Citrus Sinensis ID: 025387

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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---
Protein Sequence
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSEPGGVMDYEEDRGRPKR
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHcccccEEcHHHHcccccccccccccHHHHHHHHHHHcccHHHHHHHHcccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHccccccHHHHHHHHHHHHHHcccEEEEcccccEEEEEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHccccEEEHHHHHccHHHHHHHccccHHHHHHHHHHHHccHHHHHHcccccccccHHHHHHHHHHHHHHHHHccccccHHHHHHHcccccHHHHHHHHHHHHHHHccEEEEccccccEEEEEEcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHcccccccccccccccccc
Coil and Loop (DISEMBL)
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEatsqpslfafseilavpniaefegtenskyLDMLRLFAHGtwsdyknnaghlpqlvpdqvLKLKQLTVLTLAetnkvlpydelmeELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFaagrdlrpgqlgSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLShkadvdcrgheeiysepggvmdyeedrgrpkr
Flexible Loop (DISEMBL)
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLaetnkvlpydelMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFaagrdlrpgqLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKkslshkadvdcrgheeiysepggvmdyeedrgrpkr
Low Complexity Region (SEG)
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDqvlklkqltvltlAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSEPGGVMDYEEDRGRPKR
Disordered region (IsUnstruct)
*************F*********AALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWA**********************************************************
Disordered Region (DISOPRED)
******Q**LIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEK**************************************************************
Disordered Region (DISEMBL)
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMN**************************VDCRGHEEIYSEPGGVMD**********
Disordered Region (DISPRO)
*DIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKA*****************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMxxxxxxxxxxxxxxxxxxxxxxxxxxxxDCRGHEEIYSEPGGVMDYEEDRGRPKR
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	253	2.2.26 [Sep-21-2011]
Q94JU3	260	COP9 signalosome complex	yes	no	1.0	0.973	0.770	1e-114
Q55BD5	259	COP9 signalosome complex	yes	no	0.743	0.725	0.444	3e-43
Q9H9Q2	264	COP9 signalosome complex	yes	no	0.905	0.867	0.343	7e-37
Q2KI56	264	COP9 signalosome complex	yes	no	0.905	0.867	0.343	8e-37
Q8BV13	264	COP9 signalosome complex	yes	no	0.905	0.867	0.343	1e-36
Q9V4S8	278	COP9 signalosome complex	yes	no	0.956	0.870	0.340	1e-33
Q9CZ04	275	COP9 signalosome complex	no	no	0.822	0.756	0.349	4e-32
Q5R762	275	COP9 signalosome complex	no	no	0.822	0.756	0.344	1e-31
Q9UBW8	275	COP9 signalosome complex	no	no	0.822	0.756	0.344	1e-31
Q7SGS1	417	COP9 signalosome complex	N/A	no	0.679	0.412	0.328	2e-20

>sp|Q94JU3|CSN7_ARATH COP9 signalosome complex subunit 7 OS=Arabidopsis thaliana GN=CSN7 PE=1 SV=1

 Score =  409 bits (1051), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 195/253 (77%), Positives = 220/253 (86%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQ+QAE+ID  VK+AS  K  ALG +I+EATS PSLFAFSEILA+PN+A+ EGT +S
Sbjct: 1   MDIEQKQAEIIDQLVKRASTCKSEALGPLIIEATSHPSLFAFSEILALPNVAQLEGTTDS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
            YLD+LRLFAHGTW DYK NA  LP L PDQ+LKLKQLTVLTLAE+NKVLPYD LM ELD
Sbjct: 61  VYLDLLRLFAHGTWGDYKCNATRLPHLSPDQILKLKQLTVLTLAESNKVLPYDTLMVELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTT 180
           V+NVRELEDFLINECMY GIVRGKLDQL+RCFEV FAAGRDLRPGQLG+M+ TLSNWL T
Sbjct: 121 VSNVRELEDFLINECMYAGIVRGKLDQLKRCFEVPFAAGRDLRPGQLGNMLHTLSNWLNT 180

Query: 181 SDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSEPGG 240
           S+NLLISIQ+KIKWAD+M+EMDKKHRK+ EE VEE KKSLS K DVD RG++E++ EP G
Sbjct: 181 SENLLISIQDKIKWADNMSEMDKKHRKEAEEGVEEVKKSLSMKGDVDIRGNKEMFGEPSG 240

Query: 241 VMDYEEDRGRPKR 253
           VMDYEED  RPKR
Sbjct: 241 VMDYEEDGIRPKR 253

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes such as photomorphogenesis and auxin and jasmonate responses. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF. It is involved in repression of photomorphogenesis in darkness by regulating the activity of COP1-containing Ubl ligase complexes. The complex is also required for degradation of IAA6 by regulating the activity of the Ubl ligase SCF-TIR complex.
Arabidopsis thaliana (taxid: 3702)

>sp|Q55BD5|CSN7_DICDI COP9 signalosome complex subunit 7 OS=Dictyostelium discoideum GN=csn7 PE=1 SV=1

 Score =  175 bits (443), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 84/189 (44%), Positives = 126/189 (66%), Gaps = 1/189 (0%)

Query: 11  IDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFA 70
           +  FV  A + KG A+ S+I +A + PS+F F E+L +PN+ + + TE   Y D+L +FA
Sbjct: 14  LKQFVVLAKSSKGRAIVSIIEKALNHPSVFVFGELLDMPNVQQLKETEFKNYYDLLLIFA 73

Query: 71  HGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF 130
           +G++ DYKN    LPQL P  + KLKQLT++ L+ T+ V+PY  L E++++TNVRELED 
Sbjct: 74  YGSFIDYKNKKDSLPQLTPQMITKLKQLTIVFLSSTSNVIPYSVLQEQIEITNVRELEDL 133

Query: 131 LINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQE 190
           +I + +Y  I++GKLDQ  +  E+ F+ GRD++P QL SMI  L+NW +TS  LL  I  
Sbjct: 134 II-DSIYQNIIKGKLDQKNKHLEIDFSIGRDVQPEQLDSMINCLNNWSSTSQKLLDDISG 192

Query: 191 KIKWADSMN 199
            I  +D ++
Sbjct: 193 LITHSDKVH 201

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of E3 ligase complexes, leading to modify the Ubl ligase activity.

Dictyostelium discoideum (taxid: 44689)

>sp|Q9H9Q2|CSN7B_HUMAN COP9 signalosome complex subunit 7b OS=Homo sapiens GN=COPS7B PE=1 SV=1

 Score =  154 bits (388), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 79/230 (34%), Positives = 135/230 (58%), Gaps = 1/230 (0%)

Query: 8   AELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLR 67
           + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N+ YL +L 
Sbjct: 9   SNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGANAAYLQLLN 68

Query: 68  LFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVREL 127
           LFA+GT+ DY  N   LP+L   Q  KLK LT+++LA   K +PY  L+++L++ N+REL
Sbjct: 69  LFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDLEMRNLREL 128

Query: 128 EDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLIS 187
           ED +I E +YT I++GKLDQ  +  EV F  GRD+R   + ++++TL  W    + +L+ 
Sbjct: 129 EDLII-EAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDGCEAVLLG 187

Query: 188 IQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSE 237
           I++++  A+   E   + ++ +E +V   KK+L   A    +  E+  +E
Sbjct: 188 IEQQVLRANQYKENHNRTQQQVEAEVTNIKKTLKATASSSAQEMEQQLAE 237

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, JUN, I-kappa-B-alpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.

Homo sapiens (taxid: 9606)

>sp|Q2KI56|CSN7B_BOVIN COP9 signalosome complex subunit 7b OS=Bos taurus GN=COPS7B PE=2 SV=1

 Score =  154 bits (388), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 79/230 (34%), Positives = 135/230 (58%), Gaps = 1/230 (0%)

Query: 8   AELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLR 67
           + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N+ YL +L 
Sbjct: 9   SNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGANAAYLQLLN 68

Query: 68  LFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVREL 127
           LFA+GT+ DY  N   LP+L   Q  KLK LT+++LA   K +PY  L+++L++ N+REL
Sbjct: 69  LFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDLEMRNLREL 128

Query: 128 EDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLIS 187
           ED +I E +YT I++GKLDQ  +  EV F  GRD+R   + ++++TL  W    + +L+ 
Sbjct: 129 EDLII-EAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDGCEAVLLG 187

Query: 188 IQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSE 237
           I++++  A+   E   + ++ +E +V   KK+L   A    +  E+  +E
Sbjct: 188 IEQQVLRANQYKENHSRTQQQVEAEVTNIKKTLKATASSSAQEMEQQLAE 237

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, JUN, I-kappa-B-alpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.

Bos taurus (taxid: 9913)

>sp|Q8BV13|CSN7B_MOUSE COP9 signalosome complex subunit 7b OS=Mus musculus GN=Cops7b PE=1 SV=1

 Score =  153 bits (387), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 79/230 (34%), Positives = 135/230 (58%), Gaps = 1/230 (0%)

Query: 8   AELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLR 67
           + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N+ YL +L 
Sbjct: 9   SNLLEQFILLAKGTSGSALTTLISQVLEAPGVYVFGELLELANVQELAEGANAAYLQLLN 68

Query: 68  LFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVREL 127
           LFA+GT+ DY  N   LP+L   Q  KLK LT+++LA   K +PY  L+++L++ N+REL
Sbjct: 69  LFAYGTYPDYIANKESLPELSVAQQNKLKHLTIVSLASRMKCIPYSVLLKDLEMRNLREL 128

Query: 128 EDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLIS 187
           ED +I E +YT I++GKLDQ  +  EV F  GRD+R   + ++++TL  W    + +L+ 
Sbjct: 129 EDLII-EAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDGCEAVLLG 187

Query: 188 IQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSE 237
           I++++  A+   E   + ++ +E +V   KK+L   A    +  E+  +E
Sbjct: 188 IEQQVLRANQYKENHHRTQQQVEAEVSNIKKTLKATASSSAQEMEQQLAE 237

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, JUN, I-kappa-B-alpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.

Mus musculus (taxid: 10090)

>sp|Q9V4S8|CSN7_DROME COP9 signalosome complex subunit 7 OS=Drosophila melanogaster GN=CSN7 PE=1 SV=2

 Score =  143 bits (360), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 84/247 (34%), Positives = 140/247 (56%), Gaps = 5/247 (2%)

Query: 10  LIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLF 69
            ++ F   A +  GAAL  VI +A   P++F F E+LA P++ + +   +SK+ + L LF
Sbjct: 19  FLEKFCVLAKSSTGAALLDVIRQALEAPNVFVFGELLAEPSVLQLKDGPDSKHFETLNLF 78

Query: 70  AHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELED 129
           A+GT+ +Y+       +L P    KL+ LT+++LA   K +PY  L+ EL++ NVR LED
Sbjct: 79  AYGTYKEYRAQPEKFIELTPAMQKKLQHLTIVSLAIKAKSIPYALLLSELEIDNVRHLED 138

Query: 130 FLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQ 189
            +I E +Y  I+ GKL Q  R  EV +A GRD+ PG  G +++TL  W+ + D++   I+
Sbjct: 139 III-EAIYADIIHGKLFQNTRILEVDYAQGRDIPPGYTGQIVETLQAWVNSCDSVSNCIE 197

Query: 190 EKIKWADSMNEMDKKHRKDLEEKVEEAKKSL-SHKADVDCRGHEEIYSEPG--GVMDYEE 246
            +IK+A++       +++ +E+ +   KK L S  +D D     + +  PG  G +   E
Sbjct: 198 MQIKYANAEKSKRLINKERVEQDLINLKKVLKSQTSDSDESMQIDTHG-PGTSGGLGQSE 256

Query: 247 DRGRPKR 253
            R +P +
Sbjct: 257 LRKKPSK 263

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of the SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF. The CSN complex plays an essential role in oogenesis and embryogenesis and is required for proper photoreceptor R cell differentiation and promote lamina glial cell migration or axon targeting. It also promotes Ubl-dependent degradation of cyclin E (CycE) during early oogenesis.

Drosophila melanogaster (taxid: 7227)

>sp|Q9CZ04|CSN7A_MOUSE COP9 signalosome complex subunit 7a OS=Mus musculus GN=Cops7a PE=1 SV=2

 Score =  138 bits (347), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 73/209 (34%), Positives = 123/209 (58%), Gaps = 1/209 (0%)

Query: 12  DHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAH 71
           + F+  A + KGAAL ++I +    P ++ F E+L +PN+ E   ++ +    +L +FA+
Sbjct: 13  EQFLLLAKSAKGAALATLIHQVLEAPGVYVFGELLDMPNVRELAESDFASTFRLLTVFAY 72

Query: 72  GTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131
           GT++DY   A +LP L   Q  KL+ L+V+TLA   K +PY  L+E L + NVR+LED +
Sbjct: 73  GTYADYLAEARNLPPLTDAQKNKLRHLSVVTLAAKVKCIPYAVLLEALALRNVRQLEDLV 132

Query: 132 INECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEK 191
           I E +Y  ++RG LDQ  +  EV ++ GRD++   L ++ QTL  W    + +L  I+E+
Sbjct: 133 I-EAVYADVLRGSLDQRNQRLEVDYSIGRDIQRQDLSAIAQTLQEWCVGCEVVLSGIEEQ 191

Query: 192 IKWADSMNEMDKKHRKDLEEKVEEAKKSL 220
           +  A+   E     ++ +E +V   KK++
Sbjct: 192 VSRANQHKEQQLGLKQQIESEVANLKKTI 220

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, JUN, I-kappa-B-alpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.

Mus musculus (taxid: 10090)

>sp|Q5R762|CSN7A_PONAB COP9 signalosome complex subunit 7a OS=Pongo abelii GN=COPS7A PE=2 SV=1

 Score =  136 bits (343), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 72/209 (34%), Positives = 123/209 (58%), Gaps = 1/209 (0%)

Query: 12  DHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAH 71
           + F+  A + KGAAL ++I +    P ++ F E+L +PN+ E   ++ +    +L +FA+
Sbjct: 13  EQFLLLAKSAKGAALATLIHQVLEAPGVYVFGELLDMPNVRELAESDFASTFRLLTVFAY 72

Query: 72  GTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131
           GT++DY   A +LP L   Q  KL+ L+V+TLA   K +PY  L+E L + NVR+LED +
Sbjct: 73  GTYADYLAEARNLPPLTEAQKNKLRHLSVVTLAAKVKCIPYAVLLEALALRNVRQLEDLV 132

Query: 132 INECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEK 191
           I E +Y  ++RG LDQ  +  EV ++ GRD++   L ++ +TL  W    + +L  I+E+
Sbjct: 133 I-EAVYADVLRGSLDQRNQRLEVDYSIGRDIQRQDLSAIARTLQEWCVGCEVVLSGIEEQ 191

Query: 192 IKWADSMNEMDKKHRKDLEEKVEEAKKSL 220
           +  A+   E     ++ +E +V   KK++
Sbjct: 192 VSRANQHKEQQLGLKQQIESEVANLKKTI 220

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, JUN, I-kappa-B-alpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.

Pongo abelii (taxid: 9601)

>sp|Q9UBW8|CSN7A_HUMAN COP9 signalosome complex subunit 7a OS=Homo sapiens GN=COPS7A PE=1 SV=1

 Score =  136 bits (343), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 72/209 (34%), Positives = 123/209 (58%), Gaps = 1/209 (0%)

Query: 12  DHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAH 71
           + F+  A + KGAAL ++I +    P ++ F E+L +PN+ E   ++ +    +L +FA+
Sbjct: 13  EQFLLLAKSAKGAALATLIHQVLEAPGVYVFGELLDMPNVRELAESDFASTFRLLTVFAY 72

Query: 72  GTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131
           GT++DY   A +LP L   Q  KL+ L+V+TLA   K +PY  L+E L + NVR+LED +
Sbjct: 73  GTYADYLAEARNLPPLTEAQKNKLRHLSVVTLAAKVKCIPYAVLLEALALRNVRQLEDLV 132

Query: 132 INECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEK 191
           I E +Y  ++RG LDQ  +  EV ++ GRD++   L ++ +TL  W    + +L  I+E+
Sbjct: 133 I-EAVYADVLRGSLDQRNQRLEVDYSIGRDIQRQDLSAIARTLQEWCVGCEVVLSGIEEQ 191

Query: 192 IKWADSMNEMDKKHRKDLEEKVEEAKKSL 220
           +  A+   E     ++ +E +V   KK++
Sbjct: 192 VSRANQHKEQQLGLKQQIESEVANLKKTI 220

Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2. The complex is also involved in phosphorylation of p53/TP53, JUN, I-kappa-B-alpha/NFKBIA, ITPK1 and IRF8/ICSBP, possibly via its association with CK2 and PKD kinases. CSN-dependent phosphorylation of TP53 and JUN promotes and protects degradation by the Ubl system, respectively.

Homo sapiens (taxid: 9606)

>sp|Q7SGS1|CSN7A_NEUCR COP9 signalosome complex subunit 7a OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) GN=csn-7a PE=1 SV=1

 Score = 99.4 bits (246), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 66/201 (32%), Positives = 108/201 (53%), Gaps = 29/201 (14%)

Query: 3   IEQRQA-ELIDHFV---KQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGT- 57
           +EQ +A   ++ F+   K A++ + AA   ++   TS P+ F F+E+L  P I   E + 
Sbjct: 1   MEQTKALNALEPFIVLSKSATSPRAAA--DLVTRVTSAPNTFIFTELLQTPQIQSLEYSH 58

Query: 58  ENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLA------------- 104
           E S YL +L++F+HGT++DY  NA  LP L  DQ LKL+QL++LTL              
Sbjct: 59  EFSSYLTLLQIFSHGTYADYIANASALPALNDDQKLKLRQLSLLTLVANDGSNVPLDYDA 118

Query: 105 ---ETNKVLP----YDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV-QF 156
              E N+  P    Y  L   L++++ RELE+ +I+  +Y G++ G+LD      ++   
Sbjct: 119 MQRENNQAQPPNQSYASLTRRLELSSARELEELVIS-AIYAGLIEGQLDPANEMVQINSV 177

Query: 157 AAGRDLRPGQLGSMIQTLSNW 177
           AA RD+    +  ++ +L  W
Sbjct: 178 AALRDVPARGVNGLLSSLQGW 198

Component of the COP9 signalosome (CSN) complex that acts as an regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunit of SCF-type E3 ubiquitin-protein ligase complexes (By similarity). The CSN complex is involved in the regulation of the circadian clock through its control of the stability of the SCF(FWD1) complex.

