Citrus Sinensis ID: 024781

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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--
Protein Sequence
MPVVSGYNSSDCPIRYFQNPSSRSLLFESRSEEKKKKIRMAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVRL
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccHHHHHHHcccccccccccccccccccccccEEEEEcEEEEEEEHHEEcccccccEEEEEEEEEEEcccEEEEEEEEEEcccccccccEEcHHHHHHHHHHHHcccccccEEEEEccccccccccHHHHHHHHHHccccEEEEEEcccccccccEEEEEEEEccccccccccEEcccccccccccHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccEEEccccccccEEEcccccccEEEEEEEcccccccEEEcccccccccccccccccccEEEEEEEEEEEEEEcccccccccccEEEEEEEEEEccccEEEEEEcEEEccccccccEEEcHHHHHHHHHHHHHcccccEEEEEEcccccccHcHHHHHHHHHHHccccEEEEEEcccccccccEEEEEEEEEEcccccccEEEEEccEEEEEEcHHHHHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
mpvvsgynssdcpiryfqnpssrsllFESRSEEKKKKIRMaasdrtvlqfgpssaatsnvtakvHPLVIFNicdcyvrrpdQAERVIGTLLgsvlpdgtvdirnsyvvphnefsdqVALDIEYHHTMLKshlkvnpqeVIVGWFStglgvtggsaLIHEFycrevpnpvhltvdtgfrngegTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDilkstsvdklpsdlEGMEVLMERLLTLINDIYKYVDDTVRL
Flexible Loop (DISEMBL)
mpvvsgynssdcpiryfqnpssrsllFESRSEEKKKKirmaasdrtvlqfgpssaatsnvtakvhPLVIFNICDCYVRRPDQAERVIGTllgsvlpdgtvDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDIlkstsvdklpsdlEGMEVLMERLLTLIndiykyvddtvrl
Low Complexity Region (SEG)
MPVVSGYNSSDCPIRYFQNPssrsllfesrseekkkkIRMAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVRL
Disordered region (IsUnstruct)
**********************************************************NVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDD****
Disordered Region (DISOPRED)
*************************************************************AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDIL******************MERLLTLINDIYKYVDDTVRL
Disordered Region (DISEMBL)
********SSDCPIRYFQNPSSRSLLFESRSEEKKKKIRMAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVRL
Disordered Region (DISPRO)
*PVVSGYNSSDCPIRYFQNPSSRSLLFESRSEEK**KIRM**SDRTVLQFGP***ATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVRL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MPVVSGYNSSDCPIRYFQNPSSRSLLFESRSEEKKKKIRMAASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVRL
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	262	2.2.26 [Sep-21-2011]
O04202	293	Eukaryotic translation in	yes	no	0.839	0.750	0.772	1e-102
Q9DCH4	361	Eukaryotic translation in	yes	no	0.751	0.545	0.394	4e-39
O00303	357	Eukaryotic translation in	yes	no	0.751	0.551	0.394	4e-39
A5A6I3	361	Eukaryotic translation in	yes	no	0.751	0.545	0.394	4e-39
Q4R5B8	361	Eukaryotic translation in	N/A	no	0.751	0.545	0.394	4e-39
B3M123	280	Eukaryotic translation in	N/A	no	0.763	0.714	0.410	6e-38
Q54C49	284	Eukaryotic translation in	yes	no	0.755	0.697	0.415	4e-37
B4JGX4	280	Eukaryotic translation in	N/A	no	0.767	0.717	0.402	5e-37
Q295I4	280	Eukaryotic translation in	yes	no	0.763	0.714	0.396	6e-37
B4GDU3	280	Eukaryotic translation in	N/A	no	0.763	0.714	0.396	6e-37

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

 Score =  372 bits (954), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 173/224 (77%), Positives = 198/224 (88%), Gaps = 4/224 (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 RVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTV 260
           RVGFD+LK+TSVDKLP+DLEGME+ MERLLTLIND+YKYVD  V
Sbjct: 183 RVGFDVLKATSVDKLPNDLEGMELTMERLLTLINDVYKYVDSVV 226

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|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|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 = 80/203 (39%), Positives = 126/203 (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: 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

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|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 = 80/203 (39%), Positives = 126/203 (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+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

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

Pan troglodytes (taxid: 9598)

EC: 3

EC: .

EC: 4

EC: .

EC: 1

EC: 9

EC: .

EC: 1

EC: 2

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

 Score =  161 bits (408), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 80/203 (39%), Positives = 126/203 (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+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

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

 Score =  157 bits (397), Expect = 6e-38,   Method: Compositional matrix adjust.
 Identities = 87/212 (41%), Positives = 122/212 (57%), Gaps = 12/212 (5%)

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 NGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFDILKSTSVDKLPS----- 233
            G   ++AYV + L +   +    F  IP++L   E E  G  +L+ T V   P+     
Sbjct: 124 GGRMGLRAYVCIQLGVPGGKSGCMFTPIPVELTSYEPETFGLKLLQKT-VGVSPAHRPKT 182

Query: 234 -----DLEGMEVLMERLLTLINDIYKYVDDTV 260
                DL  +    ++L  L++ I KYVDD +
Sbjct: 183 VPPMLDLAQISEASQKLQQLLDLILKYVDDVI 214

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

Drosophila ananassae (taxid: 7217)

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

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

 Score =  154 bits (390), Expect = 5e-37,   Method: Compositional matrix adjust.
 Identities = 85/211 (40%), Positives = 122/211 (57%), Gaps = 10/211 (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 ----DLEGMEVLMERLLTLINDIYKYVDDTV 260
               DL  +    ++L +L++ I KYVDD +
Sbjct: 184 PPMLDLAQISEASQKLQSLLDLILKYVDDVI 214

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|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 (389), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 84/212 (39%), Positives = 122/212 (57%), Gaps = 12/212 (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 -----DLEGMEVLMERLLTLINDIYKYVDDTV 260
                DL  +     +L +L++ I KYVDD +
Sbjct: 183 VPPMLDLAQISEASTKLQSLLDLILKYVDDVI 214

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 (389), Expect = 6e-37,   Method: Compositional matrix adjust.
 Identities = 84/212 (39%), Positives = 122/212 (57%), Gaps = 12/212 (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 -----DLEGMEVLMERLLTLINDIYKYVDDTV 260
                DL  +     +L +L++ I KYVDD +
Sbjct: 183 VPPMLDLAQISEASTKLQSLLDLILKYVDDVI 214

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	262
260586249	288	putative eukaryotic translation initiati	0.847	0.770	0.977	1e-124
255571843	287	eukaryotic translation initiation factor	0.839	0.766	0.850	1e-108
449441322	285	PREDICTED: eukaryotic translation initia	0.835	0.768	0.819	1e-106
224109362	287	predicted protein [Populus trichocarpa]	0.835	0.763	0.809	1e-105
297788583	293	26S proteasome regulatory subunit [Arabi	0.843	0.754	0.791	1e-104
356539943	288	PREDICTED: eukaryotic translation initia	0.847	0.770	0.806	1e-103
358249108	289	uncharacterized protein LOC100811797 [Gl	0.847	0.768	0.811	1e-103
357461161	288	Eukaryotic translation initiation factor	0.847	0.770	0.810	1e-103
225449198	285	PREDICTED: eukaryotic translation initia	0.835	0.768	0.806	1e-102
388507086	288	unknown [Medicago truncatula]	0.847	0.770	0.806	1e-102

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

 Score =  451 bits (1161), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 217/222 (97%), Positives = 218/222 (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 FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVR 261
           FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTV 
Sbjct: 181 FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVE 222

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 =  397 bits (1020), 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 =  390 bits (1002), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 182/222 (81%), Positives = 202/222 (90%), Gaps = 3/222 (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 FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVR 261
           FDILK+TS+DKLP+DLEGME  MERLL LI+DIYKYVD+ V 
Sbjct: 178 FDILKTTSIDKLPNDLEGMEASMERLLALIDDIYKYVDNVVE 219

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 =  385 bits (989), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 179/221 (80%), Positives = 202/221 (91%), Gaps = 2/221 (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 DILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVR 261
           D+LK+T VDK+PSDLEGME+ M+RLL LI+D+YKYVDD V 
Sbjct: 181 DVLKTTMVDKIPSDLEGMEISMQRLLALIDDVYKYVDDVVE 221

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 (986), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 178/225 (79%), Positives = 203/225 (90%), Gaps = 4/225 (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 RVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVR 261
           RVGF++LK+TSVDKLP+DLEGME+ MERLLTLIND+YKYVD  V 
Sbjct: 183 RVGFNVLKATSVDKLPNDLEGMELTMERLLTLINDVYKYVDSVVE 227

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 =  379 bits (973), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 179/222 (80%), Positives = 203/222 (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 FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVR 261
           FD+LK+T+VDK+PSDLEGME  M+ LL LI+DIYKYV+D V 
Sbjct: 181 FDMLKATAVDKIPSDLEGMEASMQHLLVLIDDIYKYVNDVVE 222

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 (973), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 181/223 (81%), Positives = 203/223 (91%), Gaps = 1/223 (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 GFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVR 261
           GFD+LK+T+VDK+PSDLEGME  M+ LL LI+DIYKYVDD V 
Sbjct: 181 GFDMLKATAVDKIPSDLEGMEASMQHLLVLIDDIYKYVDDVVE 223

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-103,   Method: Compositional matrix adjust.
 Identities = 180/222 (81%), Positives = 201/222 (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 FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVR 261
           FDILK+T+VDK+PSDLEGME  ME LL LINDIYKYVDD V 
Sbjct: 181 FDILKATTVDKIPSDLEGMEASMEHLLALINDIYKYVDDVVE 222

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 =  377 bits (969), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 179/222 (80%), Positives = 199/222 (89%), Gaps = 3/222 (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 FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVR 261
           FDILK+T V+KLPSDLEGME  MERLL LI+D+YKYVD  V 
Sbjct: 178 FDILKTTMVEKLPSDLEGMEASMERLLALIDDVYKYVDSVVE 219

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 = 179/222 (80%), Positives = 201/222 (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 FDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTVR 261
           FDILK+T+VDK+PSDLEGME  ME LL LINDIYKYVDD V 
Sbjct: 181 FDILKATTVDKIPSDLEGMEASMEHLLALINDIYKYVDDVVE 222

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	262
TAIR|locus:2061206	293	EIF2 "AT2G39990" [Arabidopsis	0.839	0.750	0.772	5.5e-93
MGI|MGI:1913335	361	Eif3f "eukaryotic translation	0.751	0.545	0.394	3.4e-38
UNIPROTKB|E1BLZ8	384	EIF3F "Uncharacterized protein	0.751	0.513	0.394	4.3e-38
UNIPROTKB|B3KSH1	372	EIF3F "HCG1784554, isoform CRA	0.751	0.529	0.394	4.3e-38
UNIPROTKB|O00303	357	EIF3F "Eukaryotic translation	0.751	0.551	0.394	4.3e-38
UNIPROTKB|A5A6I3	361	EIF3F "Eukaryotic translation	0.751	0.545	0.394	4.3e-38
UNIPROTKB|Q4R5B8	361	EIF3F "Eukaryotic translation	0.751	0.545	0.394	4.3e-38
DICTYBASE|DDB_G0293254	284	eif3F "eukaryotic translation	0.755	0.697	0.415	8e-37
UNIPROTKB|E1C050	332	EIF3F "Uncharacterized protein	0.793	0.626	0.374	7.2e-36
FB|FBgn0037270	280	CG9769 [Drosophila melanogaste	0.767	0.717	0.402	9.2e-36

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

 Score = 926 (331.0 bits), Expect = 5.5e-93, P = 5.5e-93
 Identities = 173/224 (77%), Positives = 198/224 (88%)

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 RVGFDILKSTSVDKLPSDLEGMEVLMERLLTLINDIYKYVDDTV 260
             RVGFD+LK+TSVDKLP+DLEGME+ MERLLTLIND+YKYVD  V
Sbjct:   183 RVGFDVLKATSVDKLPNDLEGMELTMERLLTLINDVYKYVDSVV 226

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 = 3.4e-38, P = 3.4e-38
 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|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

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

 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:   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 = 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:    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 = 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:    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 = 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:    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

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

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

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

 Score = 386 (140.9 bits), Expect = 9.2e-36, P = 9.2e-36
 Identities = 85/211 (40%), Positives = 120/211 (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 ----DLEGMEVLMERLLTLINDIYKYVDDTV 260
                 DL  +     +L +L++ I KYVDD +
Sbjct:   184 PPMLDLAQISEASTKLQSLLDLILKYVDDVI 214

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

GO:0006413 "translational initiation" evidence=ISS

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

GO:0048102 "autophagic cell death" evidence=IEP

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
O04202	EIF3F_ARATH	No assigned EC number	0.7723	0.8396	0.7508	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

---

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	262
cd08064	265	cd08064, MPN_eIF3f, Mpr1p, Pad1p N-terminal (MPN)	5e-94
cd08057	157	cd08057, MPN_euk_non_mb, Mpr1p, Pad1p N-terminal (	7e-36
pfam01398	117	pfam01398, JAB, JAB1/Mov34/MPN/PAD-1 ubiquitin pro	4e-28
cd08062	280	cd08062, MPN_RPN7_8, Mpr1p, Pad1p N-terminal (MPN)	3e-26
PLN03246	303	PLN03246, PLN03246, 26S proteasome regulatory subu	2e-24
smart00232	135	smart00232, JAB_MPN, JAB/MPN domain	4e-24
cd08063	288	cd08063, MPN_CSN6, Mpr1p, Pad1p N-terminal (MPN) d	1e-16

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

 Score =  277 bits (710), Expect = 5e-94
 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 =  124 bits (314), Expect = 7e-36
 Identities = 50/163 (30%), Positives = 77/163 (47%), Gaps = 11/163 (6%)

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

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

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

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

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

 Score =  103 bits (259), Expect = 4e-28
 Identities = 40/117 (34%), Positives = 58/117 (49%), Gaps = 7/117 (5%)

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

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

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

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

 Score =  103 bits (259), Expect = 3e-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 = 2e-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 = 93.6 bits (233), Expect = 4e-24
 Identities = 40/135 (29%), Positives = 55/135 (40%), Gaps = 9/135 (6%)

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

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

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

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

>gnl|CDD|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 = 56/171 (32%), Positives = 82/171 (47%), Gaps = 12/171 (7%)

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

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

Query: 173 VDTG--FRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVGFD 221
           +D        +  V  Y SV L L D +   +F+E+P  +   EAER+G D
Sbjct: 119 LDPEANASGKDLPVTIYESV-LELVDGEATLRFRELPYTIETGEAERIGVD 168

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	262
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	99.94
KOG1560	339	consensus Translation initiation factor 3, subunit	99.91
smart00232	135	JAB_MPN JAB/MPN domain. Domain in Jun kinase activ	99.89
KOG1554	347	consensus COP9 signalosome, subunit CSN5 [Posttran	99.84
cd07767	116	MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (al	99.68
cd08067	187	MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deu	99.63
cd08058	119	MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains w	99.57
cd08068	244	MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subun	99.33
cd08066	173	MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associ	99.09
KOG1555	316	consensus 26S proteasome regulatory complex, subun	99.06
cd08070	128	MPN_like Mpr1p, Pad1p N-terminal (MPN) domains wit	98.52
cd08060	182	MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family	98.51
PF03665	196	UPF0172: Uncharacterised protein family (UPF0172);	98.42
COG1310	134	Predicted metal-dependent protease of the PAD1/JAB	98.21
PF13012	115	MitMem_reg: Maintenance of mitochondrial structure	97.7
KOG3289	199	consensus Uncharacterized conserved protein encode	97.66
cd08056	252	MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains wit	96.88
TIGR02256	131	ICE_VC0181 integrative and conjugative element pro	96.81
cd08072	117	MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1	96.66
PF14464	104	Prok-JAB: Prokaryotic homologs of the JAB domain;	96.34
cd08073	108	MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains	90.1
cd08061	274	MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein l	89.25
PF05021	306	NPL4: NPL4 family; InterPro: IPR007717 The HRD4 ge	87.74
cd08059	101	MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains	85.5
KOG2880	424	consensus SMAD6 interacting protein AMSH, contains	80.95

