1flk_A          223 SDLP  226 (228)
T ss_dssp             TTSC
T ss_pred             cccc
Confidence            7653

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

Probab=99.87  E-value=2.3e-22  Score=194.23  Aligned_cols=134  Identities=18%  Similarity=0.232  Sum_probs=110.5

Q ss_pred             CCCceEEEEEecccccccceeecccc--cceEeeeccCCceEEEEecCCCCCC-CCCeEEEEEEccCCCCCCCCeEEEEE
Q 041904          173 PPTYYHTWKVSNFSSLLDEFYESESF--GCYKWYANYSMDVKILLYPNGNGEA-KGNCISLFLDVSQSSIPPNTKLLTKY  249 (317)
Q Consensus       173 ~~~~~~~~~i~nfs~~~~~~~~S~~f--~g~~W~~~~~~~~~i~~yp~g~~~~-~~~~lS~yL~~~~~~~~~~~~~~~~~  249 (317)
                      ...++|+|+|+|||.+++ .+.|++|  ||++|        +|.+||+|+..+ +++|||+||.+.....+..|.+.|+|
T Consensus        28 ~~~~~~~w~I~nfS~~~~-~~~S~~F~vgg~~W--------~i~~yP~G~~~~~~~~~lSlyL~~~~~~~~~~w~v~a~f   98 (522)
T 2f1z_A           28 RSEATFQFTVERFSRLSE-SVLSPPCFVRNLPW--------KIMVMPRFYPDRPHQKSVGFFLQCNAESDSTSWSCHAQA   98 (522)
T ss_dssp             CSEEEEEEEESSCTTCCS-CEECCCEEETTEEE--------EEEECBC--------CBBCEEEEESTTCCCSSCBEEEEE
T ss_pred             cCCcEEEEEECChhhcCC-ceeCCCEEECCEee--------EEEEEeCCCCCCCCCCeEEEEEEecCCCCCCCceEEEEE
Confidence            456899999999999986 8889999  99999        999999997543 56899999995433556789999999


Q ss_pred             EEEEEECCCCC-ceeeeeeEEeeCCCCCccccccccccccCCCCCCceeCCEEEEEEEEEEEeeecc
Q 041904          250 FLCVENQMNGK-NSEVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGLVLA  315 (317)
Q Consensus       250 ~l~l~n~~~~~-~~~~~~~~~F~~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v~~~~~~  315 (317)
                      +|.|+|+.++. +..+...++|.....+|||++||++++|.++++|||+||+++|+|+|+|...+|+
T Consensus        99 ~l~l~n~~~~~~~~~~~~~~~F~~~~~~wG~~~Fi~~~~L~~~~~g~L~nD~l~i~~~V~v~~p~g~  165 (522)
T 2f1z_A           99 VLKIINYRDDEKSFSRRISHLFFHKENDWGFSNFMAWSEVTDPEKGFIDDDKVTFEVFVQADAPHGV  165 (522)
T ss_dssp             EEEECCTTCGGGCEEEECCEEECGGGCEEEESSSSBHHHHSCGGGSSCBTTBEEEEEEEEECCCBSS
T ss_pred             EEEEEcCCCCccceeccceeEecCCCCCcchhheeEhhHhcCcccCcccCCcEEEEEEeeccccccc
Confidence            99999998765 3455677889876788999999999999877789999999999999999776654

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

Probab=99.55  E-value=7.7e-15  Score=141.18  Aligned_cols=147  Identities=13%  Similarity=0.142  Sum_probs=110.5

Q ss_pred             eccccCCcEEEEEEcCcccccccccceEEcccEEe-CCeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC-CCCCCEEE-
Q 041904           10 AGRNAAPSHYLFKIESFSLLSKASVEQLILDNFEA-GGYKWKLSIHLTGSKSVNVTDHISIYLELAETSS-LPTGWEVN-   86 (317)
Q Consensus        10 ~~~~~~~~~~~w~I~~fs~~~~~~~~~~~S~~F~~-gG~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~-~~~~w~v~-   86 (317)
                      .+.+.+|+.+.|+|.||++++...+..++||+|+. .||+++|.++|++      ..|+|+|+++.++.. ..++||+. 
T Consensus       399 s~t~G~CP~~vw~i~nfs~~l~~~~~~~~Sp~Fys~~GY~~~v~l~~~~------~~~~~~~~~l~sG~~D~~L~WP~~~  472 (592)
T 4gwm_A          399 NLSETRCPHHIWHIRNFTQFIGSPNGTLYSPPFYSSKGYAFQIYLNLAH------VTNAGIYFHLISGANDDQLQWPCPW  472 (592)
T ss_dssp             EEESSCCCSEEEEECSCGGGTTCTTCEEECCCEECTTSCEEEEEEECCS------SSEEEEEEEEECCTTGGGSCSSCCS
T ss_pred             EEeeCCCCCCceeecCHHHhhcCCCCceeCCCccCCCCeEEEEEEecCC------CceEEEEEEEecCCCCCCccCCCCC
Confidence            35778999999999999999874567899999997 5999999999874      478999999999876 47899994 