Neurospora crassa (strain ATCC 24698 / 74-OR23-1A / CBS 708.71 / DSM 1257 / FGSC 987) (taxid: 367110)

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	253
449445513	259	PREDICTED: COP9 signalosome complex subu	1.0	0.976	0.818	1e-122
118485804	259	unknown [Populus trichocarpa]	1.0	0.976	0.830	1e-121
225453392	259	PREDICTED: COP9 signalosome complex subu	1.0	0.976	0.849	1e-118
388506722	259	unknown [Medicago truncatula]	0.996	0.972	0.779	1e-113
18378920	260	COP9 signalosome complex subunit 7 [Arab	1.0	0.973	0.770	1e-112
297842906	260	hypothetical protein ARALYDRAFT_470065 [	1.0	0.973	0.762	1e-111
356548799	259	PREDICTED: COP9 signalosome complex subu	0.996	0.972	0.811	1e-109
224067485	225	predicted protein [Populus trichocarpa]	0.885	0.995	0.834	1e-109
356556751	259	PREDICTED: COP9 signalosome complex subu	0.996	0.972	0.807	1e-107
255541046	275	cop9 complex subunit 7a, putative [Ricin	0.984	0.905	0.752	1e-107

>gi|449445513|ref|XP_004140517.1| PREDICTED: COP9 signalosome complex subunit 7-like [Cucumis sativus] gi|449514708|ref|XP_004164457.1| PREDICTED: COP9 signalosome complex subunit 7-like [Cucumis sativus]

 Score =  442 bits (1137), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 207/253 (81%), Positives = 233/253 (92%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQ+Q E IDHFVKQAS+ KG+ALGSV+ +ATS PSLFAFSEILAVPN+ E EGTE+S
Sbjct: 1   MDIEQKQTEFIDHFVKQASSLKGSALGSVVTDATSHPSLFAFSEILAVPNVVELEGTEHS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
            YLD+LRLFA+GTWSDYK+N+  LP+L  DQ LKLKQLTVLTLAETNKVL YD+LM+ELD
Sbjct: 61  IYLDVLRLFAYGTWSDYKSNSSRLPELSSDQALKLKQLTVLTLAETNKVLAYDQLMQELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTT 180
           VTNVRELEDFLINECMY GIVRGKLDQLRRCFEVQFAAGRDLRPGQLG+MI+TLSNWLTT
Sbjct: 121 VTNVRELEDFLINECMYAGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGNMIRTLSNWLTT 180

Query: 181 SDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSEPGG 240
           SDNLL+SIQEKIKWAD+M+E+DKKHRKD++++VEE KKSLS KA++D R HEEIYSEPGG
Sbjct: 181 SDNLLVSIQEKIKWADNMSELDKKHRKDVDDRVEEVKKSLSLKANIDIREHEEIYSEPGG 240

Query: 241 VMDYEEDRGRPKR 253
           VMDYEEDR RPKR
Sbjct: 241 VMDYEEDRSRPKR 253

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118485804|gb|ABK94750.1| unknown [Populus trichocarpa]

 Score =  441 bits (1135), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 210/253 (83%), Positives = 231/253 (91%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQ+QAELIDHFV QAS  K +AL  +I+EATS PSLFAFSEIL+ P ++E EGTENS
Sbjct: 1   MDIEQKQAELIDHFVNQASTLKASALWPLIIEATSHPSLFAFSEILSSPTVSELEGTENS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
             LD+LRLFAHGTWSDYK+NAG LPQLVPDQVLKLKQLTVLTLAE NKVLPYD+LM+ELD
Sbjct: 61  FCLDVLRLFAHGTWSDYKSNAGRLPQLVPDQVLKLKQLTVLTLAEMNKVLPYDQLMQELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTT 180
           VTNVRELEDFLINECMY GIVRGKLDQLRRCFEVQFAAGRDLRPGQLG+M+QTLSNWL T
Sbjct: 121 VTNVRELEDFLINECMYAGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGNMLQTLSNWLDT 180

Query: 181 SDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSEPGG 240
           SD+LL+SIQEKIKWADS +E+DKKH+KD+E +VEE KKSLS KAD+D RGHEEIYSEPGG
Sbjct: 181 SDDLLVSIQEKIKWADSTSELDKKHQKDVEYRVEEVKKSLSLKADIDFRGHEEIYSEPGG 240

Query: 241 VMDYEEDRGRPKR 253
           VMDYEEDR RPKR
Sbjct: 241 VMDYEEDRSRPKR 253

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225453392|ref|XP_002273686.1| PREDICTED: COP9 signalosome complex subunit 7 isoform 1 [Vitis vinifera] gi|297734611|emb|CBI16662.3| unnamed protein product [Vitis vinifera]

 Score =  431 bits (1107), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 215/253 (84%), Positives = 231/253 (91%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQRQAELID FVKQAS   G+AL +VI++ATS PSLFAFSEILAVPN+ E  GTENS
Sbjct: 1   MDIEQRQAELIDAFVKQASTHNGSALATVILDATSHPSLFAFSEILAVPNVVELGGTENS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
            YLDMLRLFAHGTWSDYK+N   LPQLVPDQ LKLKQLTVLTLAETNKVLPYD+LM+ELD
Sbjct: 61  VYLDMLRLFAHGTWSDYKSNVDRLPQLVPDQALKLKQLTVLTLAETNKVLPYDQLMQELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTT 180
           VTNVRELEDFLINECMY GIVRGKLDQLRRCFEVQFAAGRDLRPGQLG MIQTLSNWL T
Sbjct: 121 VTNVRELEDFLINECMYAGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGCMIQTLSNWLGT 180

Query: 181 SDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSEPGG 240
           SDNLL+SIQEKIKWAD+M+E+DKKHRK++EE+VEE KKS S KAD+D RGHEEIYSEPGG
Sbjct: 181 SDNLLLSIQEKIKWADTMSELDKKHRKEVEERVEEVKKSFSVKADIDFRGHEEIYSEPGG 240

Query: 241 VMDYEEDRGRPKR 253
           VMDYEEDR RPKR
Sbjct: 241 VMDYEEDRSRPKR 253

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388506722|gb|AFK41427.1| unknown [Medicago truncatula]

 Score =  414 bits (1063), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 198/254 (77%), Positives = 225/254 (88%), Gaps = 2/254 (0%)

Query: 1   MDIEQRQAELIDHFVKQASNQKG-AALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTEN 59
           MDIEQRQ+ELID FVKQAS     +A+ SVIV+ATS P LFAFSEILA+PN+ + E T+ 
Sbjct: 1   MDIEQRQSELIDQFVKQASAASNTSAISSVIVDATSHPLLFAFSEILALPNVLQLEATDE 60

Query: 60  SKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEEL 119
             YLD+LRLFAHG WSDYK+NA  LPQLVPDQ+LKLKQLTVLTL ET KVLPYD+LM+EL
Sbjct: 61  EFYLDLLRLFAHGIWSDYKSNADRLPQLVPDQILKLKQLTVLTLVETYKVLPYDQLMQEL 120

Query: 120 DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLT 179
           DVTNVRELEDFLINECMY GIVRGKLDQLRRCFEVQFAAGRDLRPGQLG MIQTLS+WL+
Sbjct: 121 DVTNVRELEDFLINECMYAGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGDMIQTLSDWLS 180

Query: 180 TSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSEPG 239
           TS+N+L+SIQ+KIKWADSM+E+DKKHRK++EEKV+E KKS+  KAD+D RGHEEI +E G
Sbjct: 181 TSENMLVSIQDKIKWADSMSEVDKKHRKEVEEKVDEVKKSI-FKADIDFRGHEEICAESG 239

Query: 240 GVMDYEEDRGRPKR 253
           GVMDYEEDR RPKR
Sbjct: 240 GVMDYEEDRSRPKR 253

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18378920|ref|NP_563645.1| COP9 signalosome complex subunit 7 [Arabidopsis thaliana] gi|55976565|sp|Q94JU3.1|CSN7_ARATH RecName: Full=COP9 signalosome complex subunit 7; Short=CSN complex subunit 7; AltName: Full=Protein FUSCA 5 gi|13937161|gb|AAK50074.1|AF372934_1 At1g02090/T7I23_24 [Arabidopsis thaliana] gi|18056671|gb|AAL58109.1|AF395066_1 CSN complex subunit 7ii [Arabidopsis thaliana] gi|21593551|gb|AAM65518.1| FUS5 [Arabidopsis thaliana] gi|22137006|gb|AAM91348.1| At1g02090/T7I23_24 [Arabidopsis thaliana] gi|332189259|gb|AEE27380.1| COP9 signalosome complex subunit 7 [Arabidopsis thaliana]

 Score =  409 bits (1051), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 195/253 (77%), Positives = 220/253 (86%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQ+QAE+ID  VK+AS  K  ALG +I+EATS PSLFAFSEILA+PN+A+ EGT +S
Sbjct: 1   MDIEQKQAEIIDQLVKRASTCKSEALGPLIIEATSHPSLFAFSEILALPNVAQLEGTTDS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
            YLD+LRLFAHGTW DYK NA  LP L PDQ+LKLKQLTVLTLAE+NKVLPYD LM ELD
Sbjct: 61  VYLDLLRLFAHGTWGDYKCNATRLPHLSPDQILKLKQLTVLTLAESNKVLPYDTLMVELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTT 180
           V+NVRELEDFLINECMY GIVRGKLDQL+RCFEV FAAGRDLRPGQLG+M+ TLSNWL T
Sbjct: 121 VSNVRELEDFLINECMYAGIVRGKLDQLKRCFEVPFAAGRDLRPGQLGNMLHTLSNWLNT 180

Query: 181 SDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSEPGG 240
           S+NLLISIQ+KIKWAD+M+EMDKKHRK+ EE VEE KKSLS K DVD RG++E++ EP G
Sbjct: 181 SENLLISIQDKIKWADNMSEMDKKHRKEAEEGVEEVKKSLSMKGDVDIRGNKEMFGEPSG 240

Query: 241 VMDYEEDRGRPKR 253
           VMDYEED  RPKR
Sbjct: 241 VMDYEEDGIRPKR 253

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297842906|ref|XP_002889334.1| hypothetical protein ARALYDRAFT_470065 [Arabidopsis lyrata subsp. lyrata] gi|297335176|gb|EFH65593.1| hypothetical protein ARALYDRAFT_470065 [Arabidopsis lyrata subsp. lyrata]

 Score =  406 bits (1043), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 193/253 (76%), Positives = 220/253 (86%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQ+QAE+ID  VK+AS  K  ALG +I+EATS PSLFAFSEILA+P +A+ +GT +S
Sbjct: 1   MDIEQKQAEIIDQLVKRASTCKPEALGPLIIEATSHPSLFAFSEILALPTVAQLQGTTDS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
            YLD+LRLFAHGTW DYK NA  +PQL PDQ+LKLKQLTVLTLAE+NKVLPYD LM ELD
Sbjct: 61  VYLDVLRLFAHGTWGDYKCNASRIPQLSPDQILKLKQLTVLTLAESNKVLPYDTLMVELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTT 180
           VTNVR+LEDFLINECMY GIVRGKLDQL+RCFEV FAAGRDLRPGQLG+M+ TLS+WL T
Sbjct: 121 VTNVRQLEDFLINECMYAGIVRGKLDQLKRCFEVPFAAGRDLRPGQLGNMLDTLSSWLNT 180

Query: 181 SDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSEPGG 240
           S+NLLISIQ+KIKWADSM+EMDKKHRK+ EE VEE KKSLS K DVD RG++E++ EP G
Sbjct: 181 SENLLISIQDKIKWADSMSEMDKKHRKEAEEGVEEVKKSLSMKGDVDIRGNKEMFGEPSG 240

Query: 241 VMDYEEDRGRPKR 253
           VMDYEED  RPKR
Sbjct: 241 VMDYEEDGIRPKR 253

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356548799|ref|XP_003542787.1| PREDICTED: COP9 signalosome complex subunit 7-like [Glycine max]

 Score =  400 bits (1027), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 206/254 (81%), Positives = 230/254 (90%), Gaps = 2/254 (0%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGS-VIVEATSQPSLFAFSEILAVPNIAEFEGTEN 59
           MDIEQ+Q+ELIDHFVK+AS    AA  S V+VEATS PSLFAFSEILA+PN+ + E TEN
Sbjct: 1   MDIEQKQSELIDHFVKRASAASDAAALSSVLVEATSHPSLFAFSEILALPNLLQLEATEN 60

Query: 60  SKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEEL 119
           S YLDMLRLFAHGTW+DYK+NA  LPQL+PDQ+LKLKQLTVLTLAET KVLPYD+LM+EL
Sbjct: 61  SAYLDMLRLFAHGTWNDYKSNADRLPQLIPDQILKLKQLTVLTLAETYKVLPYDQLMQEL 120

Query: 120 DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLT 179
           DVTNVRELEDFLINECMY GIVRGKLDQLRRCFEVQFAAGRDLRP QLG+MIQTLSNWL+
Sbjct: 121 DVTNVRELEDFLINECMYAGIVRGKLDQLRRCFEVQFAAGRDLRPDQLGNMIQTLSNWLS 180

Query: 180 TSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSEPG 239
           TS+N+L+SIQEKIKWAD+M+E+DKKHRKD+EEKVEE KKS+  KAD+D RGHEEI SE G
Sbjct: 181 TSENMLVSIQEKIKWADAMSEIDKKHRKDVEEKVEEVKKSI-FKADIDFRGHEEICSESG 239

Query: 240 GVMDYEEDRGRPKR 253
           GVMDYEEDR RPKR
Sbjct: 240 GVMDYEEDRSRPKR 253

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224067485|ref|XP_002302493.1| predicted protein [Populus trichocarpa] gi|222844219|gb|EEE81766.1| predicted protein [Populus trichocarpa]

 Score =  399 bits (1026), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 187/224 (83%), Positives = 208/224 (92%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           MDIEQ+QAELIDHFV QAS  K +AL  +I+EATS PSLFAFSEIL+VP ++E +GTENS
Sbjct: 1   MDIEQKQAELIDHFVNQASTLKASALWPLIIEATSHPSLFAFSEILSVPTVSELQGTENS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
            YLD+LRLFAHGTW+DYKNNAGHLPQLVPDQVLKLKQLTVLTLAE NKVLPYD+LM+ELD
Sbjct: 61  LYLDVLRLFAHGTWTDYKNNAGHLPQLVPDQVLKLKQLTVLTLAEMNKVLPYDQLMQELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTT 180
           VTNVRELEDFLINECMY GIVRGKLDQLRRCFEVQFAAGRDLRPGQLG+M+QTLSNWL T
Sbjct: 121 VTNVRELEDFLINECMYAGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGNMLQTLSNWLAT 180

Query: 181 SDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKA 224
           SDNLL+SIQEKIKWADSM+E+DKKHRKD++++VEE KKSLS K 
Sbjct: 181 SDNLLVSIQEKIKWADSMSELDKKHRKDVDDRVEEVKKSLSLKV 224

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356556751|ref|XP_003546686.1| PREDICTED: COP9 signalosome complex subunit 7-like [Glycine max]

 Score =  394 bits (1012), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 205/254 (80%), Positives = 229/254 (90%), Gaps = 2/254 (0%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGS-VIVEATSQPSLFAFSEILAVPNIAEFEGTEN 59
           MDIEQ+Q+ELIDHFVK+AS    AA  + V+VEATS PSLFAFSEILA+PN+ + E TEN
Sbjct: 1   MDIEQKQSELIDHFVKRASAASDAAALASVLVEATSHPSLFAFSEILALPNLLQLEATEN 60

Query: 60  SKYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEEL 119
           S YLDMLRLFAHGTWSDYK+NA  LPQL+ DQ+LKLKQLTVLTLAET KVLPYD+LM+EL
Sbjct: 61  SAYLDMLRLFAHGTWSDYKSNADRLPQLISDQILKLKQLTVLTLAETYKVLPYDQLMQEL 120

Query: 120 DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLT 179
           DVTNVRELEDFLINECMY GIVRGKLDQLRRCFEVQFAAGRDLRP QLG+MIQTLS+WLT
Sbjct: 121 DVTNVRELEDFLINECMYAGIVRGKLDQLRRCFEVQFAAGRDLRPDQLGNMIQTLSSWLT 180

Query: 180 TSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSEPG 239
           TS+NLL+SIQEKIKWAD+M+E+DKKHRK++EEKVEE KKS+  KAD+D RGHEEI SE G
Sbjct: 181 TSENLLVSIQEKIKWADAMSEIDKKHRKEVEEKVEEVKKSI-FKADIDFRGHEEICSESG 239

Query: 240 GVMDYEEDRGRPKR 253
           GVMDYEEDR RPKR
Sbjct: 240 GVMDYEEDRSRPKR 253

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255541046|ref|XP_002511587.1| cop9 complex subunit 7a, putative [Ricinus communis] gi|223548767|gb|EEF50256.1| cop9 complex subunit 7a, putative [Ricinus communis]

 Score =  394 bits (1011), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 195/259 (75%), Positives = 221/259 (85%), Gaps = 10/259 (3%)

Query: 1   MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
           M+IEQ+QAELIDHFVK AS  KG+ALG VIVEATS PSLFAFSEILAVP +AE EG +NS
Sbjct: 1   MEIEQKQAELIDHFVKIASALKGSALGPVIVEATSHPSLFAFSEILAVPTVAELEGVDNS 60

Query: 61  KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELD 120
            YLD+LRLFAHGTW+DYKNN+G LPQL+PDQVLKLKQLTVLTLAETNKVLPYD+LM+ELD
Sbjct: 61  VYLDVLRLFAHGTWTDYKNNSGRLPQLIPDQVLKLKQLTVLTLAETNKVLPYDQLMQELD 120

Query: 121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTT 180
           VTNVRELEDFLINECMY GIVRGKLDQLRRCFEVQFAAGRDLRP QLG+M+QTLSNWL+T
Sbjct: 121 VTNVRELEDFLINECMYAGIVRGKLDQLRRCFEVQFAAGRDLRPEQLGNMLQTLSNWLST 180

Query: 181 SDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADV-------DCRGHEE 233
           S+NLL+SIQEKIKWAD+M+E+DK+HRKD+E+KVEE KK+LS K ++        C    E
Sbjct: 181 SENLLVSIQEKIKWADTMSELDKRHRKDVEDKVEEVKKTLSLKMELVLLNVPFYC-STAE 239

Query: 234 IYSEPGGVMDYEE--DRGR 250
                GG + Y E  DR R
Sbjct: 240 FGKNAGGGIQYPESIDRSR 258

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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	253
TAIR|locus:2205593	260	FUS5 "FUSCA 5" [Arabidopsis th	1.0	0.973	0.723	4.2e-95
DICTYBASE|DDB_G0271282	259	csn7 "proteasome component reg	0.901	0.880	0.379	1.1e-39
UNIPROTKB|Q2KI56	264	COPS7B "COP9 signalosome compl	0.920	0.882	0.314	3.7e-32
UNIPROTKB|E2R501	264	COPS7B "Uncharacterized protei	0.920	0.882	0.314	3.7e-32
UNIPROTKB|Q9H9Q2	264	COPS7B "COP9 signalosome compl	0.920	0.882	0.314	3.7e-32
MGI|MGI:1349388	264	Cops7b "COP9 (constitutive pho	0.920	0.882	0.314	4.7e-32
RGD|1306918	322	Cops7b "COP9 signalosome subun	0.920	0.723	0.310	9.8e-32
UNIPROTKB|E1C3R1	267	COPS7B "Uncharacterized protei	0.905	0.857	0.307	8.8e-31
FB|FBgn0028836	278	CSN7 "COP9 complex homolog sub	0.952	0.866	0.321	7.9e-30
UNIPROTKB|F1NGK0	275	COPS7A "Uncharacterized protei	0.822	0.756	0.320	5e-28

TAIR|locus:2205593 FUS5 "FUSCA 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 946 (338.1 bits), Expect = 4.2e-95, P = 4.2e-95
 Identities = 183/253 (72%), Positives = 207/253 (81%)

Query:     1 MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENS 60
             MDIEQ+QAE+ID  VK+AS  K  ALG +I+EATS PSLFAFSEILA+PN+A+ EGT +S
Sbjct:     1 MDIEQKQAEIIDQLVKRASTCKSEALGPLIIEATSHPSLFAFSEILALPNVAQLEGTTDS 60

Query:    61 KYLDMLRLFAHGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELD 120
              YLD+LRLFAHGTW DYK NA  LP L PD             AE+NKVLPYD LM ELD
Sbjct:    61 VYLDLLRLFAHGTWGDYKCNATRLPHLSPDQILKLKQLTVLTLAESNKVLPYDTLMVELD 120

Query:   121 VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTT 180
             V+NVRELEDFLINECMY GIVRGKLDQL+RCFEV FAAGRDLRPGQLG+M+ TLSNWL T
Sbjct:   121 VSNVRELEDFLINECMYAGIVRGKLDQLKRCFEVPFAAGRDLRPGQLGNMLHTLSNWLNT 180

Query:   181 SDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSEPGG 240
             S+NLLISIQ+KIKWAD+M+EMDKKHRK+ EE VEE KKSLS K DVD RG++E++ EP G
Sbjct:   181 SENLLISIQDKIKWADNMSEMDKKHRKEAEEGVEEVKKSLSMKGDVDIRGNKEMFGEPSG 240

Query:   241 VMDYEEDRGRPKR 253
             VMDYEED  RPKR
Sbjct:   241 VMDYEEDGIRPKR 253

GO:0005737 "cytoplasm" evidence=ISM

GO:0004708 "MAP kinase kinase activity" evidence=ISS

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISS

GO:0008180 "signalosome" evidence=TAS;IPI

GO:0009640 "photomorphogenesis" evidence=RCA;TAS

GO:0010387 "signalosome assembly" evidence=IMP

GO:0010388 "cullin deneddylation" evidence=RCA;IMP

GO:0005829 "cytosol" evidence=IDA

GO:0016567 "protein ubiquitination" evidence=RCA

GO:0016571 "histone methylation" evidence=RCA

GO:0016579 "protein deubiquitination" evidence=RCA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=RCA

