Citrus Sinensis ID: 024476

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------
Protein Sequence
MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPPLDYKEPEKPIASASSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTYQPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQKPVAEKEIKQELPEKKEEPKFRPFTGKKYSLKG
Secondary Structure (PSIPRED)
cEEEEEEcccccEEEEEEEEEEccccEEEEcHHHHHHcccccccEEEEEEEEcccccEEEEEEccccccccccccHHHHccccccEEcccccEEEEEEccEEEEEEEEEEcccccEEEEEccEEEEEccccccccccccccccccHHHHHcccccccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccEEEEEEcccccccccccccccHHcccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cEEEEEcccccccccccEEEEEcccccEEcHHHHHHHcccccccEEEEEEccccccEEEEEccccccHcccccHHHHHHHHHHHHHHHccccEEEEEEcccEEEEEEEEEcccccEEEEEEccEEEccccccccccccccccccccccHHccHHHcccccccccccccccEccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccccccccccEccc
Coil and Loop (DISEMBL)
MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLqegdivrvknvtlpkgtyvklqphtkdfldisnpkAILETTLRnysclttgDSIMVAYNNKKYYIDIIetkpsnaisiietdcevdfappldykepekpiasaSSRATAKAEeasvetepkfspftgvarrldgkpltyqpppvpslgskdkqpatsngtgqpsagstsqnaarqsqgklvfgsnaslhpketqkpvAEKEIKqelpekkeepkfrpftgkkyslkg
Flexible Loop (DISEMBL)
mlfelrnnaaervshcgVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKgtyvklqphtkdfldisnPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPPLDYKEPEKPIASASSRATAKAeeasvetepkfspftgvARRLDGKPLTYQPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFgsnaslhpketqkpvaekeikqelpekkeepkfrpftgkkyslkg
Low Complexity Region (SEG)
MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPPLDYKEPEKPIASASSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTYQPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQKPVAekeikqelpekkeepkFRPFTGKKYSLKG
Disordered region (IsUnstruct)
**********ERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAP******************************************************************************************************************************************
Disordered Region (DISOPRED)
MLFE***NAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPPL**************************************************************************************GKLVFGSNA**********************************KKYSL**
Disordered Region (DISEMBL)
MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPPLDYKEPE***********************KFSPFTGVARRLDGKPLTYQPPPVP********************************GKLVFGSNASLHPKETQKPVAEKEIKQELPEKKEEPKFRPFTGKKYSLKG
Disordered Region (DISPRO)
MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPPLDYKE************************************************************************************************************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPPLDYKEPEKPIASASSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTYQPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQKPVAEKEIKQELPEKKEEPKFRPFTGKKYSLKG
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	267	2.2.26 [Sep-21-2011]
Q9ES53	307	Ubiquitin fusion degradat	yes	no	0.689	0.599	0.518	1e-53
P70362	307	Ubiquitin fusion degradat	yes	no	0.689	0.599	0.518	2e-53
Q92890	307	Ubiquitin fusion degradat	yes	no	0.689	0.599	0.513	8e-53
Q55BK0	330	Ubiquitin fusion degradat	yes	no	0.677	0.548	0.473	2e-49
Q9VTF9	316	Ubiquitin fusion degradat	yes	no	0.655	0.553	0.505	4e-47
Q19584	342	Ubiquitin fusion degradat	yes	no	0.655	0.511	0.443	3e-40
P53044	361	Ubiquitin fusion degradat	yes	no	0.513	0.379	0.528	4e-39
O42915	342	Ubiquitin fusion degradat	yes	no	0.677	0.529	0.412	2e-38

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

 Score =  209 bits (532), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 96/185 (51%), Positives = 129/185 (69%), Gaps = 1/185 (0%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLF+L N  ++R++HCGVLEF+A+EG+ Y+P+WMM+NLLL+EG +V+V++V L   TY K
Sbjct: 65  MLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSK 124

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
            QP + DFLDI+NPKA+LE  LRN++CLTTGD I + YN K Y + ++ETKP  A+SIIE
Sbjct: 125 FQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIE 184

Query: 121 TDCEVDFAPPLDYKEPEKPIASASSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTYQ 180
            D  VDF  PL YKEPE+P+    S    +A+ +    E  F  F+G   RLDGK    +
Sbjct: 185 CDMNVDFDAPLGYKEPERPVQHEES-IEGEADHSGYAGEVGFRAFSGSGNRLDGKKKGVE 243

Query: 181 PPPVP 185
           P P P
Sbjct: 244 PSPSP 248

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

 Score =  209 bits (532), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 96/185 (51%), Positives = 129/185 (69%), Gaps = 1/185 (0%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLF+L N  ++R++HCGVLEF+A+EG+ Y+P+WMM+NLLL+EG +V+V++V L   TY K
Sbjct: 65  MLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSK 124

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
            QP + DFLDI+NPKA+LE  LRN++CLTTGD I + YN K Y + ++ETKP  A+SIIE
Sbjct: 125 FQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIE 184

Query: 121 TDCEVDFAPPLDYKEPEKPIASASSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTYQ 180
            D  VDF  PL YKEPE+P+    S    +A+ +    E  F  F+G   RLDGK    +
Sbjct: 185 CDMNVDFDAPLGYKEPERPVQHEES-IEGEADHSGYAGEVGFRAFSGSGNRLDGKKKGVE 243

Query: 181 PPPVP 185
           P P P
Sbjct: 244 PSPSP 248

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

 Score =  207 bits (526), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 95/185 (51%), Positives = 128/185 (69%), Gaps = 1/185 (0%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLF+L N  ++R++HCGVLEF+A+EG+ Y+P+WMM+NLLL+EG +V+V++V L   TY K
Sbjct: 65  MLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSK 124

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
            QP + DFLDI+NPKA+LE  LRN++CLTTGD I + YN K Y + ++ETKP  A+SIIE
Sbjct: 125 FQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIE 184

Query: 121 TDCEVDFAPPLDYKEPEKPIASASSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTYQ 180
            D  VDF  PL YKEPE+ +    S    +A+ +    E  F  F+G   RLDGK    +
Sbjct: 185 CDMNVDFDAPLGYKEPERQVQHEES-TEGEADHSGYAGELGFRAFSGSGNRLDGKKKGVE 243

Query: 181 PPPVP 185
           P P P
Sbjct: 244 PSPSP 248

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

 Score =  196 bits (497), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 100/211 (47%), Positives = 130/211 (61%), Gaps = 30/211 (14%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLFE+ N  + + SHCGVLEFIAEEG+ Y+P WMM+NL L+EG+ + +KN TL KGT+VK
Sbjct: 69  MLFEISNPISGKKSHCGVLEFIAEEGICYLPLWMMQNLQLKEGEFIDIKNATLAKGTFVK 128

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
           +QP T +F+DISNPKA+LE +LR ++ LT  D IM+ YNN KYY+ ++E KP+NAISIIE
Sbjct: 129 IQPRTSNFIDISNPKAVLENSLRKFATLTKDDEIMIDYNNTKYYLKVVELKPANAISIIE 188

Query: 121 TDCEVDFAPPLDYKE---------------PEKPIASASSRATA------------KAEE 153
            D  VDFAPP+D KE               P K +    +  +A               +
Sbjct: 189 ADVSVDFAPPMDSKEATSPSTSSPGSHVSGPSKGLTFGPASTSAKPIPGGKKKKDESDSD 248

Query: 154 ASVETEPKFSPFTGVARRLDGK---PLTYQP 181
           +  + EPKF  F G   RLDGK   PL   P
Sbjct: 249 SDSDDEPKFKAFAGTGARLDGKVGTPLGTSP 279

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 =  188 bits (477), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 92/182 (50%), Positives = 118/182 (64%), Gaps = 7/182 (3%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLF+L N    R SH GVLEF+A+EG  Y+P+WMMENLLL EGDI+ +++V+LP  T+ K
Sbjct: 62  MLFKLTNVKKSRSSHAGVLEFVADEGKCYLPHWMMENLLLGEGDILNIESVSLPVATFSK 121