Q ss_pred             EEEEEEEEecCCCcEEE---EEee----ecccceeeeecc-----------------cccccccccceeecccccCCCCc
Q 041904           87 AITISFYSIKFKTNILV---SKVR----NSTINVIVKHFH-----------------AMKSKYGVAKFIDLKTFSDPLNG  142 (317)
Q Consensus        87 ~~f~~~l~n~~~~~~~~---~~~~----~~~~~~~~~~F~-----------------~~~~~~G~~~fi~~~~l~~~~~~  142 (317)
                      -+++|.|+||+......   ....    ..+.+.....|.                 ..+.+|||+.||++++|+  +++
T Consensus       473 ~q~t~~llDQ~pd~~~rms~~~s~ttdp~~~~~~~~~~w~~P~~~g~~~~~~~~~~~~r~~~~G~~~fish~~l~--~r~  550 (592)
T 4gwm_A          473 QQATMTLLDQNPDIRQRMSNQRSITTDPFMTTDNGNYFWDRPSKVGTVALFSNGTQFRRGGGYGTSAFITHERLK--SRD  550 (592)
T ss_dssp             EEEEEEECCCCSSGGGCCCEEEEEECCTTCBCTTSCBTTSCHHHHCEEEECTTCCEEEEEEEEEEEEEEEHHHHT--STT
T ss_pred             CEEEEEEeCCCCChHhcCceeEEEEcCCcccCcccccccCCcccccccccccCCcceeecCCcCccccccHHHHh--hcC
Confidence            78999999997543321   1110    000000111121                 124579999999999998  678


Q ss_pred             eEeCCEEEEEEEEEEEeecCcc
Q 041904          143 YLINDACVFGAEVFVVKNTFKG  164 (317)
Q Consensus       143 yl~~d~l~i~~~v~v~~~~~~~  164 (317)
                      ||+||.|.|.+.|+-+......
T Consensus       551 fiK~d~~~i~~~~eD~~~l~~~  572 (592)
T 4gwm_A          551 FIKGDDVYILLTVEDISHLNST  572 (592)
T ss_dssp             SSBTTBEEEEEEEEECGGGSSC
T ss_pred             cccCCeEEEEEEEEeCcccccc
Confidence            9999999999999876554433

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

Probab=99.20  E-value=3.8e-11  Score=115.62  Aligned_cols=125  Identities=16%  Similarity=0.234  Sum_probs=96.8

Q ss_pred             cCCCCceEEEEEecccccc---cceeecccc---cceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-cc-CCCCCCC
Q 041904          171 HDPPTYYHTWKVSNFSSLL---DEFYESESF---GCYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VS-QSSIPPN  242 (317)
Q Consensus       171 ~~~~~~~~~~~i~nfs~~~---~~~~~S~~f---~g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~-~~~~~~~  242 (317)
                      ...++..+.|+|.||+++.   +..++||.|   .||.+        +|.+||++     ..++|+|++ +. ..+.-..
T Consensus       401 t~G~CP~~vw~i~nfs~~l~~~~~~~~Sp~Fys~~GY~~--------~v~l~~~~-----~~~~~~~~~l~sG~~D~~L~  467 (592)
T 4gwm_A          401 SETRCPHHIWHIRNFTQFIGSPNGTLYSPPFYSSKGYAF--------QIYLNLAH-----VTNAGIYFHLISGANDDQLQ  467 (592)
T ss_dssp             ESSCCCSEEEEECSCGGGTTCTTCEEECCCEECTTSCEE--------EEEEECCS-----SSEEEEEEEEECCTTGGGSC
T ss_pred             eeCCCCCCceeecCHHHhhcCCCCceeCCCccCCCCeEE--------EEEEecCC-----CceEEEEEEEecCCCCCCcc
Confidence            3456678999999999987   458999999   99999        99999975     469999999 54 4444589


Q ss_pred             CeE-EEEEEEEEEECCCCCceeeeeeEEeeC--------------------------------CCCCccccccccccccC
Q 041904          243 TKL-LTKYFLCVENQMNGKNSEVEGEWLYTL--------------------------------TNRAIGGRQFMTLAKLK  289 (317)
Q Consensus       243 ~~~-~~~~~l~l~n~~~~~~~~~~~~~~F~~--------------------------------~~~~~G~~~fi~~~~L~  289 (317)
                      |++ .-+++|.|++|+......+.....|..                                .+.+|||+.||+++.|.
T Consensus       468 WP~~~~q~t~~llDQ~pd~~~rms~~~s~ttdp~~~~~~~~~~w~~P~~~g~~~~~~~~~~~~r~~~~G~~~fish~~l~  547 (592)
T 4gwm_A          468 WPCPWQQATMTLLDQNPDIRQRMSNQRSITTDPFMTTDNGNYFWDRPSKVGTVALFSNGTQFRRGGGYGTSAFITHERLK  547 (592)
T ss_dssp             SSCCSEEEEEEECCCCSSGGGCCCEEEEEECCTTCBCTTSCBTTSCHHHHCEEEECTTCCEEEEEEEEEEEEEEEHHHHT
T ss_pred             CCCCCCEEEEEEeCCCCChHhcCceeEEEEcCCcccCcccccccCCcccccccccccCCcceeecCCcCccccccHHHHh
Confidence            999 578999999997543222222222321                                12358999999999999


Q ss_pred             CCCCCceeCCEEEEEEEEEEE
Q 041904          290 DPTEGYLVDDSCIIKAEVTLH  310 (317)
Q Consensus       290 ~~~~gyl~dd~l~i~~~V~v~  310 (317)
                      .  +.||+||.|.|.+.|+-+
T Consensus       548 ~--r~fiK~d~~~i~~~~eD~  566 (592)
T 4gwm_A          548 S--RDFIKGDDVYILLTVEDI  566 (592)
T ss_dssp             S--TTSSBTTBEEEEEEEEEC
T ss_pred             h--cCcccCCeEEEEEEEEeC
Confidence            6  679999999999999654

---

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	317
d2cr2a1	146	b.8.1.1 (A:8-153) Speckle-type poz protein SPOP {H	9e-16
d2cr2a1	146	b.8.1.1 (A:8-153) Speckle-type poz protein SPOP {H	3e-13
d1czya1	152	b.8.1.1 (A:350-501) TNF receptor associated factor	1e-14
d1czya1	152	b.8.1.1 (A:350-501) TNF receptor associated factor	9e-12
d1l0aa1	155	b.8.1.1 (A:350-504) TNF receptor associated factor	9e-14
d1l0aa1	155	b.8.1.1 (A:350-504) TNF receptor associated factor	7e-08
d1lb6a_	155	b.8.1.1 (A:) TNF receptor associated factor 6 (TRA	1e-10
d1lb6a_	155	b.8.1.1 (A:) TNF receptor associated factor 6 (TRA	5e-09

