Citrus Sinensis ID: 023811

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------
Protein Sequence
MPVVSGYNSSDCPIRYFQNPSSRSLLFESRSEEKKKKIRMAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIVLI
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccHHHHHHHcccccccccccccccccccccccEEEEEcEEEEEHHHHHHHccccccEEEEEEEEEEEcccEEEEEEEEEEcccccccccEEcHHHHHHHHHHHHcccccccEEEEEccccccccccHHHHHHHHHHccccEEEEEEcccccccccEEEEEEEEccccccccccEEcccccccccccHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHcccc
Secondary Structure Prediction (SSPRO)
ccEEEccccccccEEEcccccccEEEEEEEcccccccEEEcccccccccccccccccccEEEEEEEEEEEEEEcccccccccccEEEEEEEEEEccccEEEEEEcEEEccccccccEEEcHHHHHHHHHHHHHcccccEEEEEEcccccccHcHHHHHHHHHHHccccEEEEEEcccccccccEEEEEEEEEEcccccccEEEEEccEEEEEEcHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEEEEEEEEc
Coil and Loop (DISEMBL)
mpvvsgynssdcpiryfqnpssrsllFESRSEEKKKKIRMaasdrtvlqfgpssaatsnvtakvHPLVIFNicdcyvrrpdQAERVIGTLLgsvlpdgtvdirnsyvvphnefsdqVALDIEYHHTMLKshlkvnpqeVIVGWFStglgvtggsaLIHEFycrevpnpvhltvdtgfrngegTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDilkstsvdklpsdlEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIVLI
Flexible Loop (DISEMBL)
mpvvsgynssdcpiryfqnpssrsllFESRSEEKKKKirmaasdrtvlqfgpssaatsnvtakvhPLVIFNICDCYVRRPDQAERVIGTllgsvlpdgtvDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDIlkstsvdklpsdlEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIVLI
Low Complexity Region (SEG)
MPVVSGYNSSDCPIRYFQNPssrsllfesrseekkkkIRMAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIVLI
Disordered region (IsUnstruct)
**********************************************************NVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIVL*
Disordered Region (DISOPRED)
*************************************************************AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDIL******************MERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIVLI
Disordered Region (DISEMBL)
********SSDCPIRYFQNPSSRSLLFESRSEEKKKKIRMAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIVLI
Disordered Region (DISPRO)
*PVVSGYNSSDCPIRYFQNPSSRSLLFESRSEEKKKKIRMA*SDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIVLI
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHi
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHi
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPVVSGYNSSDCPIRYFQNPSSRSLLFESRSEEKKKKIRMAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIVLI
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	277	2.2.26 [Sep-21-2011]
O04202	293	Eukaryotic translation in	yes	no	0.808	0.764	0.763	1e-102
O00303	357	Eukaryotic translation in	yes	no	0.703	0.546	0.398	4e-39
Q4R5B8	361	Eukaryotic translation in	N/A	no	0.703	0.540	0.398	4e-39
Q9DCH4	361	Eukaryotic translation in	yes	no	0.711	0.545	0.394	4e-39
A5A6I3	361	Eukaryotic translation in	yes	no	0.703	0.540	0.398	4e-39
B3M123	280	Eukaryotic translation in	N/A	no	0.740	0.732	0.404	4e-38
B4JGX4	280	Eukaryotic translation in	N/A	no	0.740	0.732	0.395	4e-37
Q54C49	284	Eukaryotic translation in	yes	no	0.714	0.697	0.415	4e-37
Q295I4	280	Eukaryotic translation in	yes	no	0.736	0.728	0.388	5e-37
B4GDU3	280	Eukaryotic translation in	N/A	no	0.736	0.728	0.388	5e-37

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

 Score =  372 bits (955), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 174/228 (76%), Positives = 199/228 (87%), Gaps = 4/228 (1%)

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 RVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMI 264
           RVGFD+LK+TSVDKLP+DLEGME+ MERLLTLIND+YKYVD  V   I
Sbjct: 183 RVGFDVLKATSVDKLPNDLEGMELTMERLLTLINDVYKYVDSVVGGQI 230

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

 Score =  161 bits (408), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 80/201 (39%), Positives = 125/201 (62%), Gaps = 6/201 (2%)

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 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTS-----VDKLPSDLEG 237
           ++KAYVS  + +  R +   F  + +     + ER+G D++  T      V  L SDL+ 
Sbjct: 212 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQQ 271

Query: 238 MEVLMERLLTLINDIYKYVDD 258
           +     R+   ++ + +Y +D
Sbjct: 272 VGGASARIQDALSTVLQYAED 292

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

 Score =  161 bits (408), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 80/201 (39%), Positives = 125/201 (62%), Gaps = 6/201 (2%)

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 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTS-----VDKLPSDLEG 237
           ++KAYVS  + +  R +   F  + +     + ER+G D++  T      V  L SDL+ 
Sbjct: 216 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQQ 275

Query: 238 MEVLMERLLTLINDIYKYVDD 258
           +     R+   ++ + +Y +D
Sbjct: 276 VGGASARIQDALSTVLQYAED 296

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

 Score =  161 bits (408), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 80/203 (39%), Positives = 127/203 (62%), Gaps = 6/203 (2%)

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 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTS-----VDKLPSDLEG 237
           ++KAYVS  + +  R +   F  + +     + ER+G D++  T      V  L SDL+ 
Sbjct: 216 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQQ 275

Query: 238 MEVLMERLLTLINDIYKYVDDTV 260
           +     R+   ++ + +Y +D +
Sbjct: 276 VGGASARIQDALSTVLQYAEDVL 298

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

 Score =  161 bits (408), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 80/201 (39%), Positives = 125/201 (62%), Gaps = 6/201 (2%)

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 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTS-----VDKLPSDLEG 237
           ++KAYVS  + +  R +   F  + +     + ER+G D++  T      V  L SDL+ 
Sbjct: 216 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQQ 275

Query: 238 MEVLMERLLTLINDIYKYVDD 258
           +     R+   ++ + +Y +D
Sbjct: 276 VGGASARIQDALSTVLQYAED 296

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

 Score =  158 bits (399), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 87/215 (40%), Positives = 122/215 (56%), Gaps = 10/215 (4%)

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 NGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKST---SVDKLPS-- 233
            G   ++AYV + L +   +    F  IP++L   E E  G  +L+ T   S    P   
Sbjct: 124 GGRMGLRAYVCIQLGVPGGKSGCMFTPIPVELTSYEPETFGLKLLQKTVGVSPAHRPKTV 183

Query: 234 ----DLEGMEVLMERLLTLINDIYKYVDDTVVSMI 264
               DL  +    ++L  L++ I KYVDD +   +
Sbjct: 184 PPMLDLAQISEASQKLQQLLDLILKYVDDVIAHKV 218

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|B4JGX4|EI3F1_DROGR Eukaryotic translation initiation factor 3 subunit F-1 OS=Drosophila grimshawi GN=eIF3-S5-1 PE=3 SV=1

 Score =  155 bits (391), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 85/215 (39%), Positives = 123/215 (57%), Gaps = 10/215 (4%)

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  AELSYALDMYDLNRKVNSNESVVGWWATGNEVTNHSSVIHEYYARECNNPVHLTVDTSLQ 123

Query: 179 NGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKST---SVDKLPS-- 233
            G   ++AYV + L +   +    F  IP++L   E E  G  +L+ T   S  + P   
Sbjct: 124 GGRMGLRAYVCIQLGVPGGKTGCMFTPIPVELTSYEPETFGLKLLQKTVGVSPAQRPKTV 183

Query: 234 ----DLEGMEVLMERLLTLINDIYKYVDDTVVSMI 264
               DL  +    ++L +L++ I KYVDD +   +
Sbjct: 184 PPMLDLAQISEASQKLQSLLDLILKYVDDVIAHKV 218

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 grimshawi (taxid: 7222)

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

 Score =  155 bits (391), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 86/207 (41%), Positives = 129/207 (62%), Gaps = 9/207 (4%)

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-DRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDK---- 230
           G  N    + AY++ NLSL  +  L + F ++PL++   EAE  G + +  T  D+    
Sbjct: 129 GLTNDTMGIHAYMAHNLSLNPESSLGSYFSQLPLEILTFEAENAGLESIAQTKYDQQSTS 188

Query: 231 LPSDLEGMEVLMERLLTLINDIYKYVD 257
           L S+LE ++  + +L  ++  I  Y++
Sbjct: 189 LLSELESLQGSLTKLDEMLESITSYIE 215

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

 Score =  154 bits (390), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 84/216 (38%), Positives = 123/216 (56%), Gaps = 12/216 (5%)

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 NGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDKLPS----- 233
            G   +++YV + L +   +    F  IP++L   E E  G  +L+ T V   P+     
Sbjct: 124 GGRMGLRSYVCIQLGVPGGKTGCMFTPIPVELTSYEPETFGLKLLQKT-VGVAPANRPKT 182

Query: 234 -----DLEGMEVLMERLLTLINDIYKYVDDTVVSMI 264
                DL  +     +L +L++ I KYVDD +   +
Sbjct: 183 VPPMLDLAQISEASTKLQSLLDLILKYVDDVIAHKV 218

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 =  154 bits (390), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 84/216 (38%), Positives = 123/216 (56%), Gaps = 12/216 (5%)

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 NGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDKLPS----- 233
            G   +++YV + L +   +    F  IP++L   E E  G  +L+ T V   P+     
Sbjct: 124 GGRMGLRSYVCIQLGVPGGKTGCMFTPIPVELTSYEPETFGLKLLQKT-VGVAPANRPKT 182

Query: 234 -----DLEGMEVLMERLLTLINDIYKYVDDTVVSMI 264
                DL  +     +L +L++ I KYVDD +   +
Sbjct: 183 VPPMLDLAQISEASTKLQSLLDLILKYVDDVIAHKV 218

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	277
260586249	288	putative eukaryotic translation initiati	0.797	0.767	0.981	1e-125
255571843	287	eukaryotic translation initiation factor	0.794	0.766	0.850	1e-108
449441322	285	PREDICTED: eukaryotic translation initia	0.787	0.764	0.823	1e-106
224109362	287	predicted protein [Populus trichocarpa]	0.787	0.759	0.813	1e-105
297788583	293	26S proteasome regulatory subunit [Arabi	0.794	0.750	0.794	1e-104
356539943	288	PREDICTED: eukaryotic translation initia	0.812	0.781	0.795	1e-103
358249108	289	uncharacterized protein LOC100811797 [Gl	0.797	0.764	0.815	1e-103
357461161	288	Eukaryotic translation initiation factor	0.797	0.767	0.814	1e-102
225449198	285	PREDICTED: eukaryotic translation initia	0.805	0.782	0.792	1e-102
388507086	288	unknown [Medicago truncatula]	0.797	0.767	0.809	1e-102

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

 Score =  452 bits (1163), Expect = e-125,   Method: Compositional matrix adjust.
 Identities = 217/221 (98%), Positives = 218/221 (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

Query: 220 FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTV 260
           FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTV
Sbjct: 181 FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTV 221

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 =  398 bits (1022), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 188/221 (85%), Positives = 207/221 (93%), Gaps = 1/221 (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

Query: 220 FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTV 260
           +DILK+T VDK+PSDLEGMEV M+RLL LI+D+YKYVDD V
Sbjct: 180 YDILKTTMVDKIPSDLEGMEVSMQRLLALIDDVYKYVDDVV 220

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 =  391 bits (1004), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 182/221 (82%), Positives = 202/221 (91%), Gaps = 3/221 (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

Query: 220 FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTV 260
           FDILK+TS+DKLP+DLEGME  MERLL LI+DIYKYVD+ V
Sbjct: 178 FDILKTTSIDKLPNDLEGMEASMERLLALIDDIYKYVDNVV 218

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 =  386 bits (991), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 179/220 (81%), Positives = 202/220 (91%), Gaps = 2/220 (0%)

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 YCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGF 220
           Y REVPNP+HLTVDTGF NGEGT+KAYVSVNLSLGDR LAAQFQE+PLDLRM+EAER+GF
Sbjct: 121 YSREVPNPIHLTVDTGFSNGEGTIKAYVSVNLSLGDRPLAAQFQEVPLDLRMVEAERIGF 180

Query: 221 DILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTV 260
           D+LK+T VDK+PSDLEGME+ M+RLL LI+D+YKYVDD V
Sbjct: 181 DVLKTTMVDKIPSDLEGMEISMQRLLALIDDVYKYVDDVV 220

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

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 =  384 bits (987), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 178/224 (79%), Positives = 203/224 (90%), Gaps = 4/224 (1%)

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 RVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTV 260
           RVGF++LK+TSVDKLP+DLEGME+ MERLLTLIND+YKYVD  V
Sbjct: 183 RVGFNVLKATSVDKLPNDLEGMELTMERLLTLINDVYKYVDSVV 226

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  380 bits (976), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 179/225 (79%), Positives = 205/225 (91%)

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

Query: 220 FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMI 264
           FD+LK+T+VDK+PSDLEGME  M+ LL LI+DIYKYV+D V  ++
Sbjct: 181 FDMLKATAVDKIPSDLEGMEASMQHLLVLIDDIYKYVNDVVEGLV 225

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  379 bits (974), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 181/222 (81%), Positives = 203/222 (91%), Gaps = 1/222 (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 GFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTV 260
           GFD+LK+T+VDK+PSDLEGME  M+ LL LI+DIYKYVDD V
Sbjct: 181 GFDMLKATAVDKIPSDLEGMEASMQHLLVLIDDIYKYVDDVV 222

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357461161|ref|XP_003600862.1| Eukaryotic translation initiation factor 3 subunit F [Medicago truncatula] gi|217073538|gb|ACJ85129.1| unknown [Medicago truncatula] gi|355489910|gb|AES71113.1| Eukaryotic translation initiation factor 3 subunit F [Medicago truncatula]

 Score =  379 bits (972), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 180/221 (81%), Positives = 201/221 (90%)

Query: 40  MAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT 99
           MA+++RTVLQF  SS+++ +++AKVHPLV+FNICDCYVRRPDQAERVIGTLLGSVLPDGT
Sbjct: 1   MASTNRTVLQFSSSSSSSQSLSAKVHPLVVFNICDCYVRRPDQAERVIGTLLGSVLPDGT 60

Query: 100 VDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHE 159
           VDIRNSY VPHNE  DQVALDIEYHH ML SH KVN +E+IVGW+STGLGVTGGSALIHE
Sbjct: 61  VDIRNSYAVPHNESVDQVALDIEYHHNMLLSHQKVNQKEIIVGWYSTGLGVTGGSALIHE 120

Query: 160 FYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
           FY REVPNP+HLTVDTGF  G GT+KAYVS NLSLGDRQ+AAQFQEIPLDLRM+EAER+G
Sbjct: 121 FYSREVPNPIHLTVDTGFTAGGGTIKAYVSNNLSLGDRQIAAQFQEIPLDLRMVEAERIG 180

Query: 220 FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTV 260
           FDILK+T+VDK+PSDLEGME  ME LL LINDIYKYVDD V
Sbjct: 181 FDILKATTVDKIPSDLEGMEASMEHLLALINDIYKYVDDVV 221

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

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 =  379 bits (972), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 179/226 (79%), Positives = 201/226 (88%), Gaps = 3/226 (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

Query: 220 FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMII 265
           FDILK+T V+KLPSDLEGME  MERLL LI+D+YKYVD  V   ++
Sbjct: 178 FDILKTTMVEKLPSDLEGMEASMERLLALIDDVYKYVDSVVEGQVV 223

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|388507086|gb|AFK41609.1| unknown [Medicago truncatula]

 Score =  377 bits (969), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 179/221 (80%), Positives = 201/221 (90%)

Query: 40  MAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT 99
           MA+++RTVLQF  SS+++ +++A+VHPLV+FNICDCYVRRPDQAERVIGTLLGSVLPDGT
Sbjct: 1   MASTNRTVLQFSSSSSSSQSLSARVHPLVVFNICDCYVRRPDQAERVIGTLLGSVLPDGT 60

Query: 100 VDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHE 159
           VDIRNSY VPHNE  DQVALDIEYHH ML SH KVN +E+IVGW+STGLGVTGGSALIHE
Sbjct: 61  VDIRNSYAVPHNESVDQVALDIEYHHNMLLSHQKVNQKEIIVGWYSTGLGVTGGSALIHE 120

Query: 160 FYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG 219
           FY REVPNP+HLTVDTGF  G GT+KAYVS NLSLGDRQ+AAQFQEIPLDLRM+EAER+G
Sbjct: 121 FYSREVPNPIHLTVDTGFTAGGGTIKAYVSNNLSLGDRQIAAQFQEIPLDLRMVEAERIG 180

