Citrus Sinensis ID: 035839

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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-------24
Protein Sequence
MASNKRDEYYTCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKEPDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK
Secondary Structure (PSIPRED)
cccccccccccccEEEEEEEEEEcccccccccccEEEEcHHHHHHHHHccccccEEEEEEEcccccEEEEEEEEEEccccEEEccHHHHHccccccccEEEEEEEEccccEEEEEEEccccccccccccHHHHHHHHHcccccccccEEEEEEccEEEEEEEEEEccccEEEEEcccEEEEEccccccccccHHHHcccccccccHHHHccccccHHHHHccccccccEEEcEEcccc
Secondary Structure Prediction (SSPRO)
ccccccccHHcHHccEEEEcEEEcccccccccccEEEccHHHHHHHHHccccccEEEEEEcccccccccccEEEEEcccccEEcHHHHHHHcccccccEEEEEEccccccEEEEEccccHHHHHHcccHHHHHHHHHHHHHHHccccEEEEEEcccEEEEEEEEEcccccEEEEEEcEEEEcccccccccccccccccccccccccccccccccHHcccccccccEEEcccccEcccc
Coil and Loop (DISEMBL)
MASNKRDEYYTCFekhyhcyslshvakpqhepgdkiimpqsafdrlahtevgyPMMFELcnlssgktthcgvveftadegfiylpnwmmdnmKLQEYELVRVTNVSLAKATymklqphtkgfldelsNPRAVLEAILRKFSclttgdtimIMHNESKYYIDVletkpsnavsitetdcevdfappldykepdeklvkrkvpfpsqveeqskqQPQAVKEEANNKFKaftgkgkllgfk
Flexible Loop (DISEMBL)
masnkrdeYYTCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKEPDEKLVKRKVPfpsqveeqskqqpqavkEEANNkfkaftgkgkllgfk
Low Complexity Region (SEG)
MASNKRDEYYTCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKEPDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK
Disordered region (IsUnstruct)
*******EYYTCFEKHYHCYSLSHVAK******DKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFA*******************************************************
Disordered Region (DISOPRED)
*************EKHYHCYSLSHVA****EPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPL*****************************************FTGKGKLL***
Disordered Region (DISEMBL)
********YYTCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKEPDEKLVKRKVPF*****************EANNKFKAFTGKGKLLGFK
Disordered Region (DISPRO)
*******EYYTCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKE************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MASNKRDEYYTCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKEPDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK
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	238	2.2.26 [Sep-21-2011]
Q9ES53	307	Ubiquitin fusion degradat	yes	no	0.894	0.693	0.480	9e-53
Q92890	307	Ubiquitin fusion degradat	yes	no	0.894	0.693	0.475	9e-53
P70362	307	Ubiquitin fusion degradat	yes	no	0.894	0.693	0.480	1e-52
Q55BK0	330	Ubiquitin fusion degradat	yes	no	0.743	0.536	0.505	7e-50
Q9VTF9	316	Ubiquitin fusion degradat	yes	no	0.756	0.569	0.489	2e-45
O42915	342	Ubiquitin fusion degradat	yes	no	0.760	0.529	0.425	1e-39
P53044	361	Ubiquitin fusion degradat	yes	no	0.777	0.512	0.398	1e-38
Q19584	342	Ubiquitin fusion degradat	yes	no	0.861	0.599	0.366	2e-32

>sp|Q9ES53|UFD1_RAT Ubiquitin fusion degradation protein 1 homolog OS=Rattus norvegicus GN=Ufd1l PE=1 SV=1

 Score =  206 bits (525), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 109/227 (48%), Positives = 139/227 (61%), Gaps = 14/227 (6%)

Query: 13  FEKHYHCYSLSHVAKPQH----EPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTT 68
           F   Y C+S+S +A P      E G KIIMP SA D+L+   + YPM+F+L N +S + T
Sbjct: 19  FSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMT 78

Query: 69  HCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSN 128
           HCGV+EF ADEG  YLP+WMM N+ L+E  LV+V +V+L  ATY K QP +  FLD ++N
Sbjct: 79  HCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLD-ITN 137

Query: 129 PRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDY 188
           P+AVLE  LR F+CLTTGD I I +NE  Y + V+ETKP  AVSI E D  VDF  PL Y
Sbjct: 138 PKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDFDAPLGY 197

Query: 189 KEPDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLL 235
           KEP+          P Q EE  + +           F+AF+G G  L
Sbjct: 198 KEPER---------PVQHEESIEGEADHSGYAGEVGFRAFSGSGNRL 235

Essential component of the ubiquitin-dependent proteolytic pathway which degrades ubiquitin fusion proteins. The ternary complex containing UFD1L, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1L-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope. It may be involved in the development of some ectoderm-derived structures.
Rattus norvegicus (taxid: 10116)

>sp|Q92890|UFD1_HUMAN Ubiquitin fusion degradation protein 1 homolog OS=Homo sapiens GN=UFD1L PE=1 SV=3

 Score =  206 bits (525), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 108/227 (47%), Positives = 141/227 (62%), Gaps = 14/227 (6%)

Query: 13  FEKHYHCYSLSHVAKPQH----EPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTT 68
           F   Y C+S+S +A P      E G KIIMP SA D+L+   + YPM+F+L N +S + T
Sbjct: 19  FSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMT 78

Query: 69  HCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSN 128
           HCGV+EF ADEG  YLP+WMM N+ L+E  LV+V +V+L  ATY K QP +  FLD ++N
Sbjct: 79  HCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLD-ITN 137

Query: 129 PRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDY 188
           P+AVLE  LR F+CLTTGD I I +NE  Y + V+ETKP  AVSI E D  VDF  PL Y
Sbjct: 138 PKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDFDAPLGY 197

Query: 189 KEPDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLL 235
           KEP+ ++         Q EE ++ +           F+AF+G G  L
Sbjct: 198 KEPERQV---------QHEESTEGEADHSGYAGELGFRAFSGSGNRL 235

Essential component of the ubiquitin-dependent proteolytic pathway which degrades ubiquitin fusion proteins. The ternary complex containing UFD1L, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1L-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope. It may be involved in the development of some ectoderm-derived structures.

Homo sapiens (taxid: 9606)

>sp|P70362|UFD1_MOUSE Ubiquitin fusion degradation protein 1 homolog OS=Mus musculus GN=Ufd1l PE=1 SV=2

 Score =  206 bits (525), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 109/227 (48%), Positives = 139/227 (61%), Gaps = 14/227 (6%)

Query: 13  FEKHYHCYSLSHVAKPQH----EPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTT 68
           F   Y C+S+S +A P      E G KIIMP SA D+L+   + YPM+F+L N +S + T
Sbjct: 19  FSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMT 78

Query: 69  HCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSN 128
           HCGV+EF ADEG  YLP+WMM N+ L+E  LV+V +V+L  ATY K QP +  FLD ++N
Sbjct: 79  HCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLD-ITN 137

Query: 129 PRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDY 188
           P+AVLE  LR F+CLTTGD I I +NE  Y + V+ETKP  AVSI E D  VDF  PL Y
Sbjct: 138 PKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDFDAPLGY 197

Query: 189 KEPDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLL 235
           KEP+          P Q EE  + +           F+AF+G G  L
Sbjct: 198 KEPER---------PVQHEESIEGEADHSGYAGEVGFRAFSGSGNRL 235

Essential component of the ubiquitin-dependent proteolytic pathway which degrades ubiquitin fusion proteins. The ternary complex containing UFD1L, VCP and NPLOC4 binds ubiquitinated proteins and is necessary for the export of misfolded proteins from the ER to the cytoplasm, where they are degraded by the proteasome. The NPLOC4-UFD1L-VCP complex regulates spindle disassembly at the end of mitosis and is necessary for the formation of a closed nuclear envelope (By similarity). It may be involved in the development of some ectoderm-derived structures.

Mus musculus (taxid: 10090)

>sp|Q55BK0|UFD1_DICDI Ubiquitin fusion degradation protein 1 homolog OS=Dictyostelium discoideum GN=ufd1 PE=3 SV=1

 Score =  197 bits (500), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 91/180 (50%), Positives = 128/180 (71%), Gaps = 3/180 (1%)

Query: 13  FEKHYHCYSLSHVAKPQH--EPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHC 70
           +E+ +  + +S + K +H  E G KI++P SA + L+   + YPM+FE+ N  SGK +HC
Sbjct: 25  YEQKFKAFPISFLPKEKHSLESGGKILLPPSALNALSRLNIQYPMLFEISNPISGKKSHC 84

Query: 71  GVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPR 130
           GV+EF A+EG  YLP WMM N++L+E E + + N +LAK T++K+QP T  F+D +SNP+
Sbjct: 85  GVLEFIAEEGICYLPLWMMQNLQLKEGEFIDIKNATLAKGTFVKIQPRTSNFID-ISNPK 143

Query: 131 AVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKE 190
           AVLE  LRKF+ LT  D IMI +N +KYY+ V+E KP+NA+SI E D  VDFAPP+D KE
Sbjct: 144 AVLENSLRKFATLTKDDEIMIDYNNTKYYLKVVELKPANAISIIEADVSVDFAPPMDSKE 203

Functions at a post-ubiquitation step in the ubiquitin fusion degradation (UFD) pathway.

Dictyostelium discoideum (taxid: 44689)

>sp|Q9VTF9|UFD1_DROME Ubiquitin fusion degradation protein 1 homolog OS=Drosophila melanogaster GN=Ufd1-like PE=2 SV=1

 Score =  182 bits (462), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 90/184 (48%), Positives = 122/184 (66%), Gaps = 4/184 (2%)

Query: 13  FEKHYHCYSLSHVAKPQH---EPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTH 69
           F  +Y C+S+S +   +    E G KIIMP SA D L    V YPM+F+L N+   +++H
Sbjct: 17  FHANYKCFSVSMLPGNERTDVEKGGKIIMPPSALDTLTRLNVEYPMLFKLTNVKKSRSSH 76

Query: 70  CGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNP 129
            GV+EF ADEG  YLP+WMM+N+ L E +++ + +VSL  AT+ K QPH+  FLD ++NP
Sbjct: 77  AGVLEFVADEGKCYLPHWMMENLLLGEGDILNIESVSLPVATFSKFQPHSTDFLD-ITNP 135

Query: 130 RAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYK 189
           +AVLE  LR F+CLT GD I I +N+  Y + VLETKP NAVSI E D  V+F  P+ YK
Sbjct: 136 KAVLENALRNFACLTRGDVIAIKYNKKVYELCVLETKPGNAVSIIECDMNVEFEAPVGYK 195

Query: 190 EPDE 193
           +  E
Sbjct: 196 DHSE 199

Functions at a post-ubiquitation step in the ubiquitin fusion degradation (UFD) pathway.

Drosophila melanogaster (taxid: 7227)

>sp|O42915|UFD1_SCHPO Ubiquitin fusion degradation protein 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=ufd1 PE=2 SV=4

 Score =  163 bits (412), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 80/188 (42%), Positives = 120/188 (63%), Gaps = 7/188 (3%)

Query: 13  FEKHYHCYSLSHVA---KPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTH 69
           F+  Y CY ++ +    +P    G K+I+P SA ++L+   V YPM+F+  N ++ K TH
Sbjct: 32  FDTRYRCYPVAMIPGEERPNVNYGGKVILPPSALEKLSRLNVSYPMLFDFENEAAEKKTH 91

Query: 70  CGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNP 129
            GV+EF A+EG +YLP WMM  + L+  +LVRV N  +A+ +Y+KLQP +  FLD +++ 
Sbjct: 92  GGVLEFIAEEGRVYLPYWMMTTLSLEPGDLVRVINTDIAQGSYVKLQPQSVNFLD-ITDH 150

Query: 130 RAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNA---VSITETDCEVDFAPPL 186
           RAVLE  LR FS LT  D   I++N+  Y I V++ +P ++   VS+ ETD  VDF PP+
Sbjct: 151 RAVLENALRNFSTLTKSDIFEILYNDQVYQIKVIDVQPDDSRHVVSVVETDLVVDFDPPI 210

Query: 187 DYKEPDEK 194
            Y+E  +K
Sbjct: 211 GYEESLQK 218

Functions at a post-ubiquitation step in the ubiquitin fusion degradation (UFD) pathway. It is required for vegetative growth.

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (taxid: 284812)

>sp|P53044|UFD1_YEAST Ubiquitin fusion degradation protein 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=UFD1 PE=1 SV=1

 Score =  160 bits (404), Expect = 1e-38,   Method: Compositional matrix adjust.
 Identities = 77/193 (39%), Positives = 118/193 (61%), Gaps = 8/193 (4%)

Query: 12  CFEKHYHCYSLS----HVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKT 67
            FE+ + CY ++     + K     G KI +P SA  +L+   + YPM+F+L    +G+ 
Sbjct: 20  TFEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANETGRV 79

Query: 68  THCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELS 127
           TH GV+EF A+EG +YLP WMM+ + +Q   L+++++  +    ++KL+P +  FLD +S
Sbjct: 80  THGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFLD-IS 138

Query: 128 NPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKP---SNAVSITETDCEVDFAP 184
           +P+AVLE +LR FS LT  D I I +N   + I +LE KP   S ++ + ETD   DFAP
Sbjct: 139 DPKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSICVIETDLVTDFAP 198

Query: 185 PLDYKEPDEKLVK 197
           P+ Y EPD K +K
Sbjct: 199 PVGYVEPDYKALK 211

Functions at a post-ubiquitation step in the ubiquitin fusion degradation (UFD) pathway. Has a role in the endoplasmic reticulum-associated degradation (ERAD) pathway. Required for the proteasome-dependent processing/activation of MGA2 and SPT23 transcription factors leading to the subsequent expression of OLE1. Has an additional role in the turnover of OLE1 where it targets ubiquitinated OLE1 and other proteins to the ERAD.

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (taxid: 559292)

>sp|Q19584|UFD1_CAEEL Ubiquitin fusion degradation protein 1 homolog OS=Caenorhabditis elegans GN=ufd-1 PE=2 SV=1

 Score =  139 bits (350), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 77/210 (36%), Positives = 116/210 (55%), Gaps = 5/210 (2%)

Query: 33  GDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWMMDNM 92
           G KI++P SA + L    +  PM+F+L N++  + THCGV+EF+A EG   LP WMM  +
Sbjct: 47  GGKILLPSSALNLLMQYNIPMPMLFKLTNMAVQRVTHCGVLEFSAPEGQAILPLWMMQQL 106

Query: 93  KLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIM 152
            L + + +R+ + +L KAT+ KL+P +  FL+ ++NP+AVLE  LRK++CLT  D I   
Sbjct: 107 GLDDGDTIRIESATLPKATFAKLKPMSLEFLN-ITNPKAVLEVELRKYACLTKNDRIPTS 165

Query: 153 HNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKEPDEKL---VKRKVPFP-SQVEE 208
           +        V++ KP+N+V I E D  +DF PP  Y E   ++   V  K P P +    
Sbjct: 166 YAGQTLEFLVVDLKPANSVCIIECDVNLDFDPPEGYVEQPRQVTPAVTAKPPAPDASAFI 225

Query: 209 QSKQQPQAVKEEANNKFKAFTGKGKLLGFK 238
            + Q+         N    F G G+ L  K
Sbjct: 226 GAGQKAGGSGGTGQNATSVFGGAGRRLDGK 255

Functions at a post-ubiquitation step in the ubiquitin fusion degradation (UFD) pathway.