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

Probab=100.00  E-value=2.7e-57  Score=397.55  Aligned_cols=220  Identities=46%  Similarity=0.784  Sum_probs=209.2

Q ss_pred             cccccceeeecCCCCCCCCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeec
Q 024781           41 AASDRTVLQFGPSSAATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALD  120 (262)
Q Consensus        41 ~~~~~~~~~~~~~~~~~~~~~V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~~iD  120 (262)
                      +..+..+.+.+.|++.++..+|.|||+|+|+|+|+|.||.+++.||||+|||+ .++|.|||||||++||+|.++++.+|
T Consensus         2 ~~~~~~v~~~~~~~~~ss~ltv~ihP~Vlf~ivD~~~RR~~~~~rviGTLLG~-~~~g~ieitNCFaVPhnEssdqvevd   80 (288)
T KOG2975|consen    2 QTPAPHVPGPALPSPFSSNLTVRLHPVVLFSIVDAYERRNKGAERVIGTLLGT-VDKGSVEVTNCFAVPHNESSDQVEVD   80 (288)
T ss_pred             CCCcCcCCCcCCCCCCCCCceEEEcceEEeEeehhhhcCCccchhhhhheeec-ccCCeEEEEEeeeccCccccccceee
Confidence            44555677778888899999999999999999999999999999999999999 78999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhCCCCcEEEeecCCCCCCCchhHHHHHHhhhCCCcEEEEEeCCCCCCcceeEEEEeeeeccCCcccc
Q 024781          121 IEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLA  200 (262)
Q Consensus       121 ~~y~~~m~~l~kkV~p~e~vVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikAy~~~~~~~~~~~~~  200 (262)
                      ++|...|+++|+|+||+|.|||||+||++++.+++.||++|.+++++||||+||++.+++.+++|||.+++.|+++++.+
T Consensus        81 m~y~~~M~~l~~k~npnE~vvGWyaTg~dvt~~sslihdyYare~~~pvhLtVDT~~~n~rm~ikaYvss~~Gvpg~~~~  160 (288)
T KOG2975|consen   81 MEYAKNMYELHKKVNPNELVVGWYATGHDVTEHSSLIHDYYAREAPNPVHLTVDTSLQNGRMSIKAYVSSLMGVPGRTMG  160 (288)
T ss_pred             HHHHHHHHHHhcccCCCceeEEEEecCCCcccchhHHHHHhhccCCCCeEEEEeccccCCccceeEEEEeccCCCCcccc
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cceEEeeeEEecchhhHHHHHHhhccCCC-----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024781          201 AQFQEIPLDLRMIEAERVGFDILKSTSVD-----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVR  261 (262)
Q Consensus       201 ~~F~~ip~~I~~~e~E~i~l~~l~k~~~~-----~~~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~  261 (262)
                      ..|.|+|++|.+.|+||+|++.|.|++.+     .+..+|+++..|..+|+++++++++|+++|++
T Consensus       161 ~mF~plpvel~~~~~ervgl~li~kt~~sp~r~~~l~~dLqQv~~at~~l~~~L~~Vl~YVedVl~  226 (288)
T KOG2975|consen  161 VMFTPLPVELAYYDAERVGLDLIEKTSFSPSRVAGLSSDLQQVEGATARLQSLLERVLKYVEDVLA  226 (288)
T ss_pred             eeeeeeeeEEeecchhhhHHHHHHHhccChhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            99999999999999999999999998743     47889999999999999999999999999975

>PLN03246 26S proteasome regulatory subunit; Provisional

Probab=100.00  E-value=3.7e-52  Score=381.18  Aligned_cols=205  Identities=31%  Similarity=0.481  Sum_probs=186.6

Q ss_pred             CCCCcEEEEehhhHhHHHHHHhhcCCC-CceEEEEeeeeEecCCeEEEEeeeecccCCCCcc---eeecHHHHHHHHHHH
Q 024781           56 ATSNVTAKVHPLVIFNICDCYVRRPDQ-AERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSH  131 (262)
Q Consensus        56 ~~~~~~V~VhPlVll~I~dH~~R~~~~-~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~---~~iD~~y~~~m~~l~  131 (262)
                      .++..+|.|||+|||+|+|||+|+..+ +.+|+|+|||. +.++.|||+|||++|+++++++   |++|.+|+++|+++|
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            356779999999999999999999765 68999999999 7889999999999999876554   789999999999999


Q ss_pred             hhhCCCCcEEEeecCCCCCCCchhHHHHHHhhhCCCcEEEEEeCCCCCCcceeEEEEeeeeccCCcc--cccceEEeeeE
Q 024781          132 LKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQ--LAAQFQEIPLD  209 (262)
Q Consensus       132 kkV~p~e~vVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikAy~~~~~~~~~~~--~~~~F~~ip~~  209 (262)
                      ++|||++.+||||+||++++++|+.||++|++++++||||++|+...++++|++||++.+.+.++++  .+..|+++|++
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            9999999999999999999999999999999999999999999988888899999999988776443  45789999999


Q ss_pred             EecchhhHHHHHHhhccCCC----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024781          210 LRMIEAERVGFDILKSTSVD----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVR  261 (262)
Q Consensus       210 I~~~e~E~i~l~~l~k~~~~----~~~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~  261 (262)
                      |.++|+||||++|+++...+    .+..+|.++.+|+++|.+||+.|++||++|.+
T Consensus       161 i~~~EaE~Igve~l~r~~~~~~~s~l~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~  216 (303)
T PLN03246        161 IGAHEAEEIGVEHLLRDVKDTTVSTLATEVTGKLTALKGLDARLREIRSYLDLVVE  216 (303)
T ss_pred             eeecCHHHHHHHHHHhcccCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            99999999999999985543    35568999999999999999999999999975

>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=1.8e-51  Score=373.61  Aligned_cols=200  Identities=32%  Similarity=0.491  Sum_probs=184.3

Q ss_pred             EEEEehhhHhHHHHHHhhcCCC-CceEEEEeeeeEecCCeEEEEeeeecccCCCCcc---eeecHHHHHHHHHHHhhhCC
Q 024781           61 TAKVHPLVIFNICDCYVRRPDQ-AERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSHLKVNP  136 (262)
Q Consensus        61 ~V~VhPlVll~I~dH~~R~~~~-~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~---~~iD~~y~~~m~~l~kkV~p  136 (262)
                      +|+|||+|||+|+|||+|+..+ +.+|+|+|||+ ..++.+||+|||++|+++++++   +++|.+|+++|+++|++|||
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 78999999999 7899999999999999887665   57999999999999999999


Q ss_pred             CCcEEEeecCCCCCCCchhHHHHHHhhhCCCcEEEEEeCCCCCCcceeEEEEeeeeccCCcc-cccceEEeeeEEecchh
Q 024781          137 QEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQ-LAAQFQEIPLDLRMIEA  215 (262)
Q Consensus       137 ~e~vVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikAy~~~~~~~~~~~-~~~~F~~ip~~I~~~e~  215 (262)
                      ++.+||||+||++++..|+.||++|++++++||+|++||..+++++|++||++.+.+.++++ ....|.|+|++|.++|+
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            99999999999999999999999999999999999999999888999999999998876665 78899999999999999


Q ss_pred             hHHHHHHhhccCCC----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024781          216 ERVGFDILKSTSVD----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVR  261 (262)
Q Consensus       216 E~i~l~~l~k~~~~----~~~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~  261 (262)
                      ||||++|+++...+    .+..++.++.+|+++|+.||+.+++||++|.+
T Consensus       161 E~igve~l~r~~~~~~~~~l~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~  210 (280)
T cd08062         161 EEVGVEHLLRDIKDVTVSTLSTRVTNKLNSLKGLQSKLKEIKDYLQLVVE  210 (280)
T ss_pred             HHHHHHHHHhhccCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Confidence            99999999975332    35568999999999999999999999999974

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=2.7e-51  Score=370.25  Aligned_cols=199  Identities=50%  Similarity=0.859  Sum_probs=185.7

Q ss_pred             EEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeecHHHHHHHHHHHhhhCCCCcEE
Q 024781           62 AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIV  141 (262)
Q Consensus        62 V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~~iD~~y~~~m~~l~kkV~p~e~vV  141 (262)
                      |+|||+|||+|+|||+|++.++.+|+|+|||+ ..++.+||||||++|++++++++.+|.+|+++|+++|++|||++.+|
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            68999999999999999987789999999999 78899999999999999988889999999999999999999999999


Q ss_pred             EeecCCCCCCCchhHHHHHHhhhCC--CcEEEEEeCCCCCCcceeEEEEeeeeccCCcccccceEEeeeEEecchhhHHH
Q 024781          142 GWFSTGLGVTGGSALIHEFYCREVP--NPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIEAERVG  219 (262)
Q Consensus       142 GWY~t~~~~~~~~~~ih~~~~~~~~--~PI~L~vD~~~~~~~l~ikAy~~~~~~~~~~~~~~~F~~ip~~I~~~e~E~i~  219 (262)
                      |||+||+.++.++..||++|+++++  +||+|++||...++++|++||++.+.++.+++....|+|+|++|.++|+||||
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  99999999998777999999999998877777889999999999999999999


Q ss_pred             HHHhhccCCC-----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024781          220 FDILKSTSVD-----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVR  261 (262)
Q Consensus       220 l~~l~k~~~~-----~~~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~  261 (262)
                      ++++.+...+     .+.++++++.+|+++|..||+.+++||++|.+
T Consensus       160 v~~l~~~~~~~~~~~~~~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~  206 (265)
T cd08064         160 LDLLAKTLASPSRSAPLTSDLEQLEASLEKLQEMLDRVLRYVEDVLA  206 (265)
T ss_pred             HHHHHhhccCCcccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            9999986543     24578999999999999999999999999964

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=4.9e-50  Score=365.95  Aligned_cols=200  Identities=28%  Similarity=0.425  Sum_probs=183.1

Q ss_pred             cEEEEehhhHhHHHHHHhhcCCC----CceEEEEeeeeEecCCeEEEEeeeecccCCCC-cceeecHHHHHHHHHHHhhh
Q 024781           60 VTAKVHPLVIFNICDCYVRRPDQ----AERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS-DQVALDIEYHHTMLKSHLKV  134 (262)
Q Consensus        60 ~~V~VhPlVll~I~dH~~R~~~~----~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~-~~~~iD~~y~~~m~~l~kkV  134 (262)
                      .+|.|||+|||+|+|||+|+..+    +.+|+|+|||+ ++|++|||+|||++|+++++ +++.+|.+|+++|+++||+|
T Consensus         1 ~~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~-~~~~~veItnsF~~p~~~~~~~~~~id~~y~~~m~~~~kkV   79 (288)
T cd08063           1 LSVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQ-QDGREIEIENSFELKYDTNEDGEIVLDKEFLETRLEQFKQV   79 (288)
T ss_pred             CeEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEE-EcCCEEEEEEEEecccccCCCCceeeCHHHHHHHHHHHHHh
Confidence            37999999999999999998653    58999999998 89999999999999999887 67899999999999999999


Q ss_pred             CCCCcEEEeecCCCC-CCCchhHHHHHHhhhCCCcEEEEEeCCC--CCCcceeEEEEeeeeccCCcccccceEEeeeEEe
Q 024781          135 NPQEVIVGWFSTGLG-VTGGSALIHEFYCREVPNPVHLTVDTGF--RNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLR  211 (262)
Q Consensus       135 ~p~e~vVGWY~t~~~-~~~~~~~ih~~~~~~~~~PI~L~vD~~~--~~~~l~ikAy~~~~~~~~~~~~~~~F~~ip~~I~  211 (262)
                      ||++.+||||+||+. ++.+++.||++|++.+++||+|++||..  .++++|++||++...+.++ .....|+|+|++|+
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  5788999999999887765 56688999999999


Q ss_pred             cchhhHHHHHHhhccCC--C----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024781          212 MIEAERVGFDILKSTSV--D----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVR  261 (262)
Q Consensus       212 ~~e~E~i~l~~l~k~~~--~----~~~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~  261 (262)
                      ++|+||||++|+++...  +    .+..+++.+.+|+++|++||+.|++||++|.+
T Consensus       159 ~~eaErIgv~~l~~~~~~~~~~~~~~~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~  214 (288)
T cd08063         159 TGEAERIGVDHVARGGASGSSEKSTVAAHLQAQHNAIKMLNSRVELILEYLKAVPV  214 (288)
T ss_pred             eccCceeeHHHHHhcCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            99999999999998652  1    24578999999999999999999999999974

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=2.4e-46  Score=325.78  Aligned_cols=205  Identities=30%  Similarity=0.470  Sum_probs=187.6

Q ss_pred             CCCCcEEEEehhhHhHHHHHHhhcCC-CCceEEEEeeeeEecCCeEEEEeeeecccCCCCcc---eeecHHHHHHHHHHH
Q 024781           56 ATSNVTAKVHPLVIFNICDCYVRRPD-QAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSH  131 (262)
Q Consensus        56 ~~~~~~V~VhPlVll~I~dH~~R~~~-~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~---~~iD~~y~~~m~~l~  131 (262)
                      ..+..+|.|||||||+++|||.|... +++||+|+|||. ..++++.|+|||++|++|++++   |++|.+|++.|+++|
T Consensus         5 ~~~~~kViVhPLVLLS~VDhynR~~k~~~KRvvGvLLG~-~~~~~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~mf   83 (309)
T KOG1556|consen    5 ELTVEKVIVHPLVLLSAVDHYNRVGKDTNKRVVGVLLGS-WNGDVIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGMF   83 (309)
T ss_pred             ccccceeeeehhHHHHHHHHHhhhccCcCceEEEEEEec-CCCCeEEeecceeccccccCCCCceEEeccHHHHHHHHHH
Confidence            45567999999999999999999864 468999999999 7788999999999999998877   899999999999999


Q ss_pred             hhhCCCCcEEEeecCCCCCCCchhHHHHHHhhhCCCcEEEEEeCCCCCCcceeEEEEeeeeccCC-cccccceEEeeeEE
Q 024781          132 LKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGD-RQLAAQFQEIPLDL  210 (262)
Q Consensus       132 kkV~p~e~vVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikAy~~~~~~~~~-~~~~~~F~~ip~~I  210 (262)
                      +|||.+|.+||||||||.+..+|+.|++++.+++++|+.+++|..+++-++|..||...+....+ .+....|+.+|++|
T Consensus        84 kKvNakekivGWYhTGPkl~~nDl~In~l~k~y~pnpvLvIIdvkpk~~gLPT~AY~aVeev~dDgt~t~ktF~Hvps~I  163 (309)
T KOG1556|consen   84 KKVNAKEKVVGWYHTGPKLRENDLDINELLKRYVPNPVLVIIDVKPKELGLPTEAYIAVEEVKDDGTPTSKTFVHVPSEI  163 (309)
T ss_pred             HHhcchhheeeeeccCCccccchhhHHHHHhhcCCCceEEEEecccccCCCCchheeeeeeeecCCCCccceeEecCccc
Confidence            99999999999999999999999999999999999999999999988888999999999876653 45577899999999


