Citrus Sinensis ID: 026931

---

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
Protein Sequence
MPVVSGYNSSDCPIRYFQNPSSRSLLFESRSEEKKKKIRMAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGCMYMLVILIHI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccEEEEEccHHHHccccccccccccccccccccccccEEEEEEcEEEEEEEEEEEEccccccEEEEEEEEEEEcccEEEEEEEEEEccccccccEEEcHHHHHHHHHHHHccccccEEEEEEEcccccccccHHHHHHHHHHccccEEEEEEcccccccccEEEEEEEEEcccccccccEEEEEcEEEEcccHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccEEEccccccccEEEcccccccEEEEEEcccccccEEEEcccccccccccccccccccEEEEEEEEEEEEEEHcHccccccccEEEEEEEEEEccccEEEEEEcEEEccccccccEEEcHHHHHHHHHHHHHcccccEEEEEEcccccccHcHHHHHHHHHHHccccEEEEEEcccccccccEEEEEEEEEEcccccccEEEEEccEEEEEccHHHHHHHHHHHHEccc
Coil and Loop (DISEMBL)
mpvvsgynssdcpiryfqnpssrsllFESRSEEKKKKIRMaasdrtvlqfgpssaatsnvtakvHPLVIFNicdcyvrrpdQAERVIGTLLgsvlpdgtvdirnsyvvphnefsdqVALDIEYHHTMLKshlkvnpqeVIVGWFStglgvtggsaLIHEFycrevpnpvhltvdtgfrngegTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGCMYMLVILIHI
Flexible Loop (DISEMBL)
mpvvsgynssdcpiryfqnpssrsllFESRSEEKKKKirmaasdrtvlqfgpssaatsnvtakvhPLVIFNICDCYVRRPDQAERVIGTllgsvlpdgtvDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGCMYMLVILIHI
Low Complexity Region (SEG)
MPVVSGYNSSDCPIRYFQNPssrsllfesrseekkkkIRMAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGCMYMLVILIHI
Disordered region (IsUnstruct)
**********************************************************NVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGCMYMLVILIH*
Disordered Region (DISOPRED)
*************************************************************AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGCMYMLVILIH*
Disordered Region (DISEMBL)
********SSDCPIRYFQNPSSRSLLFESRSEEKKKKIRMAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGCMYMLVILIHI
Disordered Region (DISPRO)
*PVVSGYNSSDCPIRYFQNPSSRSLLFESRSEEKKKKIRMAASDRTVLQFGP***ATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGCMYMLVILIHI
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MPVVSGYNSSDCPIRYFQNPSSRSLLFESRSEEKKKKIRMAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGCMYMLVILIHI
Positional Conservation
no confident homologs detected

---

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	230	2.2.26 [Sep-21-2011]
O04202	293	Eukaryotic translation in	yes	no	0.778	0.610	0.765	2e-81
A5A6I3	361	Eukaryotic translation in	yes	no	0.682	0.434	0.443	2e-36
Q4R5B8	361	Eukaryotic translation in	N/A	no	0.682	0.434	0.443	2e-36
O00303	357	Eukaryotic translation in	yes	no	0.682	0.439	0.443	2e-36
Q9DCH4	361	Eukaryotic translation in	yes	no	0.682	0.434	0.443	3e-36
B3M123	280	Eukaryotic translation in	N/A	no	0.695	0.571	0.453	3e-34
Q54C49	284	Eukaryotic translation in	yes	no	0.7	0.566	0.463	7e-34
Q1HR47	287	Eukaryotic translation in	N/A	no	0.695	0.557	0.447	3e-33
Q295I4	280	Eukaryotic translation in	yes	no	0.695	0.571	0.434	3e-33
B4GDU3	280	Eukaryotic translation in	N/A	no	0.695	0.571	0.434	3e-33

>sp|O04202|EIF3F_ARATH Eukaryotic translation initiation factor 3 subunit F OS=Arabidopsis thaliana GN=TIF3F1 PE=2 SV=1

 Score =  301 bits (772), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 140/183 (76%), Positives = 160/183 (87%), Gaps = 4/183 (2%)

Query: 41  AASDRTVLQF-GPSSAA---TSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLP 96
           A S+ T+LQF  PSS A   TS +TA++HPLVIFN+CDC+VRRPD AERVIGTLLGS+LP
Sbjct: 3   ATSEHTILQFVSPSSTASATTSVLTARIHPLVIFNVCDCFVRRPDSAERVIGTLLGSILP 62

Query: 97  DGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSAL 156
           DGTVDIRNSY VPHNE SDQVA+DI+YHH ML SHLKVN +E IVGW+STG GV GGS+L
Sbjct: 63  DGTVDIRNSYAVPHNESSDQVAVDIDYHHNMLASHLKVNSKETIVGWYSTGAGVNGGSSL 122

Query: 157 IHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAE 216
           IH+FY REVPNP+HLTVDTGF NGEGT+KA+VS NLSLGDRQL A FQEIP+DLRM++AE
Sbjct: 123 IHDFYAREVPNPIHLTVDTGFTNGEGTIKAFVSSNLSLGDRQLVAHFQEIPVDLRMVDAE 182

Query: 217 RVG 219
           RVG
Sbjct: 183 RVG 185

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome.
Arabidopsis thaliana (taxid: 3702)

>sp|A5A6I3|EIF3F_PANTR Eukaryotic translation initiation factor 3 subunit F OS=Pan troglodytes GN=EIF3F PE=2 SV=1

 Score =  152 bits (383), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 70/158 (44%), Positives = 105/158 (66%), Gaps = 1/158 (0%)

Query: 63  KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIE 122
           ++HP+++ +I D Y RR + A RVIGTLLG+V    +V++ N + VPHNE  D+VA+D+E
Sbjct: 97  RLHPVILASIVDSYERRNEGAARVIGTLLGTV-DKHSVEVTNCFSVPHNESEDEVAVDME 155

Query: 123 YHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEG 182
           +   M + H KV+P E+I+GW++TG  +T  S LIHE+Y RE PNP+HLTVDT  +NG  
Sbjct: 156 FAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVDTSLQNGRM 215

Query: 183 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGC 220
           ++KAYVS  + +  R +   F  + +     + ER+G 
Sbjct: 216 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGV 253

Deubiquitinates activated NOTCH1, promoting its nuclear import, thereby acting as a positive regulator of Notch signaling.

Pan troglodytes (taxid: 9598)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: 1

EC: 2

>sp|Q4R5B8|EIF3F_MACFA Eukaryotic translation initiation factor 3 subunit F OS=Macaca fascicularis GN=EIF3F PE=2 SV=1

 Score =  152 bits (383), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 70/158 (44%), Positives = 105/158 (66%), Gaps = 1/158 (0%)

Query: 63  KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIE 122
           ++HP+++ +I D Y RR + A RVIGTLLG+V    +V++ N + VPHNE  D+VA+D+E
Sbjct: 97  RLHPVILASIVDSYERRNEGAARVIGTLLGTV-DKHSVEVTNCFSVPHNESEDEVAVDME 155

Query: 123 YHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEG 182
           +   M + H KV+P E+I+GW++TG  +T  S LIHE+Y RE PNP+HLTVDT  +NG  
Sbjct: 156 FAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVDTSLQNGRM 215

Query: 183 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGC 220
           ++KAYVS  + +  R +   F  + +     + ER+G 
Sbjct: 216 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGV 253

Deubiquitinates activated NOTCH1, promoting its nuclear import, thereby acting as a positive regulator of Notch signaling.

Macaca fascicularis (taxid: 9541)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: 1

EC: 2

>sp|O00303|EIF3F_HUMAN Eukaryotic translation initiation factor 3 subunit F OS=Homo sapiens GN=EIF3F PE=1 SV=1

 Score =  152 bits (383), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 70/158 (44%), Positives = 105/158 (66%), Gaps = 1/158 (0%)

Query: 63  KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIE 122
           ++HP+++ +I D Y RR + A RVIGTLLG+V    +V++ N + VPHNE  D+VA+D+E
Sbjct: 93  RLHPVILASIVDSYERRNEGAARVIGTLLGTV-DKHSVEVTNCFSVPHNESEDEVAVDME 151

Query: 123 YHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEG 182
           +   M + H KV+P E+I+GW++TG  +T  S LIHE+Y RE PNP+HLTVDT  +NG  
Sbjct: 152 FAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVDTSLQNGRM 211

Query: 183 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGC 220
           ++KAYVS  + +  R +   F  + +     + ER+G 
Sbjct: 212 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGV 249

Deubiquitinates activated NOTCH1, promoting its nuclear import, thereby acting as a positive regulator of Notch signaling.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: 1

EC: 2

>sp|Q9DCH4|EIF3F_MOUSE Eukaryotic translation initiation factor 3 subunit F OS=Mus musculus GN=Eif3f PE=1 SV=2

 Score =  152 bits (383), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 70/158 (44%), Positives = 106/158 (67%), Gaps = 1/158 (0%)

Query: 63  KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIE 122
           ++HP+++ +I D Y RR + A RVIGTLLG+V    +V++ N + VPHNE  D+VA+D+E
Sbjct: 97  RLHPVILASIVDSYERRNEGAARVIGTLLGTV-DKHSVEVTNCFSVPHNESEDEVAVDME 155

Query: 123 YHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEG 182
           +   M + H KV+P E+I+GW++TG  +T  S LIHE+Y RE PNP+HLTVDTG ++G  
Sbjct: 156 FAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVDTGLQHGRM 215

Query: 183 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGC 220
           ++KAYVS  + +  R +   F  + +     + ER+G 
Sbjct: 216 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGV 253

Deubiquitinates activated NOTCH1, promoting its nuclear import, thereby acting as a positive regulator of Notch signaling.

Mus musculus (taxid: 10090)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: 1

EC: 2

>sp|B3M123|EI3F1_DROAN Eukaryotic translation initiation factor 3 subunit F-1 OS=Drosophila ananassae GN=eIF3-S5-1 PE=3 SV=1

 Score =  145 bits (365), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 73/161 (45%), Positives = 99/161 (61%), Gaps = 1/161 (0%)

Query: 59  NVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVA 118
           N+T +VHP+V+F + D Y RR   + RVIGTLLGSV   G V++ N + VPH E  DQV 
Sbjct: 5   NLTVRVHPVVLFQVVDAYERRNADSHRVIGTLLGSV-DKGVVEVTNCFCVPHKEHDDQVE 63

Query: 119 LDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFR 178
            ++ Y   M   + KVNP E +VGW++TG  VT  S++IHE+Y RE  NPVHLTVDT  +
Sbjct: 64  AELSYALDMYDLNRKVNPNESVVGWWATGNDVTNHSSVIHEYYARECNNPVHLTVDTSLQ 123

Query: 179 NGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
            G   ++AYV + L +   +    F  IP++L   E E  G
Sbjct: 124 GGRMGLRAYVCIQLGVPGGKSGCMFTPIPVELTSYEPETFG 164

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome.

Drosophila ananassae (taxid: 7217)

>sp|Q54C49|EIF3F_DICDI Eukaryotic translation initiation factor 3 subunit F OS=Dictyostelium discoideum GN=eif3f PE=3 SV=1

 Score =  144 bits (362), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 77/166 (46%), Positives = 108/166 (65%), Gaps = 5/166 (3%)

Query: 58  SNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV 117
           S VT KVHP+VIFNI D Y+RR    +RVIGTLLG    DG ++IRN + V H+E ++Q+
Sbjct: 11  SQVTVKVHPVVIFNILDHYIRRNVGQDRVIGTLLG-FNNDGVLEIRNCFPVVHSE-TEQI 68

Query: 118 ALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPN--PVHLTVDT 175
           A+++EY   ML  HLK +P+E I+GW++TG  +   S  I+ FY  E+ N  P+HLTVDT
Sbjct: 69  AVEMEYQRKMLDLHLKSSPREPIIGWYATGNDINENSVHINNFYRDEMGNSTPIHLTVDT 128

Query: 176 GFRNGEGTVKAYVSVNLSLG-DRQLAAQFQEIPLDLRMIEAERVGC 220
           G  N    + AY++ NLSL  +  L + F ++PL++   EAE  G 
Sbjct: 129 GLTNDTMGIHAYMAHNLSLNPESSLGSYFSQLPLEILTFEAENAGL 174

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome.

Dictyostelium discoideum (taxid: 44689)

>sp|Q1HR47|EIF3F_AEDAE Eukaryotic translation initiation factor 3 subunit F OS=Aedes aegypti GN=eIF3-S5 PE=2 SV=1

 Score =  142 bits (357), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 72/161 (44%), Positives = 100/161 (62%), Gaps = 1/161 (0%)

Query: 59  NVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVA 118
           N+T +VHP+V+F I D Y RR   +ERVIGTLLGSV   G V++ N + VPH E +DQV 
Sbjct: 9   NLTVRVHPVVLFQIVDAYERRNADSERVIGTLLGSV-DKGVVEVTNCFCVPHKEHADQVE 67

Query: 119 LDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFR 178
            ++ Y   +   + +VNP E IVGW++TG  VT  S++IHE+Y RE  NP+HLT+DT   
Sbjct: 68  AELGYASDLYDLNRRVNPSENIVGWWATGQEVTNHSSVIHEYYARECNNPIHLTLDTSLS 127

Query: 179 NGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
                +KAYV V+L +   +    F  I +++   E E VG
Sbjct: 128 AARMGIKAYVCVSLGVPGGKTGCMFTPINVEISSYEPEVVG 168

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome.

Aedes aegypti (taxid: 7159)

>sp|Q295I4|EI3F1_DROPS Eukaryotic translation initiation factor 3 subunit F-1 OS=Drosophila pseudoobscura pseudoobscura GN=eIF3-S5-1 PE=3 SV=1

 Score =  141 bits (356), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 70/161 (43%), Positives = 99/161 (61%), Gaps = 1/161 (0%)

Query: 59  NVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVA 118
           N+T +VHP+V+F + D + RR  ++ RVIGTLLGSV   G V++ N + VPH E  DQV 
Sbjct: 5   NLTVRVHPVVLFQVVDAFERRNAESHRVIGTLLGSV-EKGVVEVTNCFCVPHKEHDDQVE 63

Query: 119 LDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFR 178
            ++ Y   M   + KVN  E +VGW++TG  VT  S++IHE+Y RE  NPVHLTVDT  +
Sbjct: 64  AELSYALDMYDLNRKVNSNEAVVGWWATGNDVTNHSSVIHEYYARECNNPVHLTVDTSLQ 123

Query: 179 NGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
            G   +++YV + L +   +    F  IP++L   E E  G
Sbjct: 124 GGRMGLRSYVCIQLGVPGGKTGCMFTPIPVELTSYEPETFG 164

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome.

Drosophila pseudoobscura pseudoobscura (taxid: 46245)

>sp|B4GDU3|EI3F1_DROPE Eukaryotic translation initiation factor 3 subunit F-1 OS=Drosophila persimilis GN=eIF3-S5-1 PE=3 SV=1

 Score =  141 bits (356), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 70/161 (43%), Positives = 99/161 (61%), Gaps = 1/161 (0%)

Query: 59  NVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVA 118
           N+T +VHP+V+F + D + RR  ++ RVIGTLLGSV   G V++ N + VPH E  DQV 
Sbjct: 5   NLTVRVHPVVLFQVVDAFERRNAESHRVIGTLLGSV-EKGVVEVTNCFCVPHKEHDDQVE 63

Query: 119 LDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFR 178
            ++ Y   M   + KVN  E +VGW++TG  VT  S++IHE+Y RE  NPVHLTVDT  +
Sbjct: 64  AELSYALDMYDLNRKVNSNEAVVGWWATGNDVTNHSSVIHEYYARECNNPVHLTVDTSLQ 123

Query: 179 NGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
            G   +++YV + L +   +    F  IP++L   E E  G
Sbjct: 124 GGRMGLRSYVCIQLGVPGGKTGCMFTPIPVELTSYEPETFG 164

Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome.

Drosophila persimilis (taxid: 7234)

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	230
260586249	288	putative eukaryotic translation initiati	0.782	0.625	0.977	1e-100
255571843	287	eukaryotic translation initiation factor	0.778	0.623	0.872	7e-89
449441322	285	PREDICTED: eukaryotic translation initia	0.769	0.621	0.833	2e-86
224109362	287	predicted protein [Populus trichocarpa]	0.769	0.616	0.832	3e-85
356539943	288	PREDICTED: eukaryotic translation initia	0.782	0.625	0.833	2e-84
255635179	210	unknown [Glycine max]	0.782	0.857	0.833	5e-84
297788583	293	26S proteasome regulatory subunit [Arabi	0.778	0.610	0.797	5e-84
358249108	289	uncharacterized protein LOC100811797 [Gl	0.782	0.622	0.834	7e-84
225449198	285	PREDICTED: eukaryotic translation initia	0.769	0.621	0.822	2e-83
357492587	284	Eukaryotic translation initiation factor	0.765	0.619	0.816	4e-83

>gi|260586249|gb|ACX45995.1| putative eukaryotic translation initiation factor 1 [Citrus sinensis]

 Score =  370 bits (949), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 176/180 (97%), Positives = 177/180 (98%)

Query: 40  MAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT 99
           MAASDRTVLQFGPSSA TSN+TAKVHPLVIFNI DCYVRRPDQAERVIGTLLGSVLPDGT
Sbjct: 1   MAASDRTVLQFGPSSAVTSNITAKVHPLVIFNISDCYVRRPDQAERVIGTLLGSVLPDGT 60

Query: 100 VDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHE 159
           VDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHE
Sbjct: 61  VDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHE 120

Query: 160 FYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
           FYCREVPNPVHLTV TGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG
Sbjct: 121 FYCREVPNPVHLTVGTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 180

Source: Citrus sinensis

Species: Citrus sinensis

Genus: Citrus

Family: Rutaceae

Order: Sapindales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255571843|ref|XP_002526864.1| eukaryotic translation initiation factor 3f, eif3f, putative [Ricinus communis] gi|223533763|gb|EEF35495.1| eukaryotic translation initiation factor 3f, eif3f, putative [Ricinus communis]

 Score =  332 bits (851), Expect = 7e-89,   Method: Compositional matrix adjust.
 Identities = 157/180 (87%), Positives = 170/180 (94%), Gaps = 1/180 (0%)

Query: 40  MAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT 99
           MAAS++TVLQF  S+ +++ ++AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT
Sbjct: 1   MAASEQTVLQF-TSAPSSTGLSAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT 59

Query: 100 VDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHE 159
           VDIRNSY VPHNE SDQVALDI+YHH ML SH KVNP+EVIVGW+STGLGVTGGSALIHE
Sbjct: 60  VDIRNSYAVPHNESSDQVALDIDYHHNMLLSHQKVNPKEVIVGWYSTGLGVTGGSALIHE 119

Query: 160 FYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
           FY REVPNPVHLTVDTGFRNGEGT+KAYVSVNLSLGDRQLAAQFQEIPLDLRM+EAERVG
Sbjct: 120 FYSREVPNPVHLTVDTGFRNGEGTIKAYVSVNLSLGDRQLAAQFQEIPLDLRMLEAERVG 179

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449441322|ref|XP_004138431.1| PREDICTED: eukaryotic translation initiation factor 3 subunit F-like [Cucumis sativus] gi|449517876|ref|XP_004165970.1| PREDICTED: eukaryotic translation initiation factor 3 subunit F-like [Cucumis sativus]

 Score =  324 bits (830), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 150/180 (83%), Positives = 165/180 (91%), Gaps = 3/180 (1%)

Query: 40  MAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT 99
           MA ++ TVLQF  SS   + ++AKVHPLVIFNICDCYVRRPDQA+RVIGTLLGSVLPDGT
Sbjct: 1   MATTETTVLQFSHSS---NTLSAKVHPLVIFNICDCYVRRPDQADRVIGTLLGSVLPDGT 57

Query: 100 VDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHE 159
           VDIRNSY VPHNEFSDQVALDI+YHH ML SH KVNP+EVIVGW+STG GVTGGSALIHE
Sbjct: 58  VDIRNSYAVPHNEFSDQVALDIDYHHNMLSSHQKVNPKEVIVGWYSTGTGVTGGSALIHE 117

Query: 160 FYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
           FY REV NP+HLTVDTGF+NGEGT+KAY+SVNLSLGDRQLAAQFQEIPLDLRM+EAER+G
Sbjct: 118 FYSREVANPIHLTVDTGFKNGEGTIKAYISVNLSLGDRQLAAQFQEIPLDLRMVEAERLG 177

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224109362|ref|XP_002315172.1| predicted protein [Populus trichocarpa] gi|118484603|gb|ABK94175.1| unknown [Populus trichocarpa] gi|222864212|gb|EEF01343.1| predicted protein [Populus trichocarpa]

 Score =  320 bits (820), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 149/179 (83%), Positives = 165/179 (92%), Gaps = 2/179 (1%)

Query: 41  AASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTV 100
           A   +TVLQF PSS++T  ++AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTV
Sbjct: 3   AIEQQTVLQFAPSSSST--LSAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTV 60

Query: 101 DIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEF 160
           DIRNSY VPHNE S+QVALDI+YHH +L SH KVNP+EVIVGW+STGLGVTGGSALIH+F
Sbjct: 61  DIRNSYAVPHNESSEQVALDIDYHHNLLLSHQKVNPKEVIVGWYSTGLGVTGGSALIHDF 120

Query: 161 YCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
           Y REVPNP+HLTVDTGF NGEGT+KAYVSVNLSLGDR LAAQFQE+PLDLRM+EAER+G
Sbjct: 121 YSREVPNPIHLTVDTGFSNGEGTIKAYVSVNLSLGDRPLAAQFQEVPLDLRMVEAERIG 179

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356539943|ref|XP_003538452.1| PREDICTED: eukaryotic translation initiation factor 3 subunit F-like [Glycine max]

 Score =  317 bits (813), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 150/180 (83%), Positives = 167/180 (92%)

Query: 40  MAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT 99
           MAASDRTVLQF  SS+++ +++AKVHPLVIFNICDCYVRRPDQA+RVIGTLLGSVLPDGT
Sbjct: 1   MAASDRTVLQFSSSSSSSQSLSAKVHPLVIFNICDCYVRRPDQADRVIGTLLGSVLPDGT 60

Query: 100 VDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHE 159
           VDIRNSY VPHNE  +QVALDIEYHH ML SH KVNP+E+IVGW+STGLGVTGGSALIHE
Sbjct: 61  VDIRNSYAVPHNESIEQVALDIEYHHNMLISHQKVNPKEIIVGWYSTGLGVTGGSALIHE 120

Query: 160 FYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
           FY REVPNP+HLTVDTGF NG GT+KAYVS NLSLG+RQ+AAQFQEIPLDLRM+EAER+G
Sbjct: 121 FYSREVPNPIHLTVDTGFTNGAGTIKAYVSNNLSLGERQIAAQFQEIPLDLRMVEAERIG 180

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255635179|gb|ACU17945.1| unknown [Glycine max]

 Score =  316 bits (809), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 150/180 (83%), Positives = 167/180 (92%)

Query: 40  MAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT 99
           MAASDRTVLQF  SS+++ +++AKVHPLVIFNICDCYVRRPDQA+RVIGTLLGSVLPDGT
Sbjct: 1   MAASDRTVLQFSSSSSSSQSLSAKVHPLVIFNICDCYVRRPDQADRVIGTLLGSVLPDGT 60