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
            QPH+ DFLDI+NPKA+LE  LRN++CLT GD I + YN K Y + ++ETKP NA+SIIE
Sbjct: 122 FQPHSTDFLDITNPKAVLENALRNFACLTRGDVIAIKYNKKVYELCVLETKPGNAVSIIE 181

Query: 121 TDCEVDFAPPLDYKEPEKPIASASSR----ATAKAEEASVET---EPKFSPFTGVARRLD 173
            D  V+F  P+ YK+  +  AS S +     T   E A       E     F G   RLD
Sbjct: 182 CDMNVEFEAPVGYKDHSETQASGSGQQGAAGTVGGEIAGATNAILEEVVETFKGSGVRLD 241

Query: 174 GK 175
           GK
Sbjct: 242 GK 243

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

Drosophila melanogaster (taxid: 7227)

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

 Score =  165 bits (418), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 83/187 (44%), Positives = 112/187 (59%), Gaps = 12/187 (6%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLF+L N A +RV+HCGVLEF A EG   +P WMM+ L L +GD +R+++ TLPK T+ K
Sbjct: 69  MLFKLTNMAVQRVTHCGVLEFSAPEGQAILPLWMMQQLGLDDGDTIRIESATLPKATFAK 128

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
           L+P + +FL+I+NPKA+LE  LR Y+CLT  D I  +Y  +     +++ KP+N++ IIE
Sbjct: 129 LKPMSLEFLNITNPKAVLEVELRKYACLTKNDRIPTSYAGQTLEFLVVDLKPANSVCIIE 188

Query: 121 TDCEVDFAPPLDYKE------------PEKPIASASSRATAKAEEASVETEPKFSPFTGV 168
            D  +DF PP  Y E            P  P ASA   A  KA  +    +   S F G 
Sbjct: 189 CDVNLDFDPPEGYVEQPRQVTPAVTAKPPAPDASAFIGAGQKAGGSGGTGQNATSVFGGA 248

Query: 169 ARRLDGK 175
            RRLDGK
Sbjct: 249 GRRLDGK 255

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

Caenorhabditis elegans (taxid: 6239)

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

 Score =  161 bits (408), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 74/140 (52%), Positives = 99/140 (70%), Gaps = 3/140 (2%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLF+L  N   RV+H GVLEFIAEEG +Y+P WMME L +Q G ++++ +  +P G +VK
Sbjct: 67  MLFKLTANETGRVTHGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVK 126

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKP---SNAIS 117
           L+P + DFLDIS+PKA+LE  LRN+S LT  D I ++YN K + I I+E KP   S +I 
Sbjct: 127 LEPQSVDFLDISDPKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSIC 186

Query: 118 IIETDCEVDFAPPLDYKEPE 137
           +IETD   DFAPP+ Y EP+
Sbjct: 187 VIETDLVTDFAPPVGYVEPD 206

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

 Score =  159 bits (402), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 78/189 (41%), Positives = 116/189 (61%), Gaps = 8/189 (4%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLF+  N AAE+ +H GVLEFIAEEG +Y+PYWMM  L L+ GD+VRV N  + +G+YVK
Sbjct: 77  MLFDFENEAAEKKTHGGVLEFIAEEGRVYLPYWMMTTLSLEPGDLVRVINTDIAQGSYVK 136

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNA---IS 117
           LQP + +FLDI++ +A+LE  LRN+S LT  D   + YN++ Y I +I+ +P ++   +S
Sbjct: 137 LQPQSVNFLDITDHRAVLENALRNFSTLTKSDIFEILYNDQVYQIKVIDVQPDDSRHVVS 196

Query: 118 IIETDCEVDFAPPLDYKEP-----EKPIASASSRATAKAEEASVETEPKFSPFTGVARRL 172
           ++ETD  VDF PP+ Y+E      ++ IA        K     +  +   +   G   +L
Sbjct: 197 VVETDLVVDFDPPIGYEESLQKNKQQNIAGVQGTMVTKIGYDELVRQGDSNLMKGTGTKL 256

Query: 173 DGKPLTYQP 181
           +GK +   P
Sbjct: 257 NGKEVAEVP 265

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)

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	267
118488238	324	unknown [Populus trichocarpa]	1.0	0.824	0.832	1e-126
224103317	323	predicted protein [Populus trichocarpa]	1.0	0.826	0.832	1e-126
255543881	356	ubiquitin fusion degradaton protein, put	0.996	0.747	0.828	1e-119
357521303	320	Ubiquitin fusion degradation protein [Me	0.992	0.828	0.783	1e-116
224080470	258	predicted protein [Populus trichocarpa]	0.876	0.906	0.864	1e-115
449526164	321	PREDICTED: ubiquitin fusion degradation	0.996	0.828	0.776	1e-114
449464840	321	PREDICTED: ubiquitin fusion degradation	0.996	0.828	0.772	1e-113
297744721	309	unnamed protein product [Vitis vinifera]	0.988	0.854	0.802	1e-110
225427780	319	PREDICTED: ubiquitin fusion degradation	0.988	0.827	0.802	1e-109
297821317	319	hypothetical protein ARALYDRAFT_480987 [	0.988	0.827	0.75	1e-109

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

 Score =  455 bits (1171), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 224/269 (83%), Positives = 241/269 (89%), Gaps = 2/269 (0%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLFEL+N+AAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGD VRVKNVTLPKG YVK
Sbjct: 56  MLFELQNDAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDTVRVKNVTLPKGKYVK 115

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
           LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE
Sbjct: 116 LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 175

Query: 121 TDCEVDFAPPLDYKEPEKPIASA-SSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTY 179
           TDCEVDFAPPLDYKEPEKP+AS   S+AT++AEE   ETEPKF+PFTG  RRLDGKPL+Y
Sbjct: 176 TDCEVDFAPPLDYKEPEKPVASVPPSKATSQAEEVPAETEPKFNPFTGAGRRLDGKPLSY 235

Query: 180 QPPP-VPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQKPVA 238
           QPPP + S  SKDKQPA ++G+ QPS GS+SQN AR+SQGKLVFGSN    PKETQ+  +
Sbjct: 236 QPPPALSSSVSKDKQPAVADGSRQPSLGSSSQNTARKSQGKLVFGSNTGRTPKETQREES 295

Query: 239 EKEIKQELPEKKEEPKFRPFTGKKYSLKG 267
            KE KQE PEKKEEPKF+ FTGKKYSLKG
Sbjct: 296 GKETKQEQPEKKEEPKFQAFTGKKYSLKG 324

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  455 bits (1170), Expect = e-126,   Method: Compositional matrix adjust.
 Identities = 224/269 (83%), Positives = 241/269 (89%), Gaps = 2/269 (0%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLFEL+N+AAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGD VRVKNVTLPKG YVK
Sbjct: 55  MLFELQNDAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDTVRVKNVTLPKGKYVK 114

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
           LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE
Sbjct: 115 LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 174

Query: 121 TDCEVDFAPPLDYKEPEKPIASA-SSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTY 179
           TDCEVDFAPPLDYKEPEKP+AS   S+AT++AEE   ETEPKF+PFTG  RRLDGKPL+Y
Sbjct: 175 TDCEVDFAPPLDYKEPEKPVASVPPSKATSQAEEVPAETEPKFNPFTGAGRRLDGKPLSY 234

Query: 180 QPPP-VPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQKPVA 238
           QPPP + S  SKDKQPA ++G+ QPS GS+SQN AR+SQGKLVFGSN    PKETQ+  +
Sbjct: 235 QPPPALSSSVSKDKQPAVADGSRQPSLGSSSQNTARKSQGKLVFGSNTGRTPKETQREES 294

Query: 239 EKEIKQELPEKKEEPKFRPFTGKKYSLKG 267
            KE KQE PEKKEEPKF+ FTGKKYSLKG
Sbjct: 295 GKETKQEQPEKKEEPKFQAFTGKKYSLKG 323

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255543881|ref|XP_002513003.1| ubiquitin fusion degradaton protein, putative [Ricinus communis] gi|223548014|gb|EEF49506.1| ubiquitin fusion degradaton protein, putative [Ricinus communis]