Q ss_pred             ecchhhHHHHHHhhccCCC----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024781          211 RMIEAERVGFDILKSTSVD----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVR  261 (262)
Q Consensus       211 ~~~e~E~i~l~~l~k~~~~----~~~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~  261 (262)
                      ++.|||+||++|+.|...+    .++..+.++..+++-|+.++..|.+||++|.+
T Consensus       164 ~AeEAEEvGVEHLlRDikd~t~gtla~rit~ql~sLkgl~~~L~eI~~YL~~Vi~  218 (309)
T KOG1556|consen  164 EAEEAEEVGVEHLLRDIKDTTVGTLATRITNQLMSLKGLQSRLREIRSYLDKVID  218 (309)
T ss_pred             chhHHHHhhHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            9999999999999986543    46778889999999999999999999999975

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

Probab=100.00  E-value=5e-43  Score=304.57  Aligned_cols=206  Identities=26%  Similarity=0.392  Sum_probs=183.1

Q ss_pred             CCCCCCcEEEEehhhHhHHHHHHhhcCCC--C--ceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeecHHHHHHHHH
Q 024781           54 SAATSNVTAKVHPLVIFNICDCYVRRPDQ--A--ERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLK  129 (262)
Q Consensus        54 ~~~~~~~~V~VhPlVll~I~dH~~R~~~~--~--~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~~iD~~y~~~m~~  129 (262)
                      ++++++.+|.+|||||+||+|||+|.+.+  +  .+|+|+|+|. +.|++|||.|||++..+..++...+|.+|++++-+
T Consensus         3 ps~S~s~tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~-Q~GR~vEi~NSFeL~~d~~~~~~~~dke~l~kk~e   81 (299)
T KOG3050|consen    3 PSSSGSVTVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGK-QRGRNVEIMNSFELKMDTEEDTETIDKEYLEKKEE   81 (299)
T ss_pred             CCCCCceeEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheec-ccCceEEEeeeeEEEecchhhhhhccHHHHHHHHH
Confidence            44577889999999999999999999742  2  4899999998 99999999999999988776666899999999999


Q ss_pred             HHhhhCCCCcEEEeecCCCCCCCchhHHHHHHhhhCCCcEEEEEeCCCC-CCcceeEEEEeeeeccCCcccccceEEeee
Q 024781          130 SHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFR-NGEGTVKAYVSVNLSLGDRQLAAQFQEIPL  208 (262)
Q Consensus       130 l~kkV~p~e~vVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~-~~~l~ikAy~~~~~~~~~~~~~~~F~~ip~  208 (262)
                      +||+|||+..++|||+||.+.++.|+.||.+++..++.|++|.++|..+ ..+.|+..|++.-..+ ++.....|+|+.|
T Consensus        82 qykqVFpdl~vlGwYttG~d~t~sd~~i~k~l~~i~esplflkLNp~t~~t~~~pv~lfese~dvi-dg~~q~~f~~~ty  160 (299)
T KOG3050|consen   82 QYKQVFPDLYVLGWYTTGSDPTPSDIHIHKQLMDINESPLFLKLNPATNHTDKDPVTLFESEIDVI-DGEAQMLFVPLTY  160 (299)
T ss_pred             HHHHhcccceEEEEeecCCCCChhhhHHHHHHHhhhcCceEEEecchhccccCCCceeeeeeheee-cCcceeeeeeeEE
Confidence            9999999999999999999999999999999999999999999999874 4556999998874444 4556788999999


Q ss_pred             EEecchhhHHHHHHhhccCC------CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024781          209 DLRMIEAERVGFDILKSTSV------DKLPSDLEGMEVLMERLLTLINDIYKYVDDTVR  261 (262)
Q Consensus       209 ~I~~~e~E~i~l~~l~k~~~------~~~~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~  261 (262)
                      +|.+.|+||||+||+++-..      +.+..|++.+..|+++|+.|++.|++||++|.+
T Consensus       161 tl~teEaERIgVdHVA~lt~~~gge~s~VaeHl~AQdsA~~ml~~Rvklil~Y~k~~e~  219 (299)
T KOG3050|consen  161 TLATEEAERIGVDHVARLTPSDGGEGSSVAEHLEAQDSAIKMLDNRVKLILAYLKKVEA  219 (299)
T ss_pred             EEeehhhhhccchhheeeccCCCCCcchHHHHHhhHHHHHHHHhhHHHHHHHHHhhhhc
Confidence            99999999999999998432      236789999999999999999999999999975

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

Probab=100.00  E-value=2.9e-40  Score=276.69  Aligned_cols=150  Identities=31%  Similarity=0.552  Sum_probs=137.1

Q ss_pred             EEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeecHHHHHHHHHHHhhhCCCCcEE
Q 024781           62 AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIV  141 (262)
Q Consensus        62 V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~~iD~~y~~~m~~l~kkV~p~e~vV  141 (262)
                      |+|||+|||||+|||+|+..++.+|+|+|||+ ..+++++|+|||++|++++++.+.+|.+|+++|++++++|+|++.+|
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            68999999999999999976678999999999 78999999999999999887778899999999999999999999999


Q ss_pred             EeecCCCC----CCCchhHHHHHHhhh-CCCcEEEEEeCCC--CCCcceeEEEEeeeeccCCcccccceEEeeeEEecch
Q 024781          142 GWFSTGLG----VTGGSALIHEFYCRE-VPNPVHLTVDTGF--RNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMIE  214 (262)
Q Consensus       142 GWY~t~~~----~~~~~~~ih~~~~~~-~~~PI~L~vD~~~--~~~~l~ikAy~~~~~~~~~~~~~~~F~~ip~~I~~~e  214 (262)
                      |||++++.    ++..+..||++|.++ .++||+|++||..  .+++++++||++.+...       .+.++|++|.+.|
T Consensus        80 GWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~~~~-------~~~~~~~~i~~~e  152 (157)
T cd08057          80 GWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQREE-------NGAEITYEIGTEE  152 (157)
T ss_pred             EEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEecCCC-------CCceeeeEEeccc
Confidence            99999987    889999999999998 8889999999987  47899999999985432       1339999999999


Q ss_pred             hhHHH
Q 024781          215 AERVG  219 (262)
Q Consensus       215 ~E~i~  219 (262)
                      +||||
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=4.8e-35  Score=264.54  Aligned_cols=196  Identities=22%  Similarity=0.277  Sum_probs=163.1

Q ss_pred             EEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcc---eeecHHHHHHHHHHHhhhCCC
Q 024781           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQ---VALDIEYHHTMLKSHLKVNPQ  137 (262)
Q Consensus        61 ~V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~---~~iD~~y~~~m~~l~kkV~p~  137 (262)
                      +|+|||+|+++|+|||.|+.  +.+|+|+|||. ..++.+||||||++|+.+++++   +..|.+|+.+|++++++++++
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  78999999999 6789999999999999887665   466789999999999999999


Q ss_pred             CcEEEeecCCC-CCCCchhHHHHHHhhhC--CCcEEEEEeCCC-CCCcceeEEEEeeeeccC---------------Ccc
Q 024781          138 EVIVGWFSTGL-GVTGGSALIHEFYCREV--PNPVHLTVDTGF-RNGEGTVKAYVSVNLSLG---------------DRQ  198 (262)
Q Consensus       138 e~vVGWY~t~~-~~~~~~~~ih~~~~~~~--~~PI~L~vD~~~-~~~~l~ikAy~~~~~~~~---------------~~~  198 (262)
                      +.+||||+|++ +...+...||.++..+.  +++|+|++||.+ +++.++++||++.+.+++               +.+
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  778999999988 578899999999998764               356


Q ss_pred             cccceEEeeeEEecchhhHHHHHHhhccCCCC-------CcccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024781          199 LAAQFQEIPLDLRMIEAERVGFDILKSTSVDK-------LPSDLEGMEVLMERLLTLINDIYKYVDDT  259 (262)
Q Consensus       199 ~~~~F~~ip~~I~~~e~E~i~l~~l~k~~~~~-------~~~~l~~l~~sl~~L~~~l~~i~~Yl~~V  259 (262)
                      ...+|.|||++|++++.+++.+..+.......       .......+...+..|.+.+|.+..+.++.
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            78999999999999999999999996533221       11234456666666666666666666554

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=6.1e-29  Score=224.90  Aligned_cols=167  Identities=16%  Similarity=0.223  Sum_probs=149.2

Q ss_pred             CCCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeecHHHHHHHHH--HHhhh
Q 024781           57 TSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLK--SHLKV  134 (262)
Q Consensus        57 ~~~~~V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~~iD~~y~~~m~~--l~kkV  134 (262)
                      ....+|.|+|+|+++|++|+.|.  .+.+|+|+|+|. .+++.++|++||++|+.++++.+..+.+|++.|++  +++++
T Consensus         7 ~~~~~V~Is~~allkil~Ha~~~--~p~Ev~GlLlG~-~~~~~v~Vt~~fp~p~~~t~~~v~~~~e~~~~m~~~~~~~~~   83 (268)
T cd08069           7 DYFEKVYISSLALLKMLKHARAG--GPIEVMGLMLGK-VDDYTIIVVDVFALPVEGTETRVNAQDEFQEYMVQYEMLKQT   83 (268)
T ss_pred             CcccEEEECHHHHHHHHHHHhcc--CCceEEEEEEee-ecCCeEEEEEEEECCcCCCCCceeccHHHHHHHHHHHHHHHh
Confidence            44668999999999999999874  578999999998 78899999999999998888878888899999999  99999


Q ss_pred             CCCCcEEEeecCCCC----CCCchhHHHHHHhhhCCCcEEEEEeCCCC--CCcceeEEEEeeeeccC----Cc-------
Q 024781          135 NPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFR--NGEGTVKAYVSVNLSLG----DR-------  197 (262)
Q Consensus       135 ~p~e~vVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~--~~~l~ikAy~~~~~~~~----~~-------  197 (262)
                      ++++.+||||||+++    ++..|+.+|..|++.++++|+|++||..+  .|++.++||++.+.+..    +.       
T Consensus        84 ~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~~~~~~~~~~~~~~s~~~~  163 (268)
T cd08069          84 GRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIPPGYKPLEPRQTTSNIGH  163 (268)
T ss_pred             CCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEECccccccCcccCccccCc
Confidence            999999999999997    78999999999999888889999998764  78899999999988754    12       


Q ss_pred             ----------ccccceEEeeeEEecchhhHHHHHHhhcc
Q 024781          198 ----------QLAAQFQEIPLDLRMIEAERVGFDILKST  226 (262)
Q Consensus       198 ----------~~~~~F~~ip~~I~~~e~E~i~l~~l~k~  226 (262)
                                .....|.+||++|..++.|+..++.+.+.
T Consensus       164 ~~~~~~~~~~~~~~~y~~l~i~~~~s~l~~~~L~~l~~~  202 (268)
T cd08069         164 LPKPKIEDFGGHNKQYYSLPIEYFKSSLDRKLLLNLWNK  202 (268)
T ss_pred             cCcHHHHHhCchhcEEEEeeeEEecCHHHHHHHHHHHHH
Confidence                      25678999999999999999999999764

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=99.94  E-value=1.5e-26  Score=183.15  Aligned_cols=107  Identities=36%  Similarity=0.576  Sum_probs=94.1

Q ss_pred             CCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCC-eEEEEeeeecccCCCCcce-eecHHHHHHHHHHHhhhC
Q 024781           58 SNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDG-TVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKVN  135 (262)
Q Consensus        58 ~~~~V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~-~veVtnsF~vP~~~~~~~~-~iD~~y~~~m~~l~kkV~  135 (262)
                      +..+|.|||+|+++|+||+.|+..  .+|+|+|+|+ .+++ .++|+|||++|+.+++++. ..+.++.++|++++++++
T Consensus         2 s~~~V~i~p~vll~i~~h~~r~~~--~~v~G~LlG~-~~~~~~v~I~~~f~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~   78 (114)
T PF01398_consen    2 SVQTVQIHPLVLLKIIDHATRSSP--NEVIGLLLGT-QDGDNTVEITNSFPVPHSESEDDCDMDDEDFQKKMIELLKKVN   78 (114)
T ss_dssp             SCEEEEEEHHHHHHHHHHHHHHHC--TEEEEEEEEE-EETT-EEEEEEEEEESEEEESSEEEEECCHHHHHHHHHHHHCS
T ss_pred             CcEEEEECHHHHHHHHHHHhcCCC--CEEEEEEEEE-ecCceEEEEEEEEEeeEecCccccccchhhHHHHHHhhhcccc
Confidence            467999999999999999999853  4999999999 7787 9999999999999877664 456667799999999999


Q ss_pred             CCCcEEEeecCCCCC----CCchhHHHHHHhhhCCC
Q 024781          136 PQEVIVGWFSTGLGV----TGGSALIHEFYCREVPN  167 (262)
Q Consensus       136 p~e~vVGWY~t~~~~----~~~~~~ih~~~~~~~~~  167 (262)
                      |++.+||||+|++..    +..|+.+|.+|++.+++
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    89999999999987653

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

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

Probab=99.91  E-value=3.2e-24  Score=190.31  Aligned_cols=168  Identities=23%  Similarity=0.362  Sum_probs=137.6

Q ss_pred             CCCCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCC--CCcce---eecH---HHHHHH
Q 024781           56 ATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNE--FSDQV---ALDI---EYHHTM  127 (262)
Q Consensus        56 ~~~~~~V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~--~~~~~---~iD~---~y~~~m  127 (262)
                      +.+...|.+..||+|+|++||.....+..-+.|+|+|. .-++.+|||||||.|...  +++.+   ..|.   .|+..|
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            46678999999999999999987766667899999998 679999999999999754  22322   2332   599999


Q ss_pred             HHHHhhhCCCCcEEEeecCCC-CCCCchhHHHHHHhhh--CCCcEEEEEeCCC-CCCcceeEEEEeeeeccC--------
Q 024781          128 LKSHLKVNPQEVIVGWFSTGL-GVTGGSALIHEFYCRE--VPNPVHLTVDTGF-RNGEGTVKAYVSVNLSLG--------  195 (262)
Q Consensus       128 ~~l~kkV~p~e~vVGWY~t~~-~~~~~~~~ih~~~~~~--~~~PI~L~vD~~~-~~~~l~ikAy~~~~~~~~--------  195 (262)
                      ++.++.+|.+..+||||++.- +..-+-..+..+|.++  +++.|+|++||.+ ++|.|.++||+..|..+.        
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 3333345667777776  5677999999999 689999999999987542        


Q ss_pred             -------CcccccceEEeeeEEecchhhHHHHHHhh
Q 024781          196 -------DRQLAAQFQEIPLDLRMIEAERVGFDILK  224 (262)
Q Consensus       196 -------~~~~~~~F~~ip~~I~~~e~E~i~l~~l~  224 (262)
                             +.+..+.|.++|+.|+++..-.+-+..+.
T Consensus       168 pealk~~nltyenmfeElPIVIknS~L~nvlmseLs  203 (339)
T KOG1560|consen  168 PEALKSANLTYENMFEELPIVIKNSHLANVLMSELS  203 (339)
T ss_pred             HHHHHhcCCCHHHHHhhcCeeeeccHHHHHHHHhcc
Confidence                   35677899999999999999888888887

>smart00232 JAB_MPN JAB/MPN domain

Probab=99.89  E-value=2.8e-22  Score=161.54  Aligned_cols=128  Identities=31%  Similarity=0.442  Sum_probs=113.0

Q ss_pred             EEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcce-eecHHHHHHHHHHHhhhCCCCc
Q 024781           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKVNPQEV  139 (262)
Q Consensus        61 ~V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~-~iD~~y~~~m~~l~kkV~p~e~  139 (262)
                      .|+|||+|+++|++|+.|.  .+.+++|+|+|. ..++.++|+++|++|...+++.+ ..+.+|.+.|.++++++++++.
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  478999999998 67889999999999987765554 6789999999999999999999