Query: 100 VDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHE 159
           VDIRNSY VPHNE  +QVALDIEYHH ML SH KVNP+E+IVGW+STGLGVTGGSALIHE
Sbjct: 61  VDIRNSYAVPHNESIEQVALDIEYHHNMLISHQKVNPKEIIVGWYSTGLGVTGGSALIHE 120

Query: 160 FYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
           FY REVPNP+HLTVDTGF NG GT+KAYVS NLSLG+RQ+AAQFQEIPLDLRM+EAER+G
Sbjct: 121 FYSREVPNPIHLTVDTGFTNGAGTIKAYVSNNLSLGERQIAAQFQEIPLDLRMVEAERIG 180

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297788583|ref|XP_002862370.1| 26S proteasome regulatory subunit [Arabidopsis lyrata subsp. lyrata] gi|297827613|ref|XP_002881689.1| 26S proteasome regulatory subunit [Arabidopsis lyrata subsp. lyrata] gi|297307815|gb|EFH38628.1| 26S proteasome regulatory subunit [Arabidopsis lyrata subsp. lyrata] gi|297327528|gb|EFH57948.1| 26S proteasome regulatory subunit [Arabidopsis lyrata subsp. lyrata]

 Score =  316 bits (809), Expect = 5e-84,   Method: Compositional matrix adjust.
 Identities = 146/183 (79%), Positives = 165/183 (90%), Gaps = 4/183 (2%)

Query: 41  AASDRTVLQF-GPSSAATSN---VTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLP 96
           AAS+ TVLQF  PSS AT+    +TA++HPLVIFN+CDC+VRRPD AERVIGTLLGS+LP
Sbjct: 3   AASEHTVLQFVAPSSTATATTSVLTARIHPLVIFNVCDCFVRRPDSAERVIGTLLGSILP 62

Query: 97  DGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSAL 156
           DGTVDIRNSY VPHNEFSDQVA+DI+YHH ML SHLKVNP+E+IVGW+STG GV GGSAL
Sbjct: 63  DGTVDIRNSYAVPHNEFSDQVAVDIDYHHNMLASHLKVNPKEIIVGWYSTGAGVNGGSAL 122

Query: 157 IHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAE 216
           IHEFY REV NP+HLTVDTGF NGEGT+KA+VS NLSLGDRQLAAQFQEIP+DLRM++AE
Sbjct: 123 IHEFYAREVTNPIHLTVDTGFTNGEGTIKAFVSSNLSLGDRQLAAQFQEIPVDLRMVDAE 182

Query: 217 RVG 219
           RVG
Sbjct: 183 RVG 185

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|358249108|ref|NP_001239738.1| uncharacterized protein LOC100811797 [Glycine max] gi|255638221|gb|ACU19424.1| unknown [Glycine max]

 Score =  315 bits (808), Expect = 7e-84,   Method: Compositional matrix adjust.
 Identities = 151/181 (83%), Positives = 167/181 (92%), Gaps = 1/181 (0%)

Query: 40  MAASDRTVLQFGPSSAATSNV-TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDG 98
           MAASDRTVLQF  SS+++S + +AKVHPLVIFNICDCYVRRPDQA+RVIGTLLGSVLPDG
Sbjct: 1   MAASDRTVLQFSSSSSSSSQILSAKVHPLVIFNICDCYVRRPDQADRVIGTLLGSVLPDG 60

Query: 99  TVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIH 158
           TVDIRNSY VPHNE  +QVALDIEYHH ML SH KVNP+E+IVGW+STGLGVTGGSALIH
Sbjct: 61  TVDIRNSYAVPHNESIEQVALDIEYHHNMLISHQKVNPKEIIVGWYSTGLGVTGGSALIH 120

Query: 159 EFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERV 218
           EFY REVPNP+HLTVDTGF NG GT+KAYVS NLSLG+RQ+AAQFQEIPLDLRM+EAER+
Sbjct: 121 EFYSREVPNPIHLTVDTGFTNGAGTIKAYVSNNLSLGERQIAAQFQEIPLDLRMVEAERI 180

Query: 219 G 219
           G
Sbjct: 181 G 181

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225449198|ref|XP_002279347.1| PREDICTED: eukaryotic translation initiation factor 3 subunit F [Vitis vinifera] gi|296086088|emb|CBI31529.3| unnamed protein product [Vitis vinifera]

 Score =  314 bits (805), Expect = 2e-83,   Method: Compositional matrix adjust.
 Identities = 148/180 (82%), Positives = 164/180 (91%), Gaps = 3/180 (1%)

Query: 40  MAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT 99
           MA+S+  VLQF PSS   ++++AKVHPLVIFNICDCYVRRPDQAERVIGTLLGS+ PDGT
Sbjct: 1   MASSESAVLQFFPSS---TSLSAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSISPDGT 57

Query: 100 VDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHE 159
           VDIRNSY VPHNE SDQVALDI+YHH ML SH KVNP+EVIVGW+STGLGVTGGSALIHE
Sbjct: 58  VDIRNSYAVPHNESSDQVALDIDYHHNMLLSHQKVNPKEVIVGWYSTGLGVTGGSALIHE 117

Query: 160 FYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
           FY REV NP+HLTVDT FRNGE T+KA+VSV+LSLG+RQLAAQFQEIPLDLRM+EAERVG
Sbjct: 118 FYSREVQNPIHLTVDTTFRNGEATIKAFVSVSLSLGERQLAAQFQEIPLDLRMVEAERVG 177

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357492587|ref|XP_003616582.1| Eukaryotic translation initiation factor 3 subunit F [Medicago truncatula] gi|355517917|gb|AES99540.1| Eukaryotic translation initiation factor 3 subunit F [Medicago truncatula]

 Score =  313 bits (802), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 147/180 (81%), Positives = 161/180 (89%), Gaps = 4/180 (2%)

Query: 40  MAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT 99
           MAAS RTVLQF    +++  ++ KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT
Sbjct: 1   MAASKRTVLQF----SSSQTLSGKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT 56

Query: 100 VDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHE 159
           VDIRNSY VPHNE  DQVALDIEYHH ML SH KVNP+EVIVGW+STGLGVTGGSALIHE
Sbjct: 57  VDIRNSYAVPHNESVDQVALDIEYHHNMLLSHQKVNPKEVIVGWYSTGLGVTGGSALIHE 116

Query: 160 FYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
           FY REV NP+HLTVDTGF +GEG +KAYVS NLSLGD+Q+AAQFQEIPLDLRM+EAER+G
Sbjct: 117 FYSREVSNPIHLTVDTGFADGEGAIKAYVSNNLSLGDQQIAAQFQEIPLDLRMVEAERIG 176

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	230
TAIR|locus:2061206	293	EIF2 "AT2G39990" [Arabidopsis	0.778	0.610	0.765	2.5e-74
MGI|MGI:1913335	361	Eif3f "eukaryotic translation	0.678	0.432	0.445	3.1e-35
UNIPROTKB|E1BLZ8	384	EIF3F "Uncharacterized protein	0.678	0.406	0.445	4e-35
UNIPROTKB|B3KSH1	372	EIF3F "HCG1784554, isoform CRA	0.678	0.419	0.445	4e-35
UNIPROTKB|O00303	357	EIF3F "Eukaryotic translation	0.678	0.436	0.445	4e-35
UNIPROTKB|A5A6I3	361	EIF3F "Eukaryotic translation	0.678	0.432	0.445	4e-35
UNIPROTKB|Q4R5B8	361	EIF3F "Eukaryotic translation	0.678	0.432	0.445	4e-35
DICTYBASE|DDB_G0293254	284	eif3F "eukaryotic translation	0.695	0.563	0.466	2e-33
UNIPROTKB|E1C050	332	EIF3F "Uncharacterized protein	0.726	0.503	0.416	4.1e-33
FB|FBgn0037270	280	CG9769 [Drosophila melanogaste	0.695	0.571	0.440	8.5e-33

TAIR|locus:2061206 EIF2 "AT2G39990" [Arabidopsis thaliana (taxid:3702)]

 Score = 750 (269.1 bits), Expect = 2.5e-74, P = 2.5e-74
 Identities = 140/183 (76%), Positives = 160/183 (87%)

Query:    41 AASDRTVLQF-GPSSAA---TSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLP 96
             A S+ T+LQF  PSS A   TS +TA++HPLVIFN+CDC+VRRPD AERVIGTLLGS+LP
Sbjct:     3 ATSEHTILQFVSPSSTASATTSVLTARIHPLVIFNVCDCFVRRPDSAERVIGTLLGSILP 62

Query:    97 DGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSAL 156
             DGTVDIRNSY VPHNE SDQVA+DI+YHH ML SHLKVN +E IVGW+STG GV GGS+L
Sbjct:    63 DGTVDIRNSYAVPHNESSDQVAVDIDYHHNMLASHLKVNSKETIVGWYSTGAGVNGGSSL 122

Query:   157 IHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAE 216
             IH+FY REVPNP+HLTVDTGF NGEGT+KA+VS NLSLGDRQL A FQEIP+DLRM++AE
Sbjct:   123 IHDFYAREVPNPIHLTVDTGFTNGEGTIKAFVSSNLSLGDRQLVAHFQEIPVDLRMVDAE 182

Query:   217 RVG 219
             RVG
Sbjct:   183 RVG 185

GO:0003743 "translation initiation factor activity" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISM;IDA

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISS

GO:0006413 "translational initiation" evidence=ISS

GO:0005634 "nucleus" evidence=IDA

GO:0016020 "membrane" evidence=IDA

GO:0009790 "embryo development" evidence=IMP

GO:0009846 "pollen germination" evidence=IMP

GO:0005829 "cytosol" evidence=IDA

MGI|MGI:1913335 Eif3f "eukaryotic translation initiation factor 3, subunit F" [Mus musculus (taxid:10090)]

 Score = 381 (139.2 bits), Expect = 3.1e-35, P = 3.1e-35
 Identities = 70/157 (44%), Positives = 106/157 (67%)

Query:    63 KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIE 122
             ++HP+++ +I D Y RR + A RVIGTLLG+V    +V++ N + VPHNE  D+VA+D+E
Sbjct:    97 RLHPVILASIVDSYERRNEGAARVIGTLLGTV-DKHSVEVTNCFSVPHNESEDEVAVDME 155

Query:   123 YHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEG 182
             +   M + H KV+P E+I+GW++TG  +T  S LIHE+Y RE PNP+HLTVDTG ++G  
Sbjct:   156 FAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVDTGLQHGRM 215

Query:   183 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
             ++KAYVS  + +  R +   F  + +     + ER+G
Sbjct:   216 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIG 252

GO:0003743 "translation initiation factor activity" evidence=IDA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISO;IDA

GO:0006412 "translation" evidence=IEA

GO:0006413 "translational initiation" evidence=ISO;IDA

GO:0006508 "proteolysis" evidence=IEA

GO:0008233 "peptidase activity" evidence=IEA

GO:0008234 "cysteine-type peptidase activity" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

UNIPROTKB|E1BLZ8 EIF3F "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 380 (138.8 bits), Expect = 4.0e-35, P = 4.0e-35
 Identities = 70/157 (44%), Positives = 105/157 (66%)

Query:    63 KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIE 122
             ++HP+++ +I D Y RR + A RVIGTLLG+V    +V++ N + VPHNE  D+VA+D+E
Sbjct:   120 RLHPVILASIVDSYERRNEGAARVIGTLLGTV-DKHSVEVTNCFSVPHNESEDEVAVDME 178

Query:   123 YHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEG 182
             +   M + H KV+P E+I+GW++TG  +T  S LIHE+Y RE PNP+HLTVDT  +NG  
Sbjct:   179 FAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVDTSLQNGRM 238

Query:   183 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
             ++KAYVS  + +  R +   F  + +     + ER+G
Sbjct:   239 SIKAYVSTLMGVPGRTMGVMFTPLTVKYTYYDTERIG 275

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

UNIPROTKB|B3KSH1 EIF3F "HCG1784554, isoform CRA_a" [Homo sapiens (taxid:9606)]

 Score = 380 (138.8 bits), Expect = 4.0e-35, P = 4.0e-35
 Identities = 70/157 (44%), Positives = 105/157 (66%)

Query:    63 KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIE 122
             ++HP+++ +I D Y RR + A RVIGTLLG+V    +V++ N + VPHNE  D+VA+D+E
Sbjct:   108 RLHPVILASIVDSYERRNEGAARVIGTLLGTV-DKHSVEVTNCFSVPHNESEDEVAVDME 166

Query:   123 YHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEG 182
             +   M + H KV+P E+I+GW++TG  +T  S LIHE+Y RE PNP+HLTVDT  +NG  
Sbjct:   167 FAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVDTSLQNGRM 226

Query:   183 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
             ++KAYVS  + +  R +   F  + +     + ER+G
Sbjct:   227 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIG 263

GO:0003743 "translation initiation factor activity" evidence=IEA

UNIPROTKB|O00303 EIF3F "Eukaryotic translation initiation factor 3 subunit F" [Homo sapiens (taxid:9606)]

 Score = 380 (138.8 bits), Expect = 4.0e-35, P = 4.0e-35
 Identities = 70/157 (44%), Positives = 105/157 (66%)

Query:    63 KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIE 122
             ++HP+++ +I D Y RR + A RVIGTLLG+V    +V++ N + VPHNE  D+VA+D+E
Sbjct:    93 RLHPVILASIVDSYERRNEGAARVIGTLLGTV-DKHSVEVTNCFSVPHNESEDEVAVDME 151

Query:   123 YHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEG 182
             +   M + H KV+P E+I+GW++TG  +T  S LIHE+Y RE PNP+HLTVDT  +NG  
Sbjct:   152 FAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVDTSLQNGRM 211

Query:   183 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
             ++KAYVS  + +  R +   F  + +     + ER+G
Sbjct:   212 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIG 248

GO:0006508 "proteolysis" evidence=IEA

GO:0008234 "cysteine-type peptidase activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IDA;TAS

GO:0003743 "translation initiation factor activity" evidence=IC;IDA;TAS

GO:0006413 "translational initiation" evidence=IC;IDA;TAS

GO:0005829 "cytosol" evidence=TAS

GO:0006412 "translation" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0044267 "cellular protein metabolic process" evidence=TAS

UNIPROTKB|A5A6I3 EIF3F "Eukaryotic translation initiation factor 3 subunit F" [Pan troglodytes (taxid:9598)]

 Score = 380 (138.8 bits), Expect = 4.0e-35, P = 4.0e-35
 Identities = 70/157 (44%), Positives = 105/157 (66%)

Query:    63 KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIE 122
             ++HP+++ +I D Y RR + A RVIGTLLG+V    +V++ N + VPHNE  D+VA+D+E
Sbjct:    97 RLHPVILASIVDSYERRNEGAARVIGTLLGTV-DKHSVEVTNCFSVPHNESEDEVAVDME 155

Query:   123 YHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEG 182
             +   M + H KV+P E+I+GW++TG  +T  S LIHE+Y RE PNP+HLTVDT  +NG  
Sbjct:   156 FAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVDTSLQNGRM 215

Query:   183 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
             ++KAYVS  + +  R +   F  + +     + ER+G
Sbjct:   216 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIG 252

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISS

GO:0006413 "translational initiation" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

UNIPROTKB|Q4R5B8 EIF3F "Eukaryotic translation initiation factor 3 subunit F" [Macaca fascicularis (taxid:9541)]

 Score = 380 (138.8 bits), Expect = 4.0e-35, P = 4.0e-35
 Identities = 70/157 (44%), Positives = 105/157 (66%)

Query:    63 KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIE 122
             ++HP+++ +I D Y RR + A RVIGTLLG+V    +V++ N + VPHNE  D+VA+D+E
Sbjct:    97 RLHPVILASIVDSYERRNEGAARVIGTLLGTV-DKHSVEVTNCFSVPHNESEDEVAVDME 155

Query:   123 YHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEG 182
             +   M + H KV+P E+I+GW++TG  +T  S LIHE+Y RE PNP+HLTVDT  +NG  
Sbjct:   156 FAKNMYELHKKVSPNELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVDTSLQNGRM 215

Query:   183 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
             ++KAYVS  + +  R +   F  + +     + ER+G
Sbjct:   216 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIG 252

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISS

GO:0006413 "translational initiation" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

DICTYBASE|DDB_G0293254 eif3F "eukaryotic translation initiation factor 3 (eIF3) subunit 5" [Dictyostelium discoideum (taxid:44689)]

 Score = 364 (133.2 bits), Expect = 2.0e-33, P = 2.0e-33
 Identities = 77/165 (46%), Positives = 108/165 (65%)

Query:    58 SNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV 117
             S VT KVHP+VIFNI D Y+RR    +RVIGTLLG    DG ++IRN + V H+E ++Q+
Sbjct:    11 SQVTVKVHPVVIFNILDHYIRRNVGQDRVIGTLLG-FNNDGVLEIRNCFPVVHSE-TEQI 68

Query:   118 ALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPN--PVHLTVDT 175
             A+++EY   ML  HLK +P+E I+GW++TG  +   S  I+ FY  E+ N  P+HLTVDT
Sbjct:    69 AVEMEYQRKMLDLHLKSSPREPIIGWYATGNDINENSVHINNFYRDEMGNSTPIHLTVDT 128

Query:   176 GFRNGEGTVKAYVSVNLSLG-DRQLAAQFQEIPLDLRMIEAERVG 219
             G  N    + AY++ NLSL  +  L + F ++PL++   EAE  G
Sbjct:   129 GLTNDTMGIHAYMAHNLSLNPESSLGSYFSQLPLEILTFEAENAG 173

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISS

GO:0006413 "translational initiation" evidence=IEA

GO:0006412 "translation" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

UNIPROTKB|E1C050 EIF3F "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 361 (132.1 bits), Expect = 4.1e-33, P = 4.1e-33
 Identities = 72/173 (41%), Positives = 108/173 (62%)

Query:    52 PSSAATSNV-----TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSY 106
             P SAA S         ++HP+V+ +I D + RR + A RVIGTLLG+V    +V++ N +
Sbjct:    52 PLSAALSGPFPGGRVVRLHPVVLASIVDSFERRNEGAARVIGTLLGTV-DKHSVEVTNCF 110

Query:   107 VVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVP 166
              VPHNE  D+VA+D+E+   M + H KV+P E+I+GW++TG  +T  S LIHE+Y RE  
Sbjct:   111 SVPHNESEDEVAVDMEFAKNMYELHKKVSPSEIILGWYATGHDITEHSVLIHEYYSREAH 170

Query:   167 NPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
             NP+HLTVDT  +N   ++KAYVS  + +  + +   F  + +     + ER+G
Sbjct:   171 NPIHLTVDTSLQNSRMSIKAYVSAPMGVPGKTMGVMFTPLTVKYVYYDTERIG 223

GO:0003743 "translation initiation factor activity" evidence=IEA

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=IEA

FB|FBgn0037270 CG9769 [Drosophila melanogaster (taxid:7227)]

 Score = 358 (131.1 bits), Expect = 8.5e-33, P = 8.5e-33
 Identities = 71/161 (44%), Positives = 98/161 (60%)

Query:    59 NVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVA 118
             N+T +VHP+V+F + D + RR   + RVIGTLLGSV   G V++ N + VPH E  DQV 
Sbjct:     5 NLTVRVHPVVLFQVVDAFERRNADSHRVIGTLLGSV-DKGVVEVTNCFCVPHKEHDDQVE 63

Query:   119 LDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFR 178
              ++ Y   M   + KVN  E +VGW++TG  VT  S++IHE+Y RE  NPVHLTVDT  +
Sbjct:    64 AELSYALDMYDLNRKVNSNESVVGWWATGNDVTNHSSVIHEYYARECNNPVHLTVDTSLQ 123

Query:   179 NGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
              G   ++AYV + L +   +    F  IP++L   E E  G
Sbjct:   124 GGRMGLRAYVCIQLGVPGGKSGCMFTPIPVELTSYEPETFG 164

GO:0005852 "eukaryotic translation initiation factor 3 complex" evidence=ISS

GO:0006413 "translational initiation" evidence=ISS

GO:0003743 "translation initiation factor activity" evidence=ISS

GO:0048102 "autophagic cell death" evidence=IEP

GO:0035071 "salivary gland cell autophagic cell death" evidence=IEP

---

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)
O04202	EIF3F_ARATH	No assigned EC number	0.7650	0.7782	0.6109	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

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.4.17.n1	LOW CONFIDENCE prediction!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	grail3.0022015701	SubName- Full=Putative uncharacterized protein; (287 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	grail3.0022009302	hypothetical protein (343 aa)				•		•			0.841
	estExt_fgenesh4_pm.C_LG_VIII0284	hypothetical protein (343 aa)				•		•			0.840
	estExt_Genewise1_v1.C_290097	hypothetical protein (465 aa)						•			0.834
	eugene3.00030772	hypothetical protein (464 aa)				•		•			0.833
	estExt_fgenesh4_pm.C_LG_XIII0470	SubName- Full=Putative uncharacterized protein; (271 aa)						•			0.818
	estExt_Genewise1_v1.C_LG_XIV3582	SubName- Full=Putative uncharacterized protein;; Seems to be required for maximal rate of prote [...] (145 aa)						•			0.814
	grail3.0038004701	hypothetical protein (452 aa)						•			0.811
	eugene3.03280006	hypothetical protein (455 aa)						•			0.811
	eugene3.01650024	hypothetical protein (444 aa)						•			0.811
	fgenesh4_pg.C_scaffold_1866000002	annotation not avaliable (150 aa)						•			0.807

---

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	230
cd08064	265	cd08064, MPN_eIF3f, Mpr1p, Pad1p N-terminal (MPN)	3e-83
cd08057	157	cd08057, MPN_euk_non_mb, Mpr1p, Pad1p N-terminal (	1e-36
pfam01398	117	pfam01398, JAB, JAB1/Mov34/MPN/PAD-1 ubiquitin pro	4e-28
cd08062	280	cd08062, MPN_RPN7_8, Mpr1p, Pad1p N-terminal (MPN)	2e-25
smart00232	135	smart00232, JAB_MPN, JAB/MPN domain	4e-24
PLN03246	303	PLN03246, PLN03246, 26S proteasome regulatory subu	9e-24
cd08063	288	cd08063, MPN_CSN6, Mpr1p, Pad1p N-terminal (MPN) d	1e-16

>gnl|CDD|163695 cd08064, MPN_eIF3f, Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f

 Score =  248 bits (635), Expect = 3e-83
 Identities = 86/159 (54%), Positives = 113/159 (71%), Gaps = 3/159 (1%)

Query: 63  KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIE 122
           +VHP+V+F+I D Y RR +  ERVIGTLLG+   +G V+I N + VPHNE  DQVA+D+E
Sbjct: 2   RVHPVVLFSILDSYERRNEGQERVIGTLLGTRS-EGEVEITNCFAVPHNESEDQVAVDME 60

Query: 123 YHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCRE--VPNPVHLTVDTGFRNG 180
           YH TM + H KVNP+EVIVGW++TG  +T  SALIH++Y RE    NP+HLTVDT   +G
Sbjct: 61  YHRTMYELHQKVNPKEVIVGWYATGSEITEHSALIHDYYSRECTSYNPIHLTVDTSLDDG 120