Query: 220 FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTV 260
           FDILK+T+VDK+PSDLEGME  ME LL LINDIYKYVDD V
Sbjct: 181 FDILKATTVDKIPSDLEGMEASMEHLLALINDIYKYVDDVV 221

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	277
TAIR|locus:2061206	293	EIF2 "AT2G39990" [Arabidopsis	0.808	0.764	0.763	4.3e-93
MGI|MGI:1913335	361	Eif3f "eukaryotic translation	0.711	0.545	0.394	2.2e-40
UNIPROTKB|B3KSH1	372	EIF3F "HCG1784554, isoform CRA	0.711	0.529	0.394	2.8e-40
UNIPROTKB|O00303	357	EIF3F "Eukaryotic translation	0.711	0.551	0.394	2.8e-40
UNIPROTKB|A5A6I3	361	EIF3F "Eukaryotic translation	0.711	0.545	0.394	2.8e-40
UNIPROTKB|Q4R5B8	361	EIF3F "Eukaryotic translation	0.711	0.545	0.394	2.8e-40
UNIPROTKB|E1BLZ8	384	EIF3F "Uncharacterized protein	0.711	0.513	0.394	4.3e-38
DICTYBASE|DDB_G0293254	284	eif3F "eukaryotic translation	0.714	0.697	0.415	8e-37
FB|FBgn0037270	280	CG9769 [Drosophila melanogaste	0.740	0.732	0.395	7.2e-36
UNIPROTKB|E1C050	332	EIF3F "Uncharacterized protein	0.750	0.626	0.374	7.2e-36

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

 Score = 927 (331.4 bits), Expect = 4.3e-93, P = 4.3e-93
 Identities = 174/228 (76%), Positives = 199/228 (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 RVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMI 264
             RVGFD+LK+TSVDKLP+DLEGME+ MERLLTLIND+YKYVD  V   I
Sbjct:   183 RVGFDVLKATSVDKLPNDLEGMELTMERLLTLINDVYKYVDSVVGGQI 230

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 = 409 (149.0 bits), Expect = 2.2e-40, Sum P(2) = 2.2e-40
 Identities = 80/203 (39%), Positives = 127/203 (62%)

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 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTS-----VDKLPSDLEG 237
             ++KAYVS  + +  R +   F  + +     + ER+G D++  T      V  L SDL+ 
Sbjct:   216 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQQ 275

Query:   238 MEVLMERLLTLINDIYKYVDDTV 260
             +     R+   ++ + +Y +D +
Sbjct:   276 VGGASARIQDALSTVLQYAEDVL 298

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

 Score = 408 (148.7 bits), Expect = 2.8e-40, Sum P(2) = 2.8e-40
 Identities = 80/203 (39%), Positives = 126/203 (62%)

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 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTS-----VDKLPSDLEG 237
             ++KAYVS  + +  R +   F  + +     + ER+G D++  T      V  L SDL+ 
Sbjct:   227 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQQ 286

Query:   238 MEVLMERLLTLINDIYKYVDDTV 260
             +     R+   ++ + +Y +D +
Sbjct:   287 VGGASARIQDALSTVLQYAEDVL 309

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

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

 Score = 408 (148.7 bits), Expect = 2.8e-40, Sum P(2) = 2.8e-40
 Identities = 80/203 (39%), Positives = 126/203 (62%)

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 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTS-----VDKLPSDLEG 237
             ++KAYVS  + +  R +   F  + +     + ER+G D++  T      V  L SDL+ 
Sbjct:   212 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQQ 271

Query:   238 MEVLMERLLTLINDIYKYVDDTV 260
             +     R+   ++ + +Y +D +
Sbjct:   272 VGGASARIQDALSTVLQYAEDVL 294

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 = 408 (148.7 bits), Expect = 2.8e-40, Sum P(2) = 2.8e-40
 Identities = 80/203 (39%), Positives = 126/203 (62%)

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 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTS-----VDKLPSDLEG 237
             ++KAYVS  + +  R +   F  + +     + ER+G D++  T      V  L SDL+ 
Sbjct:   216 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQQ 275

Query:   238 MEVLMERLLTLINDIYKYVDDTV 260
             +     R+   ++ + +Y +D +
Sbjct:   276 VGGASARIQDALSTVLQYAEDVL 298

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 = 408 (148.7 bits), Expect = 2.8e-40, Sum P(2) = 2.8e-40
 Identities = 80/203 (39%), Positives = 126/203 (62%)

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 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTS-----VDKLPSDLEG 237
             ++KAYVS  + +  R +   F  + +     + ER+G D++  T      V  L SDL+ 
Sbjct:   216 SIKAYVSTLMGVPGRTMGVMFTPLTVKYAYYDTERIGVDLIMKTCFSPNRVIGLSSDLQQ 275

Query:   238 MEVLMERLLTLINDIYKYVDDTV 260
             +     R+   ++ + +Y +D +
Sbjct:   276 VGGASARIQDALSTVLQYAEDVL 298

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

 Score = 408 (148.7 bits), Expect = 4.3e-38, P = 4.3e-38
 Identities = 80/203 (39%), Positives = 126/203 (62%)

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 TVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTS-----VDKLPSDLEG 237
             ++KAYVS  + +  R +   F  + +     + ER+G D++  T      V  L SDL+ 
Sbjct:   239 SIKAYVSTLMGVPGRTMGVMFTPLTVKYTYYDTERIGVDLIMKTCFSPNRVIGLSSDLQQ 298

Query:   238 MEVLMERLLTLINDIYKYVDDTV 260
             +     R+   ++ + +Y +D +
Sbjct:   299 VGGASARIQDALSTVLQYAEDVL 321

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

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

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

 Score = 396 (144.5 bits), Expect = 8.0e-37, P = 8.0e-37
 Identities = 86/207 (41%), Positives = 129/207 (62%)

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-DRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDK---- 230
             G  N    + AY++ NLSL  +  L + F ++PL++   EAE  G + +  T  D+    
Sbjct:   129 GLTNDTMGIHAYMAHNLSLNPESSLGSYFSQLPLEILTFEAENAGLESIAQTKYDQQSTS 188

Query:   231 LPSDLEGMEVLMERLLTLINDIYKYVD 257
             L S+LE ++  + +L  ++  I  Y++
Sbjct:   189 LLSELESLQGSLTKLDEMLESITSYIE 215

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

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

 Score = 387 (141.3 bits), Expect = 7.2e-36, P = 7.2e-36
 Identities = 85/215 (39%), Positives = 121/215 (56%)

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 NGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKST---SVDKLPS-- 233
              G   ++AYV + L +   +    F  IP++L   E E  G  +L+ T   S    P   
Sbjct:   124 GGRMGLRAYVCIQLGVPGGKSGCMFTPIPVELTSYEPETFGLKLLQKTVGVSPAHRPKTV 183

Query:   234 ----DLEGMEVLMERLLTLINDIYKYVDDTVVSMI 264
                 DL  +     +L +L++ I KYVDD +   +
Sbjct:   184 PPMLDLAQISEASTKLQSLLDLILKYVDDVIAHKV 218

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

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

 Score = 387 (141.3 bits), Expect = 7.2e-36, P = 7.2e-36
 Identities = 82/219 (37%), Positives = 128/219 (58%)

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 NPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKST 226
             NP+HLTVDT  +N   ++KAYVS  + +  + +   F  + +     + ER+G D++  T
Sbjct:   171 NPIHLTVDTSLQNSRMSIKAYVSAPMGVPGKTMGVMFTPLTVKYVYYDTERIGVDLIMKT 230

Query:   227 S-----VDKLPSDLEGMEVLMERLLTLINDIYKYVDDTV 260
                   V  L SDL+ +     R+   +  + +Y +D +
Sbjct:   231 CFSPNRVIGLSSDLQQVGSASARIQDTLGMVLQYAEDVL 269

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

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

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Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O04202	EIF3F_ARATH	No assigned EC number	0.7631	0.8086	0.7645	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

Fail to connect to STRING server

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	277
cd08064	265	cd08064, MPN_eIF3f, Mpr1p, Pad1p N-terminal (MPN)	2e-93
cd08057	157	cd08057, MPN_euk_non_mb, Mpr1p, Pad1p N-terminal (	1e-34
pfam01398	117	pfam01398, JAB, JAB1/Mov34/MPN/PAD-1 ubiquitin pro	9e-28
cd08062	280	cd08062, MPN_RPN7_8, Mpr1p, Pad1p N-terminal (MPN)	7e-26
PLN03246	303	PLN03246, PLN03246, 26S proteasome regulatory subu	3e-24
smart00232	135	smart00232, JAB_MPN, JAB/MPN domain	1e-23
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 =  276 bits (708), Expect = 2e-93
 Identities = 100/203 (49%), Positives = 137/203 (67%), Gaps = 8/203 (3%)

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 EGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDK-----LPSDL 235
           + ++KAYVS  L +  + L + F  IPL+L   EAERV  D+L  T         L SDL
Sbjct: 121 KMSIKAYVSSPLGVPGKTLGSMFVPIPLELLYSEAERVALDLLAKTLASPSRSAPLTSDL 180

Query: 236 EGMEVLMERLLTLINDIYKYVDD 258
           E +E  +E+L  +++ + +YV+D
Sbjct: 181 EQLEASLEKLQEMLDRVLRYVED 203

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 =  122 bits (308), Expect = 1e-34
 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 =  103 bits (258), Expect = 9e-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 =  102 bits (257), Expect = 7e-26
 Identities = 65/210 (30%), Positives = 100/210 (47%), Gaps = 18/210 (8%)

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-QLAAQFQEIPLDLRMIEAERVGFDIL----KSTSVDKLPSD 234
                +AY++V     D    +  F  +P ++   EAE VG + L    K  +V  L + 
Sbjct: 124 LGLPTEAYIAVEEVHDDGTPTSKTFVHVPSEIGAEEAEEVGVEHLLRDIKDVTVSTLSTR 183

Query: 235 LE----GMEVLMERLLTLINDIYKYVDDTV 260
           +      ++ L  +L     +I  Y+   V
Sbjct: 184 VTNKLNSLKGLQSKL----KEIKDYLQLVV 209

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|215645 PLN03246, PLN03246, 26S proteasome regulatory subunit; Provisional

 Score = 98.7 bits (246), Expect = 3e-24
 Identities = 68/208 (32%), Positives = 100/208 (48%), Gaps = 19/208 (9%)

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--LSLGDRQLAAQFQEIPLDLRMIEAERVGFDIL----KSTSVDKLPS 233
                KAY +V        ++    F  +P ++   EAE +G + L    K T+V  L +
Sbjct: 129 LGIPTKAYYAVEEVKENATQKSQKVFVHVPSEIGAHEAEEIGVEHLLRDVKDTTVSTLAT 188

Query: 234 D----LEGMEVLMERLLTLINDIYKYVD 257
           +    L  ++ L  RL      I  Y+D
Sbjct: 189 EVTGKLTALKGLDARLRE----IRSYLD 212

Length = 303

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

 Score = 92.8 bits (231), Expect = 1e-23
 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|163694 cd08063, MPN_CSN6, Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6

 Score = 77.3 bits (191), Expect = 1e-16
 Identities = 62/218 (28%), Positives = 100/218 (45%), Gaps = 18/218 (8%)

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--FRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFD-ILK----- 224
           +D        +  V  Y SV L L D +   +F+E+P  +   EAER+G D + +     
Sbjct: 119 LDPEANASGKDLPVTIYESV-LELVDGEATLRFRELPYTIETGEAERIGVDHVARGGASG 177

Query: 225 STSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVVS 262
           S+    + + L+     ++ L + +  I +Y+    V 
Sbjct: 178 SSEKSTVAAHLQAQHNAIKMLNSRVELILEYLKAVPVG 215

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	277
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
KOG3050	299	consensus COP9 signalosome, subunit CSN6 [Posttran	100.0
cd08057	157	MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domai	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	99.93
KOG1560	339	consensus Translation initiation factor 3, subunit	99.92
smart00232	135	JAB_MPN JAB/MPN domain. Domain in Jun kinase activ	99.88
KOG1554	347	consensus COP9 signalosome, subunit CSN5 [Posttran	99.76
cd07767	116	MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (al	99.66
cd08067	187	MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deu	99.59
cd08058	119	MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains w	99.56
cd08068	244	MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subun	99.27
KOG1555	316	consensus 26S proteasome regulatory complex, subun	99.07
cd08066	173	MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associ	99.03
PF13012	115	MitMem_reg: Maintenance of mitochondrial structure	98.81
cd08070	128	MPN_like Mpr1p, Pad1p N-terminal (MPN) domains wit	98.47
cd08060	182	MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family	98.47
PF03665	196	UPF0172: Uncharacterised protein family (UPF0172);	98.38
COG1310	134	Predicted metal-dependent protease of the PAD1/JAB	98.09
KOG3289	199	consensus Uncharacterized conserved protein encode	97.63
cd08056	252	MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains wit	96.7
cd08072	117	MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1	96.51
TIGR02256	131	ICE_VC0181 integrative and conjugative element pro	96.5
PF14464	104	Prok-JAB: Prokaryotic homologs of the JAB domain;	96.07
cd08073	108	MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains	88.72
cd08061	274	MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein l	88.03
PF05021	306	NPL4: NPL4 family; InterPro: IPR007717 The HRD4 ge	86.62
cd08059	101	MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains	81.8

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

Probab=100.00  E-value=3.5e-59  Score=412.55  Aligned_cols=233  Identities=43%  Similarity=0.721  Sum_probs=222.4

Q ss_pred             ccccceeeecCCCCCCCCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccH
Q 023811           42 ASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDI  121 (277)
Q Consensus        42 ~~~~~~~~~~~~~~~~~~~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~  121 (277)
                      .....+.+.+.|++.++..+|.|||+|+++|+|||.||.+++.||||+|||+ .++|.|||||||++||+|.++++.+|+
T Consensus         3 ~~~~~v~~~~~~~~~ss~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~-~~~g~ieitNCFaVPhnEssdqvevdm   81 (288)
T KOG2975|consen    3 TPAPHVPGPALPSPFSSNLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGT-VDKGSVEVTNCFAVPHNESSDQVEVDM   81 (288)
T ss_pred             CCcCcCCCcCCCCCCCCCceEEEcceEEeEeehhhhcCCccchhhhhheeec-ccCCeEEEEEeeeccCccccccceeeH
Confidence            3445667778888899999999999999999999999999999999999999 779999999999999999999999999


Q ss_pred             HHHHHHHHHhhhcCCCCcEEEeeecCCCCCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEeeeeccCCccccc
Q 023811          122 EYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAA  201 (277)
Q Consensus       122 ~y~~~m~~l~kkv~p~e~iVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~~~~~~~~~~~~  201 (277)
                      +|.+.|+++|+|+||+|.+||||+||++++.+++.||++|.+++++||||++|++.+++.+++|||.+++.++++++.+.
T Consensus        82 ~y~~~M~~l~~k~npnE~vvGWyaTg~dvt~~sslihdyYare~~~pvhLtVDT~~~n~rm~ikaYvss~~Gvpg~~~~~  161 (288)
T KOG2975|consen   82 EYAKNMYELHKKVNPNELVVGWYATGHDVTEHSSLIHDYYAREAPNPVHLTVDTSLQNGRMSIKAYVSSLMGVPGRTMGV  161 (288)
T ss_pred             HHHHHHHHHhcccCCCceeEEEEecCCCcccchhHHHHHhhccCCCCeEEEEeccccCCccceeEEEEeccCCCCcccce
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999899


Q ss_pred             ceEEeceEEEcChhhHHHHHHhhccCCC-----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeeec
Q 023811          202 QFQEIPLDLRMIEAERVGFDILKSTSVD-----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIV  275 (277)
Q Consensus       202 ~F~~ip~~I~~~eaErIav~~l~k~~~~-----~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~~  275 (277)
                      .|.|+|++|.+.|+||+|++.|.|++.+     .+.++|+++..|..+|+++++.+++|+++|.+|++++|..++||+.
T Consensus       162 mF~plpvel~~~~~ervgl~li~kt~~sp~r~~~l~~dLqQv~~at~~l~~~L~~Vl~YVedVl~gk~~pdn~VGR~Lm  240 (288)
T KOG2975|consen  162 MFTPLPVELAYYDAERVGLDLIEKTSFSPSRVAGLSSDLQQVEGATARLQSLLERVLKYVEDVLAGKVKPDNAVGRFLM  240 (288)
T ss_pred             eeeeeeeEEeecchhhhHHHHHHHhccChhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcchHHHHHH
Confidence            9999999999999999999999998843     5789999999999999999999999999999999999999999975