Caenorhabditis elegans (taxid: 6239)

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	238
449461623	322	PREDICTED: ubiquitin fusion degradation	0.915	0.677	0.605	1e-73
357521303	320	Ubiquitin fusion degradation protein [Me	0.924	0.687	0.574	8e-72
449464840	321	PREDICTED: ubiquitin fusion degradation	0.924	0.685	0.587	1e-71
449526164	321	PREDICTED: ubiquitin fusion degradation	0.924	0.685	0.587	1e-71
224103317	323	predicted protein [Populus trichocarpa]	0.924	0.681	0.578	7e-71
118488238	324	unknown [Populus trichocarpa]	0.924	0.679	0.578	8e-71
118485222	314	unknown [Populus trichocarpa]	0.945	0.716	0.548	1e-70
168052703	322	predicted protein [Physcomitrella patens	0.924	0.683	0.575	3e-70
18399646	319	ubiquitin fusion degradation 1 [Arabidop	0.907	0.677	0.564	2e-69
356557947	318	PREDICTED: ubiquitin fusion degradation	0.945	0.707	0.549	3e-69

>gi|449461623|ref|XP_004148541.1| PREDICTED: ubiquitin fusion degradation protein 1 homolog [Cucumis sativus] gi|449520152|ref|XP_004167098.1| PREDICTED: ubiquitin fusion degradation protein 1 homolog [Cucumis sativus]

 Score =  281 bits (719), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 138/228 (60%), Positives = 170/228 (74%), Gaps = 10/228 (4%)

Query: 11  TCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHC 70
           T FE+ Y C+S S + KP  E GD+IIMP SA DRLA  ++ YPM+FEL N +  + +HC
Sbjct: 11  TSFEQSYQCFSTSFIDKPHLETGDRIIMPPSALDRLASLQIDYPMLFELRNDAVERVSHC 70

Query: 71  GVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPR 130
           GV+EF A+EG IY+P WMM+NM LQE +LVRV NV+L K TY+KLQPHTK FLD +SNP+
Sbjct: 71  GVLEFVAEEGMIYMPYWMMENMVLQEGDLVRVKNVTLPKGTYVKLQPHTKDFLD-ISNPK 129

Query: 131 AVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKE 190
           A+LE  LR FSCLTTGD+IM+ +N  KYYID++ETKPSNA+SI ETDCEVDFAPPLDYKE
Sbjct: 130 AILETTLRNFSCLTTGDSIMVAYNNKKYYIDIVETKPSNAISIIETDCEVDFAPPLDYKE 189

Query: 191 PDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK 238
           P EKLV      P++ +EQ  + P +   EA  KF AFTG G+ L  K
Sbjct: 190 P-EKLVA-----PTKGKEQVAEAPDS---EAEPKFSAFTGTGRRLDGK 228

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357521303|ref|XP_003630940.1| Ubiquitin fusion degradation protein [Medicago truncatula] gi|355524962|gb|AET05416.1| Ubiquitin fusion degradation protein [Medicago truncatula]

 Score =  275 bits (704), Expect = 8e-72,   Method: Compositional matrix adjust.
 Identities = 131/228 (57%), Positives = 163/228 (71%), Gaps = 8/228 (3%)

Query: 11  TCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHC 70
           T FE+ Y CY  S + KPQ E GDKIIMP SA DRLA   + YPM+FEL N ++ + +HC
Sbjct: 11  TSFEQTYRCYPASFIEKPQLESGDKIIMPPSALDRLASLHIDYPMLFELRNAAAERVSHC 70

Query: 71  GVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPR 130
           GV+EF A+EG IY+P WMM+NM LQE ++VRV NV+L K TY+KLQPHTK FLD +SNP+
Sbjct: 71  GVLEFIAEEGMIYMPYWMMENMLLQEGDVVRVKNVTLPKGTYVKLQPHTKDFLD-ISNPK 129

Query: 131 AVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKE 190
           A+LE  LR FSCLTTGD+IM+ +N  KYYID++E+KP+NA+SI ETDCEVDFAPPLDYKE
Sbjct: 130 AILETTLRNFSCLTTGDSIMVAYNNKKYYIDIVESKPANAISIIETDCEVDFAPPLDYKE 189

Query: 191 PDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK 238
           P+  +  R      +  E  K+ P     E   KF  FTG G+ L  K
Sbjct: 190 PERPVAPRSA---GKAPEADKEAPA----ETEPKFNPFTGSGRRLDGK 230

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449464840|ref|XP_004150137.1| PREDICTED: ubiquitin fusion degradation protein 1 homolog [Cucumis sativus]

 Score =  275 bits (703), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 134/228 (58%), Positives = 164/228 (71%), Gaps = 8/228 (3%)

Query: 11  TCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHC 70
           T FE+ Y CY  S + KPQ E GDKIIMP SA DRLA   + YPM+FEL N  + + +HC
Sbjct: 11  TSFEQTYRCYPASFIEKPQLETGDKIIMPPSALDRLASLHIDYPMLFELRNDVTERLSHC 70

Query: 71  GVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPR 130
           GV+EF A+EG IY+P WMM+NM LQE ++VRV NV+L K TY+KLQPHTK FLD +SNP+
Sbjct: 71  GVLEFIAEEGMIYMPYWMMENMLLQEGDVVRVKNVTLPKGTYVKLQPHTKDFLD-ISNPK 129

Query: 131 AVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKE 190
           A+LE  LR FSCLTTGD+IM+ +N  KYYID++ETKPSNA+SI ETDCEVDFAPPLDYKE
Sbjct: 130 AILETTLRNFSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPPLDYKE 189

Query: 191 PDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK 238
           P++       P PS    ++  Q +    EA  KF  FTG G+ L  K
Sbjct: 190 PEK-------PVPSLPTGKAPVQDEEPPAEAEPKFNPFTGAGRRLDGK 230

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449526164|ref|XP_004170084.1| PREDICTED: ubiquitin fusion degradation protein 1 homolog [Cucumis sativus]

 Score =  275 bits (703), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 134/228 (58%), Positives = 164/228 (71%), Gaps = 8/228 (3%)

Query: 11  TCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHC 70
           T FE+ Y CY  S + KPQ E GDKIIMP SA DRLA   + YPM+FEL N  + + +HC
Sbjct: 11  TSFEQTYRCYPASFIEKPQLETGDKIIMPPSALDRLASLHIDYPMLFELRNDVTERLSHC 70

Query: 71  GVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPR 130
           GV+EF A+EG IY+P WMM+NM LQE ++VRV NV+L K TY+KLQPHTK FLD +SNP+
Sbjct: 71  GVLEFIAEEGMIYMPYWMMENMLLQEGDVVRVKNVTLPKGTYVKLQPHTKDFLD-ISNPK 129

Query: 131 AVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKE 190
           A+LE  LR FSCLTTGD+IM+ +N  KYYID++ETKPSNA+SI ETDCEVDFAPPLDYKE
Sbjct: 130 AILETTLRNFSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPPLDYKE 189

Query: 191 PDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK 238
           P++       P PS    ++  Q +    EA  KF  FTG G+ L  K
Sbjct: 190 PEK-------PVPSLPTGKAPVQDEEPPAEAEPKFNPFTGAGRRLDGK 230

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224103317|ref|XP_002313007.1| predicted protein [Populus trichocarpa] gi|222849415|gb|EEE86962.1| predicted protein [Populus trichocarpa]

 Score =  272 bits (696), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 132/228 (57%), Positives = 166/228 (72%), Gaps = 8/228 (3%)

Query: 11  TCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHC 70
           T FE+ Y CY  S + KPQ E GDKIIMP SA DRLA   + YPM+FEL N ++ + +HC
Sbjct: 11  TSFEQTYRCYPASFIEKPQIESGDKIIMPPSALDRLASLHIDYPMLFELQNDAAERVSHC 70

Query: 71  GVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPR 130
           GV+EF A+EG IY+P WMM+N+ LQE + VRV NV+L K  Y+KLQPHTK FLD +SNP+
Sbjct: 71  GVLEFIAEEGMIYMPYWMMENLLLQEGDTVRVKNVTLPKGKYVKLQPHTKDFLD-ISNPK 129

Query: 131 AVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKE 190
           A+LE  LR +SCLTTGD+IM+ +N  KYYID++ETKPSNA+SI ETDCEVDFAPPLDYKE
Sbjct: 130 AILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPPLDYKE 189

Query: 191 PDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK 238
           P++ +    VP PS+   Q+++ P     E   KF  FTG G+ L  K
Sbjct: 190 PEKPVA--SVP-PSKATSQAEEVPA----ETEPKFNPFTGAGRRLDGK 230

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118488238|gb|ABK95938.1| unknown [Populus trichocarpa]

 Score =  272 bits (696), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 132/228 (57%), Positives = 166/228 (72%), Gaps = 8/228 (3%)

Query: 11  TCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHC 70
           T FE+ Y CY  S + KPQ E GDKIIMP SA DRLA   + YPM+FEL N ++ + +HC
Sbjct: 12  TSFEQTYRCYPASFIEKPQIESGDKIIMPPSALDRLASLHIDYPMLFELQNDAAERVSHC 71

Query: 71  GVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPR 130
           GV+EF A+EG IY+P WMM+N+ LQE + VRV NV+L K  Y+KLQPHTK FLD +SNP+
Sbjct: 72  GVLEFIAEEGMIYMPYWMMENLLLQEGDTVRVKNVTLPKGKYVKLQPHTKDFLD-ISNPK 130

Query: 131 AVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKE 190
           A+LE  LR +SCLTTGD+IM+ +N  KYYID++ETKPSNA+SI ETDCEVDFAPPLDYKE
Sbjct: 131 AILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPPLDYKE 190

Query: 191 PDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK 238
           P++ +    VP PS+   Q+++ P     E   KF  FTG G+ L  K
Sbjct: 191 PEKPVA--SVP-PSKATSQAEEVPA----ETEPKFNPFTGAGRRLDGK 231

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118485222|gb|ABK94471.1| unknown [Populus trichocarpa]

 Score =  271 bits (693), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 130/237 (54%), Positives = 170/237 (71%), Gaps = 12/237 (5%)

Query: 4   NKRDEYYTCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLS 63
           +++D + + FE+ Y CY +S + K   E GDKIIMP SA DRLA   + YPM+FEL N S
Sbjct: 2   DRQDHHSSSFEQSYRCYPVSFIDKAHLEKGDKIIMPPSALDRLATLHIDYPMLFELHNPS 61

Query: 64  SGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFL 123
           +G+T+HCGV+EF ADEG IYLP WMM+NM LQE ++V++ N SL K T++KLQPHTK FL
Sbjct: 62  AGRTSHCGVLEFIADEGMIYLPYWMMENMLLQEGDIVQLRNTSLEKGTFVKLQPHTKDFL 121

Query: 124 DELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFA 183
           D +SNP+A+LE  LR +SCLTTGDTIM+ +N  KYYID++E KPS+A+SI ETDCEVDFA
Sbjct: 122 D-ISNPKAILETSLRNYSCLTTGDTIMVAYNNKKYYIDIVEAKPSSAISIIETDCEVDFA 180

Query: 184 PPLDYKEPDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANN--KFKAFTGKGKLLGFK 238
           PPLDYKEP++         P  +   +K  P+ ++E A    +F AFTG  + L  K
Sbjct: 181 PPLDYKEPEK---------PKSIPRSNKIPPEGMEEPAAKMPRFSAFTGSARRLDGK 228

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|168052703|ref|XP_001778779.1| predicted protein [Physcomitrella patens subsp. patens] gi|162669785|gb|EDQ56365.1| predicted protein [Physcomitrella patens subsp. patens]

 Score =  270 bits (691), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 130/226 (57%), Positives = 161/226 (71%), Gaps = 6/226 (2%)

Query: 13  FEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGV 72
           FE++Y CYS S + KP  E GDK++MP SA DRLA   + YPM+FE+ N S+ +T+HCGV
Sbjct: 15  FEQNYRCYSASFIDKPHLENGDKVVMPPSALDRLASLRIDYPMLFEVHNPSTLRTSHCGV 74

Query: 73  VEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAV 132
           +EF A+EG IY+P WMM NM LQE ++VRV + +L K T++KLQPHTK FLD +SNP+AV
Sbjct: 75  LEFVAEEGMIYMPYWMMQNMLLQEGDIVRVKSATLPKGTFVKLQPHTKDFLD-ISNPKAV 133

Query: 133 LEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKEPD 192
           LE  LR FSCLT GD IM+ +N  KYYID++E+KP+NA+SI ETDCEVDFAPPLDYKEP+
Sbjct: 134 LETTLRNFSCLTIGDNIMVAYNNKKYYIDIIESKPANAISIIETDCEVDFAPPLDYKEPE 193

Query: 193 EKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK 238
                R  P P  V  QS Q      E    KF AFTG G+ L  K
Sbjct: 194 -----RVTPPPVSVPAQSSQDATPPPEPEEPKFSAFTGTGRRLDGK 234

Source: Physcomitrella patens subsp. patens

Species: Physcomitrella patens

Genus: Physcomitrella

Family: Funariaceae

Order: Funariales

Class: Bryopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|18399646|ref|NP_565504.1| ubiquitin fusion degradation 1 [Arabidopsis thaliana] gi|79322611|ref|NP_001031384.1| ubiquitin fusion degradation 1 [Arabidopsis thaliana] gi|20197912|gb|AAD23675.2| putative ubiquitin fusion-degradation protein [Arabidopsis thaliana] gi|110741145|dbj|BAE98665.1| putative ubiquitin fusion-degradation protein [Arabidopsis thaliana] gi|111609940|gb|ABH11520.1| UFD1a [synthetic construct] gi|193885163|gb|ACF28395.1| At2g21270 [Arabidopsis thaliana] gi|330252058|gb|AEC07152.1| ubiquitin fusion degradation 1 [Arabidopsis thaliana] gi|330252059|gb|AEC07153.1| ubiquitin fusion degradation 1 [Arabidopsis thaliana]

 Score =  268 bits (684), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 127/225 (56%), Positives = 158/225 (70%), Gaps = 9/225 (4%)

Query: 11  TCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHC 70
           T FE+ Y CY  S + KPQ E GDKIIMP SA DRLA   + YPM+FEL N    + THC
Sbjct: 11  TTFEQSYRCYPASFIDKPQLESGDKIIMPPSALDRLASLHIDYPMLFELRNAGIERVTHC 70

Query: 71  GVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPR 130
           GV+EF A+EG IY+P WMM N+ LQE ++VRV NV+L K TY+KLQPHT  FLD +SNP+
Sbjct: 71  GVLEFIAEEGMIYMPYWMMQNLLLQEGDIVRVRNVTLPKGTYVKLQPHTTDFLD-ISNPK 129

Query: 131 AVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKE 190
           A+LE  LR +SCLT+GD+IM+ +N  KY+ID++ETKP+NA+SI ETDCEVDFAPPLDYKE
Sbjct: 130 AILETALRNYSCLTSGDSIMVPYNNKKYFIDIVETKPANAISIIETDCEVDFAPPLDYKE 189

Query: 191 PDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLL 235
           P+          P++ EE        V +E   KF  FTG G+ L
Sbjct: 190 PERPTAPSAAKGPAKAEE--------VVDEPEPKFNPFTGSGRRL 226

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356557947|ref|XP_003547271.1| PREDICTED: ubiquitin fusion degradation protein 1 homolog [Glycine max]

 Score =  267 bits (683), Expect = 3e-69,   Method: Compositional matrix adjust.
 Identities = 128/233 (54%), Positives = 166/233 (71%), Gaps = 8/233 (3%)

Query: 6   RDEYYTCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSG 65
           RD+ +  FE+ Y CY +S + KP  E GDKIIMP SA DRLA   + YPM+F++ N S+ 
Sbjct: 5   RDDRFATFEQFYRCYPVSFIEKPDLEKGDKIIMPPSALDRLASLHIEYPMLFQIKNPSAE 64

Query: 66  KTTHCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDE 125
           + THCGV+EF +DEG IY+P WMM+NM LQE ++V+V N +LAK TY+KLQPHTK FLD 
Sbjct: 65  RVTHCGVLEFVSDEGIIYIPYWMMENMLLQEGDIVKVKNTNLAKGTYVKLQPHTKDFLD- 123

Query: 126 LSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPP 185
           +SNP+A+LE  LR +SCLTTGDTIM+ +N  KYYID++ETKPS AVSI ETDCEVDFAPP
Sbjct: 124 ISNPKAILETTLRSYSCLTTGDTIMVPYNNKKYYIDIVETKPSPAVSIIETDCEVDFAPP 183

Query: 186 LDYKEPDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK 238
           LDYKEP+++   + V F  +  +   + P  +      +   FTG G+ L  K
Sbjct: 184 LDYKEPEKQA--KPVVFDRKRPKVEDEPPTKIA-----RLTPFTGSGRRLDGK 229

Source: Glycine max

Species: Glycine max

Genus: Glycine

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	238
TAIR|locus:2050054	340	UFD1 "AT2G21270" [Arabidopsis	0.907	0.635	0.564	3.2e-65
TAIR|locus:2120247	315	AT4G38930 "AT4G38930" [Arabido	0.911	0.688	0.564	5.2e-65
TAIR|locus:2066122	312	AT2G29070 [Arabidopsis thalian	0.915	0.698	0.578	1.1e-64
MGI|MGI:109353	307	Ufd1l "ubiquitin fusion degrad	0.907	0.703	0.482	2e-51
UNIPROTKB|J9NYF2	307	UFD1L "Uncharacterized protein	0.907	0.703	0.482	2e-51
UNIPROTKB|Q92890	307	UFD1L "Ubiquitin fusion degrad	0.907	0.703	0.482	2e-51
UNIPROTKB|F1RK61	307	UFD1L "Uncharacterized protein	0.907	0.703	0.473	2.6e-51
ZFIN|ZDB-GENE-040718-150	308	ufd1l "ubiquitin fusion degrad	0.911	0.704	0.491	6.5e-51
DICTYBASE|DDB_G0271122	330	ufd1 "ubiquitin fusion degrada	0.743	0.536	0.505	2e-49
UNIPROTKB|F1PAI5	310	UFD1L "Uncharacterized protein	0.907	0.696	0.474	3.3e-49

TAIR|locus:2050054 UFD1 "AT2G21270" [Arabidopsis thaliana (taxid:3702)]

 Score = 664 (238.8 bits), Expect = 3.2e-65, P = 3.2e-65
 Identities = 127/225 (56%), Positives = 158/225 (70%)

Query:    11 TCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHC 70
             T FE+ Y CY  S + KPQ E GDKIIMP SA DRLA   + YPM+FEL N    + THC
Sbjct:    32 TTFEQSYRCYPASFIDKPQLESGDKIIMPPSALDRLASLHIDYPMLFELRNAGIERVTHC 91

Query:    71 GVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPR 130
             GV+EF A+EG IY+P WMM N+ LQE ++VRV NV+L K TY+KLQPHT  FLD +SNP+
Sbjct:    92 GVLEFIAEEGMIYMPYWMMQNLLLQEGDIVRVRNVTLPKGTYVKLQPHTTDFLD-ISNPK 150

Query:   131 AVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKE 190
             A+LE  LR +SCLT+GD+IM+ +N  KY+ID++ETKP+NA+SI ETDCEVDFAPPLDYKE
Sbjct:   151 AILETALRNYSCLTSGDSIMVPYNNKKYFIDIVETKPANAISIIETDCEVDFAPPLDYKE 210

Query:   191 PDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLL 235
             P+          P++ EE        V +E   KF  FTG G+ L
Sbjct:   211 PERPTAPSAAKGPAKAEE--------VVDEPEPKFNPFTGSGRRL 247

GO:0003674 "molecular_function" evidence=ND

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM

GO:0005829 "cytosol" evidence=IDA

TAIR|locus:2120247 AT4G38930 "AT4G38930" [Arabidopsis thaliana (taxid:3702)]

 Score = 662 (238.1 bits), Expect = 5.2e-65, P = 5.2e-65
 Identities = 127/225 (56%), Positives = 162/225 (72%)

Query:    11 TCFEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHC 70
             T FE+ Y CY  S + KPQ E GDKIIMP SA DRLA  ++ YPM+FEL N S+   +HC
Sbjct:    11 TTFEQTYRCYPSSFIDKPQIESGDKIIMPPSALDRLASLQIDYPMLFELRNASTDSFSHC 70