Query: 181 EGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
           + ++KAYVS  L +  + L + F  IPL+L   EAERV 
Sbjct: 121 KMSIKAYVSSPLGVPGKTLGSMFVPIPLELLYSEAERVA 159

Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and apoptosis. It enhances its association with the core eIF3 subunits during apoptosis, suggesting that eIF3f may inhibit translation by increasing the binding to the eIF3 complex during apoptosis. Thus, eIF3f may be an important negative regulator of cell growth and proliferation. Length = 265

>gnl|CDD|163688 cd08057, MPN_euk_non_mb, Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic

 Score =  125 bits (316), Expect = 1e-36
 Identities = 50/163 (30%), Positives = 77/163 (47%), Gaps = 11/163 (6%)

Query: 62  AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDI 121
            ++HPLV+ NI D Y RR    +RVIG LLG V     +++ NS+ +P +E  + + +D 
Sbjct: 1   VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGYVD-GDKIEVTNSFELPFDEEEESIFIDT 59

Query: 122 EYHHTMLKSHLKVNPQEVIVGWFSTG----LGVTGGSALIHEFYCREV-PNPVHLTVDTG 176
           EY       H KV PQE IVGW+S G      ++     +H  +      NP+ L +D  
Sbjct: 60  EYLEKRYNLHKKVYPQEKIVGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPS 119

Query: 177 FRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
            ++     K  +S   S    +      EI  ++   E ER+ 
Sbjct: 120 LQSDSE--KLEISTFTSAQREEN---GAEITYEIGTEETERIA 157

This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. It cleaves ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. EIF3f s a potent inhibitor of HIV-1 replication as well as an important negative regulator of cell growth and proliferation. EIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. Length = 157

>gnl|CDD|216478 pfam01398, JAB, JAB1/Mov34/MPN/PAD-1 ubiquitin protease

 Score =  102 bits (257), Expect = 4e-28
 Identities = 40/117 (34%), Positives = 58/117 (49%), Gaps = 7/117 (5%)

Query: 58  SNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV 117
           S  T  +HPLV+  I D   R     E V+G LLG++  D  +++ NS+ +P +E  D V
Sbjct: 1   SVRTVVIHPLVLLKIVDHARRGGKSGEEVMGVLLGTLEGDRVIEVTNSFALPQSETEDDV 60

Query: 118 ---ALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPN 167
               LD EY   ML+   KVN  E +VGW+ +  G    ++       E Y R +P 
Sbjct: 61  EAVELDHEYMEKMLEMLKKVNRDEEVVGWYHSHPGYGCWLSSVDVHTQELYQRMIPE 117

Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain and PAD-1-like domain, JABP1 domain or JAMM domain. These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signaling and protein turnover pathways in eukaryotes. Versions of the domain in prokaryotic cognates of the ubiquitin-modification pathway are predicted to have a similar role. Length = 117

>gnl|CDD|163693 cd08062, MPN_RPN7_8, Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8

 Score =   99 bits (250), Expect = 2e-25
 Identities = 56/161 (34%), Positives = 82/161 (50%), Gaps = 6/161 (3%)

Query: 64  VHPLVIFNICDCYVR-RPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVA---L 119
           VHPLV+ ++ D Y R     ++RV+G LLGS    G +D+ NS+ VP  E     +   L
Sbjct: 5   VHPLVLLSVVDHYNRVAKGTSKRVVGVLLGSWK-KGVLDVTNSFAVPFEEDEKDPSVWFL 63

Query: 120 DIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRN 179
           D  Y   M     KVN +E IVGW+STG  +      I+E + R  PNPV + +D   ++
Sbjct: 64  DHNYLENMYGMFKKVNAKEKIVGWYSTGPKLRPNDLDINELFRRYCPNPVLVIIDVRPKD 123

Query: 180 GEGTVKAYVSVNLSLGDR-QLAAQFQEIPLDLRMIEAERVG 219
                +AY++V     D    +  F  +P ++   EAE VG
Sbjct: 124 LGLPTEAYIAVEEVHDDGTPTSKTFVHVPSEIGAEEAEEVG 164

This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. Rpn7 and Rpn8 are ATP-independent components of the 19S regulator subunit, and contain the MPN structural motif on its N-terminal region. However, while they show a typical MPN metalloprotease fold, they lack the canonical JAMM motif, and therefore do not show catalytic isopeptidase activity. It is suggested that Rpn7 function is primarily structural. Length = 280

>gnl|CDD|214573 smart00232, JAB_MPN, JAB/MPN domain

 Score = 92.8 bits (231), Expect = 4e-24
 Identities = 40/135 (29%), Positives = 55/135 (40%), Gaps = 9/135 (6%)

Query: 63  KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVP-HNEFSDQVALDI 121
           KVHPLV  NI    +R  D  E V G LLG    D   +++  + VP   +       D 
Sbjct: 3   KVHPLVPLNILKHAIR--DGPEEVCGVLLGKSNKD-RPEVKEVFAVPNEPQDDSVQEYDE 59

Query: 122 EYHHTMLKSHLKVNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGF 177
           +Y H M +   KVN    IVGW+ +        +      HE Y    P  V L VD   
Sbjct: 60  DYSHLMDEELKKVNKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIK 119

Query: 178 -RNGEGTVKAYVSVN 191
              G  +++A+    
Sbjct: 120 SFQGRLSLRAFRLTP 134

Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function. Length = 135

>gnl|CDD|215645 PLN03246, PLN03246, 26S proteasome regulatory subunit; Provisional

 Score = 96.0 bits (239), Expect = 9e-24
 Identities = 57/167 (34%), Positives = 84/167 (50%), Gaps = 7/167 (4%)

Query: 64  VHPLVIFNICDCYVR-RPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVA---L 119
           VHPLV+ +I D Y R   D  +RV+G LLGS    G VD+ NS+ VP  E     +   L
Sbjct: 10  VHPLVLLSIVDHYNRVAKDTRKRVVGVLLGS-SFRGRVDVTNSFAVPFEEDDKDPSIWFL 68

Query: 120 DIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRN 179
           D  Y  +M     ++N +E +VGW+STG  +      IHE +   VPNPV + +D   + 
Sbjct: 69  DHNYLESMFGMFKRINAKEHVVGWYSTGPKLRENDLDIHELFNDYVPNPVLVIIDVQPKE 128

Query: 180 GEGTVKAYVSVN--LSLGDRQLAAQFQEIPLDLRMIEAERVGCMYML 224
                KAY +V        ++    F  +P ++   EAE +G  ++L
Sbjct: 129 LGIPTKAYYAVEEVKENATQKSQKVFVHVPSEIGAHEAEEIGVEHLL 175

Length = 303

>gnl|CDD|163694 cd08063, MPN_CSN6, Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6

 Score = 76.1 bits (188), Expect = 1e-16
 Identities = 55/169 (32%), Positives = 81/169 (47%), Gaps = 12/169 (7%)

Query: 60  VTAKVHPLVIFNICDCYVR----RPDQAERVIGTLLGSVLPDG-TVDIRNSY-VVPHNEF 113
           ++ K+HPLVI NI D   R       +  RV+G LLG    DG  ++I NS+ +      
Sbjct: 1   LSVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQ--DGREIEIENSFELKYDTNE 58

Query: 114 SDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGL-GVTGGSALIHEFYCREVPNPVHLT 172
             ++ LD E+  T L+   +V      VGW++TG  G T     IH+       +PV L 
Sbjct: 59  DGEIVLDKEFLETRLEQFKQVFKDLDFVGWYTTGPGGPTESDLPIHKQILEINESPVLLL 118

Query: 173 VDTG--FRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
           +D        +  V  Y SV L L D +   +F+E+P  +   EAER+G
Sbjct: 119 LDPEANASGKDLPVTIYESV-LELVDGEATLRFRELPYTIETGEAERIG 166

CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleavage of Rbx1 and increased deneddylation of cullins inactivate CRLs and presumably stabilize pro-apoptotic factors for final apoptotic steps. While CSN6 shows a typical MPN metalloprotease fold, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. Length = 288

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	230
KOG2975	288	consensus Translation initiation factor 3, subunit	100.0
PLN03246	303	26S proteasome regulatory subunit; Provisional	100.0
cd08062	280	MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains w	100.0
cd08064	265	MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains wi	100.0
cd08063	288	MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains wit	100.0
KOG1556	309	consensus 26S proteasome regulatory complex, subun	100.0
cd08057	157	MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domai	100.0
KOG3050	299	consensus COP9 signalosome, subunit CSN6 [Posttran	100.0
cd08065	266	MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains wi	100.0
cd08069	268	MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal	99.97
PF01398	114	JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; Inte	99.95
KOG1560	339	consensus Translation initiation factor 3, subunit	99.91
smart00232	135	JAB_MPN JAB/MPN domain. Domain in Jun kinase activ	99.9
KOG1554	347	consensus COP9 signalosome, subunit CSN5 [Posttran	99.72
cd07767	116	MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (al	99.72
cd08067	187	MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deu	99.65
cd08058	119	MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains w	99.63
cd08068	244	MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subun	99.37
cd08066	173	MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associ	99.13
KOG1555	316	consensus 26S proteasome regulatory complex, subun	99.1
cd08070	128	MPN_like Mpr1p, Pad1p N-terminal (MPN) domains wit	98.48
cd08060	182	MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family	98.47
PF03665	196	UPF0172: Uncharacterised protein family (UPF0172);	98.39
COG1310	134	Predicted metal-dependent protease of the PAD1/JAB	98.15
KOG3289	199	consensus Uncharacterized conserved protein encode	97.69
cd08056	252	MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains wit	97.44
TIGR02256	131	ICE_VC0181 integrative and conjugative element pro	96.53
cd08072	117	MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1	96.49
PF14464	104	Prok-JAB: Prokaryotic homologs of the JAB domain;	96.0
cd08061	274	MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein l	92.53
PF05021	306	NPL4: NPL4 family; InterPro: IPR007717 The HRD4 ge	90.43
cd08073	108	MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains	89.45
cd08059	101	MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains	82.98
KOG2880	424	consensus SMAD6 interacting protein AMSH, contains	81.84

>KOG2975 consensus Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis]

Probab=100.00  E-value=4.7e-53  Score=367.85  Aligned_cols=186  Identities=46%  Similarity=0.775  Sum_probs=177.2

Q ss_pred             ecccccceeeccCCCCCCCcEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeec
Q 026931           41 AASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALD  120 (230)
Q Consensus        41 ~~~~~~~~~~~~~~~~~~~~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD  120 (230)
                      +.....+.+.+++++.++..+|.|||+|+++|+|||.||..++.||||+|||+ .++|.|||||||++||+|.+|++.+|
T Consensus         2 ~~~~~~v~~~~~~~~~ss~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~-~~~g~ieitNCFaVPhnEssdqvevd   80 (288)
T KOG2975|consen    2 QTPAPHVPGPALPSPFSSNLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGT-VDKGSVEVTNCFAVPHNESSDQVEVD   80 (288)
T ss_pred             CCCcCcCCCcCCCCCCCCCceEEEcceEEeEeehhhhcCCccchhhhhheeec-ccCCeEEEEEeeeccCccccccceee
Confidence            34455666777888899999999999999999999999999999999999997 78999999999999999999999999


Q ss_pred             HHHHHHHHHhhcccCCCCcEEEEeecCCCCCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeEeeecCCcccc
Q 026931          121 IEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLA  200 (230)
Q Consensus       121 ~~y~~~m~~l~kkV~p~e~iVGWY~tg~~~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~~~~~~~~~~~  200 (230)
                      ++|+++|+++|+|+||+|.+||||+||+++++++..||++|.+++++||||++|++.+++.+++|||.+++.+++|++.+
T Consensus        81 m~y~~~M~~l~~k~npnE~vvGWyaTg~dvt~~sslihdyYare~~~pvhLtVDT~~~n~rm~ikaYvss~~Gvpg~~~~  160 (288)
T KOG2975|consen   81 MEYAKNMYELHKKVNPNELVVGWYATGHDVTEHSSLIHDYYAREAPNPVHLTVDTSLQNGRMSIKAYVSSLMGVPGRTMG  160 (288)
T ss_pred             HHHHHHHHHHhcccCCCceeEEEEecCCCcccchhHHHHHhhccCCCCeEEEEeccccCCccceeEEEEeccCCCCcccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999998888


Q ss_pred             ccEEEeceEEecCchHHHHHHHHHHHh
Q 026931          201 AQFQEIPLDLRMIEAERVGCMYMLVIL  227 (230)
Q Consensus       201 ~~F~~lp~~I~~~eaErI~v~~i~k~~  227 (230)
                      .+|.|+|++|.++|+||+|++.|.|..
T Consensus       161 ~mF~plpvel~~~~~ervgl~li~kt~  187 (288)
T KOG2975|consen  161 VMFTPLPVELAYYDAERVGLDLIEKTS  187 (288)
T ss_pred             eeeeeeeeEEeecchhhhHHHHHHHhc
Confidence            999999999999999999999999876

>PLN03246 26S proteasome regulatory subunit; Provisional

Probab=100.00  E-value=1.7e-48  Score=351.89  Aligned_cols=171  Identities=33%  Similarity=0.497  Sum_probs=157.2

Q ss_pred             CCCCcEEEEehhhHhhHhhhhhhccCC-CceEEEEEeeeEeeCCeEEEEEeeeecccCCCcc---eeecHHHHHHHHHhh
Q 026931           56 ATSNVTAKVHPLVIFNICDCYVRRPDQ-AERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSH  131 (230)
Q Consensus        56 ~~~~~~V~IhPlVlL~I~DH~~R~~~~-~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~---~~iD~~y~~~m~~l~  131 (230)
                      +++..+|.|||+|||+|+|||+|+..+ +.||+|+|||+ +.|+.|||+|||++|+++++++   +++|.+|+++|+++|
T Consensus         2 ~~~~~~V~vhPlVll~I~dh~~R~~~~~~~rviG~LLG~-~~~~~ieItnsF~~p~~e~~~~~~~~~~D~~y~~~m~~~~   80 (303)
T PLN03246          2 PRGIEKVVVHPLVLLSIVDHYNRVAKDTRKRVVGVLLGS-SFRGRVDVTNSFAVPFEEDDKDPSIWFLDHNYLESMFGMF   80 (303)
T ss_pred             CCCCcEEEECcHHHHHHHHHHHhccCCCCCeeEEEEEee-ecCCEEEEEeccccCcccCCCCccceeecHHHHHHHHHHH
Confidence            467889999999999999999998765 68999999995 8899999999999999876543   789999999999999


Q ss_pred             cccCCCCcEEEEeecCCCCCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeEeeecCCcc--ccccEEEeceE
Q 026931          132 LKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQ--LAAQFQEIPLD  209 (230)
Q Consensus       132 kkV~p~e~iVGWY~tg~~~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~~~~~~~~~--~~~~F~~lp~~  209 (230)
                      |+|||++.+||||+||++++++|+.||++|++++++||||++|+...+++||++||++...+..++.  .+..|.++|++
T Consensus        81 k~V~~~~~vVGWY~tg~~i~~~d~~IH~~~~~~~~~Pv~L~vD~~~~~~~lpi~aY~s~~~~~~~~~~~~~~~F~~vp~~  160 (303)
T PLN03246         81 KRINAKEHVVGWYSTGPKLRENDLDIHELFNDYVPNPVLVIIDVQPKELGIPTKAYYAVEEVKENATQKSQKVFVHVPSE  160 (303)
T ss_pred             HHhCCCCcEEeeecCCCCCCcchHHHHHHHHhhCCCCeEEEEecCCCCCCCceEEEEEEEeccCCCCcccccEEEECCee
Confidence            9999999999999999999999999999999999999999999999888999999999988776543  56789999999


Q ss_pred             EecCchHHHHHHHHHHHh
Q 026931          210 LRMIEAERVGCMYMLVIL  227 (230)
Q Consensus       210 I~~~eaErI~v~~i~k~~  227 (230)
                      |+++|||||||+|+++..
T Consensus       161 i~~~EaE~Igve~l~r~~  178 (303)
T PLN03246        161 IGAHEAEEIGVEHLLRDV  178 (303)
T ss_pred             eeecCHHHHHHHHHHhcc
Confidence            999999999999999853

>cd08062 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8

Probab=100.00  E-value=1.3e-47  Score=343.03  Aligned_cols=165  Identities=35%  Similarity=0.535  Sum_probs=153.9

Q ss_pred             EEEEehhhHhhHhhhhhhccCC-CceEEEEEeeeEeeCCeEEEEEeeeecccCCCcc---eeecHHHHHHHHHhhcccCC
Q 026931           61 TAKVHPLVIFNICDCYVRRPDQ-AERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSHLKVNP  136 (230)
Q Consensus        61 ~V~IhPlVlL~I~DH~~R~~~~-~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~---~~iD~~y~~~m~~l~kkV~p  136 (230)
                      +|+|||+|||+|+|||+|+..+ +.+|+|+|||+ +.|+++||+|||++|+++++++   +++|.+|+++|+++||+|||
T Consensus         2 ~V~ihplVLl~I~dh~~R~~~~~~~~ViG~LLG~-~~~~~veItnsF~~p~~~~~~~~~~~~~d~~y~~~m~~~~kkv~~   80 (280)
T cd08062           2 KVVVHPLVLLSVVDHYNRVAKGTSKRVVGVLLGS-WKKGVLDVTNSFAVPFEEDEKDPSVWFLDHNYLENMYGMFKKVNA   80 (280)
T ss_pred             eEEEehHHHHHHHHHHhhhcCCCCceEEEEEEEE-EeCCEEEEEEeeecCccCCCCCcchhhhhHHHHHHHHHHHHHhCC
Confidence            7999999999999999998654 78999999995 8899999999999999887654   57999999999999999999


Q ss_pred             CCcEEEEeecCCCCCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeEeeecCCcc-ccccEEEeceEEecCch
Q 026931          137 QEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQ-LAAQFQEIPLDLRMIEA  215 (230)
Q Consensus       137 ~e~iVGWY~tg~~~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~~~~~~~~~-~~~~F~~lp~~I~~~ea  215 (230)
                      ++.+||||+||++++++|+.+|++|++++++||+|++||..+++++|++||++.+....+++ .+..|.++|++|+++||
T Consensus        81 ~e~vVGWY~tg~~~~~~d~~ih~~~~~~~~~pv~l~vd~~~~~~~lpi~aY~s~~~~~~~g~~~~~~F~~vp~~i~~~ea  160 (280)
T cd08062          81 KEKIVGWYSTGPKLRPNDLDINELFRRYCPNPVLVIIDVRPKDLGLPTEAYIAVEEVHDDGTPTSKTFVHVPSEIGAEEA  160 (280)
T ss_pred             CCCeEEEecCCCCCCcchHHHHHHHHHhCCCCEEEEEecCCCCCCCceEEEEEeeeccCCCCcceeEEEEcceEeeccch
Confidence            99999999999999999999999999999999999999999888999999999987775554 78899999999999999


Q ss_pred             HHHHHHHHHHH
Q 026931          216 ERVGCMYMLVI  226 (230)
Q Consensus       216 ErI~v~~i~k~  226 (230)
                      |||||+|+++.
T Consensus       161 E~igve~l~r~  171 (280)
T cd08062         161 EEVGVEHLLRD  171 (280)
T ss_pred             HHHHHHHHHhh
Confidence            99999999984

This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. Rpn7 and Rpn8 are ATP-independent components of the 19S regulator subunit, and contain the MPN structural motif on its N-terminal region. However, while they show a typical MPN metalloprotease fold, they lack the canonical JAMM motif, and therefore do not show catalytic isopeptidase activity. It is suggested that Rpn7 function is primarily structural.