DICTYBASE|DDB_G0271282 csn7 "proteasome component region PCI (PINT) domain-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 423 (154.0 bits), Expect = 1.1e-39, P = 1.1e-39
 Identities = 90/237 (37%), Positives = 140/237 (59%)

Query:    11 IDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFA 70
             +  FV  A + KG A+ S+I +A + PS+F F E+L +PN+ + + TE   Y D+L +FA
Sbjct:    14 LKQFVVLAKSSKGRAIVSIIEKALNHPSVFVFGELLDMPNVQQLKETEFKNYYDLLLIFA 73

Query:    71 HGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDVTNVRELEDF 130
             +G++ DYKN    LPQL P              + T+ V+PY  L E++++TNVRELED 
Sbjct:    74 YGSFIDYKNKKDSLPQLTPQMITKLKQLTIVFLSSTSNVIPYSVLQEQIEITNVRELEDL 133

Query:   131 LINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQE 190
             +I+  +Y  I++GKLDQ  +  E+ F+ GRD++P QL SMI  L+NW +TS  LL  I  
Sbjct:   134 IIDS-IYQNIIKGKLDQKNKHLEIDFSIGRDVQPEQLDSMINCLNNWSSTSQKLLDDISG 192

Query:   191 KIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSEPGGVMDYEED 247
              I  +D ++   +K +++ E K E AK  L+ K D      E++Y +    M+Y ++
Sbjct:   193 LITHSDKVHLQYRKEKEEFESKFEIAK--LNTKNDSPA---EQLYYDS---MEYSDE 241

GO:0008180 "signalosome" evidence=IEA;ISS;IPI

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

UNIPROTKB|Q2KI56 COPS7B "COP9 signalosome complex subunit 7b" [Bos taurus (taxid:9913)]

 Score = 352 (129.0 bits), Expect = 3.7e-32, P = 3.7e-32
 Identities = 74/235 (31%), Positives = 128/235 (54%)

Query:     4 EQR-QAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKY 62
             EQ+  + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N+ Y
Sbjct:     4 EQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGANAAY 63

Query:    63 LDMLRLFAHGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDVT 122
             L +L LFA+GT+ DY  N   LP+L                A   K +PY  L+++L++ 
Sbjct:    64 LQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDLEMR 123

Query:   123 NVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSD 182
             N+RELED +I E +YT I++GKLDQ  +  EV F  GRD+R   + ++++TL  W    +
Sbjct:   124 NLRELEDLII-EAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDGCE 182

Query:   183 NLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSE 237
              +L+ I++++  A+   E   + ++ +E +V   KK+L   A    +  E+  +E
Sbjct:   183 AVLLGIEQQVLRANQYKENHSRTQQQVEAEVTNIKKTLKATASSSAQEMEQQLAE 237

GO:0005737 "cytoplasm" evidence=IEA

GO:0010388 "cullin deneddylation" evidence=IEA

GO:0008180 "signalosome" evidence=IEA

UNIPROTKB|E2R501 COPS7B "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 352 (129.0 bits), Expect = 3.7e-32, P = 3.7e-32
 Identities = 74/235 (31%), Positives = 128/235 (54%)

Query:     4 EQR-QAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKY 62
             EQ+  + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N+ Y
Sbjct:     4 EQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGANAAY 63

Query:    63 LDMLRLFAHGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDVT 122
             L +L LFA+GT+ DY  N   LP+L                A   K +PY  L+++L++ 
Sbjct:    64 LQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDLEMR 123

Query:   123 NVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSD 182
             N+RELED +I E +YT I++GKLDQ  +  EV F  GRD+R   + ++++TL  W    +
Sbjct:   124 NLRELEDLII-EAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDGCE 182

Query:   183 NLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSE 237
              +L+ I++++  A+   E   + ++ +E +V   KK+L   A    +  E+  +E
Sbjct:   183 AVLLGIEQQVLRANQYKENHSRTQQQVEAEVTNIKKTLKATASSSAQEMEQQLAE 237

GO:0010388 "cullin deneddylation" evidence=IEA

GO:0008180 "signalosome" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

UNIPROTKB|Q9H9Q2 COPS7B "COP9 signalosome complex subunit 7b" [Homo sapiens (taxid:9606)]

 Score = 352 (129.0 bits), Expect = 3.7e-32, P = 3.7e-32
 Identities = 74/235 (31%), Positives = 128/235 (54%)

Query:     4 EQR-QAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKY 62
             EQ+  + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N+ Y
Sbjct:     4 EQKPSSNLLEQFILLAKGTSGSALTALISQVLEAPGVYVFGELLELANVQELAEGANAAY 63

Query:    63 LDMLRLFAHGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDVT 122
             L +L LFA+GT+ DY  N   LP+L                A   K +PY  L+++L++ 
Sbjct:    64 LQLLNLFAYGTYPDYIANKESLPELSTAQQNKLKHLTIVSLASRMKCIPYSVLLKDLEMR 123

Query:   123 NVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSD 182
             N+RELED +I E +YT I++GKLDQ  +  EV F  GRD+R   + ++++TL  W    +
Sbjct:   124 NLRELEDLII-EAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDGCE 182

Query:   183 NLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSE 237
              +L+ I++++  A+   E   + ++ +E +V   KK+L   A    +  E+  +E
Sbjct:   183 AVLLGIEQQVLRANQYKENHNRTQQQVEAEVTNIKKTLKATASSSAQEMEQQLAE 237

GO:0008180 "signalosome" evidence=IDA

GO:0010388 "cullin deneddylation" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

MGI|MGI:1349388 Cops7b "COP9 (constitutive photomorphogenic) homolog, subunit 7b (Arabidopsis thaliana)" [Mus musculus (taxid:10090)]

 Score = 351 (128.6 bits), Expect = 4.7e-32, P = 4.7e-32
 Identities = 74/235 (31%), Positives = 128/235 (54%)

Query:     4 EQR-QAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKY 62
             EQ+  + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N+ Y
Sbjct:     4 EQKPSSNLLEQFILLAKGTSGSALTTLISQVLEAPGVYVFGELLELANVQELAEGANAAY 63

Query:    63 LDMLRLFAHGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDVT 122
             L +L LFA+GT+ DY  N   LP+L                A   K +PY  L+++L++ 
Sbjct:    64 LQLLNLFAYGTYPDYIANKESLPELSVAQQNKLKHLTIVSLASRMKCIPYSVLLKDLEMR 123

Query:   123 NVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSD 182
             N+RELED +I E +YT I++GKLDQ  +  EV F  GRD+R   + ++++TL  W    +
Sbjct:   124 NLRELEDLII-EAVYTDIIQGKLDQRNQLLEVDFCIGRDIRKKDINNIVKTLHEWCDGCE 182

Query:   183 NLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSE 237
              +L+ I++++  A+   E   + ++ +E +V   KK+L   A    +  E+  +E
Sbjct:   183 AVLLGIEQQVLRANQYKENHHRTQQQVEAEVSNIKKTLKATASSSAQEMEQQLAE 237

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0008180 "signalosome" evidence=ISO

GO:0010388 "cullin deneddylation" evidence=ISO

RGD|1306918 Cops7b "COP9 signalosome subunit 7B" [Rattus norvegicus (taxid:10116)]

 Score = 348 (127.6 bits), Expect = 9.8e-32, P = 9.8e-32
 Identities = 73/235 (31%), Positives = 128/235 (54%)

Query:     4 EQR-QAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKY 62
             EQ+  + L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N+ Y
Sbjct:    62 EQKPSSNLLEQFILLAKGTSGSALTTLISQVLEAPGVYVFGELLELANVQELAEGANAAY 121

Query:    63 LDMLRLFAHGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDVT 122
             L +L LFA+GT+ DY  N   LP+L                A   K +PY  L+++L++ 
Sbjct:   122 LQLLNLFAYGTYPDYIANKESLPELSAAQQNKLKHLTIVSLASRMKCIPYSVLLKDLEMR 181

Query:   123 NVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSD 182
             N+RELED +I E +YT I++GKLDQ  +  EV F  GRD++   + ++++TL  W    +
Sbjct:   182 NLRELEDLII-EAVYTDIIQGKLDQRNQLLEVDFCIGRDIQKKDINNIVKTLHEWCDGCE 240

Query:   183 NLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSE 237
              +L+ I++++  A+   E   + ++ +E +V   KK+L   A    +  E+  +E
Sbjct:   241 AVLLGIEQQVLRANQYKENHHRTQQQVEAEVSNIKKTLKATASSSAQEMEQQLAE 295

GO:0005737 "cytoplasm" evidence=ISO

GO:0008180 "signalosome" evidence=ISO

GO:0010388 "cullin deneddylation" evidence=ISO

UNIPROTKB|E1C3R1 COPS7B "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 339 (124.4 bits), Expect = 8.8e-31, P = 8.8e-31
 Identities = 72/234 (30%), Positives = 126/234 (53%)

Query:     4 EQRQA-ELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKY 62
             EQ+ +  L++ F+  A    G+AL ++I +    P ++ F E+L + N+ E     N+ Y
Sbjct:     4 EQKPSCNLLEQFILLAKGTSGSALTALINQVLEAPGVYVFGELLELTNVQELAEGSNAAY 63

Query:    63 LDMLRLFAHGTWSDY---KNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEEL 119
               +L LFA+GT+ DY     N  +LP+L                A   K +PY  L+++L
Sbjct:    64 FQLLNLFAYGTYPDYVALTANKDNLPELTATQKNKLKHLTIVSLASRMKCIPYSVLLKDL 123

Query:   120 DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLT 179
             D+ N+RELED +I E +YT I++GKLDQ  +  EV F  GRD++   + ++++TL  W  
Sbjct:   124 DMRNLRELEDLII-EAVYTDIIQGKLDQRNQMLEVDFCIGRDIQKKDISNIVKTLQEWCD 182

Query:   180 TSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEE 233
               + +L+ I++++  A+   E   + ++ +E +V   KK+L   A    +  E+
Sbjct:   183 GCEAVLLGIEQQVLRANQYKENHHRTQQQVEMEVTNIKKTLKATASSSAQEMEQ 236

GO:0005737 "cytoplasm" evidence=IEA

GO:0008180 "signalosome" evidence=IEA

GO:0010388 "cullin deneddylation" evidence=IEA

FB|FBgn0028836 CSN7 "COP9 complex homolog subunit 7" [Drosophila melanogaster (taxid:7227)]

 Score = 330 (121.2 bits), Expect = 7.9e-30, P = 7.9e-30
 Identities = 79/246 (32%), Positives = 131/246 (53%)

Query:    11 IDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFA 70
             ++ F   A +  GAAL  VI +A   P++F F E+LA P++ + +   +SK+ + L LFA
Sbjct:    20 LEKFCVLAKSSTGAALLDVIRQALEAPNVFVFGELLAEPSVLQLKDGPDSKHFETLNLFA 79

Query:    71 HGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDVTNVRELEDF 130
             +GT+ +Y+       +L P              A   K +PY  L+ EL++ NVR LED 
Sbjct:    80 YGTYKEYRAQPEKFIELTPAMQKKLQHLTIVSLAIKAKSIPYALLLSELEIDNVRHLEDI 139

Query:   131 LINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQE 190
             +I E +Y  I+ GKL Q  R  EV +A GRD+ PG  G +++TL  W+ + D++   I+ 
Sbjct:   140 II-EAIYADIIHGKLFQNTRILEVDYAQGRDIPPGYTGQIVETLQAWVNSCDSVSNCIEM 198

Query:   191 KIKWADSMNEMDKKHRKDLEEKVEEAKKSL-SHKADVDCRGHEEIYSEPG--GVMDYEED 247
             +IK+A++       +++ +E+ +   KK L S  +D D     + +  PG  G +   E 
Sbjct:   199 QIKYANAEKSKRLINKERVEQDLINLKKVLKSQTSDSDESMQIDTHG-PGTSGGLGQSEL 257

Query:   248 RGRPKR 253
             R +P +
Sbjct:   258 RKKPSK 263

GO:0005515 "protein binding" evidence=IPI

GO:0008180 "signalosome" evidence=ISS;IDA;IPI

GO:0050821 "protein stabilization" evidence=IMP

GO:0007095 "mitotic G2 DNA damage checkpoint" evidence=IGI

GO:0046331 "lateral inhibition" evidence=IMP

UNIPROTKB|F1NGK0 COPS7A "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 313 (115.2 bits), Expect = 5.0e-28, P = 5.0e-28
 Identities = 67/209 (32%), Positives = 112/209 (53%)

Query:    12 DHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAH 71
             + F+  A   +GAAL S+I +    P ++ F E+L +P + E   +E S    +L +FA 
Sbjct:    13 EQFLLLAKAARGAALASLIHQVLEAPGIYVFGELLDMPAVRELADSEFSPVFHLLTIFAC 72

Query:    72 GTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDVTNVRELEDFL 131
             GT++DY   A +LP L                A   K +PY  L+E+L + NVR+LED +
Sbjct:    73 GTYADYLAEAANLPPLTEAQKNKLRHLSVVTLAAKIKCIPYSVLLEQLQLKNVRQLEDLV 132

Query:   132 INECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEK 191
             I E +Y  ++RG LDQ  +  EV ++ GRD+R  +L ++ +TL  W    + +L  I+E+
Sbjct:   133 I-EAVYADVLRGSLDQRNQRLEVDYSIGRDIRREELSTITRTLQEWCQGCEVVLSGIEEQ 191

Query:   192 IKWADSMNEMDKKHRKDLEEKVEEAKKSL 220
             +  A+   E     ++ +E +V   KK++
Sbjct:   192 VSRANQHKEQQLALKQQIESEVANLKKTI 220

GO:0005737 "cytoplasm" evidence=IEA

GO:0008180 "signalosome" evidence=IEA

GO:0010388 "cullin deneddylation" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8BV13	CSN7B_MOUSE	No assigned EC number	0.3434	0.9051	0.8674	yes	no
Q2KI56	CSN7B_BOVIN	No assigned EC number	0.3434	0.9051	0.8674	yes	no
Q94JU3	CSN7_ARATH	No assigned EC number	0.7707	1.0	0.9730	yes	no
Q9V4S8	CSN7_DROME	No assigned EC number	0.3400	0.9565	0.8705	yes	no
Q9H9Q2	CSN7B_HUMAN	No assigned EC number	0.3434	0.9051	0.8674	yes	no

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:
	GSVIVG00019091001	SubName- Full=Chromosome chr15 scaffold_19, whole genome shotgun sequence; (259 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00026238001	SubName- Full=Chromosome chr15 scaffold_37, whole genome shotgun sequence; (441 aa)				•	•		•		0.729
	GSVIVG00014641001	SubName- Full=Chromosome chr18 scaffold_1, whole genome shotgun sequence; (397 aa)					•		•		0.727
	GSVIVG00036331001	SubName- Full=Chromosome chr3 scaffold_8, whole genome shotgun sequence; (329 aa)					•		•		0.722
	GSVIVG00025658001	SubName- Full=Chromosome chr8 scaffold_34, whole genome shotgun sequence; (437 aa)					•		•		0.721
	GSVIVG00020552001	SubName- Full=Chromosome chr14 scaffold_21, whole genome shotgun sequence; (424 aa)					•		•		0.682
	GSVIVG00003356001	SubName- Full=Chromosome undetermined scaffold_142, whole genome shotgun sequence; (310 aa)					•		•		0.670
	GSVIVG00023341001	SubName- Full=Chromosome chr8 scaffold_29, whole genome shotgun sequence; (433 aa)					•		•		0.557
	GSVIVG00032816001	SubName- Full=Chromosome chr4 scaffold_6, whole genome shotgun sequence; (395 aa)					•		•		0.405

---

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	253
pfam01399	100	pfam01399, PCI, PCI domain	3e-13
smart00753	88	smart00753, PAM, PCI/PINT associated module	2e-12
smart00088	88	smart00088, PINT, motif in proteasome subunits, In	2e-12

>gnl|CDD|216479 pfam01399, PCI, PCI domain

 Score = 63.8 bits (156), Expect = 3e-13
 Identities = 27/102 (26%), Positives = 47/102 (46%), Gaps = 11/102 (10%)

Query: 62  YLDMLRLFAHGTWSDYKNNAG---------HLPQLVPDQVLKLKQLTVLTLAETNKVLPY 112
           Y D+LR F  G  SD++              L +L+ D   K+++L +  LA+    +  
Sbjct: 1   YRDLLRAFYSGDLSDFEEILADNEDELLDDGLAELLEDLRRKIRELNLRRLAKPYSSISL 60

Query: 113 DELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154
            +L + L ++ V E+E  L    +  G +RGK+DQ+      
Sbjct: 61  SDLAKLLGLS-VDEVEKILSK-LIRDGRIRGKIDQVNGIVVF 100

This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15). Length = 100

>gnl|CDD|214803 smart00753, PAM, PCI/PINT associated module

 Score = 61.1 bits (149), Expect = 2e-12
 Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 4/92 (4%)

Query: 86  QLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145
           QLV     K++   +L L+E    +   +L + L ++   E+E  +    +  G +  K+
Sbjct: 1   QLVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVP-EVEKLVSK-AIRDGEISAKI 58

Query: 146 DQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNW 177
           DQ+    E +    R  R   L    +TL   
Sbjct: 59  DQVNGIVEFEEVDPR--RSEPLAQFAETLKKL 88

Length = 88

>gnl|CDD|214509 smart00088, PINT, motif in proteasome subunits, Int-6, Nip-1 and TRIP-15

 Score = 61.1 bits (149), Expect = 2e-12
 Identities = 21/92 (22%), Positives = 38/92 (41%), Gaps = 4/92 (4%)

Query: 86  QLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145
           QLV     K++   +L L+E    +   +L + L ++   E+E  +    +  G +  K+
Sbjct: 1   QLVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVP-EVEKLVSK-AIRDGEISAKI 58

Query: 146 DQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNW 177
           DQ+    E +    R  R   L    +TL   
Sbjct: 59  DQVNGIVEFEEVDPR--RSEPLAQFAETLKKL 88

Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function. Length = 88

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	253
KOG3250	258	consensus COP9 signalosome, subunit CSN7 [Posttran	100.0
KOG2753	378	consensus Uncharacterized conserved protein, conta	99.97
KOG2908	380	consensus 26S proteasome regulatory complex, subun	99.97
smart00088	88	PINT motif in proteasome subunits, Int-6, Nip-1 an	99.51
smart00753	88	PAM PCI/PINT associated module.	99.51
PF01399	105	PCI: PCI domain; InterPro: IPR000717 A homology do	99.51
KOG1464	440	consensus COP9 signalosome, subunit CSN2 [Posttran	98.86
KOG2581	493	consensus 26S proteasome regulatory complex, subun	97.73
KOG1498	439	consensus 26S proteasome regulatory complex, subun	96.44
KOG2758	432	consensus Translation initiation factor 3, subunit	96.04
KOG1497	399	consensus COP9 signalosome, subunit CSN4 [Posttran	95.68
KOG0686	466	consensus COP9 signalosome, subunit CSN1 [Posttran	95.5
COG5071	439	RPN5 26S proteasome regulatory complex component [	95.3
KOG2688	394	consensus Transcription-associated recombination p	94.38
KOG1463	411	consensus 26S proteasome regulatory complex, subun	93.1
KOG2582	422	consensus COP9 signalosome, subunit CSN3 [Posttran	93.01
COG5600	413	Transcription-associated recombination protein [DN	92.61
KOG0687	393	consensus 26S proteasome regulatory complex, subun	90.88
KOG2072	988	consensus Translation initiation factor 3, subunit	90.62
PF10075	143	PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro	90.38
PF09756	188	DDRGK: DDRGK domain; InterPro: IPR019153 This is a	88.79
COG5159	421	RPN6 26S proteasome regulatory complex component [	88.12
COG3355	126	Predicted transcriptional regulator [Transcription	85.85
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	83.62
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	81.39
KOG3054	299	consensus Uncharacterized conserved protein [Funct	80.1

>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=100.00  E-value=2.2e-65  Score=441.50  Aligned_cols=251  Identities=42%  Similarity=0.652  Sum_probs=247.8