Query:    71 GVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPR 130
             GV+EF A+EG IY+P WMM N+ LQE ++VRV NV+L K TY+KLQPHT  FLD ++NP+
Sbjct:    71 GVLEFIAEEGVIYIPYWMMQNLLLQEGDMVRVRNVTLPKGTYVKLQPHTTDFLD-IANPK 129

Query:   131 AVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKE 190
             A+LE  LR +SCLT GD+IM+ +N  KY+ID++E KPSN +SI ETDCEVDFAPPLDYKE
Sbjct:   130 AILETALRNYSCLTVGDSIMVPYNNKKYFIDIVEAKPSNGISIIETDCEVDFAPPLDYKE 189

Query:   191 PDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLL 235
             P+  +     P P++ E ++K+   A   EA  KF  FTG G+ L
Sbjct:   190 PERPVA----PAPAKGEAKAKEVDVA---EAEPKFNPFTGSGRRL 227

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA;ISS

TAIR|locus:2066122 AT2G29070 [Arabidopsis thaliana (taxid:3702)]

 Score = 659 (237.0 bits), Expect = 1.1e-64, P = 1.1e-64
 Identities = 132/228 (57%), Positives = 167/228 (73%)

Query:    13 FEKHYHCYSLSHVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGV 72
             FE+ Y CY ++ + K   E GDKIIMP SA DRLA   + YPM+F+L N+S  KT+HCGV
Sbjct:     8 FEQCYRCYPVTFIDKAHLEKGDKIIMPPSALDRLASLHIEYPMLFQLSNVSVEKTSHCGV 67

Query:    73 VEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAV 132
             +EFTADEG +YLP WMM NM L+E ++++V N+SL K TY+KLQPHT+ FLD +SNP+A+
Sbjct:    68 LEFTADEGLVYLPYWMMQNMSLEEGDVMQVKNISLVKGTYIKLQPHTQDFLD-ISNPKAI 126

Query:   133 LEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKEPD 192
             LE  LR +SCLTTGDTIM+ +N  +YYI+V+E KPS+AVSI ETDCEVDFAPPLDYKEP+
Sbjct:   127 LETTLRSYSCLTTGDTIMVPYNNKQYYINVVEAKPSSAVSIIETDCEVDFAPPLDYKEPE 186

Query:   193 --EKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK 238
               +KL       P QV+E+  ++P A K     KF  FTG GK L  K
Sbjct:   187 KPQKLTPSNKR-PLQVKEE--EEP-ASKVP---KFTPFTGSGKRLDGK 227

GO:0005634 "nucleus" evidence=ISM

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA;ISS

GO:0009507 "chloroplast" evidence=ISM

MGI|MGI:109353 Ufd1l "ubiquitin fusion degradation 1 like" [Mus musculus (taxid:10090)]

 Score = 507 (183.5 bits), Expect = 2.0e-51, Sum P(2) = 2.0e-51
 Identities = 111/230 (48%), Positives = 142/230 (61%)

Query:    13 FEKHYHCYSLSHVAKPQH----EPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTT 68
             F   Y C+S+S +A P      E G KIIMP SA D+L+   + YPM+F+L N +S + T
Sbjct:    19 FSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMT 78

Query:    69 HCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSN 128
             HCGV+EF ADEG  YLP+WMM N+ L+E  LV+V +V+L  ATY K QP +  FLD ++N
Sbjct:    79 HCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLD-ITN 137

Query:   129 PRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDY 188
             P+AVLE  LR F+CLTTGD I I +NE  Y + V+ETKP  AVSI E D  VDF  PL Y
Sbjct:   138 PKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDFDAPLGY 197

Query:   189 KEPDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK 238
             KEP+     R V     +E ++     A   E    F+AF+G G  L  K
Sbjct:   198 KEPE-----RPVQHEESIEGEADHSGYA--GEVG--FRAFSGSGNRLDGK 238

GO:0005102 "receptor binding" evidence=ISO

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=IDA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0032403 "protein complex binding" evidence=ISO

UNIPROTKB|J9NYF2 UFD1L "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 506 (183.2 bits), Expect = 2.0e-51, Sum P(2) = 2.0e-51
 Identities = 111/230 (48%), Positives = 143/230 (62%)

Query:    13 FEKHYHCYSLSHVAKPQH----EPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTT 68
             F   Y C+S+S +A P      E G KIIMP SA D+L+   + YPM+F+L N +S + T
Sbjct:    19 FSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMT 78

Query:    69 HCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSN 128
             HCGV+EF ADEG  YLP+WMM N+ L+E  LV+V +V+L  ATY K QP +  FLD ++N
Sbjct:    79 HCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLD-ITN 137

Query:   129 PRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDY 188
             P+AVLE  LR F+CLTTGD I I +NE  Y + V+ETKP  AVSI E D  VDF  PL Y
Sbjct:   138 PKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDFDAPLGY 197

Query:   189 KEPDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK 238
             KEP+     R+V    Q EE ++ +           F+AF+G G  L  K
Sbjct:   198 KEPE-----RQV----QHEESAEGEADHSGYAGELGFRAFSGSGNRLDGK 238

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

UNIPROTKB|Q92890 UFD1L "Ubiquitin fusion degradation protein 1 homolog" [Homo sapiens (taxid:9606)]

 Score = 506 (183.2 bits), Expect = 2.0e-51, Sum P(2) = 2.0e-51
 Identities = 111/230 (48%), Positives = 143/230 (62%)

Query:    13 FEKHYHCYSLSHVAKPQH----EPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTT 68
             F   Y C+S+S +A P      E G KIIMP SA D+L+   + YPM+F+L N +S + T
Sbjct:    19 FSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMT 78

Query:    69 HCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSN 128
             HCGV+EF ADEG  YLP+WMM N+ L+E  LV+V +V+L  ATY K QP +  FLD ++N
Sbjct:    79 HCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLD-ITN 137

Query:   129 PRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDY 188
             P+AVLE  LR F+CLTTGD I I +NE  Y + V+ETKP  AVSI E D  VDF  PL Y
Sbjct:   138 PKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDFDAPLGY 197

Query:   189 KEPDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK 238
             KEP+     R+V    Q EE ++ +           F+AF+G G  L  K
Sbjct:   198 KEPE-----RQV----QHEESTEGEADHSGYAGELGFRAFSGSGNRLDGK 238

GO:0005102 "receptor binding" evidence=IEA

GO:0032403 "protein complex binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0001501 "skeletal system development" evidence=TAS

GO:0004843 "ubiquitin-specific protease activity" evidence=TAS

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=TAS

UNIPROTKB|F1RK61 UFD1L "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 505 (182.8 bits), Expect = 2.6e-51, Sum P(2) = 2.6e-51
 Identities = 109/230 (47%), Positives = 142/230 (61%)

Query:    13 FEKHYHCYSLSHVAKPQH----EPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTT 68
             F   Y C+S+S +A P      E G KIIMP SA D+L+   + YPM+F+L N +S + T
Sbjct:    19 FSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMT 78

Query:    69 HCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSN 128
             HCGV+EF ADEG  YLP+WMM N+ L+E  LV+V +V+L  ATY K QP +  FLD ++N
Sbjct:    79 HCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLD-ITN 137

Query:   129 PRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDY 188
             P+AVLE  LR F+CLTTGD I I +NE  Y + V+ETKP  AVSI E D  VDF  PL Y
Sbjct:   138 PKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDFDAPLGY 197

Query:   189 KEPDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK 238
             KEP+ ++         Q EE ++ +           F+AF+G G  L  K
Sbjct:   198 KEPERQI---------QHEESAEGEADHGGYAGELGFRAFSGSGNRLDGK 238

GO:0005737 "cytoplasm" evidence=IEA

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

ZFIN|ZDB-GENE-040718-150 ufd1l "ubiquitin fusion degradation 1-like" [Danio rerio (taxid:7955)]

 Score = 529 (191.3 bits), Expect = 6.5e-51, P = 6.5e-51
 Identities = 113/230 (49%), Positives = 146/230 (63%)

Query:    13 FEKHYHCYSLSHVAKPQH----EPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTT 68
             F   Y CYS+S +A P      E G KIIMP SA D+L+   + YPM+F+L N +S + T
Sbjct:    19 FSTQYRCYSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMT 78

Query:    69 HCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSN 128
             HCGV+EF ADEGF YLP+WMM N+ L+E  LV+V +V+L  ATY K QP +  FLD ++N
Sbjct:    79 HCGVLEFVADEGFCYLPHWMMQNLLLEEGGLVQVESVNLMVATYSKFQPQSPDFLD-ITN 137

Query:   129 PRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDY 188
             P+AVLE  LR F+CLTTGD I I +NE  Y + V+ETKP  AVSI E D  VDF  PL Y
Sbjct:   138 PKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDFDAPLGY 197

Query:   189 KEPDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK 238
             KEP+     R +  P   EE ++++      + +  F+AFTG G  L  K
Sbjct:   198 KEPE-----RHMQHP---EEPAEEETDPSNYDMDLGFRAFTGSGNRLDGK 239

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0042221 "response to chemical stimulus" evidence=IDA

DICTYBASE|DDB_G0271122 ufd1 "ubiquitin fusion degradation protein UFD1 family protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 488 (176.8 bits), Expect = 2.0e-49, Sum P(2) = 2.0e-49
 Identities = 91/180 (50%), Positives = 128/180 (71%)

Query:    13 FEKHYHCYSLSHVAKPQH--EPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHC 70
             +E+ +  + +S + K +H  E G KI++P SA + L+   + YPM+FE+ N  SGK +HC
Sbjct:    25 YEQKFKAFPISFLPKEKHSLESGGKILLPPSALNALSRLNIQYPMLFEISNPISGKKSHC 84

Query:    71 GVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPR 130
             GV+EF A+EG  YLP WMM N++L+E E + + N +LAK T++K+QP T  F+D +SNP+
Sbjct:    85 GVLEFIAEEGICYLPLWMMQNLQLKEGEFIDIKNATLAKGTFVKIQPRTSNFID-ISNPK 143

Query:   131 AVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPPLDYKE 190
             AVLE  LRKF+ LT  D IMI +N +KYY+ V+E KP+NA+SI E D  VDFAPP+D KE
Sbjct:   144 AVLENSLRKFATLTKDDEIMIDYNNTKYYLKVVELKPANAISIIEADVSVDFAPPMDSKE 203

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA;ISS

GO:0005789 "endoplasmic reticulum membrane" evidence=ISS

GO:0043161 "proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

UNIPROTKB|F1PAI5 UFD1L "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 485 (175.8 bits), Expect = 3.3e-49, Sum P(2) = 3.3e-49
 Identities = 111/234 (47%), Positives = 144/234 (61%)

Query:    13 FEKHYHCYSLSHVAKPQH----EPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTT 68
             F   Y C+S+S +A P      E G KIIMP SA D+L+   + YPM+F+L N +S + T
Sbjct:    18 FSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMT 77

Query:    69 HCGVVEFTADEGFIYLPNW-MMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELS 127
             HCGV+EF ADEG  YLP+W MM N+ L+E  LV+V +V+L  ATY K QP +  FLD ++
Sbjct:    78 HCGVLEFVADEGICYLPHWWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLD-IT 136

Query:   128 NPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDC---EVDFAP 184
             NP+AVLE  LR F+CLTTGD I I +NE  Y + V+ETKP  AVSI E D    +VDF  
Sbjct:   137 NPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNGPKVDFDA 196

Query:   185 PLDYKEPDEKLVKRKVPFPSQVEEQSKQQPQAVKEEANNKFKAFTGKGKLLGFK 238
             PL YKEP+     R+V    Q EE ++ +           F+AF+G G  L  K
Sbjct:   197 PLGYKEPE-----RQV----QHEESAEGEADHSGYAGELGFRAFSGSGNRLDGK 241

GO:0006511 "ubiquitin-dependent protein catabolic process" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

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	238
pfam03152	176	pfam03152, UFD1, Ubiquitin fusion degradation prot	2e-91
COG5140	331	COG5140, UFD1, Ubiquitin fusion-degradation protei	3e-53
PLN03086	567	PLN03086, PLN03086, PRLI-interacting factor K; Pro	3e-31

>gnl|CDD|217391 pfam03152, UFD1, Ubiquitin fusion degradation protein UFD1

 Score =  265 bits (681), Expect = 2e-91
 Identities = 99/177 (55%), Positives = 127/177 (71%), Gaps = 4/177 (2%)

Query: 12  CFEKHYHCYSLSHVAK---PQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTT 68
            FE+ Y CY +S +        E G KII+P SA DRL+   + YPM+FEL N ++ K T
Sbjct: 1   RFEQTYRCYPVSFLPGNEREDIEYGGKIILPPSALDRLSRLNIEYPMLFELQNPANKKVT 60

Query: 69  HCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSN 128
           HCGV+EF A+EG IYLP WMM N+ L+E +LV++T+ SL K T++KLQP +  FLD +SN
Sbjct: 61  HCGVLEFIAEEGTIYLPYWMMQNLGLEEGDLVQITSASLPKGTFVKLQPQSTDFLD-ISN 119

Query: 129 PRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFAPP 185
           P+AVLE  LR FS LT GDTI+I +N+  Y ID+LE KP+NA+SI ETD EVDFAPP
Sbjct: 120 PKAVLENALRNFSTLTKGDTIVINYNDKIYEIDILEVKPANAISIIETDLEVDFAPP 176

Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified. This family includes UFD1, a 40kD protein that is essential for vegetative cell viability. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterized by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation. Length = 176

>gnl|CDD|227469 COG5140, UFD1, Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]

 Score =  174 bits (442), Expect = 3e-53
 Identities = 70/194 (36%), Positives = 105/194 (54%), Gaps = 7/194 (3%)

Query: 13  FEKHYHCYSLSHV---AKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTH 69
           F +   CY  +      +     G K+I+P SA  +L+   + YPM+FE+ +      TH
Sbjct: 22  FGEKPRCYPRAMKFDGCRQNANFGGKVILPPSALVKLSSLNIQYPMLFEISHSDGIYRTH 81

Query: 70  CGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNP 129
            GV+EF A+EG +YLP+WMM  + ++  +LV +         ++KL P +  FLD + +P
Sbjct: 82  GGVLEFIAEEGRVYLPSWMMQTLSMEPGDLVVLRYTDFPLGKFVKLIPQSVDFLD-IEDP 140

Query: 130 RAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKP---SNAVSITETDCEVDFAPPL 186
           +AVLE  LR FS LT GD I I +N+    I      P   +NA+ + ETD  VDF PP+
Sbjct: 141 KAVLENCLRNFSTLTEGDEIEIQYNDEVGSIKFTVVHPEPSANAIYVVETDLVVDFLPPI 200

Query: 187 DYKEPDEKLVKRKV 200
            YKE  ++  +R  
Sbjct: 201 GYKEKAQQDKERNS 214

Length = 331

>gnl|CDD|178635 PLN03086, PLN03086, PRLI-interacting factor K; Provisional

 Score =  120 bits (302), Expect = 3e-31
 Identities = 69/184 (37%), Positives = 96/184 (52%), Gaps = 21/184 (11%)

Query: 21  SLSHV--AKPQHEPGDKIIMPQSAFDRLAHT---EVGYPMMFELCNL-----------SS 64
             S +  A      GDKI +P S F  L+     + G P+ F L  +            S
Sbjct: 77  VFSRIFEAVSFQGNGDKIKLPPSCFTELSDQGAFDKG-PLYFRLSVVHQEGSGEMKDTDS 135

Query: 65  GKTTHCGVVEFTADEGFIYLPNWMMDNM---KLQEYELVRVTNVSLAKATYMKLQPHTKG 121
            KTTH GV+EFTA+EG + LP  +  N+      +  LV V  + L K TY KLQP   G
Sbjct: 136 QKTTHSGVLEFTAEEGSVGLPPHVWSNLFPSDPPDVPLVEVRYIWLPKGTYAKLQPDGVG 195

Query: 122 FLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVD 181
           F D L N +AVLE  LR+ + L+  D +++ + +  Y + VLE KP+++VS+ ETD EVD
Sbjct: 196 FSD-LPNHKAVLETALRQHATLSEDDVLVVNYGQLTYKLKVLELKPASSVSVLETDIEVD 254

Query: 182 FAPP 185
              P
Sbjct: 255 IVGP 258

Length = 567

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	238
KOG1816	308	consensus Ubiquitin fusion-degradation protein [Po	100.0
PF03152	176	UFD1: Ubiquitin fusion degradation protein UFD1; I	100.0
COG5140	331	UFD1 Ubiquitin fusion-degradation protein [Posttra	100.0
PLN03086	567	PRLI-interacting factor K; Provisional	100.0
PF02933	64	CDC48_2: Cell division protein 48 (CDC48), domain	96.73
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	96.34
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	95.93
PF09262	80	PEX-1N: Peroxisome biogenesis factor 1, N-terminal	93.59
TIGR01439	43	lp_hng_hel_AbrB looped-hinge helix DNA binding dom	86.38
PF04014	47	Antitoxin-MazE: Antidote-toxin recognition MazE; I	86.35
PF02359	87	CDC48_N: Cell division protein 48 (CDC48), N-termi	82.03
PF07497	78	Rho_RNA_bind: Rho termination factor, RNA-binding	80.6

>KOG1816 consensus Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=4.4e-89  Score=615.93  Aligned_cols=219  Identities=50%  Similarity=0.886  Sum_probs=198.5