 Score =  433 bits (1114), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 222/268 (82%), Positives = 236/268 (88%), Gaps = 2/268 (0%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLFELRN+AAER+SHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK
Sbjct: 90  MLFELRNDAAERISHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 149

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
           LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDI+ETKPSNAISIIE
Sbjct: 150 LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIVETKPSNAISIIE 209

Query: 121 TDCEVDFAPPLDYKEPEKPIASA-SSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTY 179
           TDCEVDFAPPLDYKEPE+   S    +ATA+ EE   ETEPKF+PFTGVARRLDGKPL  
Sbjct: 210 TDCEVDFAPPLDYKEPERTTPSIPQKKATAQVEEVPEETEPKFNPFTGVARRLDGKPLKQ 269

Query: 180 QPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQKPVAE 239
           QP PV S GSKDKQ A  +G GQPS  S+SQN+ARQSQGKLVFGSN +  PKETQK VA 
Sbjct: 270 QPFPVSSQGSKDKQAAVPSGRGQPSLESSSQNSARQSQGKLVFGSNVNRAPKETQKEVA- 328

Query: 240 KEIKQELPEKKEEPKFRPFTGKKYSLKG 267
           KE K E  +K EEPKF+PFTG+KYSLKG
Sbjct: 329 KETKPEQSQKNEEPKFQPFTGRKYSLKG 356

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

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 =  423 bits (1088), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 210/268 (78%), Positives = 231/268 (86%), Gaps = 3/268 (1%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLFELRN AAERVSHCGVLEFIAEEGMIYMPYWMMEN+LLQEGD+VRVKNVTLPKGTYVK
Sbjct: 55  MLFELRNAAAERVSHCGVLEFIAEEGMIYMPYWMMENMLLQEGDVVRVKNVTLPKGTYVK 114

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
           LQPHTKDFLDISNPKAILETTLRN+SCLTTGDSIMVAYNNKKYYIDI+E+KP+NAISIIE
Sbjct: 115 LQPHTKDFLDISNPKAILETTLRNFSCLTTGDSIMVAYNNKKYYIDIVESKPANAISIIE 174

Query: 121 TDCEVDFAPPLDYKEPEKPIASASSRATAKAE-EASVETEPKFSPFTGVARRLDGKPLTY 179
           TDCEVDFAPPLDYKEPE+P+A  S+    +A+ EA  ETEPKF+PFTG  RRLDGKPL Y
Sbjct: 175 TDCEVDFAPPLDYKEPERPVAPRSAGKAPEADKEAPAETEPKFNPFTGSGRRLDGKPLNY 234

Query: 180 QPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQKPVAE 239
           QPPPV S GSKDK PA  N   QPS  S+SQ+ A Q+QGKLVFGSN +   KET K   E
Sbjct: 235 QPPPVSSSGSKDKNPAAQNVNSQPSTASSSQSNAPQTQGKLVFGSNPN-RGKETGK-ATE 292

Query: 240 KEIKQELPEKKEEPKFRPFTGKKYSLKG 267
            + KQE P++KEE KF+PFTGKKYSL+G
Sbjct: 293 AKAKQEPPKEKEEDKFQPFTGKKYSLRG 320

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224080470|ref|XP_002306140.1| predicted protein [Populus trichocarpa] gi|222849104|gb|EEE86651.1| predicted protein [Populus trichocarpa]

 Score =  421 bits (1082), Expect = e-115,   Method: Compositional matrix adjust.
 Identities = 204/236 (86%), Positives = 216/236 (91%), Gaps = 2/236 (0%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLFELRN AAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKG YVK
Sbjct: 18  MLFELRNAAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGKYVK 77

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
           LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDI+ETKPSNAISIIE
Sbjct: 78  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIVETKPSNAISIIE 137

Query: 121 TDCEVDFAPPLDYKEPEKPIASA-SSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTY 179
           TDCEVDFAPPLDYKEPEKP+AS   S+AT++AEE   ETEPKF+PFTG  RRLDGKP++Y
Sbjct: 138 TDCEVDFAPPLDYKEPEKPVASVPPSKATSQAEEVPAETEPKFNPFTGTGRRLDGKPMSY 197

Query: 180 QPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQK 235
           QPPPV S GSKDKQPA +N + QPS GS S+N ARQSQGKLVFGSNAS  PKETQ+
Sbjct: 198 QPPPVSS-GSKDKQPAVANDSRQPSLGSISKNTARQSQGKLVFGSNASRSPKETQQ 252

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  416 bits (1069), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 208/268 (77%), Positives = 228/268 (85%), Gaps = 2/268 (0%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLFELRN+  ER+SHCGVLEFIAEEGMIYMPYWMMEN+LLQEGD+VRVKNVTLPKGTYVK
Sbjct: 55  MLFELRNDVTERLSHCGVLEFIAEEGMIYMPYWMMENMLLQEGDVVRVKNVTLPKGTYVK 114

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
           LQPHTKDFLDISNPKAILETTLRN+SCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE
Sbjct: 115 LQPHTKDFLDISNPKAILETTLRNFSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 174

Query: 121 TDCEVDFAPPLDYKEPEKPIASA-SSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTY 179
           TDCEVDFAPPLDYKEPEKP+ S  + +A  + EE   E EPKF+PFTG  RRLDGKP   
Sbjct: 175 TDCEVDFAPPLDYKEPEKPVPSLPTGKAPVQDEEPPAEAEPKFNPFTGAGRRLDGKPSMQ 234

Query: 180 QPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQKPVAE 239
           Q P   +  SKDKQ  T   TGQPSAGSTS+NA+RQS+GKLVFG NAS  PKET+K   E
Sbjct: 235 QAPLSWTSISKDKQVDTRTVTGQPSAGSTSRNASRQSEGKLVFGGNASRTPKETKKE-GE 293

Query: 240 KEIKQELPEKKEEPKFRPFTGKKYSLKG 267
           K+ KQE  ++KEE KF+PF GKKYSL+G
Sbjct: 294 KDGKQEQTKEKEEAKFQPFGGKKYSLRG 321

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  415 bits (1066), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 207/268 (77%), Positives = 228/268 (85%), Gaps = 2/268 (0%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLFELRN+  ER+SHCGVLEFIAEEGMIYMPYWMMEN+LLQEGD+VRVKNVTLPKGTYVK
Sbjct: 55  MLFELRNDVTERLSHCGVLEFIAEEGMIYMPYWMMENMLLQEGDVVRVKNVTLPKGTYVK 114

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
           LQPHTKDFLDISNPKAILETTLRN+SCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE
Sbjct: 115 LQPHTKDFLDISNPKAILETTLRNFSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 174

Query: 121 TDCEVDFAPPLDYKEPEKPIASA-SSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTY 179
           TDCEVDFAPPLDYKEPEKP+ S  + +A  + EE   E EPKF+PFTG  RRLDGKP   
Sbjct: 175 TDCEVDFAPPLDYKEPEKPVPSLPTGKAPVQDEEPPAEAEPKFNPFTGAGRRLDGKPSMQ 234

Query: 180 QPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQKPVAE 239
           Q P   +  SKDKQ  T   TGQPS+GSTS+NA+RQS+GKLVFG NAS  PKET+K   E
Sbjct: 235 QAPLSWTSISKDKQVDTRTVTGQPSSGSTSRNASRQSEGKLVFGGNASRTPKETKKE-GE 293

Query: 240 KEIKQELPEKKEEPKFRPFTGKKYSLKG 267
           K+ KQE  ++KEE KF+PF GKKYSL+G
Sbjct: 294 KDGKQEQTKEKEEAKFQPFGGKKYSLRG 321

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297744721|emb|CBI37983.3| unnamed protein product [Vitis vinifera]

 Score =  402 bits (1033), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 215/268 (80%), Positives = 236/268 (88%), Gaps = 4/268 (1%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLFEL N AA+RVSHCGVLEFIAEEGMIYMPYWMMEN+LLQEGD V+VKNVTLPKGTYVK
Sbjct: 45  MLFELSNPAAQRVSHCGVLEFIAEEGMIYMPYWMMENMLLQEGDTVQVKNVTLPKGTYVK 104