Q ss_pred             CcHhHHHHHHHHHHHHhcccccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhh
Q 025387            1 MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN   80 (253)
Q Consensus         1 ~~~~~~~~~~l~~fl~lak~~~~~aa~~lI~~AL~~p~vf~F~eLL~~p~v~~L~~t~~~~~~~LL~iFa~Gt~~dy~~~   80 (253)
                      |++||++++.+|||+++||+.+|+|...+|.+||++|+||+|||||.+|+|.+|..+.++.+++||++||||||.||.++
T Consensus         1 m~~ek~~~~~~eqfvllak~~kg~al~~lIsqale~P~vf~F~ELl~l~nv~qlae~~dsa~lrlL~lFa~Gt~~Dy~ae   80 (258)
T KOG3250|consen    1 MDIEKKQAEIIEQFVLLAKTCKGEALEELISQALEAPGVFVFGELLILPNVVQLAEPIDSAYLRLLELFAYGTYRDYSAE   80 (258)
T ss_pred             CCcchhhHHHHHHHHHHHhccchhHHHHHHHHHhcCCCeeeHHHHHhhhhHHHHcccccHHHHHHHHHHhcCchhhhhhh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hCCCCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCC
Q 025387           81 AGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGR  160 (253)
Q Consensus        81 ~~~l~~L~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~R  160 (253)
                      +-.+|.|+++++.||++||++|||+..++|||..+.+.|.+.|+++||++|| +|||+++++|||||.+|+++|.|+.+|
T Consensus        81 a~rlp~Ls~~q~~kLk~ltV~slas~~k~lpy~~Ll~~l~~~nvrelEd~ii-eamya~IlrGkldqr~q~leV~faigR  159 (258)
T KOG3250|consen   81 ALRLPKLSLAQLNKLKHLTVVSLASFEKCLPYLVLLRLLPSRNVRELEDLII-EAMYADILRGKLDQRNQTLEVDFAIGR  159 (258)
T ss_pred             hhcCCCCCHHHHHhhhcceehhhhhhchhhhHHHHHhhccCCchhHHHHHHH-HHHHHHHHHhhHHhhcceEeechhhcc
Confidence            9999999999999999999999999999999999999999999999999999 999999999999999999999999999


Q ss_pred             CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhccccccCCccccchhhccCCC
Q 025387          161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSEPGG  240 (253)
Q Consensus       161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~~~k~~~~~~~~~~~~~~~~~  240 (253)
                      |+++.++.+|..+|++||+.|+++|..|++++.|||++++...+++++.|.+|.++||+++.+++.|+++.+..+.+| |
T Consensus       160 dlr~k~i~nm~~TL~~w~~~cenvL~~ie~qv~~anq~~e~~~r~~qq~e~ev~~~kKtlk~~ad~d~~~~eq~l~ep-p  238 (258)
T KOG3250|consen  160 DLRSKDIDNMKYTLDEWCEGCENVLFGIEAQVPRANQSKERASRMSQQDEIEVMNFKKTLKPTADTDFQLNEQMLGEP-P  238 (258)
T ss_pred             cccHhHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHhhhhhhhhhHHhhhcccCCCccccccchHHHhCCC-C
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999999999 9


Q ss_pred             ccccccccCCCCC
Q 025387          241 VMDYEEDRGRPKR  253 (253)
Q Consensus       241 ~~~~~~~~~~~~~  253 (253)
                      +|++..++.+|++
T Consensus       239 ~~~qrqp~kk~sk  251 (258)
T KOG3250|consen  239 VMDQRQPGKKPSK  251 (258)
T ss_pred             CccccCCCcCccc
Confidence            9999999999875

>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]

Probab=99.97  E-value=3.1e-32  Score=248.31  Aligned_cols=150  Identities=27%  Similarity=0.523  Sum_probs=139.6

Q ss_pred             HHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhh----hCCCCC---cchHHHHHHH
Q 025387           24 AALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN----AGHLPQ---LVPDQVLKLK   96 (253)
Q Consensus        24 ~aa~~lI~~AL~~p~vf~F~eLL~~p~v~~L~~t~~~~~~~LL~iFa~Gt~~dy~~~----~~~l~~---L~~~~~~KLr   96 (253)
                      .+|.+||+.|+.+|++|.|+.|+++|+|+.|+++.   +|+||.||..|..++|.++    ++++..   ..+++.+|||
T Consensus       205 edA~rcV~~av~dP~~F~fD~Ll~L~pV~qLE~d~---i~qLL~IF~s~~L~aYveF~~~N~~Fvqs~gl~~E~~~~KMR  281 (378)
T KOG2753|consen  205 EDAMRCVVEAVKDPKIFLFDHLLTLPPVKQLEGDL---IHQLLKIFVSGKLDAYVEFVAANSGFVQSQGLVHEQNMAKMR  281 (378)
T ss_pred             HHHHHHHHHHHcCCceeccchhccCchHHHhccch---HHHHHHHHHhcchHHHHHHHHhChHHHHHhcccHHHHHHHHH
Confidence            46999999999999999999999999999999765   8999999999999999874    444443   3367899999


Q ss_pred             HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHH
Q 025387           97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSN  176 (253)
Q Consensus        97 ~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~  176 (253)
                      +||+++||+.+.+|||++|+++|+|. .+|||.||| +||.+++|.|||||.+++|.|+.+.+|.|+..||..|.++|..
T Consensus       282 LLTlm~LA~es~eisy~~l~k~LqI~-edeVE~fVI-daI~aklV~~kidq~~~~viVs~~~hR~FG~~qW~~L~~kL~a  359 (378)
T KOG2753|consen  282 LLTLMSLAEESNEISYDTLAKELQIN-EDEVELFVI-DAIRAKLVEGKIDQMNRTVIVSSSTHRTFGKQQWQQLRDKLAA  359 (378)
T ss_pred             HHHHHHHhccCCCCCHHHHHHHhccC-HHHHHHHHH-HHHHHHHHHhhHHhhcceEEeehhhhhhcccHHHHHHHHHHHH
Confidence            99999999999999999999999996 999999999 9999999999999999999999999999999999999999999


Q ss_pred             HH
Q 025387          177 WL  178 (253)
Q Consensus       177 W~  178 (253)
                      |.
T Consensus       360 w~  361 (378)
T KOG2753|consen  360 WG  361 (378)
T ss_pred             HH
Confidence            95

>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]

Probab=99.97  E-value=5.3e-31  Score=241.29  Aligned_cols=179  Identities=18%  Similarity=0.358  Sum_probs=161.9

Q ss_pred             HHHHHhc------ccccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhh---hC
Q 025387           12 DHFVKQA------SNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN---AG   82 (253)
Q Consensus        12 ~~fl~la------k~~~~~aa~~lI~~AL~~p~vf~F~eLL~~p~v~~L~~t~~~~~~~LL~iFa~Gt~~dy~~~---~~   82 (253)
                      -.|+...      .+.+...|..|..+||.+.++|||||||.||+...|.||++.|++++|.+|+.||+..|...   .+
T Consensus       181 L~YL~~~d~~~l~~se~~~lA~~L~~aALLGe~iyNfGELL~HPilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~~~~  260 (380)
T KOG2908|consen  181 LLYLGCSDIDDLSESEKQDLAFDLSLAALLGENIYNFGELLAHPILESLKGTNREWLKDLLIAFNSGDLKRFESLKGVWG  260 (380)
T ss_pred             HHHhccccccccCHHHHHHHHHHHHHHHHhccccccHHHHHhhHHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHHHhc
Confidence            3566665      44455789999999999999999999999999999999999999999999999999999974   34


Q ss_pred             CCCCcchH---HHHHHHHHHhhhccc----CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025387           83 HLPQLVPD---QVLKLKQLTVLTLAE----TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ  155 (253)
Q Consensus        83 ~l~~L~~~---~~~KLr~LtLlsLa~----~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~  155 (253)
                      ..|.|...   ..+|+++++|+-++.    ..|.+||++|+++++|| .++||.+|| +|++.|||+|.|||++++|+++
T Consensus       261 ~~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip-~~eVE~LVM-KAlslgLikG~Idqv~~~v~~s  338 (380)
T KOG2908|consen  261 KQPDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIP-NKEVELLVM-KALSLGLIKGSIDQVEGVVYMS  338 (380)
T ss_pred             cCchHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCC-HHHHHHHHH-HHHhccceeeeecccccEEEEe
Confidence            57777633   478999999998875    57999999999999999 899999998 9999999999999999999999


Q ss_pred             eecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025387          156 FAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKI  192 (253)
Q Consensus       156 ~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i  192 (253)
                      |++||.++.+|+..|.+++..|++.++++...++.+-
T Consensus       339 wvqPRvl~~~qI~~Mk~rl~~W~~~v~~me~~ve~~~  375 (380)
T KOG2908|consen  339 WVQPRVLDRSQIVKMKDRLDEWNKDVKSMEGLVEHRG  375 (380)
T ss_pred             cccccccCHHHHHhHHHHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999999999999999999999998764

>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15

Probab=99.51  E-value=3.7e-14  Score=106.96  Aligned_cols=86  Identities=22%  Similarity=0.335  Sum_probs=80.9

Q ss_pred             chHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcH
Q 025387           88 VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQL  167 (253)
Q Consensus        88 ~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~  167 (253)
                      .+....|++.+++.+++..+++|+|++|++.++++ .+++|.+|+ ++|..|.|.|+|||.+++|.+.+..+|.  .++|
T Consensus         3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~-~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~   78 (88)
T smart00088        3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVS-KAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPL   78 (88)
T ss_pred             HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCeEEEEcCcCCEEEECCCchhh--hhHH
Confidence            45678999999999999999999999999999998 889999999 9999999999999999999999999997  7889


Q ss_pred             HHHHHHHHHH
Q 025387          168 GSMIQTLSNW  177 (253)
Q Consensus       168 ~~l~~~L~~W  177 (253)
                      ..+.++|..|
T Consensus        79 ~~~~~~l~~~   88 (88)
T smart00088       79 AQFAETLKKL   88 (88)
T ss_pred             HHHHHHhhcC
Confidence            9999998887

Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.

>smart00753 PAM PCI/PINT associated module

Probab=99.51  E-value=3.7e-14  Score=106.96  Aligned_cols=86  Identities=22%  Similarity=0.335  Sum_probs=80.9

Q ss_pred             chHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcH
Q 025387           88 VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQL  167 (253)
Q Consensus        88 ~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~  167 (253)
                      .+....|++.+++.+++..+++|+|++|++.++++ .+++|.+|+ ++|..|.|.|+|||.+++|.+.+..+|.  .++|
T Consensus         3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~-~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~   78 (88)
T smart00753        3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVS-KAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPL   78 (88)
T ss_pred             HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCeEEEEcCcCCEEEECCCchhh--hhHH
Confidence            45678999999999999999999999999999998 889999999 9999999999999999999999999997  7889


Q ss_pred             HHHHHHHHHH
Q 025387          168 GSMIQTLSNW  177 (253)
Q Consensus       168 ~~l~~~L~~W  177 (253)
                      ..+.++|..|
T Consensus        79 ~~~~~~l~~~   88 (88)
T smart00753       79 AQFAETLKKL   88 (88)
T ss_pred             HHHHHHhhcC
Confidence            9999998887

>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins

Probab=99.51  E-value=5.1e-14  Score=107.87  Aligned_cols=94  Identities=20%  Similarity=0.405  Sum_probs=80.9

Q ss_pred             HHHHHHHHHhcCChhhHhhhhC----------CCCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHH
Q 025387           61 KYLDMLRLFAHGTWSDYKNNAG----------HLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF  130 (253)
Q Consensus        61 ~~~~LL~iFa~Gt~~dy~~~~~----------~l~~L~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~l  130 (253)
                      |+.+|+++|..|++..|...-.          .+..+.+....+++..++.+++..++.|+++.|++.|+++ .++||.+
T Consensus         2 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~-~~~vE~~   80 (105)
T PF01399_consen    2 PYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLS-EEEVESI   80 (105)
T ss_dssp             HHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCC-HHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccc-hHHHHHH
Confidence            6899999999999999986322          2223446678999999999999999999999999999998 8999999


Q ss_pred             HHHHhHhcCccEEEecCCCCEEEEEe
Q 025387          131 LINECMYTGIVRGKLDQLRRCFEVQF  156 (253)
Q Consensus       131 lI~~AI~~gLI~GkIDQ~~~~v~V~~  156 (253)
                      |+ ++|..|.|.|+|||.+++|+++|
T Consensus        81 l~-~~I~~~~i~~~ID~~~~~v~~~k  105 (105)
T PF01399_consen   81 LI-DLISNGLIKAKIDQVNGVVVFSK  105 (105)
T ss_dssp             HH-HHHHTTSSEEEEETTTTEEEE-S
T ss_pred             HH-HHHHCCCEEEEEECCCCEEEecC
Confidence            99 99999999999999999999875

This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.

>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=98.86  E-value=6.7e-09  Score=94.72  Aligned_cols=125  Identities=14%  Similarity=0.360  Sum_probs=105.1

Q ss_pred             hHHHHHHHHHhcCChhhHhh----hhCC------CCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHH
Q 025387           60 SKYLDMLRLFAHGTWSDYKN----NAGH------LPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELED  129 (253)
Q Consensus        60 ~~~~~LL~iFa~Gt~~dy~~----~~~~------l~~L~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~  129 (253)
                      -.+.+|+..+...++..|+.    |.+.      +-+..++.++++|...|+.|..++..|....|+++|+|+ ..+||.
T Consensus       305 lAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~-~~dV~~  383 (440)
T KOG1464|consen  305 LAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVP-EADVES  383 (440)
T ss_pred             HHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCC-HHHHHH
Confidence            45889999999999999986    3332      223557889999999999999999999999999999998 999999


Q ss_pred             HHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025387          130 FLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKI  192 (253)
Q Consensus       130 llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i  192 (253)
                      +++ .||..+-|+|+|||+++.+.......      .-..+...|..|.+.++++.+.|-.++
T Consensus       384 LLV-~~ILD~~i~g~Ide~n~~l~~~~~~~------s~~k~~~al~kW~~ql~Sl~~~i~sr~  439 (440)
T KOG1464|consen  384 LLV-SCILDDTIDGRIDEVNQYLELDKSKN------SGSKLYKALDKWNNQLKSLQSNIVSRV  439 (440)
T ss_pred             HHH-HHHhccccccchHHhhhHhccCccCC------cchHHHHHHHHHHHHHHHHHHHHHhhc
Confidence            999 99999999999999999988764322      123378999999999999888776553

>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]

Probab=97.73  E-value=0.00018  Score=68.79  Aligned_cols=128  Identities=8%  Similarity=0.183  Sum_probs=83.9

Q ss_pred             hHHHHHHHHHhcCChhhHhhhhCCCCC-c----chHHHHHHHHHHhhhc----ccCCcccChHHHHHHcCCCChHHHHHH
Q 025387           60 SKYLDMLRLFAHGTWSDYKNNAGHLPQ-L----VPDQVLKLKQLTVLTL----AETNKVLPYDELMEELDVTNVRELEDF  130 (253)
Q Consensus        60 ~~~~~LL~iFa~Gt~~dy~~~~~~l~~-L----~~~~~~KLr~LtLlsL----a~~~k~Isy~~I~~~L~I~~~~evE~l  130 (253)
                      .+|+.|-+..-.||++-|....+.+.+ +    +-...-.||+=.|=+=    .-.++.|||.+|+..|+|+|..++|.+
T Consensus       319 ~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Seed~Eyi  398 (493)
T KOG2581|consen  319 RPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSEEDAEYI  398 (493)
T ss_pred             HHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCchhHHHH
Confidence            569999999999999999875433222 1    1112444555322221    115889999999999999999999999


Q ss_pred             HHHHhHhcCccEEEecCCCCEEEEEe--ecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025387          131 LINECMYTGIVRGKLDQLRRCFEVQF--AAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW  194 (253)
Q Consensus       131 lI~~AI~~gLI~GkIDQ~~~~v~V~~--~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~  194 (253)
                      |- +||+.|+|+|+||..++.+.-.-  -+.|.=.      -...+..-..-|-++.+.....+.+
T Consensus       399 Va-kAIRDGvIea~Id~~~g~m~skE~~diy~t~e------pQ~~f~~rI~fCl~LhN~~vkamRy  457 (493)
T KOG2581|consen  399 VA-KAIRDGVIEAKIDHEDGFMQSKETFDIYSTRE------PQTAFDERIRFCLQLHNEAVKAMRY  457 (493)
T ss_pred             HH-HHHHhccceeeeccccCceehhhhhhhhccCC------chhhHhHHHHHHHHHHHHHHHHhcC
Confidence            98 99999999999999999554321  1122111      1223334445555566666555543

>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]

Probab=96.44  E-value=0.027  Score=53.88  Aligned_cols=128  Identities=21%  Similarity=0.300  Sum_probs=92.2

Q ss_pred             CchHHHHHHHHHhcCChhhHhhhh---------CCCCC---cchHH--HHHHHH--HHhhhcccCCcccChHHHHHHcCC
Q 025387           58 ENSKYLDMLRLFAHGTWSDYKNNA---------GHLPQ---LVPDQ--VLKLKQ--LTVLTLAETNKVLPYDELMEELDV  121 (253)
Q Consensus        58 ~~~~~~~LL~iFa~Gt~~dy~~~~---------~~l~~---L~~~~--~~KLr~--LtLlsLa~~~k~Isy~~I~~~L~I  121 (253)
                      +.+.+-.+|.+|..|.+--+....         +.+..   ..+..  -.|.|.  .-+-=.|.=+.+||+..+++-|+.
T Consensus       286 e~p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLdl  365 (439)
T KOG1498|consen  286 ELPDYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLDL  365 (439)
T ss_pred             cCccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhCC
Confidence            345577899999998766554211         11111   11111  122222  333344556889999999999999


Q ss_pred             CChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025387          122 TNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS  197 (253)
Q Consensus       122 ~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~  197 (253)
                      | .++.|.+|- +.+..|.+.+|||+..+.+.+...          ..+.+-|..|..++++++..++..-+-..+
T Consensus       366 ~-~ee~E~~LS-~lv~t~ti~aKidrpsgII~F~k~----------K~~~~~LneW~~nve~L~~ll~K~~HLI~K  429 (439)
T KOG1498|consen  366 P-VEEMEKFLS-DLVVTGTIYAKIDRPSGIINFQKV----------KDSNEILNEWASNVEKLLGLLEKVSHLIHK  429 (439)
T ss_pred             C-HHHHHHHHH-HHHhccceEEEecCCCceEEEEec----------ccHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence            8 999999999 899999999999999999988654          347888999999999999998876555544

>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]

Probab=96.04  E-value=0.012  Score=55.20  Aligned_cols=97  Identities=16%  Similarity=0.226  Sum_probs=75.6

Q ss_pred             hHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHH
Q 025387           89 PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLG  168 (253)
Q Consensus        89 ~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~  168 (253)
                      .+-+.--|++-.=+.|.-..+|+.+.+|+.|+++ .+|.|.|++ +.|+...|++|||..-++|.+.....-     --+
T Consensus       329 ~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~-~eeaErwiv-nlIr~~rl~AkidSklg~Vvmg~~~~s-----~~q  401 (432)
T KOG2758|consen  329 DEFLENARLLIFETFCRIHQCITIDMLADKLNMD-PEEAERWIV-NLIRTARLDAKIDSKLGHVVMGHPTVS-----PHQ  401 (432)
T ss_pred             HHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCC-HHHHHHHHH-HHHHHhhhhhhhccccCceeecCCCCC-----HHH
Confidence            4446677888888889889999999999999997 999999999 899999999999999999888643322     234


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q 025387          169 SMIQTLSNWLTTSDNLLISIQEKI  192 (253)
Q Consensus       169 ~l~~~L~~W~~~~~~vl~~Ie~~i  192 (253)
                      .++++-..-.-+...+-..++..+
T Consensus       402 Q~ie~tksLS~rsq~la~~lek~~  425 (432)
T KOG2758|consen  402 QLIEKTKSLSFRSQNLAQQLEKKI  425 (432)
T ss_pred             HHHHhccccchhHHHHHHHHHHHH
Confidence            566666666666666666665544