>PLN03246 26S proteasome regulatory subunit; Provisional

Probab=100.00  E-value=1.5e-55  Score=407.13  Aligned_cols=219  Identities=29%  Similarity=0.443  Sum_probs=200.5

Q ss_pred             CCCCcEEEEehhhHhHHHHHHhhcCCC-CceEEEEeeeeEecCCeEEEEeeeecccCCCCcc---eeccHHHHHHHHHHh
Q 023811           56 ATSNVTAKVHPLVIFNICDCYVRRPDQ-AERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSH  131 (277)
Q Consensus        56 ~~~~~~V~vhPlVlL~I~dH~~R~~~~-~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~---~~iD~~y~~~m~~l~  131 (277)
                      .++..+|.|||+|||+|+|||+|+..+ +.+|+|+|||+ +.|+.|||+|||++|+++++++   |++|.+|+++|+++|
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            466789999999999999999999765 68999999998 7889999999999999876554   789999999999999


Q ss_pred             hhcCCCCcEEEeeecCCCCCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEeeeeccCCcc--cccceEEeceE
Q 023811          132 LKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQ--LAAQFQEIPLD  209 (277)
Q Consensus       132 kkv~p~e~iVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~~~~~~~~~--~~~~F~~ip~~  209 (277)
                      |+|||++.+||||+||++++++|+.||++|++++++||||++|+...++++|++||++...+.++++  .+..|.++|++
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            9999999999999999999999999999999999999999999998888899999999988775433  46789999999


Q ss_pred             EEcChhhHHHHHHhhccCCC----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeeec
Q 023811          210 LRMIEAERVGFDILKSTSVD----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIV  275 (277)
Q Consensus       210 I~~~eaErIav~~l~k~~~~----~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~~  275 (277)
                      |.++|+||||++|+++...+    .+..++.++.+|+++|.+|++.+++||++|.+|++++|+++||++-
T Consensus       161 i~~~EaE~Igve~l~r~~~~~~~s~l~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~g~~~~d~~IlR~l~  230 (303)
T PLN03246        161 IGAHEAEEIGVEHLLRDVKDTTVSTLATEVTGKLTALKGLDARLREIRSYLDLVVEGKLPLNHEILYHLQ  230 (303)
T ss_pred             eeecCHHHHHHHHHHhcccCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHH
Confidence            99999999999999985543    3556888999999999999999999999999999999999999874

>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=1.1e-54  Score=398.22  Aligned_cols=214  Identities=29%  Similarity=0.449  Sum_probs=197.7

Q ss_pred             EEEEehhhHhHHHHHHhhcCCC-CceEEEEeeeeEecCCeEEEEeeeecccCCCCcc---eeccHHHHHHHHHHhhhcCC
Q 023811           61 TAKVHPLVIFNICDCYVRRPDQ-AERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSHLKVNP  136 (277)
Q Consensus        61 ~V~vhPlVlL~I~dH~~R~~~~-~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~---~~iD~~y~~~m~~l~kkv~p  136 (277)
                      +|+|||+|||+|+|||+|+..+ +.+|+|+|||+ +.|+.|||+|||++|+++++++   +++|.+|+++|+++||+|||
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            7999999999999999998755 78999999998 7889999999999999887665   58999999999999999999


Q ss_pred             CCcEEEeeecCCCCCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEeeeeccCCcc-cccceEEeceEEEcChh
Q 023811          137 QEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQ-LAAQFQEIPLDLRMIEA  215 (277)
Q Consensus       137 ~e~iVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~~~~~~~~~-~~~~F~~ip~~I~~~ea  215 (277)
                      ++.+||||+||++++.+|+.||++|++++++||+|++||...++++|++||++.+...++++ .+..|.++|++|.++|+
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            99999999999999999999999999999999999999999888999999999988775555 78899999999999999


Q ss_pred             hHHHHHHhhccCCC----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeeec
Q 023811          216 ERVGFDILKSTSVD----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIV  275 (277)
Q Consensus       216 ErIav~~l~k~~~~----~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~~  275 (277)
                      ||||++|+++...+    .+..++.++.+|+++|+.|++.+.+||++|.+|++++|+++||++-
T Consensus       161 E~igve~l~r~~~~~~~~~l~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~d~~IlR~l~  224 (280)
T cd08062         161 EEVGVEHLLRDIKDVTVSTLSTRVTNKLNSLKGLQSKLKEIKDYLQLVVEGKLPINHQIIYNLQ  224 (280)
T ss_pred             HHHHHHHHHhhccCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH
Confidence            99999999974332    3556889999999999999999999999999999999999999874

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=1.4e-54  Score=395.30  Aligned_cols=213  Identities=47%  Similarity=0.786  Sum_probs=199.8

Q ss_pred             EEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEE
Q 023811           62 AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIV  141 (277)
Q Consensus        62 V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iV  141 (277)
                      |.|||+|||+|+|||+|+..++.+|+|+|||+ +.++.+||||||++|++++++++.+|.+|+++|+++||+|||++.+|
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            68999999999999999987789999999998 78899999999999999988889999999999999999999999999


Q ss_pred             EeeecCCCCCCchhHHHHHHhhcCC--CcEEEEEecCCCCCcceeEEEEeeeeccCCcccccceEEeceEEEcChhhHHH
Q 023811          142 GWFSTGLGVTGGSALIHEFYCREVP--NPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG  219 (277)
Q Consensus       142 GWY~t~~~~~~~~~~ih~~~~~~~~--~PI~L~vD~~~~~~~l~ikay~~~~~~~~~~~~~~~F~~ip~~I~~~eaErIa  219 (277)
                      |||+||+.++.++..||++|+++++  +||+|++||...++++|++||++.+.++.+++....|.++|++|.++|+||||
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  99999999998777999999999988877777889999999999999999999


Q ss_pred             HHHhhccCCC-----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeeec
Q 023811          220 FDILKSTSVD-----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIV  275 (277)
Q Consensus       220 v~~l~k~~~~-----~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~~  275 (277)
                      ++++++...+     .+.++++.+.+++++|+++++.+.+||++|.+|+.++|++++|++.
T Consensus       160 v~~l~~~~~~~~~~~~~~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~d~~i~r~l~  220 (265)
T cd08064         160 LDLLAKTLASPSRSAPLTSDLEQLEASLEKLQEMLDRVLRYVEDVLAGKVKADNAIGRYLM  220 (265)
T ss_pred             HHHHHhhccCCcccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence            9999986553     2457899999999999999999999999999999999999999874

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=2.2e-53  Score=391.59  Aligned_cols=214  Identities=27%  Similarity=0.395  Sum_probs=197.0

Q ss_pred             cEEEEehhhHhHHHHHHhhcCCC----CceEEEEeeeeEecCCeEEEEeeeecccCCCC-cceeccHHHHHHHHHHhhhc
Q 023811           60 VTAKVHPLVIFNICDCYVRRPDQ----AERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS-DQVALDIEYHHTMLKSHLKV  134 (277)
Q Consensus        60 ~~V~vhPlVlL~I~dH~~R~~~~----~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~-~~~~iD~~y~~~m~~l~kkv  134 (277)
                      .+|.|||+|||+|+|||+|+..+    +.+|+|+|||+ ++|+.|||+|||++|+++++ +++.+|.+|+++|+++||+|
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            37999999999999999998643    58999999998 88999999999999999877 67899999999999999999


Q ss_pred             CCCCcEEEeeecCCC-CCCchhHHHHHHhhcCCCcEEEEEecCC--CCCcceeEEEEeeeeccCCcccccceEEeceEEE
Q 023811          135 NPQEVIVGWFSTGLG-VTGGSALIHEFYCREVPNPVHLTVDTGF--RNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLR  211 (277)
Q Consensus       135 ~p~e~iVGWY~t~~~-~~~~~~~ih~~~~~~~~~PI~L~vD~~~--~~~~l~ikay~~~~~~~~~~~~~~~F~~ip~~I~  211 (277)
                      ||++.+||||+||+. ++.++..||++|++.+++||+|++||..  .++++|++||++...+.++ .....|+|+|++|+
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            999999999999998 9999999999999999999999999998  5789999999999887765 56688999999999


Q ss_pred             cChhhHHHHHHhhccCC--C----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeeec
Q 023811          212 MIEAERVGFDILKSTSV--D----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIV  275 (277)
Q Consensus       212 ~~eaErIav~~l~k~~~--~----~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~~  275 (277)
                      ++|+||||++|+++...  +    .+.++++.+.+|+++|++|++.|++||++|.+|++++|+++||++.
T Consensus       159 ~~eaErIgv~~l~~~~~~~~~~~~~~~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~g~~~~d~~ilR~l~  228 (288)
T cd08063         159 TGEAERIGVDHVARGGASGSSEKSTVAAHLQAQHNAIKMLNSRVELILEYLKAVPVGEVPPDHSILRSIS  228 (288)
T ss_pred             eccCceeeHHHHHhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHH
Confidence            99999999999998652  1    2467899999999999999999999999999999999999999874

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=2.5e-49  Score=346.97  Aligned_cols=219  Identities=28%  Similarity=0.429  Sum_probs=200.9

Q ss_pred             CCCCCcEEEEehhhHhHHHHHHhhcCC-CCceEEEEeeeeEecCCeEEEEeeeecccCCCCcc---eeccHHHHHHHHHH
Q 023811           55 AATSNVTAKVHPLVIFNICDCYVRRPD-QAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKS  130 (277)
Q Consensus        55 ~~~~~~~V~vhPlVlL~I~dH~~R~~~-~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~---~~iD~~y~~~m~~l  130 (277)
                      +.-+..+|.+||||||+++|||.|... +++||+|.|||. ..++++.|+|||++|++|++++   |++|.+|++.|++|
T Consensus         4 ~~~~~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~-~~~~~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~m   82 (309)
T KOG1556|consen    4 SELTVEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGS-WNGDVIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGM   82 (309)
T ss_pred             cccccceeeeehhHHHHHHHHHhhhccCcCceEEEEEEec-CCCCeEEeecceeccccccCCCCceEEeccHHHHHHHHH
Confidence            355677999999999999999999863 468999999998 6777999999999999998876   89999999999999


Q ss_pred             hhhcCCCCcEEEeeecCCCCCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEeeeeccC-CcccccceEEeceE
Q 023811          131 HLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLG-DRQLAAQFQEIPLD  209 (277)
Q Consensus       131 ~kkv~p~e~iVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~~~~~~-~~~~~~~F~~ip~~  209 (277)
                      |+|+|.+|.+||||+|||.+.++|+.|++++.+++|+|+++++|..+.+-+||..||...++..+ +.+...+|+.+|++
T Consensus        83 fkKvNakekivGWYhTGPkl~~nDl~In~l~k~y~pnpvLvIIdvkpk~~gLPT~AY~aVeev~dDgt~t~ktF~Hvps~  162 (309)
T KOG1556|consen   83 FKKVNAKEKVVGWYHTGPKLRENDLDINELLKRYVPNPVLVIIDVKPKELGLPTEAYIAVEEVKDDGTPTSKTFVHVPSE  162 (309)
T ss_pred             HHHhcchhheeeeeccCCccccchhhHHHHHhhcCCCceEEEEecccccCCCCchheeeeeeeecCCCCccceeEecCcc
Confidence            99999999999999999999999999999999999999999999998888999999999887654 45567899999999


Q ss_pred             EEcChhhHHHHHHhhccCCC----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeee
Q 023811          210 LRMIEAERVGFDILKSTSVD----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQI  274 (277)
Q Consensus       210 I~~~eaErIav~~l~k~~~~----~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~  274 (277)
                      |++.|||+||++|+.+...+    .+...+.++..+++.|+.++..|.+||++|.+|++|.||+++-|.
T Consensus       163 I~AeEAEEvGVEHLlRDikd~t~gtla~rit~ql~sLkgl~~~L~eI~~YL~~Vi~g~lpiNh~Il~~l  231 (309)
T KOG1556|consen  163 IEAEEAEEVGVEHLLRDIKDTTVGTLATRITNQLMSLKGLQSRLREIRSYLDKVIDGKLPINHEILYQL  231 (309)
T ss_pred             cchhHHHHhhHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHH
Confidence            99999999999999986543    467788899999999999999999999999999999999998764

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

Probab=100.00  E-value=7.7e-48  Score=337.08  Aligned_cols=221  Identities=24%  Similarity=0.360  Sum_probs=197.8

Q ss_pred             CCCCCCCcEEEEehhhHhHHHHHHhhcCCC--C--ceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHH
Q 023811           53 SSAATSNVTAKVHPLVIFNICDCYVRRPDQ--A--ERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTML  128 (277)
Q Consensus        53 ~~~~~~~~~V~vhPlVlL~I~dH~~R~~~~--~--~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~  128 (277)
                      +++++++.+|.+||||++||+|||+|.+.+  +  ++|+|+|+|. |.|++|||.|||++..+..++...+|.+|++++.
T Consensus         2 Aps~S~s~tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~-Q~GR~vEi~NSFeL~~d~~~~~~~~dke~l~kk~   80 (299)
T KOG3050|consen    2 APSSSGSVTVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGK-QRGRNVEIMNSFELKMDTEEDTETIDKEYLEKKE   80 (299)
T ss_pred             CCCCCCceeEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheec-ccCceEEEeeeeEEEecchhhhhhccHHHHHHHH
Confidence            355778899999999999999999999743  2  4899999998 9999999999999998877666689999999999


Q ss_pred             HHhhhcCCCCcEEEeeecCCCCCCchhHHHHHHhhcCCCcEEEEEecCCC-CCcceeEEEEeeeeccCCcccccceEEec
Q 023811          129 KSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFR-NGEGTVKAYVSVNLSLGDRQLAAQFQEIP  207 (277)
Q Consensus       129 ~l~kkv~p~e~iVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~-~~~l~ikay~~~~~~~~~~~~~~~F~~ip  207 (277)
                      ++||+|||+..++|||+||.+.++.|..||.+++..++.|++|.++|..+ ..+.|+..|++.--.++ +....+|.|+.
T Consensus        81 eqykqVFpdl~vlGwYttG~d~t~sd~~i~k~l~~i~esplflkLNp~t~~t~~~pv~lfese~dvid-g~~q~~f~~~t  159 (299)
T KOG3050|consen   81 EQYKQVFPDLYVLGWYTTGSDPTPSDIHIHKQLMDINESPLFLKLNPATNHTDKDPVTLFESEIDVID-GEAQMLFVPLT  159 (299)
T ss_pred             HHHHHhcccceEEEEeecCCCCChhhhHHHHHHHhhhcCceEEEecchhccccCCCceeeeeeheeec-CcceeeeeeeE
Confidence            99999999999999999999999999999999999999999999999885 45569999988744443 45578999999


Q ss_pred             eEEEcChhhHHHHHHhhccCCC------CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeeec
Q 023811          208 LDLRMIEAERVGFDILKSTSVD------KLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIV  275 (277)
Q Consensus       208 ~~I~~~eaErIav~~l~k~~~~------~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~~  275 (277)
                      |++.+.|||||||||+++-+..      ....|++.+..|++||+.|++.|++|+++|.+|++++||++|||.-
T Consensus       160 ytl~teEaERIgVdHVA~lt~~~gge~s~VaeHl~AQdsA~~ml~~Rvklil~Y~k~~e~G~l~~N~eILrea~  233 (299)
T KOG3050|consen  160 YTLATEEAERIGVDHVARLTPSDGGEGSSVAEHLEAQDSAIKMLDNRVKLILAYLKKVEAGTLQPNFEILREAY  233 (299)
T ss_pred             EEEeehhhhhccchhheeeccCCCCCcchHHHHHhhHHHHHHHHhhHHHHHHHHHhhhhcCCcCccHHHHHHHH
Confidence            9999999999999999984331      3678999999999999999999999999999999999999999864

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

Probab=100.00  E-value=8.6e-40  Score=276.27  Aligned_cols=150  Identities=31%  Similarity=0.551  Sum_probs=137.0

Q ss_pred             EEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEE
Q 023811           62 AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIV  141 (277)
Q Consensus        62 V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iV  141 (277)
                      |+|||+|||||+|||+|+..++.+|+|+|||+ +.++.++|+|||++|++++++.+.+|.+|+++|+++|++|+|++.+|
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            68999999999999999876678999999998 77999999999999998887778899999999999999999999999