>cd08064 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f

Probab=100.00  E-value=1.6e-47  Score=339.92  Aligned_cols=165  Identities=53%  Similarity=0.872  Sum_probs=156.4

Q ss_pred             EEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEE
Q 026931           62 AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIV  141 (230)
Q Consensus        62 V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iV  141 (230)
                      |+|||+|||+|+|||+|++.++.+|+|+|||+ +.|+++||+|||++|++++++++.+|.+|+++|+++||+|||++.+|
T Consensus         1 v~ihPlVll~I~dH~~R~~~~~~~V~G~LLG~-~~~~~veItnsF~~p~~~~~~~~~~d~~y~~~m~~~~kkv~~~~~vV   79 (265)
T cd08064           1 VRVHPVVLFSILDSYERRNEGQERVIGTLLGT-RSEGEVEITNCFAVPHNESEDQVAVDMEYHRTMYELHQKVNPKEVIV   79 (265)
T ss_pred             CEEccHHHHhHHHHHhhhcCCCcEEEEEEEEE-EeCCEEEEEeCeecceeCCCCeEEEcHHHHHHHHHHHHHhCCCCcEE
Confidence            68999999999999999987889999999996 88999999999999999988889999999999999999999999999


Q ss_pred             EEeecCCCCCcChHHHHHHHhhhCC--CcEEEEEeccCCCCceeEEEEEeEeeecCCccccccEEEeceEEecCchHHHH
Q 026931          142 GWFSTGLGVTGGSALIHEFYCREVP--NPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG  219 (230)
Q Consensus       142 GWY~tg~~~~~~~~~ih~~~~~~~~--~pI~L~vDp~~~~~~l~ikAY~~~~~~~~~~~~~~~F~~lp~~I~~~eaErI~  219 (230)
                      |||+||+.++.++..||++|++.++  +||+|++||..+++++|++||++.+.++.+++.+.+|.++|++|.++|+||||
T Consensus        80 GWY~tg~~~~~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~~~~l~i~ay~~~~~~~~~~~~~~~F~~ip~~i~~~eaE~i~  159 (265)
T cd08064          80 GWYATGSEITEHSALIHDYYSRECTSYNPIHLTVDTSLDDGKMSIKAYVSSPLGVPGKTLGSMFVPIPLELLYSEAERVA  159 (265)
T ss_pred             eeeeCCCCCCccHHHHHHHHHhhCCCCCCEEEEEeCCCCCCCcceEEEEEEecccCCCCcceEEEEcceeeecCcHHHHH
Confidence            9999999999999999999999988  99999999998888999999999988887777889999999999999999999


Q ss_pred             HHHHHHHh
Q 026931          220 CMYMLVIL  227 (230)
Q Consensus       220 v~~i~k~~  227 (230)
                      |+|+++..
T Consensus       160 v~~l~~~~  167 (265)
T cd08064         160 LDLLAKTL  167 (265)
T ss_pred             HHHHHhhc
Confidence            99999853

Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and ap

>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6

Probab=100.00  E-value=1.9e-46  Score=336.58  Aligned_cols=166  Identities=31%  Similarity=0.434  Sum_probs=153.6

Q ss_pred             cEEEEehhhHhhHhhhhhhccCC----CceEEEEEeeeEeeCCeEEEEEeeeecccCCC-cceeecHHHHHHHHHhhccc
Q 026931           60 VTAKVHPLVIFNICDCYVRRPDQ----AERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS-DQVALDIEYHHTMLKSHLKV  134 (230)
Q Consensus        60 ~~V~IhPlVlL~I~DH~~R~~~~----~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e-~~~~iD~~y~~~m~~l~kkV  134 (230)
                      .+|.|||+|||+|+|||+|+..+    +.+|+|+|||+ ++|++|||+|||++|+.+++ +++.+|.+|+++|+++||+|
T Consensus         1 ~~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~-~~~~~veItnsF~~p~~~~~~~~~~id~~y~~~m~~~~kkV   79 (288)
T cd08063           1 LSVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQ-QDGREIEIENSFELKYDTNEDGEIVLDKEFLETRLEQFKQV   79 (288)
T ss_pred             CeEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEE-EcCCEEEEEEEEecccccCCCCceeeCHHHHHHHHHHHHHh
Confidence            37999999999999999998653    58999999995 99999999999999999877 77899999999999999999


Q ss_pred             CCCCcEEEEeecCCC-CCcChHHHHHHHhhhCCCcEEEEEeccC--CCCceeEEEEEeEeeecCCccccccEEEeceEEe
Q 026931          135 NPQEVIVGWFSTGLG-VTGGSALIHEFYCREVPNPVHLTVDTGF--RNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLR  211 (230)
Q Consensus       135 ~p~e~iVGWY~tg~~-~~~~~~~ih~~~~~~~~~pI~L~vDp~~--~~~~l~ikAY~~~~~~~~~~~~~~~F~~lp~~I~  211 (230)
                      ||++.+||||+||+. ++.+++.||++|++.+++||+|++||..  +.+++|++||++...+.++ .....|+++|++|+
T Consensus        80 ~~~~~vVGWY~tg~~~~~~~~~~Ih~~~~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~~~~~~-~~~~~F~~i~~~i~  158 (288)
T cd08063          80 FKDLDFVGWYTTGPGGPTESDLPIHKQILEINESPVLLLLDPEANASGKDLPVTIYESVLELVDG-EATLRFRELPYTIE  158 (288)
T ss_pred             ccCCceEEEEecCCCCCCHHHHHHHHHHHhhCCCcEEEEEccccccCCCCCceeEEEEEEeccCC-ccccEEEeeeeEEE
Confidence            999999999999999 9999999999999999999999999998  5688999999999877765 56788999999999


Q ss_pred             cCchHHHHHHHHHHHh
Q 026931          212 MIEAERVGCMYMLVIL  227 (230)
Q Consensus       212 ~~eaErI~v~~i~k~~  227 (230)
                      ++|+|||||+|+++..
T Consensus       159 ~~eaErIgv~~l~~~~  174 (288)
T cd08063         159 TGEAERIGVDHVARGG  174 (288)
T ss_pred             eccCceeeHHHHHhcC
Confidence            9999999999999754

CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav

>KOG1556 consensus 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=3e-43  Score=304.39  Aligned_cols=171  Identities=32%  Similarity=0.478  Sum_probs=157.0

Q ss_pred             CCCCcEEEEehhhHhhHhhhhhhccC-CCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcc---eeecHHHHHHHHHhh
Q 026931           56 ATSNVTAKVHPLVIFNICDCYVRRPD-QAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSH  131 (230)
Q Consensus        56 ~~~~~~V~IhPlVlL~I~DH~~R~~~-~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~---~~iD~~y~~~m~~l~  131 (230)
                      .-...+|.+||||||+++|||.|... +++||+|.|||. ..++++.|+|||++|++|++.+   |++|.+|++.|+++|
T Consensus         5 ~~~~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~-~~~~~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~mf   83 (309)
T KOG1556|consen    5 ELTVEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGS-WNGDVIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGMF   83 (309)
T ss_pred             ccccceeeeehhHHHHHHHHHhhhccCcCceEEEEEEec-CCCCeEEeecceeccccccCCCCceEEeccHHHHHHHHHH
Confidence            34467999999999999999999753 468999999996 7777899999999999998765   899999999999999


Q ss_pred             cccCCCCcEEEEeecCCCCCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeEeeecC-CccccccEEEeceEE
Q 026931          132 LKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLG-DRQLAAQFQEIPLDL  210 (230)
Q Consensus       132 kkV~p~e~iVGWY~tg~~~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~~~~~~-~~~~~~~F~~lp~~I  210 (230)
                      +|||.+|.+||||+|||.+.++|+.|++.+.++||+|+++++|..+++-+||..||...+..-. |.+....|+.+|++|
T Consensus        84 kKvNakekivGWYhTGPkl~~nDl~In~l~k~y~pnpvLvIIdvkpk~~gLPT~AY~aVeev~dDgt~t~ktF~Hvps~I  163 (309)
T KOG1556|consen   84 KKVNAKEKVVGWYHTGPKLRENDLDINELLKRYVPNPVLVIIDVKPKELGLPTEAYIAVEEVKDDGTPTSKTFVHVPSEI  163 (309)
T ss_pred             HHhcchhheeeeeccCCccccchhhHHHHHhhcCCCceEEEEecccccCCCCchheeeeeeeecCCCCccceeEecCccc
Confidence            9999999999999999999999999999999999999999999999999999999999876554 455677999999999


Q ss_pred             ecCchHHHHHHHHHHHh
Q 026931          211 RMIEAERVGCMYMLVIL  227 (230)
Q Consensus       211 ~~~eaErI~v~~i~k~~  227 (230)
                      +++|||+|||+|+++.+
T Consensus       164 ~AeEAEEvGVEHLlRDi  180 (309)
T KOG1556|consen  164 EAEEAEEVGVEHLLRDI  180 (309)
T ss_pred             chhHHHHhhHHHHHHHH
Confidence            99999999999999875

>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic

Probab=100.00  E-value=1.9e-41  Score=279.15  Aligned_cols=150  Identities=31%  Similarity=0.552  Sum_probs=135.8

Q ss_pred             EEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEE
Q 026931           62 AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIV  141 (230)
Q Consensus        62 V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iV  141 (230)
                      |+|||+|||||+|||+|+..++.+|+|+|||+ +.|++++|+|||++|++++++.+.+|.+|+++|++++|+|+|++.+|
T Consensus         1 V~ihplvll~I~dh~~R~~~~~~~v~G~LlG~-~~~~~veV~nsF~lp~~~~~~~~~~d~~y~~~m~~~~~~v~~~~~vV   79 (157)
T cd08057           1 VQLHPLVLLNISDHYTRRKYGIKRVIGVLLGY-VDGDKIEVTNSFELPFDEEEESIFIDTEYLEKRYNLHKKVYPQEKIV   79 (157)
T ss_pred             CEEccHHHhhHHHHHHhccCCCCeEEEEEEeE-EeCCEEEEEEeEEccccCCCcchhhhHHHHHHHHHHHHHhCCCCCEE
Confidence            68999999999999999876688999999995 88999999999999998887778899999999999999999999999


Q ss_pred             EEeecCCC----CCcChHHHHHHHhhh-CCCcEEEEEeccC--CCCceeEEEEEeEeeecCCccccccEEEeceEEecCc
Q 026931          142 GWFSTGLG----VTGGSALIHEFYCRE-VPNPVHLTVDTGF--RNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIE  214 (230)
Q Consensus       142 GWY~tg~~----~~~~~~~ih~~~~~~-~~~pI~L~vDp~~--~~~~l~ikAY~~~~~~~~~~~~~~~F~~lp~~I~~~e  214 (230)
                      |||++++.    ++..+..+|++|++. +++||+|++||..  .+++++++||++.+...       .+.++|++|.++|
T Consensus        80 GWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~~~~-------~~~~~~~~i~~~e  152 (157)
T cd08057          80 GWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQREE-------NGAEITYEIGTEE  152 (157)
T ss_pred             EEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEecCCC-------CCceeeeEEeccc
Confidence            99999998    788899999999987 8899999999987  46789999999984222       2339999999999


Q ss_pred             hHHHH
Q 026931          215 AERVG  219 (230)
Q Consensus       215 aErI~  219 (230)
                      +||||
T Consensus       153 ~E~I~  157 (157)
T cd08057         153 TERIA  157 (157)
T ss_pred             ccccC
Confidence            99986

This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import

>KOG3050 consensus COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=100.00  E-value=1e-40  Score=288.24  Aligned_cols=172  Identities=27%  Similarity=0.414  Sum_probs=154.4

Q ss_pred             cCCCCCCCcEEEEehhhHhhHhhhhhhccCC---C-ceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHH
Q 026931           52 PSSAATSNVTAKVHPLVIFNICDCYVRRPDQ---A-ERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTM  127 (230)
Q Consensus        52 ~~~~~~~~~~V~IhPlVlL~I~DH~~R~~~~---~-~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m  127 (230)
                      ++.+++++++|.+||||++||+|||+|.+.+   + ++|+|+|+| +|.|++|||.|||++..+..++...+|.+|++++
T Consensus         1 ~Aps~S~s~tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG-~Q~GR~vEi~NSFeL~~d~~~~~~~~dke~l~kk   79 (299)
T KOG3050|consen    1 MAPSSSGSVTVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIG-KQRGRNVEIMNSFELKMDTEEDTETIDKEYLEKK   79 (299)
T ss_pred             CCCCCCCceeEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhhee-cccCceEEEeeeeEEEecchhhhhhccHHHHHHH
Confidence            3556788999999999999999999998643   2 489999999 6999999999999999887766668999999999


Q ss_pred             HHhhcccCCCCcEEEEeecCCCCCcChHHHHHHHhhhCCCcEEEEEeccCCC-CceeEEEEEeEeeecCCccccccEEEe
Q 026931          128 LKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRN-GEGTVKAYVSVNLSLGDRQLAAQFQEI  206 (230)
Q Consensus       128 ~~l~kkV~p~e~iVGWY~tg~~~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~-~~l~ikAY~~~~~~~~~~~~~~~F~~l  206 (230)
                      .++||+|||+..++|||+||.+.++.|+.+|.+++..++.|++|.++|.... .+.|++.|++. ..+.++.+..+|+|+
T Consensus        80 ~eqykqVFpdl~vlGwYttG~d~t~sd~~i~k~l~~i~esplflkLNp~t~~t~~~pv~lfese-~dvidg~~q~~f~~~  158 (299)
T KOG3050|consen   80 EEQYKQVFPDLYVLGWYTTGSDPTPSDIHIHKQLMDINESPLFLKLNPATNHTDKDPVTLFESE-IDVIDGEAQMLFVPL  158 (299)
T ss_pred             HHHHHHhcccceEEEEeecCCCCChhhhHHHHHHHhhhcCceEEEecchhccccCCCceeeeee-heeecCcceeeeeee
Confidence            9999999999999999999999999999999999999999999999998765 45599999986 344455778999999


Q ss_pred             ceEEecCchHHHHHHHHHH
Q 026931          207 PLDLRMIEAERVGCMYMLV  225 (230)
Q Consensus       207 p~~I~~~eaErI~v~~i~k  225 (230)
                      .|+++++|||||||||+++
T Consensus       159 tytl~teEaERIgVdHVA~  177 (299)
T KOG3050|consen  159 TYTLATEEAERIGVDHVAR  177 (299)
T ss_pred             EEEEeehhhhhccchhhee
Confidence            9999999999999999986

>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h

Probab=100.00  E-value=1.1e-33  Score=251.44  Aligned_cols=160  Identities=24%  Similarity=0.326  Sum_probs=135.6

Q ss_pred             EEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcc---eeecHHHHHHHHHhhcccCCC
Q 026931           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSHLKVNPQ  137 (230)
Q Consensus        61 ~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~---~~iD~~y~~~m~~l~kkV~p~  137 (230)
                      +|+|||+|+++|+|||.|+  .+.+|+|+|||. ..|+++||||||++|+.+++++   ...|.+|+.+|++++++++++
T Consensus         2 ~V~I~~~vllkIv~H~~~~--~p~~v~G~LLG~-~~~~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~~~   78 (266)
T cd08065           2 SVQIDGLVVLKIIKHCKEE--LPELVQGQLLGL-DVGGTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVD   78 (266)
T ss_pred             EEEEeHHHHHHHHHHHhcC--CCcEEEEEEeee-EcCCEEEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhCCC
Confidence            6999999999999999886  489999999995 7899999999999999887665   466789999999999999999


Q ss_pred             CcEEEEeecCC-CCCcChHHHHHHHhhh--CCCcEEEEEeccCC-CCceeEEEEEeEeeecC---------------Ccc
Q 026931          138 EVIVGWFSTGL-GVTGGSALIHEFYCRE--VPNPVHLTVDTGFR-NGEGTVKAYVSVNLSLG---------------DRQ  198 (230)
Q Consensus       138 e~iVGWY~tg~-~~~~~~~~ih~~~~~~--~~~pI~L~vDp~~~-~~~l~ikAY~~~~~~~~---------------~~~  198 (230)
                      +.+||||+|++ ....+...+|.+|...  .+++|+|++||..+ +++++++||++++.++.               +.+
T Consensus        79 e~iVGWY~S~p~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s~~g~l~lkAyrl~~~~~~~~~~~~~~~~~l~~~~~~  158 (266)
T cd08065          79 HNHVGWYQSTYLGSFFTRDLIETQYNYQEAIEESVVLVYDPSKTSQGSLSLKAYRLSEKFMELYKEGKFSTESLREANLT  158 (266)
T ss_pred             CcEEEeEeecCCCCcCCHHHHHHHHHHhccCCCCEEEEECCCcccccceeeEEEEEcHHHHHHhhcCCcCHHHHHHhcCc
Confidence            99999999998 2222356667666554  47899999999874 67899999999998774               346


Q ss_pred             ccccEEEeceEEecCchHHHHHHHH
Q 026931          199 LAAQFQEIPLDLRMIEAERVGCMYM  223 (230)
Q Consensus       199 ~~~~F~~lp~~I~~~eaErI~v~~i  223 (230)
                      .+.+|.|||++|.++..+.+.+..+
T Consensus       159 ~~~if~eiPv~i~n~~l~~~~L~~l  183 (266)
T cd08065         159 FSNIFEEIPVVIRNSHLVNALLSEL  183 (266)
T ss_pred             hhcEEEEEEEEEEchHHHHHHHHhc
Confidence            7889999999999987777766655

Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different

>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5

Probab=99.97  E-value=9.2e-30  Score=226.73  Aligned_cols=168  Identities=15%  Similarity=0.226  Sum_probs=150.4

Q ss_pred             CCCCcEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHH--hhcc
Q 026931           56 ATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLK--SHLK  133 (230)
Q Consensus        56 ~~~~~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~--l~kk  133 (230)
                      .....+|.|+|+|+++|++|+.|  ..+.+|+|.|+|. .++++++|+|||++|+.++++++..+.+|++.|++  ++++
T Consensus         6 ~~~~~~V~Is~~allkil~Ha~~--~~p~Ev~GlLlG~-~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~~   82 (268)
T cd08069           6 PDYFEKVYISSLALLKMLKHARA--GGPIEVMGLMLGK-VDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLKQ   82 (268)
T ss_pred             CCcccEEEECHHHHHHHHHHHhc--cCCceEEEEEEee-ecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHHH
Confidence            45567899999999999999977  3688999999995 88899999999999998888888888899999999  9999


Q ss_pred             cCCCCcEEEEeecCCC----CCcChHHHHHHHhhhCCCcEEEEEeccCC--CCceeEEEEEeEeeecC----Cc------
Q 026931          134 VNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFR--NGEGTVKAYVSVNLSLG----DR------  197 (230)
Q Consensus       134 V~p~e~iVGWY~tg~~----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~--~~~l~ikAY~~~~~~~~----~~------  197 (230)
                      +++++.+||||||++.    ++..|+.+|..|++.++.+|+|++||..+  .|++.++||++.+.++.    +.      
T Consensus        83 ~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~~~~~~~~~~~~~~s~~~  162 (268)
T cd08069          83 TGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIPPGYKPLEPRQTTSNIG  162 (268)
T ss_pred             hCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEECccccccCcccCccccC
Confidence            9999999999999987    88899999999999988899999998765  57899999999998764    12      


Q ss_pred             -----------cccccEEEeceEEecCchHHHHHHHHHHH
Q 026931          198 -----------QLAAQFQEIPLDLRMIEAERVGCMYMLVI  226 (230)
Q Consensus       198 -----------~~~~~F~~lp~~I~~~eaErI~v~~i~k~  226 (230)
                                 ..+..|.+||++|.+++.|+..++.+.+.
T Consensus       163 ~~~~~~~~~~~~~~~~y~~l~i~~~~s~l~~~~L~~l~~~  202 (268)
T cd08069         163 HLPKPKIEDFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNK  202 (268)
T ss_pred             ccCcHHHHHhCchhcEEEEeeeEEecCHHHHHHHHHHHHH
Confidence                       15678999999999999999999988765

This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i

>PF01398 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; InterPro: IPR000555 Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors

Probab=99.95  E-value=1.4e-27  Score=185.88  Aligned_cols=107  Identities=36%  Similarity=0.579  Sum_probs=94.1

Q ss_pred             CCcEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCC-eEEEEEeeeecccCCCcce-eecHHHHHHHHHhhcccC
Q 026931           58 SNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDG-TVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKVN  135 (230)
Q Consensus        58 ~~~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~-~VeVtnsF~vp~~e~e~~~-~iD~~y~~~m~~l~kkV~  135 (230)
                      +..+|.|||+|+++|+||++|+.  +.+|+|+|+|+ .+++ .++|+|||++|+.+++++. ..+.++.++|++++++++
T Consensus         2 s~~~V~i~p~vll~i~~h~~r~~--~~~v~G~LlG~-~~~~~~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (114)
T PF01398_consen    2 SVQTVQIHPLVLLKIIDHATRSS--PNEVIGLLLGT-QDGDNTVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVN   78 (114)
T ss_dssp             SCEEEEEEHHHHHHHHHHHHHHH--CTEEEEEEEEE-EETT-EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCS
T ss_pred             CcEEEEECHHHHHHHHHHHhcCC--CCEEEEEEEEE-ecCceEEEEEEEEEeeEecCccccccchhhHHHHHHhhhcccc
Confidence            56799999999999999999974  34999999996 8888 9999999999999876653 456677799999999999


Q ss_pred             CCCcEEEEeecCCCC----CcChHHHHHHHhhhCCC
Q 026931          136 PQEVIVGWFSTGLGV----TGGSALIHEFYCREVPN  167 (230)
Q Consensus       136 p~e~iVGWY~tg~~~----~~~~~~ih~~~~~~~~~  167 (230)
                      |++.+||||+|++..    +..|+.+|++|++.+++
T Consensus        79 ~~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~  114 (114)
T PF01398_consen   79 PNLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN  114 (114)
T ss_dssp             TTSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred             ccceEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence            999999999999887    88999999999998764

This family is also known as the MPN domain [] and PAD-1-like domain []. It has been shown that this domain occurs in prokaryotes []. Mov34 proteins act as the regulatory subunit of the 26 proteasome, which is involved in the ATP-dependent degradation of ubiquitinated proteins. The function of this domain is unclear, but it is found in the N terminus of the proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. A number of the proteins associated with this family belong to MEROPS peptidase family M67 (clan M-). This includes the Poh1 peptidase of Saccharomyces cerevisiae (Baker's yeast) which is a component of the 19S proteasome regulatory particle.; GO: 0005515 protein binding; PDB: 2ZNV_D 2ZNR_A 4E0Q_A 2P87_A 2P8R_A 2O96_B 2O95_A 3RZU_F 3RZV_A.

>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]

Probab=99.91  E-value=6.6e-25  Score=193.22  Aligned_cols=166  Identities=22%  Similarity=0.352  Sum_probs=134.9

Q ss_pred             CCCCCcEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccC--CCcce---eec---HHHHHH
Q 026931           55 AATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNE--FSDQV---ALD---IEYHHT  126 (230)
Q Consensus        55 ~~~~~~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e--~e~~~---~iD---~~y~~~  126 (230)
                      .+.+...|.++.||+++|++||.....+-.-+.|+|+| ...++.+|||||||.|...  ++|.+   ..|   ..|+..
T Consensus         8 ~~p~vk~v~ldsLvVMkiiKHc~ee~~n~d~~~GvL~G-lvvd~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~l~   86 (339)
T KOG1560|consen    8 ESPPVKRVELDSLVVMKIIKHCREEFPNGDGTQGVLLG-LVVDGRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQLA   86 (339)
T ss_pred             CCCccceeeehhHHHHHHHHHHHhhcCCcchhhheeee-eeecceeEeecccCCCccCCCccchhhhhhhHHHHHHHHHH
Confidence            46678899999999999999997664445689999999 6889999999999999843  22221   233   369999


Q ss_pred             HHHhhcccCCCCcEEEEeec---CCCCCcChHHHHHHHhhhCCCcEEEEEeccCC-CCceeEEEEEeEeeecC-------
Q 026931          127 MLKSHLKVNPQEVIVGWFST---GLGVTGGSALIHEFYCREVPNPVHLTVDTGFR-NGEGTVKAYVSVNLSLG-------  195 (230)
Q Consensus       127 m~~l~kkV~p~e~iVGWY~t---g~~~~~~~~~ih~~~~~~~~~pI~L~vDp~~~-~~~l~ikAY~~~~~~~~-------  195 (230)
                      |++.++.+|-+...||||++   |+.++..-+.-+-.|+.-+++.|+|++||..+ +|.|.++||++++..+.       
T Consensus        87 mlrrlr~vnid~~hVGwYqs~~vgs~lS~~lveSqy~YQ~a~pesVvliYD~~kssqG~L~lrAyrLTp~am~~~kekdw  166 (339)
T KOG1560|consen   87 MLRRLRYVNIDHLHVGWYQSAYVGSFLSPALVESQYAYQKAIPESVVLIYDPIKSSQGTLSLRAYRLTPEAMAAHKEKDW  166 (339)
T ss_pred             HHHHhhhcCccceeeeeeeeehhccccCHHHHHHHHHHHhcCCccEEEEeccccccCceEEeehhhcCHHHHHHHhcCCC
Confidence            99999999999999999997   56666444555666888899999999999987 58899999999987652       


Q ss_pred             --------CccccccEEEeceEEecCchHHHHHHHHHHHhcc
Q 026931          196 --------DRQLAAQFQEIPLDLRMIEAERVGCMYMLVILIH  229 (230)
Q Consensus       196 --------~~~~~~~F~~lp~~I~~~eaErI~v~~i~k~~~~  229 (230)
                              +-+...+|.++|+.|++        +|+++.+|+
T Consensus       167 tpealk~~nltyenmfeElPIVIkn--------S~L~nvlms  200 (339)
T KOG1560|consen  167 TPEALKSANLTYENMFEELPIVIKN--------SHLANVLMS  200 (339)
T ss_pred             CHHHHHhcCCCHHHHHhhcCeeeec--------cHHHHHHHH
Confidence                    12567899999999999        777777765

>smart00232 JAB_MPN JAB/MPN domain

Probab=99.90  E-value=3.9e-23  Score=163.31  Aligned_cols=128  Identities=31%  Similarity=0.418  Sum_probs=113.1

Q ss_pred             EEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcce-eecHHHHHHHHHhhcccCCCCc
Q 026931           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKVNPQEV  139 (230)
Q Consensus        61 ~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~-~iD~~y~~~m~~l~kkV~p~e~  139 (230)
                      +|.|||+|+++|++|+.|.  .+.+++|.|+|. ..++.++|+++|++|...+.+.+ ..+.+|+++|.++++++++++.
T Consensus         1 ~v~i~~~v~~~i~~h~~~~--~p~e~~G~L~G~-~~~~~~~i~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (135)
T smart00232        1 EVKVHPLVPLNILKHAIRD--GPEEVCGVLLGK-SNKDRPEVKEVFAVPNEPQDDSVQEYDEDYSHLMDEELKKVNKDLE   77 (135)
T ss_pred             CEEEcHHHHHHHHHHHhcC--CCcEEEEEEEEE-EcCCEEEEEEEEecCcCCCCcchhhhhhhHHHHHHHHHHhhCCCce
Confidence            4789999999999999875  678999999995 77889999999999987655544 6789999999999999999999


Q ss_pred             EEEEeecCC----CCCcChHHHHHHHhhhCCCcEEEEEeccCCC-CceeEEEEEeEe
Q 026931          140 IVGWFSTGL----GVTGGSALIHEFYCREVPNPVHLTVDTGFRN-GEGTVKAYVSVN  191 (230)
Q Consensus       140 iVGWY~tg~----~~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~-~~l~ikAY~~~~  191 (230)
                      +||||+|++    .++..|+.+|..++...+.++++.+|+..+. ++++++||++++
T Consensus        78 ~vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~~g~~~~~af~~~~  134 (135)
T smart00232       78 IVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQGRLSLRAFRLTP  134 (135)
T ss_pred             EEEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccccCcEEEEEEEecC
Confidence            999999987    3667789999999988889999999998875 889999999863

Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.