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
           LQPHT DFLDISNPKAILETTLRN+SCLTTGDSIMVAYNNKKYYIDI+ETKPSNAISIIE
Sbjct: 105 LQPHTTDFLDISNPKAILETTLRNFSCLTTGDSIMVAYNNKKYYIDIVETKPSNAISIIE 164

Query: 121 TDCEVDFAPPLDYKEPEKPIASAS-SRATAKAEEASVETEPKFSPFTGVARRLDGKPLTY 179
           TDCEVDFAPPLD+KEPEKP+A     +A A+ +EA VE EPKF+PF GV RRLDGKP  Y
Sbjct: 165 TDCEVDFAPPLDFKEPEKPVAPVPLGKAAAEVQEAPVEPEPKFNPFCGVGRRLDGKPQKY 224

Query: 180 QPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQKPVAE 239
           +PPPV S GSKDKQP  + G+GQPSAGS+SQ+++RQSQGKLVFGSN +  PKETQK  A 
Sbjct: 225 EPPPVSSSGSKDKQP-VNRGSGQPSAGSSSQSSSRQSQGKLVFGSNVNRSPKETQKEAA- 282

Query: 240 KEIKQELPEKKEEPKFRPFTGKKYSLKG 267
           K  KQE P KKEEPKF+PF+GKKYSLKG
Sbjct: 283 KATKQEEP-KKEEPKFQPFSGKKYSLKG 309

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225427780|ref|XP_002268781.1| PREDICTED: ubiquitin fusion degradation protein 1 homolog [Vitis vinifera]

 Score =  401 bits (1031), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 215/268 (80%), Positives = 236/268 (88%), Gaps = 4/268 (1%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLFEL N AA+RVSHCGVLEFIAEEGMIYMPYWMMEN+LLQEGD V+VKNVTLPKGTYVK
Sbjct: 55  MLFELSNPAAQRVSHCGVLEFIAEEGMIYMPYWMMENMLLQEGDTVQVKNVTLPKGTYVK 114

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
           LQPHT DFLDISNPKAILETTLRN+SCLTTGDSIMVAYNNKKYYIDI+ETKPSNAISIIE
Sbjct: 115 LQPHTTDFLDISNPKAILETTLRNFSCLTTGDSIMVAYNNKKYYIDIVETKPSNAISIIE 174

Query: 121 TDCEVDFAPPLDYKEPEKPIASAS-SRATAKAEEASVETEPKFSPFTGVARRLDGKPLTY 179
           TDCEVDFAPPLD+KEPEKP+A     +A A+ +EA VE EPKF+PF GV RRLDGKP  Y
Sbjct: 175 TDCEVDFAPPLDFKEPEKPVAPVPLGKAAAEVQEAPVEPEPKFNPFCGVGRRLDGKPQKY 234

Query: 180 QPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQKPVAE 239
           +PPPV S GSKDKQP  + G+GQPSAGS+SQ+++RQSQGKLVFGSN +  PKETQK  A 
Sbjct: 235 EPPPVSSSGSKDKQP-VNRGSGQPSAGSSSQSSSRQSQGKLVFGSNVNRSPKETQKEAA- 292

Query: 240 KEIKQELPEKKEEPKFRPFTGKKYSLKG 267
           K  KQE P KKEEPKF+PF+GKKYSLKG
Sbjct: 293 KATKQEEP-KKEEPKFQPFSGKKYSLKG 319

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297821317|ref|XP_002878541.1| hypothetical protein ARALYDRAFT_480987 [Arabidopsis lyrata subsp. lyrata] gi|297324380|gb|EFH54800.1| hypothetical protein ARALYDRAFT_480987 [Arabidopsis lyrata subsp. lyrata]

 Score =  400 bits (1028), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 201/268 (75%), Positives = 225/268 (83%), Gaps = 4/268 (1%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLFE+RN   ERV+HCGVLEFIAEEGMIYMPYWMM+NLLLQEGDIVRV+NVTLPKGTYVK
Sbjct: 55  MLFEVRNAGIERVTHCGVLEFIAEEGMIYMPYWMMQNLLLQEGDIVRVRNVTLPKGTYVK 114

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
           LQPHT DFLDISNPKAILET LRNYSCLTTGDSIMV YNNKKY+IDI+ETKP+NAISIIE
Sbjct: 115 LQPHTTDFLDISNPKAILETALRNYSCLTTGDSIMVPYNNKKYFIDIVETKPANAISIIE 174

Query: 121 TDCEVDFAPPLDYKEPEKPIASASSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTYQ 180
           TDCEVDFAPPLDYKEPE+P A A+++  AKAEE   E EPKF+PFTG  RRLDG+PL Y+
Sbjct: 175 TDCEVDFAPPLDYKEPERPTAPAAAKGPAKAEEVVTEPEPKFNPFTGSGRRLDGRPLAYE 234

Query: 181 PPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQKPV-AE 239
           P P  S  SKDKQP  +NG GQ S  S+S+ A R +QGKLVFG+NA+  PKE    V A 
Sbjct: 235 PAPASS--SKDKQPVVANGNGQSSVASSSEKATR-AQGKLVFGANANRAPKEAAPKVGAA 291

Query: 240 KEIKQELPEKKEEPKFRPFTGKKYSLKG 267
           KE KQE  EKK+EPKF+ F+GKKYSL+G
Sbjct: 292 KETKQEEQEKKDEPKFQAFSGKKYSLRG 319

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

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	267
TAIR|locus:2050054	340	UFD1 "AT2G21270" [Arabidopsis	0.988	0.776	0.697	2.9e-96
TAIR|locus:2120247	315	AT4G38930 "AT4G38930" [Arabido	0.962	0.815	0.653	7.5e-89
TAIR|locus:2066122	312	AT2G29070 [Arabidopsis thalian	0.973	0.833	0.562	1.1e-76
DICTYBASE|DDB_G0271122	330	ufd1 "ubiquitin fusion degrada	0.535	0.433	0.594	6.2e-55
MGI|MGI:109353	307	Ufd1l "ubiquitin fusion degrad	0.689	0.599	0.518	1.5e-49
RGD|619822	307	Ufd1l "ubiquitin fusion degrad	0.689	0.599	0.518	1.5e-49
UNIPROTKB|J9NYF2	307	UFD1L "Uncharacterized protein	0.689	0.599	0.518	4.1e-49
UNIPROTKB|F1RK61	307	UFD1L "Uncharacterized protein	0.689	0.599	0.524	4.1e-49
ZFIN|ZDB-GENE-040718-150	308	ufd1l "ubiquitin fusion degrad	0.692	0.600	0.508	4.1e-49
UNIPROTKB|A6NJ11	296	UFD1L "Ubiquitin fusion degrad	0.689	0.621	0.513	1.1e-48

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

 Score = 957 (341.9 bits), Expect = 2.9e-96, P = 2.9e-96
 Identities = 187/268 (69%), Positives = 211/268 (78%)

Query:     1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
             MLFELRN   ERV+HCGVLEFIAEEGMIYMPYWMM+NLLLQEGDIVRV+NVTLPKGTYVK
Sbjct:    76 MLFELRNAGIERVTHCGVLEFIAEEGMIYMPYWMMQNLLLQEGDIVRVRNVTLPKGTYVK 135

Query:    61 LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
             LQPHT DFLDISNPKAILET LRNYSCLT+GDSIMV YNNKKY+IDI+ETKP+NAISIIE
Sbjct:   136 LQPHTTDFLDISNPKAILETALRNYSCLTSGDSIMVPYNNKKYFIDIVETKPANAISIIE 195

Query:   121 TDCEVDFAPPLDYKEPEKPIASASSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTYQ 180
             TDCEVDFAPPLDYKEPE+P A ++++  AKAEE   E EPKF+PFTG  RRLDG+PL Y+
Sbjct:   196 TDCEVDFAPPLDYKEPERPTAPSAAKGPAKAEEVVDEPEPKFNPFTGSGRRLDGRPLAYE 255