>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=95.68  E-value=0.02  Score=53.66  Aligned_cols=154  Identities=11%  Similarity=0.131  Sum_probs=89.7

Q ss_pred             HHHHHHHHhcCCCcccc-hhhhcCchhhhccCCC-chHHHHHHHHHhcC-ChhhHhhh-----hCCCCCcchHHHHHHHH
Q 025387           26 LGSVIVEATSQPSLFAF-SEILAVPNIAEFEGTE-NSKYLDMLRLFAHG-TWSDYKNN-----AGHLPQLVPDQVLKLKQ   97 (253)
Q Consensus        26 a~~lI~~AL~~p~vf~F-~eLL~~p~v~~L~~t~-~~~~~~LL~iFa~G-t~~dy~~~-----~~~l~~L~~~~~~KLr~   97 (253)
                      |..|..-|.-+|..--| ..|...|.+++|..=+ -.++|  |+-|-.+ +...|...     +...+.=+.-.-+-+.-
T Consensus       228 a~~CtlLA~~gpqrsr~Latlfkder~~~l~~y~ileKmy--l~riI~k~el~ef~~~L~pHQka~~~dgssil~ra~~E  305 (399)
T KOG1497|consen  228 ALQCTLLASAGPQRSRMLATLFKDERCQKLPAYGILEKMY--LERIIRKEELQEFEAFLQPHQKAHTMDGSSILDRAVIE  305 (399)
T ss_pred             hHhheeecCCChHHHHHHHHHhcCcccccccchHHHHHHH--HHHHhcchhHHHHHHHhcchhhhcccCcchhhhhHHHH
Confidence            44444444555544443 3555556666554211 12222  3444444 45556542     11112101111122333


Q ss_pred             HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHH
Q 025387           98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNW  177 (253)
Q Consensus        98 LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W  177 (253)
                      -.|+++++-+..|+|+++...|+|+ .+.+|...- +.|..+-+.|.|||.++.+++.-   |. ...+|+.   ....-
T Consensus       306 hNlls~Skly~nisf~~Lg~ll~i~-~ekaekiaa-~MI~qeRmng~IDQ~egiihFe~---~e-~l~~wdk---qi~sl  376 (399)
T KOG1497|consen  306 HNLLSASKLYNNISFEELGALLKID-AEKAEKIAA-QMITQERMNGSIDQIEGIIHFED---RE-ELPQWDK---QIQSL  376 (399)
T ss_pred             HhHHHHHHHHHhccHHHHHHHhCCC-HHHHHHHHH-HHHhHHHhccchHhhcceEeecc---hh-hhhhhhH---HHHHH
Confidence            4566666778899999999999998 999999999 89999999999999999999763   21 1123443   33344


Q ss_pred             HHHHHHHHHHHHH
Q 025387          178 LTTSDNLLISIQE  190 (253)
Q Consensus       178 ~~~~~~vl~~Ie~  190 (253)
                      |+.++++++.|..
T Consensus       377 ~~qvNki~~~i~~  389 (399)
T KOG1497|consen  377 CNQVNKILDKISH  389 (399)
T ss_pred             HHHHHHHHHHHHH
Confidence            5555555555543

>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=95.50  E-value=0.15  Score=49.31  Aligned_cols=98  Identities=15%  Similarity=0.223  Sum_probs=76.5

Q ss_pred             HHHHHHHHhcCChhhHhh----hhCCCC---Ccc---hHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHH
Q 025387           62 YLDMLRLFAHGTWSDYKN----NAGHLP---QLV---PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL  131 (253)
Q Consensus        62 ~~~LL~iFa~Gt~~dy~~----~~~~l~---~L~---~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~ll  131 (253)
                      +.++|.-|..+-|..-..    .++.+-   -|.   .....++|.=.++.--.++..++++.++.+.+.+ +..+|.=|
T Consensus       308 lr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~s-v~~le~~l  386 (466)
T KOG0686|consen  308 LREILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTS-VAILESEL  386 (466)
T ss_pred             HHHHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhccc-HHHHHHHH
Confidence            566777777776665333    222210   122   3457889998999988999999999999999997 99999999


Q ss_pred             HHHhHhcCccEEEecCCCCEEEEEeecCCC
Q 025387          132 INECMYTGIVRGKLDQLRRCFEVQFAAGRD  161 (253)
Q Consensus       132 I~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rd  161 (253)
                      . +.|-.|.|.||||+.++++++.-+..|.
T Consensus       387 ~-~LI~~~~i~~rIDs~~ki~~~~~~~~en  415 (466)
T KOG0686|consen  387 L-ELILEGKISGRIDSHNKILYARDADSEN  415 (466)
T ss_pred             H-HHHHccchheeeccccceeeeccccccc
Confidence            9 9999999999999999999987665554

>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

Probab=95.30  E-value=0.08  Score=49.54  Aligned_cols=75  Identities=16%  Similarity=0.256  Sum_probs=65.3

Q ss_pred             cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHH
Q 025387          105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNL  184 (253)
Q Consensus       105 ~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~v  184 (253)
                      .=++.|+-..|..-++.| ..+.|.+|- +.+..|++.+||++..+.+.+...          ++..+.|..|.++++.+
T Consensus       349 ~yYSrI~~~rl~~lld~~-~s~te~~IS-dlVN~G~~yaKiNrpa~Ii~FEK~----------~n~~~~lneW~~NV~el  416 (439)
T COG5071         349 NYYSRIHCSRLGVLLDMS-PSETEQFIS-DLVNKGHFYAKINRPAQIISFEKS----------QNVQEQLNEWGSNVTEL  416 (439)
T ss_pred             HHhhhhhHHHHHHHHcCC-HHHHHHHHH-HHHhcCcEEEEecCccceEEeecc----------ccHHHHHHHhcccHHHH
Confidence            457889999999999998 999999999 899999999999999999987643          23577899999999999


Q ss_pred             HHHHHHH
Q 025387          185 LISIQEK  191 (253)
Q Consensus       185 l~~Ie~~  191 (253)
                      +..++.-
T Consensus       417 lgklek~  423 (439)
T COG5071         417 LGKLEKV  423 (439)
T ss_pred             HHHHHHH
Confidence            9988753

>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]

Probab=94.38  E-value=0.084  Score=50.68  Aligned_cols=109  Identities=15%  Similarity=0.184  Sum_probs=74.7

Q ss_pred             CchhhhccCCCchHHHHHHHHHhcCChhhHhh----hhCCCCCcch-HHHHHHHHHHhhhcc-------cCCcccChHHH
Q 025387           48 VPNIAEFEGTENSKYLDMLRLFAHGTWSDYKN----NAGHLPQLVP-DQVLKLKQLTVLTLA-------ETNKVLPYDEL  115 (253)
Q Consensus        48 ~p~v~~L~~t~~~~~~~LL~iFa~Gt~~dy~~----~~~~l~~L~~-~~~~KLr~LtLlsLa-------~~~k~Isy~~I  115 (253)
                      +|-..-|..-.-..+-.|+.....||+..|..    +...+....- -.+.|++.++.=.|.       .+...+|++.+
T Consensus       260 ~Pt~~lL~~~~~~~~~~lv~aVr~Gnl~~f~~al~~~E~~f~~~gi~l~l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~  339 (394)
T KOG2688|consen  260 IPTKELLDFYTLDKYSPLVQAVRSGNLRLFDLALADNERFFIRSGIYLTLEKLPLVVYRNLFKKVIQLWGKTSQLPLSRF  339 (394)
T ss_pred             CcchhhHhHhhHHhHHHHHHHHHhccHHHHHHHHhhhHHHHHHhccHHHhhhhhHHHHHHHHHHHHHHhCCCCCCCHHHH
Confidence            34443343212345777999999999999985    2222211110 012334444433333       26789999999


Q ss_pred             HHHcCCCC-----hHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025387          116 MEELDVTN-----VRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA  157 (253)
Q Consensus       116 ~~~L~I~~-----~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~  157 (253)
                      ..++....     .+|||-.+. .+|+.|.|+|.|+...+++.+...
T Consensus       340 ~~al~~~~~~~~~~deveciLa-~lI~~G~ikgYish~~~~~V~sK~  385 (394)
T KOG2688|consen  340 LTALQFSGVTDVDLDEVECILA-NLIDLGRIKGYISHQLQTLVFSKK  385 (394)
T ss_pred             HHHHhhcCCCCCchhhHHHHHH-hhhhhccccchhchhhheEEEecC
Confidence            99998765     789999999 899999999999999999998854

>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]

Probab=93.10  E-value=0.25  Score=46.88  Aligned_cols=114  Identities=15%  Similarity=0.230  Sum_probs=81.2

Q ss_pred             hhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhhhCCC-CCcc-----hHHH----HHHHHHHhhhcccCCcccChH
Q 025387           44 EILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHL-PQLV-----PDQV----LKLKQLTVLTLAETNKVLPYD  113 (253)
Q Consensus        44 eLL~~p~v~~L~~t~~~~~~~LL~iFa~Gt~~dy~~~~~~l-~~L~-----~~~~----~KLr~LtLlsLa~~~k~Isy~  113 (253)
                      .|+.-.......+..-..+...=+.|..-+++||..--..+ ++|-     ...+    ..|=---|+.+.+++.++..+
T Consensus       270 ~lls~K~~l~y~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei~  349 (411)
T KOG1463|consen  270 ALLSAKLALKYAGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEIS  349 (411)
T ss_pred             HHHhhHHHHhccCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhHH
Confidence            34443333334444556677788889999999998632212 1222     1122    222223577888899999999


Q ss_pred             HHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecC
Q 025387          114 ELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAG  159 (253)
Q Consensus       114 ~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~  159 (253)
                      -|++-+|++ +..||.=+- ..|-...+.|.|||-++++.|.--.+
T Consensus       350 hIA~~IGl~-~~~VEkKLs-qMILDKkf~G~LDQg~g~Liv~~e~~  393 (411)
T KOG1463|consen  350 HIAEVIGLD-VPQVEKKLS-QMILDKKFYGTLDQGEGCLIVFEEPP  393 (411)
T ss_pred             HHHHHHCCC-cHHHHHHHH-HHHHHHHhhcccccCCCeEEEeCCCC
Confidence            999999998 999999988 89999999999999999999975443

>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=93.01  E-value=0.69  Score=44.22  Aligned_cols=106  Identities=11%  Similarity=0.247  Sum_probs=77.7

Q ss_pred             hHHHHHHHHHhcCChhhHhh----hhCCC-C----CcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHH
Q 025387           60 SKYLDMLRLFAHGTWSDYKN----NAGHL-P----QLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF  130 (253)
Q Consensus        60 ~~~~~LL~iFa~Gt~~dy~~----~~~~l-~----~L~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~l  130 (253)
                      .+|.++++++..+.-.+.+.    +++.+ .    .|......-+..-+|..|-+...+++.++|++..++.+..|||..
T Consensus       259 ~pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~l~k~av~sl~k~nI~rltktF~sLsL~dIA~~vQLa~~qevek~  338 (422)
T KOG2582|consen  259 NPYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTGLAKQAVSSLYKKNIQRLTKTFLSLSLSDIASRVQLASAQEVEKY  338 (422)
T ss_pred             chHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcchHHHHHH
Confidence            36899999999988776554    22222 1    122333445555667777777788999999997777778999999


Q ss_pred             HHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHH
Q 025387          131 LINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGS  169 (253)
Q Consensus       131 lI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~  169 (253)
                      |+ ..|..|=|-..||   +-|..+.-...+..|+...+
T Consensus       339 Il-qmie~~~i~a~iN---G~v~f~~n~e~~~SpeM~~n  373 (422)
T KOG2582|consen  339 IL-QMIEDGEIFASIN---GMVFFTDNPEKYNSPEMHEN  373 (422)
T ss_pred             HH-HHhccCceEEEec---ceEEEecCcccCCCHHHHhh
Confidence            99 8999999999999   77777766666666655543

>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]

Probab=92.61  E-value=0.36  Score=46.19  Aligned_cols=99  Identities=20%  Similarity=0.317  Sum_probs=64.7

Q ss_pred             chHHHHHHHHHhcCChhhHhhh----hCCCCC----cc-----hH-HHHHHHHHHhhhcccCCcccChHHHHHHcCCC--
Q 025387           59 NSKYLDMLRLFAHGTWSDYKNN----AGHLPQ----LV-----PD-QVLKLKQLTVLTLAETNKVLPYDELMEELDVT--  122 (253)
Q Consensus        59 ~~~~~~LL~iFa~Gt~~dy~~~----~~~l~~----L~-----~~-~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~--  122 (253)
                      .+.+--|.++.-+|++++|..-    ...+-.    ++     |. +.+.|.. -+..+.-....+|++.+...++++  
T Consensus       288 ~s~~~~LvkavrsGni~~~~~~l~~ner~~~~~~l~ltl~~~~~~V~~RNL~r-k~w~~~~~qsrlp~sil~~~~qls~~  366 (413)
T COG5600         288 CSVYSPLVKAVRSGNIEDFDLALSRNERKFAKRGLYLTLLAHYPLVCFRNLFR-KIWRLHGKQSRLPLSILLIVLQLSAI  366 (413)
T ss_pred             cchhHHHHHHHHcCCHHHHHHHHHHhHHHHHHcchHHHHHhhccHHHHHHHHH-HHHhhccccccCcHHHHHHHHHccCC
Confidence            4556678899999999999852    111110    00     10 1222222 223333345557777666555554  


Q ss_pred             C----hHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecC
Q 025387          123 N----VRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAG  159 (253)
Q Consensus       123 ~----~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~  159 (253)
                      +    ..+||-.++ .+|..|+++|.|....+++.+....|
T Consensus       367 dn~~~~~~VEciL~-tlI~~G~lrgYis~s~~~vV~sk~~p  406 (413)
T COG5600         367 DNFHSFKEVECILV-TLIGLGLLRGYISHSRRTVVFSKKDP  406 (413)
T ss_pred             CcccChHHHHHHHH-HHHhhhhhhheecccceEEEEecCCC
Confidence            2    568999999 89999999999999999999986544

>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]

Probab=90.88  E-value=3.5  Score=39.14  Aligned_cols=64  Identities=17%  Similarity=0.267  Sum_probs=56.3

Q ss_pred             HHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025387           92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA  157 (253)
Q Consensus        92 ~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~  157 (253)
                      .+-||+..--.|-+.+|.++.+..|+..|++ ++-++.=+= +-|-+|-++++||-++++|++++-
T Consensus       300 vREMR~rvY~QlLESYrsl~l~~MA~aFgVS-VefiDreL~-rFI~~grL~ckIDrVnGVVEtNrp  363 (393)
T KOG0687|consen  300 VREMRRRVYAQLLESYRSLTLESMAKAFGVS-VEFIDRELG-RFIAAGRLHCKIDRVNGVVETNRP  363 (393)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhCch-HHHHHhHHH-HhhccCceeeeeecccceeecCCc
Confidence            5778888888888899999999999999997 887777677 778899999999999999999854

>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]

Probab=90.62  E-value=3.4  Score=43.27  Aligned_cols=50  Identities=16%  Similarity=0.219  Sum_probs=43.9

Q ss_pred             cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025387          105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ  155 (253)
Q Consensus       105 ~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~  155 (253)
                      ..+.+|+|+.|.+-.-.=|.-+||.+++ +|...+.+..+||....+|.+.
T Consensus       443 qiY~sIs~~~l~~La~F~~~~~lEk~~v-~a~k~~~v~iriDH~~~~v~Fg  492 (988)
T KOG2072|consen  443 QIYESISFERLYKLAPFFSAFELEKLLV-EAAKHNDVSIRIDHESNSVSFG  492 (988)
T ss_pred             HHHHHHhHHHHHHHHhhcCHHHHHHHHH-HHHhccceeEEeccccceeeec
Confidence            3577899998887665556889999999 9999999999999999999987

>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8

Probab=90.38  E-value=2.7  Score=34.17  Aligned_cols=107  Identities=15%  Similarity=0.185  Sum_probs=72.6

Q ss_pred             HHHHHHHHHhcCCCcccchhhhcCchhhhccC-CCchHHHHHHHHHhcCChhhHhhhhCCC---C---CcchHHHHHHHH
Q 025387           25 ALGSVIVEATSQPSLFAFSEILAVPNIAEFEG-TENSKYLDMLRLFAHGTWSDYKNNAGHL---P---QLVPDQVLKLKQ   97 (253)
Q Consensus        25 aa~~lI~~AL~~p~vf~F~eLL~~p~v~~L~~-t~~~~~~~LL~iFa~Gt~~dy~~~~~~l---~---~L~~~~~~KLr~   97 (253)
                      ....+...+|..-.+-+|.-++..-.-...+. .+-..++.|.+.+-.|+|..|-+.....   +   .+.+....++|.
T Consensus         6 ~~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~iR~   85 (143)
T PF10075_consen    6 IYALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDTIRE   85 (143)
T ss_dssp             HHHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHHHHH
T ss_pred             HHHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHHHHH
Confidence            33445555555556788888877444333332 4557788999999999999987732211   1   233555778888


Q ss_pred             HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHH
Q 025387           98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI  132 (253)
Q Consensus        98 LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI  132 (253)
                      -++-.+...+..|+.+.+++-||++ ..+++.++.
T Consensus        86 ~i~~~i~~aY~sIs~~~la~~Lg~~-~~el~~~~~  119 (143)
T PF10075_consen   86 RIAHLISKAYSSISLSDLAEMLGLS-EEELEKFIK  119 (143)
T ss_dssp             HHHHHHHHH-SEE-HHHHHHHTTS--HHHHHHHHH
T ss_pred             HHHHHHHHHHhHcCHHHHHHHhCCC-HHHHHHHHH
Confidence            7777777889999999999999998 999999877

In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.

>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues

Probab=88.79  E-value=0.66  Score=40.35  Aligned_cols=57  Identities=14%  Similarity=0.268  Sum_probs=40.8

Q ss_pred             HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025387           97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ  155 (253)
Q Consensus        97 ~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~  155 (253)
                      +-.++..+...++++.++||.++++. ..++-+-|- +....|.|.|-||...+-|+|+
T Consensus       101 L~~Fi~yIK~~Kvv~ledla~~f~l~-t~~~i~ri~-~L~~~g~ltGv~DdrGkfIyIs  157 (188)
T PF09756_consen  101 LQEFINYIKEHKVVNLEDLAAEFGLR-TQDVINRIQ-ELEAEGRLTGVIDDRGKFIYIS  157 (188)
T ss_dssp             HHHHHHHHHH-SEE-HHHHHHHH-S--HHHHHHHHH-HHHHHSSS-EEE-TT--EEE--
T ss_pred             HHHHHHHHHHcceeeHHHHHHHcCCC-HHHHHHHHH-HHHHCCCceeeEcCCCCeEEec
Confidence            34566777789999999999999998 788888877 8999999999999999989887

They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.