>KOG1554 consensus COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]

Probab=99.72  E-value=2.4e-17  Score=146.03  Aligned_cols=134  Identities=17%  Similarity=0.291  Sum_probs=111.1

Q ss_pred             CCCcEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeec---HHHHHHHHHhhcc
Q 026931           57 TSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALD---IEYHHTMLKSHLK  133 (230)
Q Consensus        57 ~~~~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD---~~y~~~m~~l~kk  133 (230)
                      ..-..|+|..|+||+|.-|..|  +++-.|||.|+| +.+|+++.|.+||++|.+++|..+...   .+|+....+.-|.
T Consensus        50 ~~fk~vkISalAllKm~~hA~~--GgnlEiMGlm~G-kv~g~t~IvmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~k~  126 (347)
T KOG1554|consen   50 HYFKHVKISALALLKMVMHARS--GGNLEIMGLMQG-KVDGDTIIVMDSFALPVEGTETRVNAQAEAYEYMVQYIEEAKN  126 (347)
T ss_pred             chhhhhhhHHHHHHHHHHHHhc--CCCeEEEeeecc-cccCCeEEEEeccccccccccceechHHHHHHHHHHHHHHHHH
Confidence            3456899999999999998854  478999999999 599999999999999999988765433   5777777888889


Q ss_pred             cCCCCcEEEEeecCCC----CCcChHHHHHHHhhhCCCc-EEEEEeccCC--CCceeEEEEEeEeeec
Q 026931          134 VNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNP-VHLTVDTGFR--NGEGTVKAYVSVNLSL  194 (230)
Q Consensus       134 V~p~e~iVGWY~tg~~----~~~~~~~ih~~~~~~~~~p-I~L~vDp~~~--~~~l~ikAY~~~~~~~  194 (230)
                      ++..+++||||+++|.    ++.-|+..|..-+++ ..| |++++||..+  .+++.|.|||..+.+.
T Consensus       127 ~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~f-QePfvAvViDP~Rtlsagkv~iGAFRTyp~gy  193 (347)
T KOG1554|consen  127 VGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRF-QEPFVAVVIDPTRTLSAGKVNIGAFRTYPKGY  193 (347)
T ss_pred             hhhhhceeeeeecCCCCCccccCcchhHHHHhhhh-cCCeEEEEecCccccccCceeeceeecccCCC
Confidence            9999999999999887    566676665544443 556 9999999875  6899999999998776

>cd07767 MPN Mpr1p, Pad1p N-terminal (MPN) domains

Probab=99.72  E-value=8e-17  Score=124.34  Aligned_cols=111  Identities=25%  Similarity=0.339  Sum_probs=88.8

Q ss_pred             hhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEEEEeecCCC
Q 026931           70 FNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG  149 (230)
Q Consensus        70 L~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iVGWY~tg~~  149 (230)
                      .+|++|+.+.  .+.+|+|.|+|. ..++.++|+++|++|...++..  .+..  ..|....+.+..++.+||||+|++.
T Consensus         2 k~il~~a~~~--~~~ev~G~L~G~-~~~~~~~i~~~~~~~~~~~~~~--~~~~--~~~~~~~~~~~~~~~iVGwyhshp~   74 (116)
T cd07767           2 KMFLDAAKSI--NGKEVIGLLYGS-KTKKVLDVDEVIAVPFDEGDKD--DNVW--FLMYLDFKKLNAGLRIVGWYHTHPK   74 (116)
T ss_pred             HhHHHHHhcC--CCcEEEEEeEEE-EcCCEEEEEEEEecccCCCCCc--cHHH--HHHHHHHHHhcCCCeEEEEEEcCCC
Confidence            4688888653  478999999995 7788899999999998765432  2221  1266666778899999999999876


Q ss_pred             ----CCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEE
Q 026931          150 ----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAY  187 (230)
Q Consensus       150 ----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY  187 (230)
                          ++..|+..|..|++..+++++|++|+...+.+++++||
T Consensus        75 ~~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~~~~~~~~~~~  116 (116)
T cd07767          75 PSCFLSPNDLATHELFQRYFPEKVMIIVDVKPKDLGNSWKCY  116 (116)
T ss_pred             CCCccCHHHHHHHHHHHHhCCCCEEEEEECCCccCCCCcccC
Confidence                67788899999998888999999999887667888887

MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. J

>cd08067 MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase

Probab=99.65  E-value=4.2e-15  Score=126.38  Aligned_cols=129  Identities=14%  Similarity=0.065  Sum_probs=104.5

Q ss_pred             CcEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEee-CCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCC
Q 026931           59 NVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLP-DGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQ  137 (230)
Q Consensus        59 ~~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~-~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~  137 (230)
                      +.+|+|+++|+|+|.+|+...   ...|+|.|+|.+.. ++.++|+++|++|....+++..+|.+++.+|.+..++.+  
T Consensus         4 pf~V~Is~~all~m~~Ha~~~---~~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~~e~dp~~q~e~~~~l~~~g--   78 (187)
T cd08067           4 PFKVTVSSNALLLMDFHCHLT---TSEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLDCEMDPVSETEIRESLESRG--   78 (187)
T ss_pred             CEEEEECHHHHHHHHHHhcCC---CcEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcccccCHHHHHHHHHHHHHcC--
Confidence            679999999999999999643   28999999995333 468999999999987766667889999999999998877  


Q ss_pred             CcEEEEeecCCC----CCcChHHHHHHHhhhCC-------CcEEEEEeccCCC---CceeEEEEEeEee
Q 026931          138 EVIVGWFSTGLG----VTGGSALIHEFYCREVP-------NPVHLTVDTGFRN---GEGTVKAYVSVNL  192 (230)
Q Consensus       138 e~iVGWY~tg~~----~~~~~~~ih~~~~~~~~-------~pI~L~vDp~~~~---~~l~ikAY~~~~~  192 (230)
                      +.+|||||+++.    ++..|+..|..||...+       ..|.|++||-...   ..-.+++|...+.
T Consensus        79 l~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~  147 (187)
T cd08067          79 LSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPP  147 (187)
T ss_pred             CEEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECC
Confidence            599999999875    45567888888888654       2499999997642   3457899998754

This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it p

>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic

Probab=99.63  E-value=2.1e-15  Score=118.69  Aligned_cols=110  Identities=13%  Similarity=0.209  Sum_probs=86.4

Q ss_pred             hHhhHhhhhhhccCCCceEEEEEeeeEee----CCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEEEE
Q 026931           68 VIFNICDCYVRRPDQAERVIGTLLGSVLP----DGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGW  143 (230)
Q Consensus        68 VlL~I~DH~~R~~~~~~~ViG~LLG~~~~----~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iVGW  143 (230)
                      |+++|++|+.+.  .+..++|.|+|....    +..++|+++|+.|...+.         .+.|..+.+....++++|||
T Consensus         2 ~~~~i~~ha~~~--~p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~~~---------~~~~~~~~~~~~~g~~~vG~   70 (119)
T cd08058           2 ALLKMLQHAESN--TGIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCTG---------ENVEELFNVQTGRPLLVVGW   70 (119)
T ss_pred             HHHHHHHHhcCC--CCeEEEEEeeeEEecCccceeEEEEeecCCCCCCchh---------HHHHHHHHHHhCCCCeEEEE
Confidence            789999999663  578999999995332    346899999999875422         22455556678889999999


Q ss_pred             eecCCC----CCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeE
Q 026931          144 FSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV  190 (230)
Q Consensus       144 Y~tg~~----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~  190 (230)
                      ||+++.    ++..|+..|.+|+...++.++|++||..+  ...++||+++
T Consensus        71 YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~--~~~~~a~rl~  119 (119)
T cd08058          71 YHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHR--NKDTGIFRLT  119 (119)
T ss_pred             EecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCC--CcccceEEeC
Confidence            999883    66778887887888778889999999663  7899999873

This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot

>cd08068 MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex

Probab=99.37  E-value=4.1e-11  Score=105.65  Aligned_cols=148  Identities=17%  Similarity=0.188  Sum_probs=105.1

Q ss_pred             cEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEee-------CCeEEEEEeeeecccC-CCcceeecHHH----HHHH
Q 026931           60 VTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLP-------DGTVDIRNSYVVPHNE-FSDQVALDIEY----HHTM  127 (230)
Q Consensus        60 ~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~-------~~~VeVtnsF~vp~~e-~e~~~~iD~~y----~~~m  127 (230)
                      .+|.|.+.++.+|++|+.+.  .+..++|.|+|. .+       ++.+.|..-++.+..+ ..+.+.+|.+-    .+.+
T Consensus         2 ~~V~Is~~~l~~il~HA~~~--~P~EvCGLL~G~-~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea   78 (244)
T cd08068           2 SKVHLSADVYLVCLTHALST--EKEEVMGLLIGE-IEVSKKGEEVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEA   78 (244)
T ss_pred             cEEEECHHHHHHHHHHHHhC--CCcceeEEEEee-cccccccccceeEEEeeeccccccCCCCceEEeCHHHHHHHHHHH
Confidence            47999999999999999654  689999999995 43       3345555545543332 34567888652    3456


Q ss_pred             HHhhcccCCCCcEEEEeecCCC----CCcChHHHHHHHhhhCCCcEEEEEeccCC-----CCceeEEEEEeEeeecCCcc
Q 026931          128 LKSHLKVNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFR-----NGEGTVKAYVSVNLSLGDRQ  198 (230)
Q Consensus       128 ~~l~kkV~p~e~iVGWY~tg~~----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~-----~~~l~ikAY~~~~~~~~~~~  198 (230)
                      -++.+....++.+||||||++.    ++..|+..|..|+...+.-++|++++...     .++..+++|+..+-   .+.
T Consensus        79 ~~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~g---~~~  155 (244)
T cd08068          79 ERLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQG---NKA  155 (244)
T ss_pred             HHHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecCC---CCC
Confidence            6777788899999999999886    55667776677776667779999976432     25788999998631   112


Q ss_pred             ccccEEEeceEEecC
Q 026931          199 LAAQFQEIPLDLRMI  213 (230)
Q Consensus       199 ~~~~F~~lp~~I~~~  213 (230)
                      ......++|++|...
T Consensus       156 ~~~~~~e~pl~i~~~  170 (244)
T cd08068         156 GQYERIEVPLEIVPT  170 (244)
T ss_pred             CcceEEEeeeEEecC
Confidence            235677888888743

BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-contai

>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family

Probab=99.13  E-value=2e-09  Score=90.53  Aligned_cols=124  Identities=12%  Similarity=0.134  Sum_probs=91.5

Q ss_pred             EEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCccee-ecHHHHHHHHHhhcccCCCCc
Q 026931           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVA-LDIEYHHTMLKSHLKVNPQEV  139 (230)
Q Consensus        61 ~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~-iD~~y~~~m~~l~kkV~p~e~  139 (230)
                      .+.|-.-.+-+|+.|+.++...+..+.|.|+|. ..++..+|++.+-.|...++..+. .|.   .++++..  --.++.
T Consensus         3 ~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~-~~~~~~~I~~i~~~~q~~~~~~~~~~~~---~e~~~~~--~~~gle   76 (173)
T cd08066           3 QVVVPADLMDKFLQLAEPNTSRNLETCGILCGK-LSNNAFFITHLIIPKQSGTSDSCQTTNE---EELFDFQ--DQHDLI   76 (173)
T ss_pred             EEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeE-cCCCeEEEEEEEeccccCCCceecCCCH---HHHHHHH--HhCCCe
Confidence            456666778889999976532357999999995 777888999998878776655433 232   1122221  134789


Q ss_pred             EEEEeecCCC----CCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeE-eeec
Q 026931          140 IVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV-NLSL  194 (230)
Q Consensus       140 iVGWY~tg~~----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~-~~~~  194 (230)
                      +||||+|.+.    ++..|+..|..|+...+..++|+++|    +...++||+.. +.++
T Consensus        77 ~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp----~~~~l~afrl~~~~g~  132 (173)
T cd08066          77 TLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAP----KYNEFGIFRLTDPPGL  132 (173)
T ss_pred             eEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECC----CCcEEeEEEeecCCcc
Confidence            9999999774    67788999988888788899999997    36789999998 6655

AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, al

>KOG1555 consensus 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones]

Probab=99.10  E-value=2.3e-10  Score=103.58  Aligned_cols=135  Identities=21%  Similarity=0.326  Sum_probs=110.8

Q ss_pred             CCCCcEEEEehhhHhhHhhhhhhccCCCce-EEEEE-ee---eEeeCCeEEEEEeeeecccCCCcc--e-eecHHHHHHH
Q 026931           56 ATSNVTAKVHPLVIFNICDCYVRRPDQAER-VIGTL-LG---SVLPDGTVDIRNSYVVPHNEFSDQ--V-ALDIEYHHTM  127 (230)
Q Consensus        56 ~~~~~~V~IhPlVlL~I~DH~~R~~~~~~~-ViG~L-LG---~~~~~~~VeVtnsF~vp~~e~e~~--~-~iD~~y~~~m  127 (230)
                      .....+|.++.+++++.++|- |. ..+.. ++|.+ +|   .+.+..++.|.+.|+.|....+-.  + .+|..|+.+|
T Consensus        27 ~~~~e~v~i~slall~m~rh~-r~-~~p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg~~is~~~e~~d~V~q~q~  104 (316)
T KOG1555|consen   27 SDEKETVYISSLALLKMLRHD-RA-GSPEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAVDPVFQTQM  104 (316)
T ss_pred             ccCcceeeeehhhhhhccccc-cc-CCchhhccceeecccccceeeecceeeeeeeccccccceecccchhccHHHHHHH
Confidence            455779999999999999988 43 23444 89999 99   667888999999999998875432  1 5799999999


Q ss_pred             HHhhcccCCCCcEEEEeecCCC----CCcChHHHHHHHhhhCCCcEEEEEeccCC-CCceeEEEEEeEee
Q 026931          128 LKSHLKVNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFR-NGEGTVKAYVSVNL  192 (230)
Q Consensus       128 ~~l~kkV~p~e~iVGWY~tg~~----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~-~~~l~ikAY~~~~~  192 (230)
                      .++.++....+.+|||||+++.    ++..|+..|..|+...+..+..++||..+ .|+.-+.||+....
T Consensus       105 ~~~l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~~g~vv~d~f~~In~  174 (316)
T KOG1555|consen  105 MDLLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPYGKVVPDAFSSINP  174 (316)
T ss_pred             HHHHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCCCCccCChhhhcCc
Confidence            9999999888999999999886    45678999999999989999999999875 35555558877654

>cd08070 MPN_like Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding)

Probab=98.48  E-value=5.7e-06  Score=65.70  Aligned_cols=113  Identities=15%  Similarity=0.076  Sum_probs=78.6

Q ss_pred             hHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCC--cceeecHHHHHHHHHhhcccCCCCcEEEEee
Q 026931           68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS--DQVALDIEYHHTMLKSHLKVNPQEVIVGWFS  145 (230)
Q Consensus        68 VlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e--~~~~iD~~y~~~m~~l~kkV~p~e~iVGWY~  145 (230)
                      ++-+|++|+.+.  .+..+.|.|+|. .++....|+..+++|....+  ....+|.+.+.++.+..++.  ++.+|||||
T Consensus         3 ~~~~il~ha~~~--~P~E~cGlL~G~-~~~~~~~i~~~~p~~n~~~~~~~~f~~d~~~~~~~~~~~~~~--g~~~vG~~H   77 (128)
T cd08070           3 LLEAILAHAEAE--YPEECCGLLLGK-GGGVTAIVTEVYPVRNVAESPRRRFEIDPAEQLAAQREARER--GLEVVGIYH   77 (128)
T ss_pred             HHHHHHHHHHhC--CCCceEEEEEee-cCCCCceEEEEEEccCCCCCCCceEEECHHHHHHHHHHHHHC--CCeEEEEEe
Confidence            456888999763  588999999995 66666678899999986544  35678887777777666655  589999999


Q ss_pred             cCCCCC--cChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeE
Q 026931          146 TGLGVT--GGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV  190 (230)
Q Consensus       146 tg~~~~--~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~  190 (230)
                      |++...  .+...+..+.   ....++|++.....  .-.+++|...
T Consensus        78 SHP~~~~~PS~~D~~~~~---~~~~~~lIv~~~~~--~~~~~~~~~~  119 (128)
T cd08070          78 SHPDGPARPSETDLRLAW---PPGVSYLIVSLAGG--APELRAWRLE  119 (128)
T ss_pred             CCCCCCCCCCHHHHHhcc---CCCCeEEEEECCCC--CcEEEEEEEc
Confidence            988622  2222222211   12458888875333  5678999875

This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.

>cd08060 MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family of unknown function includes neighbor of COX4 (Noc4p)

Probab=98.47  E-value=2e-06  Score=73.06  Aligned_cols=106  Identities=22%  Similarity=0.234  Sum_probs=74.2

Q ss_pred             ehhhHhhHhhhhhhccCCCceEEEEEeeeEee-CCeEEEEEeeeecccCCCcceeecHHH--HHHHHHhhcccCCCCcEE
Q 026931           65 HPLVIFNICDCYVRRPDQAERVIGTLLGSVLP-DGTVDIRNSYVVPHNEFSDQVALDIEY--HHTMLKSHLKVNPQEVIV  141 (230)
Q Consensus        65 hPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~-~~~VeVtnsF~vp~~e~e~~~~iD~~y--~~~m~~l~kkV~p~e~iV  141 (230)
                      .+.+..+|..|..+.  .+..|.|.|+|. .. ++.+.|++++|+.+..    ..++...  ...+.+.+-+- .+..||
T Consensus         2 s~~ay~ki~~HA~k~--p~~evcGlLlG~-~~~~~~~~V~d~vPl~h~~----~~l~P~~Eval~~ve~~~~~-~gl~Iv   73 (182)
T cd08060           2 STLAYVKMLLHAAKY--PHCAVNGLLLGK-KSSGGSVEITDAVPLFHSC----LALAPMLEVALALVDAYCKS-SGLVIV   73 (182)
T ss_pred             CHHHHHHHHHHHHHc--CCchheEEEEee-ecCCCCEEEEEEEEcCCCc----cccCHHHHHHHHHHHHHHHH-CCCEEE
Confidence            356788999999874  466999999996 55 7789999999999853    3455442  22222333322 378999


Q ss_pred             EEeecCCCCCcCh-----HHHHHHHhhhCCCcEEEEEeccCC
Q 026931          142 GWFSTGLGVTGGS-----ALIHEFYCREVPNPVHLTVDTGFR  178 (230)
Q Consensus       142 GWY~tg~~~~~~~-----~~ih~~~~~~~~~pI~L~vDp~~~  178 (230)
                      |+|++.+......     ..|=+...++++++++|++|-..-
T Consensus        74 G~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~l  115 (182)
T cd08060          74 GYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEKL  115 (182)
T ss_pred             EEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCccc
Confidence            9999988654322     234455677788999999997653

This family includes Noc4p (neighbor of COX4; neighbor of Cytochrome c Oxidase 4; nucleolar complex associated 4 homolog) which belongs to the family of unknown function, UPF0172, with MPN/JAMM-like domains. Proteins in this family are homologs of the NOC4 gene which is conserved in eukaryotic members including human, dog, mouse, rat, chicken, zebrafish, fruit fly, mosquito, S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa, A.thaliana, and rice. NOC4 highly expressed in the pancreas and moderately in liver, heart, lung, kidney, brain, skeletal muscle, and placenta. This nucleolar protein forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.