Query:   181 PPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQKPV-AX 239
             P P  S  SK KQP  +NG GQ S  S+S+ A R +QGKLVFG+N +  PKE    V A 
Sbjct:   256 PAPASS--SKGKQPVVANGNGQSSVASSSEKATR-AQGKLVFGANGNRAPKEAAPKVGAA 312

Query:   240 XXXXXXXXXXXXXXXFRPFTGKKYSLKG 267
                            F+ F+GKKYSL+G
Sbjct:   313 KETKKEEQEKKDEPKFQAFSGKKYSLRG 340

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 = 887 (317.3 bits), Expect = 7.5e-89, P = 7.5e-89
 Identities = 177/271 (65%), Positives = 205/271 (75%)

Query:     1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
             MLFELRN + +  SHCGVLEFIAEEG+IY+PYWMM+NLLLQEGD+VRV+NVTLPKGTYVK
Sbjct:    55 MLFELRNASTDSFSHCGVLEFIAEEGVIYIPYWMMQNLLLQEGDMVRVRNVTLPKGTYVK 114

Query:    61 LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
             LQPHT DFLDI+NPKAILET LRNYSCLT GDSIMV YNNKKY+IDI+E KPSN ISIIE
Sbjct:   115 LQPHTTDFLDIANPKAILETALRNYSCLTVGDSIMVPYNNKKYFIDIVEAKPSNGISIIE 174

Query:   121 TDCEVDFAPPLDYKEPEKPIASASSRATAKAEEASV-ETEPKFSPFTGVARRLDGKPLTY 179
             TDCEVDFAPPLDYKEPE+P+A A ++  AKA+E  V E EPKF+PFTG  RRLDG+PL+Y
Sbjct:   175 TDCEVDFAPPLDYKEPERPVAPAPAKGEAKAKEVDVAEAEPKFNPFTGSGRRLDGRPLSY 234

Query:   180 QPPPVPSLGSKDKQPATSNGTGQPSAGSTS---QNAARQSQGKLVFGSNASLHPKETQKP 236
             +P P    G+     A SNG   P A S+S   + A +Q++GKLVFGSN     KET K 
Sbjct:   235 EPQP----GA-----ANSNGQSHPVASSSSSGSEKATQQNRGKLVFGSNVERSTKETTK- 284

Query:   237 VAXXXXXXXXXXXXXXXXFRPFTGKKYSLKG 267
             V                 F+ F+GKKYSL+G
Sbjct:   285 VGAGKDRKQEEEAEKEAKFQAFSGKKYSLRG 315

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 = 772 (276.8 bits), Expect = 1.1e-76, P = 1.1e-76
 Identities = 152/270 (56%), Positives = 188/270 (69%)

Query:     1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
             MLF+L N + E+ SHCGVLEF A+EG++Y+PYWMM+N+ L+EGD+++VKN++L KGTY+K
Sbjct:    50 MLFQLSNVSVEKTSHCGVLEFTADEGLVYLPYWMMQNMSLEEGDVMQVKNISLVKGTYIK 109

Query:    61 LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
             LQPHT+DFLDISNPKAILETTLR+YSCLTTGD+IMV YNNK+YYI+++E KPS+A+SIIE
Sbjct:   110 LQPHTQDFLDISNPKAILETTLRSYSCLTTGDTIMVPYNNKQYYINVVEAKPSSAVSIIE 169

Query:   121 TDCEVDFAPPLDYKEPEKP--IASASSRAT-AKAEEASVETEPKFSPFTGVARRLDGKPL 177
             TDCEVDFAPPLDYKEPEKP  +  ++ R    K EE      PKF+PFTG  +RLDGK  
Sbjct:   170 TDCEVDFAPPLDYKEPEKPQKLTPSNKRPLQVKEEEEPASKVPKFTPFTGSGKRLDGKAQ 229

Query:   178 TYQPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQKPV 237
             T   P      +K ++  T NG        T+    RQ  GKLVFGSN+    KET K  
Sbjct:   230 TQTEPE----DTKQQEKPTENGKDDEKLSVTTP---RQISGKLVFGSNSKSAAKETAKVD 282

Query:   238 AXXXXXXXXXXXXXXXXFRPFTGKKYSLKG 267
                              F+ FTGKKYSL G
Sbjct:   283 DPKNIVQESSTKSDEAKFKVFTGKKYSLNG 312

GO:0005634 "nucleus" evidence=ISM

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

GO:0009507 "chloroplast" evidence=ISM

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

 Score = 475 (172.3 bits), Expect = 6.2e-55, Sum P(3) = 6.2e-55
 Identities = 85/143 (59%), Positives = 110/143 (76%)

Query:     1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
             MLFE+ N  + + SHCGVLEFIAEEG+ Y+P WMM+NL L+EG+ + +KN TL KGT+VK
Sbjct:    69 MLFEISNPISGKKSHCGVLEFIAEEGICYLPLWMMQNLQLKEGEFIDIKNATLAKGTFVK 128

Query:    61 LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
             +QP T +F+DISNPKA+LE +LR ++ LT  D IM+ YNN KYY+ ++E KP+NAISIIE
Sbjct:   129 IQPRTSNFIDISNPKAVLENSLRKFATLTKDDEIMIDYNNTKYYLKVVELKPANAISIIE 188

Query:   121 TDCEVDFAPPLDYKEPEKPIASA 143
              D  VDFAPP+D KE   P  S+
Sbjct:   189 ADVSVDFAPPMDSKEATSPSTSS 211

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

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

 Score = 516 (186.7 bits), Expect = 1.5e-49, P = 1.5e-49
 Identities = 96/185 (51%), Positives = 129/185 (69%)

Query:     1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
             MLF+L N  ++R++HCGVLEF+A+EG+ Y+P+WMM+NLLL+EG +V+V++V L   TY K
Sbjct:    65 MLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSK 124

Query:    61 LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
              QP + DFLDI+NPKA+LE  LRN++CLTTGD I + YN K Y + ++ETKP  A+SIIE
Sbjct:   125 FQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIE 184

Query:   121 TDCEVDFAPPLDYKEPEKPIASASSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTYQ 180
              D  VDF  PL YKEPE+P+    S    +A+ +    E  F  F+G   RLDGK    +
Sbjct:   185 CDMNVDFDAPLGYKEPERPVQHEES-IEGEADHSGYAGEVGFRAFSGSGNRLDGKKKGVE 243

Query:   181 PPPVP 185
             P P P
Sbjct:   244 PSPSP 248

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

RGD|619822 Ufd1l "ubiquitin fusion degradation 1 like (yeast)" [Rattus norvegicus (taxid:10116)]

 Score = 516 (186.7 bits), Expect = 1.5e-49, P = 1.5e-49
 Identities = 96/185 (51%), Positives = 129/185 (69%)

Query:     1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
             MLF+L N  ++R++HCGVLEF+A+EG+ Y+P+WMM+NLLL+EG +V+V++V L   TY K
Sbjct:    65 MLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSK 124

Query:    61 LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
              QP + DFLDI+NPKA+LE  LRN++CLTTGD I + YN K Y + ++ETKP  A+SIIE
Sbjct:   125 FQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIE 184

Query:   121 TDCEVDFAPPLDYKEPEKPIASASSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTYQ 180
              D  VDF  PL YKEPE+P+    S    +A+ +    E  F  F+G   RLDGK    +
Sbjct:   185 CDMNVDFDAPLGYKEPERPVQHEES-IEGEADHSGYAGEVGFRAFSGSGNRLDGKKKGVE 243

Query:   181 PPPVP 185
             P P P
Sbjct:   244 PSPSP 248

GO:0005102 "receptor binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005737 "cytoplasm" evidence=ISO

GO:0005829 "cytosol" evidence=IEA

GO:0032403 "protein complex binding" evidence=IPI

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

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

 Score = 512 (185.3 bits), Expect = 4.1e-49, P = 4.1e-49
 Identities = 96/185 (51%), Positives = 129/185 (69%)

Query:     1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
             MLF+L N  ++R++HCGVLEF+A+EG+ Y+P+WMM+NLLL+EG +V+V++V L   TY K
Sbjct:    65 MLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSK 124