>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

Probab=88.12  E-value=3.8  Score=38.51  Aligned_cols=100  Identities=17%  Similarity=0.238  Sum_probs=73.5

Q ss_pred             chHHHHHHHHHhcCChhhHhhh-hCCCCCcc-----hHHH----HHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHH
Q 025387           59 NSKYLDMLRLFAHGTWSDYKNN-AGHLPQLV-----PDQV----LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELE  128 (253)
Q Consensus        59 ~~~~~~LL~iFa~Gt~~dy~~~-~~~l~~L~-----~~~~----~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE  128 (253)
                      -..+...-+.|..-++.||..- +..-|+|-     ...+    .-|---.|+.+.++..++..+-|++-+|++ ...||
T Consensus       283 I~am~avaea~~NRsL~df~~aL~qY~~el~~D~~iRsHl~~LYD~LLe~Nl~kiiEPfs~VeishIa~viGld-t~qvE  361 (421)
T COG5159         283 IRAMLAVAEAFGNRSLKDFSDALAQYSDELHQDSFIRSHLQYLYDVLLEKNLVKIIEPFSVVEISHIADVIGLD-TNQVE  361 (421)
T ss_pred             HHHHHHHHHHhCCCcHhhHHHHHHHhhHHhccCHHHHHHHHHHHHHHHHhhhhhhcCcceeeehhHHHHHhccc-HHHHH
Confidence            3456667788888889999762 22222222     1111    222223567778899999999999999997 99999


Q ss_pred             HHHHHHhHhcCccEEEecCCCCEEEEEeecCC
Q 025387          129 DFLINECMYTGIVRGKLDQLRRCFEVQFAAGR  160 (253)
Q Consensus       129 ~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~R  160 (253)
                      -=+- ..|-..++-|.+||.++|+.|.-....
T Consensus       362 gKLs-qMILDKifyG~LDqg~gcLivy~ep~q  392 (421)
T COG5159         362 GKLS-QMILDKIFYGTLDQGDGCLIVYGEPAQ  392 (421)
T ss_pred             HHHH-HHHHHHHHHhhhccCCceEEEeCCccc
Confidence            8888 889899999999999999999755433

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=85.85  E-value=7.1  Score=31.90  Aligned_cols=80  Identities=20%  Similarity=0.365  Sum_probs=57.5

Q ss_pred             cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE-Eec-CCCCEEEEEeecCCCCCCCcHHH-HHHHHHHHHHHH
Q 025387          105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG-KLD-QLRRCFEVQFAAGRDLRPGQLGS-MIQTLSNWLTTS  181 (253)
Q Consensus       105 ~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~G-kID-Q~~~~v~V~~~~~Rdl~~~q~~~-l~~~L~~W~~~~  181 (253)
                      +.++.++-++|++.|+++ -..|..-|= +.+..|+|.= |.. ...+..++-    +.++++++.. +...|..|++++
T Consensus        38 ~~~~~~tvdelae~lnr~-rStv~rsl~-~L~~~GlV~Rek~~~~~Ggy~yiY----~~i~~ee~k~~i~~~l~~w~~~~  111 (126)
T COG3355          38 EENGPLTVDELAEILNRS-RSTVYRSLQ-NLLEAGLVEREKVNLKGGGYYYLY----KPIDPEEIKKKILKDLDEWYDKM  111 (126)
T ss_pred             hhcCCcCHHHHHHHHCcc-HHHHHHHHH-HHHHcCCeeeeeeccCCCceeEEE----ecCCHHHHHHHHHHHHHHHHHHH
Confidence            367889999999999997 778888777 8999999873 333 223333332    2334556653 678999999999


Q ss_pred             HHHHHHHHH
Q 025387          182 DNLLISIQE  190 (253)
Q Consensus       182 ~~vl~~Ie~  190 (253)
                      ...+...+.
T Consensus       112 ~~~i~~~~~  120 (126)
T COG3355         112 KQLIEEFEK  120 (126)
T ss_pred             HHHHHHHhc
Confidence            988876653

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif

Probab=83.62  E-value=0.93  Score=32.50  Aligned_cols=43  Identities=16%  Similarity=0.287  Sum_probs=33.3

Q ss_pred             HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025387           99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG  143 (253)
Q Consensus        99 tLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~G  143 (253)
                      .|..+...++.+|+++|+.+++++ .+.||.++= ..+..|-|+-
T Consensus         4 ~i~~~l~~~~~~S~~eLa~~~~~s-~~~ve~mL~-~l~~kG~I~~   46 (69)
T PF09012_consen    4 EIRDYLRERGRVSLAELAREFGIS-PEAVEAMLE-QLIRKGYIRK   46 (69)
T ss_dssp             HHHHHHHHS-SEEHHHHHHHTT---HHHHHHHHH-HHHCCTSCEE
T ss_pred             HHHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEE
Confidence            344455578899999999999997 999999887 8898998883

FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.

>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp

Probab=81.39  E-value=4.6  Score=29.80  Aligned_cols=58  Identities=17%  Similarity=0.230  Sum_probs=39.2

Q ss_pred             HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025387           95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ  155 (253)
Q Consensus        95 Lr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~  155 (253)
                      ++.|..+......+.++-.+|++.++++ ...|+.++= +...+|+|+.+= ..++.+...
T Consensus        11 l~~l~~la~~~~~~~~s~~eiA~~~~i~-~~~l~kil~-~L~~~Gli~s~~-G~~GGy~L~   68 (83)
T PF02082_consen   11 LRILLYLARHPDGKPVSSKEIAERLGIS-PSYLRKILQ-KLKKAGLIESSR-GRGGGYRLA   68 (83)
T ss_dssp             HHHHHHHHCTTTSC-BEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEET-STTSEEEES
T ss_pred             HHHHHHHHhCCCCCCCCHHHHHHHHCcC-HHHHHHHHH-HHhhCCeeEecC-CCCCceeec
Confidence            3334444333344569999999999998 999998877 889999987552 444544443

(strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.

>KOG3054 consensus Uncharacterized conserved protein [Function unknown]

Probab=80.10  E-value=3  Score=37.90  Aligned_cols=54  Identities=19%  Similarity=0.401  Sum_probs=43.4

Q ss_pred             hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025387          100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ  155 (253)
Q Consensus       100 LlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~  155 (253)
                      ++..+.++++++.++|+.+.++. ..++=+-+= +.+..|+|.|-||...+-++|+
T Consensus       205 Fv~YIk~nKvV~ledLas~f~Lr-tqd~inriq-~~l~eg~ltGVmDDRGKfIYIS  258 (299)
T KOG3054|consen  205 FVEYIKKNKVVPLEDLASEFGLR-TQDSINRIQ-ELLAEGLLTGVMDDRGKFIYIS  258 (299)
T ss_pred             HHHHHHhcCeeeHHHHHHHhCcc-HHHHHHHHH-HHHHhhhheeeecCCCceEEec
Confidence            44555689999999999999998 444444444 5666899999999999999997

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	253
3chm_A	169	Crystal Structure Of Pci Domain From A. Thaliana Co		6e-68

>pdb|3CHM|A Chain A, Crystal Structure Of Pci Domain From A. Thaliana Cop9 Signalosome Subunit 7 (Csn7) Length = 169

Iteration: 1
 Score =  253 bits (647), Expect = 6e-68,   Method: Compositional matrix adjust.
 Identities = 120/168 (71%), Positives = 134/168 (79%)
Query: 2   DIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSK 61
           DIEQ+QAE+ID  VK+AS  K  ALG +I+EATS PSLFAFSEILA+PN+A+ EGT +S 
Sbjct: 2   DIEQKQAEIIDQLVKRASTCKSEALGPLIIEATSHPSLFAFSEILALPNVAQLEGTTDSV 61
Query: 62  YLDMLRLFAHGTWSDYKNNAGHLPQLVPDXXXXXXXXXXXXXAETNKVLPYDELMEELDV 121
           YLD+LRLFAHGTW DYK NA  LP L PD             AE+NKVLPYD LM ELDV
Sbjct: 62  YLDLLRLFAHGTWGDYKCNATRLPHLSPDQILKLKQLTVLTLAESNKVLPYDTLMVELDV 121
Query: 122 TNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGS 169
           +NVRELEDFLINECMY GIVRGKLDQL+RCFEV FAAGRDLRPGQLG+
Sbjct: 122 SNVRELEDFLINECMYAGIVRGKLDQLKRCFEVPFAAGRDLRPGQLGN 169

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	253
3chm_A	169	COP9 signalosome complex subunit 7; heat/ARM repea	7e-62
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	1e-04

>3chm_A COP9 signalosome complex subunit 7; heat/ARM repeats, winged helix motif, developmental protein, phosphoprotein; 1.50A {Arabidopsis thaliana} Length = 169

 Score =  191 bits (486), Expect = 7e-62
 Identities = 132/168 (78%), Positives = 147/168 (87%)

Query: 2   DIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSK 61
           DIEQ+QAE+ID  VK+AS  K  ALG +I+EATS PSLFAFSEILA+PN+A+ EGT +S 
Sbjct: 2   DIEQKQAEIIDQLVKRASTCKSEALGPLIIEATSHPSLFAFSEILALPNVAQLEGTTDSV 61

Query: 62  YLDMLRLFAHGTWSDYKNNAGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDV 121
           YLD+LRLFAHGTW DYK NA  LP L PDQ+LKLKQLTVLTLAE+NKVLPYD LM ELDV
Sbjct: 62  YLDLLRLFAHGTWGDYKCNATRLPHLSPDQILKLKQLTVLTLAESNKVLPYDTLMVELDV 121

Query: 122 TNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGS 169
           +NVRELEDFLINECMY GIVRGKLDQL+RCFEV FAAGRDLRPGQLG+
Sbjct: 122 SNVRELEDFLINECMYAGIVRGKLDQLKRCFEVPFAAGRDLRPGQLGN 169

>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 = 42.1 bits (98), Expect = 1e-04
 Identities = 56/371 (15%), Positives = 103/371 (27%), Gaps = 135/371 (36%)

Query: 3   IEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPS------------LFAFSEILA--- 47
           +  +Q E++  FV++        L S I     QPS            L+  +++ A   
Sbjct: 71  LLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYN 130

Query: 48  VPNIAEFEGTENSKYLDMLR----LFAHG------TW------SDYKN-----------N 80
           V  +  +     +  L  LR    +   G      TW        YK            N
Sbjct: 131 VSRLQPYLKLRQA--LLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLN 188

Query: 81  AGHL--PQLVPDQVLKL-----KQLTVLTLAETNKVLPYDELMEEL-------------- 119
             +   P+ V + + KL        T  +   +N  L    +  EL              
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLL 248

Query: 120 ---DVTNVRELEDFLINEC---------------------------MYTGIVRGK-LDQL 148
              +V N +    F ++ C                               +   +    L
Sbjct: 249 VLLNVQNAKAWNAFNLS-CKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL 307

Query: 149 RRCFEVQFAAGRDLRPGQLG------SMI-QTLSNWLTTSDNLLISIQEKIKWA--DSMN 199
            +  + +     DL    L       S+I +++ + L T DN      +K+      S+N
Sbjct: 308 LKYLDCRPQ---DLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLN 364

Query: 200 EMD----KKHRKDL----------------------EEKVEEAKKSLSHKADVDCRGHEE 233
            ++    +K    L                      +  V      L   + V+ +  E 
Sbjct: 365 VLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKES 424

Query: 234 IYSEPGGVMDY 244
             S P   ++ 
Sbjct: 425 TISIPSIYLEL 435

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	253
3chm_A	169	COP9 signalosome complex subunit 7; heat/ARM repea	100.0
4b4t_O	393	26S proteasome regulatory subunit RPN9; hydrolase,	100.0
3txn_A	394	26S proteasome regulatory complex subunit P42B; PC	99.41
4b4t_P	445	26S proteasome regulatory subunit RPN5; hydrolase,	98.98
4b4t_R	429	RPN7, 26S proteasome regulatory subunit RPN7; hydr	98.76
3t5x_A	203	PCI domain-containing protein 2; PCI, mRNA nuclear	98.57
4b4t_Q	434	26S proteasome regulatory subunit RPN6; hydrolase,	98.48
1ufm_A	84	COP9 complex subunit 4; helix-turn-helix, structur	98.35
4b4t_S	523	RPN3, 26S proteasome regulatory subunit RPN3; hydr	97.83
3t5v_B	455	Nuclear mRNA export protein THP1; PCI, mRNA nuclea	97.63
4b0z_A	229	RPN12, 26S proteasome regulatory subunit RPN12; pr	93.63
1wi9_A	72	Protein C20ORF116 homolog; helix-turn-helix motif,	91.95
3df8_A	111	Possible HXLR family transcriptional factor; APC89	85.9
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	85.43
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	83.87
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	80.41
3r0a_A	123	Putative transcriptional regulator; structural gen	80.28
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	80.07

>3chm_A COP9 signalosome complex subunit 7; heat/ARM repeats, winged helix motif, developmental protein, phosphoprotein; 1.50A {Arabidopsis thaliana}

Probab=100.00  E-value=5.4e-51  Score=344.99  Aligned_cols=168  Identities=79%  Similarity=1.223  Sum_probs=158.7

Q ss_pred             cHhHHHHHHHHHHHHhcccccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhhh
Q 025387            2 DIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNA   81 (253)
Q Consensus         2 ~~~~~~~~~l~~fl~lak~~~~~aa~~lI~~AL~~p~vf~F~eLL~~p~v~~L~~t~~~~~~~LL~iFa~Gt~~dy~~~~   81 (253)
                      ++|+++.++||||+.+||++++++|+++|++||.+|++|+|||||.+|+|++|++++++|+++||++|++|||.+|.+++
T Consensus         2 ~~~~~~~~~l~~f~~la~~~~~~~a~~li~~Al~~p~vf~F~eLL~~p~v~~L~~~~~~~~~~LL~iF~~G~~~~y~~~~   81 (169)
T 3chm_A            2 DIEQKQAEIIDQLVKRASTCKSEALGPLIIEATSHPSLFAFSEILALPNVAQLEGTTDSVYLDLLRLFAHGTWGDYKCNA   81 (169)
T ss_dssp             --CCCHHHHHHHHHHHHTTSCGGGHHHHHHHHHHCTTCCCCHHHHTCHHHHTTTTSTTHHHHHHHHHHHHCCHHHHHHHG
T ss_pred             chhHHHHHHHHHHHHHHhcCcHHHHHHHHHHHhcCCCeeehHHHhCChHHHHhcCCChhHHHHHHHHHhcCCHHHHHHhH
Confidence            68999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCC
Q 025387           82 GHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRD  161 (253)
Q Consensus        82 ~~l~~L~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rd  161 (253)
                      +.+|.|++.+.+|||+|||++||..+++|||++|+++|+|+|+++||+||||+||+.|||+|||||++++|+|+|++||+
T Consensus        82 ~~~p~L~~~~~~KlrlLtL~sLa~~~~~lsy~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkiDQ~~~~v~V~~~~~R~  161 (169)
T 3chm_A           82 TRLPHLSPDQILKLKQLTVLTLAESNKVLPYDTLMVELDVSNVRELEDFLINECMYAGIVRGKLDQLKRCFEVPFAAGRD  161 (169)
T ss_dssp             GGSCCCCHHHHHHHHHHHHHHHHHHCSEEEHHHHHHHHTCCSHHHHHHHHHHTHHHHTSEEEEEETTTTEEEEEEECCTT
T ss_pred             HhCcchHHHHHHHHHHHHHHHHHHhCCCcCHHHHHHHhCCCCHHHHHHHHHHHHHHhCCeEEEEcCcCCEEEEEeecCCc
Confidence            89999999999999999999999999999999999999999999999999988999999999999999999999999999


Q ss_pred             CCCCcHHH
Q 025387          162 LRPGQLGS  169 (253)
Q Consensus       162 l~~~q~~~  169 (253)
                      |+++||++
T Consensus       162 l~~~qi~~  169 (169)
T 3chm_A          162 LRPGQLGN  169 (169)
T ss_dssp             CCC-----
T ss_pred             cCHHhccC
Confidence            99999963

>4b4t_O 26S proteasome regulatory subunit RPN9; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=6.8e-35  Score=274.39  Aligned_cols=170  Identities=14%  Similarity=0.320  Sum_probs=118.6

Q ss_pred             cHHHHHHHHHHHhcCCCcccchhhhcCchhhhccC-CCchHHHHHHHHHhcCChhhHhh----hhCCCCCcchH---HHH
Q 025387           22 KGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEG-TENSKYLDMLRLFAHGTWSDYKN----NAGHLPQLVPD---QVL   93 (253)
Q Consensus        22 ~~~aa~~lI~~AL~~p~vf~F~eLL~~p~v~~L~~-t~~~~~~~LL~iFa~Gt~~dy~~----~~~~l~~L~~~---~~~   93 (253)
                      +...|+.+++.||.+|++|+||+|+.+|.+++|++ +++.|+++||++|++||+.+|.+    +.+.+|.|.+.   ..+
T Consensus       210 ~~~~a~~l~~~all~~~i~~f~eLL~~p~i~~L~~~~~~~~l~~Ll~~f~~g~~~~f~~~~~~~~~~~~~l~~~~~~l~~  289 (393)
T 4b4t_O          210 RQQLAYDLSISALLGDKIYNFGELLHHPIMETIVNDSNYDWLFQLLNALTVGDFDKFDSLIKVQISKIPILAQHESFLRQ  289 (393)
T ss_dssp             HHHHHHHHHHHHHHCCSSCSTHHHHHSCCTTSSCSSSSTTHHHHHHHHHHHTCHHHHHHHCCHHHHHSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCCChHHHhCChHHHHhhcCCchHHHHHHHHHHhcCCHHHHHHHHHHhhhhCcchhhhHHHHHH
Confidence            34679999999999999999999999999999975 57999999999999999999976    34566766644   478


Q ss_pred             HHHHHHhhhccc--CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHH
Q 025387           94 KLKQLTVLTLAE--TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMI  171 (253)
Q Consensus        94 KLr~LtLlsLa~--~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~  171 (253)
                      |+|.+++++|+.  +++.|||++|+++|+|+ +++||+||| +||+.|+|+|+|||++++|+|+|++||+|+++||..|.
T Consensus       290 kirll~l~~l~~~~~~~~i~f~~ia~~l~i~-~~evE~lli-~aI~~glI~GkIDQv~~~v~v~~~~pR~~~~~q~~~l~  367 (393)
T 4b4t_O          290 KICLMTLIETVFVKNIRMLSFEDISKATHLP-KDNVEHLVM-RAISLGLLKGSIDQVNELVTISWVQPRIISGDQITKMK  367 (393)
T ss_dssp             HHHHHHHHHHHCSSSCCCEEHHHHHHHHTCC-HHHHHHHHH-HHHHHSCSSSCEETTTTEECC-----------------
T ss_pred             HHHHHHHHHHhccCCCCcCcHHHHHHHhCcC-HHHHHHHHH-HHHHcCCEEEEEcCCCCEEEEEeccCCCCCHHHHHHHH
Confidence            999999999874  57899999999999997 999999999 99999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q 025387          172 QTLSNWLTTSDNLLISIQEKIK  193 (253)
Q Consensus       172 ~~L~~W~~~~~~vl~~Ie~~i~  193 (253)
                      ++|..|+++|++++..|+++..
T Consensus       368 ~~L~~W~~~v~~l~~~ve~~~~  389 (393)
T 4b4t_O          368 DRLVEWNDQVEKLGKKMEARGQ  389 (393)
T ss_dssp             ----------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHhcC
Confidence            9999999999999999998754

>3txn_A 26S proteasome regulatory complex subunit P42B; PCI domain, alpha solenoid, regulatory PART LID, hydrolase, protein binding; 2.50A {Drosophila melanogaster} PDB: 3txm_A

Probab=99.41  E-value=1e-12  Score=123.84  Aligned_cols=159  Identities=11%  Similarity=0.109  Sum_probs=111.5

Q ss_pred             HHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhh----hCCCCC---cc---hHHHH
Q 025387           24 AALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN----AGHLPQ---LV---PDQVL   93 (253)
Q Consensus        24 ~aa~~lI~~AL~~p~vf~F~eLL~~p~v~~L~~t~~~~~~~LL~iFa~Gt~~dy~~~----~~~l~~---L~---~~~~~   93 (253)
                      ..+.-++..+|..-+.+.+++++..|......+++..|+.+|+..|.+|++..|...    .+.+..   +.   ....+
T Consensus       221 ~~lkYlvL~aLl~~~r~el~~~l~~~~~~~~~~pei~~l~~L~~a~~~~dl~~f~~iL~~~~~~l~~D~~l~~h~~~L~~  300 (394)
T 3txn_A          221 TSLKYMLLCKIMLGQSDDVNQLVSGKLAITYSGRDIDAMKSVAEASHKRSLADFQAALKEYKKELAEDVIVQAHLGTLYD  300 (394)
T ss_dssp             HHHHHHHHHHHHTTCGGGHHHHHHSHHHHTTCSHHHHHHHHHHHHHHTTCHHHHHHHHHHSTTTTTTSHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCHHHHHHHhccccccccCCccHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhcChHHHHHHHHHHH
Confidence            356667888888888999999999887665655667899999999999999999863    222221   11   23467