Q ss_pred             cceeeEEEeeeecccCC---CCCCCCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeEeCCCcEeccHhH
Q 035839           12 CFEKHYHCYSLSHVAKP---QHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWM   88 (238)
Q Consensus        12 ~f~~~~~~y~~s~~~~~---~~~~gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~A~EG~i~lP~Wm   88 (238)
                      .|+++|||||++|+..+   ++++|||||||||||++|+++||.|||+|+|+|.+..|+||||||||+||||.||||+||
T Consensus        13 ~f~~~yrcy~~~~l~~~~~s~~~~GgKIilPPSaL~~Ls~lnI~yPMlFkLtn~~~~r~THcGVLEF~AeEG~vyLP~WM   92 (308)
T KOG1816|consen   13 QFETSYRCYPVSFLPGPDRSDVNKGGKIILPPSALDRLSSLNITYPMLFKLTNVDVDRVTHCGVLEFTAEEGRVYLPYWM   92 (308)
T ss_pred             ceeeeeEecccccccCccccccccCCeEEeCHHHHHHHHHhcCCCceEEEEeccccceeeeeeEEEEEecCceEEeehHh
Confidence            39999999999999655   999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhcCCCCCCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEECCEEEEEEEEEecCC
Q 035839           89 MDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPS  168 (238)
Q Consensus        89 m~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~~~~y~l~V~e~kP~  168 (238)
                      |++|+|++||+|+|++++||+|||||||||+.+|+| |+|||||||++||||+|||+||+|.|+||++.|+|+|+|+||+
T Consensus        93 mq~L~le~gdlv~i~~v~lpkgtyvKLqP~s~dFLD-ItNpKAvLE~~LRn~acLT~gDvi~i~Yn~k~y~i~V~e~kPa  171 (308)
T KOG1816|consen   93 MQNLLLEEGDLVRIRSVTLPKGTYVKLQPHSVDFLD-ITNPKAVLENALRNYACLTTGDVILINYNEKTYELKVVETKPA  171 (308)
T ss_pred             hhhccCCCCCeEEEEEeeccccceeeeccCCCCccc-cCChHHHHHHHHhhccccccCCEEEEecCCeEEEEEEEEecCC
Confidence            999999999999999999999999999999999999 9999999999999999999999999999999999999999999


Q ss_pred             CceEEEeCceEEEecCCCCCCCCchhhhcccCCCCCcchhhcccCchhh----hhhcCCcccceeeeceecCCC
Q 035839          169 NAVSITETDCEVDFAPPLDYKEPDEKLVKRKVPFPSQVEEQSKQQPQAV----KEEANNKFKAFTGKGKLLGFK  238 (238)
Q Consensus       169 ~aVsIidTDl~VDf~ppl~y~e~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~f~~F~G~G~rldgk  238 (238)
                      +|||||||||+|||+||+||+||+++.+.....       +..++..+.    ...-+++|.+|+|+|+|||||
T Consensus       172 ~aVsIiEtD~~VDF~pP~gyke~~~~~~~~~~~-------k~~~~~v~~~ag~~~~~e~~~~~f~gsg~rLdgK  238 (308)
T KOG1816|consen  172 NAVSIIETDLNVDFDPPLGYKEPERQVAPAEKA-------KGEAEVVGSYAGYKNVIENKVEPFTGSGRRLDGK  238 (308)
T ss_pred             ceeEEEEcceeecccCCcCccCcccccChhhcc-------cccceeeccccccccccccceeeeccccceeccc
Confidence            999999999999999999999999874321110       011111110    011178999999999999998

>PF03152 UFD1: Ubiquitin fusion degradation protein UFD1; InterPro: IPR004854 Post-translational ubiquitin-protein conjugates are recognised for degradation by the ubiquitin fusion degradation (UFD) pathway

Probab=100.00  E-value=2.6e-75  Score=498.70  Aligned_cols=173  Identities=57%  Similarity=0.975  Sum_probs=149.8

Q ss_pred             cceeeEEEeeeecc---cCCCCCCCCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeEeCCCcEeccHhH
Q 035839           12 CFEKHYHCYSLSHV---AKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYLPNWM   88 (238)
Q Consensus        12 ~f~~~~~~y~~s~~---~~~~~~~gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~A~EG~i~lP~Wm   88 (238)
                      +|+++|||||++|+   +++++++||||+||||||++|++++++|||+|+|+|..++++||||||||+|+||+|+||+||
T Consensus         1 ~f~~~~~~~~~~~~~~~~~~~~~~gdKiiLP~s~L~~L~~~~~~~P~~F~i~n~~~~~~th~GVlEFsA~eG~i~lP~wm   80 (176)
T PF03152_consen    1 KFDQTYRCYPVSFLPGADRPELEYGDKIILPPSALDELSRLNIPYPMLFEISNPDNGKRTHCGVLEFSAEEGTIYLPPWM   80 (176)
T ss_dssp             -EEEEEEEEECCCSSTTS-CCCCCTTEEEE-HHHHHHHHHTT--SS-EEEEEETTTTEEEEEEEEEE--CTTEEEE-CHH
T ss_pred             CccceEEEEeEEeecCCCCcccCCCCeEEcCHHHHHHHHhccCCCCEEEEEecCCCCcEEEEEEEEeEcCCCeEEeCccH
Confidence            48999999999999   899999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhcCCCCCCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEECCEEEEEEEEEecCC
Q 035839           89 MDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPS  168 (238)
Q Consensus        89 m~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~~~~y~l~V~e~kP~  168 (238)
                      |++|++++||.|+|++++||||||||||||+.+|++ |+|||+|||++||||+|||+||+|.|+|+++.|+|+|+|+||+
T Consensus        81 m~~L~l~~g~~V~v~~~~LPkgt~vkLqP~~~~F~~-i~n~KavLE~~Lr~ystLT~Gd~I~i~~~~~~y~l~V~e~kP~  159 (176)
T PF03152_consen   81 MQNLGLQEGDIVRVEYVSLPKGTFVKLQPQSSDFLD-ISNPKAVLERALRNYSTLTKGDTISIEYNNKTYELDVVEVKPE  159 (176)
T ss_dssp             HHHHT--TTEEEEEEEEE----SEEEEEESCHHHHC-SS-HHHHHHHHHCC-SEEETTSEEEEECTTEEEEEEEEEECSS
T ss_pred             HhhcCCCCCCEEEEEEeECCCCCEEEEeECCCcccc-ccchHHHHHhhcccCceeecCCEEEEEeCCEEEEEEEEEEcCC
Confidence            999999999999999999999999999999999999 9999999999999999999999999999999999999999999


Q ss_pred             CceEEEeCceEEEecCC
Q 035839          169 NAVSITETDCEVDFAPP  185 (238)
Q Consensus       169 ~aVsIidTDl~VDf~pp  185 (238)
                      +|||||||||+|||+||
T Consensus       160 ~aV~IidTDl~vDf~~P  176 (176)
T PF03152_consen  160 NAVSIIDTDLEVDFEPP  176 (176)
T ss_dssp             SCEE-SSS-SEEEE---
T ss_pred             CEEEEEeCceEEEecCC
Confidence            99999999999999997

Several proteins involved in this pathway have been identified []. This family includes UFD1, a 40kDa protein that is essential for vegetative cell viability []. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterised by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation []. ; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 1ZC1_A 2YUJ_A.

>COG5140 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]

Probab=100.00  E-value=9.6e-68  Score=470.32  Aligned_cols=189  Identities=37%  Similarity=0.657  Sum_probs=181.6

Q ss_pred             CCCcccccceeeEEEeeeecc---cCCCCCCCCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeEeCCCc
Q 035839            5 KRDEYYTCFEKHYHCYSLSHV---AKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGF   81 (238)
Q Consensus         5 ~~~~~~~~f~~~~~~y~~s~~---~~~~~~~gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~A~EG~   81 (238)
                      +++..++.|.+.|||||.+|+   .|++.++|+|||||||||..|++++|.|||+|+|++.+..+.||||||||+|+||.
T Consensus        14 f~n~~~q~F~e~~rcyp~am~~d~~r~n~NfGGKvilPpSaL~kLs~lni~yPmlF~~s~~~~~~~THgGVLEFiaEEGr   93 (331)
T COG5140          14 FLNDLFQLFGEKPRCYPRAMKFDGCRQNANFGGKVILPPSALVKLSSLNIQYPMLFEISHSDGIYRTHGGVLEFIAEEGR   93 (331)
T ss_pred             hhhhhhhhhccCccceeeecccCccccCCCcCceEEcCHHHHHHHHhhccCCceEEEEecccceeEecccEEEEeecCCc
Confidence            456688999999999999997   35778999999999999999999999999999999999999999999999999999


Q ss_pred             EeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEECCEEEEEE
Q 035839           82 IYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYID  161 (238)
Q Consensus        82 i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~~~~y~l~  161 (238)
                      ||||+|||+.|++++||.|+++|.++|.|+||||+|||.+|++ |+||||+||++||||+|||+||+|.|.||++.|.|+
T Consensus        94 VylP~WMm~tLs~epgdlv~~~~td~plG~fVKL~PqSVdFLd-I~dpkavLEn~LRNfstLt~~D~iei~ynd~v~~Ik  172 (331)
T COG5140          94 VYLPSWMMQTLSMEPGDLVVLRYTDFPLGKFVKLIPQSVDFLD-IEDPKAVLENCLRNFSTLTEGDEIEIQYNDEVGSIK  172 (331)
T ss_pred             EeehHHHHHhccCCCCcEEEEEeccccccceEEecccccceEe-ccChHHHHHHHHhhccccccCCEEEEEECCeeeEEE
Confidence            9999999999999999999999999999999999999999999 999999999999999999999999999999999999


Q ss_pred             EEEecCC---CceEEEeCceEEEecCCCCCCCCchh
Q 035839          162 VLETKPS---NAVSITETDCEVDFAPPLDYKEPDEK  194 (238)
Q Consensus       162 V~e~kP~---~aVsIidTDl~VDf~ppl~y~e~~~~  194 (238)
                      +++++|+   +||||||||+.|||+||++|+|+..+
T Consensus       173 ~~~v~pe~S~~~i~vveTDLvvDF~pPiGy~e~~qq  208 (331)
T COG5140         173 FTVVHPEPSANAIYVVETDLVVDFLPPIGYKEKAQQ  208 (331)
T ss_pred             EEEeccCCCcceEEEEecceeeeccCCccccchhhh
Confidence            9999996   89999999999999999999998543

>PLN03086 PRLI-interacting factor K; Provisional

Probab=100.00  E-value=3.6e-60  Score=462.29  Aligned_cols=159  Identities=42%  Similarity=0.613  Sum_probs=152.5

Q ss_pred             CCCCeeeecHHHHHHHHhCCC--CCceEEEEEeC-----------CCCCeEEEEEeeeEeCCCcEeccHhHHhhcCCCC-
Q 035839           31 EPGDKIIMPQSAFDRLAHTEV--GYPMMFELCNL-----------SSGKTTHCGVVEFTADEGFIYLPNWMMDNMKLQE-   96 (238)
Q Consensus        31 ~~gdKIiLP~SaL~~L~~~~i--~~Pm~F~i~n~-----------~~~~~th~GVlEF~A~EG~i~lP~Wmm~~L~l~~-   96 (238)
                      ..||||+||||||++|+++++  .|||+|+|+|.           ..+++||||||||+|+||+||||+|||++|++.+ 
T Consensus        89 ~~GdKI~LPpSaL~~L~~~~~~~~~Pm~F~l~~~~~~~~~~~~~~~~~~~th~GVlEF~A~EG~v~lP~wm~~~L~~~~~  168 (567)
T PLN03086         89 GNGDKIKLPPSCFTELSDQGAFDKGPLYFRLSVVHQEGSGEMKDTDSQKTTHSGVLEFTAEEGSVGLPPHVWSNLFPSDP  168 (567)
T ss_pred             CCCCeEEcCHHHHHHHHhcCCCCCCCeEEEEeccccccccccccccCCcEEEEEEEEEEcCCCeEEcCHHHHhhcCCCCC
Confidence            599999999999999999998  89999999984           3478999999999999999999999999999875 


Q ss_pred             --CCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEECCEEEEEEEEEecCCCceEEE
Q 035839           97 --YELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSIT  174 (238)
Q Consensus        97 --gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~~~~y~l~V~e~kP~~aVsIi  174 (238)
                        |+.|+|++++|||||||||||++.+|++ |+|||||||++||||+|||+||+|.|+|+++.|+|+|+|++|++|||||
T Consensus       169 ~~~~~v~v~~~~Lpkgt~vklqP~~~~f~d-i~npKavLE~~Lr~~stLT~Gd~i~i~~~~~~y~~~V~ev~P~~aVsii  247 (567)
T PLN03086        169 PDVPLVEVRYIWLPKGTYAKLQPDGVGFSD-LPNHKAVLETALRQHATLSEDDVLVVNYGQLTYKLKVLELKPASSVSVL  247 (567)
T ss_pred             CCCCeEEEEEeecCCCCEEEEeeccCCcCC-cccHHHHHHHHhhcCccccCCCEEEEecCCEEEEEEEEEEcCCCeeEEE
Confidence              8899999999999999999999999999 9999999999999999999999999999999999999999999999999


Q ss_pred             eCceEEEecCCCCCCC
Q 035839          175 ETDCEVDFAPPLDYKE  190 (238)
Q Consensus       175 dTDl~VDf~ppl~y~e  190 (238)
                      ||||+|||+||.++.+
T Consensus       248 eTDi~VDf~~p~~~~~  263 (567)
T PLN03086        248 ETDIEVDIVGPDSVSN  263 (567)
T ss_pred             eCceEEEeccCCcchh
Confidence            9999999999999743

>PF02933 CDC48_2: Cell division protein 48 (CDC48), domain 2; InterPro: IPR004201 This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains

Probab=96.73  E-value=0.0091  Score=42.78  Aligned_cols=46  Identities=33%  Similarity=0.405  Sum_probs=35.1

Q ss_pred             HhhccCcccccCCEEEEEECCEEEEEEEEEecCCCceEEE-eCceEEE
Q 035839          135 AILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSIT-ETDCEVD  181 (238)
Q Consensus       135 ~~Lrnys~LT~Gd~I~I~~~~~~y~l~V~e~kP~~aVsIi-dTDl~VD  181 (238)
                      +.|.+ .-+++||+|.+.+.++.+.|.|.+++|.++|.|- +|.+++.
T Consensus        12 ~~l~~-~pv~~Gd~i~~~~~~~~~~~~V~~~~P~~~v~it~~T~i~i~   58 (64)
T PF02933_consen   12 RQLEG-RPVTKGDTIVFPFFGQALPFKVVSTEPSGPVIITEDTEIEIK   58 (64)
T ss_dssp             HHHTT-EEEETT-EEEEEETTEEEEEEEEEECSSSEEEEETTSEEEES
T ss_pred             HHHcC-CCccCCCEEEEEeCCcEEEEEEEEEEcCCCEEECCCcEEEEc
Confidence            34444 4599999999999999999999999999977555 3445543

Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C terminus. The VAT-N domain found in AAA ATPases (IPR003959 from INTERPRO) is a substrate 185-residue recognition domain [].; GO: 0005524 ATP binding; PDB: 1QDN_B 1QCS_A 1CR5_C 3QQ8_A 3HU2_A 3HU1_E 3HU3_A 3QWZ_A 3TIW_B 3QQ7_A ....

>KOG0735 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=96.34  E-value=0.061  Score=55.87  Aligned_cols=147  Identities=18%  Similarity=0.182  Sum_probs=115.0

Q ss_pred             eeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeE-eCCCcEeccHhHHhhcCCCCCCeEEEEEe-eeCCcee
Q 035839           35 KIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFT-ADEGFIYLPNWMMDNMKLQEYELVRVTNV-SLAKATY  112 (238)
Q Consensus        35 KIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~-A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~-~LPkgt~  112 (238)
                      -|.||.+.+..|....-.+++.-.-+.....+.-..|  -++ ..|..+-+=.-..+.|+|.+|+.|.++-. ..++++-
T Consensus        16 fv~lP~ql~~ai~~~~~~~av~~v~~~~~~~~s~~~g--~~s~~se~~ieIn~~~A~~l~L~e~~~V~l~~~~~v~~~~~   93 (952)
T KOG0735|consen   16 FVNLPEQLLEAISEPVQNYAVQAVVSKNPIKKSWVFG--HGSGSSENVIEINRVYAHTLGLAENQEVKLSIIDHVHEATQ   93 (952)
T ss_pred             hhccHHHHHHHHhccccCceeEEEEcCCChhheeecc--cCCCCccceEEeehhhHhhccCCCCCeEEEEEcCCccceeE
Confidence            3678999999988776566665444332333344455  444 35777888888999999999999999976 7999999


Q ss_pred             EEEeecCccccccCCChHHH-HHHhhc-cCcccccCCEEEEEECC-EEEEEEEEEecCCCceEEEeCceEEEecCC
Q 035839          113 MKLQPHTKGFLDELSNPRAV-LEAILR-KFSCLTTGDTIMIMHNE-SKYYIDVLETKPSNAVSITETDCEVDFAPP  185 (238)
Q Consensus       113 vkLqP~s~~F~~~i~npKav-LE~~Lr-nys~LT~Gd~I~I~~~~-~~y~l~V~e~kP~~aVsIidTDl~VDf~pp  185 (238)
                      |.+.|.+++=|+ |-+--|. ||..|- ++.-+|. ....|+++. ..-.|.|..+.|+..+.=++++-+|=++|-
T Consensus        94 V~VeP~TsdDWE-IiElnA~~~e~~lL~Q~RIv~~-~~f~iwl~~~t~i~fqv~rl~Ps~~~gRl~~~Tev~VaPK  167 (952)
T KOG0735|consen   94 VEVEPVTSDDWE-IIELNAEWLEENLLVQTRIVTP-EIFIIWLPSGTVIQFQVDRLIPSMLYGRLLRGTEVLVAPK  167 (952)
T ss_pred             EEEeeccCccHH-HHHhhHHHHhhhhhhheeeccc-ceeEEEEcCccEEEEEEeeeecccceeeecCCceEEEecC
Confidence            999999998888 8665555 677666 7888999 777888876 456799999999999999999999998774

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=95.93  E-value=0.21  Score=51.19  Aligned_cols=134  Identities=16%  Similarity=0.160  Sum_probs=94.5