Query:    61 LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
              QP + DFLDI+NPKA+LE  LRN++CLTTGD I + YN K Y + ++ETKP  A+SIIE
Sbjct:   125 FQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIE 184

Query:   121 TDCEVDFAPPLDYKEPEKPIASASSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTYQ 180
              D  VDF  PL YKEPE+ +    S A  +A+ +    E  F  F+G   RLDGK    +
Sbjct:   185 CDMNVDFDAPLGYKEPERQVQHEES-AEGEADHSGYAGELGFRAFSGSGNRLDGKKKGVE 243

Query:   181 PPPVP 185
             P P P
Sbjct:   244 PSPSP 248

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

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

 Score = 512 (185.3 bits), Expect = 4.1e-49, P = 4.1e-49
 Identities = 97/185 (52%), Positives = 128/185 (69%)

Query:     1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
             MLF+L N  ++R++HCGVLEF+A+EG+ Y+P+WMM+NLLL+EG +V+V++V L   TY K
Sbjct:    65 MLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSK 124

Query:    61 LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
              QP + DFLDI+NPKA+LE  LRN++CLTTGD I + YN K Y + ++ETKP  A+SIIE
Sbjct:   125 FQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIE 184

Query:   121 TDCEVDFAPPLDYKEPEKPIASASSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTYQ 180
              D  VDF  PL YKEPE+ I    S A  +A+      E  F  F+G   RLDGK    +
Sbjct:   185 CDMNVDFDAPLGYKEPERQIQHEES-AEGEADHGGYAGELGFRAFSGSGNRLDGKKKGVE 243

Query:   181 PPPVP 185
             P P P
Sbjct:   244 PSPSP 248

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 = 512 (185.3 bits), Expect = 4.1e-49, P = 4.1e-49
 Identities = 94/185 (50%), Positives = 128/185 (69%)

Query:     1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
             MLF+L N  ++R++HCGVLEF+A+EG  Y+P+WMM+NLLL+EG +V+V++V L   TY K
Sbjct:    65 MLFKLTNKNSDRMTHCGVLEFVADEGFCYLPHWMMQNLLLEEGGLVQVESVNLMVATYSK 124

Query:    61 LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
              QP + DFLDI+NPKA+LE  LRN++CLTTGD I + YN K Y + ++ETKP  A+SIIE
Sbjct:   125 FQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIE 184

Query:   121 TDCEVDFAPPLDYKEPEKPIASASSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTYQ 180
              D  VDF  PL YKEPE+ +      A  + + ++ + +  F  FTG   RLDGK    +
Sbjct:   185 CDMNVDFDAPLGYKEPERHMQHPEEPAEEETDPSNYDMDLGFRAFTGSGNRLDGKKKGIE 244

Query:   181 PPPVP 185
             P P P
Sbjct:   245 PSPAP 249

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

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

UNIPROTKB|A6NJ11 UFD1L "Ubiquitin fusion degradation protein 1 homolog" [Homo sapiens (taxid:9606)]

 Score = 508 (183.9 bits), Expect = 1.1e-48, P = 1.1e-48
 Identities = 95/185 (51%), Positives = 128/185 (69%)

Query:     1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
             MLF+L N  ++R++HCGVLEF+A+EG+ Y+P+WMM+NLLL+EG +V+V++V L   TY K
Sbjct:    54 MLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSK 113

Query:    61 LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
              QP + DFLDI+NPKA+LE  LRN++CLTTGD I + YN K Y + ++ETKP  A+SIIE
Sbjct:   114 FQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIE 173

Query:   121 TDCEVDFAPPLDYKEPEKPIASASSRATAKAEEASVETEPKFSPFTGVARRLDGKPLTYQ 180
              D  VDF  PL YKEPE+ +    S    +A+ +    E  F  F+G   RLDGK    +
Sbjct:   174 CDMNVDFDAPLGYKEPERQVQHEES-TEGEADHSGYAGELGFRAFSGSGNRLDGKKKGVE 232

Query:   181 PPPVP 185
             P P P
Sbjct:   233 PSPSP 237

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	267
pfam03152	176	pfam03152, UFD1, Ubiquitin fusion degradation prot	3e-91
COG5140	331	COG5140, UFD1, Ubiquitin fusion-degradation protei	8e-56
PLN03086	567	PLN03086, PLN03086, PRLI-interacting factor K; Pro	2e-30

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

 Score =  266 bits (683), Expect = 3e-91
 Identities = 91/130 (70%), Positives = 113/130 (86%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLFEL+N A ++V+HCGVLEFIAEEG IY+PYWMM+NL L+EGD+V++ + +LPKGT+VK
Sbjct: 47  MLFELQNPANKKVTHCGVLEFIAEEGTIYLPYWMMQNLGLEEGDLVQITSASLPKGTFVK 106

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
           LQP + DFLDISNPKA+LE  LRN+S LT GD+I++ YN+K Y IDI+E KP+NAISIIE
Sbjct: 107 LQPQSTDFLDISNPKAVLENALRNFSTLTKGDTIVINYNDKIYEIDILEVKPANAISIIE 166

Query: 121 TDCEVDFAPP 130
           TD EVDFAPP
Sbjct: 167 TDLEVDFAPP 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 =  182 bits (462), Expect = 8e-56
 Identities = 77/199 (38%), Positives = 104/199 (52%), Gaps = 12/199 (6%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLFE+ ++     +H GVLEFIAEEG +Y+P WMM+ L ++ GD+V ++    P G +VK
Sbjct: 67  MLFEISHSDGIYRTHGGVLEFIAEEGRVYLPSWMMQTLSMEPGDLVVLRYTDFPLGKFVK 126

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKP---SNAIS 117
           L P + DFLDI +PKA+LE  LRN+S LT GD I + YN++   I      P   +NAI 
Sbjct: 127 LIPQSVDFLDIEDPKAVLENCLRNFSTLTEGDEIEIQYNDEVGSIKFTVVHPEPSANAIY 186

Query: 118 IIETDCEVDFAPPLDYKEP-----EKPIASASSRATAKAEEASVETEPKFSPFTGVARRL 172
           ++ETD  VDF PP+ YKE      E+             E      + K     G+   L
Sbjct: 187 VVETDLVVDFLPPIGYKEKAQQDKERNSFGVQGTMATYIEYIDSSHDVKPILMKGLGLYL 246

Query: 173 DGKPLTYQPPPVPSLGSKD 191
            GK         P    KD
Sbjct: 247 YGK----VDKAEPKQDIKD 261

Length = 331

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

 Score =  119 bits (299), Expect = 2e-30
 Identities = 52/130 (40%), Positives = 82/130 (63%), Gaps = 3/130 (2%)

Query: 4   ELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQ---EGDIVRVKNVTLPKGTYVK 60
           E+++  +++ +H GVLEF AEEG + +P  +  NL      +  +V V+ + LPKGTY K
Sbjct: 129 EMKDTDSQKTTHSGVLEFTAEEGSVGLPPHVWSNLFPSDPPDVPLVEVRYIWLPKGTYAK 188

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
           LQP    F D+ N KA+LET LR ++ L+  D ++V Y    Y + ++E KP++++S++E
Sbjct: 189 LQPDGVGFSDLPNHKAVLETALRQHATLSEDDVLVVNYGQLTYKLKVLELKPASSVSVLE 248

Query: 121 TDCEVDFAPP 130
           TD EVD   P
Sbjct: 249 TDIEVDIVGP 258

Length = 567

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	267
KOG1816	308	consensus Ubiquitin fusion-degradation protein [Po	100.0
COG5140	331	UFD1 Ubiquitin fusion-degradation protein [Posttra	100.0
PF03152	176	UFD1: Ubiquitin fusion degradation protein UFD1; I	100.0
PLN03086	567	PRLI-interacting factor K; Provisional	100.0
PF02933	64	CDC48_2: Cell division protein 48 (CDC48), domain	96.12
KOG0735	952	consensus AAA+-type ATPase [Posttranslational modi	95.0
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	94.46
PF09262	80	PEX-1N: Peroxisome biogenesis factor 1, N-terminal	93.13
TIGR01439	43	lp_hng_hel_AbrB looped-hinge helix DNA binding dom	87.53
PF02359	87	CDC48_N: Cell division protein 48 (CDC48), N-termi	85.68
PF04014	47	Antitoxin-MazE: Antidote-toxin recognition MazE; I	84.63
PF07497	78	Rho_RNA_bind: Rho termination factor, RNA-binding	80.12