Q ss_pred             EEEeecCCCC----CCCchhHHHHHHhhhCCCcEEEEEeCCCC-CCcceeEEEEeee
Q 024781          140 IVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFR-NGEGTVKAYVSVN  191 (262)
Q Consensus       140 vVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~-~~~l~ikAy~~~~  191 (262)
                      +||||||++.    ++..|+.+|..+......++++++|+..+ .++++++||++.+
T Consensus        78 ~vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~~g~~~~~af~~~~  134 (135)
T smart00232       78 IVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQGRLSLRAFRLTP  134 (135)
T ss_pred             EEEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccccCcEEEEEEEecC
Confidence            9999999873    56778888988888888899999999985 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=99.84  E-value=2.1e-20  Score=166.58  Aligned_cols=195  Identities=14%  Similarity=0.218  Sum_probs=142.3

Q ss_pred             CCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeec---HHHHHHHHHHHhhh
Q 024781           58 SNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALD---IEYHHTMLKSHLKV  134 (262)
Q Consensus        58 ~~~~V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~~iD---~~y~~~m~~l~kkV  134 (262)
                      ....|+|..|++|+|+-|..|  +++-.|||.++|+ .+|+++.|.+||++|.+++|.++...   .+|+....+..+.+
T Consensus        51 ~fk~vkISalAllKm~~hA~~--GgnlEiMGlm~Gk-v~g~t~IvmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~k~~  127 (347)
T KOG1554|consen   51 YFKHVKISALALLKMVMHARS--GGNLEIMGLMQGK-VDGDTIIVMDSFALPVEGTETRVNAQAEAYEYMVQYIEEAKNV  127 (347)
T ss_pred             hhhhhhhHHHHHHHHHHHHhc--CCCeEEEeeeccc-ccCCeEEEEeccccccccccceechHHHHHHHHHHHHHHHHHh
Confidence            355899999999999998855  4789999999999 89999999999999999998877432   67888888999999


Q ss_pred             CCCCcEEEeecCCCCC----CCchhHHHHHHhhhCCCc-EEEEEeCCC--CCCcceeEEEEeeeeccCC-----------
Q 024781          135 NPQEVIVGWFSTGLGV----TGGSALIHEFYCREVPNP-VHLTVDTGF--RNGEGTVKAYVSVNLSLGD-----------  196 (262)
Q Consensus       135 ~p~e~vVGWY~t~~~~----~~~~~~ih~~~~~~~~~P-I~L~vD~~~--~~~~l~ikAy~~~~~~~~~-----------  196 (262)
                      ...|++|||||++|+.    +..|+..|. +++.+..| +++++||.+  ..+++.|.|||+.|.+...           
T Consensus       128 gr~envVGWyHSHPgYgCWLSgIDVsTQ~-lNQ~fQePfvAvViDP~Rtlsagkv~iGAFRTyp~gyk~~d~~~seyqti  206 (347)
T KOG1554|consen  128 GRLENVVGWYHSHPGYGCWLSGIDVSTQM-LNQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTYPKGYKPPDEPPSEYQTI  206 (347)
T ss_pred             hhhhceeeeeecCCCCCccccCcchhHHH-HhhhhcCCeEEEEecCccccccCceeeceeecccCCCCCCCCCchhhhcc
Confidence            9999999999999974    445554454 34446778 899999998  5889999999999987521           


Q ss_pred             --------cccccceEEeeeEEecchhhHHHHHHhhcc------CCCCCcccHHHHHHHHHHHHHHHHHHHHHH
Q 024781          197 --------RQLAAQFQEIPLDLRMIEAERVGFDILKST------SVDKLPSDLEGMEVLMERLLTLINDIYKYV  256 (262)
Q Consensus       197 --------~~~~~~F~~ip~~I~~~e~E~i~l~~l~k~------~~~~~~~~l~~l~~sl~~L~~~l~~i~~Yl  256 (262)
                              +-.+..+..+++.+--+-.++--++.|-..      ..+++.++.+.+...+..|..++++.-+.+
T Consensus       207 pl~kied~gvHck~yysl~isyfks~ld~kll~~Lwnkywv~Tlsss~ll~N~dy~~~qi~d~~ekl~q~~~~l  280 (347)
T KOG1554|consen  207 PLNKIEDFGVHCKQYYSLEISYFKSSLDMKLLELLWNKYWVRTLSSSPLLKNIDYLNGQIRDLSEKLEQREDSL  280 (347)
T ss_pred             chhhhhhcccceEEeeccchhhhhhhhhHHHHHHHHhhhhhcccccccccccchhhcchhhhHHHHHHhhhhhc
Confidence                    112233334444443344444445544321      123466667777777777766666644443

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

Probab=99.68  E-value=4.7e-16  Score=122.34  Aligned_cols=111  Identities=25%  Similarity=0.355  Sum_probs=88.6

Q ss_pred             hHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeecHHHHHHHHHHHhhhCCCCcEEEeecCCCC
Q 024781           70 FNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG  149 (262)
Q Consensus        70 l~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~~iD~~y~~~m~~l~kkV~p~e~vVGWY~t~~~  149 (262)
                      .+|++|+.+.  .+.+|+|.|+|+ ..++.++|+++|++|...++..  .+...  -|....+.+..++.+||||+|++.
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            4688888663  368999999999 7778899999999998765432  22222  266667778899999999999975


Q ss_pred             ----CCCchhHHHHHHhhhCCCcEEEEEeCCCCCCcceeEEE
Q 024781          150 ----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAY  187 (262)
Q Consensus       150 ----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikAy  187 (262)
                          ++..|+..|..+++..+++++|++|+...+.+++++||
T Consensus        75 ~~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~~~~~~~~~~~  116 (116)
T cd07767          75 PSCFLSPNDLATHELFQRYFPEKVMIIVDVKPKDLGNSWKCY  116 (116)
T ss_pred             CCCccCHHHHHHHHHHHHhCCCCEEEEEECCCccCCCCcccC
Confidence                67888888888888788899999999886667888887

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=99.63  E-value=9.1e-15  Score=126.00  Aligned_cols=146  Identities=14%  Similarity=0.095  Sum_probs=108.0

Q ss_pred             CcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEec-CCeEEEEeeeecccCCCCcceeecHHHHHHHHHHHhhhCCC
Q 024781           59 NVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLP-DGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQ  137 (262)
Q Consensus        59 ~~~V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~-~~~veVtnsF~vP~~~~~~~~~iD~~y~~~m~~l~kkV~p~  137 (262)
                      ..+|+|+++|+|+|..|+...   ...++|.|+|.+.. ++.++|+++|++|.....++..+|.+++.+|.+..++.+  
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            679999999999999999754   28899999998433 468999999999987766667789999999999988766  


Q ss_pred             CcEEEeecCCCC----CCCchhHHHHHHhhhCC------Cc-EEEEEeCCCC---CCcceeEEEEeeeeccCCcccccce
Q 024781          138 EVIVGWFSTGLG----VTGGSALIHEFYCREVP------NP-VHLTVDTGFR---NGEGTVKAYVSVNLSLGDRQLAAQF  203 (262)
Q Consensus       138 e~vVGWY~t~~~----~~~~~~~ih~~~~~~~~------~P-I~L~vD~~~~---~~~l~ikAy~~~~~~~~~~~~~~~F  203 (262)
                      +.+|||||+++.    ++..|+..|..|+...+      .| |.+++||-..   +..-.+++|...+..-..    ..-
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            699999999974    34444555544554433      34 9999999763   234579999998654221    122


Q ss_pred             EEeeeEEecc
Q 024781          204 QEIPLDLRMI  213 (262)
Q Consensus       204 ~~ip~~I~~~  213 (262)
                      ..+|+.+.+.
T Consensus       155 ~~~p~~~~~~  164 (187)
T cd08067         155 YGVPMLMSYT  164 (187)
T ss_pred             CCcCeEEEec
Confidence            3356665554

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=99.57  E-value=1.9e-14  Score=115.08  Aligned_cols=110  Identities=13%  Similarity=0.209  Sum_probs=83.0

Q ss_pred             hHhHHHHHHhhcCCCCceEEEEeeeeEec----CCeEEEEeeeecccCCCCcceeecHHHHHHHHHHHhhhCCCCcEEEe
Q 024781           68 VIFNICDCYVRRPDQAERVIGTLLGSVLP----DGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGW  143 (262)
Q Consensus        68 Vll~I~dH~~R~~~~~~~ViG~LLG~~~~----~~~veVtnsF~vP~~~~~~~~~iD~~y~~~m~~l~kkV~p~e~vVGW  143 (262)
                      |+++|++|+.+.  .+..++|.|+|...+    ...++|+++|+.|...+.         .+.|..+.+...-++.+|||
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    345899999999875431         22455566678899999999


Q ss_pred             ecCCCC----CCCchhHHHHHHhhhCCCcEEEEEeCCCCCCcceeEEEEee
Q 024781          144 FSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV  190 (262)
Q Consensus       144 Y~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikAy~~~  190 (262)
                      ||++++    ++..|+..|.+|....++-++|++||...  ...++||+++
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            999984    45666555555555556779999999663  7889999863

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=99.33  E-value=3.4e-10  Score=101.14  Aligned_cols=148  Identities=17%  Similarity=0.185  Sum_probs=99.5

Q ss_pred             cEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEe------cCCeEEEEeeeecccCC-CCcceeecHH----HHHHHH
Q 024781           60 VTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVL------PDGTVDIRNSYVVPHNE-FSDQVALDIE----YHHTML  128 (262)
Q Consensus        60 ~~V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~------~~~~veVtnsF~vP~~~-~~~~~~iD~~----y~~~m~  128 (262)
                      .+|.|.+.++.+|++|+.+.  .+..++|.|+|.+.      .++.+.|..-++.+..+ ..+.+.+|.+    .++.+.
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  57899999999832      13345554444443332 3345778864    334556


Q ss_pred             HHHhhhCCCCcEEEeecCCCC----CCCchhHHHHHHhhhCCCcEEEEEeCCC-----CCCcceeEEEEeeeeccCCccc
Q 024781          129 KSHLKVNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGF-----RNGEGTVKAYVSVNLSLGDRQL  199 (262)
Q Consensus       129 ~l~kkV~p~e~vVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~-----~~~~l~ikAy~~~~~~~~~~~~  199 (262)
                      ++.+.+..++.+|||||++++    ++..|...|..|....+.-++|++++..     ..++..+++|+..+..   ...
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            677778899999999999985    3455544433333223444899887533     2357889999997431   122


Q ss_pred             ccceEEeeeEEec
Q 024781          200 AAQFQEIPLDLRM  212 (262)
Q Consensus       200 ~~~F~~ip~~I~~  212 (262)
                      .....++|+.|..
T Consensus       157 ~~~~~e~pl~i~~  169 (244)
T cd08068         157 QYERIEVPLEIVP  169 (244)
T ss_pred             cceEEEeeeEEec
Confidence            3557788888875

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

>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family

Probab=99.09  E-value=3.3e-09  Score=90.47  Aligned_cols=124  Identities=13%  Similarity=0.143  Sum_probs=90.9

Q ss_pred             EEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCccee-ecHHHHHHHHHHHhhhCCCCc
Q 024781           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVA-LDIEYHHTMLKSHLKVNPQEV  139 (262)
Q Consensus        61 ~V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~~-iD~~y~~~m~~l~kkV~p~e~  139 (262)
                      .+.|-.-.+-+|+.|+.++-..+..+.|.|+|. ..++..+|++.+-.|...++..+. +|..   ++++.  .-..++.
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            455666778889999977632357999999998 677888999998878777655443 3321   12221  1235899


Q ss_pred             EEEeecCCCC----CCCchhHHHHHHhhhCCCcEEEEEeCCCCCCcceeEEEEee-eecc
Q 024781          140 IVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV-NLSL  194 (262)
Q Consensus       140 vVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikAy~~~-~~~~  194 (262)
                      +||||||+++    ++..|+..|..|....+..++|+++|.    ...++||+.. +.++
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    577888888877776677799999973    6789999999 6665

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

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

Probab=99.06  E-value=3.3e-09  Score=97.21  Aligned_cols=135  Identities=21%  Similarity=0.322  Sum_probs=109.3

Q ss_pred             CCCCcEEEEehhhHhHHHHHHhhcCCCCce-EEEEe-ee---eEecCCeEEEEeeeecccCCCCcc--e-eecHHHHHHH
Q 024781           56 ATSNVTAKVHPLVIFNICDCYVRRPDQAER-VIGTL-LG---SVLPDGTVDIRNSYVVPHNEFSDQ--V-ALDIEYHHTM  127 (262)
Q Consensus        56 ~~~~~~V~VhPlVll~I~dH~~R~~~~~~~-ViG~L-LG---~~~~~~~veVtnsF~vP~~~~~~~--~-~iD~~y~~~m  127 (262)
                      +....+|.++.++++.+++|- |.. .+.. ++|.+ +|   .+.+..++.|.+.|+.|+...+-.  + ..|.-|+.+|
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            466779999999999999987 442 3344 89999 99   556778899999999999876432  2 5889999999


Q ss_pred             HHHHhhhCCCCcEEEeecCCCC----CCCchhHHHHHHhhhCCCcEEEEEeCCCC-CCcceeEEEEeeee
Q 024781          128 LKSHLKVNPQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFR-NGEGTVKAYVSVNL  192 (262)
Q Consensus       128 ~~l~kkV~p~e~vVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~-~~~l~ikAy~~~~~  192 (262)
                      .++.++....+.||||||++++    ++..|+..|+-|....+..+..++||..+ .|+.-+.||+..+.
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            9999999888999999999986    45677777877877777789999999874 56666678887654

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

Probab=98.52  E-value=4.2e-06  Score=67.49  Aligned_cols=113  Identities=15%  Similarity=0.057  Sum_probs=78.5

Q ss_pred             hHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCc--ceeecHHHHHHHHHHHhhhCCCCcEEEeec
Q 024781           68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSD--QVALDIEYHHTMLKSHLKVNPQEVIVGWFS  145 (262)
Q Consensus        68 Vll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~--~~~iD~~y~~~m~~l~kkV~p~e~vVGWY~  145 (262)
                      ++-+|++|+.+.  .+.+++|.|+|. .++....|+..|++|....+.  ...+|.+.+.+..+..++.  ++.+|||||
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 666666678999998765443  4568887777776666544  699999999


Q ss_pred             CCCCC--CCchhHHHHHHhhhCCCcEEEEEeCCCCCCcceeEEEEee
Q 024781          146 TGLGV--TGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV  190 (262)
Q Consensus       146 t~~~~--~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikAy~~~  190 (262)
                      |+++-  ..+...+..+  . ....++|++.....  ...+++|...
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            99862  2333223221  1 12357888875333  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=98.51  E-value=2.5e-06  Score=73.34  Aligned_cols=118  Identities=19%  Similarity=0.211  Sum_probs=79.9

Q ss_pred             ehhhHhHHHHHHhhcCCCCceEEEEeeeeEec-CCeEEEEeeeecccCCCCcceeecHHH--HHHHHHHHhhhCCCCcEE
Q 024781           65 HPLVIFNICDCYVRRPDQAERVIGTLLGSVLP-DGTVDIRNSYVVPHNEFSDQVALDIEY--HHTMLKSHLKVNPQEVIV  141 (262)
Q Consensus        65 hPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~-~~~veVtnsF~vP~~~~~~~~~iD~~y--~~~m~~l~kkV~p~e~vV  141 (262)
                      .+.+..+|..|+.+.  .+..|.|.|+|+ .. ++.+.|++++|+.+..    ..++...  .....+.+-+- .+..||
T Consensus         2 s~~ay~ki~~HA~k~--p~~evcGlLlG~-~~~~~~~~V~d~vPl~h~~----~~l~P~~Eval~~ve~~~~~-~gl~Iv   73 (182)
T cd08060           2 STLAYVKMLLHAAKY--PHCAVNGLLLGK-KSSGGSVEITDAVPLFHSC----LALAPMLEVALALVDAYCKS-SGLVIV   73 (182)
T ss_pred             CHHHHHHHHHHHHHc--CCchheEEEEee-ecCCCCEEEEEEEEcCCCc----cccCHHHHHHHHHHHHHHHH-CCCEEE
Confidence            356788999999885  356999999998 55 7789999999999852    3455432  22333333333 379999