Q ss_pred             CCCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEee-eE--eCCCcEeccHhHHhhcCCCCCCeEEEEEeeeC
Q 035839           32 PGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVE-FT--ADEGFIYLPNWMMDNMKLQEYELVRVTNVSLA  108 (238)
Q Consensus        32 ~gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlE-F~--A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LP  108 (238)
                      ..+.+-|.++++.+|.   +..==.-+|..  ..+.+.|-|.. ..  .+.|.|.+..-+.+++++..||.|.|+-+.+|
T Consensus        15 ~~~~~~~~~~~~~~~~---~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (733)
T TIGR01243        15 GRGIVRIDRQTAARLG---VEPGDFVEIEK--GDRSVVAIVWPLRPDDEGRGIIRMDGYLRANAGVTIGDTVTVERAEVK   89 (733)
T ss_pred             CCCeEeeCHHHHHhcC---CCCCCEEEEec--CCCceeEEEEecCccccCCCEEeecHHHHhhcCCCCCCeEEEeecCCC
Confidence            5577889999998773   22111334442  34456666664 22  24689999999999999999999999998999


Q ss_pred             CceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEECCEEEEEEEEEecCCCceEE
Q 035839          109 KATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSI  173 (238)
Q Consensus       109 kgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~~~~y~l~V~e~kP~~aVsI  173 (238)
                      .++.|.+.|... ... -.+...++...+.+ ..+++||.|.+.+....+.+.|+++.|...+.+
T Consensus        90 ~~~~~~~~~~~~-~~~-~~~~~~~~~~~~~~-~~~~~g~~~~~~~~~~~~~~~v~~~~p~~~~~~  151 (733)
T TIGR01243        90 EAKKVVLAPTQP-IRF-GRDFVDYVKEFLLG-KPISKGETVIVPVLEGALPFVVVSTQPAGFVYV  151 (733)
T ss_pred             ccceEeeccccc-ccc-ccchHHHHHHHHcC-CCCCCCCEEEecccCcceeEEEEecCCCCcEEE
Confidence            999999999531 110 12233344444444 468999999999888788899999999655543

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PF09262 PEX-1N: Peroxisome biogenesis factor 1, N-terminal ; InterPro: IPR015342 This domain adopts a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain

Probab=93.59  E-value=0.079  Score=40.37  Aligned_cols=75  Identities=21%  Similarity=0.260  Sum_probs=49.2

Q ss_pred             ceeEEEeecCccccccCCChHHHHHHhhc-cCcccccCCEEEEEE-CCEEEEEEEEEecCCCc---eEEEeCceEEEecC
Q 035839          110 ATYMKLQPHTKGFLDELSNPRAVLEAILR-KFSCLTTGDTIMIMH-NESKYYIDVLETKPSNA---VSITETDCEVDFAP  184 (238)
Q Consensus       110 gt~vkLqP~s~~F~~~i~npKavLE~~Lr-nys~LT~Gd~I~I~~-~~~~y~l~V~e~kP~~a---VsIidTDl~VDf~p  184 (238)
                      ++.|.+.|.+.|=++-|...-..||..|- +-.+++.|.++.++. ++..-.|+|..+.|...   ...+..|-|+=++|
T Consensus         1 A~~V~veP~T~dDWEIlEl~A~~lE~~lL~QiRvv~~~~~~~v~v~~~~~i~~~V~~i~p~~~~~~~~~L~~~TEv~VaP   80 (80)
T PF09262_consen    1 AKSVEVEPLTSDDWEILELHAEFLEDQLLSQIRVVFPGQVFPVWVSQNTVIKFKVVSIEPSSSAEGCARLSPDTEVIVAP   80 (80)
T ss_dssp             -SEEEEEESSHHHHHHHHHS-SSHHHHHHHH--EE-TT-EEEEESSSS-EEEEEEEEEES--S---SEE--TT-EEEE--
T ss_pred             CcEEEEEcCCccHHHHHHHhHHHHHHHHHHhheeecCCCEEEEEEcCCeEEEEEEEEccCCCCceeEEEeCCCcEEEECC
Confidence            46788999998777733555556777666 688999999999998 56788999999999866   78888898887764

It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation []. ; GO: 0005524 ATP binding, 0007031 peroxisome organization, 0005777 peroxisome; PDB: 1WLF_A.

>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family

Probab=86.38  E-value=3  Score=26.75  Aligned_cols=39  Identities=23%  Similarity=0.399  Sum_probs=31.2

Q ss_pred             eCCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeec
Q 035839           77 ADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPH  118 (238)
Q Consensus        77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~  118 (238)
                      .+.|.+.||.-+.+.|++.+||.+.+...  +.| -+.|.|.
T Consensus         4 ~~kgri~iP~~~r~~l~~~~gd~~~i~~~--~~~-~l~l~p~   42 (43)
T TIGR01439         4 DKKGQIVIPKEIREKLGLKEGDRLEVIRV--EDG-EIILRPA   42 (43)
T ss_pred             CcCCeEEecHHHHHHcCcCCCCEEEEEEe--CCC-EEEEEEC
Confidence            36799999999999999999999888753  333 5666664

This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.

>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis

Probab=86.35  E-value=3.4  Score=27.71  Aligned_cols=39  Identities=13%  Similarity=0.295  Sum_probs=30.6

Q ss_pred             CCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecC
Q 035839           78 DEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHT  119 (238)
Q Consensus        78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s  119 (238)
                      ..+.|.||.-+.+.|++++||.|.+...  ..| -+.+.|..
T Consensus         5 ~s~~v~iPk~~~~~l~l~~Gd~v~i~~~--~~g-~i~i~p~~   43 (47)
T PF04014_consen    5 NSGQVTIPKEIREKLGLKPGDEVEIEVE--GDG-KIVIRPVK   43 (47)
T ss_dssp             TCSEEEE-HHHHHHTTSSTTTEEEEEEE--TTS-EEEEEEST
T ss_pred             CCceEECCHHHHHHcCCCCCCEEEEEEe--CCC-EEEEEECC
Confidence            4688999999999999999999998865  333 67777753

The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....

>PF02359 CDC48_N: Cell division protein 48 (CDC48), N-terminal domain; InterPro: IPR003338 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=82.03  E-value=19  Score=26.96  Aligned_cols=68  Identities=12%  Similarity=0.001  Sum_probs=50.1

Q ss_pred             CCCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeEe---CCCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839           32 PGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTA---DEGFIYLPNWMMDNMKLQEYELVRVTNV  105 (238)
Q Consensus        32 ~gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~A---~EG~i~lP~Wmm~~L~l~~gd~V~v~~~  105 (238)
                      ..+-++|.|..+++   +++..--+-.|..   ++.|+|=|.--..   +.|.|-|..-+.+++++.-||.|.|+-+
T Consensus        14 ~~n~v~v~~~~m~~---l~l~~gd~v~i~g---~~~tv~~v~~~~~~~~~~g~I~l~~~~R~n~~v~igd~V~V~~~   84 (87)
T PF02359_consen   14 GTNCVRVSPEDMEE---LGLFPGDVVLISG---KRKTVAFVFPDRPDDSPPGVIRLSGIQRKNAGVSIGDRVTVRPY   84 (87)
T ss_dssp             CTTEEEEEHHHHHC---TTT-TTEEEEEET---TTEEEEEEEEECCSTTCTTEEEE-HHHHHHCT--TTSEEEEEEE
T ss_pred             CCCEEEEcHHHHHH---cCCCCccEEEEeC---CceEEEEEEECCCCCCCCCEEEECHHHHhhCCcCCCCEEEEEEC
Confidence            56789999999974   4555555667765   4458888875543   4799999999999999999999999854

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The VAT protein of the archaebacterium Thermoplasma acidophilum, like all other members of the Cdc48/p97 family of AAA ATPases, has two ATPase domains and a 185-residue amino-terminal substrate-recognition domain, VAT-N. VAT shows activity in protein folding and unfolding and thus shares the common function of these ATPases in disassembly and/or degradation of protein complexes. VAT-N is composed of two equally sized subdomains. The amino-terminal subdomain VAT-Nn forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain VAT-Nc forms a novel six-stranded beta-clam fold []. Together, VAT-Nn and VAT-Nc form a kidney-shaped structure, in close agreement with results from electron microscopy. VAT-Nn is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases. ; GO: 0005524 ATP binding; PDB: 1CZ4_A 1CZ5_A 3CF3_C 3CF1_A 3CF2_A 1S3S_D 1E32_A 1R7R_A 2PJH_B 1CR5_B ....

>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts

Probab=80.60  E-value=1.1  Score=34.06  Aligned_cols=27  Identities=15%  Similarity=0.130  Sum_probs=19.8

Q ss_pred             CCcEeccHhHHhhcCCCCCCeEEEEEe
Q 035839           79 EGFIYLPNWMMDNMKLQEYELVRVTNV  105 (238)
Q Consensus        79 EG~i~lP~Wmm~~L~l~~gd~V~v~~~  105 (238)
                      +.-||+|.++.+..+|+.||.|.=...
T Consensus        28 ~~DvYVs~~qIrrf~LR~GD~V~G~vr   54 (78)
T PF07497_consen   28 PDDVYVSPSQIRRFGLRTGDLVEGQVR   54 (78)
T ss_dssp             TTSEEE-CCCCCCTT--TTEEEEEEEE
T ss_pred             CCCEEECHHHHHHcCCCCCCEEEEEEe
Confidence            456899999999999999999875443

It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	238
2yuj_A	190	Solution Structure Of Human Ubiquitin Fusion Degrad		3e-48
1zc1_A	208	Ufd1 Exhibits The Aaa-Atpase Fold With Two Distinct		8e-39

>pdb|2YUJ|A Chain A, Solution Structure Of Human Ubiquitin Fusion Degradation Protein 1 Homolog Ufd1 Length = 190

Iteration: 1
 Score =  187 bits (476), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 93/174 (53%), Positives = 118/174 (67%), Gaps = 5/174 (2%)
Query: 13  FEKHYHCYSLSHVAKPQH----EPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTT 68
           F   Y C+S+S +A P      E G KIIMP SA D+L+   + YPM+F+L N +S + T
Sbjct: 16  FSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMT 75
Query: 69  HCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSN 128
           HCGV+EF ADEG  YLP+WMM N+ L+E  LV+V +V+L  ATY K QP +  FLD ++N
Sbjct: 76  HCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLD-ITN 134
Query: 129 PRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDF 182
           P+AVLE  LR F+CLTTGD I I +NE  Y + V+ETKP  AVSI E D  VDF
Sbjct: 135 PKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDF 188

>pdb|1ZC1|A Chain A, Ufd1 Exhibits The Aaa-Atpase Fold With Two Distinct Ubiquitin Interaction Sites Length = 208

Iteration: 1
 Score =  156 bits (395), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 76/189 (40%), Positives = 116/189 (61%), Gaps = 8/189 (4%)
Query: 13  FEKHYHCYSLS----HVAKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTT 68
           FE+ + CY ++     + K     G KI +P SA  +L+   + YPM+F+L    +G+ T
Sbjct: 21  FEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANETGRVT 80
Query: 69  HCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSN 128
           H GV+EF A+EG +YLP WMM+ + +Q   L+++++  +    ++KL+P +  FLD +S+
Sbjct: 81  HGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFLD-ISD 139
Query: 129 PRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKP---SNAVSITETDCEVDFAPP 185
           P+AVLE +LR FS LT  D I I +N   + I +LE KP   S ++ + ETD   DFAPP
Sbjct: 140 PKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSICVIETDLVTDFAPP 199
Query: 186 LDYKEPDEK 194
           + Y EPD K
Sbjct: 200 VGYVEPDYK 208

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	238
1zc1_A	208	Ubiquitin fusion degradation protein 1; UFD1, doub	7e-77
2yuj_A	190	Ubiquitin fusion degradation 1-like; ubiquitin-dep	4e-73
3tiw_A	187	Transitional endoplasmic reticulum ATPase; beta-ba	5e-08
3qwz_A	211	Transitional endoplasmic reticulum ATPase; UBX, P9	8e-05

>1zc1_A Ubiquitin fusion degradation protein 1; UFD1, double-PSI-beta-barrel, protein turnover; NMR {Saccharomyces cerevisiae} Length = 208

 Score =  230 bits (587), Expect = 7e-77
 Identities = 76/189 (40%), Positives = 116/189 (61%), Gaps = 8/189 (4%)

Query: 13  FEKHYHCYSLSHVA----KPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTT 68
           FE+ + CY ++ +     K     G KI +P SA  +L+   + YPM+F+L    +G+ T
Sbjct: 21  FEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANETGRVT 80

Query: 69  HCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSN 128
           H GV+EF A+EG +YLP WMM+ + +Q   L+++++  +    ++KL+P +  FLD +S+
Sbjct: 81  HGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFLD-ISD 139

Query: 129 PRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKP---SNAVSITETDCEVDFAPP 185
           P+AVLE +LR FS LT  D I I +N   + I +LE KP   S ++ + ETD   DFAPP
Sbjct: 140 PKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSICVIETDLVTDFAPP 199

Query: 186 LDYKEPDEK 194
           + Y EPD K
Sbjct: 200 VGYVEPDYK 208

>2yuj_A Ubiquitin fusion degradation 1-like; ubiquitin-dependent proteolytic, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 190

 Score =  220 bits (561), Expect = 4e-73
 Identities = 93/175 (53%), Positives = 118/175 (67%), Gaps = 5/175 (2%)

Query: 13  FEKHYHCYSLSHVAKPQH----EPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTT 68
           F   Y C+S+S +A P      E G KIIMP SA D+L+   + YPM+F+L N +S + T
Sbjct: 16  FSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMT 75

Query: 69  HCGVVEFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSN 128
           HCGV+EF ADEG  YLP+WMM N+ L+E  LV+V +V+L  ATY K QP +  FLD ++N
Sbjct: 76  HCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLD-ITN 134

Query: 129 PRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFA 183
           P+AVLE  LR F+CLTTGD I I +NE  Y + V+ETKP  AVSI E D  VDF 
Sbjct: 135 PKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDFD 189

>3tiw_A Transitional endoplasmic reticulum ATPase; beta-barrel alpha-helix, transport protein ATPase ubiquitin ubiquitin, phosphorylation; 1.80A {Homo sapiens} PDB: 3qq8_A 3qq7_A 3qc8_A Length = 187

 Score = 50.4 bits (120), Expect = 5e-08
 Identities = 16/122 (13%), Positives = 42/122 (34%), Gaps = 5/122 (4%)

Query: 65  GKTTHCGVV-EFTADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAK-ATYMKLQPHTKGF 122
            +   C V+ + T  +  I +   + +N++++  +++ +      K    + + P     
Sbjct: 64  RREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTV 123

Query: 123 --LDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITE-TDCE 179
             +        +    L  +  +  GD  ++          V+ET PS    +   T   
Sbjct: 124 EGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIH 183

Query: 180 VD 181
            +
Sbjct: 184 CE 185

>3qwz_A Transitional endoplasmic reticulum ATPase; UBX, P97 binding, transport protein; HET: MLY; 2.00A {Homo sapiens} PDB: 2pjh_B Length = 211

 Score = 41.6 bits (97), Expect = 8e-05
 Identities = 17/124 (13%), Positives = 44/124 (35%), Gaps = 5/124 (4%)

Query: 76  TADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAK-ATYMKLQPHTKGF--LDELSNPRAV 132
           T  +  I +   + +N++++  +++ +      K    + + P       +        +
Sbjct: 79  TCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYL 138

Query: 133 LEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITE-TDCEVDFAPPLDYKEP 191
               L  +  +  GD  ++          V+ET PS    +   T    +   P+  ++ 
Sbjct: 139 KPYFLEAYRPIRKGDIFLVRGGMRAVEFXVVETDPSPYCIVAPDTVIHCE-GEPIKREDE 197

Query: 192 DEKL 195
           +E L
Sbjct: 198 EESL 201

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	238
1zc1_A	208	Ubiquitin fusion degradation protein 1; UFD1, doub	100.0
2yuj_A	190	Ubiquitin fusion degradation 1-like; ubiquitin-dep	100.0
1cz4_A	185	VCP-like ATPase; double-PSI beta-barrel, beta-CLAM	99.47
3qwz_A	211	Transitional endoplasmic reticulum ATPase; UBX, P9	99.47
3tiw_A	187	Transitional endoplasmic reticulum ATPase; beta-ba	99.46
1wlf_A	179	PEX1, peroxisome biogenesis factor 1; N-terminal d	99.15
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.74
2jv2_A	83	Putative uncharacterized protein PH1500; AAA ATPas	97.53
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	97.29
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	96.7
1yfb_A	59	Transition state regulatory protein ABRB; , homodi	92.58
1cr5_A	189	SEC18P (residues 22 - 210); double-PSI beta barrel	90.21
2glw_A	92	PHS018, 92AA long hypothetical protein; RIFT barre	89.74
1qcs_A	211	N-ethylmaleimide sensitive factor (NSF-N); double-	89.08
1cz4_A	185	VCP-like ATPase; double-PSI beta-barrel, beta-CLAM	88.41
3tiw_A	187	Transitional endoplasmic reticulum ATPase; beta-ba	87.59
2l66_A	53	SSO7C4, transcriptional regulator, ABRB family; DN	87.57
3qwz_A	211	Transitional endoplasmic reticulum ATPase; UBX, P9	84.16
2glw_A	92	PHS018, 92AA long hypothetical protein; RIFT barre	83.66

>1zc1_A Ubiquitin fusion degradation protein 1; UFD1, double-PSI-beta-barrel, protein turnover; NMR {Saccharomyces cerevisiae}

Probab=100.00  E-value=9.1e-80  Score=536.20  Aligned_cols=184  Identities=40%  Similarity=0.777  Sum_probs=179.9