>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 = 71.0 bits (173), Expect = 9e-16
 Identities = 29/143 (20%), Positives = 54/143 (37%), Gaps = 20/143 (13%)

Query: 176 YYHTWKVSNFSSLLD---EFYESESFGC-----YKWYANYSMDVKILLYPNGNGEAKGNC 227
           + + W ++NFS   +   E  +S +F        KW         + + P G  E   + 
Sbjct: 5   FSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWC--------LRVNPKGLDEESKDY 56

Query: 228 ISLFLDVSQSSIPPNTKLLTKYFLCVENQMNGKNSEVEGEWLYTLT-NRAIGGRQFMTLA 286
           +SL+L +             K+   + N    +   +E +  Y     +  G ++F+   
Sbjct: 57  LSLYLLLVSCPKSEVR---AKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRD 113

Query: 287 KLKDPTEGYLVDDSCIIKAEVTL 309
            L D   G L DD   +  EV++
Sbjct: 114 FLLDEANGLLPDDKLTLFCEVSV 136

>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 = 64.0 bits (155), Expect = 3e-13
 Identities = 35/148 (23%), Positives = 55/148 (37%), Gaps = 17/148 (11%)

Query: 19  YLFKIESFSLLSKASVEQLILDNFEAGG---YKWKLSIHLTGSKSVNVTDHISIYLELAE 75
           Y++ I +FS   +   E +    F +G     KW L ++  G       D++S+YL L  
Sbjct: 7   YMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKG-LDEESKDYLSLYLLLVS 65

Query: 76  TSSLPTGWEVNA-ITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLK 134
                   EV A    S  + K +    +   R         +       +G  KFI   
Sbjct: 66  C----PKSEVRAKFKFSILNAKGEETKAMESQR--------AYRFVQGKDWGFKKFIRRD 113

Query: 135 TFSDPLNGYLINDACVFGAEVFVVKNTF 162
              D  NG L +D      EV VV+++ 
Sbjct: 114 FLLDEANGLLPDDKLTLFCEVSVVQDSV 141

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

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

 Score = 68.3 bits (166), Expect = 1e-14
 Identities = 34/150 (22%), Positives = 58/150 (38%), Gaps = 15/150 (10%)

Query: 177 YHTWKVSNFSSLLDEFYESESFGCYK---WYANYSMDVKILLYPNGNGEAKGNCISLFLD 233
              WK+S+F     E         +    + + Y   + + +Y NG+G  +G  +SLF  
Sbjct: 4   VFIWKISDFPRKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFV 63

Query: 234 V--SQSSIPPNTKLLTKYFLCVENQMNGKNSEVEGEWLYTLTN---------RAIGGRQF 282
           V    +          K  L + +Q N ++         T ++          A G   F
Sbjct: 64  VMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLF 123

Query: 283 MTLAKLKDPTEGYLVDDSCIIKAEVTLHGL 312
             ++K+ +    Y+ DD+  IKA V L GL
Sbjct: 124 CPVSKM-EAKNSYVRDDAIFIKAIVDLTGL 152

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

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

 Score = 59.8 bits (144), Expect = 9e-12
 Identities = 28/150 (18%), Positives = 56/150 (37%), Gaps = 10/150 (6%)

Query: 17  SHYLFKIESFSLLSKASVEQLIL----DNFEAG--GYKWKLSIHLTGSKSVNVTDHISIY 70
             +++KI  F    + +V   I       F     GYK  L I+L G        H+S++
Sbjct: 3   GVFIWKISDFPRKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNG-DGTGRGTHLSLF 61

Query: 71  LELAETSSLPTG-WEVNA-ITISFYSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVA 128
             + +  +     W  N  +T+       + +++ +   + T +   +  + M    G  
Sbjct: 62  FVVMKGPNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCP 121

Query: 129 KFIDLKTFSDPLNGYLINDACVFGAEVFVV 158
            F  +    +  N Y+ +DA    A V + 
Sbjct: 122 LFCPVSKM-EAKNSYVRDDAIFIKAIVDLT 150

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

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

 Score = 65.6 bits (159), Expect = 9e-14
 Identities = 28/152 (18%), Positives = 51/152 (33%), Gaps = 17/152 (11%)

Query: 177 YHTWKVSNFSSLLDEFYESESFGCYK---WYANYSMDVKILLYPNGNGEAKGNCISLFL- 232
              WK+ ++     E    ++   Y    +   +   +   +Y NG+G  KG  +SLF  
Sbjct: 4   VLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMGKGTHLSLFFV 63

Query: 233 -DVSQSSIPPNTKLLTKYFLCVENQMNGKNSEVE----------GEWLYTLTNRAIGGRQ 281
               +           K  L + +Q + +    +           +      N A G   
Sbjct: 64  IMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPV 123

Query: 282 FMTLAKLKDPTEGYLVDDSCIIKAEVTLHGLV 313
           F+    L++    Y+ DD+  IK  V    L 
Sbjct: 124 FVAQTVLEN--GTYIKDDTIFIKVIVDTSDLP 153

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

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

 Score = 49.1 bits (116), Expect = 7e-08
 Identities = 20/147 (13%), Positives = 45/147 (30%), Gaps = 12/147 (8%)

Query: 18  HYLFKIESFSLLSKASVEQ----LILDNFEAG--GYKWKLSIHLTGSKSVNVTDHISIYL 71
             ++KI  +    + +V      L    F  G  GYK    ++L G   +    H+S++ 
Sbjct: 4   VLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNG-DGMGKGTHLSLFF 62