Q ss_pred             EeeecCCC----CCCchhHHHHHHhhc-CCCcEEEEEecCC--CCCcceeEEEEeeeeccCCcccccceEEeceEEEcCh
Q 023811          142 GWFSTGLG----VTGGSALIHEFYCRE-VPNPVHLTVDTGF--RNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIE  214 (277)
Q Consensus       142 GWY~t~~~----~~~~~~~ih~~~~~~-~~~PI~L~vD~~~--~~~~l~ikay~~~~~~~~~~~~~~~F~~ip~~I~~~e  214 (277)
                      |||++++.    ++..+..||++|+++ .++||+|++||..  .+++++++||++.+....       +.++|+++.+.|
T Consensus        80 GWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~~~~~-------~~~~~~~i~~~e  152 (157)
T cd08057          80 GWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQREEN-------GAEITYEIGTEE  152 (157)
T ss_pred             EEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEecCCCC-------CceeeeEEeccc
Confidence            99999987    889999999999998 8889999999987  478999999999854321       339999999999


Q ss_pred             hhHHH
Q 023811          215 AERVG  219 (277)
Q Consensus       215 aErIa  219 (277)
                      +||||
T Consensus       153 ~E~I~  157 (157)
T cd08057         153 TERIA  157 (157)
T ss_pred             ccccC
Confidence            99985

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

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

Probab=100.00  E-value=6e-35  Score=266.32  Aligned_cols=196  Identities=22%  Similarity=0.277  Sum_probs=160.4

Q ss_pred             EEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcc---eeccHHHHHHHHHHhhhcCCC
Q 023811           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSHLKVNPQ  137 (277)
Q Consensus        61 ~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~---~~iD~~y~~~m~~l~kkv~p~  137 (277)
                      +|+|||+|+++|+|||.|+.  +.+|+|+|||. ..|+.+||||||++|+.+++++   ...|.+|+.+|++++++++++
T Consensus         2 ~V~I~~~vllkIv~H~~~~~--p~~v~G~LLG~-~~~~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~~~   78 (266)
T cd08065           2 SVQIDGLVVLKIIKHCKEEL--PELVQGQLLGL-DVGGTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVNVD   78 (266)
T ss_pred             EEEEeHHHHHHHHHHHhcCC--CcEEEEEEeee-EcCCEEEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhCCC
Confidence            69999999999999998874  89999999998 6789999999999999887665   466789999999999999999


Q ss_pred             CcEEEeeecCC-CCCCchhHHHHHHhhcC--CCcEEEEEecCC-CCCcceeEEEEeeeeccC---------------Ccc
Q 023811          138 EVIVGWFSTGL-GVTGGSALIHEFYCREV--PNPVHLTVDTGF-RNGEGTVKAYVSVNLSLG---------------DRQ  198 (277)
Q Consensus       138 e~iVGWY~t~~-~~~~~~~~ih~~~~~~~--~~PI~L~vD~~~-~~~~l~ikay~~~~~~~~---------------~~~  198 (277)
                      +.+||||+|++ +...+...||.++..+.  +++|+|++||.. .+|.++++||++++.+++               +.+
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            99999999999 55666788999988874  778999999997 578899999999988764               456


Q ss_pred             cccceEEeceEEEcChhhHHHHHHhhccCCCC-------CcccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023811          199 LAAQFQEIPLDLRMIEAERVGFDILKSTSVDK-------LPSDLEGMEVLMERLLTLINDIYKYVDDT  259 (277)
Q Consensus       199 ~~~~F~~ip~~I~~~eaErIav~~l~k~~~~~-------l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V  259 (277)
                      .+.+|.|||++|++++.+++.+..+.......       ..+....+...++.|.+.++.+..+.++.
T Consensus       159 ~~~if~eiPv~i~n~~l~~~~L~~l~~~~~~~~~~~~~l~l~~~~~le~~l~~l~~~id~l~~e~~~~  226 (266)
T cd08065         159 FSNIFEEIPVVIRNSHLVNALLSELEEDSPSSQSDFDRLDLSTNSFLEKNLELLMESVDELSQEQGKF  226 (266)
T ss_pred             hhcEEEEEEEEEEchHHHHHHHHhcccCCCcccCCcccccccCchhHHHHHHHHHHHHHHHHHHHHHH
Confidence            78999999999999999999999886533221       12233455555555555555555554443

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=5.3e-29  Score=227.31  Aligned_cols=171  Identities=15%  Similarity=0.204  Sum_probs=151.8

Q ss_pred             CCCCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHHH--Hhhh
Q 023811           56 ATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLK--SHLK  133 (277)
Q Consensus        56 ~~~~~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~--l~kk  133 (277)
                      .....+|.|+|+|+++|++|+.|.  .+.+|+|+|+|. .+++.++|++||++|+.++++.+..+.+|++.|.+  ++++
T Consensus         6 ~~~~~~V~Is~~allkil~Ha~~~--~p~Ev~GlLlG~-~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~~   82 (268)
T cd08069           6 PDYFEKVYISSLALLKMLKHARAG--GPIEVMGLMLGK-VDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLKQ   82 (268)
T ss_pred             CCcccEEEECHHHHHHHHHHHhcc--CCceEEEEEEee-ecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHHH
Confidence            355678999999999999999874  578999999998 67889999999999998887777777899999999  9999


Q ss_pred             cCCCCcEEEeeecCCC----CCCchhHHHHHHhhcCCCcEEEEEecCCC--CCcceeEEEEeeeeccC----Cc------
Q 023811          134 VNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFR--NGEGTVKAYVSVNLSLG----DR------  197 (277)
Q Consensus       134 v~p~e~iVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~--~~~l~ikay~~~~~~~~----~~------  197 (277)
                      +++++.+||||||+++    ++..|+.+|..|++..+.+|+|++||..+  .|++.++||++.+.+..    +.      
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            9999999999999997    88999999999999888899999998764  78899999999987753    12      


Q ss_pred             -----------ccccceEEeceEEEcChhhHHHHHHhhccCCC
Q 023811          198 -----------QLAAQFQEIPLDLRMIEAERVGFDILKSTSVD  229 (277)
Q Consensus       198 -----------~~~~~F~~ip~~I~~~eaErIav~~l~k~~~~  229 (277)
                                 .....|++||+++.+++.|+..++.+.+..|.
T Consensus       163 ~~~~~~~~~~~~~~~~y~~l~i~~~~s~l~~~~L~~l~~~~w~  205 (268)
T cd08069         163 HLPKPKIEDFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNKYWV  205 (268)
T ss_pred             ccCcHHHHHhCchhcEEEEeeeEEecCHHHHHHHHHHHHHhHH
Confidence                       25689999999999999999999999887663

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=99.93  E-value=3.4e-26  Score=182.79  Aligned_cols=107  Identities=36%  Similarity=0.579  Sum_probs=94.0

Q ss_pred             CCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCC-eEEEEeeeecccCCCCcce-eccHHHHHHHHHHhhhcC
Q 023811           58 SNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDG-TVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKVN  135 (277)
Q Consensus        58 ~~~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~-~VeVtnsF~vp~~e~~~~~-~iD~~y~~~m~~l~kkv~  135 (277)
                      +..+|.|||+|+++|+||+.|+.  +.+|+|+|+|+ .+++ .++|+|||++|+.+++++. ..+.++.++|++++++++
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            46799999999999999999985  35999999998 6777 9999999999999877654 456677799999999999


Q ss_pred             CCCcEEEeeecCCCC----CCchhHHHHHHhhcCCC
Q 023811          136 PQEVIVGWFSTGLGV----TGGSALIHEFYCREVPN  167 (277)
Q Consensus       136 p~e~iVGWY~t~~~~----~~~~~~ih~~~~~~~~~  167 (277)
                      |++.+||||+|++..    +..|+.+|.+|++.+++
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            999999999999876    89999999999987664

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=99.92  E-value=7.9e-25  Score=195.63  Aligned_cols=195  Identities=22%  Similarity=0.350  Sum_probs=150.8

Q ss_pred             CCCCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCC--CCcce---eccH---HHHHHH
Q 023811           56 ATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNE--FSDQV---ALDI---EYHHTM  127 (277)
Q Consensus        56 ~~~~~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e--~~~~~---~iD~---~y~~~m  127 (277)
                      +++...|.+..||+++|++||.....+..-+.|+|+|. .-++.+|||||||.|...  +++.+   ..|.   .|+..|
T Consensus         9 ~p~vk~v~ldsLvVMkiiKHc~ee~~n~d~~~GvL~Gl-vvd~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~l~m   87 (339)
T KOG1560|consen    9 SPPVKRVELDSLVVMKIIKHCREEFPNGDGTQGVLLGL-VVDGRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQLAM   87 (339)
T ss_pred             CCccceeeehhHHHHHHHHHHHhhcCCcchhhheeeee-eecceeEeecccCCCccCCCccchhhhhhhHHHHHHHHHHH
Confidence            67788999999999999999987765557899999998 668899999999999754  22322   2332   599999


Q ss_pred             HHHhhhcCCCCcEEEeeecCC-CCCCchhHHHHHHhhc--CCCcEEEEEecCC-CCCcceeEEEEeeeeccC--------
Q 023811          128 LKSHLKVNPQEVIVGWFSTGL-GVTGGSALIHEFYCRE--VPNPVHLTVDTGF-RNGEGTVKAYVSVNLSLG--------  195 (277)
Q Consensus       128 ~~l~kkv~p~e~iVGWY~t~~-~~~~~~~~ih~~~~~~--~~~PI~L~vD~~~-~~~~l~ikay~~~~~~~~--------  195 (277)
                      +..++.+|.+..+||||++.- +..-+...+..+|.++  +++.|+|++||.+ ++|.|.++||++.+..+.        
T Consensus        88 lrrlr~vnid~~hVGwYqs~~vgs~lS~~lveSqy~YQ~a~pesVvliYD~~kssqG~L~lrAyrLTp~am~~~kekdwt  167 (339)
T KOG1560|consen   88 LRRLRYVNIDHLHVGWYQSAYVGSFLSPALVESQYAYQKAIPESVVLIYDPIKSSQGTLSLRAYRLTPEAMAAHKEKDWT  167 (339)
T ss_pred             HHHhhhcCccceeeeeeeeehhccccCHHHHHHHHHHHhcCCccEEEEeccccccCceEEeehhhcCHHHHHHHhcCCCC
Confidence            999999999999999999652 3333356778888777  5677999999999 589999999999987642        


Q ss_pred             -------CcccccceEEeceEEEcChhhHHHHHHhh--ccCCCC--CcccH-----HHHHHHHHHHHHHHHH
Q 023811          196 -------DRQLAAQFQEIPLDLRMIEAERVGFDILK--STSVDK--LPSDL-----EGMEVLMERLLTLIND  251 (277)
Q Consensus       196 -------~~~~~~~F~~ip~~I~~~eaErIav~~l~--k~~~~~--l~~~l-----~~l~~sl~~L~~~l~~  251 (277)
                             +.++.+.|.|+|+.|+++..-.+-+..+.  +.+.+.  +.+++     ..+++.++.|.++++.
T Consensus       168 pealk~~nltyenmfeElPIVIknS~L~nvlmseLs~~e~c~sdk~~~~~fdlgs~t~leknir~lme~vDE  239 (339)
T KOG1560|consen  168 PEALKSANLTYENMFEELPIVIKNSHLANVLMSELSEPEDCESDKPLHSNFDLGSGTRLEKNIRLLMERVDE  239 (339)
T ss_pred             HHHHHhcCCCHHHHHhhcCeeeeccHHHHHHHHhccccccccccccccccccccchhhHHHHHHHHHHHHHH
Confidence                   35678999999999999999999988887  433321  11111     2555666666666554

>smart00232 JAB_MPN JAB/MPN domain

Probab=99.88  E-value=5.3e-22  Score=161.48  Aligned_cols=128  Identities=31%  Similarity=0.442  Sum_probs=112.7

Q ss_pred             EEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcce-eccHHHHHHHHHHhhhcCCCCc
Q 023811           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKVNPQEV  139 (277)
Q Consensus        61 ~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~-~iD~~y~~~m~~l~kkv~p~e~  139 (277)
                      .|.|||+|+++|++|+.|.  .+.+++|.|+|. ..++.++|+++|++|...+++.. ..+.+|++.|.++++++++++.
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            4789999999999999886  578999999998 67889999999999987765554 6789999999999999999999


Q ss_pred             EEEeeecCCC----CCCchhHHHHHHhhcCCCcEEEEEecCCC-CCcceeEEEEeee
Q 023811          140 IVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFR-NGEGTVKAYVSVN  191 (277)
Q Consensus       140 iVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~-~~~l~ikay~~~~  191 (277)
                      +||||+|++.    ++..|..+|..+......++++++|+..+ .++++++||++..
T Consensus        78 ~vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~~g~~~~~af~~~~  134 (135)
T smart00232       78 IVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQGRLSLRAFRLTP  134 (135)
T ss_pred             EEEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccccCcEEEEEEEecC
Confidence            9999999873    56678888988888888899999999985 4889999999863

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=99.76  E-value=1e-17  Score=150.63  Aligned_cols=196  Identities=14%  Similarity=0.213  Sum_probs=146.9

Q ss_pred             CCCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcce---eccHHHHHHHHHHhhh
Q 023811           57 TSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV---ALDIEYHHTMLKSHLK  133 (277)
Q Consensus        57 ~~~~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~---~iD~~y~~~m~~l~kk  133 (277)
                      ..-..|.|..|++|+|.-|..|.  ++-.|+|.++|+ .+|+++.|.+||++|.+.++..+   .--.+|+....+.-+.
T Consensus        50 ~~fk~vkISalAllKm~~hA~~G--gnlEiMGlm~Gk-v~g~t~IvmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~k~  126 (347)
T KOG1554|consen   50 HYFKHVKISALALLKMVMHARSG--GNLEIMGLMQGK-VDGDTIIVMDSFALPVEGTETRVNAQAEAYEYMVQYIEEAKN  126 (347)
T ss_pred             chhhhhhhHHHHHHHHHHHHhcC--CCeEEEeeeccc-ccCCeEEEEeccccccccccceechHHHHHHHHHHHHHHHHH
Confidence            34558999999999999998553  688999999998 88999999999999999988765   2236788888999999


Q ss_pred             cCCCCcEEEeeecCCC----CCCchhHHHHHHhhcCCCc-EEEEEecCC--CCCcceeEEEEeeeeccCC----------
Q 023811          134 VNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNP-VHLTVDTGF--RNGEGTVKAYVSVNLSLGD----------  196 (277)
Q Consensus       134 v~p~e~iVGWY~t~~~----~~~~~~~ih~~~~~~~~~P-I~L~vD~~~--~~~~l~ikay~~~~~~~~~----------  196 (277)
                      ++..+.+||||+++|+    ++..|+..|.+ .+.+..| +++++||..  +.|++.|.|||+-+.+...          
T Consensus       127 ~gr~envVGWyHSHPgYgCWLSgIDVsTQ~l-NQ~fQePfvAvViDP~Rtlsagkv~iGAFRTyp~gyk~~d~~~seyqt  205 (347)
T KOG1554|consen  127 VGRLENVVGWYHSHPGYGCWLSGIDVSTQML-NQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTYPKGYKPPDEPPSEYQT  205 (347)
T ss_pred             hhhhhceeeeeecCCCCCccccCcchhHHHH-hhhhcCCeEEEEecCccccccCceeeceeecccCCCCCCCCCchhhhc
Confidence            9999999999999997    34555555543 4446778 899999988  4789999999998876421          


Q ss_pred             ---------cccccceEEeceEEEcChhhHHHHHHhhccCC------CCCcccHHHHHHHHHHHHHHHHHHHHHH
Q 023811          197 ---------RQLAAQFQEIPLDLRMIEAERVGFDILKSTSV------DKLPSDLEGMEVLMERLLTLINDIYKYV  256 (277)
Q Consensus       197 ---------~~~~~~F~~ip~~I~~~eaErIav~~l~k~~~------~~l~~~l~~l~~sl~~L~~~l~~i~~Yl  256 (277)
                               +-.+..+..+++.+--+-.++--++.+-+..+      +++..+.+.+...+..|.+++++.-+.+
T Consensus       206 ipl~kied~gvHck~yysl~isyfks~ld~kll~~Lwnkywv~Tlsss~ll~N~dy~~~qi~d~~ekl~q~~~~l  280 (347)
T KOG1554|consen  206 IPLNKIEDFGVHCKQYYSLEISYFKSSLDMKLLELLWNKYWVRTLSSSPLLKNIDYLNGQIRDLSEKLEQREDSL  280 (347)
T ss_pred             cchhhhhhcccceEEeeccchhhhhhhhhHHHHHHHHhhhhhcccccccccccchhhcchhhhHHHHHHhhhhhc
Confidence                     11234455555555555566666666654333      2466677777777777777777655544