Q ss_pred             ccccceeeEEEeeeecc----cCCCCCCCCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeEeCCCcEec
Q 035839            9 YYTCFEKHYHCYSLSHV----AKPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYL   84 (238)
Q Consensus         9 ~~~~f~~~~~~y~~s~~----~~~~~~~gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~A~EG~i~l   84 (238)
                      ..++|+++|||||++|+    +|+++++||||+||||||++|++++++|||+|+|+|..++++||||||||+|+||+|||
T Consensus        17 ~~~~f~~~~rc~~~~~~p~~~~r~~~~~GdKIiLP~SaL~~L~~~~i~~Pm~F~l~n~~~~~~th~GVlEF~A~EG~v~l   96 (208)
T 1zc1_A           17 MPQTFEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANETGRVTHGGVLEFIAEEGRVYL   96 (208)
T ss_dssp             CCEEEEEEEEEEEGGGSCTTTSCHHHHHSSEEEECHHHHHHHHHTTCCSSCCEEEECTTTCCEEEEEEEEECCSSCEEEE
T ss_pred             ccccccceEEEEEEEeccCcccccccCCCCeEECCHHHHHHHHHCCCCcCEEEEEEeCCCCCEEEEEEEEEEcCCCeEEc
Confidence            36789999999999996    78899999999999999999999999999999999999999999999999999999999


Q ss_pred             cHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEECCEEEEEEEEE
Q 035839           85 PNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLE  164 (238)
Q Consensus        85 P~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~~~~y~l~V~e  164 (238)
                      |+|||++|++++||.|+|++++||||||||||||+++|++ |+|||||||++||||+|||+||+|.|+|+++.|+|+|+|
T Consensus        97 P~wmm~~L~l~~gd~V~i~~~~LPkgt~vklqP~~~~Fld-i~npKavLE~~LRnfstLT~Gd~I~i~~~~~~y~l~V~e  175 (208)
T 1zc1_A           97 PQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFLD-ISDPKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILE  175 (208)
T ss_dssp             CHHHHHHHTCCTTCEEEEEEEECCCCSEEEEECCHHHHHT-SSCHHHHHHHHHHHCSCEESSSEEEEEETTEEEEEEEEE
T ss_pred             CHHHHHhcCCCCCCEEEEEEeEcCCCCEEEEeECcccccc-ccCHHHHHHHHhhcCccccCCCEEEEEeCCEEEEEEEEE
Confidence            9999999999999999999999999999999999999998 999999999999999999999999999999999999999


Q ss_pred             ecCCC---ceEEEeCceEEEecCCCCCCCCch
Q 035839          165 TKPSN---AVSITETDCEVDFAPPLDYKEPDE  193 (238)
Q Consensus       165 ~kP~~---aVsIidTDl~VDf~ppl~y~e~~~  193 (238)
                      +||++   |||||||||+|||+||+||+||++
T Consensus       176 ~kP~~~~~aV~IidTDleVDf~~p~~y~ep~~  207 (208)
T 1zc1_A          176 VKPESSSKSICVIETDLVTDFAPPVGYVEPDY  207 (208)
T ss_dssp             EECSSTTCEECCSSSCSEEEECCCCCCCCCCC
T ss_pred             EcCCCCCceEEEEeCceEEEecCCCCCcCCCC
Confidence            99997   999999999999999999999986

>2yuj_A Ubiquitin fusion degradation 1-like; ubiquitin-dependent proteolytic, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=100.00  E-value=2e-75  Score=503.03  Aligned_cols=174  Identities=53%  Similarity=0.907  Sum_probs=169.6

Q ss_pred             ccc-ceeeEEEeeeeccc----CCCCCCCCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeEeCCCcEec
Q 035839           10 YTC-FEKHYHCYSLSHVA----KPQHEPGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTADEGFIYL   84 (238)
Q Consensus        10 ~~~-f~~~~~~y~~s~~~----~~~~~~gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~A~EG~i~l   84 (238)
                      .+. |+++|||||+||+.    |+++++||||+||||||++|++++++|||+|+|+|..++|+||||||||+|+||+|||
T Consensus        12 ~~~~f~~~~~cy~~s~~~~~~~r~~~~~GdKI~LP~SaL~~L~~~~i~~Pm~F~l~n~~~~r~th~GVlEFsA~EG~i~l   91 (190)
T 2yuj_A           12 FQNRFSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMTHCGVLEFVADEGICYL   91 (190)
T ss_dssp             CSSSCEEEEEEECSTTSSSSSCCSTTTTTTEEECCHHHHHHHHHTTCCSSCEEEEEETTTTEEEEEEEEECCCBTTBEEC
T ss_pred             CCccccceEEEEehhHcCCcccccccCCCCeEECcHHHHHHHHHCCCCcCeEEEEecCCCCceEEEEEEEEecCCCeEEe
Confidence            344 99999999999974    7899999999999999999999999999999999999999999999999999999999


Q ss_pred             cHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEECCEEEEEEEEE
Q 035839           85 PNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLE  164 (238)
Q Consensus        85 P~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~~~~y~l~V~e  164 (238)
                      |+|||++|++++||.|+|++++||||||||||||+++|++ |+|||||||++||||+|||+||+|.|+|+++.|+|+|+|
T Consensus        92 P~wmm~~L~l~~gd~V~v~~~~LPkgt~vklqP~~~~Fl~-i~npKavLE~~LrnfstLT~Gd~I~I~~~~~~y~l~V~e  170 (190)
T 2yuj_A           92 PHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLD-ITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVME  170 (190)
T ss_dssp             CSHHHHHHTCCTTEEEEEEEECCCCCSEEEEEESSHHHHH-SSCHHHHHHHHHTTCCEECTTCEEEEESSSCEEEEEEEE
T ss_pred             CHHHHHhcCCCCCCEEEEEEeecCCCcEEEEEECCccccc-cccHHHHHHHHHhcCcccccCCEEEEEeCCEEEEEEEEE
Confidence            9999999999999999999999999999999999999999 999999999999999999999999999999999999999


Q ss_pred             ecCCCceEEEeCceEEEecC
Q 035839          165 TKPSNAVSITETDCEVDFAP  184 (238)
Q Consensus       165 ~kP~~aVsIidTDl~VDf~p  184 (238)
                      +||++|||||||||+|||+|
T Consensus       171 ~kP~~aV~IidTDl~vDf~p  190 (190)
T 2yuj_A          171 TKPDKAVSIIECDMNVDFDA  190 (190)
T ss_dssp             ESSSSSEECSSCCCEEEECC
T ss_pred             EcCCCeEEEEeCCEEEEecC
Confidence            99999999999999999986

>1cz4_A VCP-like ATPase; double-PSI beta-barrel, beta-CLAM, substrate recognition DOM hydrolase; NMR {Thermoplasma acidophilum} SCOP: b.52.2.3 d.31.1.1 PDB: 1cz5_A

Probab=99.47  E-value=6.5e-13  Score=113.16  Aligned_cols=144  Identities=15%  Similarity=0.136  Sum_probs=119.3

Q ss_pred             CCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEee-eEeC--CCcEeccHhHHhhcCCCCCCeEEEEEeeeCC
Q 035839           33 GDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVE-FTAD--EGFIYLPNWMMDNMKLQEYELVRVTNVSLAK  109 (238)
Q Consensus        33 gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlE-F~A~--EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPk  109 (238)
                      -+.+.|+|++|++|.-..-.   +.+|+   .+|.|+|-|.. +..+  .|.|-|..|+.+|+++..||.|.|+-+.++.
T Consensus        21 r~ivrl~p~~m~~Lgl~~GD---~V~I~---G~r~t~a~v~~~~~ed~~~g~Irid~~~R~N~gv~iGD~V~V~~~~~~~   94 (185)
T 1cz4_A           21 MSRVRLDESSRRLLDAEIGD---VVEIE---KVRKTVGRVYRARPEDENKGIVRIDSVMRNNCGASIGDKVKVRKVRTEI   94 (185)
T ss_dssp             SSEEEECHHHHHTTCCCTTC---EEEEE---SSSEEEEEEEECSSTTTTTSEEECCHHHHHHHTCCTTCEEEEEEECCCB
T ss_pred             CCEEEECHHHHHHcCCCCCC---EEEEE---cCCeEEEEEEEcCcCcCCCCEEEeCHHHHhccCCCCCCEEEEEECCCCC
Confidence            35699999999877532222   46665   45789999986 3333  6899999999999999999999999999999


Q ss_pred             ceeEEEeecC---ccccccCCChHHHHHHhhccCcccccCCEEEEEE---CCE-EEEEEEEEecCCCceEEEeCceEEEe
Q 035839          110 ATYMKLQPHT---KGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMH---NES-KYYIDVLETKPSNAVSITETDCEVDF  182 (238)
Q Consensus       110 gt~vkLqP~s---~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~---~~~-~y~l~V~e~kP~~aVsIidTDl~VDf  182 (238)
                      |+.|.|.|.+   ..+ ....|....|...|+++. |++||+|.+.+   .++ ...|.|++++|+.++++|..|-+|++
T Consensus        95 A~~V~l~P~~~~~~~~-~~~~~~~~~l~~~l~~rp-v~~Gd~v~v~~~~~~g~~~~~f~Vv~t~P~~~~v~Vt~~T~I~i  172 (185)
T 1cz4_A           95 AKKVTLAPIIRKDQRL-KFGEGIEEYVQRALIRRP-MLEQDNISVPGLTLAGQTGLLFKVVKTLPSKVPVEIGEETKIEI  172 (185)
T ss_dssp             CSEEEEEEECSTTCCS-CCCSSHHHHHHHHHTTCE-ECTTCEECCSSCCCSSCCCCEEEEEEESSSSSCEECCTTCEEEE
T ss_pred             ccEEEEeccccccccc-ccccchHHHHHHHHCCCc-ccCCCEEEEeeeccCCCeEEEEEEEEEcCCCceEEEcCCeEEEE
Confidence            9999999985   443 313688899999999974 99999999986   667 89999999999987889989999988


Q ss_pred             cC
Q 035839          183 AP  184 (238)
Q Consensus       183 ~p  184 (238)
                      ..
T Consensus       173 ~~  174 (185)
T 1cz4_A          173 RE  174 (185)
T ss_dssp             CS
T ss_pred             CC
Confidence            53

>3qwz_A Transitional endoplasmic reticulum ATPase; UBX, P97 binding, transport protein; HET: MLY; 2.00A {Homo sapiens} PDB: 2pjh_B

Probab=99.47  E-value=9.1e-13  Score=114.74  Aligned_cols=145  Identities=14%  Similarity=0.220  Sum_probs=121.0

Q ss_pred             CCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeee-EeCCCcEeccHhHHhhcCCCCCCeEEEEEe-eeCCc
Q 035839           33 GDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEF-TADEGFIYLPNWMMDNMKLQEYELVRVTNV-SLAKA  110 (238)
Q Consensus        33 gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF-~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~-~LPkg  110 (238)
                      .+.+.|+|+++++|.-..-.   +.+|+. ...+.|+|-|+.. ..++|.|.|..|+.+||++..||.|.|+-+ .++.|
T Consensus        39 rgivrl~p~~m~~Lgl~~GD---~V~I~G-kr~k~Tva~v~~~~~~~~g~Irid~~~R~N~gV~iGD~V~V~~~~~v~~A  114 (211)
T 3qwz_A           39 NSVVSLSQPKMDELQLFRGD---TVLLKG-XKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYG  114 (211)
T ss_dssp             TTEEEECHHHHHHHTCCBTC---EEEEEC-STTCEEEEEEEECTTSCTTEEEECHHHHHHTTCCTTCEEEEEECTTCCBC
T ss_pred             CcEEEECHHHHHHcCCCCCC---EEEEeC-CCCCcEEEEEEeCCCCCCCEEEeCHHHHhhcCCCCCCEEEEEECCCCCCc
Confidence            77899999999987633222   577875 2344899999864 457899999999999999999999999999 89999


Q ss_pred             eeEEEeecCccccccCC-C-hHHHHHHhhc-cCcccccCCEEEEEECCEEEEEEEEEecCCCceEEEeCceEEEec
Q 035839          111 TYMKLQPHTKGFLDELS-N-PRAVLEAILR-KFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDFA  183 (238)
Q Consensus       111 t~vkLqP~s~~F~~~i~-n-pKavLE~~Lr-nys~LT~Gd~I~I~~~~~~y~l~V~e~kP~~aVsIidTDl~VDf~  183 (238)
                      +.|.|.|.+..+-. |. | ....|...|. +|-.+++||+|.|.+.++..+|.|++++|+ .+|+|..|-+|++.
T Consensus       115 ~~V~LaP~~~~i~~-i~~~~~~~~lk~~l~~~~rPV~~GD~i~v~~~~~~v~f~Vv~t~P~-g~viV~~~T~I~~~  188 (211)
T 3qwz_A          115 KRIHVLPIDDTVEG-ITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFXVVETDPS-PYCIVAPDTVIHCE  188 (211)
T ss_dssp             SEEEEEEBGGGCTT-CCSCHHHHTTHHHHTTCCEEEETTCEEECCCTTSCCEEEEEEEESS-SEEEECTTCEEECC
T ss_pred             eEEEEeccCcchhc-cCchhHHHHHHHHHhhCCceeecCCEEEEccCCcEEEEEEEeecCC-CCEEECCCcEEEEc
Confidence            99999998655433 43 3 4677888888 499999999999999999999999999997 57889888888884

>3tiw_A Transitional endoplasmic reticulum ATPase; beta-barrel alpha-helix, transport protein ATPase ubiquitin ubiquitin, phosphorylation; 1.80A {Homo sapiens} PDB: 3qq8_A 3qq7_A 3qc8_A

Probab=99.46  E-value=1.9e-12  Score=110.73  Aligned_cols=144  Identities=15%  Similarity=0.221  Sum_probs=115.7

Q ss_pred             CCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeee-EeCCCcEeccHhHHhhcCCCCCCeEEEEEe-eeCCc
Q 035839           33 GDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEF-TADEGFIYLPNWMMDNMKLQEYELVRVTNV-SLAKA  110 (238)
Q Consensus        33 gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF-~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~-~LPkg  110 (238)
                      .+.+.|+|+++++|.-..-.   +.+|+. ...+.|+|-|+.- ..++|.|.|..|+.+||++..||.|.|+-+ .++.|
T Consensus        36 ~givrl~p~~m~~Lgl~~GD---~V~I~G-kr~k~Tva~v~~~~~~~~g~Irid~~~R~N~gV~iGD~V~V~~~~~v~~A  111 (187)
T 3tiw_A           36 NSVVSLSQPKMDELQLFRGD---TVLLKG-KKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYG  111 (187)
T ss_dssp             TTEEEECHHHHHHHTCCTTC---EEEEEC-STTCEEEEEEEECTTSCTTEEEECHHHHHHTTCCTTCEEEEEECTTCEEC
T ss_pred             CcEEEECHHHHHHcCCCCCC---EEEEEC-CCCCeEEEEEEECCCCCCCEEEeCHHHHhhcCCCCCCEEEEEECCCCCCc
Confidence            67899999999988633222   577774 2344899999875 357899999999999999999999999999 89999


Q ss_pred             eeEEEeecCccccccCC-C-hHHHHHHhhc-cCcccccCCEEEEEECCEEEEEEEEEecCCCceEEEeCceEEEe
Q 035839          111 TYMKLQPHTKGFLDELS-N-PRAVLEAILR-KFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDF  182 (238)
Q Consensus       111 t~vkLqP~s~~F~~~i~-n-pKavLE~~Lr-nys~LT~Gd~I~I~~~~~~y~l~V~e~kP~~aVsIidTDl~VDf  182 (238)
                      +.|.|.|.+...-. ++ | ....|...|. +|-.+++||+|.|.+.++.++|.|++++|+ .+|+|..|-+|..
T Consensus       112 ~~V~LaP~~~~i~~-i~~~~~~~~lk~~l~~~~rpV~~GD~i~v~~~~~~v~f~Vv~t~P~-~~v~V~~~T~I~~  184 (187)
T 3tiw_A          112 KRIHVLPIDDTVEG-ITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPS-PYCIVAPDTVIHC  184 (187)
T ss_dssp             SEEEEEECCCC------CCHHHHTHHHHHTTTCCEEETTCEEEEECSSSEEEEEEEEEESS-SEEECCTTCEEEC
T ss_pred             eEEEEeccccchhh-ccchhHHHHHHHHhccCCceeeCCCEEEEccCCCEEEEEEEEecCC-CCEEECCCcEEEe
Confidence            99999998644422 43 3 4677888888 499999999999999999999999999998 5677766666654

>1wlf_A PEX1, peroxisome biogenesis factor 1; N-terminal domain, protein transport; 2.05A {Mus musculus} SCOP: b.52.2.3 d.31.1.1

Probab=99.15  E-value=1.6e-10  Score=97.95  Aligned_cols=147  Identities=13%  Similarity=0.132  Sum_probs=120.5

Q ss_pred             CCCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEeeeEe----CCCcEeccHhHHhhcCCCCCCeEEEEE-ee
Q 035839           32 PGDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVEFTA----DEGFIYLPNWMMDNMKLQEYELVRVTN-VS  106 (238)
Q Consensus        32 ~gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlEF~A----~EG~i~lP~Wmm~~L~l~~gd~V~v~~-~~  106 (238)
                      ..+-+-||+++++.|.-   ..=-.-+|+-  ..++.++|...+..    ..+.|-|..-+.+|||+..||.|.|+- ..
T Consensus        23 ~~~~vrL~~~~~~~L~~---~~gd~VeI~g--~~~t~~~~w~~~~~~~d~~~~~I~Id~~~r~n~gv~~Gd~V~V~~~~~   97 (179)
T 1wlf_A           23 RDCFLHLPRRLVAQLHL---LQNQAIEVAS--DHQPTYLSWVEGRHFNDQSENVAEINRQVGQKLGLSSGDQVFLRPCSH   97 (179)
T ss_dssp             SSSCEEECHHHHHHTTC---CTTCCEEEES--SSCCEEECEEECSSCC---CCEEEEEHHHHHHTTCCTTCEEEEEECSC
T ss_pred             CCcEEECCHHHHHHcCC---CCCcEEEEEe--CCeeEEEEEECCCCcccCCCCEEEECHHHHhHCCCCCCCEEEEEECCC
Confidence            45678999999998752   2223667764  34577888887754    467999999999999999999999998 79