Query: 72  ELAETSSLPTGWEVNAITISFYSI---KFKTNILVSKVRNSTINVIVKHFHAMKSKYGVA 128
            +                ++   +     + ++  +   +   +   K    M    G  
Sbjct: 63  VIMRGEYDALLPWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCP 122

Query: 129 KFIDLKTFSDPLNGYLINDACVFGAEV 155
            F+      +    Y+ +D       V
Sbjct: 123 VFVAQTVLEN--GTYIKDDTIFIKVIV 147

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

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

 Score = 57.2 bits (137), Expect = 1e-10
 Identities = 26/151 (17%), Positives = 49/151 (32%), Gaps = 21/151 (13%)

Query: 177 YHTWKVSNFSSLLDEFYESESFGCY--KWYA-NYSMDVKILLYPNGNG-EAKGNCISLFL 232
            + WK+ NF   L    E +    +   +Y       + + L+      +   N ISLF+
Sbjct: 6   IYIWKIGNFGMHLKCQEEEKPVVIHSPGFYTGKPGYKLCMRLHLQLPTAQRCANYISLFV 65

Query: 233 DVSQ--SSIPPNTKLLTKYFLCVENQMNGKNSEVEGEWLYTL-------------TNRAI 277
              Q                L + +Q      +   E +                  +  
Sbjct: 66  HTMQGEYDSHLPWPFQGTIRLTILDQSEAPVRQNHEEIMDAKPELLAFQRPTIPRNPKGF 125

Query: 278 GGRQFMTLAKLKDPTEGYLVDDSCIIKAEVT 308
           G   FM L  L+     ++ DD+ +++ EV+
Sbjct: 126 GYVTFMHLEALRQ--RTFIKDDTLLVRCEVS 154

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

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

 Score = 52.1 bits (124), Expect = 5e-09
 Identities = 22/150 (14%), Positives = 45/150 (30%), Gaps = 14/150 (9%)

Query: 18  HYLFKIESFSLLSKASV----EQLILDNFEAG--GYKWKLSIHLTGSKSVNVTDHISIYL 71
            Y++KI +F +  K         +    F  G  GYK  + +HL    +    ++IS+++
Sbjct: 6   IYIWKIGNFGMHLKCQEEEKPVVIHSPGFYTGKPGYKLCMRLHLQLPTAQRCANYISLFV 65

Query: 72  ELAETSSLPTGWEVNAITISFYSIKFKTNILVSKVRNSTINVIVKH------FHAMKSKY 125
              +             TI    +      +                            +
Sbjct: 66  HTMQGEYDSHLPWPFQGTIRLTILDQSEAPVRQNHEEIMDAKPELLAFQRPTIPRNPKGF 125

Query: 126 GVAKFIDLKTFSDPLNGYLINDACVFGAEV 155
           G   F+ L+        ++ +D  +   EV
Sbjct: 126 GYVTFMHLEALRQ--RTFIKDDTLLVRCEV 153

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	317
d2cr2a1	146	Speckle-type poz protein SPOP {Human (Homo sapiens	99.94
d1czya1	152	TNF receptor associated factor 2 (TRAF2) {Human (H	99.94
d1lb6a_	155	TNF receptor associated factor 6 (TRAF6) {Human (H	99.94
d1l0aa1	155	TNF receptor associated factor 3 (TRAF3) {Human (H	99.94
d2cr2a1	146	Speckle-type poz protein SPOP {Human (Homo sapiens	99.91
d1czya1	152	TNF receptor associated factor 2 (TRAF2) {Human (H	99.9
d1l0aa1	155	TNF receptor associated factor 3 (TRAF3) {Human (H	99.88
d1lb6a_	155	TNF receptor associated factor 6 (TRAF6) {Human (H	99.87

>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=99.94  E-value=2e-27  Score=189.69  Aligned_cols=134  Identities=24%  Similarity=0.271  Sum_probs=114.3

Q ss_pred             CcEEEEEEcCcccccccccceEEcccEEeCC---eEEEEEEEecCCCCCCCCCcEEEEEEeccCCCCCCCCEEEEEEEEE
Q 041904           16 PSHYLFKIESFSLLSKASVEQLILDNFEAGG---YKWKLSIHLTGSKSVNVTDHISIYLELAETSSLPTGWEVNAITISF   92 (317)
Q Consensus        16 ~~~~~w~I~~fs~~~~~~~~~~~S~~F~~gG---~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~~~~~w~v~~~f~~~   92 (317)
                      ..+|+|+|+|||.+++..++.++||.|.+||   ++|+|.+||+|.... ..+||||||.+.+..    .|++.++|+|.
T Consensus         4 ~~~~~W~I~nfs~~~~~~~~~~~Sp~F~~~~~~~~~W~l~lyp~G~~~~-~~~~lSv~L~~~~~~----~~~v~~~~~~~   78 (146)
T d2cr2a1           4 KFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKWCLRVNPKGLDEE-SKDYLSLYLLLVSCP----KSEVRAKFKFS   78 (146)
T ss_dssp             EEEEEEEEETGGGCCCCSSCCEECCCBCSSSCCSCCBEEEECTTCSSSS-SSSBCCEEEECCCCS----SSEEEEECEEE
T ss_pred             EEEEEEEECCchHHhhcCCCEEECCCEEeCCcCCeEEEEEEEECCCCCC-CCCEEEEEEEeccCC----CceEEEEEEEE
Confidence            4689999999998876567899999999887   589999999998763 678999999998754    48999999999