Q ss_pred             HHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHH
Q 025387           94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQT  173 (253)
Q Consensus        94 KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~  173 (253)
                      +++...|+.+..++++|+++.|++.++++ ++++|.+|+ ++|..|.|.|+|||++++|++....+|+   ...+...+.
T Consensus       301 ~Ir~~~L~~i~~pYsrIsl~~iA~~l~ls-~~evE~~L~-~lI~dg~I~a~IDq~~giv~~~~~~~r~---~~y~~ale~  375 (394)
T 3txn_A          301 TMLEQNLCRIIEPYSRVQVAHVAESIQLP-MPQVEKKLS-QMILDKKFSGILDQGEGVLIVFEETPVD---KTYERVLET  375 (394)
T ss_dssp             HHHHHHHHHHHTTCSEEEHHHHHHHHTCC-HHHHHHHHH-HHHHTTSSCEEEETTTTEEEECCC----------------
T ss_pred             HHHHHHHHHHhHhhceeeHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeeEEEcCCCCEEEECCCcchh---hHHHHHHHH
Confidence            88899999999999999999999999996 999999999 9999999999999999999998776665   345556778


Q ss_pred             HHHHHHHHHHHHHH
Q 025387          174 LSNWLTTSDNLLIS  187 (253)
Q Consensus       174 L~~W~~~~~~vl~~  187 (253)
                      +.+|...++.++..
T Consensus       376 l~~ls~vVd~L~~~  389 (394)
T 3txn_A          376 IQSMGKVVDTLYQK  389 (394)
T ss_dssp             --------------
T ss_pred             HHHHHHHHHHHHHH
Confidence            99999988877653

>4b4t_P 26S proteasome regulatory subunit RPN5; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.98  E-value=8.4e-10  Score=104.86  Aligned_cols=161  Identities=14%  Similarity=0.152  Sum_probs=98.6

Q ss_pred             HHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhh----hhCCCC---Cc---------
Q 025387           24 AALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKN----NAGHLP---QL---------   87 (253)
Q Consensus        24 ~aa~~lI~~AL~~p~vf~F~eLL~~p~v~~L~~t~~~~~~~LL~iFa~Gt~~dy~~----~~~~l~---~L---------   87 (253)
                      .+...+|...+.+|..-.++.++.-+.... ...+...+..|+.+|..+.+..|..    +...+.   ..         
T Consensus       259 ~~L~~~v~~~iLa~~~~~~~~ll~~~~~~~-~~~~l~~~~~L~k~f~~~~L~~~~~~~~~~~~~L~~~~~~~~~~~~~~~  337 (445)
T 4b4t_P          259 PVLSHIVYFLVLSPYGNLQNDLIHKIQNDN-NLKKLESQESLVKLFTTNELMRWPIVQKTYEPVLNEDDLAFGGEANKHH  337 (445)
T ss_dssp             HHHHHHHHHHHHSSCSSTTHHHHHSHHHHS-SCHHHHHHHHHHHHHHHCCSSSHHHHHHHTCSSTTTCCSSCCCSCSSHH
T ss_pred             HHHHHHHHHHHhCCCCchHHHHHHHHhhcc-cccccHHHHHHHHHHHhchHhhhHHHHHHHHHHhcccchhhhcchhhHH
Confidence            356667778888888888888886543211 1123567899999999999887764    222111   11         


Q ss_pred             chHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcH
Q 025387           88 VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQL  167 (253)
Q Consensus        88 ~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~  167 (253)
                      .....+.++...|..++..++.|+++.|++.|+++ ++++|.++. ++|..|.|.|+|||++|+|++....+        
T Consensus       338 ~~~L~~~v~ehnl~~i~k~Ys~I~l~~la~lL~l~-~~evE~~ls-~mI~~g~i~akIDq~~giV~F~~~~~--------  407 (445)
T 4b4t_P          338 WEDLQKRVIEHNLRVISEYYSRITLLRLNELLDLT-ESQTETYIS-DLVNQGIIYAKVNRPAKIVNFEKPKN--------  407 (445)
T ss_dssp             HHHHHHHHHHHHHHHHHHHEEEEEHHHHHHHHTSC-HHHHHHHHH-HHHHHTSSCCEEETTTTEEEC-------------
T ss_pred             HHHHHHHHHHHHHHHHHHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCEEEEEcCCCCEEEECCCCC--------
Confidence            12346677778888999999999999999999997 999999999 99999999999999999887654321        


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025387          168 GSMIQTLSNWLTTSDNLLISIQEKIKWADS  197 (253)
Q Consensus       168 ~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~  197 (253)
                        -.+.|..|.+++++++..|+.-.+-.++
T Consensus       408 --~~~~l~~W~~~i~~l~~~v~k~~~lI~k  435 (445)
T 4b4t_P          408 --SSQLLNEWSHNVDELLEHIETIGHLITK  435 (445)
T ss_dssp             ------------------------------
T ss_pred             --hHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence              2357899999999999999765555554

>4b4t_R RPN7, 26S proteasome regulatory subunit RPN7; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.76  E-value=3.6e-08  Score=92.96  Aligned_cols=153  Identities=14%  Similarity=0.136  Sum_probs=96.6

Q ss_pred             HHHHHHHHHhcCCCcccc-hhhhcCchhhhcc-CCC-chHHHHHHHHHhcCChhhHhhh-----hCC------CCCcchH
Q 025387           25 ALGSVIVEATSQPSLFAF-SEILAVPNIAEFE-GTE-NSKYLDMLRLFAHGTWSDYKNN-----AGH------LPQLVPD   90 (253)
Q Consensus        25 aa~~lI~~AL~~p~vf~F-~eLL~~p~v~~L~-~t~-~~~~~~LL~iFa~Gt~~dy~~~-----~~~------l~~L~~~   90 (253)
                      .+.-.+.-++..++--.+ ..++.-|.+...- ..+ ..++.+++..|-.+.+..|...     ...      +.+-...
T Consensus       249 ~~~y~~l~al~~~~r~~l~~~v~~~~~~~~~l~~~p~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~d~~l~~h~~~  328 (429)
T 4b4t_R          249 IATYASVTGLFTLERTDLKSKVIDSPELLSLISTTAALQSISSLTISLYASDYASYFPYLLETYANVLIPCKYLNRHADF  328 (429)
T ss_dssp             HHHHHHHHHHHTTCHHHHHHSSSSSHHHHHGGGSHHHHHHHHHHHHHHHHTCHHHHHHHHHHHHSTTTTTCTTSTTTHHH
T ss_pred             HHHHHHHHHHhcCCHHHHHHHHhcCHHHHhhccCChhHHHHHHHHHHHHhccHHHHHHHHHHHHHhhhccCHHHHHHHHH
Confidence            344455555555444332 2355556554433 222 3567788888888988886531     111      1122345


Q ss_pred             HHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHH
Q 025387           91 QVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSM  170 (253)
Q Consensus        91 ~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l  170 (253)
                      ..+.+|...++.++.++++|+++.+++.++++ +.++|.++. +.|..|-|.|||||++|+|++....+|.         
T Consensus       329 l~~~ir~~~l~q~~~~Ys~I~l~~mA~~l~~s-~~~~E~~L~-~lI~~g~l~akID~~~giv~~~~~d~~~---------  397 (429)
T 4b4t_R          329 FVREMRRKVYAQLLESYKTLSLKSMASAFGVS-VAFLDNDLG-KFIPNKQLNCVIDRVNGIVETNRPDNKN---------  397 (429)
T ss_dssp             HHHHHHHHHHHHHHHTCSEEEHHHHHHHHTSC-HHHHHHHHH-HHHHHTSSCEEEETTTTEEEECC--------------
T ss_pred             HHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHcCCeEEEEcCCCCEEEECCCCchh---------
Confidence            78999999999999999999999999999997 999999999 9999999999999999999988776664         


Q ss_pred             HHHHHHHHHHHHHHHHHHH
Q 025387          171 IQTLSNWLTTSDNLLISIQ  189 (253)
Q Consensus       171 ~~~L~~W~~~~~~vl~~Ie  189 (253)
                       ...+.|.+..+.+++.|+
T Consensus       398 -~~y~~~i~~gd~Ll~riq  415 (429)
T 4b4t_R          398 -AQYHLLVKQGDGLLTKLQ  415 (429)
T ss_dssp             -------------------
T ss_pred             -HHHHHHHHHHHHHHHHHH
Confidence             234445555555555444

>3t5x_A PCI domain-containing protein 2; PCI, mRNA nuclear export, transcription; 2.12A {Homo sapiens}

Probab=98.57  E-value=2.7e-08  Score=85.56  Aligned_cols=97  Identities=18%  Similarity=0.232  Sum_probs=77.2

Q ss_pred             hHHHHHHHHHhcCChhhHhhhh----CCCC-CcchHHHHHHHHHHhhhccc------CCcccChHHHHHHcCCC-----C
Q 025387           60 SKYLDMLRLFAHGTWSDYKNNA----GHLP-QLVPDQVLKLKQLTVLTLAE------TNKVLPYDELMEELDVT-----N  123 (253)
Q Consensus        60 ~~~~~LL~iFa~Gt~~dy~~~~----~~l~-~L~~~~~~KLr~LtLlsLa~------~~k~Isy~~I~~~L~I~-----~  123 (253)
                      ..+.+|...+..||+..|.+.-    +.+. .-.--.+.|+|.+.+.+|..      ++..||++.|+.+|++.     +
T Consensus        81 ~~y~~L~~Avr~Gdl~~f~~~l~~~~~~f~~~~~~lll~rlr~~v~r~l~rkv~~~~~~~rI~l~~i~~~l~~~~~~~~~  160 (203)
T 3t5x_A           81 MQFAEVTRAVSEGNLLLLHEALAKHEAFFIRCGIFLILEKLKIITYRNLFKKVYLLLKTHQLSLDAFLVALKFMQVEDVD  160 (203)
T ss_dssp             GGGHHHHHHHHHTCHHHHHHHHHHTHHHHHHHTCHHHHHTHHHHHHHHHHHHHHHHHCCSEEEHHHHHHHHHHTTCTTCC
T ss_pred             hHHHHHHHHHHhCCHHHHHHHHHHhHHHHHHCChHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCCC
Confidence            3588999999999999998622    1111 11112468888888877765      68899999999999652     5


Q ss_pred             hHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025387          124 VRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA  157 (253)
Q Consensus       124 ~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~  157 (253)
                      .+|||.+|. .+|+.|.|+|+||+.++++.++..
T Consensus       161 ~~evE~ila-~lI~~G~Ikg~I~~~~~~lVlsk~  193 (203)
T 3t5x_A          161 IDEVQCILA-NLIYMGHVKGYISHQHQKLVVSKQ  193 (203)
T ss_dssp             HHHHHHHHH-HHHHHTSSCEEEETTTTEEEECSS
T ss_pred             HHHHHHHHH-HHHHcCceEEEEcccccEEEECCC
Confidence            899999999 899999999999999999988754

>4b4t_Q 26S proteasome regulatory subunit RPN6; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=98.48  E-value=1.4e-07  Score=85.02  Aligned_cols=124  Identities=13%  Similarity=0.111  Sum_probs=79.3

Q ss_pred             chHHHHHHHHHhcCChhhHhhhhCC----CCC------cchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHH
Q 025387           59 NSKYLDMLRLFAHGTWSDYKNNAGH----LPQ------LVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELE  128 (253)
Q Consensus        59 ~~~~~~LL~iFa~Gt~~dy~~~~~~----l~~------L~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE  128 (253)
                      ..++..++..|..+++..|......    +..      ........++...+..++..++.|+++.|++.|+++ ++++|
T Consensus       296 ~~~~~~l~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~l~~~~~~y~~i~l~~la~~l~~~-~~~~E  374 (434)
T 4b4t_Q          296 IDAMKAVAEAYNNRSLLDFNTALKQYEKELMGDELTRSHFNALYDTLLESNLCKIIEPFECVEISHISKIIGLD-TQQVE  374 (434)
T ss_dssp             HHHHHHHHHHHHHTCHHHHHHHHHHTHHHHTCSHHHHHHHHHHHHHHHHHHHHHHHSSCSCEEHHHHHHHHTCC-HHHHH
T ss_pred             hhHHHHHHHHHHhhhHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHhCcC-HHHHH
Confidence            4678889999999999998863211    111      113345677888899999999999999999999997 99999


Q ss_pred             HHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025387          129 DFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW  194 (253)
Q Consensus       129 ~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~  194 (253)
                      .+|. ++|..|.|.|+|||.+++|++.....++          .....|.+.++++...++.....
T Consensus       375 ~~l~-~lI~~~~i~a~id~~~g~v~~~~~~~~~----------~~~~~~l~~~~~l~~~vd~L~~k  429 (434)
T 4b4t_Q          375 GKLS-QMILDKIFYGVLDQGNGWLYVYETPNQD----------ATYDSALELVGQLNKVVDQLFEK  429 (434)
T ss_dssp             HHHH-HHHHHTSSCCEEETTTTEEECC---------------------------------------
T ss_pred             HHHH-HHHhCCCcceecccccCeEeeCCCcchh----------HHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999 9999999999999999999986554443          23455666666655555544333

>1ufm_A COP9 complex subunit 4; helix-turn-helix, structural genomics, riken structural genomics/proteomics initiative, RSGI, signaling protein; NMR {Mus musculus} SCOP: a.4.5.47

Probab=98.35  E-value=1.1e-06  Score=65.69  Aligned_cols=62  Identities=15%  Similarity=0.261  Sum_probs=54.1

Q ss_pred             HHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025387           94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA  157 (253)
Q Consensus        94 KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~  157 (253)
                      ++..-.|..+++.++.|+++.|++.++++ .+++|.++. ++|..|-|.|+|||++++|.+...
T Consensus        15 ~v~E~nl~~is~~Y~~Isl~~La~ll~ls-~~~vE~~ls-~mI~~~~l~akIDq~~g~V~f~~~   76 (84)
T 1ufm_A           15 AVIEHNLLSASKLYNNITFEELGALLEIP-AAKAEKIAS-QMITEGRMNGFIDQIDGIVHFETR   76 (84)
T ss_dssp             HHHHHHHHHHHHSCSEEEHHHHHHHTTSC-HHHHHHHHH-HHHHTTSSCEEEETTTTEEEECCS
T ss_pred             HHHHHHHHHHHHhcCeeeHHHHHHHHCcC-HHHHHHHHH-HHHhCCcEEEEEeCCCCEEEeCCc
Confidence            34444555677899999999999999998 999999999 999999999999999999987543

>4b4t_S RPN3, 26S proteasome regulatory subunit RPN3; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=97.83  E-value=1.7e-05  Score=77.04  Aligned_cols=94  Identities=12%  Similarity=0.239  Sum_probs=71.8

Q ss_pred             hHHHHHHHHHhcCChhhHhhh----hCC-CCCcchHHHHHHHHH----HhhhcccCCcccChHHHHHHcCCCChHHHHHH
Q 025387           60 SKYLDMLRLFAHGTWSDYKNN----AGH-LPQLVPDQVLKLKQL----TVLTLAETNKVLPYDELMEELDVTNVRELEDF  130 (253)
Q Consensus        60 ~~~~~LL~iFa~Gt~~dy~~~----~~~-l~~L~~~~~~KLr~L----tLlsLa~~~k~Isy~~I~~~L~I~~~~evE~l  130 (253)
                      .+|+.|..+|..|++..|.+.    ... ...=+-..+.++|+.    -|..+...+..||+++|+..|++++.+++|.+
T Consensus       343 ~pY~~Lv~Avr~GdL~~F~~~L~~h~~~F~~Dgty~LI~rLr~~vir~~irkis~~YsrIsL~dIa~kL~L~s~eeaE~i  422 (523)
T 4b4t_S          343 LPYYHLTKAVKLGDLKKFTSTITKYKQLLLKDDTYQLCVRLRSNVIKTGIRIISLTYKKISLRDICLKLNLDSEQTVEYM  422 (523)
T ss_dssp             HHHHHHHHHHHHTCHHHHHHHHHHTHHHHHHTTCTHHHHHHHHHHHHHHHHHSCCCSSEECHHHHHHHHHHHHSSCHHHH
T ss_pred             HHHHHHHHHHHcCCHHHHHHHHHHhcceeccCChhHHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHhCCCCHHHHHHH
Confidence            569999999999999999862    111 111111234444443    34556667899999999999999878899999


Q ss_pred             HHHHhHhcCccEEEecCCCCEEEE
Q 025387          131 LINECMYTGIVRGKLDQLRRCFEV  154 (253)
Q Consensus       131 lI~~AI~~gLI~GkIDQ~~~~v~V  154 (253)
                      |- ++|+.|.|+|+|||.++.|..
T Consensus       423 VA-kmI~dG~I~A~Idh~~g~v~s  445 (523)
T 4b4t_S          423 VS-RAIRDGVIEAKINHEDGFIET  445 (523)
T ss_dssp             HH-HHHHHTSSCCEECTTTCCEEC
T ss_pred             HH-HHHHcCCceEEEecCCCEEEe
Confidence            99 999999999999999997753

>3t5v_B Nuclear mRNA export protein THP1; PCI, mRNA nuclear export, mRNA, nuclear, transcription; 2.90A {Saccharomyces cerevisiae}

Probab=97.63  E-value=2.2e-05  Score=75.08  Aligned_cols=95  Identities=16%  Similarity=0.161  Sum_probs=72.6

Q ss_pred             HHHHHHHHhcCChhhHhhh----hCC-CCCcc-hHHHHHHHHHHhhhcc----------cCCcccChHHHHHHcCC----
Q 025387           62 YLDMLRLFAHGTWSDYKNN----AGH-LPQLV-PDQVLKLKQLTVLTLA----------ETNKVLPYDELMEELDV----  121 (253)
Q Consensus        62 ~~~LL~iFa~Gt~~dy~~~----~~~-l~~L~-~~~~~KLr~LtLlsLa----------~~~k~Isy~~I~~~L~I----  121 (253)
                      +..|...+..||+..|.+.    ... +..=. --.+.|+|++++-.|.          .+...||++.|+.+|++    
T Consensus       299 y~~L~~AVr~Gdl~~F~~~L~~~~~~f~~~gily~LlerLr~~v~RnLirkv~~~~~~~~~~srI~l~~i~~aL~~~~~~  378 (455)
T 3t5v_B          299 WSVLYKHVRYGNIQGVSLWLRQNERHLCARQLLIVLLEKLPMVTYRNLIKTVIKSWTTEWGQNKLPYSLIERVLQLSIGP  378 (455)
T ss_dssp             HHHHHHHHHHTCHHHHHHHHHHTHHHHHHTTCHHHHHHHHHHHHHHHHHHHHHHHHTTTTCCCEEEHHHHHHHHHHHHCC
T ss_pred             HHHHHHHHHhCCHHHHHHHHHHhHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeeeHHHHHHHHhhccCc
Confidence            7889999999999999873    211 11112 3446777776543332          23479999999999984    


Q ss_pred             ----------------CChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025387          122 ----------------TNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA  157 (253)
Q Consensus       122 ----------------~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~  157 (253)
                                      .+.+|||.+|. .+|+.|+|+|+||+.++++.++..
T Consensus       379 ~~~~~~~~~~~~~~~~~~~devEcIlA-~LI~~G~IkGyIsh~~~~lVlSK~  429 (455)
T 3t5v_B          379 TFEDPGAQEITIYNGIHSPKNVENVLV-TLINLGLLRANCFPQLQLCVVKKT  429 (455)
T ss_dssp             CTTSTTCCCCCTTTSSCCSSCHHHHHH-HHHHHTSCCEEEETTTTEEEECCC
T ss_pred             cccccccccccccccCCCHHHHHHHHH-HHHHcCCeEEEEecCCCEEEECCC
Confidence                            24889999999 899999999999999999998765

>4b0z_A RPN12, 26S proteasome regulatory subunit RPN12; protein binding, proteasome ubitquitin; HET: SGM GOL; 1.58A {Schizosaccharomyces pombe}

Probab=93.63  E-value=0.1  Score=45.03  Aligned_cols=107  Identities=13%  Similarity=0.120  Sum_probs=72.1