Q ss_pred             eCCceeEEEeecCccccccC-CChHHHHHHhhc-cCcccccCCEEEEEECC-EEEEEEEEEecCCCceEEEeCceEEEec
Q 035839          107 LAKATYMKLQPHTKGFLDEL-SNPRAVLEAILR-KFSCLTTGDTIMIMHNE-SKYYIDVLETKPSNAVSITETDCEVDFA  183 (238)
Q Consensus       107 LPkgt~vkLqP~s~~F~~~i-~npKavLE~~Lr-nys~LT~Gd~I~I~~~~-~~y~l~V~e~kP~~aVsIidTDl~VDf~  183 (238)
                      .+.|+.|.|.|.+.+-++ | .+.-..||..|. ++..+++||+|.++..+ ....|.|.++.|...+++|..|-+|.++
T Consensus        98 ~~~A~~V~laP~~~dD~e-i~e~~a~~le~~Ll~QiR~v~~G~~i~v~~~g~~~i~f~V~~~~P~~~~v~It~~TeI~v~  176 (179)
T 1wlf_A           98 VVSCQQVEVEPLSADDWE-ILELHAISLEQHLLDQIRIVFPKAVVPIWVDQQTYIFIQIVTLMPAAPYGRLETNTKLLIQ  176 (179)
T ss_dssp             CEECSEEEEEESSHHHHH-HHHHSCSSHHHHHHHHCCEECTTCEEEEESSSSCEEEEEEEEEESCCSSEECCTTCEEEEC
T ss_pred             CccceEEEEEcCCcCCeE-EehhHHHHHHHHHhcCceeccCCCEEEEEecCCeEEEEEEEEeeCCCCeEEECCCcEEEEe
Confidence            999999999999866455 4 455567888888 58899999999999766 8899999999997778899999999886


Q ss_pred             C
Q 035839          184 P  184 (238)
Q Consensus       184 p  184 (238)
                      |
T Consensus       177 p  177 (179)
T 1wlf_A          177 P  177 (179)
T ss_dssp             C
T ss_pred             c
Confidence            5

>3cf2_A TER ATPase, transitional endoplasmic reticulum ATPase, valosi; AAA, CDC48, ERAD, transport protein; HET: ADP ANP; 3.50A {Mus musculus} PDB: 3cf1_A* 3cf3_A* 1r7r_A*

Probab=97.74  E-value=0.00022  Score=72.41  Aligned_cols=142  Identities=13%  Similarity=0.183  Sum_probs=100.4

Q ss_pred             CeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEee-eEeCCCcEeccHhHHhhcCCCCCCeEEEEEe-eeCCce
Q 035839           34 DKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVE-FTADEGFIYLPNWMMDNMKLQEYELVRVTNV-SLAKAT  111 (238)
Q Consensus        34 dKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlE-F~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~-~LPkgt  111 (238)
                      .-|.|.|..+++|.-..=.   +-+|+... .+.+.|-++. =..+.|.|.|..-+.+|+++..||.|.|+-+ .++.++
T Consensus        37 ~~~~~~~~~~~~l~~~~gd---~v~i~g~~-~~~~~~~~~~~~~~~~~~i~~~~~~r~n~~v~~gd~V~v~~~~~~~~a~  112 (806)
T 3cf2_A           37 SVVSLSQPKMDELQLFRGD---TVLLKGKK-RREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGK  112 (806)
T ss_dssp             TEEEECHHHHHHTTCCSSC---EEEEECGG-GCBCCEEEEECTTSBTTBCEECHHHHHTTTCCTTCEEEEEECCCCCBCS
T ss_pred             CEEEECHHHHHHcCCCCCC---EEEEEcCC-CceEEEEEcCCCCCCCCEEEeCHHHHHhcCCCCCCEEEEEECCCCCcCC
Confidence            4588999999877532112   34554322 2233344332 1246799999999999999999999999988 799999


Q ss_pred             eEEEeecCccccccCC--ChHHHHHHhhc-cCcccccCCEEEEEECCEEEEEEEEEecCCCceEEE-eCceEE
Q 035839          112 YMKLQPHTKGFLDELS--NPRAVLEAILR-KFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSIT-ETDCEV  180 (238)
Q Consensus       112 ~vkLqP~s~~F~~~i~--npKavLE~~Lr-nys~LT~Gd~I~I~~~~~~y~l~V~e~kP~~aVsIi-dTDl~V  180 (238)
                      .|.|.|.+...-. +.  .....|...|. .+-.+++||+|.+.+.+....|.|++++|...+.|- +|.+.+
T Consensus       113 ~v~l~p~~~~~~~-~~~~~~~~~l~~~~~~~~~~v~~gd~~~v~~~~~~~~f~V~~~~P~~~~~v~~~T~i~~  184 (806)
T 3cf2_A          113 RIHVLPIDDTVEG-ITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHC  184 (806)
T ss_dssp             BEEEEEBTTTSTT-CCSCHHHHTHHHHHTTTCCEEETTCEEEECCTTSCEEEEEEEESSSSEEECCTTSBCCB
T ss_pred             EEEEeccccchhc-cchhHHHHHHHHHHHhcCCcccCCCEEEEecCCcEEEEEEEEEeCCCCeEECCCcEEEE
Confidence            9999997533222 22  23455555555 467899999999999999999999999998755433 344443

>2jv2_A Putative uncharacterized protein PH1500; AAA ATPase NC-domain-like, unknown function; NMR {Pyrococcus horikoshii}

Probab=97.53  E-value=0.00035  Score=52.51  Aligned_cols=68  Identities=24%  Similarity=0.285  Sum_probs=54.9

Q ss_pred             CceeEEEeecCccccccC-CChHHHHHHhhccCcccccCCEEEEEECCEEEEEEEEEecCCCceEEEeCceEEEe
Q 035839          109 KATYMKLQPHTKGFLDEL-SNPRAVLEAILRKFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDF  182 (238)
Q Consensus       109 kgt~vkLqP~s~~F~~~i-~npKavLE~~Lrnys~LT~Gd~I~I~~~~~~y~l~V~e~kP~~aVsIidTDl~VDf  182 (238)
                      -|+.|.|.|.+.  ++ + .|.-..|-+.|+++. +++||+|.|..-++...|.|++++|.  +++|.-|-++++
T Consensus        11 ~A~kVvLAP~~~--i~-~~~~~~~~lk~~L~grP-V~~GD~I~i~~~G~~i~F~Vv~t~P~--~V~Vt~~T~I~i   79 (83)
T 2jv2_A           11 IMSELKLKPLPK--VE-LPPDFVDVIRIKLQGKT-VRTGDVIGISILGKEVKFKVVQAYPS--PLRVEDRTKITL   79 (83)
T ss_dssp             CCCEEEEEESSS--CC-CCHHHHHHHHHHHTTSE-ECTTCEEEEEETTEEEEEEEEEEESS--SEECCTTSEEEE
T ss_pred             EEEEEEEcCCCc--ee-cCccHHHHHHHHHCCCC-ccCCCEEEEeeCCCEEEEEEEEecCc--cEEECCCcEEEE
Confidence            478899999842  33 4 455677778888855 99999999998889999999999997  778877777776

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=96.70  E-value=0.053  Score=51.57  Aligned_cols=144  Identities=14%  Similarity=0.176  Sum_probs=103.4

Q ss_pred             CCeeeecHHHHHHHHhCCCCCceEEEEEeCCCCCeEEEEEee-eEeCCCcEeccHhHHhhcCCCCCCeEEEEEe-eeCCc
Q 035839           33 GDKIIMPQSAFDRLAHTEVGYPMMFELCNLSSGKTTHCGVVE-FTADEGFIYLPNWMMDNMKLQEYELVRVTNV-SLAKA  110 (238)
Q Consensus        33 gdKIiLP~SaL~~L~~~~i~~Pm~F~i~n~~~~~~th~GVlE-F~A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~-~LPkg  110 (238)
                      .+.|.|.|+++++|.   +..==+=+|+. ...+.|.|.|+- -.-+.|.|-|..-+.+|+|+.-||.|+|+-+ .+|.|
T Consensus        36 ~~~~~~~~~~~~~l~---~~~gd~v~~~g-~~~~~~~~~~~~~~~~~~~~i~~~~~~r~n~~~~~gd~v~v~~~~~~~~a  111 (489)
T 3hu3_A           36 NSVVSLSQPKMDELQ---LFRGDTVLLKG-KKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYG  111 (489)
T ss_dssp             TTEEEECHHHHHHHT---CCTTCEEEEEC-STTCEEEEEEEECTTSCTTEEECCHHHHHHTTCCTTCEEEEEECTTCCBC
T ss_pred             CCEEEECHHHHHHcC---CCCCCEEEEec-CccCcEEEEEeeCCCCCCCEEEecHHHHhhcCCCCCCEEEEEECCCCCcc
Confidence            389999999999886   22222344543 333578899862 2235789999999999999999999999999 99999


Q ss_pred             eeEEEeecCccccccCCC-hHHHHHHhhc--cCcccccCCEEEEEECCEEEEEEEEEecCCCceEEEeCceEEEe
Q 035839          111 TYMKLQPHTKGFLDELSN-PRAVLEAILR--KFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDF  182 (238)
Q Consensus       111 t~vkLqP~s~~F~~~i~n-pKavLE~~Lr--nys~LT~Gd~I~I~~~~~~y~l~V~e~kP~~aVsIidTDl~VDf  182 (238)
                      +.|.|.|-+.+--. +.. --..++.-+.  .+-.+..||.+.+....+.+++.+++.+|... +++..+-.+.+
T Consensus       112 ~~v~~~~~~~av~a-~~~ga~d~~~Kp~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~t~~~~  184 (489)
T 3hu3_A          112 KRIHVLPIDDTVEG-ITGNLFEVYLKPYFLEAYRPIRKGDIFLVHGGMRAVEFKVVETDPSPY-CIVAPDTVIHC  184 (489)
T ss_dssp             SEEEEEEBGGGSSS-CCSCHHHHTHHHHHTTTCEEEETTCEEEEEETTEEEEEEEEEEESSSE-EEECTTCEEEC
T ss_pred             CEEEEcCCCccccc-ccchhHHHHhHHHHhhcCcccccCCEEEecCCCceEEEEEEeecCCCc-eEEcCCeEEEE
Confidence            99999997654322 322 1122333322  36678889999999999999999999998644 34444444444

>1yfb_A Transition state regulatory protein ABRB; , homodimer, bioinformatics, swapped-hairpin barrel, transcription; NMR {Bacillus subtilis} SCOP: b.129.1.3 PDB: 1ysf_A 2k1n_A* 1z0r_A 2ro4_A 2fy9_A 2ro3_A

Probab=92.58  E-value=0.24  Score=34.59  Aligned_cols=40  Identities=10%  Similarity=0.130  Sum_probs=32.9

Q ss_pred             eCCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCc
Q 035839           77 ADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTK  120 (238)
Q Consensus        77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~  120 (238)
                      ...|.|.+|.=+.+.|+|++||.|.+...    +.-+.|+|...
T Consensus        19 ~~kGqItIPkeiR~~Lgi~~Gd~l~i~~~----~~~IiL~p~~p   58 (59)
T 1yfb_A           19 DELGRVVIPIELRRTLGIAEKDALEIYVD----DEKIILKKYKP   58 (59)
T ss_dssp             CTTCEEECCHHHHHHTTCCTTCEEEEEEE----TTEEEEEECCC
T ss_pred             CCCCEEEeCHHHHHHcCCCCCCEEEEEEE----CCEEEEEECCC
Confidence            36799999999999999999999988763    23588888643

>1cr5_A SEC18P (residues 22 - 210); double-PSI beta barrel, vesicle fusion, endocytosis/exocytosis complex; 2.30A {Saccharomyces cerevisiae} SCOP: b.52.2.3 d.31.1.1

Probab=90.21  E-value=1.8  Score=36.28  Aligned_cols=89  Identities=8%  Similarity=0.078  Sum_probs=62.1

Q ss_pred             CCCcEeccHhHHhhcCCCCCCeEEEEEeeeC-Cc---eeEEEeecCcccccc------CCChHHHHHHhhccCc--cccc
Q 035839           78 DEGFIYLPNWMMDNMKLQEYELVRVTNVSLA-KA---TYMKLQPHTKGFLDE------LSNPRAVLEAILRKFS--CLTT  145 (238)
Q Consensus        78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LP-kg---t~vkLqP~s~~F~~~------i~npKavLE~~Lrnys--~LT~  145 (238)
                      +.|+|.|-.-.-+-+++.-|+.|.|+.-..| .+   .++---=.+.+|+..      -=|-..+-..-+++|.  .||.
T Consensus        54 ~~G~I~ls~~QR~wa~lsl~~~v~V~~y~p~~~~~~~~~l~si~lEidf~~k~~~~~~~~D~dela~~f~~~F~~Qift~  133 (189)
T 1cr5_A           54 PPGTIGFNGNQRTWGGWSLNQDVQAKAFDLFKYSGKQSYLGSIDIDISFRARGKAVSTVFDQDELAKQFVRCYESQIFSP  133 (189)
T ss_dssp             CTTEEEECHHHHHHHTCCTTCEEEEEECCHHHHHTTCCEEEEEEEEEEECC-------CCCHHHHHHHHHHHHTTCEECT
T ss_pred             CCCEEecCHHHHHhhcccCCCeEEEEEeCCccCCCCcceEEEEEEEEEehhcCCCCCCccCHHHHHHHHHHHHcCCCCCC
Confidence            7899999998888899999999999977442 12   233222233344420      1244444455555666  5999


Q ss_pred             CCEEEEEECCEEEEEEEEEec
Q 035839          146 GDTIMIMHNESKYYIDVLETK  166 (238)
Q Consensus       146 Gd~I~I~~~~~~y~l~V~e~k  166 (238)
                      |..+.+.|++..|.|.|.++.
T Consensus       134 gQ~l~f~~~g~~l~l~V~~i~  154 (189)
T 1cr5_A          134 TQYLIMEFQGHFFDLKIRNVQ  154 (189)
T ss_dssp             TCEEEEEETTEEEEEEEEEEE
T ss_pred             CCEEEEEECCcEEEEEEEEEE
Confidence            999999999999999998764

>2glw_A PHS018, 92AA long hypothetical protein; RIFT barrel, bioinformatics, transcription; NMR {Pyrococcus horikoshii}

Probab=89.74  E-value=1.5  Score=32.89  Aligned_cols=68  Identities=15%  Similarity=0.190  Sum_probs=47.4

Q ss_pred             CCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCce----eEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEE
Q 035839           78 DEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKAT----YMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMH  153 (238)
Q Consensus        78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt----~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~  153 (238)
                      ..|.|-+|..+.+.|++.+||.|.++.++...|.    +...+-  +.--+ |.=||.+     |..--|..||.+.+.-
T Consensus        13 ~~gqvtiP~~iR~~LgI~~GD~V~v~~i~~~~g~~~~~~~~~~v--~~kGq-itIPkei-----R~~lgi~~Gd~l~~~~   84 (92)
T 2glw_A           13 RIGRIIIPAGTRKFYGIEQGDFVEIKIVKYEGEEPKEGTFTARV--GEQGS-VIIPKAL-----RDVIGIKPGEVIEVLL   84 (92)
T ss_dssp             GGGEEECCHHHHHHHTCCTTCEEEEEEEEEETTEEEEEEEEEEC--CGGGE-EECCHHH-----HHHHTCCTTCEEEEEE
T ss_pred             CCCEEEecHHHHHHcCCCCCCEEEEEEEEecCCccceeEEEEEE--CcCce-EECcHHH-----HHHcCCCCCCEEEEEE
Confidence            5799999999999999999999999876666665    111111  11112 4457765     4445789999998864

>1qcs_A N-ethylmaleimide sensitive factor (NSF-N); double-PSI beta barrel alpha beta roll, fusion protein; 1.90A {Cricetulus griseus} SCOP: b.52.2.3 d.31.1.1 PDB: 1qdn_A

Probab=89.08  E-value=1.8  Score=36.82  Aligned_cols=89  Identities=13%  Similarity=0.156  Sum_probs=61.5

Q ss_pred             CCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCc-eeEEEeecCcccccc-C-----CChHHHHHHhhccCc--ccccCCE
Q 035839           78 DEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKA-TYMKLQPHTKGFLDE-L-----SNPRAVLEAILRKFS--CLTTGDT  148 (238)
Q Consensus        78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkg-t~vkLqP~s~~F~~~-i-----~npKavLE~~Lrnys--~LT~Gd~  148 (238)
                      +.|+|.|-.-.-+.+++.-|+.|.|+.-..+.. .++-.-=.+.+|+.. -     =|-..+-..-+++|.  .||.|..
T Consensus        60 ~~G~Igls~~QR~wa~lsl~~~v~V~~y~~~~~~~~l~si~lEidf~~k~~~~~~~~D~dela~~f~~~F~~Qift~gQ~  139 (211)
T 1qcs_A           60 VPGSVAFSLPQRKWAGLSIGQEIEVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKMAAEFIQQFNNQAFSVGQQ  139 (211)
T ss_dssp             CTTEEEECHHHHHHHTCCTTCEEEEEEECCCHHHHBEEEEEEEEEESCGGGCCCCEEEHHHHHHHHHHHHTTCEEETTCE
T ss_pred             CCCEeecCHHHHhhhcccCCCcEEEEEecCCCCCceEEEEEEEEEehhcCCCCCcccCHHHHHHHHHHHHcCCCCCCCCE
Confidence            789999999999999999999999986644422 223222233445420 1     133444444445666  5999999


Q ss_pred             EEEEECCEEEEEEEEEec
Q 035839          149 IMIMHNESKYYIDVLETK  166 (238)
Q Consensus       149 I~I~~~~~~y~l~V~e~k  166 (238)
                      |.+.|++..|.|.|.+++
T Consensus       140 l~f~~~g~~l~l~V~~v~  157 (211)
T 1qcs_A          140 LVFSFNDKLFGLLVKDIE  157 (211)
T ss_dssp             EEEEETTEEEEEEEEEEE
T ss_pred             EEEEECCcEEEEEEeEEE
Confidence            999999999999998753