Q ss_pred             EeecCCCCCC-----CchhHHHHHHhhhCCCcEEEEEeCCCC--C-CcceeEEEEee
Q 024781          142 GWFSTGLGVT-----GGSALIHEFYCREVPNPVHLTVDTGFR--N-GEGTVKAYVSV  190 (262)
Q Consensus       142 GWY~t~~~~~-----~~~~~ih~~~~~~~~~PI~L~vD~~~~--~-~~l~ikAy~~~  190 (262)
                      |+||+++...     .....|-+.+.+.++++++|++|-.+-  + ..-.+.+|...
T Consensus        74 G~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~l~~~~~~~~~~~~~~~  130 (182)
T cd08060          74 GYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEKLTLDCKGNALVVYKDK  130 (182)
T ss_pred             EEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCccccccccCCceEEEEec
Confidence            9999998543     233334455666778899999997652  1 22234555554

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=98.42  E-value=4.9e-06  Score=72.37  Aligned_cols=123  Identities=16%  Similarity=0.198  Sum_probs=87.3

Q ss_pred             EEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCe--EEEEeeeecccCCCCcceeecHHHHHHHHHHHhhhCCCC
Q 024781           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGT--VDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQE  138 (262)
Q Consensus        61 ~V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~--veVtnsF~vP~~~~~~~~~iD~~y~~~m~~l~kkV~p~e  138 (262)
                      +|.+++.+..+|+=|+.+..  ...|.|+|||. ..++.  |+|+||.|+=|....  ..--.|---.+.+.|-+. .+.
T Consensus         3 ~v~is~~AY~K~~LHaaKyP--~~aVnGvLlg~-~~~~~~~v~i~DaVPLfH~~~~--L~PmlEvAL~qvd~~~~~-~gl   76 (196)
T PF03665_consen    3 SVEISSRAYAKMILHAAKYP--HCAVNGVLLGK-SSKSSSEVEIVDAVPLFHHWLS--LSPMLEVALAQVDAYAKS-NGL   76 (196)
T ss_pred             eEEEcHHHHHHHHHHhccCC--CCceeeEEEec-cCCCCceEEEeeceeccccccC--cchHHHHHHHHHHHHHhh-CCC
Confidence            78999999999999998864  47899999999 54443  999999999985421  222344445556666654 579


Q ss_pred             cEEEeecCCCCC-----CCchhHHHHHHhhhCCCcEEEEEeCCC-C--CCcceeEEEEe
Q 024781          139 VIVGWFSTGLGV-----TGGSALIHEFYCREVPNPVHLTVDTGF-R--NGEGTVKAYVS  189 (262)
Q Consensus       139 ~vVGWY~t~~~~-----~~~~~~ih~~~~~~~~~PI~L~vD~~~-~--~~~l~ikAy~~  189 (262)
                      .|||+|+....+     +.....|-+.+.+.++++++|++|-.+ .  .+...+.+|..
T Consensus        77 ~IvGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~kl~~~~~~~~~~~~~~  135 (196)
T PF03665_consen   77 VIVGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKKLSSDCKAPAISVYQR  135 (196)
T ss_pred             EEEEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcccccccCCCcceeeee
Confidence            999999987533     333334555666678889999999766 2  22334566763

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

Probab=98.21  E-value=1.7e-05  Score=64.53  Aligned_cols=100  Identities=19%  Similarity=0.245  Sum_probs=64.8

Q ss_pred             EEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCC--cceeecHHHHHHHHHHHhhhCCCCc
Q 024781           62 AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS--DQVALDIEYHHTMLKSHLKVNPQEV  139 (262)
Q Consensus        62 V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~--~~~~iD~~y~~~m~~l~kkV~p~e~  139 (262)
                      +.+-..++-.|+.|..|.  .+.+++|.|+|+ ..+     ...|+++....+  ....++.++.. ++......  ++.
T Consensus         2 ~~i~~~~l~~il~~a~~~--~p~E~~g~l~~~-~~~-----~~~~~~~n~~~~~~~~~~~~~~~~~-~~~~~~~~--g~~   70 (134)
T COG1310           2 LVIPKEVLGAILEHARRE--HPREVCGLLAGT-REG-----ERYFPLKNVSVEPVEYFEIDPEYSL-FYLAAEDA--GEV   70 (134)
T ss_pred             ceecHHHHHHHHHHHHhc--CChheEEEEEee-ccc-----ceeeccccccCCcceeEeeCHHHHH-HHHHHhhC--CCE
Confidence            345677888999999886  358999999998 555     444555443322  22355666555 44444333  399


Q ss_pred             EEEeecCCCC--CCCchhHHHHHHhhhCCCcEEEEEe
Q 024781          140 IVGWFSTGLG--VTGGSALIHEFYCREVPNPVHLTVD  174 (262)
Q Consensus       140 vVGWY~t~~~--~~~~~~~ih~~~~~~~~~PI~L~vD  174 (262)
                      +||||||+++  ...++..++  ++...+.|.+++..
T Consensus        71 vvg~yHSHP~~~~~pS~~D~~--~~~~~~~~~~iv~~  105 (134)
T COG1310          71 VVGWYHSHPGGPPYPSEADRR--LSKLGPLPWLIVSV  105 (134)
T ss_pred             EEEEEcCCCCCCCCcCHHHHh--hccccCCCEEEEEc
Confidence            9999999985  445555555  66655666566554

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

Probab=97.70  E-value=1.4e-05  Score=63.16  Aligned_cols=48  Identities=31%  Similarity=0.419  Sum_probs=12.5

Q ss_pred             chhhHHHHHHhhccCC----CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024781          213 IEAERVGFDILKSTSV----DKLPSDLEGMEVLMERLLTLINDIYKYVDDTV  260 (262)
Q Consensus       213 ~e~E~i~l~~l~k~~~----~~~~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~  260 (262)
                      .||||||++|+.+...    +.+.++++.++.++.+|..+++.+..||++|.
T Consensus         1 eEaErigv~~l~~~~~~~~~s~~~~~l~~~~~al~~L~~~l~~i~~Yl~~v~   52 (115)
T PF13012_consen    1 EEAERIGVDHLARGLGDHYYSSLSSQLENEQNALKMLHKRLWQILDYLEDVI   52 (115)
T ss_dssp             SHHHHHHHHHHHHH--S-----------------------------------
T ss_pred             CchHHHHHHHHHccCCCccccHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Confidence            4899999999988533    35778999999999999999999999999994

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

Probab=97.66  E-value=0.0011  Score=56.54  Aligned_cols=124  Identities=16%  Similarity=0.167  Sum_probs=87.3

Q ss_pred             EEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeE-ecCCeEEEEeeeecccCCCCcceeecHHHHHHHHHHHhhhCCCCc
Q 024781           61 TAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSV-LPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEV  139 (262)
Q Consensus        61 ~V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~-~~~~~veVtnsF~vP~~~~~~~~~iD~~y~~~m~~l~kkV~p~e~  139 (262)
                      .|++..++..+|+=|+.|..  ..-|-|.|+|.. ..|+.++|++|.|+=|+.-.  +.--.|-.-.|++-+-+ --+..
T Consensus         3 ~veis~~aY~kmiLH~akyp--h~aVnGLLla~~~~kg~~v~itdcVPLfH~~la--LaPmlEvAl~lId~~~~-~~Glv   77 (199)
T KOG3289|consen    3 EVEISALAYVKMILHAAKYP--HAAVNGLLLAPATGKGECVEITDCVPLFHSHLA--LAPMLEVALNLIDVWGA-QAGLV   77 (199)
T ss_pred             ceeehhhHHHHHHHHhccCc--ccceeeEEEeccCCCCCeEEEEecchhhccccc--cccHHHHHHHHHHHHHH-hcCeE
Confidence            58899999999999999875  468999999931 56778999999999877531  22234555555555543 45899


Q ss_pred             EEEeecCCCCCCC-----chhHHHHHHhhhCCCcEEEEEeCCC-C--CCcceeEEEEe
Q 024781          140 IVGWFSTGLGVTG-----GSALIHEFYCREVPNPVHLTVDTGF-R--NGEGTVKAYVS  189 (262)
Q Consensus       140 vVGWY~t~~~~~~-----~~~~ih~~~~~~~~~PI~L~vD~~~-~--~~~l~ikAy~~  189 (262)
                      |+|.|++...+..     --..|-+-.++.+++..+|++|-.+ .  -+.-++-+|+-
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            9999998864432     2234556677778887777777654 1  23457888883

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

Probab=96.88  E-value=0.006  Score=55.03  Aligned_cols=102  Identities=23%  Similarity=0.302  Sum_probs=73.0

Q ss_pred             ceEEEEeeeeEecC---CeEEEEeeeecccCCCCcceeecHHHHHHHHHHHhhhCCCCcEEEeecCCCC----CCCchhH
Q 024781           84 ERVIGTLLGSVLPD---GTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG----VTGGSAL  156 (262)
Q Consensus        84 ~~ViG~LLG~~~~~---~~veVtnsF~vP~~~~~~~~~iD~~y~~~m~~l~kkV~p~e~vVGWY~t~~~----~~~~~~~  156 (262)
                      ..+.|.|.|. ...   +.-||+.-...|...+.+.+.+..+-     -.+. ---++..|||=+|.+.    +++.|+.
T Consensus        56 tQ~~GyLyG~-~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~~-----~~~~-~l~~Le~LGWIHTqp~e~~~Lss~Dv~  128 (252)
T cd08056          56 TQIAGYLYGK-SPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQL-----PQHE-YLEDLEPLGWIHTQPNELPQLSPQDVT  128 (252)
T ss_pred             ceEEEEEecc-CCCCCCCeEEEEEEEECCEeCCcCcEECCccC-----ccch-hhCCCEeeEEEEcCCCCccccCHHHHH
Confidence            5799999998 655   56789888888888877666442110     1111 1236889999999863    5788888


Q ss_pred             HHHHHhhhCC-----CcEEEEEeCCCCCCcceeEEEEeeeecc
Q 024781          157 IHEFYCREVP-----NPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (262)
Q Consensus       157 ih~~~~~~~~-----~PI~L~vD~~~~~~~l~ikAy~~~~~~~  194 (262)
                      .|..+...++     +.|.+++  +...|..++.||...+.++
T Consensus       129 tha~~~~~~~~w~~~~~V~it~--SftpGs~sl~ay~LT~~G~  169 (252)
T cd08056         129 THAKILADNPSWDGEKTVILTC--SFTPGSCSLTAYKLTPEGY  169 (252)
T ss_pred             HHHHHHHhccccCCCcEEEEEE--cCCCCceEEEEEecCHHHH
Confidence            8988887765     3455554  4457789999999998765

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

>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family

Probab=96.81  E-value=0.03  Score=45.81  Aligned_cols=80  Identities=16%  Similarity=0.161  Sum_probs=54.4

Q ss_pred             hHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCC-Ccc--eeecHHHHHHHHHH-HhhhCCCCcEEEe
Q 024781           68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEF-SDQ--VALDIEYHHTMLKS-HLKVNPQEVIVGW  143 (262)
Q Consensus        68 Vll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~-~~~--~~iD~~y~~~m~~l-~kkV~p~e~vVGW  143 (262)
                      +++.++..|......+.+.-|+|+|. ..+..+.|++.- .|..++ ...  ..-+.+.+++.++. +++.+-....||=
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            46777888866655678999999998 566677777744 444332 122  23456677766654 4455555899999


Q ss_pred             ecCCCC
Q 024781          144 FSTGLG  149 (262)
Q Consensus       144 Y~t~~~  149 (262)
                      +||+|.
T Consensus        79 WHtHP~   84 (131)
T TIGR02256        79 WHTHPE   84 (131)
T ss_pred             cCcCCC
Confidence            999986

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

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

Probab=96.66  E-value=0.045  Score=43.60  Aligned_cols=99  Identities=18%  Similarity=0.213  Sum_probs=62.4

Q ss_pred             hHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcce-eecHHHHHHHHHHHhhhCCCCcEEEeecC
Q 024781           68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKVNPQEVIVGWFST  146 (262)
Q Consensus        68 Vll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~-~iD~~y~~~m~~l~kkV~p~e~vVGWY~t  146 (262)
                      .+-.|++|+.+.  .+.++.|.|+|+ ..    .|++.+++|....++.- ..+.+    |.      -.+..+||-|||
T Consensus         5 ~~~~i~~ha~~~--~P~E~CGlL~G~-~~----~v~~~~~~~n~~~~~~~~~f~~~----~~------~~g~~ivgi~HS   67 (117)
T cd08072           5 LLDSILEAAKSS--HPNEFAALLRGK-DG----VITELLILPGTESGEVSAVFPLL----ML------PLDMSIVGSVHS   67 (117)
T ss_pred             HHHHHHHHHhhc--CCceEEEEEEee-cc----EEEEEEECCCCCCCCcceeechH----Hh------cCCCeEEEEEEc
Confidence            345788998765  478999999997 32    58899999965443221 22221    11      248999999999


Q ss_pred             CCC----CCCchhHHHHHHhhhCCCcEEEEEeCCCCCCcceeEEEEee
Q 024781          147 GLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV  190 (262)
Q Consensus       147 ~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikAy~~~  190 (262)
                      +++    ++..|.  .  ++.. +.-.+|++....  +.-.++||...
T Consensus        68 HP~~~~~PS~~D~--~--~~~~-~~~~~lIvs~~~--~~~~~~a~~~~  108 (117)
T cd08072          68 HPSGSPRPSDADL--S--FFSK-TGLVHIIVGYPY--DEDDWRAYDSD  108 (117)
T ss_pred             CCCCCCCCCHHHH--H--hhhc-CCCEEEEEECcC--CCCCEEEEecC
Confidence            985    344442  2  2222 334777776432  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.