Q ss_pred             HHHHHHHHhcCCCcccchhhhc-CchhhhccCCC-chHHHHHHHHHhcCChhhHhhhhCCCCC-----cchHHHHHHHHH
Q 025387           26 LGSVIVEATSQPSLFAFSEILA-VPNIAEFEGTE-NSKYLDMLRLFAHGTWSDYKNNAGHLPQ-----LVPDQVLKLKQL   98 (253)
Q Consensus        26 a~~lI~~AL~~p~vf~F~eLL~-~p~v~~L~~t~-~~~~~~LL~iFa~Gt~~dy~~~~~~l~~-----L~~~~~~KLr~L   98 (253)
                      +..++.. |.-.++-.|.-.+. +|.-..+++++ -...+++-+.+..|+|..|-......|.     +.+-...++|.-
T Consensus       101 ~~~LL~l-L~~~~~~ef~~~le~l~~~~~~~~~~~I~~al~l~~al~~GnY~kff~l~~~~p~~~~~~~~~~l~~~vR~~  179 (229)
T 4b0z_A          101 GLNLLYL-LSENRIAEFHTALESVPDKSLFERDPYVEWVISLEQNVMEGAFDKVASMIRSCNFPEFSYFMKIVMSMVRNE  179 (229)
T ss_dssp             HHHHHHH-HHTTCHHHHHHHHHHCSCTTHHHHCHHHHHHHHHHHHHHTTCHHHHHHHHHTCCCGGGHHHHHHHHHHHHHH
T ss_pred             HHHHHHH-HHcCCchHHHHHHHhcChHHHhhcCHHHHHHHHHHHHHHcCCHHHHHHHHhcCccchHHHHHHHHHHHHHHH
Confidence            4444443 33334555543332 33222223333 2456789999999999998775444453     223457788888


Q ss_pred             HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHH
Q 025387           99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINE  134 (253)
Q Consensus        99 tLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~  134 (253)
                      .+-+++..+..||.+++++.|+++|.++++.++- +
T Consensus       180 ~l~~i~kaY~~i~l~~~~~~L~f~s~~e~~~f~~-~  214 (229)
T 4b0z_A          180 IATCAEKVYSEIPLSNATSLLYLENTKETEKLAE-E  214 (229)
T ss_dssp             HHHHHHHHCSEEEHHHHHHHTTCSSHHHHHHHHH-H
T ss_pred             HHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHH-H
Confidence            8888888889999999999999999999999988 6

>1wi9_A Protein C20ORF116 homolog; helix-turn-helix motif, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: a.4.5.47

Probab=91.95  E-value=0.19  Score=36.14  Aligned_cols=54  Identities=11%  Similarity=0.280  Sum_probs=46.4

Q ss_pred             hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025387          100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ  155 (253)
Q Consensus       100 LlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~  155 (253)
                      ++.....+++++.++||.++++. ..++-+-|- +....|.|.|-||...+-++|+
T Consensus        12 Fi~yIk~~Kvv~LedLA~~F~l~-t~~~i~RI~-~Le~~g~ltGViDDRGKfIyIs   65 (72)
T 1wi9_A           12 FINYIKKSKVVLLEDLAFQMGLR-TQDAINRIQ-DLLTEGTLTGVIDDRGKFIYIT   65 (72)
T ss_dssp             HHHHHHHCSEECHHHHHHHHCSC-HHHHHHHHH-HHHHHSSSCEEECTTCCEEECC
T ss_pred             HHHHHHHcCeeeHHHHHHHhCCC-hHHHHHHHH-HHHHCCCeEEEEeCCCCEEEec
Confidence            34555678999999999999998 777777777 8888999999999999998886

>3df8_A Possible HXLR family transcriptional factor; APC89000, structural genomics, midwest center for structural genomics, MCSG; 1.65A {Thermoplasma volcanium} SCOP: a.4.5.0

Probab=85.90  E-value=3.3  Score=31.01  Aligned_cols=81  Identities=11%  Similarity=0.206  Sum_probs=52.1

Q ss_pred             HHHHHHHhhhcccCCcccChHHHHHHc-CCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHH
Q 025387           93 LKLKQLTVLTLAETNKVLPYDELMEEL-DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMI  171 (253)
Q Consensus        93 ~KLr~LtLlsLa~~~k~Isy~~I~~~L-~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~  171 (253)
                      .|-|.+.|..|......++|.+|++.+ +|+ ..-|=.-+= .....|+|.-+.+  .++.+--.-.++.     +....
T Consensus        26 ~~wrl~IL~~L~~g~~~~~~~eL~~~l~gis-~~~ls~~L~-~Le~~GlV~r~~~--r~~~y~LT~~G~~-----l~~~l   96 (111)
T 3df8_A           26 KKYTMLIISVLGNGSTRQNFNDIRSSIPGIS-STILSRRIK-DLIDSGLVERRSG--QITTYALTEKGMN-----VRNSL   96 (111)
T ss_dssp             STTHHHHHHHHTSSSSCBCHHHHHHTSTTCC-HHHHHHHHH-HHHHTTSEEEEES--SSEEEEECHHHHH-----HHHHH
T ss_pred             CccHHHHHHHHhcCCCCCCHHHHHHHccCCC-HHHHHHHHH-HHHHCCCEEEeec--CcEEEEECccHHH-----HHHHH
Confidence            344554555555444446699999999 897 777766666 7788999999888  2222211222332     44567


Q ss_pred             HHHHHHHHHHH
Q 025387          172 QTLSNWLTTSD  182 (253)
Q Consensus       172 ~~L~~W~~~~~  182 (253)
                      ..+..|....+
T Consensus        97 ~~l~~w~~~~~  107 (111)
T 3df8_A           97 MPLLQYISVLD  107 (111)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHhc
Confidence            77888877543

>2hzt_A Putative HTH-type transcriptional regulator YTCD; DNA-binding protein, HTH-type transcription regulators, structural genomics, PSI-2; HET: CSU MSE; 2.00A {Bacillus subtilis} SCOP: a.4.5.69

Probab=85.43  E-value=5.9  Score=29.17  Aligned_cols=69  Identities=14%  Similarity=0.092  Sum_probs=48.3

Q ss_pred             CcccChHHHHHHc-CCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHH
Q 025387          107 NKVLPYDELMEEL-DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTT  180 (253)
Q Consensus       107 ~k~Isy~~I~~~L-~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~  180 (253)
                      ....++.+|++.+ +++ ...|=..|= .....|+|..+-+..++....-+.++.  + .++-.....+..|...
T Consensus        25 ~~~~~~~eLa~~l~~is-~~tls~~L~-~Le~~GlI~r~~~~~d~r~~~y~LT~~--G-~~l~~~~~~l~~w~~~   94 (107)
T 2hzt_A           25 HGKKRTSELKRLMPNIT-QKMLTQQLR-ELEADGVINRIVYNQVPPKVEYELSEY--G-RSLEGILDMLXAWGAN   94 (107)
T ss_dssp             TCCBCHHHHHHHCTTSC-HHHHHHHHH-HHHHTTSEEEEEECSSSCEEEEEECTT--G-GGGHHHHHHHHHHHHH
T ss_pred             hCCCCHHHHHHHhcCCC-HHHHHHHHH-HHHHCCCEEEeecCCCCCeEEEEECcc--H-HHHHHHHHHHHHHHHH
Confidence            3578999999999 997 777776666 788899999998876654433333332  1 2234556777788754

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=83.87  E-value=2.9  Score=30.17  Aligned_cols=58  Identities=14%  Similarity=0.175  Sum_probs=41.4

Q ss_pred             HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025387           95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ  155 (253)
Q Consensus        95 Lr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~  155 (253)
                      .+.|.++.-..+++.+++.+||+.|+++ ...|...|- +....|+|.-. +.....-.|.
T Consensus        13 ~~IL~~L~~~~pg~~~t~~eLA~~Lgvs-r~tV~~~L~-~Le~~G~I~~~-g~~~~~W~i~   70 (81)
T 1qbj_A           13 QRILKFLEELGEGKATTAHDLSGKLGTP-KKEINRVLY-SLAKKGKLQKE-AGTPPLWKIA   70 (81)
T ss_dssp             HHHHHHHHHHCTTCCBCHHHHHHHHTCC-HHHHHHHHH-HHHHTTSEEEE-SSSSCEEEEC
T ss_pred             HHHHHHHHHcCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEec-CCCCCeeEEe
Confidence            3345555533456799999999999997 899999888 88889998643 3444444443

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=80.41  E-value=1.1  Score=34.37  Aligned_cols=71  Identities=15%  Similarity=0.320  Sum_probs=42.5

Q ss_pred             CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE---ecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHH
Q 025387          106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK---LDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWL  178 (253)
Q Consensus       106 ~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~Gk---IDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~  178 (253)
                      .+..+|+.+|++.++++ ...+=..+= .....|+|.+.   +|...--..++....-.+.+.....+.+.|..|-
T Consensus        15 ~~~~~~~~ela~~lg~s-~~tv~~~l~-~L~~~G~i~~~~~~~~~~~~g~~~~~~v~~~~~~~~~~~~~~~l~~~~   88 (141)
T 1i1g_A           15 KDARTPFTEIAKKLGIS-ETAVRKRVK-ALEEKGIIEGYTIKINPKKLGYSLVTITGVDTKPEKLFEVAEKLKEYD   88 (141)
T ss_dssp             HCTTCCHHHHHHHHTSC-HHHHHHHHH-HHHHHTSSCCCCCCCCSGGGTCCEEEEEEEEECGGGHHHHHHHHHHST
T ss_pred             HcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEeccccccChHHhCccEEEEEEEEECchhHHHHHHHHhcCC
Confidence            34568999999999997 777766666 77778999765   3332111111110000113356667777777763

>3r0a_A Putative transcriptional regulator; structural genomics, PSI-biology, midwest center for structu genomics, MCSG; 2.31A {Methanosarcina mazei}

Probab=80.28  E-value=3.2  Score=31.68  Aligned_cols=82  Identities=10%  Similarity=0.098  Sum_probs=55.1

Q ss_pred             hcccCCcc-cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCC--CCEEEEEeecCCCCCCCcHHHHHHHHHHHH
Q 025387          102 TLAETNKV-LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQL--RRCFEVQFAAGRDLRPGQLGSMIQTLSNWL  178 (253)
Q Consensus       102 sLa~~~k~-Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~--~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~  178 (253)
                      .|...... ++-.+|++.++++ ...|-..|= .....|+|.-.-+..  .+..++..+.+.   .+-.+.+...+..|.
T Consensus        34 ~L~~~~~~~~t~~eLa~~l~~s-~sTV~r~L~-~L~~~GlV~r~~~~~d~~~~~~~y~~~~~---~~~~~~i~~~~~~~~  108 (123)
T 3r0a_A           34 SFLNEPDRWIDTDALSKSLKLD-VSTVQRSVK-KLHEKEILQRSQQNLDGGGYVYIYKIYSK---NQIRNIIQKIVQSWA  108 (123)
T ss_dssp             HHHHSTTCCEEHHHHHHHHTSC-HHHHHHHHH-HHHHTTSEEEEEEECTTSCEEEEEEECCH---HHHHHHHHHHHHHHH
T ss_pred             HHHHCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEeeCCccCCCcceEEEecCCH---HHHHHHHHHHHHHHH
Confidence            34444455 9999999999997 888877766 788899998765443  233333333221   122455788899999


Q ss_pred             HHHHHHHHHH
Q 025387          179 TTSDNLLISI  188 (253)
Q Consensus       179 ~~~~~vl~~I  188 (253)
                      +.+...++.+
T Consensus       109 ~~~~~~l~~~  118 (123)
T 3r0a_A          109 DRLGQELKEW  118 (123)
T ss_dssp             HHHHHTTTTT
T ss_pred             HHHHHHHHHH
Confidence            8887766544

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=80.07  E-value=4  Score=28.90  Aligned_cols=47  Identities=17%  Similarity=0.186  Sum_probs=37.4

Q ss_pred             HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 025387           97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL  145 (253)
Q Consensus        97 ~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkI  145 (253)
                      .|.++.-...+..+++.+||+.|+++ ...|...|= +....|+|.+.-
T Consensus        19 IL~~L~~~~~~~~~t~~eLA~~Lgvs-~~tV~~~L~-~L~~~G~I~~~g   65 (77)
T 1qgp_A           19 ILKFLEELGEGKATTAHDLSGKLGTP-KKEINRVLY-SLAKKGKLQKEA   65 (77)
T ss_dssp             HHHHHHHHCSSSCEEHHHHHHHHCCC-HHHHHHHHH-HHHHHTSEEEEC
T ss_pred             HHHHHHHcCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEecC
Confidence            44555444446689999999999998 899998877 888999998864

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	253
d1ufma_	84	COP9 signalosome complex subunit 4, GSN4 {Mouse (M	98.42
d1wi9a_	72	Hypothetical protein C20orf116 homolog {Mouse (Mus	89.91
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	88.98
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	88.38
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	87.83
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	87.34
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	86.24

>d1ufma_ a.4.5.47 (A:) COP9 signalosome complex subunit 4, GSN4 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: COP9 signalosome complex subunit 4, GSN4
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.42  E-value=2.6e-07  Score=67.26  Aligned_cols=63  Identities=14%  Similarity=0.245  Sum_probs=56.1

Q ss_pred             HHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025387           93 LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA  157 (253)
Q Consensus        93 ~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~  157 (253)
                      +.++...|..++..+.+|+++.|++.|+++ .+++|.+|. ++|..|-|.|+|||.+++|+++.-
T Consensus        14 ~~i~Ehni~~is~~Y~~Isl~~la~~l~l~-~~evE~~l~-~mI~~~~i~akIDq~~g~V~F~~~   76 (84)
T d1ufma_          14 RAVIEHNLLSASKLYNNITFEELGALLEIP-AAKAEKIAS-QMITEGRMNGFIDQIDGIVHFETR   76 (84)
T ss_dssp             HHHHHHHHHHHHHSCSEEEHHHHHHHTTSC-HHHHHHHHH-HHHHTTSSCEEEETTTTEEEECCS
T ss_pred             HHHHHHHHHHHHHhhceeeHHHHHHHHCCC-HHHHHHHHH-HHHhcCeEEEEEeCCCCEEEECCC
Confidence            445556677788899999999999999997 999999999 999999999999999999988754

>d1wi9a_ a.4.5.47 (A:) Hypothetical protein C20orf116 homolog {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PCI domain (PINT motif)
domain: Hypothetical protein C20orf116 homolog
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.91  E-value=0.17  Score=34.51  Aligned_cols=57  Identities=11%  Similarity=0.243  Sum_probs=46.4

Q ss_pred             hhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecC
Q 025387          101 LTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAG  159 (253)
Q Consensus       101 lsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~  159 (253)
                      +......|+++.++|+.+.++. ..++=+-|- +....|.|.|-||...+-++|+-+-|
T Consensus        13 I~~Ik~~Kvv~LedLAa~F~lk-tqd~i~RIq-~Le~~g~ltGViDDRGKfIyIS~s~~   69 (72)
T d1wi9a_          13 INYIKKSKVVLLEDLAFQMGLR-TQDAINRIQ-DLLTEGTLTGVIDDRGKFIYITPSGP   69 (72)
T ss_dssp             HHHHHHCSEECHHHHHHHHCSC-HHHHHHHHH-HHHHHSSSCEEECTTCCEEECCCSSC
T ss_pred             HHHHHHCCEeeHHHHHHHcCCc-HHHHHHHHH-HHHHCCCeeeEEcCCCCEEEEcCCCC
Confidence            3445578999999999999998 666555666 78889999999999999999875543

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=88.98  E-value=0.18  Score=33.16  Aligned_cols=42  Identities=12%  Similarity=0.218  Sum_probs=34.5

Q ss_pred             hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025387          100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG  143 (253)
Q Consensus       100 LlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~G  143 (253)
                      |+..-..+..+||.+|++.++++ ...|-.-+= +....|+|.|
T Consensus        10 IL~~L~~n~r~s~~~iA~~lgis-~~tv~~Ri~-~L~~~giI~~   51 (63)
T d2cfxa1          10 IIEELKKDSRLSMRELGRKIKLS-PPSVTERVR-QLESFGIIKQ   51 (63)
T ss_dssp             HHHHHHHCSCCCHHHHHHHHTCC-HHHHHHHHH-HHHHTTSEEE
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeee
Confidence            34434456788999999999998 899988777 8899999987

>d2cg4a1 a.4.5.32 (A:4-66) Regulatory protein AsnC {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Regulatory protein AsnC
species: Escherichia coli [TaxId: 562]

Probab=88.38  E-value=0.19  Score=32.95  Aligned_cols=43  Identities=21%  Similarity=0.299  Sum_probs=35.3

Q ss_pred             hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025387          100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK  144 (253)
Q Consensus       100 LlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~Gk  144 (253)
                      |+++-+.+..+||.+|++.++++ ...|-.=+= +....|+|.|.
T Consensus        10 IL~~L~~~~r~s~~eiA~~l~ls-~~~v~~Ri~-rL~~~GiI~~~   52 (63)
T d2cg4a1          10 ILEALMGNARTAYAELAKQFGVS-PETIHVRVE-KMKQAGIITGA   52 (63)
T ss_dssp             HHHHHHHCTTSCHHHHHHHHTSC-HHHHHHHHH-HHHHHTSEEEE
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEeE
Confidence            44444566889999999999997 889988777 88889999864

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=87.83  E-value=0.17  Score=32.76  Aligned_cols=42  Identities=7%  Similarity=0.256  Sum_probs=33.4

Q ss_pred             hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025387          100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG  143 (253)
Q Consensus       100 LlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~G  143 (253)
                      |+.+-+.+..+||.+|++.|+++ ...|-.-+= +....|+|.|
T Consensus         8 Il~~L~~n~r~s~~eiA~~l~ls-~~~v~~Ri~-~L~~~giI~~   49 (60)
T d2cyya1           8 IIKILQNDGKAPLREISKITGLA-ESTIHERIR-KLRESGVIKK   49 (60)
T ss_dssp             HHHHHHHCTTCCHHHHHHHHCSC-HHHHHHHHH-HHHHHTSSCC
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEe
Confidence            44444567888999999999997 888887766 7778898874

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=87.34  E-value=0.19  Score=32.67  Aligned_cols=42  Identities=19%  Similarity=0.414  Sum_probs=33.8

Q ss_pred             hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025387          100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG  143 (253)
Q Consensus       100 LlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~G  143 (253)
                      |+.+-+.+..+||.+|++.++++ ...|-.-+= +....|+|.+
T Consensus         8 Il~~L~~n~r~s~~~lA~~~gls-~~~v~~Ri~-~L~~~giI~~   49 (60)
T d1i1ga1           8 ILEILEKDARTPFTEIAKKLGIS-ETAVRKRVK-ALEEKGIIEG   49 (60)
T ss_dssp             HHHHHHHCTTCCHHHHHHHHTSC-HHHHHHHHH-HHHHHTSSCC
T ss_pred             HHHHHHHcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEe
Confidence            44444567889999999999997 888888776 7888898864

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=86.24  E-value=0.93  Score=31.46  Aligned_cols=79  Identities=13%  Similarity=0.169  Sum_probs=50.1

Q ss_pred             HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHH
Q 025387           99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWL  178 (253)
Q Consensus        99 tLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~  178 (253)
                      .|+.+......+++.+|++.++++ ...|=..+= .....|+|..+-+..++...+-...+.         =.+.+..|.
T Consensus        20 ~IL~~L~~~~~~~~~eLa~~l~is-~~~vs~~l~-~L~~~glV~~~~~~~d~r~~~~~LT~~---------G~~~~~~~~   88 (100)
T d1ub9a_          20 GIMIFLLPRRKAPFSQIQKVLDLT-PGNLDSHIR-VLERNGLVKTYKVIADRPRTVVEITDF---------GMEEAKRFL   88 (100)
T ss_dssp             HHHHHHHHHSEEEHHHHHHHTTCC-HHHHHHHHH-HHHHTTSEEEEEECSSSCEEEEEECHH---------HHHHHHHHH
T ss_pred             HHHHHhccCCCeeHHHHHHHHhhc-cccccHHHH-HHhhhceeEEEEcCcCCccccccCCHH---------HHHHHHHHH
Confidence            344333334569999999999997 666655444 777899999988877665444333221         123455666


Q ss_pred             HHHHHHHHHH
Q 025387          179 TTSDNLLISI  188 (253)
Q Consensus       179 ~~~~~vl~~I  188 (253)
                      +.+..+++.+
T Consensus        89 ~~~~~~~~~l   98 (100)
T d1ub9a_          89 SSLKAVIDGL   98 (100)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHhh
Confidence            6666666554