Q ss_pred             EEecCCCcEEEEEeeecccceeeeecccccccccccceeecccccCCCCceEeCCEEEEEEEEEEEeec
Q 041904           93 YSIKFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVVKNT  161 (317)
Q Consensus        93 l~n~~~~~~~~~~~~~~~~~~~~~~F~~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v~~~~  161 (317)
                      |+|+.++.......       ..+.|.....+|||++||++++|.++.+|||.||+|+|+|+|+|+.+.
T Consensus        79 l~n~~~~~~~~~~~-------~~~~~~~~~~~~G~~~fi~~~~l~~~~~g~l~~d~l~I~~~I~v~~e~  140 (146)
T d2cr2a1          79 ILNAKGEETKAMES-------QRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQDS  140 (146)
T ss_dssp             EECTTSCEEEEEEC-------SCCEEEETTCEEEESCCSBHHHHSCTTTTSCTTSEEEEEEEEEEECCS
T ss_pred             EEcCCCCcccceEe-------cceEeCCCCCeeeccEEEEHHHhcCcccCceeCCEEEEEEEEEEEeCC
Confidence            99998877666543       333444566889999999999999989999999999999999998764

>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=99.94  E-value=1.7e-27  Score=191.38  Aligned_cols=141  Identities=18%  Similarity=0.285  Sum_probs=109.7

Q ss_pred             CcEEEEEEcCccccccc----ccceEEcccEEeC--CeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC-CCCCCEEEEE
Q 041904           16 PSHYLFKIESFSLLSKA----SVEQLILDNFEAG--GYKWKLSIHLTGSKSVNVTDHISIYLELAETSS-LPTGWEVNAI   88 (317)
Q Consensus        16 ~~~~~w~I~~fs~~~~~----~~~~~~S~~F~~g--G~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~-~~~~w~v~~~   88 (317)
                      .|+|+|+|+|||.+++.    .++.++||+|++|  ||+|+|.+||+|+..+ .++|+||||++.++.. .++.|++.++
T Consensus         2 ~g~f~W~I~nFs~l~~~~~~~~~~~~~Sp~F~~g~~Gy~w~l~~yP~G~~~~-~~~~lSlyL~l~~~~~d~~~~~~~~~~   80 (152)
T d1czya1           2 DGVFIWKISDFPRKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTG-RGTHLSLFFVVMKGPNDALLRWPFNQK   80 (152)
T ss_dssp             SSEEEEEECSHHHHHHHHHTTSCCCEECCCEESSTTSCEEEEEEETTCCGGG-TTTEEEEEEEEECCTTGGGSCSSCCCC
T ss_pred             CCEEEEEECCcHHHHHhhhcCCCceEECcCEEcCCCCeEEEEEEEeCCCCCC-CCCEEEEEEEEccCCcCcccccceeeE
Confidence            58999999999998751    3567999999998  9999999999998753 6789999999988754 3568999999


Q ss_pred             EEEEEEecCCCcEEEEEeee-cccceeeeecccccccccccceeecccccCCCCceEeCCEEEEEEEEEEE
Q 041904           89 TISFYSIKFKTNILVSKVRN-STINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFVV  158 (317)
Q Consensus        89 f~~~l~n~~~~~~~~~~~~~-~~~~~~~~~F~~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v~  158 (317)
                      |+|.|+||.++......... .......+.+.....+|||++||++++|. +++|||.||+|+|+|+|.|.
T Consensus        81 ~~~~l~d~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~G~~~fi~~~~L~-~~~gfl~dD~l~I~~~V~v~  150 (152)
T d1czya1          81 VTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKME-AKNSYVRDDAIFIKAIVDLT  150 (152)
T ss_dssp             EEEEECCTTSSCCEEEEECCCTTSGGGSCCSSSBCCCEEEEEEEETCCCC-CSTTTSCSSCEEEEEEECCT
T ss_pred             EEEEEEcCCCCccceeeeccccccccccCCCcccccccchhhEEEHHHhc-ccCCcEeCCEEEEEEEEEec
Confidence            99999999876644421110 00000112234456789999999999984 46799999999999999764

>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=99.94  E-value=6.2e-27  Score=188.63  Aligned_cols=141  Identities=15%  Similarity=0.228  Sum_probs=110.2

Q ss_pred             cCCcEEEEEEcCcccccc----cccceEEcccEEeC--CeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC-CCCCCEEE
Q 041904           14 AAPSHYLFKIESFSLLSK----ASVEQLILDNFEAG--GYKWKLSIHLTGSKSVNVTDHISIYLELAETSS-LPTGWEVN   86 (317)
Q Consensus        14 ~~~~~~~w~I~~fs~~~~----~~~~~~~S~~F~~g--G~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~-~~~~w~v~   86 (317)
                      ...|+|.|+|+|||.+++    ..+..++||+|++|  ||+|||.+||+|...+...+|||+||++.++.. ..++|++.
T Consensus         2 ~~~G~f~W~I~nfs~~~~~~~~~~~~~i~Sp~F~~g~~Gy~wrl~~yp~g~~~~~~~~~lsvyL~l~~~~~d~~~~~~~~   81 (155)
T d1lb6a_           2 QCNGIYIWKIGNFGMHLKCQEEEKPVVIHSPGFYTGKPGYKLCMRLHLQLPTAQRCANYISLFVHTMQGEYDSHLPWPFQ   81 (155)
T ss_dssp             CCCEEEEEEECCHHHHHHHHHTTCCEEEECCCEESSSSCCEEEEEEEECCTTCTTTTTEEEEEEEEECCTTGGGSCSSCC
T ss_pred             ccccEEEEEECChHHHHHhhhcCCCcEEECcCEEeCCCCcEEEEEEEeCCCCCCCCCCEEEEEEEEecCcccccCCCcEE
Confidence            567999999999999876    13568999999998  999999999999876434689999999988754 46789999