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

Probab=100.00  E-value=9.5e-83  Score=586.02  Aligned_cols=242  Identities=54%  Similarity=0.915  Sum_probs=198.3

Q ss_pred             CeEEEEeCCCCcEEEEEeeeeeeCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhh
Q 024476            1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILET   80 (267)
Q Consensus         1 MlF~l~N~~~~r~th~GVLEF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~   80 (267)
                      |||+|+|.+..|+||||||||+||||+||||+|||++|+|++||+|+|++++||+||||||||||.|||||+|||||||+
T Consensus        59 MlFkLtn~~~~r~THcGVLEF~AeEG~vyLP~WMmq~L~le~gdlv~i~~v~lpkgtyvKLqP~s~dFLDItNpKAvLE~  138 (308)
T KOG1816|consen   59 MLFKLTNVDVDRVTHCGVLEFTAEEGRVYLPYWMMQNLLLEEGDLVRIRSVTLPKGTYVKLQPHSVDFLDITNPKAVLEN  138 (308)
T ss_pred             eEEEEeccccceeeeeeEEEEEecCceEEeehHhhhhccCCCCCeEEEEEeeccccceeeeccCCCCccccCChHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccceecccCCEEEEEECCEEEEEEEEEecCCCeeEEEeCceeeeecCCCCCCCCCCcccccc-cchhhhhhhcccc--
Q 024476           81 TLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPPLDYKEPEKPIASAS-SRATAKAEEASVE--  157 (267)
Q Consensus        81 ~LRnystLT~Gd~I~I~yn~~~y~l~V~e~kP~~aVsIIeTDleVDf~pPldy~Epe~~~~~~~-~~~~~~~~~~~~~--  157 (267)
                      +||||+|||+||+|+|+||++.|+|+|+|+||++|||||||||+|||+||+||+||+++.++.. .+..+...+..+.  
T Consensus       139 ~LRn~acLT~gDvi~i~Yn~k~y~i~V~e~kPa~aVsIiEtD~~VDF~pP~gyke~~~~~~~~~~~k~~~~~v~~~ag~~  218 (308)
T KOG1816|consen  139 ALRNYACLTTGDVILINYNEKTYELKVVETKPANAVSIIETDLNVDFDPPLGYKEPERQVAPAEKAKGEAEVVGSYAGYK  218 (308)
T ss_pred             HHhhccccccCCEEEEecCCeEEEEEEEEecCCceeEEEEcceeecccCCcCccCcccccChhhcccccceeeccccccc
Confidence            9999999999999999999999999999999999999999999999999999999999855432 2211111110111  


Q ss_pred             --CCCcccceeeeccccCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCeEEEccCCCCCCCCCCC
Q 024476          158 --TEPKFSPFTGVARRLDGKPLTYQPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKETQK  235 (267)
Q Consensus       158 --~~~~~~~F~G~G~rLdGK~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~g~L~Fg~~~~~~~~~~~~  235 (267)
                        -++++.+|.|+|+|||||+...++.+.+  +..        +    ......+...+++.|+|+||+|..+.++... 
T Consensus       219 ~~~e~~~~~f~gsg~rLdgK~~~~e~~~~p--v~~--------~----~~~~~~~~~~d~~~G~l~F~~~~~~~~~~~~-  283 (308)
T KOG1816|consen  219 NVIENKVEPFTGSGRRLDGKKKVEEVSKHP--VKN--------G----DLIQRGVPNHDFKLGKLVFGRNVDPLKKESE-  283 (308)
T ss_pred             cccccceeeeccccceecccccccccCCCc--ccC--------c----ccccCCCCccccCCceEEEecCCCccccccc-
Confidence              1678999999999999998865542221  110        1    1122344556999999999998633322111 


Q ss_pred             chhhhhhhccCccccCCCCcCCccccccccCC
Q 024476          236 PVAEKEIKQELPEKKEEPKFRPFTGKKYSLKG  267 (267)
Q Consensus       236 ~~~~~~~~~~~~~~~~~~~f~aF~G~g~SLr~  267 (267)
                               + ++....++|++|+|+||||||
T Consensus       284 ---------E-~~a~k~~~~~~F~G~~~slr~  305 (308)
T KOG1816|consen  284 ---------E-KEAGKDSKFEAFSGAGYSLRK  305 (308)
T ss_pred             ---------h-hhcccccceeEecCCceeccc
Confidence                     1 122223899999999999996

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

Probab=100.00  E-value=1.3e-63  Score=453.10  Aligned_cols=236  Identities=36%  Similarity=0.560  Sum_probs=191.7

Q ss_pred             CeEEEEeCCCCcEEEEEeeeeeeCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhh
Q 024476            1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILET   80 (267)
Q Consensus         1 MlF~l~N~~~~r~th~GVLEF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~   80 (267)
                      |||+|+|.++.++||||||||+|+||.||||+|||++|.+++||+|+|+|.++|.|+||||+|||+|||||+|||||||+
T Consensus        67 mlF~~s~~~~~~~THgGVLEFiaEEGrVylP~WMm~tLs~epgdlv~~~~td~plG~fVKL~PqSVdFLdI~dpkavLEn  146 (331)
T COG5140          67 MLFEISHSDGIYRTHGGVLEFIAEEGRVYLPSWMMQTLSMEPGDLVVLRYTDFPLGKFVKLIPQSVDFLDIEDPKAVLEN  146 (331)
T ss_pred             eEEEEecccceeEecccEEEEeecCCcEeehHHHHHhccCCCCcEEEEEeccccccceEEecccccceEeccChHHHHHH
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccceecccCCEEEEEECCEEEEEEEEEecCC---CeeEEEeCceeeeecCCCCCCCCCCccccc-c-c-chhhhh-h-
Q 024476           81 TLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPS---NAISIIETDCEVDFAPPLDYKEPEKPIASA-S-S-RATAKA-E-  152 (267)
Q Consensus        81 ~LRnystLT~Gd~I~I~yn~~~y~l~V~e~kP~---~aVsIIeTDleVDf~pPldy~Epe~~~~~~-~-~-~~~~~~-~-  152 (267)
                      +||||+|||+||+|.|.||++.|.|++++++|+   ++||||||||.|||+||+||+|+..+-+.. . . +.+... . 
T Consensus       147 ~LRNfstLt~~D~iei~ynd~v~~Ik~~~v~pe~S~~~i~vveTDLvvDF~pPiGy~e~~qq~ke~n~~gvqgtm~t~I~  226 (331)
T COG5140         147 CLRNFSTLTEGDEIEIQYNDEVGSIKFTVVHPEPSANAIYVVETDLVVDFLPPIGYKEKAQQDKERNSFGVQGTMATYIE  226 (331)
T ss_pred             HHhhccccccCCEEEEEECCeeeEEEEEEeccCCCcceEEEEecceeeeccCCccccchhhhhhhhccccccceeEEEEe
Confidence            999999999999999999999999999999995   899999999999999999999984331111 0 0 101000 0 


Q ss_pred             hccccCCCcccceeeeccccCCccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCeEEEccCCCCCCCC
Q 024476          153 EASVETEPKFSPFTGVARRLDGKPLTYQPPPVPSLGSKDKQPATSNGTGQPSAGSTSQNAARQSQGKLVFGSNASLHPKE  232 (267)
Q Consensus       153 ~~~~~~~~~~~~F~G~G~rLdGK~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~g~L~Fg~~~~~~~~~  232 (267)
                      -.......+-.--.|.|..|.||..+..+....               .+ ..-.+.|+++++|.|+||||+|.+.|+.+
T Consensus       227 y~~~~~~~~~~lmKg~G~~l~gk~~~~~pk~~i---------------~d-~~~~~~pa~l~lp~g~~ffg~p~~~p~~d  290 (331)
T COG5140         227 YIDSSHDVKPILMKGLGLYLYGKVDKAEPKQDI---------------KD-MKIDGEPAKLDLPEGQLFFGFPMVLPKED  290 (331)
T ss_pred             eeccccccchhhhhcccceecccccccccccch---------------hh-hhccCCcccccccCcceEeccccccCccc
Confidence            011112233345669999999998765532211               11 11256899999999999999999999763