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

Probab=96.34  E-value=0.031  Score=42.66  Aligned_cols=91  Identities=15%  Similarity=0.068  Sum_probs=50.4

Q ss_pred             hHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeee-cccCCCCcceeecHHHHHHHHHHHhhhCCCCcEEEeecC
Q 024781           68 VIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYV-VPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFST  146 (262)
Q Consensus        68 Vll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~-vP~~~~~~~~~iD~~y~~~m~~l~kkV~p~e~vVGWY~t  146 (262)
                      ++-.|+.|+.+.  .+.+..|.|+|. ..+..+.++.... .|.+           +.....  ++....+..+||+|||
T Consensus         4 ~~~~i~~~~~~~--~p~E~~G~L~g~-~~~~~~~~~~~~~~~p~~-----------~~~~~~--~~~~~~~~~~vg~~HS   67 (104)
T PF14464_consen    4 VLEQIIAHARAA--YPNEACGLLLGR-RDDQRFIVVPNVNPDPRD-----------SFRRER--FEARERGLEIVGIWHS   67 (104)
T ss_dssp             HHHHHHHHHHHH--TTS-EEEEEEEE-EECCEEEEEEEEE--HHC-----------HHHHHH---HHHHHT-EEEEEEEE
T ss_pred             HHHHHHHHHhhC--CCCeEEEEEEEE-ecCCEEEEEeCCCCCcHH-----------HHHHHh--hhhhcccceeeEEEEc
Confidence            455788888776  468999999998 5666666766655 1111           111111  0445678999999999


Q ss_pred             CCCCCCchhHHHHHHhhhCCCcEEEEEe
Q 024781          147 GLGVTGGSALIHEFYCREVPNPVHLTVD  174 (262)
Q Consensus       147 ~~~~~~~~~~ih~~~~~~~~~PI~L~vD  174 (262)
                      +++-...=+............+++|++.
T Consensus        68 HP~~~a~pS~~D~~~~~~~~~~~~iI~~   95 (104)
T PF14464_consen   68 HPSGPAFPSSTDIRSMRDLAPPSYIIVG   95 (104)
T ss_dssp             ESSSSSS--HHHHHTHCCS-SCEEEEEE
T ss_pred             CCCCCCCCCHHHHHhhhccCCeEEEEEe
Confidence            9864322222222222222255666664

>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=90.10  E-value=3.4  Score=32.32  Aligned_cols=65  Identities=8%  Similarity=-0.059  Sum_probs=40.5

Q ss_pred             HhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCC--cceeecH-HHHHHHHHHHhhhCCCCcEEEeec
Q 024781           69 IFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS--DQVALDI-EYHHTMLKSHLKVNPQEVIVGWFS  145 (262)
Q Consensus        69 ll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~--~~~~iD~-~y~~~m~~l~kkV~p~e~vVGWY~  145 (262)
                      +-.|++|..+.  .+.+..|.|+|. .  +   ++..++++....+  ....+|. ++++-+    +    ...+||-||
T Consensus         3 ~~~i~~ha~~~--~P~E~CGll~g~-~--~---~~~~~p~~N~~~~p~~~F~idp~e~~~a~----~----~~~ivgi~H   66 (108)
T cd08073           3 EDAILAHAKAE--YPREACGLVVRK-G--R---KLRYIPCRNIAADPEEHFEISPEDYAAAE----D----EGEIVAVVH   66 (108)
T ss_pred             HHHHHHHHhHC--CCCcceEEEEec-C--C---ceEEEECccCCCCccceEEeCHHHHHHHh----c----CCCEEEEEE
Confidence            34688888665  468899999997 3  2   3344666532221  3356775 444322    1    238999999


Q ss_pred             CCCC
Q 024781          146 TGLG  149 (262)
Q Consensus       146 t~~~  149 (262)
                      |+++
T Consensus        67 SHP~   70 (108)
T cd08073          67 SHPD   70 (108)
T ss_pred             cCCC
Confidence            9974

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=89.25  E-value=4.3  Score=37.18  Aligned_cols=108  Identities=19%  Similarity=0.232  Sum_probs=68.4

Q ss_pred             ceEEEEeeeeEecC------CeEEEEeeeecccCCCCcceeecHHHHHHHHHHHhhhCCCCcEEEeecCCC------C--
Q 024781           84 ERVIGTLLGSVLPD------GTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGL------G--  149 (262)
Q Consensus        84 ~~ViG~LLG~~~~~------~~veVtnsF~vP~~~~~~~~~iD~~y~~~m~~l~kkV~p~e~vVGWY~t~~------~--  149 (262)
                      ..-+|.|.|++.+.      .++.|.--|+=|...+.+.+.+..+-.++..+... ..-+...|||=-|..      +  
T Consensus        34 ~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~~~~l~d~~~~~vd~iA-~~lGL~~VG~IfT~l~~~~~d~~~  112 (274)
T cd08061          34 QQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDGFELLEDPNADTVDAIA-AALGLERVGWIFTDLPREDKDGYF  112 (274)
T ss_pred             ceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCCeEEccchhhhHHHHHH-HHcCCeEEEEEEecCCCCCCCcee
Confidence            56799999995443      37889888898988877766544333333344443 334899999966553      2  


Q ss_pred             CCCchhHHHHHHhh-----hCCCc-EEEEEeCCCCCCcceeEEEEeeeec
Q 024781          150 VTGGSALIHEFYCR-----EVPNP-VHLTVDTGFRNGEGTVKAYVSVNLS  193 (262)
Q Consensus       150 ~~~~~~~ih~~~~~-----~~~~P-I~L~vD~~~~~~~l~ikAy~~~~~~  193 (262)
                      +++..+.....++.     ...+. +-+++.+.. ++.+.+.||..++..
T Consensus       113 LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~-~g~i~~~ayQvSdq~  161 (274)
T cd08061         113 LSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDK-DGQIHFEAYQVSDQA  161 (274)
T ss_pred             ECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCC-CCceeeeeeeecHHH
Confidence            23333333444442     23333 557777654 477899999998754

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=87.74  E-value=6.2  Score=36.74  Aligned_cols=105  Identities=18%  Similarity=0.165  Sum_probs=62.7

Q ss_pred             EEEeeeeEecCC------eEEEEeeeecccCCCCcceeecHHHHHHHHHHHhhhCCCCcEEEeecCCCC-----------
Q 024781           87 IGTLLGSVLPDG------TVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG-----------  149 (262)
Q Consensus        87 iG~LLG~~~~~~------~veVtnsF~vP~~~~~~~~~iD~~y~~~m~~l~kkV~p~e~vVGWY~t~~~-----------  149 (262)
                      +|.|.|++.+..      ++.|.--|+=|...+.+.+.+..+-.++..+...+-- +...|||=-|...           
T Consensus         2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~~~l~~d~~~~~vd~iA~~l-GL~rVG~IfTdl~~~~~~~g~v~~   80 (306)
T PF05021_consen    2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDGFTLLPDENEERVDAIASAL-GLERVGWIFTDLTDDGSGDGTVKC   80 (306)
T ss_pred             eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCCEEEcCCccHHHHHHHHHHC-CCEEEEEEEecCcccccCCCceee
Confidence            799999854444      6889889999998877777653333333333333222 8999999444321           


Q ss_pred             --------CCCchhHHHHHHhhhC------------CCc-EEEEEeCCCCCCcceeEEEEeeeec
Q 024781          150 --------VTGGSALIHEFYCREV------------PNP-VHLTVDTGFRNGEGTVKAYVSVNLS  193 (262)
Q Consensus       150 --------~~~~~~~ih~~~~~~~------------~~P-I~L~vD~~~~~~~l~ikAy~~~~~~  193 (262)
                              +++..+..-..++...            .+. |-+++.+. .++.+.+.||..++..
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                    2222222222232222            222 55566553 5678999999998754

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=85.50  E-value=4  Score=30.98  Aligned_cols=63  Identities=13%  Similarity=0.080  Sum_probs=39.9

Q ss_pred             HHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeecHHHHHHHHHHHhhhCCCCcEEEeecCCCC
Q 024781           71 NICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIVGWFSTGLG  149 (262)
Q Consensus        71 ~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~~iD~~y~~~m~~l~kkV~p~e~vVGWY~t~~~  149 (262)
                      .|.+|+.+.  -+.+..|.|+|. .. +  .+.+..++|...    ..++..+      ......-+..+||-||++++
T Consensus         5 ~i~~~~~~~--~p~E~~gll~~~-~~-~--~~~~~~~~~~~~----~~~~~~~------~~~a~~~~~~~v~i~HsHP~   67 (101)
T cd08059           5 TILVHAKDA--HPDEFCGFLSGS-KD-N--VMDELIFLPFVS----GSVSAVI------DLAALEIGMKVVGLVHSHPS   67 (101)
T ss_pred             HHHHHHHhc--CChhhheeeecC-CC-C--eEEEEEeCCCcC----CccChHH------HHHHhhCCCcEEEEEecCcC
Confidence            456666543  257899999997 43 3  567778887443    1233333      22333457789999999974

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

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

Probab=80.95  E-value=3  Score=39.57  Aligned_cols=100  Identities=15%  Similarity=0.211  Sum_probs=61.8

Q ss_pred             CceEEEEeeeeEecCCeEEEEeeeecccC-CCCcce-eecHHHHHHHHHHHh-hhCCCCcEEEeecCCCC--CCCchhHH
Q 024781           83 AERVIGTLLGSVLPDGTVDIRNSYVVPHN-EFSDQV-ALDIEYHHTMLKSHL-KVNPQEVIVGWFSTGLG--VTGGSALI  157 (262)
Q Consensus        83 ~~~ViG~LLG~~~~~~~veVtnsF~vP~~-~~~~~~-~iD~~y~~~m~~l~k-kV~p~e~vVGWY~t~~~--~~~~~~~i  157 (262)
                      +-.-.|+|-|. -..|..-||+-. +|.. .+.|-+ ..|.+-      +|. +---++--+||-||++.  ..-+++.+
T Consensus       275 nlETCGiL~g~-L~~n~f~IThli-iPkQeatsd~C~t~neee------lF~vQdq~~L~tlGWIHTHPTQt~FmSSVDl  346 (424)
T KOG2880|consen  275 NLETCGILAGK-LERNEFYITHLI-IPKQEATSDSCNTMNEEE------LFEVQDQHELLTLGWIHTHPTQTCFMSSVDL  346 (424)
T ss_pred             cchHHHHhhhH-hhcCcEEEEEEE-eecccCCCccccccCHHH------HheecccccceeeeeeecCCccchhheeccc
Confidence            45678999999 788888897755 4544 333322 122111      111 11235667999999985  33455566


Q ss_pred             HHHHhhh--CCCcEEEEEeCCCCCCcceeEEEEee-eecc
Q 024781          158 HEFYCRE--VPNPVHLTVDTGFRNGEGTVKAYVSV-NLSL  194 (262)
Q Consensus       158 h~~~~~~--~~~PI~L~vD~~~~~~~l~ikAy~~~-~~~~  194 (262)
                      |.-++++  .+..|++++-|..++    -.+|++. +.|+
T Consensus       347 HTHcSYQiMlPEAiAIV~aPk~~~----tGiFrLt~~~Gm  382 (424)
T KOG2880|consen  347 HTHCSYQIMLPEAIAIVCAPKSKT----TGIFRLTDPGGM  382 (424)
T ss_pred             cccceeeeecchheeEEeccccCC----cceEEecCCcch
Confidence            7767776  577899999887432    3467776 4444

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	262
2o95_A	187	Crystal Structure Of The Metal-Free Dimeric Human M		9e-12
2o96_A	178	Crystal Structure Of The Metal-Free Dimeric Human M		1e-11
4b4t_U	338	Near-Atomic Resolution Structural Model Of The Yeas		2e-07
4e0q_A	141	Crystal Structure Of Mpn Domain From Cop9 Signaloso		1e-04

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

Iteration: 1
 Score = 67.0 bits (162), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 47/132 (35%), Positives = 69/132 (52%), Gaps = 6/132 (4%)
Query: 64  VHPLVIFNICDCYVR--RPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNE--FSDQVA- 118
           VHPLV+ ++ D + R  +    +RV+G LLGS      +D+ NS+ VP +E    D V  
Sbjct: 12  VHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGS-WQKKVLDVSNSFAVPFDEDDKDDSVWF 70
Query: 119 LDIEYHHTMLKSHLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFR 178
           LD +Y   M     KVN +E IVGW+ TG  +      I+E   R  PN V + +D   +
Sbjct: 71  LDHDYLENMYGMFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSVLVIIDVKPK 130
Query: 179 NGEGTVKAYVSV 190
           +     +AY+SV
Sbjct: 131 DLGLPTEAYISV 142

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 2e-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 = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/92 (28%), Positives = 49/92 (53%), Gaps = 4/92 (4%)
Query: 59  NVTAKVHPLVIFNICDCYVR-RPDQAE--RVIGTLLGSVLPDGTVDIRNSYVVPHNEFSD 115
           +VT  +HPLVI NI + + R R    E  +V G L+G       ++I NS+ +  +   D
Sbjct: 5   SVTISLHPLVIXNISEHWTRFRAQHGEPRQVYGALIGK-QKGRNIEIXNSFELKTDVIGD 63
Query: 116 QVALDIEYHHTMLKSHLKVNPQEVIVGWFSTG 147
           +  ++ +Y++   + + +V      +GW++TG
Sbjct: 64  ETVINKDYYNKKEQQYKQVFSDLDFIGWYTTG 95

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	262
2o95_A	187	26S proteasome non-ATPase regulatory subunit 7; PS	6e-48
4e0q_A	141	COP9 signalosome complex subunit 6; MPN (MPR1P and	6e-43

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

 Score =  156 bits (395), Expect = 6e-48
 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 =  141 bits (358), Expect = 6e-43
 Identities = 31/140 (22%), Positives = 65/140 (46%), Gaps = 5/140 (3%)

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

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

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

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	262
4b4t_U	338	RPN8, 26S proteasome regulatory subunit RPN8; hydr	100.0
2o95_A	187	26S proteasome non-ATPase regulatory subunit 7; PS	100.0
4e0q_A	141	COP9 signalosome complex subunit 6; MPN (MPR1P and	100.0
4b4t_V	306	26S proteasome regulatory subunit RPN11; hydrolase	99.98
2znr_A	178	AMSH-like protease; metal binding protein, alterna	99.47
3rzv_A	211	STAM-binding protein; ubiquitin hydrolase, endosom	99.36
2kks_A	146	Uncharacterized protein; NESG, structural genomics	99.06
2kcq_A	153	MOV34/MPN/PAD-1 family; NESG, structure, structura	98.86
1oi0_A	124	AF2198, hypothetical protein AF2198; proteasome, d	98.1
2p8r_A	273	PRP8, PRE-mRNA-splicing factor PRP8; alpha-beta, t	96.47
2og4_A	254	PRE-mRNA-splicing factor 8; isopeptidase, JAB1/MPN	96.2
3sbg_A	565	PRE-mRNA-splicing factor 8; PRP8P, rnaseh domain,	94.67

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

Probab=100.00  E-value=1.4e-49  Score=368.85  Aligned_cols=203  Identities=25%  Similarity=0.432  Sum_probs=181.5

Q ss_pred             CCcEEEEehhhHhHHHHHHhhcC-CCCceEEEEeeeeEecCCeEEEEeeeecccCCCCc---ceeecHHHHHHHHHHHhh
Q 024781           58 SNVTAKVHPLVIFNICDCYVRRP-DQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSD---QVALDIEYHHTMLKSHLK  133 (262)
Q Consensus        58 ~~~~V~VhPlVll~I~dH~~R~~-~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~---~~~iD~~y~~~m~~l~kk  133 (262)
                      ...+|.|||||||+|+|||+|.+ .++.+|+|+|||. ++|+.|||+|||++|++++++   .+++|.+|+++|+++|++
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 4568999999998 899999999999999987653   368999999999999999


Q ss_pred             hCCCCcEEEeecCCCCCCCchhHHHHHHhhhCC-CcEEEEEeCCCCCCcceeEEEEeeeeccCC-cccccceEEeeeEEe
Q 024781          134 VNPQEVIVGWFSTGLGVTGGSALIHEFYCREVP-NPVHLTVDTGFRNGEGTVKAYVSVNLSLGD-RQLAAQFQEIPLDLR  211 (262)
Q Consensus       134 V~p~e~vVGWY~t~~~~~~~~~~ih~~~~~~~~-~PI~L~vD~~~~~~~l~ikAy~~~~~~~~~-~~~~~~F~~ip~~I~  211 (262)
                      |||++.+||||+||++++..|+.||++|+++++ +|++|++|+...++++|++||++.+.+..+ ......|+++|++|.
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 899999999998999999999998876653 345678999999999


Q ss_pred             cchhhHHHHHHhhccCCC----CCcccHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024781          212 MIEAERVGFDILKSTSVD----KLPSDLEGMEVLMERLLTLINDIYKYVDDTVR  261 (262)
Q Consensus       212 ~~e~E~i~l~~l~k~~~~----~~~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~  261 (262)
                      ++|+||||++|+++...+    .+..++.++.+++++|+.+++.|++||++|.+
T Consensus       163 ~~eaE~Igv~~l~r~~~~~~~~~l~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~  216 (338)
T 4b4t_U          163 AEEAEEIGVEHLLRDVRDQAAGGLSIRLTNQLKSLKGLQSKLKDVVEYLDKVIN  216 (338)
T ss_dssp             SCHHHHHHHHHHHHHHSSCC---CHHHHHHHHHHHHHHHHHHHHHHHHHHHC--
T ss_pred             cCcHHHHHHHHHHhccccCcccccchhHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence            999999999999986433    36678999999999999999999999999874