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

Probab=99.66  E-value=9.8e-16  Score=121.64  Aligned_cols=111  Identities=25%  Similarity=0.355  Sum_probs=88.1

Q ss_pred             hHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEEEeeecCCC
Q 023811           70 FNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG  149 (277)
Q Consensus        70 L~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iVGWY~t~~~  149 (277)
                      .+|++|+.+.  .+.+|+|.|+|+ ..++.++|+++|++|...++..  .+...  -|....+.+..++.+||||+|++.
T Consensus         2 k~il~~a~~~--~~~ev~G~L~G~-~~~~~~~i~~~~~~~~~~~~~~--~~~~~--~~~~~~~~~~~~~~iVGwyhshp~   74 (116)
T cd07767           2 KMFLDAAKSI--NGKEVIGLLYGS-KTKKVLDVDEVIAVPFDEGDKD--DNVWF--LMYLDFKKLNAGLRIVGWYHTHPK   74 (116)
T ss_pred             HhHHHHHhcC--CCcEEEEEeEEE-EcCCEEEEEEEEecccCCCCCc--cHHHH--HHHHHHHHhcCCCeEEEEEEcCCC
Confidence            4678888663  468999999998 6777899999999998765432  22222  266667778899999999999975


Q ss_pred             ----CCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEE
Q 023811          150 ----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAY  187 (277)
Q Consensus       150 ----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay  187 (277)
                          ++..|+..|..+++..+++++|++|+...+.+++++||
T Consensus        75 ~~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~~~~~~~~~~~  116 (116)
T cd07767          75 PSCFLSPNDLATHELFQRYFPEKVMIIVDVKPKDLGNSWKCY  116 (116)
T ss_pred             CCCccCHHHHHHHHHHHHhCCCCEEEEEECCCccCCCCcccC
Confidence                67888888888888788899999999887667888886

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=99.59  E-value=3.7e-14  Score=123.30  Aligned_cols=146  Identities=14%  Similarity=0.095  Sum_probs=107.2

Q ss_pred             CcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEec-CCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCC
Q 023811           59 NVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLP-DGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQ  137 (277)
Q Consensus        59 ~~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~-~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~  137 (277)
                      ..+|+|+++|+|+|..|+...   ...|+|.|+|.+.. ++.++|+++|++|.....++..+|.+++.+|.+..++.+  
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            578999999999999999653   28899999998433 468999999999987765666789999999999988766  


Q ss_pred             CcEEEeeecCCC----CCCchhHHHHHHhhcCC------Cc-EEEEEecCCC---CCcceeEEEEeeeeccCCcccccce
Q 023811          138 EVIVGWFSTGLG----VTGGSALIHEFYCREVP------NP-VHLTVDTGFR---NGEGTVKAYVSVNLSLGDRQLAAQF  203 (277)
Q Consensus       138 e~iVGWY~t~~~----~~~~~~~ih~~~~~~~~------~P-I~L~vD~~~~---~~~l~ikay~~~~~~~~~~~~~~~F  203 (277)
                      +.+|||||+++.    ++..|+..|..|+...+      .| |.++++|-..   ...-.|++|...+..-.+    ..-
T Consensus        79 l~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~~~~~----~~~  154 (187)
T cd08067          79 LSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPPPENR----PNE  154 (187)
T ss_pred             CEEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECCCCCC----Ccc
Confidence            699999999984    33444544444544433      24 9999999763   235679999998653221    122


Q ss_pred             EEeceEEEcC
Q 023811          204 QEIPLDLRMI  213 (277)
Q Consensus       204 ~~ip~~I~~~  213 (277)
                      ..+|+.+.+.
T Consensus       155 ~~~p~~~~~~  164 (187)
T cd08067         155 YGVPMLMSYT  164 (187)
T ss_pred             CCcCeEEEec
Confidence            3356655554

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=99.56  E-value=2.5e-14  Score=115.38  Aligned_cols=110  Identities=13%  Similarity=0.209  Sum_probs=83.4

Q ss_pred             hHhHHHHHHhhcCCCCceEEEEeeeeEec----CCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEEEe
Q 023811           68 VIFNICDCYVRRPDQAERVIGTLLGSVLP----DGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGW  143 (277)
Q Consensus        68 VlL~I~dH~~R~~~~~~~ViG~LLG~~~~----~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iVGW  143 (277)
                      |+++|++|+.+.  .+..++|.|+|...+    ++.++|+++|+.|...+.         .+.|..+.+....++.+|||
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            789999999774  478999999998432    346899999999875432         22455556678899999999


Q ss_pred             eecCCC----CCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEee
Q 023811          144 FSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV  190 (277)
Q Consensus       144 Y~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~  190 (277)
                      ||++++    ++..|+..|.+|....++.++|++||..+  .++++||+++
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            999983    45566555555555567779999999663  7899999874

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=99.27  E-value=3.1e-10  Score=102.25  Aligned_cols=148  Identities=17%  Similarity=0.185  Sum_probs=99.9

Q ss_pred             cEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEe------cCCeEEEEeeeecccCC-CCcceeccHH----HHHHHH
Q 023811           60 VTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVL------PDGTVDIRNSYVVPHNE-FSDQVALDIE----YHHTML  128 (277)
Q Consensus        60 ~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~------~~~~VeVtnsF~vp~~e-~~~~~~iD~~----y~~~m~  128 (277)
                      .+|.|.+.++..|++|..+.  .+..++|.|+|.+.      .++.+.|..-++.+..+ ..+.+.+|.+    ..+.+.
T Consensus         2 ~~V~Is~~~l~~il~HA~~~--~P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~~s~~r~eidPee~~~a~~ea~   79 (244)
T cd08068           2 SKVHLSADVYLVCLTHALST--EKEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSDKRKDRVEISPEQLSAASTEAE   79 (244)
T ss_pred             cEEEECHHHHHHHHHHHHhC--CCcceeEEEEeecccccccccceeEEEeeeccccccCCCCceEEeCHHHHHHHHHHHH
Confidence            37999999999999999775  58899999999832      13445555555544333 2344677854    335566


Q ss_pred             HHhhhcCCCCcEEEeeecCCC----CCCchhHHHHHHhhcCCCcEEEEEecCC-----CCCcceeEEEEeeeeccCCccc
Q 023811          129 KSHLKVNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGF-----RNGEGTVKAYVSVNLSLGDRQL  199 (277)
Q Consensus       129 ~l~kkv~p~e~iVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~-----~~~~l~ikay~~~~~~~~~~~~  199 (277)
                      ++.+.+..++.+|||||++++    ++..|...+..|....+.-++|++.+..     ..++..+++|+..+..   ...
T Consensus        80 ~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~g~---~~~  156 (244)
T cd08068          80 RLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQGN---KAG  156 (244)
T ss_pred             HHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecCCC---CCC
Confidence            777788999999999999985    3445544433343333555899887543     2367889999997431   122


Q ss_pred             ccceEEeceEEEc
Q 023811          200 AAQFQEIPLDLRM  212 (277)
Q Consensus       200 ~~~F~~ip~~I~~  212 (277)
                      .....++|+.|..
T Consensus       157 ~~~~~e~pl~i~~  169 (244)
T cd08068         157 QYERIEVPLEIVP  169 (244)
T ss_pred             cceEEEeeeEEec
Confidence            3456788887774

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

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

Probab=99.07  E-value=2.4e-09  Score=98.94  Aligned_cols=135  Identities=21%  Similarity=0.321  Sum_probs=110.2

Q ss_pred             CCCCcEEEEehhhHhHHHHHHhhcCCCCc-eEEEEe-ee---eEecCCeEEEEeeeecccCCCCcc--e-eccHHHHHHH
Q 023811           56 ATSNVTAKVHPLVIFNICDCYVRRPDQAE-RVIGTL-LG---SVLPDGTVDIRNSYVVPHNEFSDQ--V-ALDIEYHHTM  127 (277)
Q Consensus        56 ~~~~~~V~vhPlVlL~I~dH~~R~~~~~~-~ViG~L-LG---~~~~~~~VeVtnsF~vp~~e~~~~--~-~iD~~y~~~m  127 (277)
                      +....+|.++.++++.+++|- |.. .+. .++|.+ +|   .+.+..++.|.+.|+.|+...+=.  + +.|.-|+.+|
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-RAG-SPEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAVDPVFQTQM  104 (316)
T ss_pred             ccCcceeeeehhhhhhccccc-ccC-CchhhccceeecccccceeeecceeeeeeeccccccceecccchhccHHHHHHH
Confidence            466789999999999999987 442 233 489999 99   666788999999999998875432  2 6889999999


Q ss_pred             HHHhhhcCCCCcEEEeeecCCC----CCCchhHHHHHHhhcCCCcEEEEEecCCC-CCcceeEEEEeeee
Q 023811          128 LKSHLKVNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFR-NGEGTVKAYVSVNL  192 (277)
Q Consensus       128 ~~l~kkv~p~e~iVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~-~~~l~ikay~~~~~  192 (277)
                      .++.++....+.+|||||++++    ++..|+..|+-|+...+..+..++||..+ .|+..+.||+....
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            9999999988999999999986    45677777777877778889999999884 56666778887654

>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family

Probab=99.03  E-value=1e-08  Score=88.24  Aligned_cols=124  Identities=13%  Similarity=0.143  Sum_probs=90.0

Q ss_pred             EEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCccee-ccHHHHHHHHHHhhhcCCCCc
Q 023811           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVA-LDIEYHHTMLKSHLKVNPQEV  139 (277)
Q Consensus        61 ~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~-iD~~y~~~m~~l~kkv~p~e~  139 (277)
                      .+.|-.-.+-+|+.|..++...+..+.|.|+|. ..++..+|++.+-.|...++..+. .|..   ++++.  .-..++.
T Consensus         3 ~l~Ipk~il~~~l~~A~~~~~~p~E~cGlL~G~-~~~~~~~I~~i~~~~q~~~~~~~~~~~~~---e~~~~--~~~~gle   76 (173)
T cd08066           3 QVVVPADLMDKFLQLAEPNTSRNLETCGILCGK-LSNNAFFITHLIIPKQSGTSDSCQTTNEE---ELFDF--QDQHDLI   76 (173)
T ss_pred             EEEECHHHHHHHHHHHHhCCCCCCeEEEEEEeE-cCCCeEEEEEEEeccccCCCceecCCCHH---HHHHH--HHhCCCe
Confidence            355666678889999977532357999999998 667788999998778776654432 3321   12211  1235899


Q ss_pred             EEEeeecCCC----CCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEee-eecc
Q 023811          140 IVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV-NLSL  194 (277)
Q Consensus       140 iVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~-~~~~  194 (277)
                      +||||+|+++    ++..|+..|..|....+..++|+++|.    ...++||+.. +.++
T Consensus        77 ~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~----~~~l~afrl~~~~g~  132 (173)
T cd08066          77 TLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK----YNEFGIFRLTDPPGL  132 (173)
T ss_pred             eEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC----CcEEeEEEeecCCcc
Confidence            9999999874    567888888877776777899999973    6789999998 6654

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

>PF13012 MitMem_reg: Maintenance of mitochondrial structure and function; PDB: 2O96_B 2O95_A

Probab=98.81  E-value=1.3e-09  Score=87.13  Aligned_cols=63  Identities=27%  Similarity=0.283  Sum_probs=12.6

Q ss_pred             ChhhHHHHHHhhccCC----CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeeec
Q 023811          213 IEAERVGFDILKSTSV----DKLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIV  275 (277)
Q Consensus       213 ~eaErIav~~l~k~~~----~~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~~  275 (277)
                      .||||||++|+++...    +.+.++++.+.+++.+|+++++.+.+||++|.+|++++|++++||+-
T Consensus         1 eEaErigv~~l~~~~~~~~~s~~~~~l~~~~~al~~L~~~l~~i~~Yl~~v~~g~~~~d~~i~r~l~   67 (115)
T PF13012_consen    1 EEAERIGVDHLARGLGDHYYSSLSSQLENEQNALKMLHKRLWQILDYLEDVISGEIPPDHEILRQLQ   67 (115)
T ss_dssp             SHHHHHHHHHHHHH--S--------------------------------------------------
T ss_pred             CchHHHHHHHHHccCCCccccHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHcCcCCCchhHHHHHH
Confidence            4899999999998543    25678899999999999999999999999999999999999999984

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

Probab=98.47  E-value=6.7e-06  Score=66.95  Aligned_cols=113  Identities=15%  Similarity=0.067  Sum_probs=78.4

Q ss_pred             hHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCc--ceeccHHHHHHHHHHhhhcCCCCcEEEeee
Q 023811           68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSD--QVALDIEYHHTMLKSHLKVNPQEVIVGWFS  145 (277)
Q Consensus        68 VlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~--~~~iD~~y~~~m~~l~kkv~p~e~iVGWY~  145 (277)
                      ++-+|++|+.+.  .+..+.|.|+|. .++....|+..+++|....+.  ...+|.+.+.++.+..++.  ++.+|||||
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            456889999774  478999999998 656555678999998765443  4568887777776666544  699999999


Q ss_pred             cCCC--CCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEee
Q 023811          146 TGLG--VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV  190 (277)
Q Consensus       146 t~~~--~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~  190 (277)
                      |+++  ...+...+..+  . ....++|++.....  ...+++|...
T Consensus        78 SHP~~~~~PS~~D~~~~--~-~~~~~~lIv~~~~~--~~~~~~~~~~  119 (128)
T cd08070          78 SHPDGPARPSETDLRLA--W-PPGVSYLIVSLAGG--APELRAWRLE  119 (128)
T ss_pred             CCCCCCCCCCHHHHHhc--c-CCCCeEEEEECCCC--CcEEEEEEEc
Confidence            9985  23333222222  1 12457888886433  4678999886

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=3.7e-06  Score=72.99  Aligned_cols=105  Identities=22%  Similarity=0.248  Sum_probs=74.3

Q ss_pred             ehhhHhHHHHHHhhcCCCCceEEEEeeeeEec-CCeEEEEeeeecccCCCCcceeccHHH--HHHHHHHhhhcCCCCcEE
Q 023811           65 HPLVIFNICDCYVRRPDQAERVIGTLLGSVLP-DGTVDIRNSYVVPHNEFSDQVALDIEY--HHTMLKSHLKVNPQEVIV  141 (277)
Q Consensus        65 hPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~-~~~VeVtnsF~vp~~e~~~~~~iD~~y--~~~m~~l~kkv~p~e~iV  141 (277)
                      .+.+..+|..|..+..  +..|.|.|+|+ .. ++.+.|++++|+.+..    ..++...  ...+.+.+-+. .+..||
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 STLAYVKMLLHAAKYP--HCAVNGLLLGK-KSSGGSVEITDAVPLFHSC----LALAPMLEVALALVDAYCKS-SGLVIV   73 (182)
T ss_pred             CHHHHHHHHHHHHHcC--CchheEEEEee-ecCCCCEEEEEEEEcCCCc----cccCHHHHHHHHHHHHHHHH-CCCEEE
Confidence            3567889999998853  56999999998 55 7789999999999852    3455442  22233333333 389999


Q ss_pred             EeeecCCCCC-----CchhHHHHHHhhcCCCcEEEEEecCC
Q 023811          142 GWFSTGLGVT-----GGSALIHEFYCREVPNPVHLTVDTGF  177 (277)
Q Consensus       142 GWY~t~~~~~-----~~~~~ih~~~~~~~~~PI~L~vD~~~  177 (277)
                      |+|++++...     .....|=+.+.+.++++++|++|-.+
T Consensus        74 G~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~  114 (182)
T cd08060          74 GYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEK  114 (182)
T ss_pred             EEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCcc
Confidence            9999998543     23334455566677889999999765

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=98.38  E-value=7.5e-06  Score=71.85  Aligned_cols=124  Identities=16%  Similarity=0.181  Sum_probs=86.8