>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function

Probab=98.39  E-value=4.3e-06  Score=71.74  Aligned_cols=122  Identities=16%  Similarity=0.191  Sum_probs=84.9

Q ss_pred             EEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCe--EEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCC
Q 026931           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT--VDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQE  138 (230)
Q Consensus        61 ~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~--VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e  138 (230)
                      +|.+.+.+..+|+=|..+.  ....|.|.|||. ..++.  |+|+||.|+=|....  ..--.|-.-.+.+.|-+. .+.
T Consensus         3 ~v~is~~AY~K~~LHaaKy--P~~aVnGvLlg~-~~~~~~~v~i~DaVPLfH~~~~--L~PmlEvAL~qvd~~~~~-~gl   76 (196)
T PF03665_consen    3 SVEISSRAYAKMILHAAKY--PHCAVNGVLLGK-SSKSSSEVEIVDAVPLFHHWLS--LSPMLEVALAQVDAYAKS-NGL   76 (196)
T ss_pred             eEEEcHHHHHHHHHHhccC--CCCceeeEEEec-cCCCCceEEEeeceeccccccC--cchHHHHHHHHHHHHHhh-CCC
Confidence            7899999999999999876  356899999997 54443  999999999995422  122234444556666543 469


Q ss_pred             cEEEEeecCCCCCcC-----hHHHHHHHhhhCCCcEEEEEeccCCC---CceeEEEEE
Q 026931          139 VIVGWFSTGLGVTGG-----SALIHEFYCREVPNPVHLTVDTGFRN---GEGTVKAYV  188 (230)
Q Consensus       139 ~iVGWY~tg~~~~~~-----~~~ih~~~~~~~~~pI~L~vDp~~~~---~~l~ikAY~  188 (230)
                      .|||+|+....+...     -..|=+.+.+.++++++|++|-..-.   +..++.+|.
T Consensus        77 ~IvGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~kl~~~~~~~~~~~~~  134 (196)
T PF03665_consen   77 VIVGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKKLSSDCKAPAISVYQ  134 (196)
T ss_pred             EEEEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcccccccCCCcceeee
Confidence            999999997644322     22334456667889999999976422   234456666

>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]

Probab=98.15  E-value=2.6e-05  Score=62.46  Aligned_cols=100  Identities=19%  Similarity=0.249  Sum_probs=65.9

Q ss_pred             EEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCC--cceeecHHHHHHHHHhhcccCCCCcE
Q 026931           63 KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS--DQVALDIEYHHTMLKSHLKVNPQEVI  140 (230)
Q Consensus        63 ~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e--~~~~iD~~y~~~m~~l~kkV~p~e~i  140 (230)
                      .+-..++-.|++|..|.  .+.+++|.|+|+ ..+     ...|+++..+.+  ....++.++.. ++...++.+  +.+
T Consensus         3 ~i~~~~l~~il~~a~~~--~p~E~~g~l~~~-~~~-----~~~~~~~n~~~~~~~~~~~~~~~~~-~~~~~~~~g--~~v   71 (134)
T COG1310           3 VIPKEVLGAILEHARRE--HPREVCGLLAGT-REG-----ERYFPLKNVSVEPVEYFEIDPEYSL-FYLAAEDAG--EVV   71 (134)
T ss_pred             eecHHHHHHHHHHHHhc--CChheEEEEEee-ccc-----ceeeccccccCCcceeEeeCHHHHH-HHHHHhhCC--CEE
Confidence            45677888999999775  468999999996 444     455555544332  23355666665 555444444  999


Q ss_pred             EEEeecCCCC--CcChHHHHHHHhhhCCCcEEEEEec
Q 026931          141 VGWFSTGLGV--TGGSALIHEFYCREVPNPVHLTVDT  175 (230)
Q Consensus       141 VGWY~tg~~~--~~~~~~ih~~~~~~~~~pI~L~vDp  175 (230)
                      ||||||+++.  ..++..++  +++..+.|.+++..+
T Consensus        72 vg~yHSHP~~~~~pS~~D~~--~~~~~~~~~~iv~~~  106 (134)
T COG1310          72 VGWYHSHPGGPPYPSEADRR--LSKLGPLPWLIVSVP  106 (134)
T ss_pred             EEEEcCCCCCCCCcCHHHHh--hccccCCCEEEEEcC
Confidence            9999999863  34445554  666666666666653

>KOG3289 consensus Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only]

Probab=97.69  E-value=0.0016  Score=55.08  Aligned_cols=123  Identities=16%  Similarity=0.173  Sum_probs=86.0

Q ss_pred             EEEEehhhHhhHhhhhhhccCCCceEEEEEee--eEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCC
Q 026931           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLG--SVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQE  138 (230)
Q Consensus        61 ~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG--~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e  138 (230)
                      .|.+.-++..+|+=|+.|..  ..-|-|.|+|  + ..|+.|||++|.|+=|+...  +.--.|-...|.+-+-+- -..
T Consensus         3 ~veis~~aY~kmiLH~akyp--h~aVnGLLla~~~-~kg~~v~itdcVPLfH~~la--LaPmlEvAl~lId~~~~~-~Gl   76 (199)
T KOG3289|consen    3 EVEISALAYVKMILHAAKYP--HAAVNGLLLAPAT-GKGECVEITDCVPLFHSHLA--LAPMLEVALNLIDVWGAQ-AGL   76 (199)
T ss_pred             ceeehhhHHHHHHHHhccCc--ccceeeEEEeccC-CCCCeEEEEecchhhccccc--cccHHHHHHHHHHHHHHh-cCe
Confidence            57888999999999998863  4679999999  5 56678999999999877531  122334455566655533 468


Q ss_pred             cEEEEeecCCCCCcC-----hHHHHHHHhhhCCCcEEEEEeccC-CC--CceeEEEEEe
Q 026931          139 VIVGWFSTGLGVTGG-----SALIHEFYCREVPNPVHLTVDTGF-RN--GEGTVKAYVS  189 (230)
Q Consensus       139 ~iVGWY~tg~~~~~~-----~~~ih~~~~~~~~~pI~L~vDp~~-~~--~~l~ikAY~~  189 (230)
                      .|+|.|++...++..     -..|-+.++++++++..|++|... ..  ..-++-+|+-
T Consensus        77 viaGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn~~l~~~~e~~~v~v~e~  135 (199)
T KOG3289|consen   77 VIAGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDNKKLVPQCERPPVIVLED  135 (199)
T ss_pred             EEEEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEeccccccccCCCCEEEeec
Confidence            999999997654321     133445677888887777777653 22  3457888884

>cd08056 MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8

Probab=97.44  E-value=0.00084  Score=59.77  Aligned_cols=103  Identities=22%  Similarity=0.298  Sum_probs=73.6

Q ss_pred             CceEEEEEeeeEeeC---CeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEEEEeecCCC----CCcChH
Q 026931           83 AERVIGTLLGSVLPD---GTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG----VTGGSA  155 (230)
Q Consensus        83 ~~~ViG~LLG~~~~~---~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iVGWY~tg~~----~~~~~~  155 (230)
                      ..++.|.|.|. ...   +.-||+-....|+.++.+.+.+-.+-     -.+. ---++..|||=+|.+.    +++.|+
T Consensus        55 rtQ~~GyLyG~-~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~~-----~~~~-~l~~Le~LGWIHTqp~e~~~Lss~Dv  127 (252)
T cd08056          55 RTQIAGYLYGK-SPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQL-----PQHE-YLEDLEPLGWIHTQPNELPQLSPQDV  127 (252)
T ss_pred             cceEEEEEecc-CCCCCCCeEEEEEEEECCEeCCcCcEECCccC-----ccch-hhCCCEeeEEEEcCCCCccccCHHHH
Confidence            35899999995 665   45688888888888766655442210     1111 1236889999999753    677889


Q ss_pred             HHHHHHhhhCC-----CcEEEEEeccCCCCceeEEEEEeEeeec
Q 026931          156 LIHEFYCREVP-----NPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (230)
Q Consensus       156 ~ih~~~~~~~~-----~pI~L~vDp~~~~~~l~ikAY~~~~~~~  194 (230)
                      ..|..|+..++     +.|.+++-  .+.|..++.||.+++.++
T Consensus       128 ~tha~~~~~~~~w~~~~~V~it~S--ftpGs~sl~ay~LT~~G~  169 (252)
T cd08056         128 TTHAKILADNPSWDGEKTVILTCS--FTPGSCSLTAYKLTPEGY  169 (252)
T ss_pred             HHHHHHHHhccccCCCcEEEEEEc--CCCCceEEEEEecCHHHH
Confidence            99998888776     46777664  457789999999997665

Members of this family are found in pre-mRNA-processing factor 8 (Prp8) which is a critical splicing factor, interacting with several other spliceosomal proteins, snRNAs, and the pre-mRNA, thus organizing and stabilizing the spliceosome catalytic core. Prp8 is one of the largest and most highly conserved of nuclear proteins, occupying a central position in the catalytic core of the spliceosome. Its C-terminal domain exhibits a JAB1/MPN-like core similar to deubiquitinating enzymes, but does not show catalytic isopeptidase activity, possibly because the putative isopeptidase center is covered by insertions and terminal appendices that are grafted onto this core, thus impairing the metal binding site. It is proposed that this domain is a protein interaction domain instead of a Zn(2+)-dependent metalloenzyme as proposed for some MPN proteins. The DEAD-box protein Brr2 and t

>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family

Probab=96.53  E-value=0.054  Score=43.81  Aligned_cols=80  Identities=16%  Similarity=0.158  Sum_probs=54.2

Q ss_pred             hHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCC---cceeecHHHHHHHH-HhhcccCCCCcEEEE
Q 026931           68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS---DQVALDIEYHHTML-KSHLKVNPQEVIVGW  143 (230)
Q Consensus        68 VlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e---~~~~iD~~y~~~m~-~l~kkV~p~e~iVGW  143 (230)
                      ++++++..|......+...-|.|+|. ..+..+.|+++- .|..++-   ....-+.+.+++.+ +.+++.+-...-||=
T Consensus         1 ~v~~~~~~~~Q~~~~~~EtGGiLiG~-~~~~~~ii~~~t-~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~ylGe   78 (131)
T TIGR02256         1 VVVAMLKSYRQWHDLSTETGGVLIGE-RRGAHAVITKIS-EPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYLGE   78 (131)
T ss_pred             CHHHHHHHHHhCcCCCCccceEEEEE-EcCCcEEEEEEE-cCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEEEe
Confidence            46778888866655678999999996 667777777744 4443322   12334556655554 455555556899999


Q ss_pred             eecCCC
Q 026931          144 FSTGLG  149 (230)
Q Consensus       144 Y~tg~~  149 (230)
                      +||++.
T Consensus        79 WHtHP~   84 (131)
T TIGR02256        79 WHTHPE   84 (131)
T ss_pred             cCcCCC
Confidence            999886

This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize.

>cd08072 MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme

Probab=96.49  E-value=0.069  Score=41.95  Aligned_cols=99  Identities=18%  Similarity=0.206  Sum_probs=61.4

Q ss_pred             hHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcce-eecHHHHHHHHHhhcccCCCCcEEEEeec
Q 026931           68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKVNPQEVIVGWFST  146 (230)
Q Consensus        68 VlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~-~iD~~y~~~m~~l~kkV~p~e~iVGWY~t  146 (230)
                      .+-.|++|+.+.  -+..+.|.|+|. ..    .|++.+++|.....+.. ..+.+    |.      -.+..+||-|||
T Consensus         5 ~~~~i~~ha~~~--~P~E~CGlL~G~-~~----~v~~~~~~~n~~~~~~~~~f~~~----~~------~~g~~ivgi~HS   67 (117)
T cd08072           5 LLDSILEAAKSS--HPNEFAALLRGK-DG----VITELLILPGTESGEVSAVFPLL----ML------PLDMSIVGSVHS   67 (117)
T ss_pred             HHHHHHHHHhhc--CCceEEEEEEee-cc----EEEEEEECCCCCCCCcceeechH----Hh------cCCCeEEEEEEc
Confidence            355788888654  688999999995 32    58899999966543221 12221    11      247899999999


Q ss_pred             CCC----CCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeE
Q 026931          147 GLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV  190 (230)
Q Consensus       147 g~~----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~  190 (230)
                      +++    ++..|+.    ++.. +..++|++....  +.=.++||...
T Consensus        68 HP~~~~~PS~~D~~----~~~~-~~~~~lIvs~~~--~~~~~~a~~~~  108 (117)
T cd08072          68 HPSGSPRPSDADLS----FFSK-TGLVHIIVGYPY--DEDDWRAYDSD  108 (117)
T ss_pred             CCCCCCCCCHHHHH----hhhc-CCCEEEEEECcC--CCCCEEEEecC
Confidence            885    3333422    2222 345788886422  22457888764

This family contains only archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.

>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A

Probab=96.00  E-value=0.056  Score=40.55  Aligned_cols=69  Identities=14%  Similarity=0.013  Sum_probs=41.6

Q ss_pred             hHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEEEEeecC
Q 026931           68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTG  147 (230)
Q Consensus        68 VlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iVGWY~tg  147 (230)
                      ++-.|+.|+.+.  .+....|.|+|. ..+..+.++......-.+          +......  +....+..+||+|||+
T Consensus         4 ~~~~i~~~~~~~--~p~E~~G~L~g~-~~~~~~~~~~~~~~~p~~----------~~~~~~~--~~~~~~~~~vg~~HSH   68 (104)
T PF14464_consen    4 VLEQIIAHARAA--YPNEACGLLLGR-RDDQRFIVVPNVNPDPRD----------SFRRERF--EARERGLEIVGIWHSH   68 (104)
T ss_dssp             HHHHHHHHHHHH--TTS-EEEEEEEE-EECCEEEEEEEEE--HHC----------HHHHHH---HHHHHT-EEEEEEEEE
T ss_pred             HHHHHHHHHhhC--CCCeEEEEEEEE-ecCCEEEEEeCCCCCcHH----------HHHHHhh--hhhcccceeeEEEEcC
Confidence            455677887664  578999999996 566777777666511010          1111110  3445678999999998


Q ss_pred             CCCC
Q 026931          148 LGVT  151 (230)
Q Consensus       148 ~~~~  151 (230)
                      +.-.
T Consensus        69 P~~~   72 (104)
T PF14464_consen   69 PSGP   72 (104)
T ss_dssp             SSSS
T ss_pred             CCCC
Confidence            7643

>cd08061 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain

Probab=92.53  E-value=1.4  Score=39.93  Aligned_cols=109  Identities=17%  Similarity=0.202  Sum_probs=71.0

Q ss_pred             ceEEEEEeeeEeeC------CeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEEEEeecCCC--------
Q 026931           84 ERVIGTLLGSVLPD------GTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG--------  149 (230)
Q Consensus        84 ~~ViG~LLG~~~~~------~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iVGWY~tg~~--------  149 (230)
                      ..-+|-|.|+....      .++.|.--++=|...+.+.+.+..+-.++..+... ..-.+..|||=-|...        
T Consensus        34 ~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~vd~iA-~~lGL~~VG~IfT~l~~~~~d~~~  112 (274)
T cd08061          34 QQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADTVDAIA-AALGLERVGWIFTDLPREDKDGYF  112 (274)
T ss_pred             ceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhHHHHHH-HHcCCeEEEEEEecCCCCCCCcee
Confidence            46699999975544      37889989999988777766654443333344443 2347999999988652        


Q ss_pred             CCcChHHHHHHHhh-----hC-CCcEEEEEeccCCCCceeEEEEEeEeeec
Q 026931          150 VTGGSALIHEFYCR-----EV-PNPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (230)
Q Consensus       150 ~~~~~~~ih~~~~~-----~~-~~pI~L~vDp~~~~~~l~ikAY~~~~~~~  194 (230)
                      +++..+.....+|.     .. .+=|-+++.+..+ +...+.||..+...+
T Consensus       113 LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~~-g~i~~~ayQvSdq~~  162 (274)
T cd08061         113 LSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDKD-GQIHFEAYQVSDQAM  162 (274)
T ss_pred             ECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCCC-CceeeeeeeecHHHH
Confidence            33334444455552     22 2336677876544 679999999987543

Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.

>PF05021 NPL4: NPL4 family; InterPro: IPR007717 The HRD4 gene is identical to NPL4, a gene previously implicated in nuclear transport

Probab=90.43  E-value=2.4  Score=38.92  Aligned_cols=106  Identities=20%  Similarity=0.197  Sum_probs=65.1

Q ss_pred             EEEEeeeEeeCC------eEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEEEEeecCCC-----------
Q 026931           87 IGTLLGSVLPDG------TVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG-----------  149 (230)
Q Consensus        87 iG~LLG~~~~~~------~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iVGWY~tg~~-----------  149 (230)
                      +|-|.|......      ++.|.--|+=|+..+.+.+.+..+-.++..+...+.- ++..|||=-|...           
T Consensus         2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA~~l-GL~rVG~IfTdl~~~~~~~g~v~~   80 (306)
T PF05021_consen    2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEERVDAIASAL-GLERVGWIFTDLTDDGSGDGTVKC   80 (306)
T ss_pred             eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHHHHHHHHHC-CCEEEEEEEecCcccccCCCceee
Confidence            799999655445      6899999999988777766663333333333333222 7899999877532           


Q ss_pred             --------CCcChHHHHHHHhhhCCC-------------cEEEEEeccCCCCceeEEEEEeEeeec
Q 026931          150 --------VTGGSALIHEFYCREVPN-------------PVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (230)
Q Consensus       150 --------~~~~~~~ih~~~~~~~~~-------------pI~L~vDp~~~~~~l~ikAY~~~~~~~  194 (230)
                              +++..+..=..+|...++             -|-+++.+. .++.+.+.||..+...+
T Consensus        81 ~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~-~~g~i~~~ayQvS~q~~  145 (306)
T PF05021_consen   81 KRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGD-EEGEIHFEAYQVSNQCV  145 (306)
T ss_pred             ccccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCC-CCCceeeEEeeehHHHH
Confidence                    222222222233332221             266677653 45789999999987543

Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterised step in ER-associated degradation following ubiquitination of target proteins but preceding their recognition by the 26S proteasome []. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing [].

>cd08073 MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains

Probab=89.45  E-value=2.1  Score=33.08  Aligned_cols=65  Identities=8%  Similarity=-0.059  Sum_probs=41.4

Q ss_pred             HhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCC--cceeecH-HHHHHHHHhhcccCCCCcEEEEee
Q 026931           69 IFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS--DQVALDI-EYHHTMLKSHLKVNPQEVIVGWFS  145 (230)
Q Consensus        69 lL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e--~~~~iD~-~y~~~m~~l~kkV~p~e~iVGWY~  145 (230)
                      +-.|++|..+.  -+....|.|+|. .  +   ++..+++.....+  ....+|. ++.+.+    +    ...+||-||
T Consensus         3 ~~~i~~ha~~~--~P~E~CGll~g~-~--~---~~~~~p~~N~~~~p~~~F~idp~e~~~a~----~----~~~ivgi~H   66 (108)
T cd08073           3 EDAILAHAKAE--YPREACGLVVRK-G--R---KLRYIPCRNIAADPEEHFEISPEDYAAAE----D----EGEIVAVVH   66 (108)
T ss_pred             HHHHHHHHhHC--CCCcceEEEEec-C--C---ceEEEECccCCCCccceEEeCHHHHHHHh----c----CCCEEEEEE
Confidence            34678888654  578999999994 3  2   3445666643222  3466775 444332    2    228999999


Q ss_pred             cCCC
Q 026931          146 TGLG  149 (230)
Q Consensus       146 tg~~  149 (230)
                      |+++
T Consensus        67 SHP~   70 (108)
T cd08073          67 SHPD   70 (108)
T ss_pred             cCCC
Confidence            9875

This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.

>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic

Probab=82.98  E-value=5.1  Score=29.92  Aligned_cols=63  Identities=13%  Similarity=0.080  Sum_probs=39.0

Q ss_pred             hHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcEEEEeecCCC
Q 026931           71 NICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG  149 (230)
Q Consensus        71 ~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~iVGWY~tg~~  149 (230)
                      .|.+|+.+.  -+....|.|+|. .. +  .+.+..++|...    ...+..+      ......-+..+||-|++++.
T Consensus         5 ~i~~~~~~~--~p~E~~gll~~~-~~-~--~~~~~~~~~~~~----~~~~~~~------~~~a~~~~~~~v~i~HsHP~   67 (101)
T cd08059           5 TILVHAKDA--HPDEFCGFLSGS-KD-N--VMDELIFLPFVS----GSVSAVI------DLAALEIGMKVVGLVHSHPS   67 (101)
T ss_pred             HHHHHHHhc--CChhhheeeecC-CC-C--eEEEEEeCCCcC----CccChHH------HHHHhhCCCcEEEEEecCcC
Confidence            455666432  367899999994 33 3  577888887543    1233333      22223346789999999875

This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.

>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]

Probab=81.84  E-value=2.4  Score=39.76  Aligned_cols=96  Identities=16%  Similarity=0.221  Sum_probs=62.5

Q ss_pred             CceEEEEEeeeEeeCCeEEEEEeeeecccC-CCcce-eecHHHHHHHHHhhc-ccCCCCcEEEEeecCCC----CCcChH
Q 026931           83 AERVIGTLLGSVLPDGTVDIRNSYVVPHNE-FSDQV-ALDIEYHHTMLKSHL-KVNPQEVIVGWFSTGLG----VTGGSA  155 (230)
Q Consensus        83 ~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e-~e~~~-~iD~~y~~~m~~l~k-kV~p~e~iVGWY~tg~~----~~~~~~  155 (230)
                      +-.-.|.|-|. -..+.+-||.-. +|..+ +.|.. .-+.      .++|. +---++--|||-+|++.    +++-|+
T Consensus       275 nlETCGiL~g~-L~~n~f~IThli-iPkQeatsd~C~t~ne------eelF~vQdq~~L~tlGWIHTHPTQt~FmSSVDl  346 (424)
T KOG2880|consen  275 NLETCGILAGK-LERNEFYITHLI-IPKQEATSDSCNTMNE------EELFEVQDQHELLTLGWIHTHPTQTCFMSSVDL  346 (424)
T ss_pred             cchHHHHhhhH-hhcCcEEEEEEE-eecccCCCccccccCH------HHHheecccccceeeeeeecCCccchhheeccc
Confidence            45679999995 788888888765 44443 33311 1111      11222 11235778999999875    445677


Q ss_pred             HHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeE
Q 026931          156 LIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV  190 (230)
Q Consensus       156 ~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~  190 (230)
                      ..|-.||--.|.+|++++-|..++    -.+|+++
T Consensus       347 HTHcSYQiMlPEAiAIV~aPk~~~----tGiFrLt  377 (424)
T KOG2880|consen  347 HTHCSYQIMLPEAIAIVCAPKSKT----TGIFRLT  377 (424)
T ss_pred             cccceeeeecchheeEEeccccCC----cceEEec
Confidence            777778877899999999987543    2367776

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	230
2o96_A	178	Crystal Structure Of The Metal-Free Dimeric Human M		6e-12
2o95_A	187	Crystal Structure Of The Metal-Free Dimeric Human M		7e-12
4b4t_U	338	Near-Atomic Resolution Structural Model Of The Yeas		3e-07
4e0q_A	141	Crystal Structure Of Mpn Domain From Cop9 Signaloso		1e-04

>pdb|2O96|A Chain A, Crystal Structure Of The Metal-Free Dimeric Human Mov34 Mpn Domain (Residues 1-177) Length = 178

Iteration: 1
 Score = 67.4 bits (163), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 47/132 (35%), Positives = 69/132 (52%), Gaps = 6/132 (4%)
Query: 64  VHPLVIFNICDCYVR--RPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNE--FSDQVA- 118
           VHPLV+ ++ D + R  +    +RV+G LLGS      +D+ NS+ VP +E    D V  
Sbjct: 12  VHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGS-WQKKVLDVSNSFAVPFDEDDKDDSVWF 70
Query: 119 LDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFR 178
           LD +Y   M     KVN +E IVGW+ TG  +      I+E   R  PN V + +D   +
Sbjct: 71  LDHDYLENMYGMFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSVLVIIDVKPK 130
Query: 179 NGEGTVKAYVSV 190
           +     +AY+SV
Sbjct: 131 DLGLPTEAYISV 142

>pdb|2O95|A Chain A, Crystal Structure Of The Metal-Free Dimeric Human Mov34 Mpn Domain (Residues 1-186) Length = 187

Iteration: 1
 Score = 67.0 bits (162), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 47/132 (35%), Positives = 69/132 (52%), Gaps = 6/132 (4%)
Query: 64  VHPLVIFNICDCYVR--RPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNE--FSDQVA- 118
           VHPLV+ ++ D + R  +    +RV+G LLGS      +D+ NS+ VP +E    D V  
Sbjct: 12  VHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGS-WQKKVLDVSNSFAVPFDEDDKDDSVWF 70
Query: 119 LDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFR 178
           LD +Y   M     KVN +E IVGW+ TG  +      I+E   R  PN V + +D   +
Sbjct: 71  LDHDYLENMYGMFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSVLVIIDVKPK 130
Query: 179 NGEGTVKAYVSV 190
           +     +AY+SV
Sbjct: 131 DLGLPTEAYISV 142

>pdb|4B4T|U Chain U, Near-Atomic Resolution Structural Model Of The Yeast 26s Proteasome Length = 338