Q ss_pred             EEEEEEEEecCCCcEEEEEeeecccc-----eeeeecccccccccccceeecccccCCCCceEeCCEEEEEEEEE
Q 041904           87 AITISFYSIKFKTNILVSKVRNSTIN-----VIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVF  156 (317)
Q Consensus        87 ~~f~~~l~n~~~~~~~~~~~~~~~~~-----~~~~~F~~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~  156 (317)
                      ++++|.|+||++..............     -..+.|.....+|||++||++++|+  ++|||+||+|+|+|+|+
T Consensus        82 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~fi~~~~L~--~~gyl~dD~l~I~~~V~  154 (155)
T d1lb6a_          82 GTIRLTILDQSEAPVRQNHEEIMDAKPELLAFQRPTIPRNPKGFGYVTFMHLEALR--QRTFIKDDTLLVRCEVS  154 (155)
T ss_dssp             SEEEEEECCCSCTTSCCCEEEEEECCTTSGGGSCCSSSBCSEEEEEEEEEEGGGGG--TSCCCBTTBEEEEEEEE
T ss_pred             EEEEEEEECCCCCccceeeEEeeecCCccccccCCcccCCcCCcChHHeeEHHHhc--cCCCEECCEEEEEEEEE
Confidence            99999999998765432211100000     0112344456789999999999998  58999999999999986

>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=99.94  E-value=3.6e-27  Score=190.11  Aligned_cols=139  Identities=14%  Similarity=0.181  Sum_probs=110.0

Q ss_pred             CcEEEEEEcCccccccc----ccceEEcccEEeC--CeEEEEEEEecCCCCCCCCCcEEEEEEeccCCC-CCCCCEEEEE
Q 041904           16 PSHYLFKIESFSLLSKA----SVEQLILDNFEAG--GYKWKLSIHLTGSKSVNVTDHISIYLELAETSS-LPTGWEVNAI   88 (317)
Q Consensus        16 ~~~~~w~I~~fs~~~~~----~~~~~~S~~F~~g--G~~W~l~~~p~G~~~~~~~~~lSvyL~~~~~~~-~~~~w~v~~~   88 (317)
                      .|+|+|+|+|||.+++.    .+..++||+|++|  ||+|+|.+||+|+..+ .++||||||++.++.. ..+.|++.++
T Consensus         2 ~g~f~W~I~nfs~~~~~~~~~~~~~~~S~~F~~~~~Gy~w~l~~yp~G~~~~-~~~~lSlyL~l~~~~~d~~~~~~~~~~   80 (155)
T d1l0aa1           2 NGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKMCARVYLNGDGMG-KGTHLSLFFVIMRGEYDALLPWPFKQK   80 (155)
T ss_dssp             SSEEEEEEECHHHHHHHHHTTSCSEEECCCEESSTTSCEEEEEEETTCCGGG-TTTEEEEEEEEECCTTTTTSCSSCCCC
T ss_pred             CCEEEEEECCcHHHHHhhhcCCCcEEECcCEEeCCCCcEEEEEEEeCCCCCC-CCCEEEEEEEEccCCcCcccCCcEEEE
Confidence            68999999999998751    4568999999998  9999999999998763 6789999999988654 3568999999


Q ss_pred             EEEEEEecCCCcEEEEEeee--cccceeeeecccccccccccceeecccccCCCCceEeCCEEEEEEEEEE
Q 041904           89 TISFYSIKFKTNILVSKVRN--STINVIVKHFHAMKSKYGVAKFIDLKTFSDPLNGYLINDACVFGAEVFV  157 (317)
Q Consensus        89 f~~~l~n~~~~~~~~~~~~~--~~~~~~~~~F~~~~~~~G~~~fi~~~~l~~~~~~yl~~d~l~i~~~v~v  157 (317)
                      |+|.|+||.++.........  .......+.+.....+|||++||++++|+  ++|||+||+|+|+|+|.+
T Consensus        81 ~~~~l~~q~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~G~~~fi~~~~L~--~~gfl~dD~l~I~~~V~~  149 (155)
T d1l0aa1          81 VTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLE--NGTYIKDDTIFIKVIVDT  149 (155)
T ss_dssp             EEEEECCCSSSCCCEEEEECCCTTSTTSSCCSSSBCCCEEEEEEEEHHHHH--TTTTCBTTEEEEEEEECC
T ss_pred             EEEEEecCCCCccceeEEEeeccccccccccccccccCcChhheeEHHHhh--hCCCEECCEEEEEEEEEe
Confidence            99999999877654432210  00001123344556789999999999998  589999999999999864

>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=99.91  E-value=6.2e-25  Score=175.05  Aligned_cols=128  Identities=23%  Similarity=0.366  Sum_probs=106.7

Q ss_pred             CceEEEEEecccccc---cceeecccc--cc---eEeeeccCCceEEEEecCCCCCCCCCeEEEEEEccCCCCCCCCeEE
Q 041904          175 TYYHTWKVSNFSSLL---DEFYESESF--GC---YKWYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQSSIPPNTKLL  246 (317)
Q Consensus       175 ~~~~~~~i~nfs~~~---~~~~~S~~f--~g---~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~~~~~~~~~~~~~~  246 (317)
                      ..+++|+|+||+.++   ++++.||.|  +|   ++|        +|.+||+|.....++||||||.+..   ...|++.
T Consensus         4 ~~~~~W~I~nfs~~~~~~~~~~~Sp~F~~~~~~~~~W--------~l~lyp~G~~~~~~~~lSv~L~~~~---~~~~~v~   72 (146)
T d2cr2a1           4 KFSYMWTINNFSFCREEMGEVIKSSTFSSGANDKLKW--------CLRVNPKGLDEESKDYLSLYLLLVS---CPKSEVR   72 (146)
T ss_dssp             EEEEEEEEETGGGCCCCSSCCEECCCBCSSSCCSCCB--------EEEECTTCSSSSSSSBCCEEEECCC---CSSSEEE
T ss_pred             EEEEEEEECCchHHhhcCCCEEECCCEEeCCcCCeEE--------EEEEEECCCCCCCCCEEEEEEEecc---CCCceEE
Confidence            357999999999887   368999999  66   489        9999999998877889999999432   2469999