Q ss_pred             EEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCe-EEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCc
Q 023811           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT-VDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEV  139 (277)
Q Consensus        61 ~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~-VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~  139 (277)
                      +|.+.+.+..+|+=|..+..  ...|.|.|||....++. |+|++|.|+=|....  ..--.|-.-.+.+.|-+. .+..
T Consensus         3 ~v~is~~AY~K~~LHaaKyP--~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~~~--L~PmlEvAL~qvd~~~~~-~gl~   77 (196)
T PF03665_consen    3 SVEISSRAYAKMILHAAKYP--HCAVNGVLLGKSSKSSSEVEIVDAVPLFHHWLS--LSPMLEVALAQVDAYAKS-NGLV   77 (196)
T ss_pred             eEEEcHHHHHHHHHHhccCC--CCceeeEEEeccCCCCceEEEeeceeccccccC--cchHHHHHHHHHHHHHhh-CCCE
Confidence            68999999999999998874  46899999999433333 999999999995432  122234444556666643 5799


Q ss_pred             EEEeeecCCC-----CCCchhHHHHHHhhcCCCcEEEEEecCC-C--CCcceeEEEEe
Q 023811          140 IVGWFSTGLG-----VTGGSALIHEFYCREVPNPVHLTVDTGF-R--NGEGTVKAYVS  189 (277)
Q Consensus       140 iVGWY~t~~~-----~~~~~~~ih~~~~~~~~~PI~L~vD~~~-~--~~~l~ikay~~  189 (277)
                      |||+|++...     ++..-..|=+...+.++++++|++|-.+ .  .+...+.+|..
T Consensus        78 IvGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~kl~~~~~~~~~~~~~~  135 (196)
T PF03665_consen   78 IVGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKKLSSDCKAPAISVYQR  135 (196)
T ss_pred             EEEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcccccccCCCcceeeee
Confidence            9999998753     3333334555666678899999999765 2  23344567763

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

Probab=98.09  E-value=4.1e-05  Score=62.80  Aligned_cols=99  Identities=19%  Similarity=0.251  Sum_probs=63.9

Q ss_pred             EEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCC--cceeccHHHHHHHHHHhhhcCCCCcE
Q 023811           63 KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS--DQVALDIEYHHTMLKSHLKVNPQEVI  140 (277)
Q Consensus        63 ~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~--~~~~iD~~y~~~m~~l~kkv~p~e~i  140 (277)
                      .+-..++-.|+.|..|.  .+.+++|.|+|+ ..+     ...|+++....+  +...++.++.. ++....+.  ++.+
T Consensus         3 ~i~~~~l~~il~~a~~~--~p~E~~g~l~~~-~~~-----~~~~~~~n~~~~~~~~~~~~~~~~~-~~~~~~~~--g~~v   71 (134)
T COG1310           3 VIPKEVLGAILEHARRE--HPREVCGLLAGT-REG-----ERYFPLKNVSVEPVEYFEIDPEYSL-FYLAAEDA--GEVV   71 (134)
T ss_pred             eecHHHHHHHHHHHHhc--CChheEEEEEee-ccc-----ceeeccccccCCcceeEeeCHHHHH-HHHHHhhC--CCEE
Confidence            45667888999999886  368999999998 545     344444433322  22355666555 44444333  3999


Q ss_pred             EEeeecCCC--CCCchhHHHHHHhhcCCCcEEEEEe
Q 023811          141 VGWFSTGLG--VTGGSALIHEFYCREVPNPVHLTVD  174 (277)
Q Consensus       141 VGWY~t~~~--~~~~~~~ih~~~~~~~~~PI~L~vD  174 (277)
                      ||||||+++  ...++..++  +++..+.|-+++..
T Consensus        72 vg~yHSHP~~~~~pS~~D~~--~~~~~~~~~~iv~~  105 (134)
T COG1310          72 VGWYHSHPGGPPYPSEADRR--LSKLGPLPWLIVSV  105 (134)
T ss_pred             EEEEcCCCCCCCCcCHHHHh--hccccCCCEEEEEc
Confidence            999999995  445555555  66666666566554

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

Probab=97.63  E-value=0.0012  Score=56.64  Aligned_cols=124  Identities=16%  Similarity=0.164  Sum_probs=86.6

Q ss_pred             EEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeE-ecCCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCc
Q 023811           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSV-LPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEV  139 (277)
Q Consensus        61 ~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~-~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~  139 (277)
                      .|++..++..+|+=|+.|.+  ...|.|.|+|.. ..|+.|+|++|.|+=|+.-.  +.--.|-.-.|++-+- +--+..
T Consensus         3 ~veis~~aY~kmiLH~akyp--h~aVnGLLla~~~~kg~~v~itdcVPLfH~~la--LaPmlEvAl~lId~~~-~~~Glv   77 (199)
T KOG3289|consen    3 EVEISALAYVKMILHAAKYP--HAAVNGLLLAPATGKGECVEITDCVPLFHSHLA--LAPMLEVALNLIDVWG-AQAGLV   77 (199)
T ss_pred             ceeehhhHHHHHHHHhccCc--ccceeeEEEeccCCCCCeEEEEecchhhccccc--cccHHHHHHHHHHHHH-HhcCeE
Confidence            57889999999999999874  467999999932 45678999999999877531  1223344445555544 235899


Q ss_pred             EEEeeecCCCCC-----CchhHHHHHHhhcCCCcEEEEEecCC-C--CCcceeEEEEe
Q 023811          140 IVGWFSTGLGVT-----GGSALIHEFYCREVPNPVHLTVDTGF-R--NGEGTVKAYVS  189 (277)
Q Consensus       140 iVGWY~t~~~~~-----~~~~~ih~~~~~~~~~PI~L~vD~~~-~--~~~l~ikay~~  189 (277)
                      |+|.|++...+.     ..-..|-+..++.+++..+|++|-.. .  -..-++.+|+-
T Consensus        78 iaGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn~~l~~~~e~~~v~v~e~  135 (199)
T KOG3289|consen   78 IAGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDNKKLVPQCERPPVIVLED  135 (199)
T ss_pred             EEEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEeccccccccCCCCEEEeec
Confidence            999999875432     23334556677788887777777554 2  23457888884

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

Probab=96.70  E-value=0.01  Score=54.05  Aligned_cols=103  Identities=22%  Similarity=0.298  Sum_probs=72.3

Q ss_pred             CceEEEEeeeeEecC---CeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEEEeeecCCC----CCCchh
Q 023811           83 AERVIGTLLGSVLPD---GTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG----VTGGSA  155 (277)
Q Consensus        83 ~~~ViG~LLG~~~~~---~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iVGWY~t~~~----~~~~~~  155 (277)
                      ...+.|.|.|. ...   +.-||+.-...|+..+.+.+.+..+-     -.|. ---+++.|||=+|.+.    ++..|+
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            35899999998 554   56688888888888876665432110     1111 1247899999999863    567888


Q ss_pred             HHHHHHhhcCC-----CcEEEEEecCCCCCcceeEEEEeeeecc
Q 023811          156 LIHEFYCREVP-----NPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (277)
Q Consensus       156 ~ih~~~~~~~~-----~PI~L~vD~~~~~~~l~ikay~~~~~~~  194 (277)
                      ..|..+...++     +.|.+++  +...|..++.||.+.+.++
T Consensus       128 ~tha~~~~~~~~w~~~~~V~it~--SftpGs~sl~ay~LT~~G~  169 (252)
T cd08056         128 TTHAKILADNPSWDGEKTVILTC--SFTPGSCSLTAYKLTPEGY  169 (252)
T ss_pred             HHHHHHHHhccccCCCcEEEEEE--cCCCCceEEEEEecCHHHH
Confidence            88988887766     3455544  4457789999999997764

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

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

Probab=96.51  E-value=0.064  Score=43.10  Aligned_cols=98  Identities=18%  Similarity=0.214  Sum_probs=62.2

Q ss_pred             HhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcce-eccHHHHHHHHHHhhhcCCCCcEEEeeecC
Q 023811           69 IFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKVNPQEVIVGWFSTG  147 (277)
Q Consensus        69 lL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~-~iD~~y~~~m~~l~kkv~p~e~iVGWY~t~  147 (277)
                      +-.|++|..+.  .+..+.|.|+|+ . +   .|++.+++|....++.. ..+.+    |.      -.+.++||-||++
T Consensus         6 ~~~i~~ha~~~--~P~E~CGlL~G~-~-~---~v~~~~~~~n~~~~~~~~~f~~~----~~------~~g~~ivgi~HSH   68 (117)
T cd08072           6 LDSILEAAKSS--HPNEFAALLRGK-D-G---VITELLILPGTESGEVSAVFPLL----ML------PLDMSIVGSVHSH   68 (117)
T ss_pred             HHHHHHHHhhc--CCceEEEEEEee-c-c---EEEEEEECCCCCCCCcceeechH----Hh------cCCCeEEEEEEcC
Confidence            45788888765  478999999997 3 2   58899999966543321 12221    21      2489999999999


Q ss_pred             CC----CCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEee
Q 023811          148 LG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV  190 (277)
Q Consensus       148 ~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~  190 (277)
                      ++    ++..|.  .  ++.. +.-.+|++....  +.-.++||...
T Consensus        69 P~~~~~PS~~D~--~--~~~~-~~~~~lIvs~~~--~~~~~~a~~~~  108 (117)
T cd08072          69 PSGSPRPSDADL--S--FFSK-TGLVHIIVGYPY--DEDDWRAYDSD  108 (117)
T ss_pred             CCCCCCCCHHHH--H--hhhc-CCCEEEEEECcC--CCCCEEEEecC
Confidence            85    334442  2  2222 334778776433  22468898875

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.

>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family

Probab=96.50  E-value=0.058  Score=44.46  Aligned_cols=80  Identities=16%  Similarity=0.160  Sum_probs=54.2

Q ss_pred             hHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCC-Ccc--eeccHHHHHHHHH-HhhhcCCCCcEEEe
Q 023811           68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEF-SDQ--VALDIEYHHTMLK-SHLKVNPQEVIVGW  143 (277)
Q Consensus        68 VlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~-~~~--~~iD~~y~~~m~~-l~kkv~p~e~iVGW  143 (277)
                      ++++++..|......+...-|.|+|. ..+..+.|+..- .|..++ ...  ..-+.+.+++.++ .+++.+-....||=
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            46777778866655678999999998 556677777744 443332 111  2345666666655 55556566999999


Q ss_pred             eecCCC
Q 023811          144 FSTGLG  149 (277)
Q Consensus       144 Y~t~~~  149 (277)
                      +||+|.
T Consensus        79 WHtHP~   84 (131)
T TIGR02256        79 WHTHPE   84 (131)
T ss_pred             cCcCCC
Confidence            999985

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.

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

Probab=96.07  E-value=0.055  Score=41.70  Aligned_cols=93  Identities=14%  Similarity=0.028  Sum_probs=50.9

Q ss_pred             hHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEEEeeecC
Q 023811           68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTG  147 (277)
Q Consensus        68 VlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iVGWY~t~  147 (277)
                      ++-.|+.|..+.  .+....|.|+|. ..+..+.++........+          +......  +....+..+||+|||+
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            455678888775  478999999998 566666677666511111          1111110  4455799999999999


Q ss_pred             CCCCCchhHHHHHHhhcCCCcEEEEEec
Q 023811          148 LGVTGGSALIHEFYCREVPNPVHLTVDT  175 (277)
Q Consensus       148 ~~~~~~~~~ih~~~~~~~~~PI~L~vD~  175 (277)
                      ++-...=+............+++|++..
T Consensus        69 P~~~a~pS~~D~~~~~~~~~~~~iI~~~   96 (104)
T PF14464_consen   69 PSGPAFPSSTDIRSMRDLAPPSYIIVGN   96 (104)
T ss_dssp             SSSSSS--HHHHHTHCCS-SCEEEEEEE
T ss_pred             CCCCCCCCHHHHHhhhccCCeEEEEEeC
Confidence            8643222222222233222556666653

>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=88.72  E-value=2.6  Score=33.29  Aligned_cols=64  Identities=8%  Similarity=-0.046  Sum_probs=40.2

Q ss_pred             hHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCC--cceeccH-HHHHHHHHHhhhcCCCCcEEEeeec
Q 023811           70 FNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS--DQVALDI-EYHHTMLKSHLKVNPQEVIVGWFST  146 (277)
Q Consensus        70 L~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~--~~~~iD~-~y~~~m~~l~kkv~p~e~iVGWY~t  146 (277)
                      -.|++|..+.  .+....|.|+|. .  +   ++..++++....+  ....+|. ++++-+    +    ...+||-|||
T Consensus         4 ~~i~~ha~~~--~P~E~CGll~g~-~--~---~~~~~p~~N~~~~p~~~F~idp~e~~~a~----~----~~~ivgi~HS   67 (108)
T cd08073           4 DAILAHAKAE--YPREACGLVVRK-G--R---KLRYIPCRNIAADPEEHFEISPEDYAAAE----D----EGEIVAVVHS   67 (108)
T ss_pred             HHHHHHHhHC--CCCcceEEEEec-C--C---ceEEEECccCCCCccceEEeCHHHHHHHh----c----CCCEEEEEEc
Confidence            4678888665  478899999996 3  2   3344666533222  3356775 454432    1    2389999999


Q ss_pred             CCC
Q 023811          147 GLG  149 (277)
Q Consensus       147 ~~~  149 (277)
                      +++
T Consensus        68 HP~   70 (108)
T cd08073          68 HPD   70 (108)
T ss_pred             CCC
Confidence            974

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.

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

Probab=88.03  E-value=5.7  Score=36.72  Aligned_cols=109  Identities=17%  Similarity=0.207  Sum_probs=68.7

Q ss_pred             CceEEEEeeeeEecC------CeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEEEeeecCCC-------
Q 023811           83 AERVIGTLLGSVLPD------GTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG-------  149 (277)
Q Consensus        83 ~~~ViG~LLG~~~~~------~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iVGWY~t~~~-------  149 (277)
                      ...-+|-|.|+..+.      .++.|.--|+=|+..+.+.+.+..+-.++..+... ..-+...|||=-|...       
T Consensus        33 ~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~vd~iA-~~lGL~~VG~IfT~l~~~~~d~~  111 (274)
T cd08061          33 GQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADTVDAIA-AALGLERVGWIFTDLPREDKDGY  111 (274)
T ss_pred             cceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhHHHHHH-HHcCCeEEEEEEecCCCCCCCce
Confidence            356799999995443      37889889999988777766443333323233333 2348999999888752       


Q ss_pred             -CCCchhHHHHHHhh-----cCCCc-EEEEEecCCCCCcceeEEEEeeeec
Q 023811          150 -VTGGSALIHEFYCR-----EVPNP-VHLTVDTGFRNGEGTVKAYVSVNLS  193 (277)
Q Consensus       150 -~~~~~~~ih~~~~~-----~~~~P-I~L~vD~~~~~~~l~ikay~~~~~~  193 (277)
                       ++...+.....++.     ...+. +-+++.+.. ++...+.||..++..
T Consensus       112 ~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~-~g~i~~~ayQvSdq~  161 (274)
T cd08061         112 FLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDK-DGQIHFEAYQVSDQA  161 (274)
T ss_pred             eECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCC-CCceeeeeeeecHHH
Confidence             22333333344442     23333 557777654 478999999998654

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=86.62  E-value=7.1  Score=36.70  Aligned_cols=105  Identities=18%  Similarity=0.167  Sum_probs=62.5

Q ss_pred             EEEeeeeEecCC------eEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEEEeeecCCC-----------
Q 023811           87 IGTLLGSVLPDG------TVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG-----------  149 (277)
Q Consensus        87 iG~LLG~~~~~~------~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iVGWY~t~~~-----------  149 (277)
                      +|-|.|+..+..      ++.|.--|+=|+..+.+.+.+..+-.++..+...+. -+...|||=-|...           
T Consensus         2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA~~-lGL~rVG~IfTdl~~~~~~~g~v~~   80 (306)
T PF05021_consen    2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEERVDAIASA-LGLERVGWIFTDLTDDGSGDGTVKC   80 (306)
T ss_pred             eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHHHHHHHHH-CCCEEEEEEEecCcccccCCCceee
Confidence            799999844434      688999999999887776655322233333333322 28999999876532           


Q ss_pred             --------CCCchhHHHHHHhhcC------------CCc-EEEEEecCCCCCcceeEEEEeeeec
Q 023811          150 --------VTGGSALIHEFYCREV------------PNP-VHLTVDTGFRNGEGTVKAYVSVNLS  193 (277)
Q Consensus       150 --------~~~~~~~ih~~~~~~~------------~~P-I~L~vD~~~~~~~l~ikay~~~~~~  193 (277)
                              ++...+..=..++...            .+. |-+++.+. .++.+.+.||..++..
T Consensus        81 ~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~-~~g~i~~~ayQvS~q~  144 (306)
T PF05021_consen   81 KRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGD-EEGEIHFEAYQVSNQC  144 (306)
T ss_pred             ccccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCC-CCCceeeEEeeehHHH
Confidence                    1222222212222222            222 55666654 5678999999998653

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 [].