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 37/132 (28%), Positives = 64/132 (48%), Gaps = 6/132 (4%)
Query: 64  VHPLVIFNICDCYVR-RPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNE---FSDQVAL 119
           + PLV+ +  D Y R +  + +R +G +LG      T+ + NS+ +P  E    SD   L
Sbjct: 10  IAPLVLLSALDHYERTQTKENKRCVGVILGDA-NSSTIRVTNSFALPFEEDEKNSDVWFL 68
Query: 120 DIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVP-NPVHLTVDTGFR 178
           D  Y   M +   K+N +E ++GW+ +G  +      I+E + +    NP+ L VD   +
Sbjct: 69  DHNYIENMNEMCKKINAKEKLIGWYHSGPKLRASDLKINELFKKYTQNNPLLLIVDVKQQ 128
Query: 179 NGEGTVKAYVSV 190
                  AYV++
Sbjct: 129 GVGLPTDAYVAI 140

>pdb|4E0Q|A Chain A, Crystal Structure Of Mpn Domain From Cop9 Signalosome Length = 141

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/92 (28%), Positives = 49/92 (53%), Gaps = 4/92 (4%)
Query: 59  NVTAKVHPLVIFNICDCYVR-RPDQAE--RVIGTLLGSVLPDGTVDIRNSYVVPHNEFSD 115
           +VT  +HPLVI NI + + R R    E  +V G L+G       ++I NS+ +  +   D
Sbjct: 5   SVTISLHPLVIXNISEHWTRFRAQHGEPRQVYGALIGK-QKGRNIEIXNSFELKTDVIGD 63
Query: 116 QVALDIEYHHTMLKSHLKVNPQEVIVGWFSTG 147
           +  ++ +Y++   + + +V      +GW++TG
Sbjct: 64  ETVINKDYYNKKEQQYKQVFSDLDFIGWYTTG 95

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	230
2o95_A	187	26S proteasome non-ATPase regulatory subunit 7; PS	7e-45
4e0q_A	141	COP9 signalosome complex subunit 6; MPN (MPR1P and	3e-43

>2o95_A 26S proteasome non-ATPase regulatory subunit 7; PSMD7, MOV34, JAB1/MPN, metal-free dimer, UN function; HET: SO4 12P ETE PG4 PGE; 1.95A {Homo sapiens} PDB: 2o96_A Length = 187

 Score =  147 bits (372), Expect = 7e-45
 Identities = 52/170 (30%), Positives = 81/170 (47%), Gaps = 7/170 (4%)

Query: 56  ATSNVTAKVHPLVIFNICDCYVR--RPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEF 113
             +     VHPLV+ ++ D + R  +    +RV+G LLGS      +D+ NS+ VP +E 
Sbjct: 4   ELAVQKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQ-KKVLDVSNSFAVPFDED 62

Query: 114 SDQV---ALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVH 170
                   LD +Y   M     KVN +E IVGW+ TG  +      I+E   R  PN V 
Sbjct: 63  DKDDSVWFLDHDYLENMYGMFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSVL 122

Query: 171 LTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQ-FQEIPLDLRMIEAERVG 219
           + +D   ++     +AY+SV     D    ++ F+ +  ++   EAE VG
Sbjct: 123 VIIDVKPKDLGLPTEAYISVEEVHDDGTPTSKTFEHVTSEIGAEEAEEVG 172

>4e0q_A COP9 signalosome complex subunit 6; MPN (MPR1P and PAD1P N-terminal) domain, unknown function; 2.50A {Drosophila melanogaster} Length = 141

 Score =  141 bits (357), Expect = 3e-43
 Identities = 31/140 (22%), Positives = 65/140 (46%), Gaps = 5/140 (3%)

Query: 55  AATSNVTAKVHPLVIFNICDCYVR---RPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHN 111
            +  +VT  +HPLVI NI + + R   +  +  +V G L+G       ++I NS+ +  +
Sbjct: 1   GSHMSVTISLHPLVIMNISEHWTRFRAQHGEPRQVYGALIGKQK-GRNIEIMNSFELKTD 59

Query: 112 EFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHL 171
              D+  ++ +Y++   + + +V      +GW++TG   T     I          P+ L
Sbjct: 60  VIGDETVINKDYYNKKEQQYKQVFSDLDFIGWYTTGDNPTADDIKIQRQIAAINECPIML 119

Query: 172 TVDTGFRNGEG-TVKAYVSV 190
            ++   R+ +   +K + S+
Sbjct: 120 QLNPLSRSVDHLPLKLFESL 139

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	230
4b4t_U	338	RPN8, 26S proteasome regulatory subunit RPN8; hydr	100.0
2o95_A	187	26S proteasome non-ATPase regulatory subunit 7; PS	100.0
4e0q_A	141	COP9 signalosome complex subunit 6; MPN (MPR1P and	100.0
4b4t_V	306	26S proteasome regulatory subunit RPN11; hydrolase	99.97
2znr_A	178	AMSH-like protease; metal binding protein, alterna	99.51
3rzv_A	211	STAM-binding protein; ubiquitin hydrolase, endosom	99.39
2kks_A	146	Uncharacterized protein; NESG, structural genomics	99.03
2kcq_A	153	MOV34/MPN/PAD-1 family; NESG, structure, structura	98.85
1oi0_A	124	AF2198, hypothetical protein AF2198; proteasome, d	98.04
2p8r_A	273	PRP8, PRE-mRNA-splicing factor PRP8; alpha-beta, t	97.17
2og4_A	254	PRE-mRNA-splicing factor 8; isopeptidase, JAB1/MPN	97.04
3sbg_A	565	PRE-mRNA-splicing factor 8; PRP8P, rnaseh domain,	95.82

>4b4t_U RPN8, 26S proteasome regulatory subunit RPN8; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=100.00  E-value=1.8e-46  Score=342.23  Aligned_cols=169  Identities=25%  Similarity=0.436  Sum_probs=153.6

Q ss_pred             CCcEEEEehhhHhhHhhhhhhc-cCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCc---ceeecHHHHHHHHHhhcc
Q 026931           58 SNVTAKVHPLVIFNICDCYVRR-PDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSD---QVALDIEYHHTMLKSHLK  133 (230)
Q Consensus        58 ~~~~V~IhPlVlL~I~DH~~R~-~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~---~~~iD~~y~~~m~~l~kk  133 (230)
                      ...+|.|||||||+|+|||+|. ..++.||+|+|||+ ++|++|||+|||++|++++++   .+.+|.+|+++|+++||+
T Consensus         4 ~~~~V~vhPlVll~I~dH~~R~~~~~~~rViG~LLG~-~~~~~veV~nsF~~p~~e~~~~~~~~~~D~~y~~~m~~~~kk   82 (338)
T 4b4t_U            4 QHEKVTIAPLVLLSALDHYERTQTKENKRCVGVILGD-ANSSTIRVTNSFALPFEEDEKNSDVWFLDHNYIENMNEMCKK   82 (338)
T ss_dssp             CCSEEEECHHHHHHHHHHHHHHTTTCCSCCEEEEEEE-ECSSEEEEEEEEECCEEECSSSTTCEEECHHHHHHHHHHHHH
T ss_pred             CCCEEEEecHHHHHHHHHHHHhhcCCCCeEEEEEEeE-EcCCEEEEEEEEEeccccCCCCCccccccHHHHHHHHHHHhh
Confidence            3569999999999999999994 44578999999995 999999999999999987653   468999999999999999


Q ss_pred             cCCCCcEEEEeecCCCCCcChHHHHHHHhhhCC-CcEEEEEeccCCCCceeEEEEEeEeeecC-CccccccEEEeceEEe
Q 026931          134 VNPQEVIVGWFSTGLGVTGGSALIHEFYCREVP-NPVHLTVDTGFRNGEGTVKAYVSVNLSLG-DRQLAAQFQEIPLDLR  211 (230)
Q Consensus       134 V~p~e~iVGWY~tg~~~~~~~~~ih~~~~~~~~-~pI~L~vDp~~~~~~l~ikAY~~~~~~~~-~~~~~~~F~~lp~~I~  211 (230)
                      |||++.+||||+||+.++.+|+.||++|+++++ +|++|++|+...++++|++||++.+...+ +......|+++|++|+
T Consensus        83 V~~~e~iVGWY~tg~~~~~~d~~Ih~~~~~~~~~~pi~l~~d~~~~~~~lpi~aY~s~~~~~~~~~~~~~~F~~lp~~i~  162 (338)
T 4b4t_U           83 INAKEKLIGWYHSGPKLRASDLKINELFKKYTQNNPLLLIVDVKQQGVGLPTDAYVAIEQVKDDGTSTEKTFLHLPCTIE  162 (338)
T ss_dssp             HCCSCEEEEEEECCSSCCSTHHHHHHHHGGGCCSCCCEEEECSCCCSSSCSEEEEEEEEECSSCSTTCEEEEEEECEEEC
T ss_pred             cCccCCEEEEEecCCCCCccHHHHHHHHHhccCCCcEEEEecCCCCCCCcceEEEEeehhccCCCcccccEEEEeeeEee
Confidence            999999999999999999999999999999984 89999999999999999999999876664 3456678999999999


Q ss_pred             cCchHHHHHHHHHHHh
Q 026931          212 MIEAERVGCMYMLVIL  227 (230)
Q Consensus       212 ~~eaErI~v~~i~k~~  227 (230)
                      ++|+|||||+|++++.
T Consensus       163 ~~eaE~Igv~~l~r~~  178 (338)
T 4b4t_U          163 AEEAEEIGVEHLLRDV  178 (338)
T ss_dssp             SCHHHHHHHHHHHHHH
T ss_pred             cCcHHHHHHHHHHhcc
Confidence            9999999999999864

>2o95_A 26S proteasome non-ATPase regulatory subunit 7; PSMD7, MOV34, JAB1/MPN, metal-free dimer, UN function; HET: SO4 12P ETE PG4 PGE; 1.95A {Homo sapiens} PDB: 2o96_A

Probab=100.00  E-value=9.2e-44  Score=298.77  Aligned_cols=171  Identities=31%  Similarity=0.463  Sum_probs=152.6

Q ss_pred             CCCCcEEEEehhhHhhHhhhhhhcc--CCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCc---ceeecHHHHHHHHHh
Q 026931           56 ATSNVTAKVHPLVIFNICDCYVRRP--DQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSD---QVALDIEYHHTMLKS  130 (230)
Q Consensus        56 ~~~~~~V~IhPlVlL~I~DH~~R~~--~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~---~~~iD~~y~~~m~~l  130 (230)
                      +.+..+|+|||+|+++|+|||+|..  ..+.+|+|+|||. +.|++++|+|||++|+.+++.   .+.+|.+|+++|+++
T Consensus         4 ~~~~~~V~i~plvllkI~~H~~r~~~~~~~~~V~G~LLG~-~~~~~v~V~~~f~lp~~~~~~~~~~~~~d~ey~~~m~~~   82 (187)
T 2o95_A            4 ELAVQKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGS-WQKKVLDVSNSFAVPFDEDDKDDSVWFLDHDYLENMYGM   82 (187)
T ss_dssp             CCSCSEEEECHHHHHHHHHHHHHHHHTTCCSCCEEEEEEE-ESSSEEEEEEEEEECEEECSSCTTSEEECHHHHHHHHHH
T ss_pred             CCCCCEEEEchHHHHHHHHHHhhhcccCCCcEEEEEEEEE-EcCCEEEEEEEEEeCCcccCCCcchhhcCHHHHHHHHHH
Confidence            3556899999999999999999974  3678999999995 889999999999999987654   358999999999999


Q ss_pred             hcccCCCCcEEEEeecCCCCCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeEeeecCC-ccccccEEEeceE
Q 026931          131 HLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGD-RQLAAQFQEIPLD  209 (230)
Q Consensus       131 ~kkV~p~e~iVGWY~tg~~~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~~~~~~~-~~~~~~F~~lp~~  209 (230)
                      +|+++|++.+||||++++..+..|..+|++|++.+++|++|++||....++++++||++.+...++ .+....|.++|++
T Consensus        83 ~~~v~~~~~iVGWY~s~~~~s~~d~~i~~~~~~~~~~~v~Livd~~~~~~~l~i~ay~~~~~~~~~~~~~~~~F~~ip~~  162 (187)
T 2o95_A           83 FKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSVLVIIDVKPKDLGLPTEAYISVEEVHDDGTPTSKTFEHVTSE  162 (187)
T ss_dssp             HHTTSSSCEEEEEEECCSSCCTTHHHHHHHHTTTCTTCEEEEECCCTTC-CCSEEEEEEEEECC----CCEEEEEEEEEE
T ss_pred             HHHhCCCCCEEEEEcCCCcCCcccHHHHHHHHhcCCCCEEEEECCCCCCCCcCeEEEEEechhcCCCCcccCEEEEeeEE
Confidence            999999999999999999999999999999999999999999999887667999999999877643 3557899999999


Q ss_pred             EecCchHHHHHHHHHHHh
Q 026931          210 LRMIEAERVGCMYMLVIL  227 (230)
Q Consensus       210 I~~~eaErI~v~~i~k~~  227 (230)
                      |+++|+|||||+||++..
T Consensus       163 I~~~eaE~i~v~~l~~~~  180 (187)
T 2o95_A          163 IGAEEAEEVGVEHLLRDI  180 (187)
T ss_dssp             ECCCHHHHHHHHHHHHHC
T ss_pred             EecCcHHHHHHHHHHhcC
Confidence            999999999999999975

>4e0q_A COP9 signalosome complex subunit 6; MPN (MPR1P and PAD1P N-terminal) domain, unknown function; 2.50A {Drosophila melanogaster}

Probab=100.00  E-value=8.1e-43  Score=282.59  Aligned_cols=134  Identities=23%  Similarity=0.389  Sum_probs=114.6

Q ss_pred             CCCCcEEEEehhhHhhHhhhhhhccC---CCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhc
Q 026931           56 ATSNVTAKVHPLVIFNICDCYVRRPD---QAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHL  132 (230)
Q Consensus        56 ~~~~~~V~IhPlVlL~I~DH~~R~~~---~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~k  132 (230)
                      .++..+|+|||||||+|+|||+|++.   .+.+|+|+|||. ++|++|||+|||++|++++++++++|.+|+++|++++|
T Consensus         2 ~~~~~~V~ihplvll~I~dH~~R~~~~~g~~~~V~G~LLG~-~~~~~veV~nsF~~p~~~~~~~~~~d~~y~~~m~~~~k   80 (141)
T 4e0q_A            2 SHMSVTISLHPLVIMNISEHWTRFRAQHGEPRQVYGALIGK-QKGRNIEIMNSFELKTDVIGDETVINKDYYNKKEQQYK   80 (141)
T ss_dssp             ---CEEEEECHHHHHHHHHHHHCC------CCEEEEEEEEE-EETTEEEEEEEEECCEEEETTEEEECHHHHHHHHHHHH
T ss_pred             CCCcEEEEEecHHHHHHHHHHhhhcccCCCCcEEEEEEEEE-EeCCEEEEEEEEEecccCCCCceeecHHHHHHHHHHHH
Confidence            45678999999999999999999642   368999999995 89999999999999999888889999999999999999


Q ss_pred             ccCCCCcEEEEeecCCCCCcChHHHHHHHhhhCCCcEEEEEeccCCC-CceeEEEEEeE
Q 026931          133 KVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRN-GEGTVKAYVSV  190 (230)
Q Consensus       133 kV~p~e~iVGWY~tg~~~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~-~~l~ikAY~~~  190 (230)
                      +|||++.+||||+||+.++.+|+.+|++|++++++||+|++||.++. ++||++||++.
T Consensus        81 ~v~~~e~iVGWY~s~~~~~~~d~~i~~~~~~~~~~pV~L~~Dp~~~~~g~Lp~~ay~sv  139 (141)
T 4e0q_A           81 QVFSDLDFIGWYTTGDNPTADDIKIQRQIAAINECPIMLQLNPLSRSVDHLPLKLFESL  139 (141)
T ss_dssp             HHSTTCEEEEEEEEEC-------CHHHHHHHTTCCCEEEEESCSCCCCTTHHHHHHCC-
T ss_pred             HhCCCccEEEEEeCCCCCCcchHHHHHHHHHHCCCCEEEEECCCccCCCeEEEEEEEEE
Confidence            99999999999999999999999999999999999999999999876 56999999874

>4b4t_V 26S proteasome regulatory subunit RPN11; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=99.97  E-value=1.2e-30  Score=234.94  Aligned_cols=169  Identities=15%  Similarity=0.266  Sum_probs=142.5

Q ss_pred             CCCCcEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcce-eecHHHHHHHHHhhccc
Q 026931           56 ATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKV  134 (230)
Q Consensus        56 ~~~~~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~-~iD~~y~~~m~~l~kkV  134 (230)
                      ..+..+|.|+|+|||+|++|+.+  ..+.+|+|.|||...+|++++|+|||++|+.++++++ .+|.+|+.+|+++++++
T Consensus        21 ~~~~~~V~is~lallkm~~Ha~~--~~~~eV~GlLlG~~~~~~~v~Vt~~f~~P~~~~~~~v~~~d~~y~~~m~~~~~~v   98 (306)
T 4b4t_V           21 DDTKETVYISSIALLKMLKHGRA--GVPMEVMGLMLGEFVDDYTVNVVDVFAMPQSGTGVSVEAVDDVFQAKMMDMLKQT   98 (306)
T ss_dssp             CSSCCEEEECHHHHHHHHHHTCS--CSSSCCEEEEEEEEETTTEEEEEEEECCCCEESSSCEECCCHHHHHHHHHHHHHH
T ss_pred             CCCCCEEEEeHHHHHHHHHHhcC--CCCceEEEEEeeEEcCCeEEEEEEEEeCCcCCCCCchhcCCHHHHHHHHHHHHHh
Confidence            35588999999999999999943  3678999999996466778999999999999888776 58999999999999999


Q ss_pred             CCCCcEEEEeecCCC----CCcChHHHHHHHhhhCCCcEEEEEeccCC-CCceeEEEEEeEeeecC--C-----------
Q 026931          135 NPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFR-NGEGTVKAYVSVNLSLG--D-----------  196 (230)
Q Consensus       135 ~p~e~iVGWY~tg~~----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~-~~~l~ikAY~~~~~~~~--~-----------  196 (230)
                      ++++.+||||||++.    ++..|+..|..|++.++.+|+|++||..+ .|+++++||++.+.+..  +           
T Consensus        99 ~~~~~vVGWYhShP~~~~~~S~~Di~tq~~yQ~~~~~~V~lV~Dp~~t~~G~~~i~Afr~~~~~~~~~~~~~~~~~s~~~  178 (306)
T 4b4t_V           99 GRDQMVVGWYHSHPGFGCWLSSVDVNTQKSFEQLNSRAVAVVVDPIQSVKGKVVIDAFRLIDTGALINNLEPRQTTSNTG  178 (306)
T ss_dssp             SCCCCCSEEEEECCSSSCCCCHHHHHHHHHHHHHCSSCEEEEECSSSSSSCSSCEEEEECCHHHHHHCCCCCSCC-----
T ss_pred             CCCcceeeEEecCCCCCCcCCHHHHHHHHHHHhcCCCcEEEEECCCcCCCCceeeeEEEecCccccccccCccccccccc
Confidence            999999999999876    45678888999999999999999999876 48899999999875321  0           


Q ss_pred             -----------ccccccEEEeceEEecCchHHHHHHHHHHH
Q 026931          197 -----------RQLAAQFQEIPLDLRMIEAERVGCMYMLVI  226 (230)
Q Consensus       197 -----------~~~~~~F~~lp~~I~~~eaErI~v~~i~k~  226 (230)
                                 ......|.++|+++..++.|+..++.+.+.
T Consensus       179 ~~~~~~~~~~~~~~~~~yy~l~i~~~ks~le~~~L~~L~~~  219 (306)
T 4b4t_V          179 LLNKANIQALIHGLNRHYYSLNIDYHKTAKETKMLMNLHKE  219 (306)
T ss_dssp             -----------------CEEECSCCCCCSSCTHHHHHHHHC
T ss_pred             ccCchhhhhhhccccceEEEeeeEEEeCcHHHHHHHHHHhc
Confidence                       011346999999999999999999998764

>2znr_A AMSH-like protease; metal binding protein, alternative splicing, hydrolase, metal-binding, metalloprotease, UBL conjugation pathway, zinc; 1.20A {Homo sapiens} PDB: 2znv_A

Probab=99.51  E-value=7.2e-14  Score=116.59  Aligned_cols=127  Identities=12%  Similarity=0.165  Sum_probs=98.7

Q ss_pred             CCcEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceee-cHHHHHHHHHhhcccCC
Q 026931           58 SNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVAL-DIEYHHTMLKSHLKVNP  136 (230)
Q Consensus        58 ~~~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~i-D~~y~~~m~~l~kkV~p  136 (230)
                      +...|.|...++.+|+.|+.++..++..++|.|+|. ..++..+|+++|++|...+++.++. +.+   ..++.  ....
T Consensus         7 ~~~~v~i~~~~l~k~l~hA~~~~~~~~EvcGlL~G~-~~~~~~~V~~v~~~pq~~t~~~~~~~~~~---e~~~~--~~~~   80 (178)
T 2znr_A            7 GLRCVVLPEDLCHKFLQLAESNTVRGIETCGILCGK-LTHNEFTITHVIVPKQSAGPDYCDMENVE---ELFNV--QDQH   80 (178)
T ss_dssp             SCCCEEEETTHHHHHHHHHHHHHTTTCCCEEEEEEE-EETTEEEEEEEEECCEEEETTEEEECCHH---HHHHH--HHHH
T ss_pred             CcEEEEECHHHHHHHHHHHHhCCCCCceEEEEEeeE-ecCCCeEEEEEEeCCcCCCCCeeccCCHH---HHHHH--HHhC
Confidence            356899999999999999987643456899999995 7778899999999998776665543 322   11222  2345


Q ss_pred             CCcEEEEeecCCC----CCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeEeeec
Q 026931          137 QEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (230)
Q Consensus       137 ~e~iVGWY~tg~~----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~~~~~  194 (230)
                      ++.+||||+|.+.    ++..|+..|..|+...+..|+|++||..+    .++||++.+.++
T Consensus        81 ~l~~vGwyHSHP~~~~~pS~~Dv~tq~~yq~~~~~~v~iIvsp~~~----~~~afrl~~~g~  138 (178)
T 2znr_A           81 DLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHK----DTGIFRLTNAGM  138 (178)
T ss_dssp             TCEEEEEEEECSSSCSCCCHHHHHHHHHHHHHCTTCEEEEEEGGGT----EEEEEEECHHHH
T ss_pred             CCEEEEEEeCCCCCCCCCCHHHHHHHHHHHhhcCCEEEEEEcCCCC----cceEEEEECCcE
Confidence            8999999999864    66778888888988888899999999763    279999987654

>3rzv_A STAM-binding protein; ubiquitin hydrolase, endosome-associated deubiquitinat enzyme, hydrolase; 1.67A {Homo sapiens} PDB: 3rzu_A

Probab=99.39  E-value=2.5e-12  Score=110.06  Aligned_cols=126  Identities=14%  Similarity=0.129  Sum_probs=97.8