Q ss_pred             EEEEEEEEECCCCCce-eeeeeEEeeCCCCCccccccccccccCCCCCCceeCCEEEEEEEEEEEeee
Q 041904          247 TKYFLCVENQMNGKNS-EVEGEWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLHGLV  313 (317)
Q Consensus       247 ~~~~l~l~n~~~~~~~-~~~~~~~F~~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v~~~~  313 (317)
                      ++|+|.|+|+.++... .....+.+...+.+|||++||++++|.++.+|||+||+|+|+|+|+|++.+
T Consensus        73 ~~~~~~l~n~~~~~~~~~~~~~~~~~~~~~~~G~~~fi~~~~l~~~~~g~l~~d~l~I~~~I~v~~e~  140 (146)
T d2cr2a1          73 AKFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCEVSVVQDS  140 (146)
T ss_dssp             EECEEEEECTTSCEEEEEECSCCEEEETTCEEEESCCSBHHHHSCTTTTSCTTSEEEEEEEEEEECCS
T ss_pred             EEEEEEEEcCCCCcccceEecceEeCCCCCeeeccEEEEHHHhcCcccCceeCCEEEEEEEEEEEeCC
Confidence            9999999999876533 233333444467899999999999999988999999999999999999874

>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=99.90  E-value=2.1e-24  Score=173.18  Aligned_cols=127  Identities=26%  Similarity=0.293  Sum_probs=101.8

Q ss_pred             CceEEEEEecccccc-------cceeecccc--c--ceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccCC-CCCC
Q 041904          175 TYYHTWKVSNFSSLL-------DEFYESESF--G--CYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQS-SIPP  241 (317)
Q Consensus       175 ~~~~~~~i~nfs~~~-------~~~~~S~~f--~--g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~~-~~~~  241 (317)
                      .++++|+|+|||.++       +..+.||.|  +  ||+|        +|.+||+|+..++++|+||||+ ++.. +.+.
T Consensus         2 ~g~f~W~I~nFs~l~~~~~~~~~~~~~Sp~F~~g~~Gy~w--------~l~~yP~G~~~~~~~~lSlyL~l~~~~~d~~~   73 (152)
T d1czya1           2 DGVFIWKISDFPRKRQEAVAGRIPAIFSPAFYTSRYGYKM--------CLRIYLNGDGTGRGTHLSLFFVVMKGPNDALL   73 (152)
T ss_dssp             SSEEEEEECSHHHHHHHHHTTSCCCEECCCEESSTTSCEE--------EEEEETTCCGGGTTTEEEEEEEEECCTTGGGS
T ss_pred             CCEEEEEECCcHHHHHhhhcCCCceEECcCEEcCCCCeEE--------EEEEEeCCCCCCCCCEEEEEEEEccCCcCccc
Confidence            478999999999885       236899999  6  9999        9999999998777899999999 5432 2346


Q ss_pred             CCeEEEEEEEEEEECCCCCceeeeee-----EE----eeCCCCCccccccccccccCCCCCCceeCCEEEEEEEEEEE
Q 041904          242 NTKLLTKYFLCVENQMNGKNSEVEGE-----WL----YTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLH  310 (317)
Q Consensus       242 ~~~~~~~~~l~l~n~~~~~~~~~~~~-----~~----F~~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v~  310 (317)
                      .|++.++|+|.|+||.++++......     ..    +...+.+|||++||++++|+. ++|||+||+|+|+|+|.|.
T Consensus        74 ~~~~~~~~~~~l~d~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~G~~~fi~~~~L~~-~~gfl~dD~l~I~~~V~v~  150 (152)
T d1czya1          74 RWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLFCPVSKMEA-KNSYVRDDAIFIKAIVDLT  150 (152)
T ss_dssp             CSSCCCCEEEEECCTTSSCCEEEEECCCTTSGGGSCCSSSBCCCEEEEEEEETCCCCC-STTTSCSSCEEEEEEECCT
T ss_pred             ccceeeEEEEEEEcCCCCccceeeeccccccccccCCCcccccccchhhEEEHHHhcc-cCCcEeCCEEEEEEEEEec
Confidence            89999999999999988764432211     12    223357899999999999964 5799999999999999764

>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=99.88  E-value=1.3e-23  Score=168.99  Aligned_cols=126  Identities=24%  Similarity=0.256  Sum_probs=101.4

Q ss_pred             CceEEEEEecccccc-------cceeecccc--c--ceEeeeccCCceEEEEecCCCCCCCCCeEEEEEE-ccC-CCCCC
Q 041904          175 TYYHTWKVSNFSSLL-------DEFYESESF--G--CYKWYANYSMDVKILLYPNGNGEAKGNCISLFLD-VSQ-SSIPP  241 (317)
Q Consensus       175 ~~~~~~~i~nfs~~~-------~~~~~S~~f--~--g~~W~~~~~~~~~i~~yp~g~~~~~~~~lS~yL~-~~~-~~~~~  241 (317)
                      .++++|+|+|||.++       +..++|+.|  +  ||+|        +|.+||+|+..+.++|+||||+ +.. .+...
T Consensus         2 ~g~f~W~I~nfs~~~~~~~~~~~~~~~S~~F~~~~~Gy~w--------~l~~yp~G~~~~~~~~lSlyL~l~~~~~d~~~   73 (155)
T d1l0aa1           2 NGVLIWKIRDYKRRKQEAVMGKTLSLYSQPFYTGYFGYKM--------CARVYLNGDGMGKGTHLSLFFVIMRGEYDALL   73 (155)
T ss_dssp             SSEEEEEEECHHHHHHHHHTTSCSEEECCCEESSTTSCEE--------EEEEETTCCGGGTTTEEEEEEEEECCTTTTTS
T ss_pred             CCEEEEEECCcHHHHHhhhcCCCcEEECcCEEeCCCCcEE--------EEEEEeCCCCCCCCCEEEEEEEEccCCcCccc
Confidence            578999999999875       247899999  5  9999        9999999998877899999999 543 23356