>1cz4_A VCP-like ATPase; double-PSI beta-barrel, beta-CLAM, substrate recognition DOM hydrolase; NMR {Thermoplasma acidophilum} SCOP: b.52.2.3 d.31.1.1 PDB: 1cz5_A

Probab=88.41  E-value=0.31  Score=40.86  Aligned_cols=82  Identities=10%  Similarity=0.142  Sum_probs=58.0

Q ss_pred             CCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecC-ccccccCCChHHHHHHhhccCcccccCCEEEEEECCEE
Q 035839           79 EGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHT-KGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHNESK  157 (238)
Q Consensus        79 EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s-~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~~~~  157 (238)
                      .|.|+|+.=.|+.|+|.+||.|.|+.   .+.+.++.-|.. .+.    .+=.--|-..+|+-.-+..||.+.|.-    
T Consensus        21 r~ivrl~p~~m~~Lgl~~GD~V~I~G---~r~t~a~v~~~~~ed~----~~g~Irid~~~R~N~gv~iGD~V~V~~----   89 (185)
T 1cz4_A           21 MSRVRLDESSRRLLDAEIGDVVEIEK---VRKTVGRVYRARPEDE----NKGIVRIDSVMRNNCGASIGDKVKVRK----   89 (185)
T ss_dssp             SSEEEECHHHHHTTCCCTTCEEEEES---SSEEEEEEEECSSTTT----TTSEEECCHHHHHHHTCCTTCEEEEEE----
T ss_pred             CCEEEECHHHHHHcCCCCCCEEEEEc---CCeEEEEEEEcCcCcC----CCCEEEeCHHHHhccCCCCCCEEEEEE----
Confidence            47799999999999999999999974   567888888863 221    111111234566667789999999964    


Q ss_pred             EEEEEEEecCCCceEEEeC
Q 035839          158 YYIDVLETKPSNAVSITET  176 (238)
Q Consensus       158 y~l~V~e~kP~~aVsIidT  176 (238)
                           .+++++.-|.+--+
T Consensus        90 -----~~~~~A~~V~l~P~  103 (185)
T 1cz4_A           90 -----VRTEIAKKVTLAPI  103 (185)
T ss_dssp             -----ECCCBCSEEEEEEE
T ss_pred             -----CCCCCccEEEEecc
Confidence                 25667776666533

>3tiw_A Transitional endoplasmic reticulum ATPase; beta-barrel alpha-helix, transport protein ATPase ubiquitin ubiquitin, phosphorylation; 1.80A {Homo sapiens} PDB: 3qq8_A 3qq7_A 3qc8_A

Probab=87.59  E-value=0.32  Score=41.09  Aligned_cols=71  Identities=17%  Similarity=0.207  Sum_probs=52.0

Q ss_pred             CCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEEC
Q 035839           78 DEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHN  154 (238)
Q Consensus        78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~  154 (238)
                      |.|.+.|+.-.|+.|+|.+||.|.|+..+ -+-|.++..|..    + ...-+--|-..+|+-..+..||.+.|.--
T Consensus        35 D~givrl~p~~m~~Lgl~~GD~V~I~Gkr-~k~Tva~v~~~~----~-~~~g~Irid~~~R~N~gV~iGD~V~V~~~  105 (187)
T 3tiw_A           35 DNSVVSLSQPKMDELQLFRGDTVLLKGKK-RREAVCIVLSDD----T-CSDEKIRMNRVVRNNLRVRLGDVISIQPC  105 (187)
T ss_dssp             CTTEEEECHHHHHHHTCCTTCEEEEECST-TCEEEEEEEECT----T-SCTTEEEECHHHHHHTTCCTTCEEEEEEC
T ss_pred             CCcEEEECHHHHHHcCCCCCCEEEEECCC-CCeEEEEEEECC----C-CCCCEEEeCHHHHhhcCCCCCCEEEEEEC
Confidence            47899999999999999999999999742 124777777753    2 22212223456677778999999999754

>2l66_A SSO7C4, transcriptional regulator, ABRB family; DNA binding protein, transcription regulator; NMR {Sulfolobus solfataricus}

Probab=87.57  E-value=0.51  Score=31.69  Aligned_cols=38  Identities=16%  Similarity=0.205  Sum_probs=30.9

Q ss_pred             eCCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeec
Q 035839           77 ADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPH  118 (238)
Q Consensus        77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~  118 (238)
                      ...|.|.+|.=+.+.|++++||.|.+...   .+. +.|+|.
T Consensus         9 ~~kgqi~IPk~ir~~lgi~~Gd~v~i~~~---~~~-ivl~p~   46 (53)
T 2l66_A            9 SRNYQVTIPAKVRQKFQIKEGDLVKVTFD---ESE-GVVKIQ   46 (53)
T ss_dssp             CSSSCBCCCHHHHHHSCCCTTCEEEEEEC---SSS-CCEEEE
T ss_pred             CCCCEEEeCHHHHHHcCcCCCCEEEEEEE---CCE-EEEEEC
Confidence            36799999999999999999999988753   232 667775

>3qwz_A Transitional endoplasmic reticulum ATPase; UBX, P97 binding, transport protein; HET: MLY; 2.00A {Homo sapiens} PDB: 2pjh_B

Probab=84.16  E-value=0.54  Score=40.42  Aligned_cols=71  Identities=17%  Similarity=0.210  Sum_probs=51.3

Q ss_pred             CCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEEEC
Q 035839           78 DEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIMHN  154 (238)
Q Consensus        78 ~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~~~  154 (238)
                      |.|.+.|+.-.|+.|+|.+||.|.|+..+ -+-|.++..|.. +    ...-+--|-..+|+-..+..||.+.|.--
T Consensus        38 Drgivrl~p~~m~~Lgl~~GD~V~I~Gkr-~k~Tva~v~~~~-~----~~~g~Irid~~~R~N~gV~iGD~V~V~~~  108 (211)
T 3qwz_A           38 DNSVVSLSQPKMDELQLFRGDTVLLKGXK-RREAVCIVLSDD-T----CSDEKIRMNRVVRNNLRVRLGDVISIQPC  108 (211)
T ss_dssp             CTTEEEECHHHHHHHTCCBTCEEEEECST-TCEEEEEEEECT-T----SCTTEEEECHHHHHHTTCCTTCEEEEEEC
T ss_pred             CCcEEEECHHHHHHcCCCCCCEEEEeCCC-CCcEEEEEEeCC-C----CCCCEEEeCHHHHhhcCCCCCCEEEEEEC
Confidence            47899999999999999999999999742 224777777753 1    11112223456677778999999999644

>2glw_A PHS018, 92AA long hypothetical protein; RIFT barrel, bioinformatics, transcription; NMR {Pyrococcus horikoshii}

Probab=83.66  E-value=4.1  Score=30.48  Aligned_cols=72  Identities=13%  Similarity=0.144  Sum_probs=46.0

Q ss_pred             CCCCCeeeecHHHHHHHHhCCCCCceEEE-EEeCCCCCeEEEEEeeeE-eCCCcEeccHhHHhhcCCCCCCeEEEEE
Q 035839           30 HEPGDKIIMPQSAFDRLAHTEVGYPMMFE-LCNLSSGKTTHCGVVEFT-ADEGFIYLPNWMMDNMKLQEYELVRVTN  104 (238)
Q Consensus        30 ~~~gdKIiLP~SaL~~L~~~~i~~Pm~F~-i~n~~~~~~th~GVlEF~-A~EG~i~lP~Wmm~~L~l~~gd~V~v~~  104 (238)
                      +...++|.+|.++-+.|.-..-. -+.++ +.-....+  ..+..... ...|.+.+|.-+.+.|++++||.|.+..
T Consensus        11 v~~~gqvtiP~~iR~~LgI~~GD-~V~v~~i~~~~g~~--~~~~~~~~v~~kGqitIPkeiR~~lgi~~Gd~l~~~~   84 (92)
T 2glw_A           11 VHRIGRIIIPAGTRKFYGIEQGD-FVEIKIVKYEGEEP--KEGTFTARVGEQGSVIIPKALRDVIGIKPGEVIEVLL   84 (92)
T ss_dssp             CBGGGEEECCHHHHHHHTCCTTC-EEEEEEEEEETTEE--EEEEEEEECCGGGEEECCHHHHHHHTCCTTCEEEEEE
T ss_pred             EeCCCEEEecHHHHHHcCCCCCC-EEEEEEEEecCCcc--ceeEEEEEECcCceEECcHHHHHHcCCCCCCEEEEEE
Confidence            45678999999999877522112 22232 21111111  22222232 5789999999999999999999988764

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	238
d1e32a3	94	Membrane fusion atpase p97 domain 2, P97-Nc {Mouse	96.94
d1cz5a2	94	C-terminal domain of VAT-N, VAT-Nc {Archaeon Therm	95.45
d1wlfa1	80	Peroxisome biogenesis factor 1 (PEX-1), domain 2 {	94.02
d1e32a1	86	Membrane fusion ATPase p97 N-terminal domain , P97	89.8

>d1e32a3 d.31.1.1 (A:107-200) Membrane fusion atpase p97 domain 2, P97-Nc {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Cdc48 domain 2-like
superfamily: Cdc48 domain 2-like
family: Cdc48 domain 2-like
domain: Membrane fusion atpase p97 domain 2, P97-Nc
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.94  E-value=0.0023  Score=47.39  Aligned_cols=74  Identities=16%  Similarity=0.248  Sum_probs=56.0

Q ss_pred             eCCceeEEEeecCccccccCC-C-hHHHHHHhhc-cCcccccCCEEEEEECCEEEEEEEEEecCCCceEEEeCceEEEe
Q 035839          107 LAKATYMKLQPHTKGFLDELS-N-PRAVLEAILR-KFSCLTTGDTIMIMHNESKYYIDVLETKPSNAVSITETDCEVDF  182 (238)
Q Consensus       107 LPkgt~vkLqP~s~~F~~~i~-n-pKavLE~~Lr-nys~LT~Gd~I~I~~~~~~y~l~V~e~kP~~aVsIidTDl~VDf  182 (238)
                      +|-|+.|.+-|-+..--. ++ | .+.+|.-.+. +|--+++||++.|....+..+|+|++++|++ .|||-.|-.+.-
T Consensus         2 i~~~krV~vlP~~DTieg-lsgnlf~~ylkPYf~~~yrPv~~gD~f~v~g~~r~VEFKVv~~dp~~-~~iV~~~T~I~~   78 (94)
T d1e32a3           2 VKYGKRIHVLPIDDTVEG-ITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSP-YCIVAPDTVIHC   78 (94)
T ss_dssp             CCBCSCEEEEEBGGGTTT-CBSCHHHHTHHHHHTTSCEEEETTCEEEEEETTEEEEEEEEEESSSS-EEEECTTCCCBC
T ss_pred             CCcccEEEEEecccccCC-CCccHHHHHHhHHHhhcCccccCCCEEEEccCCeeEEEEEEeecCCC-ceEEcCCCEEEe
Confidence            688889999997643322 42 2 4456666666 6889999999999999999999999999998 466655555443

>d1cz5a2 d.31.1.1 (A:92-185) C-terminal domain of VAT-N, VAT-Nc {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: Alpha and beta proteins (a+b)
fold: Cdc48 domain 2-like
superfamily: Cdc48 domain 2-like
family: Cdc48 domain 2-like
domain: C-terminal domain of VAT-N, VAT-Nc
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=95.45  E-value=0.015  Score=42.61  Aligned_cols=73  Identities=15%  Similarity=0.170  Sum_probs=53.2

Q ss_pred             CceeEEEeecCccccccC---CChHHHHHHhhccCcccccCCEEEEEE----CCEEEEEEEEEecCCCceEEEeCceEEE
Q 035839          109 KATYMKLQPHTKGFLDEL---SNPRAVLEAILRKFSCLTTGDTIMIMH----NESKYYIDVLETKPSNAVSITETDCEVD  181 (238)
Q Consensus       109 kgt~vkLqP~s~~F~~~i---~npKavLE~~Lrnys~LT~Gd~I~I~~----~~~~y~l~V~e~kP~~aVsIidTDl~VD  181 (238)
                      .|+.|.|.|-...=.. |   .|.-..|-+.|..+ -+++||+|.|..    .++...|.|++++|.+..++|.-|=+++
T Consensus         3 ~A~kVvLAP~~~~~~~-i~~~~~~~~ylk~~L~gr-PV~~GD~i~v~~~~~~g~~~i~F~Vv~t~P~g~~ViIt~~TeI~   80 (94)
T d1cz5a2           3 IAKKVTLAPIIRKDQR-LKFGEGIEEYVQRALIRR-PMLEQDNISVPGLTLAGQTGLLFKVVKTLPSKVPVEIGEETKIE   80 (94)
T ss_dssp             BCSEEEEEECSCTTTT-CCCCSSHHHHHHHHHSSC-EECTTCEECCSSCCCSSCCCCSEEEEEESSSSSCEECCTTCEEE
T ss_pred             cccEEEECcCCCccce-EEEcCCHHHHHHHHHcCC-CCcCCCEEEEeeccccCCceEeEEEEEEeCCCCeEEECCCeEEE
Confidence            5788999996433222 3   36777788888874 689999999964    3477899999999998655665555555


Q ss_pred             ec
Q 035839          182 FA  183 (238)
Q Consensus       182 f~  183 (238)
                      +.
T Consensus        81 i~   82 (94)
T d1cz5a2          81 IR   82 (94)
T ss_dssp             EC
T ss_pred             Ee
Confidence            53

>d1wlfa1 d.31.1.1 (A:100-179) Peroxisome biogenesis factor 1 (PEX-1), domain 2 {Mouse (Mus musculus) [TaxId: 10090]}

class: Alpha and beta proteins (a+b)
fold: Cdc48 domain 2-like
superfamily: Cdc48 domain 2-like
family: Cdc48 domain 2-like
domain: Peroxisome biogenesis factor 1 (PEX-1), domain 2
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=94.02  E-value=0.016  Score=41.42  Aligned_cols=77  Identities=14%  Similarity=0.206  Sum_probs=62.6

Q ss_pred             CCceeEEEeecCccccccCCChHHHHHHhhc-cCcccccCCEEEEEEC-CEEEEEEEEEecCCCceEEEeCceEEEecC
Q 035839          108 AKATYMKLQPHTKGFLDELSNPRAVLEAILR-KFSCLTTGDTIMIMHN-ESKYYIDVLETKPSNAVSITETDCEVDFAP  184 (238)
Q Consensus       108 Pkgt~vkLqP~s~~F~~~i~npKavLE~~Lr-nys~LT~Gd~I~I~~~-~~~y~l~V~e~kP~~aVsIidTDl~VDf~p  184 (238)
                      .+++.|-+.|.+.+=++-|.-.-..||..|- +-.+++.|.++.++-+ +..-.|+|..++|+.....+..|-||=++|
T Consensus         2 ~~~~~V~veP~T~dDWEIiEl~a~~lE~~LL~QiRiV~~~~~~~v~v~~~~~~~~~V~~i~P~~~~~~L~~~TEv~VaP   80 (80)
T d1wlfa1           2 VSCQQVEVEPLSADDWEILELHAISLEQHLLDQIRIVFPKAVVPIWVDQQTYIFIQIVTLMPAAPYGRLETNTKLLIQP   80 (80)
T ss_dssp             EECSEEEEEESSHHHHHHHHHSCSSHHHHHHHHCCEECTTCEEEEESSSSCEEEEEEEEEESCCSSEECCTTCEEEECC
T ss_pred             cceEEEEEecCChhhHHHHHHHHHHHHHHHHhheeeccCCCEEEEEECCCcEEEEEEEEecCCCeeEEecCCCEEEeCC
Confidence            3578899999998777723445556777766 6999999999999987 478899999999998888899999987765

>d1e32a1 b.52.2.3 (A:21-106) Membrane fusion ATPase p97 N-terminal domain , P97-Nn {Mouse (Mus musculus) [TaxId: 10090]}

class: All beta proteins
fold: Double psi beta-barrel
superfamily: ADC-like
family: Cdc48 N-terminal domain-like
domain: Membrane fusion ATPase p97 N-terminal domain , P97-Nn
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=89.80  E-value=0.096  Score=37.41  Aligned_cols=70  Identities=19%  Similarity=0.178  Sum_probs=47.2

Q ss_pred             eCCCcEeccHhHHhhcCCCCCCeEEEEEeeeCCceeEEEeecCccccccCCChHHHHHHhhccCcccccCCEEEEE
Q 035839           77 ADEGFIYLPNWMMDNMKLQEYELVRVTNVSLAKATYMKLQPHTKGFLDELSNPRAVLEAILRKFSCLTTGDTIMIM  152 (238)
Q Consensus        77 A~EG~i~lP~Wmm~~L~l~~gd~V~v~~~~LPkgt~vkLqP~s~~F~~~i~npKavLE~~Lrnys~LT~Gd~I~I~  152 (238)
                      .+.|.+.|..-.|+.|+|.+||.|.|+-.   +.+-...-|...+=   ...=.--|-...|+=...+.||++.|.
T Consensus        14 ~D~~iarl~p~~m~~Lgl~~GD~V~I~Gk---r~t~av~~~~~~~d---~~~g~Irid~~~R~Nagv~iGD~V~V~   83 (86)
T d1e32a1          14 EDNSVVSLSQPKMDELQLFRGDTVLLKGK---KRREAVCIVLSDDT---CSDEKIRMNRVVRNNLRVRLGDVISIQ   83 (86)
T ss_dssp             CCTTEEEECHHHHHHTTCCTTCEEEEECS---TTCEEEEEEEECTT---SCSSEEEECHHHHHHTTCCTTCEEEEE
T ss_pred             CCCCEEEECHHHHHHcCCCCCCEEEEEcC---CceeEEEEEeccCC---CCCCEEEecHHHHhhcCcCCCCEEEEE
Confidence            36788999999999999999999999876   34444444432111   111111134566666778899999885