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

Probab=81.80  E-value=6.8  Score=29.97  Aligned_cols=63  Identities=14%  Similarity=0.098  Sum_probs=39.7

Q ss_pred             HHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcEEEeeecCCC
Q 023811           71 NICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG  149 (277)
Q Consensus        71 ~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~iVGWY~t~~~  149 (277)
                      .|.+|+.+.  .+....|.|+|. . ++  .+.+..++|....    ..+..+      ......-+..+||-|+++++
T Consensus         5 ~i~~~~~~~--~p~E~~gll~~~-~-~~--~~~~~~~~~~~~~----~~~~~~------~~~a~~~~~~~v~i~HsHP~   67 (101)
T cd08059           5 TILVHAKDA--HPDEFCGFLSGS-K-DN--VMDELIFLPFVSG----SVSAVI------DLAALEIGMKVVGLVHSHPS   67 (101)
T ss_pred             HHHHHHHhc--CChhhheeeecC-C-CC--eEEEEEeCCCcCC----ccChHH------HHHHhhCCCcEEEEEecCcC
Confidence            455666543  367899999996 4 33  5778788875431    233333      22223357789999999974

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	277
2o96_A	178	Crystal Structure Of The Metal-Free Dimeric Human M		1e-11
2o95_A	187	Crystal Structure Of The Metal-Free Dimeric Human M		1e-11
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 = 67.0 bits (162), Expect = 1e-11,   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 = 66.6 bits (161), Expect = 1e-11,   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 = 34/130 (26%), Positives = 60/130 (46%), Gaps = 11/130 (8%)
Query: 55  AATSNVTAKVHPLVIFNICDCYVR-RPDQAE--RVIGTLLGSVLPDGTVDIRNSYVVPHN 111
            +  +VT  +HPLVI NI + + R R    E  +V G L+G       ++I NS+ +  +
Sbjct: 1   GSHXSVTISLHPLVIXNISEHWTRFRAQHGEPRQVYGALIGK-QKGRNIEIXNSFELKTD 59
Query: 112 EFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYC--REVP--- 166
              D+  ++ +Y++   + + +V      +GW++TG   T     I        E P   
Sbjct: 60  VIGDETVINKDYYNKKEQQYKQVFSDLDFIGWYTTGDNPTADDIKIQRQIAAINECPIXL 119
Query: 167 --NPVHLTVD 174
             NP+  +VD
Sbjct: 120 QLNPLSRSVD 129

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	277
2o95_A	187	26S proteasome non-ATPase regulatory subunit 7; PS	3e-47
4e0q_A	141	COP9 signalosome complex subunit 6; MPN (MPR1P and	3e-42

>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 =  155 bits (392), Expect = 3e-47
 Identities = 54/184 (29%), Positives = 84/184 (45%), Gaps = 7/184 (3%)

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-FQEIPLDLRMIEAERVGFDILKSTSVD 229
           + +D   ++     +AY+SV     D    ++ F+ +  ++   EAE VG + L     D
Sbjct: 123 VIIDVKPKDLGLPTEAYISVEEVHDDGTPTSKTFEHVTSEIGAEEAEEVGVEHLLRDIKD 182

Query: 230 KLPS 233
               
Sbjct: 183 TTVG 186

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

 Score =  140 bits (355), Expect = 3e-42
 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	277
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	100.0
2znr_A	178	AMSH-like protease; metal binding protein, alterna	99.4
3rzv_A	211	STAM-binding protein; ubiquitin hydrolase, endosom	99.29
2kks_A	146	Uncharacterized protein; NESG, structural genomics	99.0
2kcq_A	153	MOV34/MPN/PAD-1 family; NESG, structure, structura	98.79
1oi0_A	124	AF2198, hypothetical protein AF2198; proteasome, d	98.01
2p8r_A	273	PRP8, PRE-mRNA-splicing factor PRP8; alpha-beta, t	96.32
2og4_A	254	PRE-mRNA-splicing factor 8; isopeptidase, JAB1/MPN	95.77
3sbg_A	565	PRE-mRNA-splicing factor 8; PRP8P, rnaseh domain,	94.44

>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=6.4e-53  Score=394.94  Aligned_cols=217  Identities=23%  Similarity=0.392  Sum_probs=181.7

Q ss_pred             CCcEEEEehhhHhHHHHHHhhcC-CCCceEEEEeeeeEecCCeEEEEeeeecccCCCCc---ceeccHHHHHHHHHHhhh
Q 023811           58 SNVTAKVHPLVIFNICDCYVRRP-DQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSD---QVALDIEYHHTMLKSHLK  133 (277)
Q Consensus        58 ~~~~V~vhPlVlL~I~dH~~R~~-~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~---~~~iD~~y~~~m~~l~kk  133 (277)
                      ...+|.|||||||+|+|||+|.+ .++.+|+|+|||+ ++|+.|||+|||++|++++++   .+++|.+|+++|+++||+
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            45699999999999999999954 4578999999998 899999999999999987653   368999999999999999


Q ss_pred             cCCCCcEEEeeecCCCCCCchhHHHHHHhhcCC-CcEEEEEecCCCCCcceeEEEEeeeeccC-CcccccceEEeceEEE
Q 023811          134 VNPQEVIVGWFSTGLGVTGGSALIHEFYCREVP-NPVHLTVDTGFRNGEGTVKAYVSVNLSLG-DRQLAAQFQEIPLDLR  211 (277)
Q Consensus       134 v~p~e~iVGWY~t~~~~~~~~~~ih~~~~~~~~-~PI~L~vD~~~~~~~l~ikay~~~~~~~~-~~~~~~~F~~ip~~I~  211 (277)
                      |||++.+||||+||++++.+|+.||++|+++++ +|++|++|+...++++|++||++.....+ +...+..|.++|++|.
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            999999999999999999999999999999974 89999999999899999999999877654 3455678999999999


Q ss_pred             cChhhHHHHHHhhccCCC----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHcCCcccCceeeeeec
Q 023811          212 MIEAERVGFDILKSTSVD----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVVSMIIFLFLFYSQIV  275 (277)
Q Consensus       212 ~~eaErIav~~l~k~~~~----~l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G~~~~d~~~~~~~~  275 (277)
                      ++|+||||++|+++...+    .+..++.++.+++++|+.+++.|.+||++|.+|++++|+++||++-
T Consensus       163 ~~eaE~Igv~~l~r~~~~~~~~~l~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~n~~ilr~l~  230 (338)
T 4b4t_U          163 AEEAEEIGVEHLLRDVRDQAAGGLSIRLTNQLKSLKGLQSKLKDVVEYLDKVINKELPINHTILGKLQ  230 (338)
T ss_dssp             SCHHHHHHHHHHHHHHSSCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHC----------------
T ss_pred             cCcHHHHHHHHHHhccccCcccccchhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCHHHHHHHH
Confidence            999999999999986543    4667899999999999999999999999999999999999999974

>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=2.8e-41  Score=291.43  Aligned_cols=174  Identities=30%  Similarity=0.455  Sum_probs=154.0

Q ss_pred             CCCCCcEEEEehhhHhHHHHHHhhcC--CCCceEEEEeeeeEecCCeEEEEeeeecccCCCCc---ceeccHHHHHHHHH
Q 023811           55 AATSNVTAKVHPLVIFNICDCYVRRP--DQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSD---QVALDIEYHHTMLK  129 (277)
Q Consensus        55 ~~~~~~~V~vhPlVlL~I~dH~~R~~--~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~---~~~iD~~y~~~m~~  129 (277)
                      |+.+..+|+|||+|+++|+||++|..  .++.+|+|+|||. ..++.++|+|||++|+.++++   .+.+|.+|+++|++
T Consensus         3 ~~~~~~~V~i~plvllkI~~H~~r~~~~~~~~~V~G~LLG~-~~~~~v~V~~~f~lp~~~~~~~~~~~~~d~ey~~~m~~   81 (187)
T 2o95_A            3 PELAVQKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGS-WQKKVLDVSNSFAVPFDEDDKDDSVWFLDHDYLENMYG   81 (187)
T ss_dssp             CCCSCSEEEECHHHHHHHHHHHHHHHHTTCCSCCEEEEEEE-ESSSEEEEEEEEEECEEECSSCTTSEEECHHHHHHHHH
T ss_pred             CCCCCCEEEEchHHHHHHHHHHhhhcccCCCcEEEEEEEEE-EcCCEEEEEEEEEeCCcccCCCcchhhcCHHHHHHHHH
Confidence            35667899999999999999999974  2578999999998 778899999999999987654   35899999999999


Q ss_pred             HhhhcCCCCcEEEeeecCCCCCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEeeeeccC-CcccccceEEece
Q 023811          130 SHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLG-DRQLAAQFQEIPL  208 (277)
Q Consensus       130 l~kkv~p~e~iVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~~~~~~-~~~~~~~F~~ip~  208 (277)
                      ++++++|++.+||||+++++.+..|..||++|++.+++|++|++||....++++++||++.+...+ +.+....|.++|+
T Consensus        82 ~~~~v~~~~~iVGWY~s~~~~s~~d~~i~~~~~~~~~~~v~Livd~~~~~~~l~i~ay~~~~~~~~~~~~~~~~F~~ip~  161 (187)
T 2o95_A           82 MFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSVLVIIDVKPKDLGLPTEAYISVEEVHDDGTPTSKTFEHVTS  161 (187)
T ss_dssp             HHHTTSSSCEEEEEEECCSSCCTTHHHHHHHHTTTCTTCEEEEECCCTTC-CCSEEEEEEEEECC----CCEEEEEEEEE
T ss_pred             HHHHhCCCCCEEEEEcCCCcCCcccHHHHHHHHhcCCCCEEEEECCCCCCCCcCeEEEEEechhcCCCCcccCEEEEeeE
Confidence            999999999999999999999999999999999989999999999988655699999999987764 3345789999999


Q ss_pred             EEEcChhhHHHHHHhhccCCC
Q 023811          209 DLRMIEAERVGFDILKSTSVD  229 (277)
Q Consensus       209 ~I~~~eaErIav~~l~k~~~~  229 (277)
                      +|.++|+|||||+|+++...+
T Consensus       162 ~I~~~eaE~i~v~~l~~~~~~  182 (187)
T 2o95_A          162 EIGAEEAEEVGVEHLLRDIKD  182 (187)
T ss_dssp             EECCCHHHHHHHHHHHHHCCS
T ss_pred             EEecCcHHHHHHHHHHhcCCC
Confidence            999999999999999987654

>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=1e-40  Score=276.41  Aligned_cols=134  Identities=23%  Similarity=0.389  Sum_probs=114.3

Q ss_pred             CCCCcEEEEehhhHhHHHHHHhhcCC---CCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhh
Q 023811           56 ATSNVTAKVHPLVIFNICDCYVRRPD---QAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHL  132 (277)
Q Consensus        56 ~~~~~~V~vhPlVlL~I~dH~~R~~~---~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~k  132 (277)
                      ++++.+|+|||||||+|+|||+|.+.   .+.+|+|+|||+ ++|++|||+|||++|++++++++++|.+|+++|++++|
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            35678999999999999999999642   367999999998 78999999999999999888889999999999999999


Q ss_pred             hcCCCCcEEEeeecCCCCCCchhHHHHHHhhcCCCcEEEEEecCCCC-CcceeEEEEee
Q 023811          133 KVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRN-GEGTVKAYVSV  190 (277)
Q Consensus       133 kv~p~e~iVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~-~~l~ikay~~~  190 (277)
                      +|||++.+||||+|+++++.+|+.||++|++++++||+|++||.++. |+||++||++.
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            99999999999999999999999999999999999999999999964 67999999874

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

Probab=100.00  E-value=5e-33  Score=256.92  Aligned_cols=211  Identities=14%  Similarity=0.183  Sum_probs=169.5

Q ss_pred             CCCCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcce-eccHHHHHHHHHHhhhc
Q 023811           56 ATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKV  134 (277)
Q Consensus        56 ~~~~~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~-~iD~~y~~~m~~l~kkv  134 (277)
                      ..+..+|+|+|+|+|+|++|+.+  ..+.+|+|.|||.+.++++++|+|||++|+.++++++ ++|.+|+.+|+++++++
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            35678999999999999999944  3578999999998566779999999999999887776 68999999999999999


Q ss_pred             CCCCcEEEeeecCCCC----CCchhHHHHHHhhcCCCcEEEEEecCC-CCCcceeEEEEeeeeccC--------------
Q 023811          135 NPQEVIVGWFSTGLGV----TGGSALIHEFYCREVPNPVHLTVDTGF-RNGEGTVKAYVSVNLSLG--------------  195 (277)
Q Consensus       135 ~p~e~iVGWY~t~~~~----~~~~~~ih~~~~~~~~~PI~L~vD~~~-~~~~l~ikay~~~~~~~~--------------  195 (277)
                      ++++.+||||||+++.    +..|+..|..|+...+++|+|++||.. ..|+++++||++.+.+..              
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            9999999999999863    355666666677778899999999987 468999999999865420              


Q ss_pred             ----------CcccccceEEeceEEEcChhhHHHHHHhhccCCCC---CcccHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Q 023811          196 ----------DRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDK---LPSDLEGMEVLMERLLTLINDIYKYVDDTVVS  262 (277)
Q Consensus       196 ----------~~~~~~~F~~ip~~I~~~eaErIav~~l~k~~~~~---l~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~G  262 (277)
                                +......|+++|+++..++.|+..++.+.+..+..   ..+-.+..+.+.+++.++++.+.+|.+.|.+|
T Consensus       179 ~~~~~~~~~~~~~~~~~yy~l~i~~~ks~le~~~L~~L~~~~w~~~l~~~~~~~~~~~~~~~i~~m~~~~~~y~k~v~~e  258 (306)
T 4b4t_V          179 LLNKANIQALIHGLNRHYYSLNIDYHKTAKETKMLMNLHKEQWQSGLKMYDYEEKEESNLAATKSMVKIAEQYSKRIEEE  258 (306)
T ss_dssp             -----------------CEEECSCCCCCSSCTHHHHHHHHC----------CHHHHHHHHHHHHHHSSCHHHHHHHHHHH
T ss_pred             ccCchhhhhhhccccceEEEeeeEEEeCcHHHHHHHHHHhcccccccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence                      00123569999999999999999999998876642   33446678888999999999999999999988


Q ss_pred             CcccCc
Q 023811          263 MIIFLF  268 (277)
Q Consensus       263 ~~~~d~  268 (277)
                      +...+.
T Consensus       259 ~~~~~~  264 (306)
T 4b4t_V          259 KELTEE  264 (306)
T ss_dssp             HHHHHH
T ss_pred             ccCCHH
Confidence            754443

>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=99.40  E-value=1.3e-12  Score=111.65  Aligned_cols=127  Identities=12%  Similarity=0.144  Sum_probs=95.8

Q ss_pred             CCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCccee-ccHHHHHHHHHHhhhcCC
Q 023811           58 SNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVA-LDIEYHHTMLKSHLKVNP  136 (277)
Q Consensus        58 ~~~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~-iD~~y~~~m~~l~kkv~p  136 (277)
                      +...|.|...++.+|+.|+.++..++..++|.|+|. ..++..+|+++|++|...+++.+. .+.+-   .++.  ....
T Consensus         7 ~~~~v~i~~~~l~k~l~hA~~~~~~~~EvcGlL~G~-~~~~~~~V~~v~~~pq~~t~~~~~~~~~~e---~~~~--~~~~   80 (178)
T 2znr_A            7 GLRCVVLPEDLCHKFLQLAESNTVRGIETCGILCGK-LTHNEFTITHVIVPKQSAGPDYCDMENVEE---LFNV--QDQH   80 (178)
T ss_dssp             SCCCEEEETTHHHHHHHHHHHHHTTTCCCEEEEEEE-EETTEEEEEEEEECCEEEETTEEEECCHHH---HHHH--HHHH
T ss_pred             CcEEEEECHHHHHHHHHHHHhCCCCCceEEEEEeeE-ecCCCeEEEEEEeCCcCCCCCeeccCCHHH---HHHH--HHhC
Confidence            356899999999999999987644456899999998 667789999999999876655543 33221   1111  2346


Q ss_pred             CCcEEEeeecCCC----CCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEeeeecc
Q 023811          137 QEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (277)
Q Consensus       137 ~e~iVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~~~~~  194 (277)
                      ++.+||||+|+++    ++..|+..|..|+...+..++|+++|...    .++||+..+.++
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            8999999999874    55667777766666677889999999763    389999987654