>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=1.1e-41  Score=291.22  Aligned_cols=173  Identities=31%  Similarity=0.466  Sum_probs=153.2

Q ss_pred             CCCCcEEEEehhhHhHHHHHHhhcC--CCCceEEEEeeeeEecCCeEEEEeeeecccCCCCc---ceeecHHHHHHHHHH
Q 024781           56 ATSNVTAKVHPLVIFNICDCYVRRP--DQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSD---QVALDIEYHHTMLKS  130 (262)
Q Consensus        56 ~~~~~~V~VhPlVll~I~dH~~R~~--~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~---~~~iD~~y~~~m~~l  130 (262)
                      +.+..+|+|||+|+++|+|||+|..  ..+.+|+|+|||. ..++.++|+|||++|+.++++   .+.+|.+|+++|+++
T Consensus         4 ~~~~~~V~i~plvllkI~~H~~r~~~~~~~~~V~G~LLG~-~~~~~v~V~~~f~lp~~~~~~~~~~~~~d~ey~~~m~~~   82 (187)
T 2o95_A            4 ELAVQKVVVHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGS-WQKKVLDVSNSFAVPFDEDDKDDSVWFLDHDYLENMYGM   82 (187)
T ss_dssp             CCSCSEEEECHHHHHHHHHHHHHHHHTTCCSCCEEEEEEE-ESSSEEEEEEEEEECEEECSSCTTSEEECHHHHHHHHHH
T ss_pred             CCCCCEEEEchHHHHHHHHHHhhhcccCCCcEEEEEEEEE-EcCCEEEEEEEEEeCCcccCCCcchhhcCHHHHHHHHHH
Confidence            4567899999999999999999974  2578999999998 778999999999999987654   358999999999999


Q ss_pred             HhhhCCCCcEEEeecCCCCCCCchhHHHHHHhhhCCCcEEEEEeCCCCCCcceeEEEEeeeeccCC-cccccceEEeeeE
Q 024781          131 HLKVNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGD-RQLAAQFQEIPLD  209 (262)
Q Consensus       131 ~kkV~p~e~vVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikAy~~~~~~~~~-~~~~~~F~~ip~~  209 (262)
                      +++++|++.+||||+++++.+..|..||++|++.+++|++|++||.+..++++++||++.+.+.++ .+....|+++|++
T Consensus        83 ~~~v~~~~~iVGWY~s~~~~s~~d~~i~~~~~~~~~~~v~Livd~~~~~~~l~i~ay~~~~~~~~~~~~~~~~F~~ip~~  162 (187)
T 2o95_A           83 FKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSVLVIIDVKPKDLGLPTEAYISVEEVHDDGTPTSKTFEHVTSE  162 (187)
T ss_dssp             HHTTSSSCEEEEEEECCSSCCTTHHHHHHHHTTTCTTCEEEEECCCTTC-CCSEEEEEEEEECC----CCEEEEEEEEEE
T ss_pred             HHHhCCCCCEEEEEcCCCcCCcccHHHHHHHHhcCCCCEEEEECCCCCCCCcCeEEEEEechhcCCCCcccCEEEEeeEE
Confidence            999999999999999999999999999999999899999999999886556999999999887653 3457889999999


Q ss_pred             EecchhhHHHHHHhhccCCC
Q 024781          210 LRMIEAERVGFDILKSTSVD  229 (262)
Q Consensus       210 I~~~e~E~i~l~~l~k~~~~  229 (262)
                      |.++|+||||++|+++...+
T Consensus       163 I~~~eaE~i~v~~l~~~~~~  182 (187)
T 2o95_A          163 IGAEEAEEVGVEHLLRDIKD  182 (187)
T ss_dssp             ECCCHHHHHHHHHHHHHCCS
T ss_pred             EecCcHHHHHHHHHHhcCCC
Confidence            99999999999999987643

>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=2.8e-41  Score=277.32  Aligned_cols=133  Identities=23%  Similarity=0.381  Sum_probs=114.4

Q ss_pred             CCCcEEEEehhhHhHHHHHHhhcCC---CCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeecHHHHHHHHHHHhh
Q 024781           57 TSNVTAKVHPLVIFNICDCYVRRPD---QAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLK  133 (262)
Q Consensus        57 ~~~~~V~VhPlVll~I~dH~~R~~~---~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~~iD~~y~~~m~~l~kk  133 (262)
                      +++.+|+|||||||+|+|||+|.+.   .+.+|+|+|||. +.|+++||+|||++|++++++++.+|.+|+++|++++|+
T Consensus         3 ~~~~~V~ihplvll~I~dH~~R~~~~~g~~~~V~G~LLG~-~~~~~veV~nsF~~p~~~~~~~~~~d~~y~~~m~~~~k~   81 (141)
T 4e0q_A            3 HMSVTISLHPLVIMNISEHWTRFRAQHGEPRQVYGALIGK-QKGRNIEIMNSFELKTDVIGDETVINKDYYNKKEQQYKQ   81 (141)
T ss_dssp             --CEEEEECHHHHHHHHHHHHCC------CCEEEEEEEEE-EETTEEEEEEEEECCEEEETTEEEECHHHHHHHHHHHHH
T ss_pred             CCcEEEEEecHHHHHHHHHHhhhcccCCCCcEEEEEEEEE-EeCCEEEEEEEEEecccCCCCceeecHHHHHHHHHHHHH
Confidence            5578999999999999999999742   368999999999 789999999999999998888899999999999999999


Q ss_pred             hCCCCcEEEeecCCCCCCCchhHHHHHHhhhCCCcEEEEEeCCCC-CCcceeEEEEee
Q 024781          134 VNPQEVIVGWFSTGLGVTGGSALIHEFYCREVPNPVHLTVDTGFR-NGEGTVKAYVSV  190 (262)
Q Consensus       134 V~p~e~vVGWY~t~~~~~~~~~~ih~~~~~~~~~PI~L~vD~~~~-~~~l~ikAy~~~  190 (262)
                      |||++.+||||+|+++++..|+.||++|++++++||+|++||.++ .|++|++||++.
T Consensus        82 v~~~e~iVGWY~s~~~~~~~d~~i~~~~~~~~~~pV~L~~Dp~~~~~g~Lp~~ay~sv  139 (141)
T 4e0q_A           82 VFSDLDFIGWYTTGDNPTADDIKIQRQIAAINECPIMLQLNPLSRSVDHLPLKLFESL  139 (141)
T ss_dssp             HSTTCEEEEEEEEEC-------CHHHHHHHTTCCCEEEEESCSCCCCTTHHHHHHCC-
T ss_pred             hCCCccEEEEEeCCCCCCcchHHHHHHHHHHCCCCEEEEECCCccCCCeEEEEEEEEE
Confidence            999999999999999999999999999999999999999999985 467999999875

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

Probab=99.98  E-value=3.1e-32  Score=249.33  Aligned_cols=204  Identities=15%  Similarity=0.220  Sum_probs=163.9

Q ss_pred             CCCCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcce-eecHHHHHHHHHHHhhh
Q 024781           56 ATSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQV-ALDIEYHHTMLKSHLKV  134 (262)
Q Consensus        56 ~~~~~~V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~-~iD~~y~~~m~~l~kkV  134 (262)
                      ..+..+|+|+|+|||+|++|+.+  ..+.+|+|.|||.+.++++++|+|||++|+.++++++ ++|.+|+.+|+++++++
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            35678999999999999999954  3578999999998566778999999999999888776 58999999999999999


Q ss_pred             CCCCcEEEeecCCCCC----CCchhHHHHHHhhhCCCcEEEEEeCCC-CCCcceeEEEEeeeeccC------C-------
Q 024781          135 NPQEVIVGWFSTGLGV----TGGSALIHEFYCREVPNPVHLTVDTGF-RNGEGTVKAYVSVNLSLG------D-------  196 (262)
Q Consensus       135 ~p~e~vVGWY~t~~~~----~~~~~~ih~~~~~~~~~PI~L~vD~~~-~~~~l~ikAy~~~~~~~~------~-------  196 (262)
                      ++++.+||||||+++.    +..|+..|..|+...+.+|+|++||.. ..|+++++||++.+.+..      .       
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    455666666677778889999999987 478999999999875421      0       


Q ss_pred             -----------cccccceEEeeeEEecchhhHHHHHHhhccCCC---CCcccHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024781          197 -----------RQLAAQFQEIPLDLRMIEAERVGFDILKSTSVD---KLPSDLEGMEVLMERLLTLINDIYKYVDDTVR  261 (262)
Q Consensus       197 -----------~~~~~~F~~ip~~I~~~e~E~i~l~~l~k~~~~---~~~~~l~~l~~sl~~L~~~l~~i~~Yl~~V~~  261 (262)
                                 ......|.++|+++..++.|+..++.+.+..-.   ...+-.+..+.+.+++.++++.+.+|.+.|++
T Consensus       179 ~~~~~~~~~~~~~~~~~yy~l~i~~~ks~le~~~L~~L~~~~w~~~l~~~~~~~~~~~~~~~i~~m~~~~~~y~k~v~~  257 (306)
T 4b4t_V          179 LLNKANIQALIHGLNRHYYSLNIDYHKTAKETKMLMNLHKEQWQSGLKMYDYEEKEESNLAATKSMVKIAEQYSKRIEE  257 (306)
T ss_dssp             -----------------CEEECSCCCCCSSCTHHHHHHHHC----------CHHHHHHHHHHHHHHSSCHHHHHHHHHH
T ss_pred             ccCchhhhhhhccccceEEEeeeEEEeCcHHHHHHHHHHhcccccccccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence                       012346999999999999999999999874321   23344567778889999999999999998864

>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=99.47  E-value=2.1e-13  Score=115.44  Aligned_cols=128  Identities=12%  Similarity=0.130  Sum_probs=97.2

Q ss_pred             CCCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCccee-ecHHHHHHHHHHHhhhC
Q 024781           57 TSNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVA-LDIEYHHTMLKSHLKVN  135 (262)
Q Consensus        57 ~~~~~V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~~-iD~~y~~~m~~l~kkV~  135 (262)
                      .+...|.|...++.+|+.|+.++..++..++|.|+|. ..++..+|+++|++|...+++.+. .+.+-+   ++.  ...
T Consensus         6 ~~~~~v~i~~~~l~k~l~hA~~~~~~~~EvcGlL~G~-~~~~~~~V~~v~~~pq~~t~~~~~~~~~~e~---~~~--~~~   79 (178)
T 2znr_A            6 EGLRCVVLPEDLCHKFLQLAESNTVRGIETCGILCGK-LTHNEFTITHVIVPKQSAGPDYCDMENVEEL---FNV--QDQ   79 (178)
T ss_dssp             CSCCCEEEETTHHHHHHHHHHHHHTTTCCCEEEEEEE-EETTEEEEEEEEECCEEEETTEEEECCHHHH---HHH--HHH
T ss_pred             CCcEEEEECHHHHHHHHHHHHhCCCCCceEEEEEeeE-ecCCCeEEEEEEeCCcCCCCCeeccCCHHHH---HHH--HHh
Confidence            3456899999999999999987644457899999998 677889999999999877666554 332211   111  234


Q ss_pred             CCCcEEEeecCCCC----CCCchhHHHHHHhhhCCCcEEEEEeCCCCCCcceeEEEEeeeecc
Q 024781          136 PQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (262)
Q Consensus       136 p~e~vVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikAy~~~~~~~  194 (262)
                      .++.+||||||+++    ++..|+..|..|+...+..++|+++|...    .++||+..+.++
T Consensus        80 ~~l~~vGwyHSHP~~~~~pS~~Dv~tq~~yq~~~~~~v~iIvsp~~~----~~~afrl~~~g~  138 (178)
T 2znr_A           80 HDLLTLGWIHTHPTQTAFLSSVDLHTHCSYQLMLPEAIAIVCSPKHK----DTGIFRLTNAGM  138 (178)
T ss_dssp             HTCEEEEEEEECSSSCSCCCHHHHHHHHHHHHHCTTCEEEEEEGGGT----EEEEEEECHHHH
T ss_pred             CCCEEEEEEeCCCCCCCCCCHHHHHHHHHHHhhcCCEEEEEEcCCCC----cceEEEEECCcE
Confidence            68999999999964    56677777766766667779999999763    389999987654

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

Probab=99.36  E-value=4.9e-12  Score=109.64  Aligned_cols=127  Identities=14%  Similarity=0.118  Sum_probs=96.1

Q ss_pred             CCcEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceee-cH-HHHHHHHHHHhhhC
Q 024781           58 SNVTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVAL-DI-EYHHTMLKSHLKVN  135 (262)
Q Consensus        58 ~~~~V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~~i-D~-~y~~~m~~l~kkV~  135 (262)
                      .-.+|.|..-++-+|+.|...+-.++.+++|.|+|+ ..++.++|+++|..|...+++.+.. +. +.++-+.+      
T Consensus        40 ~lr~v~Ipk~ll~kfL~~A~~~tp~~~EvcGlL~Gk-~~~~~~~I~~v~~ppq~gt~~~v~~~~~~e~~~~~~~------  112 (211)
T 3rzv_A           40 GLRHVVVPGRLCPQFLQLASANTARGVATCGILCGK-LMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQ------  112 (211)
T ss_dssp             TBCCEEEETTHHHHHHHHHHHHHHTTCCCEEEEEEE-EETTEEEEEEEEECCEEECSSCEEECCHHHHHHHHHH------
T ss_pred             ccEEEEECHHHHHHHHHHHHhCCCCCceEEEEEEeE-cCCCCEEEEEEEeCCccCCCCceeccChHHHHHHHhh------
Confidence            346899999999999999977533457899999998 7788999999999998776665533 22 22221111      


Q ss_pred             CCCcEEEeecCCCC----CCCchhHHHHHHhhhCCCcEEEEEeCCCCCCcceeEEEEeeeeccC
Q 024781          136 PQEVIVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLG  195 (262)
Q Consensus       136 p~e~vVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikAy~~~~~~~~  195 (262)
                      .++.+||||||++.    ++..|+..|..|+...+.-|+|++||..    .+++||+..+.|++
T Consensus       113 ~~l~~vGWyHSHP~~~~~pS~~Dl~tq~~~q~~~~~~I~IVvsP~~----~~lgaFrLtp~G~~  172 (211)
T 3rzv_A          113 QGLITLGWIHTHPTQTAFLSSVDLHTHCSYQMMLPESVAIVCSPKF----QETGFFKLTDHGLE  172 (211)
T ss_dssp             HTCEEEEEEEECTTSCSCCCHHHHHHHHHHHHHCTTCEEEEEETTT----TEEEEEEECHHHHH
T ss_pred             CCCEEEEEEeCCCCCCCCCCHHHHHHHHHHHhcCCCeEEEEEcCCC----CeeeEEEeccchhh
Confidence            49999999999864    5667777776676666777999999863    37999999987753

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

Probab=99.06  E-value=6.3e-09  Score=84.80  Aligned_cols=133  Identities=13%  Similarity=0.068  Sum_probs=93.5

Q ss_pred             EEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCC-cceeecHHHHHHHHHHHhhhCCCCcE
Q 024781           62 AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFS-DQVALDIEYHHTMLKSHLKVNPQEVI  140 (262)
Q Consensus        62 V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~-~~~~iD~~y~~~m~~l~kkV~p~e~v  140 (262)
                      +.|...++.+|++|..+.  .+.+++|.|+|. ..++...|+..|++|....+ +...+|.+.+.+..+...+  .++.+
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            578889999999999775  468999999998 67778899999999955433 3456787666555544443  36899