Q ss_pred             CCeEEEEEEEEEEECCCCCce-eeee---------eEEeeCCCCCccccccccccccCCCCCCceeCCEEEEEEEEEEE
Q 041904          242 NTKLLTKYFLCVENQMNGKNS-EVEG---------EWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAEVTLH  310 (317)
Q Consensus       242 ~~~~~~~~~l~l~n~~~~~~~-~~~~---------~~~F~~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~V~v~  310 (317)
                      .|++.++|+|.|+||.++... ....         .+.+...+.+|||++||++++|++  +|||+||+|+|+|+|.+.
T Consensus        74 ~~~~~~~~~~~l~~q~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~G~~~fi~~~~L~~--~gfl~dD~l~I~~~V~~~  150 (155)
T d1l0aa1          74 PWPFKQKVTLMLMDQGSSRRHLGDAFKPDPNSSSFKKPTGEMNIASGCPVFVAQTVLEN--GTYIKDDTIFIKVIVDTS  150 (155)
T ss_dssp             CSSCCCCEEEEECCCSSSCCCEEEEECCCTTSTTSSCCSSSBCCCEEEEEEEEHHHHHT--TTTCBTTEEEEEEEECCS
T ss_pred             CCcEEEEEEEEEecCCCCccceeEEEeeccccccccccccccccCcChhheeEHHHhhh--CCCEECCEEEEEEEEEeC
Confidence            899999999999999876532 2111         122333457899999999999985  799999999999998653

>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=99.87  E-value=1.4e-22  Score=162.76  Aligned_cols=125  Identities=22%  Similarity=0.277  Sum_probs=99.4

Q ss_pred             CCceEEEEEecccccc-------cceeecccc--c--ceEeeeccCCceEEEEecCCCCCCC-CCeEEEEEE-ccC-CCC
Q 041904          174 PTYYHTWKVSNFSSLL-------DEFYESESF--G--CYKWYANYSMDVKILLYPNGNGEAK-GNCISLFLD-VSQ-SSI  239 (317)
Q Consensus       174 ~~~~~~~~i~nfs~~~-------~~~~~S~~f--~--g~~W~~~~~~~~~i~~yp~g~~~~~-~~~lS~yL~-~~~-~~~  239 (317)
                      ..++++|+|+||+.++       +..+.||.|  |  ||+|        +|.+||+|...++ ++|+|+||+ ++. .+.
T Consensus         3 ~~G~f~W~I~nfs~~~~~~~~~~~~~i~Sp~F~~g~~Gy~w--------rl~~yp~g~~~~~~~~~lsvyL~l~~~~~d~   74 (155)
T d1lb6a_           3 CNGIYIWKIGNFGMHLKCQEEEKPVVIHSPGFYTGKPGYKL--------CMRLHLQLPTAQRCANYISLFVHTMQGEYDS   74 (155)
T ss_dssp             CCEEEEEEECCHHHHHHHHHTTCCEEEECCCEESSSSCCEE--------EEEEEECCTTCTTTTTEEEEEEEEECCTTGG
T ss_pred             cccEEEEEECChHHHHHhhhcCCCcEEECcCEEeCCCCcEE--------EEEEEeCCCCCCCCCCEEEEEEEEecCcccc
Confidence            4588999999999985       347999999  6  9999        9999999987653 689999999 443 233


Q ss_pred             CCCCeEEEEEEEEEEECCCCCce-eeee------------eEEeeCCCCCccccccccccccCCCCCCceeCCEEEEEEE
Q 041904          240 PPNTKLLTKYFLCVENQMNGKNS-EVEG------------EWLYTLTNRAIGGRQFMTLAKLKDPTEGYLVDDSCIIKAE  306 (317)
Q Consensus       240 ~~~~~~~~~~~l~l~n~~~~~~~-~~~~------------~~~F~~~~~~~G~~~fi~~~~L~~~~~gyl~dd~l~i~~~  306 (317)
                      ...|++.+.++|.|+||.+.... ....            .+.|...+.+|||++||++++|++  +|||+||+|+|+|+
T Consensus        75 ~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~~fi~~~~L~~--~gyl~dD~l~I~~~  152 (155)
T d1lb6a_          75 HLPWPFQGTIRLTILDQSEAPVRQNHEEIMDAKPELLAFQRPTIPRNPKGFGYVTFMHLEALRQ--RTFIKDDTLLVRCE  152 (155)
T ss_dssp             GSCSSCCSEEEEEECCCSCTTSCCCEEEEEECCTTSGGGSCCSSSBCSEEEEEEEEEEGGGGGT--SCCCBTTBEEEEEE
T ss_pred             cCCCcEEEEEEEEEECCCCCccceeeEEeeecCCccccccCCcccCCcCCcChHHeeEHHHhcc--CCCEECCEEEEEEE
Confidence            57899999999999999876522 1111            112333446899999999999985  79999999999999


Q ss_pred             EE
Q 041904          307 VT  308 (317)
Q Consensus       307 V~  308 (317)
                      |+
T Consensus       153 V~  154 (155)
T d1lb6a_         153 VS  154 (155)
T ss_dssp             EE
T ss_pred             EE
Confidence            86