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

Probab=99.29  E-value=1.8e-11  Score=107.02  Aligned_cols=125  Identities=14%  Similarity=0.117  Sum_probs=94.3

Q ss_pred             CcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCccee-ccH-HHHHHHHHHhhhcCC
Q 023811           59 NVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVA-LDI-EYHHTMLKSHLKVNP  136 (277)
Q Consensus        59 ~~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~-iD~-~y~~~m~~l~kkv~p  136 (277)
                      -.+|.|..-++-+|+.|...+..++..++|.|+|. ..++.++|+++|..|...+++.+. .+. +.++-+.+      .
T Consensus        41 lr~v~Ipk~ll~kfL~~A~~~tp~~~EvcGlL~Gk-~~~~~~~I~~v~~ppq~gt~~~v~~~~~~e~~~~~~~------~  113 (211)
T 3rzv_A           41 LRHVVVPGRLCPQFLQLASANTARGVATCGILCGK-LMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQ------Q  113 (211)
T ss_dssp             BCCEEEETTHHHHHHHHHHHHHHTTCCCEEEEEEE-EETTEEEEEEEEECCEEECSSCEEECCHHHHHHHHHH------H
T ss_pred             cEEEEECHHHHHHHHHHHHhCCCCCceEEEEEEeE-cCCCCEEEEEEEeCCccCCCCceeccChHHHHHHHhh------C
Confidence            46899999999999999977533356899999998 678889999999988876665442 232 22221111      4


Q ss_pred             CCcEEEeeecCCC----CCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEeeeecc
Q 023811          137 QEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (277)
Q Consensus       137 ~e~iVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~~~~~  194 (277)
                      ++.+||||+|++.    ++..|+..|..|+...+..|+|++||..    .++.||++.+.++
T Consensus       114 ~l~~vGWyHSHP~~~~~pS~~Dl~tq~~~q~~~~~~I~IVvsP~~----~~lgaFrLtp~G~  171 (211)
T 3rzv_A          114 GLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCSPKF----QETGFFKLTDHGL  171 (211)
T ss_dssp             TCEEEEEEEECTTSCSCCCHHHHHHHHHHHHHCTTCEEEEEETTT----TEEEEEEECHHHH
T ss_pred             CCEEEEEEeCCCCCCCCCCHHHHHHHHHHHhcCCCeEEEEEcCCC----CeeeEEEeccchh
Confidence            9999999999874    5566777776666667777999999873    2799999998765

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

Probab=99.00  E-value=1.6e-08  Score=83.05  Aligned_cols=133  Identities=13%  Similarity=0.068  Sum_probs=93.3

Q ss_pred             EEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCC-cceeccHHHHHHHHHHhhhcCCCCcE
Q 023811           62 AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS-DQVALDIEYHHTMLKSHLKVNPQEVI  140 (277)
Q Consensus        62 V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~-~~~~iD~~y~~~m~~l~kkv~p~e~i  140 (277)
                      +.|...++..|+.|..+.  .+..++|.|+|. .+++...|+..|++|....+ +...+|.+.+.+..+...+  .++.+
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            568889999999999775  478999999998 66777889999999955433 3456787666555544433  36899


Q ss_pred             EEeeecCCCC--CCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEeeeeccCCcccccceEEeceEEEc
Q 023811          141 VGWFSTGLGV--TGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRM  212 (277)
Q Consensus       141 VGWY~t~~~~--~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~~~~~~~~~~~~~F~~ip~~I~~  212 (277)
                      ||||+|+++.  ..+...++.  +. .+..+++++.+.. ++...++||+..         +..|.++|+.+..
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            9999999853  333333332  11 2344788887643 235679999984         2358999988753

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

Probab=98.79  E-value=2.6e-08  Score=82.49  Aligned_cols=134  Identities=15%  Similarity=0.128  Sum_probs=88.0

Q ss_pred             EEehhhHhHHHHHHhhcCCCCceEEEEeeeeEec-CCeEEEEeeeecccC--CC-CcceeccHHHHHHHHHHhhhcCCCC
Q 023811           63 KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLP-DGTVDIRNSYVVPHN--EF-SDQVALDIEYHHTMLKSHLKVNPQE  138 (277)
Q Consensus        63 ~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~-~~~VeVtnsF~vp~~--e~-~~~~~iD~~y~~~m~~l~kkv~p~e  138 (277)
                      .|.+.++.+|+.|..+.  .+..++|.|+|. .. ++.+.|+..|++|..  ++ .....+|.+.+.++.+..++  .++
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-VTDDGDNRVAALHRATNRRSEQRTRRYELTADDYRAADAAAQE--QGL   76 (153)
T ss_dssp             BCCHHHHHHHHHHHHHH--TTSCCCEEEEEE-ECTTSCEEEEEEEESSCCCCCCCSCCSSCCCCSHHHHHHHHHH--HTC
T ss_pred             EeCHHHHHHHHHHHHhc--CCcceEEEEEEe-eccCCCeEEEEEEECCCCCCCCCCcEEEECHHHHHHHHHHHHH--CCC
Confidence            35678899999999875  478999999998 55 677889999999875  32 23345664433334333333  268


Q ss_pred             cEEEeeecCCCC--CCchhHHHHHHhhcCCCcEEEEEecCCCCCc-ceeEEEEeeeeccCCcccccceEEeceEEEcC
Q 023811          139 VIVGWFSTGLGV--TGGSALIHEFYCREVPNPVHLTVDTGFRNGE-GTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMI  213 (277)
Q Consensus       139 ~iVGWY~t~~~~--~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~-l~ikay~~~~~~~~~~~~~~~F~~ip~~I~~~  213 (277)
                      .+||||+|+++.  ..+...+..  + ..+..+++++.+.  .++ ..+++|+...       ....|.+.++.|...
T Consensus        77 ~ivG~yHSHP~~~~~PS~~D~~~--~-~~~~~~~lIvs~~--~~~~~~~~af~~~~-------~~g~~~e~~i~v~~~  142 (153)
T 2kcq_A           77 DVVGVYHSHPDHPARPSATDLEE--A-TFPGFTYVIVSVR--DGAPEALTAWALAP-------DRSEFHREDIVRPDP  142 (153)
T ss_dssp             EEEEEEEECSSSSSSCCHHHHHT--C-CCTTSEEEEEEEE--TTEEEEEEEEEECT-------TCSCEEEECCBCCCS
T ss_pred             eEEEEEeCCCCCCCCCCHHHHHh--h-hcCCCeEEEEECC--CCCccEEEEEEEeC-------CCCcEEEEEEEEecC
Confidence            999999999863  233333322  1 1244578888643  233 4689999841       124688888877543

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

Probab=98.01  E-value=3.5e-05  Score=61.25  Aligned_cols=108  Identities=16%  Similarity=0.128  Sum_probs=67.0

Q ss_pred             EEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCcE
Q 023811           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVI  140 (277)
Q Consensus        61 ~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~i  140 (277)
                      .+.|...++..|++|..+.  .+..++|.|+|. . +   .|++.|++| ...+.   .+..|...|..      .++.+
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            3678888999999999875  478999999997 4 2   689999999 54322   11123222222      57999


Q ss_pred             EEeeecCCCC--CCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEee
Q 023811          141 VGWFSTGLGV--TGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV  190 (277)
Q Consensus       141 VGWY~t~~~~--~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~  190 (277)
                      ||||||+++-  ..+...+..  +.. +..+++++.+..  +...+++|...
T Consensus        66 vG~~HSHP~~~~~PS~~D~~~--~~~-~~~~~lIvs~~~--~~~~~~~f~~~  112 (124)
T 1oi0_A           66 FGTVHSHPSPSCRPSEEDLSL--FTR-FGKYHIIVCYPY--DENSWKCYNRK  112 (124)
T ss_dssp             EEEEEEESSSCCSCCHHHHHH--HHH-SCSEEEEEETTC--CTTCEEEEETT
T ss_pred             EEEEEECcCCCCccCHHHHHh--hhc-CCCEEEEEEccC--CCceEEEEecC
Confidence            9999999852  233333332  222 345788877533  23567888763

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

Probab=96.32  E-value=0.011  Score=52.91  Aligned_cols=110  Identities=22%  Similarity=0.289  Sum_probs=74.6

Q ss_pred             HHHHHHhhcCCCCceEEEEeeeeEec---CCeEEEEeeeecccCCCCcceec-----cHHHHHHHHHHhhhcCCCCcEEE
Q 023811           71 NICDCYVRRPDQAERVIGTLLGSVLP---DGTVDIRNSYVVPHNEFSDQVAL-----DIEYHHTMLKSHLKVNPQEVIVG  142 (277)
Q Consensus        71 ~I~dH~~R~~~~~~~ViG~LLG~~~~---~~~VeVtnsF~vp~~e~~~~~~i-----D~~y~~~m~~l~kkv~p~e~iVG  142 (277)
                      ||++.+.....-...+.|.|.|. ..   .+.-||+.---+|+..+.+.+..     ..+|+           -++..+|
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            55556666544456899999998 53   24677877666676655443321     11232           7999999


Q ss_pred             eeecCCC----CCCchhHHHHHHhhc---C--CCcEEEEEecCCCCCcceeEEEEeeeecc
Q 023811          143 WFSTGLG----VTGGSALIHEFYCRE---V--PNPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (277)
Q Consensus       143 WY~t~~~----~~~~~~~ih~~~~~~---~--~~PI~L~vD~~~~~~~l~ikay~~~~~~~  194 (277)
                      |=+|.+.    ++..|+..|..+...   .  ++.|++++-+  ..|..++.||++.+.++
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            9999763    567888888777654   2  3678887743  45667899999987664

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

Probab=95.77  E-value=0.019  Score=51.05  Aligned_cols=112  Identities=13%  Similarity=0.232  Sum_probs=74.0

Q ss_pred             HHHHHHhhcCCCCceEEEEeeeeEec---CCeEEEEeeeecccCCCCcceecc-----HHHHHHHHHHhhhcCCCCcEEE
Q 023811           71 NICDCYVRRPDQAERVIGTLLGSVLP---DGTVDIRNSYVVPHNEFSDQVALD-----IEYHHTMLKSHLKVNPQEVIVG  142 (277)
Q Consensus        71 ~I~dH~~R~~~~~~~ViG~LLG~~~~---~~~VeVtnsF~vp~~e~~~~~~iD-----~~y~~~m~~l~kkv~p~e~iVG  142 (277)
                      +|++-+.....-...+.|.|.|. ..   .+.-||+.---+|+..+.+.+...     .+|++         .-++..+|
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            45555655543456799999998 52   245678766666665554433110     12211         26899999


Q ss_pred             eeecCCC----CCCchhHHHHHHhhc-CCCcEEEEEecCCCCCcceeEEEEeeeecc
Q 023811          143 WFSTGLG----VTGGSALIHEFYCRE-VPNPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (277)
Q Consensus       143 WY~t~~~----~~~~~~~ih~~~~~~-~~~PI~L~vD~~~~~~~l~ikay~~~~~~~  194 (277)
                      |=+|.+.    ++..|+..|..+... .++.|++++-+  ..|..++.||++.+.++
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            9999763    567788888777663 47889988754  34567899999988764

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

Probab=94.44  E-value=0.052  Score=52.55  Aligned_cols=103  Identities=14%  Similarity=0.207  Sum_probs=68.9

Q ss_pred             CceEEEEeeeeEec-C--CeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhh--cCCCCcEEEeeecCCC----CCCc
Q 023811           83 AERVIGTLLGSVLP-D--GTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLK--VNPQEVIVGWFSTGLG----VTGG  153 (277)
Q Consensus        83 ~~~ViG~LLG~~~~-~--~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kk--v~p~e~iVGWY~t~~~----~~~~  153 (277)
                      ..++.|.|.|. .. +  +..||+.---+|+..+.+.+.+. +     +..+..  .-.+...+||=||.+.    ++..
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            45799999998 54 3  35677766666766665544322 0     000000  1268999999998763    6788


Q ss_pred             hhHHHHHHhhcCC-CcEEEEEecCCCCCcceeEEEEeeeecc
Q 023811          154 SALIHEFYCREVP-NPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (277)
Q Consensus       154 ~~~ih~~~~~~~~-~PI~L~vD~~~~~~~l~ikay~~~~~~~  194 (277)
                      |+..|..+...++ +.|.+++-  ...|..++.||.+.+++.
T Consensus       441 Dl~THakl~~~n~~~~I~itvs--ftPGS~SLsAy~LT~eGy  480 (565)
T 3sbg_A          441 EVATHSKLFADKKRDCIDISIF--STPGSVSLSAYNLTDEGY  480 (565)
T ss_dssp             HHHHHHHHHSSSCTTCEEEEEE--EETTEEEEEEEEECHHHH
T ss_pred             HHHHHHHHHHhCCCCeEEEEEE--ecCCceEEEEEecCHhHH
Confidence            8889988776653 44655543  556889999999998874

---

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	277
d1gtma2	178	c.58.1.1 (A:3-180) Glutamate dehydrogenase {Archae	0.002

>d1gtma2 c.58.1.1 (A:3-180) Glutamate dehydrogenase {Archaeon Pyrococcus furiosus [TaxId: 2261]} Length = 178

class: Alpha and beta proteins (a/b)
fold: Aminoacid dehydrogenase-like, N-terminal domain
superfamily: Aminoacid dehydrogenase-like, N-terminal domain
family: Aminoacid dehydrogenases
domain: Glutamate dehydrogenase
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 15/77 (19%), Positives = 27/77 (35%)

Query: 82  QAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIV 141
           + +R++   +   + DG+V +   + V HN         I +H     S +K     +  
Sbjct: 30  RPQRIVEVTIPVEMDDGSVKVFTGFRVQHNWARGPTKGGIRWHPEETLSTVKALAAWMTW 89

Query: 142 GWFSTGLGVTGGSALIH 158
                 L   GG   I 
Sbjct: 90  KTAVMDLPYGGGKGGII 106

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	277
d1oi0a_	121	Hypothetical protein AF2198 {Archaeon Archaeoglobu	97.28

>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=97.28  E-value=0.00064  Score=52.03  Aligned_cols=107  Identities=15%  Similarity=0.110  Sum_probs=64.4

Q ss_pred             cEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeccHHHHHHHHHHhhhcCCCCc
Q 023811           60 VTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEV  139 (277)
Q Consensus        60 ~~V~vhPlVlL~I~dH~~R~~~~~~~ViG~LLG~~~~~~~VeVtnsF~vp~~e~~~~~~iD~~y~~~m~~l~kkv~p~e~  139 (277)
                      .+++|..-++-.|++|+.+.  .+..+.|.|+|. .  +  .|+..+.+|....+. ...   |..+|   .   -.++.
T Consensus         2 ~~l~I~~~~l~~i~~hA~~~--~P~E~cGlL~G~-~--~--~i~~~~~~~n~~~~~-~~~---~~~~~---~---~~~~~   64 (121)
T d1oi0a_           2 SSMKISRGLLKTILEAAKSA--HPDEFIALLSGS-K--D--VMDELIFLPFVSGSV-SAV---IHLDM---L---PIGMK   64 (121)
T ss_dssp             CSCEECHHHHHHHHHHHHHH--TTSCCEEEEEES-T--T--EECEEEECCCCC-----------------------CCCE
T ss_pred             CeEEECHHHHHHHHHHHHhc--CCceeEEEEEec-C--C--cEEEEEEcCCCCCCc-ccc---cccch---h---hcCCe
Confidence            35678888899999999886  478999999996 2  2  356777777554321 111   11112   1   24889


Q ss_pred             EEEeeecCCC----CCCchhHHHHHHhhcCCCcEEEEEecCCCCCcceeEEEEee
Q 023811          140 IVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV  190 (277)
Q Consensus       140 iVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikay~~~  190 (277)
                      ++|||||+++    ++..|+...    .. ..-+++++-.....  -.++||...
T Consensus        65 ivgi~HSHP~~~a~PS~~D~~~~----~~-~g~~~~Ivs~p~~~--~~~~~~~~~  112 (121)
T d1oi0a_          65 VFGTVHSHPSPSCRPSEEDLSLF----TR-FGKYHIIVCYPYDE--NSWKCYNRK  112 (121)
T ss_dssp             EEEEEEEESSSCCSCCHHHHHHH----HH-SCSEEEEEETTCCT--TCEEEEETT
T ss_pred             EEEEEEecCCCCCCcCHHHHHhh----hc-cCCEEEEEeCCCCC--CCEEEEeCC
Confidence            9999999984    334443222    11 23377777654333  368898753