Q ss_pred             EEeecCCCCC--CCchhHHHHHHhhhCCCcEEEEEeCCCCCCcceeEEEEeeeeccCCcccccceEEeeeEEec
Q 024781          141 VGWFSTGLGV--TGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSVNLSLGDRQLAAQFQEIPLDLRM  212 (262)
Q Consensus       141 VGWY~t~~~~--~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikAy~~~~~~~~~~~~~~~F~~ip~~I~~  212 (262)
                      ||||||+++.  ..+...++.  +. .+..+++++.+.. ++...++||+..         +..|.++|+.+..
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            9999999863  333333332  11 1344788887643 245679999984         2358999988753

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

Probab=98.86  E-value=9.4e-09  Score=84.38  Aligned_cols=134  Identities=15%  Similarity=0.125  Sum_probs=88.6

Q ss_pred             EEehhhHhHHHHHHhhcCCCCceEEEEeeeeEec-CCeEEEEeeeecccC--CC-CcceeecHHHHHHHHHHHhhhCCCC
Q 024781           63 KVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLP-DGTVDIRNSYVVPHN--EF-SDQVALDIEYHHTMLKSHLKVNPQE  138 (262)
Q Consensus        63 ~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~-~~~veVtnsF~vP~~--~~-~~~~~iD~~y~~~m~~l~kkV~p~e  138 (262)
                      +|.+.++.+|+.|..+.  .+.+++|.|+|. .. ++.+.|+..|++|..  .+ .....+|.+.+.+..+...+.  ++
T Consensus         2 ~i~~~~l~~i~~ha~~~--~p~E~cGlL~G~-~~~~~~~~v~~~~p~~n~~~~~~~~~f~~dp~~~~~~~~~~~~~--g~   76 (153)
T 2kcq_A            2 KTTPDILDQIRVHGADA--YPEEGCGFLLGT-VTDDGDNRVAALHRATNRRSEQRTRRYELTADDYRAADAAAQEQ--GL   76 (153)
T ss_dssp             BCCHHHHHHHHHHHHHH--TTSCCCEEEEEE-ECTTSCEEEEEEEESSCCCCCCCSCCSSCCCCSHHHHHHHHHHH--TC
T ss_pred             EeCHHHHHHHHHHHHhc--CCcceEEEEEEe-eccCCCeEEEEEEECCCCCCCCCCcEEEECHHHHHHHHHHHHHC--CC
Confidence            45678899999999875  468999999998 55 678899999999865  32 234456654444444444332  68


Q ss_pred             cEEEeecCCCCC--CCchhHHHHHHhhhCCCcEEEEEeCCCCCCc-ceeEEEEeeeeccCCcccccceEEeeeEEecc
Q 024781          139 VIVGWFSTGLGV--TGGSALIHEFYCREVPNPVHLTVDTGFRNGE-GTVKAYVSVNLSLGDRQLAAQFQEIPLDLRMI  213 (262)
Q Consensus       139 ~vVGWY~t~~~~--~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~-l~ikAy~~~~~~~~~~~~~~~F~~ip~~I~~~  213 (262)
                      .+||||||+++.  ..+...+..  + ..+..+++++.+.  .++ ..+++|+....       ...|.+.++.|...
T Consensus        77 ~ivG~yHSHP~~~~~PS~~D~~~--~-~~~~~~~lIvs~~--~~~~~~~~af~~~~~-------~g~~~e~~i~v~~~  142 (153)
T 2kcq_A           77 DVVGVYHSHPDHPARPSATDLEE--A-TFPGFTYVIVSVR--DGAPEALTAWALAPD-------RSEFHREDIVRPDP  142 (153)
T ss_dssp             EEEEEEEECSSSSSSCCHHHHHT--C-CCTTSEEEEEEEE--TTEEEEEEEEEECTT-------CSCEEEECCBCCCS
T ss_pred             eEEEEEeCCCCCCCCCCHHHHHh--h-hcCCCeEEEEECC--CCCccEEEEEEEeCC-------CCcEEEEEEEEecC
Confidence            999999999863  233333332  1 1234478888642  233 46899998411       23588888877543

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

Probab=98.10  E-value=1.8e-05  Score=62.35  Aligned_cols=106  Identities=16%  Similarity=0.131  Sum_probs=66.1

Q ss_pred             EEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeecHHHHHHHHHHHhhhCCCCcEE
Q 024781           62 AKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEVIV  141 (262)
Q Consensus        62 V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~~iD~~y~~~m~~l~kkV~p~e~vV  141 (262)
                      +.|...++.+|++|..+.  .+.+++|.|+|. . +   .|++.|++| ...+.   .+..|...|..      .++.+|
T Consensus         4 v~i~~~~l~~i~~ha~~~--~P~E~cGlL~g~-~-~---~v~~~~~~p-~~~~~---~~~~f~~~~~~------~~~~iv   66 (124)
T 1oi0_A            4 MKISRGLLKTILEAAKSA--HPDEFIALLSGS-K-D---VMDELIFLP-FVSGS---VSAVIHLDMLP------IGMKVF   66 (124)
T ss_dssp             CEECHHHHHHHHHHHHHH--TTSCCEEEEEES-T-T---EECEEEECC-CCC----------------------CCCEEE
T ss_pred             EEEcHHHHHHHHHHHHhc--CCCeeEEEEecc-c-C---EEEEEEECC-CCCCC---cCceeeeeecc------CCCEEE
Confidence            678889999999999875  478999999997 4 2   688999999 44322   11122222222      579999


Q ss_pred             EeecCCCCC--CCchhHHHHHHhhhCCCcEEEEEeCCCCCCcceeEEEEe
Q 024781          142 GWFSTGLGV--TGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVS  189 (262)
Q Consensus       142 GWY~t~~~~--~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikAy~~  189 (262)
                      |||||+++-  ..+...+..  +.. +..++|++.+..  +...+++|..
T Consensus        67 G~~HSHP~~~~~PS~~D~~~--~~~-~~~~~lIvs~~~--~~~~~~~f~~  111 (124)
T 1oi0_A           67 GTVHSHPSPSCRPSEEDLSL--FTR-FGKYHIIVCYPY--DENSWKCYNR  111 (124)
T ss_dssp             EEEEEESSSCCSCCHHHHHH--HHH-SCSEEEEEETTC--CTTCEEEEET
T ss_pred             EEEEECcCCCCccCHHHHHh--hhc-CCCEEEEEEccC--CCceEEEEec
Confidence            999999853  233333332  222 345788876532  2356788876

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

Probab=96.47  E-value=0.0072  Score=53.76  Aligned_cols=110  Identities=21%  Similarity=0.273  Sum_probs=74.7

Q ss_pred             HHHHHHhhcCCCCceEEEEeeeeEec---CCeEEEEeeeecccCCCCcceeec-----HHHHHHHHHHHhhhCCCCcEEE
Q 024781           71 NICDCYVRRPDQAERVIGTLLGSVLP---DGTVDIRNSYVVPHNEFSDQVALD-----IEYHHTMLKSHLKVNPQEVIVG  142 (262)
Q Consensus        71 ~I~dH~~R~~~~~~~ViG~LLG~~~~---~~~veVtnsF~vP~~~~~~~~~iD-----~~y~~~m~~l~kkV~p~e~vVG  142 (262)
                      +|++.+.....-...+.|.|.|. ..   .+..||+.---+|...+.+.+..-     .+|+           -++..+|
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            55556655543346799999998 53   246788766666666655444221     2232           7999999


Q ss_pred             eecCCCC----CCCchhHHHHHHhhh---C--CCcEEEEEeCCCCCCcceeEEEEeeeecc
Q 024781          143 WFSTGLG----VTGGSALIHEFYCRE---V--PNPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (262)
Q Consensus       143 WY~t~~~----~~~~~~~ih~~~~~~---~--~~PI~L~vD~~~~~~~l~ikAy~~~~~~~  194 (262)
                      |=||.+.    +++.|+..|..|...   .  ++.|++++-+  ..|..++.||++.+.|+
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    577888888777654   3  3678888743  45667899999988765

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

Probab=96.20  E-value=0.008  Score=52.96  Aligned_cols=112  Identities=13%  Similarity=0.236  Sum_probs=73.9

Q ss_pred             HHHHHHhhcCCCCceEEEEeeeeEecC---CeEEEEeeeecccCCCCcceeec-----HHHHHHHHHHHhhhCCCCcEEE
Q 024781           71 NICDCYVRRPDQAERVIGTLLGSVLPD---GTVDIRNSYVVPHNEFSDQVALD-----IEYHHTMLKSHLKVNPQEVIVG  142 (262)
Q Consensus        71 ~I~dH~~R~~~~~~~ViG~LLG~~~~~---~~veVtnsF~vP~~~~~~~~~iD-----~~y~~~m~~l~kkV~p~e~vVG  142 (262)
                      +|++-+.+...-...+.|.|.|. ...   +..||+.---+|...+.+.+...     .+|.+         --++..+|
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            44555544443345799999998 532   46788665555666554433211     12211         26899999


Q ss_pred             eecCCCC----CCCchhHHHHHHhhh-CCCcEEEEEeCCCCCCcceeEEEEeeeecc
Q 024781          143 WFSTGLG----VTGGSALIHEFYCRE-VPNPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (262)
Q Consensus       143 WY~t~~~----~~~~~~~ih~~~~~~-~~~PI~L~vD~~~~~~~l~ikAy~~~~~~~  194 (262)
                      |=||.+.    +++.|+..|..|... .++.|++++-+  ..|..++.||++.+.|+
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    567888888777663 46889988754  34567899999998775

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

Probab=94.67  E-value=0.04  Score=52.86  Aligned_cols=102  Identities=14%  Similarity=0.208  Sum_probs=69.2

Q ss_pred             ceEEEEeeeeEec-C--CeEEEEeeeecccCCCCcceeecHHHHHHHHHHHhh--hCCCCcEEEeecCCCC----CCCch
Q 024781           84 ERVIGTLLGSVLP-D--GTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLK--VNPQEVIVGWFSTGLG----VTGGS  154 (262)
Q Consensus        84 ~~ViG~LLG~~~~-~--~~veVtnsF~vP~~~~~~~~~iD~~y~~~m~~l~kk--V~p~e~vVGWY~t~~~----~~~~~  154 (262)
                      ..+.|.|.|. .. +  +..||+.---+|..++.+.+.+. +     +..+..  .-.+...+||=||.+.    +++.|
T Consensus       369 TQicGyLyG~-sp~dn~nVkEI~cIVipPQ~Gt~~sv~lp-~-----lp~he~~~~l~dLe~LGWIHTqp~et~fLSs~D  441 (565)
T 3sbg_A          369 IQVAAFIYGM-SAKDHPKVKEIKTVVLVPQLGHVGSVQIS-N-----IPDIGDLPDTEGLELLGWIHTQTEELKFMAASE  441 (565)
T ss_dssp             SCCEEEEEEE-EETTEEEEEEEEEEECCCEEECSSCEEEC-C-----CCCCTTSTTCTTCEEEEEEEEESSCCSSCCHHH
T ss_pred             ceeEEEEecC-CCCCCCCeEEEEEEEECCccCCCceEECC-C-----CCccccccccccCEecceeeecCCcccccCHHH
Confidence            5799999998 55 3  45788665555676665555432 0     000000  1267999999998753    67888


Q ss_pred             hHHHHHHhhhCC-CcEEEEEeCCCCCCcceeEEEEeeeecc
Q 024781          155 ALIHEFYCREVP-NPVHLTVDTGFRNGEGTVKAYVSVNLSL  194 (262)
Q Consensus       155 ~~ih~~~~~~~~-~PI~L~vD~~~~~~~l~ikAy~~~~~~~  194 (262)
                      +..|..+...++ +.|.+++  +...|..++.||...+.|.
T Consensus       442 l~THakl~~~n~~~~I~itv--sftPGS~SLsAy~LT~eGy  480 (565)
T 3sbg_A          442 VATHSKLFADKKRDCIDISI--FSTPGSVSLSAYNLTDEGY  480 (565)
T ss_dssp             HHHHHHHHSSSCTTCEEEEE--EEETTEEEEEEEEECHHHH
T ss_pred             HHHHHHHHHhCCCCeEEEEE--EecCCceEEEEEecCHhHH
Confidence            888988876643 4466655  3456889999999999874

---

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	262
d1gtma2	178	c.58.1.1 (A:3-180) Glutamate dehydrogenase {Archae	0.001

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	262
d1oi0a_	121	Hypothetical protein AF2198 {Archaeon Archaeoglobu	97.42

>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=97.42  E-value=0.00034  Score=53.20  Aligned_cols=107  Identities=17%  Similarity=0.129  Sum_probs=64.4

Q ss_pred             cEEEEehhhHhHHHHHHhhcCCCCceEEEEeeeeEecCCeEEEEeeeecccCCCCcceeecHHHHHHHHHHHhhhCCCCc
Q 024781           60 VTAKVHPLVIFNICDCYVRRPDQAERVIGTLLGSVLPDGTVDIRNSYVVPHNEFSDQVALDIEYHHTMLKSHLKVNPQEV  139 (262)
Q Consensus        60 ~~V~VhPlVll~I~dH~~R~~~~~~~ViG~LLG~~~~~~~veVtnsF~vP~~~~~~~~~iD~~y~~~m~~l~kkV~p~e~  139 (262)
                      .+++|..-++-.|++|+.+..  +...+|.|+|. .  +  .|+..+.+|....+. ...   |...|.      -.++.
T Consensus         2 ~~l~I~~~~l~~i~~hA~~~~--P~E~cGlL~G~-~--~--~i~~~~~~~n~~~~~-~~~---~~~~~~------~~~~~   64 (121)
T d1oi0a_           2 SSMKISRGLLKTILEAAKSAH--PDEFIALLSGS-K--D--VMDELIFLPFVSGSV-SAV---IHLDML------PIGMK   64 (121)
T ss_dssp             CSCEECHHHHHHHHHHHHHHT--TSCCEEEEEES-T--T--EECEEEECCCCC-----------------------CCCE
T ss_pred             CeEEECHHHHHHHHHHHHhcC--CceeEEEEEec-C--C--cEEEEEEcCCCCCCc-ccc---cccchh------hcCCe
Confidence            367788889999999998863  68999999997 2  2  356777777543221 111   111111      24789


Q ss_pred             EEEeecCCCC----CCCchhHHHHHHhhhCCCcEEEEEeCCCCCCcceeEEEEee
Q 024781          140 IVGWFSTGLG----VTGGSALIHEFYCREVPNPVHLTVDTGFRNGEGTVKAYVSV  190 (262)
Q Consensus       140 vVGWY~t~~~----~~~~~~~ih~~~~~~~~~PI~L~vD~~~~~~~l~ikAy~~~  190 (262)
                      +||||||+++    ++..|+....    . ..-+++++-....  .-.++||...
T Consensus        65 ivgi~HSHP~~~a~PS~~D~~~~~----~-~g~~~~Ivs~p~~--~~~~~~~~~~  112 (121)
T d1oi0a_          65 VFGTVHSHPSPSCRPSEEDLSLFT----R-FGKYHIIVCYPYD--ENSWKCYNRK  112 (121)
T ss_dssp             EEEEEEEESSSCCSCCHHHHHHHH----H-SCSEEEEEETTCC--TTCEEEEETT
T ss_pred             EEEEEEecCCCCCCcCHHHHHhhh----c-cCCEEEEEeCCCC--CCCEEEEeCC
Confidence            9999999975    3444433222    2 2236777765322  2368898753