Q ss_pred             CCcEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeec-H-HHHHHHHHhhcccC
Q 026931           58 SNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALD-I-EYHHTMLKSHLKVN  135 (230)
Q Consensus        58 ~~~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD-~-~y~~~m~~l~kkV~  135 (230)
                      .-.+|.|-.-++-+|+.|...+..++.+++|.|+|. ..++.++|+++|..|...+++.+... . +.++-+.+      
T Consensus        40 ~lr~v~Ipk~ll~kfL~~A~~~tp~~~EvcGlL~Gk-~~~~~~~I~~v~~ppq~gt~~~v~~~~~~e~~~~~~~------  112 (211)
T 3rzv_A           40 GLRHVVVPGRLCPQFLQLASANTARGVATCGILCGK-LMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQ------  112 (211)
T ss_dssp             TBCCEEEETTHHHHHHHHHHHHHHTTCCCEEEEEEE-EETTEEEEEEEEECCEEECSSCEEECCHHHHHHHHHH------
T ss_pred             ccEEEEECHHHHHHHHHHHHhCCCCCceEEEEEEeE-cCCCCEEEEEEEeCCccCCCCceeccChHHHHHHHhh------
Confidence            346899999999999999976533456899999995 78889999999999887766655432 2 22222211      


Q ss_pred             CCCcEEEEeecCCC----CCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeEeeec
Q 026931          136 PQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (230)
Q Consensus       136 p~e~iVGWY~tg~~----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~~~~~  194 (230)
                      .++.+||||+|.+.    ++..|+..|..|+...+..|+|++||...    +++||++++.++
T Consensus       113 ~~l~~vGWyHSHP~~~~~pS~~Dl~tq~~~q~~~~~~I~IVvsP~~~----~lgaFrLtp~G~  171 (211)
T 3rzv_A          113 QGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCSPKFQ----ETGFFKLTDHGL  171 (211)
T ss_dssp             HTCEEEEEEEECTTSCSCCCHHHHHHHHHHHHHCTTCEEEEEETTTT----EEEEEEECHHHH
T ss_pred             CCCEEEEEEeCCCCCCCCCCHHHHHHHHHHHhcCCCeEEEEEcCCCC----eeeEEEeccchh
Confidence            48999999999754    66778888888888888889999998633    799999998776

>2kks_A Uncharacterized protein; NESG, structural genomics, PSI-2, protein structure initiati northeast structural genomics consortium; NMR {Desulfitobacterium hafniense}

Probab=99.03  E-value=8.1e-09  Score=82.78  Aligned_cols=133  Identities=12%  Similarity=0.065  Sum_probs=94.1

Q ss_pred             EEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCC-CcceeecHHHHHHHHHhhcccCCCCcE
Q 026931           62 AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEF-SDQVALDIEYHHTMLKSHLKVNPQEVI  140 (230)
Q Consensus        62 V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~-e~~~~iD~~y~~~m~~l~kkV~p~e~i  140 (230)
                      +.|...++.+|++|..+.  .+..++|.|+|. .+++...|+..|++|.... .+...+|.+.+.+..+..++  .++.+
T Consensus         2 l~i~~~~l~~i~~ha~~~--~p~E~cGlL~G~-~~~~~~~v~~~~p~~n~~~~~~~f~~dp~~~~~~~~~~~~--~g~~i   76 (146)
T 2kks_A            2 ITLTKKQMEEMLAHARQA--LPNEACGLLGGR-RDGDDRWVERVYPLNNLDQSPEHFSMDPREQLTAVKDMRK--NGWVM   76 (146)
T ss_dssp             EEEEHHHHHHHHHHHHHH--TTSCEEEEEEEE-EETTEEEEEEEECCCCCSCCSSSCCCCHHHHHHHHHHHHH--HTCEE
T ss_pred             EEECHHHHHHHHHHHHhc--CCcceEEEEEEE-EcCCCcEEEEEEECCCcCCCCceEEECHHHHHHHHHHHHH--CCCEE
Confidence            568889999999999764  578999999995 7777899999999996543 34567887666665544443  25799


Q ss_pred             EEEeecCCCCC--cChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEeEeeecCCccccccEEEeceEEec
Q 026931          141 VGWFSTGLGVT--GGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRM  212 (230)
Q Consensus       141 VGWY~tg~~~~--~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~~~~~~~~~~~~~~F~~lp~~I~~  212 (230)
                      ||||+|.+...  .+...++.  +. .+..+++++.+.. ++...++||+..         +..|.+.|+.|..
T Consensus        77 vG~~HSHP~~~~~PS~~D~~~--~~-~~~~~~lIvs~~~-~~~~~~~af~~~---------~~~~~e~~i~~~~  137 (146)
T 2kks_A           77 LGNFHSHPATPARPSAEDKRL--AF-DPSLSYLIISLAE-PQKPVCKSFLIK---------KDGVDEEEIILKE  137 (146)
T ss_dssp             EEEEEEESSSCSSCCHHHHTT--CC-SSSCEEEEEECSC-SSSCEEEEEEEC---------SSCEEEECEEEES
T ss_pred             EEEEeCCCcCCCCCCHHHHHh--hh-cCCCeEEEEEccC-CCceEEEEEEEe---------CCeEEEEEEEEeh
Confidence            99999987632  23333332  11 2445788887643 235679999974         2368999998864

>2kcq_A MOV34/MPN/PAD-1 family; NESG, structure, structural genomics, PSI-2, protein structure initiative; NMR {Salinibacter ruber dsm 13855}

Probab=98.85  E-value=8.7e-09  Score=83.21  Aligned_cols=134  Identities=15%  Similarity=0.119  Sum_probs=89.1

Q ss_pred             EEehhhHhhHhhhhhhccCCCceEEEEEeeeEee-CCeEEEEEeeeeccc--CC-CcceeecHHHHHHHHHhhcccCCCC
Q 026931           63 KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLP-DGTVDIRNSYVVPHN--EF-SDQVALDIEYHHTMLKSHLKVNPQE  138 (230)
Q Consensus        63 ~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~-~~~VeVtnsF~vp~~--e~-e~~~~iD~~y~~~m~~l~kkV~p~e  138 (230)
                      .|...++.+|+.|..+.  .+..++|.|+|. .. ++.+.|+..|++|..  ++ .+...+|.+.+.++.+..++.  ++
T Consensus         2 ~i~~~~l~~i~~ha~~~--~p~E~cGlL~G~-~~~~~~~~v~~~~p~~n~~~~~~~~~f~~dp~~~~~~~~~~~~~--g~   76 (153)
T 2kcq_A            2 KTTPDILDQIRVHGADA--YPEEGCGFLLGT-VTDDGDNRVAALHRATNRRSEQRTRRYELTADDYRAADAAAQEQ--GL   76 (153)
T ss_dssp             BCCHHHHHHHHHHHHHH--TTSCCCEEEEEE-ECTTSCEEEEEEEESSCCCCCCCSCCSSCCCCSHHHHHHHHHHH--TC
T ss_pred             EeCHHHHHHHHHHHHhc--CCcceEEEEEEe-eccCCCeEEEEEEECCCCCCCCCCcEEEECHHHHHHHHHHHHHC--CC
Confidence            45678899999999764  578999999995 65 678899999999876  32 334556644444444444332  58


Q ss_pred             cEEEEeecCCCCC--cChHHHHHHHhhhCCCcEEEEEeccCCCCc-eeEEEEEeEeeecCCccccccEEEeceEEecC
Q 026931          139 VIVGWFSTGLGVT--GGSALIHEFYCREVPNPVHLTVDTGFRNGE-GTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMI  213 (230)
Q Consensus       139 ~iVGWY~tg~~~~--~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~-l~ikAY~~~~~~~~~~~~~~~F~~lp~~I~~~  213 (230)
                      .+||||+|.+...  .+...+..+   ..+..++|++.+.  .++ ..+++|+...       ....|.+.+++|...
T Consensus        77 ~ivG~yHSHP~~~~~PS~~D~~~~---~~~~~~~lIvs~~--~~~~~~~~af~~~~-------~~g~~~e~~i~v~~~  142 (153)
T 2kcq_A           77 DVVGVYHSHPDHPARPSATDLEEA---TFPGFTYVIVSVR--DGAPEALTAWALAP-------DRSEFHREDIVRPDP  142 (153)
T ss_dssp             EEEEEEEECSSSSSSCCHHHHHTC---CCTTSEEEEEEEE--TTEEEEEEEEEECT-------TCSCEEEECCBCCCS
T ss_pred             eEEEEEeCCCCCCCCCCHHHHHhh---hcCCCeEEEEECC--CCCccEEEEEEEeC-------CCCcEEEEEEEEecC
Confidence            9999999988632  222333221   1245688888642  233 4689999741       123689999887654

>1oi0_A AF2198, hypothetical protein AF2198; proteasome, deubiquitination, archaea, hydrolase; 1.5A {Archaeoglobus fulgidus} SCOP: c.97.3.1 PDB: 1r5x_A

Probab=98.04  E-value=2.8e-05  Score=60.28  Aligned_cols=107  Identities=16%  Similarity=0.150  Sum_probs=65.5

Q ss_pred             EEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCcE
Q 026931           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVI  140 (230)
Q Consensus        61 ~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~i  140 (230)
                      .+.|...++.+|++|..+.  .+..++|.|+|. .  +  .|++.|++| .....   ....|...|..      .++.+
T Consensus         3 ~v~i~~~~l~~i~~ha~~~--~P~E~cGlL~g~-~--~--~v~~~~~~p-~~~~~---~~~~f~~~~~~------~~~~i   65 (124)
T 1oi0_A            3 SMKISRGLLKTILEAAKSA--HPDEFIALLSGS-K--D--VMDELIFLP-FVSGS---VSAVIHLDMLP------IGMKV   65 (124)
T ss_dssp             SCEECHHHHHHHHHHHHHH--TTSCCEEEEEES-T--T--EECEEEECC-CCC----------------------CCCEE
T ss_pred             EEEEcHHHHHHHHHHHHhc--CCCeeEEEEecc-c--C--EEEEEEECC-CCCCC---cCceeeeeecc------CCCEE
Confidence            3678889999999999764  678999999995 3  2  789999999 44321   11223222222      56999


Q ss_pred             EEEeecCCCCC--cChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEe
Q 026931          141 VGWFSTGLGVT--GGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVS  189 (230)
Q Consensus       141 VGWY~tg~~~~--~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~  189 (230)
                      ||||||++...  .+...+..+  .. +..++|++.+..  +.-.+++|..
T Consensus        66 vG~~HSHP~~~~~PS~~D~~~~--~~-~~~~~lIvs~~~--~~~~~~~f~~  111 (124)
T 1oi0_A           66 FGTVHSHPSPSCRPSEEDLSLF--TR-FGKYHIIVCYPY--DENSWKCYNR  111 (124)
T ss_dssp             EEEEEEESSSCCSCCHHHHHHH--HH-SCSEEEEEETTC--CTTCEEEEET
T ss_pred             EEEEEECcCCCCccCHHHHHhh--hc-CCCEEEEEEccC--CCceEEEEec
Confidence            99999987532  222222222  22 445788886532  2346777765

>2p8r_A PRP8, PRE-mRNA-splicing factor PRP8; alpha-beta, translation; 2.10A {Caenorhabditis elegans} PDB: 2p87_A

Probab=97.17  E-value=0.001  Score=58.53  Aligned_cols=110  Identities=22%  Similarity=0.289  Sum_probs=76.3

Q ss_pred             hHhhhhhhccCCCceEEEEEeeeEeeC---CeEEEEEeeeecccCCCcceee-----cHHHHHHHHHhhcccCCCCcEEE
Q 026931           71 NICDCYVRRPDQAERVIGTLLGSVLPD---GTVDIRNSYVVPHNEFSDQVAL-----DIEYHHTMLKSHLKVNPQEVIVG  142 (230)
Q Consensus        71 ~I~DH~~R~~~~~~~ViG~LLG~~~~~---~~VeVtnsF~vp~~e~e~~~~i-----D~~y~~~m~~l~kkV~p~e~iVG  142 (230)
                      +|++.+.+...-..++.|.|.|. ...   +..||+.---+|...+.+.+..     ..+|+           -++..||
T Consensus        46 nllkkFi~IADlrTq~~G~LyG~-s~~d~~~vkeI~~ivipPQ~gt~~sv~~~~~~p~~~~l-----------~dLe~LG  113 (273)
T 2p8r_A           46 NILKKFITISDLRTQIAGFMYGV-SPPDNPQVKEIRCIVLVPQTGSHQQVNLPTQLPDHELL-----------RDFEPLG  113 (273)
T ss_dssp             HHHHHHHHTSCSSSCCEEEEEEE-CCTTCTTEEEEEEEECCSBEECSSCEECCSSCCCCTTT-----------TTSEEEE
T ss_pred             HHHHHHHHHhhccceEEEEEecc-CCCCCCCeEEEEEEEECCccCCCceEECCCcCcchhhh-----------ccccccc
Confidence            55566655544456899999995 632   3567877777776655443322     12232           6899999


Q ss_pred             EeecCCC----CCcChHHHHHHHhhh---C--CCcEEEEEeccCCCCceeEEEEEeEeeec
Q 026931          143 WFSTGLG----VTGGSALIHEFYCRE---V--PNPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (230)
Q Consensus       143 WY~tg~~----~~~~~~~ih~~~~~~---~--~~pI~L~vDp~~~~~~l~ikAY~~~~~~~  194 (230)
                      |-+|.+.    +++.|+..|..|+..   .  +++|++++-+  +.|..++.||++++.++
T Consensus       114 WIHTqp~e~~~LSs~Dl~tH~~~~~~~~~~~~~e~I~Ivcsf--tpgs~sl~af~LT~~G~  172 (273)
T 2p8r_A          114 WMHTQPNELPQLSPQDVTTHAKLLTDNISWDGEKTVMITCSF--TPGSVSLTAYKLTPSGY  172 (273)
T ss_dssp             EEEEESSCCSSCCHHHHHHHHHHHHHCTTCCTTTCEEEEEEE--ETTEEEEEEEEECHHHH
T ss_pred             eEeeCCCCCCCcCHHHHHHHHHHHhcccccCCCceEEEEEec--CCCCceeEEEEcChHHh
Confidence            9999653    677899999888764   2  3789988854  45667899999987665

>2og4_A PRE-mRNA-splicing factor 8; isopeptidase, JAB1/MPN domain, protein-PR interaction, PRP8P, pseudoenzyme, spliceosome activation; 2.00A {Saccharomyces cerevisiae}

Probab=97.04  E-value=0.0012  Score=57.64  Aligned_cols=112  Identities=13%  Similarity=0.218  Sum_probs=76.2

Q ss_pred             hHhhhhhhccCCCceEEEEEeeeEeeC---CeEEEEEeeeecccCCCcceeec-----HHHHHHHHHhhcccCCCCcEEE
Q 026931           71 NICDCYVRRPDQAERVIGTLLGSVLPD---GTVDIRNSYVVPHNEFSDQVALD-----IEYHHTMLKSHLKVNPQEVIVG  142 (230)
Q Consensus        71 ~I~DH~~R~~~~~~~ViG~LLG~~~~~---~~VeVtnsF~vp~~e~e~~~~iD-----~~y~~~m~~l~kkV~p~e~iVG  142 (230)
                      +|++-+.+...-..++.|.|.|. ...   +..||+.---+|+..+.+.+..-     .+|+.         --++..+|
T Consensus        45 nLlkkFi~IAD~~Tq~cG~LyG~-~~~d~~~v~eI~~ivippQ~gt~~s~~~~~~~p~~~~~~---------l~dLe~LG  114 (254)
T 2og4_A           45 NLLKKFIEISDVKIQVAAFIYGM-SAKDHPKVKEIKTVVLVPQLGHVGSVQISNIPDIGDLPD---------TEGLELLG  114 (254)
T ss_dssp             HHHHHHHHTSCSSSCCEEEEEEE-ECSSCTTEEEEEEEECCCEEEETTEEEECCCCCCTTSTT---------CTTCEEEE
T ss_pred             HHHHHHHHHhhccceEEEEEEcc-CCCCCCCeEEEEEEEECCccCCCceEECCCcCccccchh---------hcCCEecc
Confidence            45555555544456799999996 532   35678776666766554433221     12211         25899999


Q ss_pred             EeecCC----CCCcChHHHHHHHhh-hCCCcEEEEEeccCCCCceeEEEEEeEeeec
Q 026931          143 WFSTGL----GVTGGSALIHEFYCR-EVPNPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (230)
Q Consensus       143 WY~tg~----~~~~~~~~ih~~~~~-~~~~pI~L~vDp~~~~~~l~ikAY~~~~~~~  194 (230)
                      |-+|.+    .+++.|+..|..|+. ..+++|++++-+  +.|..++.||++++.++
T Consensus       115 WIHTqptq~~fLSs~Dl~tH~~~~~~~~~eaIaIvcsf--tpgs~sl~af~LT~~G~  169 (254)
T 2og4_A          115 WIHTQTEELKFMAASEVATHSKLFADKKRDCIDISIFS--TPGSVSLSAYNLTDEGY  169 (254)
T ss_dssp             EEEEESSCCSSCCHHHHHHHHHHHTTTCTTCEEEEEEE--ETTEEEEEEEEECHHHH
T ss_pred             eEeeCCCCCcccCHHHHHHHHHHHHhcCCCeEEEEEec--CCCCceeEEEEcChhhh
Confidence            999965    366788999988877 457899998854  45567889999988765

>3sbg_A PRE-mRNA-splicing factor 8; PRP8P, rnaseh domain, JAB1/MPN domain; 3.28A {Saccharomyces cerevisiae}

Probab=95.82  E-value=0.011  Score=56.03  Aligned_cols=103  Identities=14%  Similarity=0.203  Sum_probs=69.7

Q ss_pred             CceEEEEEeeeEee-C--CeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcc--cCCCCcEEEEeecCCC----CCcC
Q 026931           83 AERVIGTLLGSVLP-D--GTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLK--VNPQEVIVGWFSTGLG----VTGG  153 (230)
Q Consensus        83 ~~~ViG~LLG~~~~-~--~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kk--V~p~e~iVGWY~tg~~----~~~~  153 (230)
                      ..++.|.|.|. .. +  +..||+..--+|..++.+.+..- +     ...+..  .-.++..+||-+|.+.    +++.
T Consensus       368 rTQicGyLyG~-sp~dn~nVkEI~cIVipPQ~Gt~~sv~lp-~-----lp~he~~~~l~dLe~LGWIHTqp~et~fLSs~  440 (565)
T 3sbg_A          368 KIQVAAFIYGM-SAKDHPKVKEIKTVVLVPQLGHVGSVQIS-N-----IPDIGDLPDTEGLELLGWIHTQTEELKFMAAS  440 (565)
T ss_dssp             SSCCEEEEEEE-EETTEEEEEEEEEEECCCEEECSSCEEEC-C-----CCCCTTSTTCTTCEEEEEEEEESSCCSSCCHH
T ss_pred             cceeEEEEecC-CCCCCCCeEEEEEEEECCccCCCceEECC-C-----CCccccccccccCEecceeeecCCcccccCHH
Confidence            45799999995 66 3  34677766666776665554432 0     000000  1267999999999643    6788


Q ss_pred             hHHHHHHHhhhC-CCcEEEEEeccCCCCceeEEEEEeEeeec
Q 026931          154 SALIHEFYCREV-PNPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (230)
Q Consensus       154 ~~~ih~~~~~~~-~~pI~L~vDp~~~~~~l~ikAY~~~~~~~  194 (230)
                      |+..|..+...+ .+.|.+++  +.+.|..++.||.+++.|.
T Consensus       441 Dl~THakl~~~n~~~~I~itv--sftPGS~SLsAy~LT~eGy  480 (565)
T 3sbg_A          441 EVATHSKLFADKKRDCIDISI--FSTPGSVSLSAYNLTDEGY  480 (565)
T ss_dssp             HHHHHHHHHSSSCTTCEEEEE--EEETTEEEEEEEEECHHHH
T ss_pred             HHHHHHHHHHhCCCCeEEEEE--EecCCceEEEEEecCHhHH
Confidence            999998776654 35566666  4567889999999998875

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	230
d1gtma2	178	c.58.1.1 (A:3-180) Glutamate dehydrogenase {Archae	0.001

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	230
d1oi0a_	121	Hypothetical protein AF2198 {Archaeon Archaeoglobu	97.63

>d1oi0a_ c.97.3.1 (A:) Hypothetical protein AF2198 {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: Cytidine deaminase-like
superfamily: JAB1/MPN domain
family: JAB1/MPN domain
domain: Hypothetical protein AF2198
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=97.63  E-value=0.00011  Score=55.25  Aligned_cols=106  Identities=16%  Similarity=0.147  Sum_probs=64.1

Q ss_pred             cEEEEehhhHhhHhhhhhhccCCCceEEEEEeeeEeeCCeEEEEEeeeecccCCCcceeecHHHHHHHHHhhcccCCCCc
Q 026931           60 VTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEV  139 (230)
Q Consensus        60 ~~V~IhPlVlL~I~DH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~e~~~~iD~~y~~~m~~l~kkV~p~e~  139 (230)
                      .+++|..-++-.|++|+.+.  .+..+.|.|+|.   ++  .|+..+.+|....+.. ..   |...|.      -.++.
T Consensus         2 ~~l~I~~~~l~~i~~hA~~~--~P~E~cGlL~G~---~~--~i~~~~~~~n~~~~~~-~~---~~~~~~------~~~~~   64 (121)
T d1oi0a_           2 SSMKISRGLLKTILEAAKSA--HPDEFIALLSGS---KD--VMDELIFLPFVSGSVS-AV---IHLDML------PIGMK   64 (121)
T ss_dssp             CSCEECHHHHHHHHHHHHHH--TTSCCEEEEEES---TT--EECEEEECCCCC-----------------------CCCE
T ss_pred             CeEEECHHHHHHHHHHHHhc--CCceeEEEEEec---CC--cEEEEEEcCCCCCCcc-cc---cccchh------hcCCe
Confidence            45778888999999999775  578999999994   23  4667778876543221 11   111121      13789


Q ss_pred             EEEEeecCCC----CCcChHHHHHHHhhhCCCcEEEEEeccCCCCceeEEEEEe
Q 026931          140 IVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVS  189 (230)
Q Consensus       140 iVGWY~tg~~----~~~~~~~ih~~~~~~~~~pI~L~vDp~~~~~~l~ikAY~~  189 (230)
                      +||||||+++    +++.|+....    . ..-++|++-.....  -.++||..
T Consensus        65 ivgi~HSHP~~~a~PS~~D~~~~~----~-~g~~~~Ivs~p~~~--~~~~~~~~  111 (121)
T d1oi0a_          65 VFGTVHSHPSPSCRPSEEDLSLFT----R-FGKYHIIVCYPYDE--NSWKCYNR  111 (121)
T ss_dssp             EEEEEEEESSSCCSCCHHHHHHHH----H-SCSEEEEEETTCCT--TCEEEEET
T ss_pred             EEEEEEecCCCCCCcCHHHHHhhh----c-cCCEEEEEeCCCCC--CCEEEEeC
Confidence            9999999875    3344443222    1 33477777643222  35888874