Q ss_pred             CCCchhhhhhhccCccccCCCCcCCccccccccC
Q 024476          233 TQKPVAEKEIKQELPEKKEEPKFRPFTGKKYSLK  266 (267)
Q Consensus       233 ~~~~~~~~~~~~~~~~~~~~~~f~aF~G~g~SLr  266 (267)
                      +.             . +..+.-+.|.|+|-|||
T Consensus       291 ee-------------s-~~~~~~~~fqg~g~slr  310 (331)
T COG5140         291 EE-------------S-AAKSSEQNFQGQGISLR  310 (331)
T ss_pred             hh-------------h-ccCchhhccccCceeee
Confidence            32             1 11244466999999998

>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=3.8e-58  Score=399.95  Aligned_cols=130  Identities=68%  Similarity=1.123  Sum_probs=112.5

Q ss_pred             CeEEEEeCCCCcEEEEEeeeeeeCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhh
Q 024476            1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILET   80 (267)
Q Consensus         1 MlF~l~N~~~~r~th~GVLEF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~   80 (267)
                      |+|+|+|..++++||||||||+|+||+||||+|||++|++++||.|+|++++||||||||||||+.+|++|+|||||||+
T Consensus        47 ~~F~i~n~~~~~~th~GVlEFsA~eG~i~lP~wmm~~L~l~~g~~V~v~~~~LPkgt~vkLqP~~~~F~~i~n~KavLE~  126 (176)
T PF03152_consen   47 MLFEISNPDNGKRTHCGVLEFSAEEGTIYLPPWMMQNLGLQEGDIVRVEYVSLPKGTFVKLQPQSSDFLDISNPKAVLER  126 (176)
T ss_dssp             -EEEEEETTTTEEEEEEEEEE--CTTEEEE-CHHHHHHT--TTEEEEEEEEE----SEEEEEESCHHHHCSS-HHHHHHH
T ss_pred             EEEEEecCCCCcEEEEEEEEeEcCCCeEEeCccHHhhcCCCCCCEEEEEEeECCCCCEEEEeECCCccccccchHHHHHh
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccceecccCCEEEEEECCEEEEEEEEEecCCCeeEEEeCceeeeecCC
Q 024476           81 TLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPP  130 (267)
Q Consensus        81 ~LRnystLT~Gd~I~I~yn~~~y~l~V~e~kP~~aVsIIeTDleVDf~pP  130 (267)
                      +||||+|||+||+|.|+|+++.|+|+|+|++|++|||||||||+|||+||
T Consensus       127 ~Lr~ystLT~Gd~I~i~~~~~~y~l~V~e~kP~~aV~IidTDl~vDf~~P  176 (176)
T PF03152_consen  127 ALRNYSTLTKGDTISIEYNNKTYELDVVEVKPENAVSIIDTDLEVDFEPP  176 (176)
T ss_dssp             HHCC-SEEETTSEEEEECTTEEEEEEEEEECSSSCEE-SSS-SEEEE---
T ss_pred             hcccCceeecCCEEEEEeCCEEEEEEEEEEcCCCEEEEEeCceEEEecCC
Confidence            99999999999999999999999999999999999999999999999997

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.

>PLN03086 PRLI-interacting factor K; Provisional

Probab=100.00  E-value=7.1e-51  Score=404.04  Aligned_cols=135  Identities=39%  Similarity=0.656  Sum_probs=129.6

Q ss_pred             CeEEEEeC-----------CCCcEEEEEeeeeeeCCCeEeccHHHHHHcCCCC---CCeEEEEEeecCCcceEEEeeCCc
Q 024476            1 MLFELRNN-----------AAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQE---GDIVRVKNVTLPKGTYVKLQPHTK   66 (267)
Q Consensus         1 MlF~l~N~-----------~~~r~th~GVLEF~A~EG~i~LP~Wmm~~L~l~~---gd~V~I~~~~LPkGt~vkLqP~s~   66 (267)
                      |+|+|+|.           ..+++||||||||+|+||.||||+|||++|++.+   |++|+|++++||+|||||||||+.
T Consensus       115 m~F~l~~~~~~~~~~~~~~~~~~~th~GVlEF~A~EG~v~lP~wm~~~L~~~~~~~~~~v~v~~~~Lpkgt~vklqP~~~  194 (567)
T PLN03086        115 LYFRLSVVHQEGSGEMKDTDSQKTTHSGVLEFTAEEGSVGLPPHVWSNLFPSDPPDVPLVEVRYIWLPKGTYAKLQPDGV  194 (567)
T ss_pred             eEEEEeccccccccccccccCCcEEEEEEEEEEcCCCeEEcCHHHHhhcCCCCCCCCCeEEEEEeecCCCCEEEEeeccC
Confidence            89999994           3579999999999999999999999999999874   899999999999999999999999


Q ss_pred             CcCCccCchHHHhhccccceecccCCEEEEEECCEEEEEEEEEecCCCeeEEEeCceeeeecCCCCCCC
Q 024476           67 DFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAPPLDYKE  135 (267)
Q Consensus        67 ~Fl~isnpKavLE~~LRnystLT~Gd~I~I~yn~~~y~l~V~e~kP~~aVsIIeTDleVDf~pPldy~E  135 (267)
                      +|+||+|||||||++||||+|||+||+|.|+||++.|+|+|+|++|++|||||||||+|||+||.++.+
T Consensus       195 ~f~di~npKavLE~~Lr~~stLT~Gd~i~i~~~~~~y~~~V~ev~P~~aVsiieTDi~VDf~~p~~~~~  263 (567)
T PLN03086        195 GFSDLPNHKAVLETALRQHATLSEDDVLVVNYGQLTYKLKVLELKPASSVSVLETDIEVDIVGPDSVSN  263 (567)
T ss_pred             CcCCcccHHHHHHHHhhcCccccCCCEEEEecCCEEEEEEEEEEcCCCeeEEEeCceEEEeccCCcchh
Confidence            999999999999999999999999999999999999999999999999999999999999999999743

>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=96.12  E-value=0.028  Score=41.02  Aligned_cols=41  Identities=27%  Similarity=0.505  Sum_probs=33.0

Q ss_pred             eecccCCEEEEEECCEEEEEEEEEecCCCeeEEEe-Cceeee
Q 024476           86 SCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE-TDCEVD  126 (267)
Q Consensus        86 stLT~Gd~I~I~yn~~~y~l~V~e~kP~~aVsIIe-TDleVD  126 (267)
                      --|++||+|.|.+.++.+.|.|.+++|.+++-|-+ |.+++-
T Consensus        17 ~pv~~Gd~i~~~~~~~~~~~~V~~~~P~~~v~it~~T~i~i~   58 (64)
T PF02933_consen   17 RPVTKGDTIVFPFFGQALPFKVVSTEPSGPVIITEDTEIEIK   58 (64)
T ss_dssp             EEEETT-EEEEEETTEEEEEEEEEECSSSEEEEETTSEEEES
T ss_pred             CCccCCCEEEEEeCCcEEEEEEEEEEcCCCEEECCCcEEEEc
Confidence            45999999999999999999999999998665553 555554

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=95.00  E-value=0.16  Score=54.05  Aligned_cols=106  Identities=22%  Similarity=0.211  Sum_probs=90.9

Q ss_pred             CCCeEeccHHHHHHcCCCCCCeEEEEEe-ecCCcceEEEeeCCcCcCCccCchHH-Hhhccc-cceecccCCEEEEEECC
Q 024476           24 EEGMIYMPYWMMENLLLQEGDIVRVKNV-TLPKGTYVKLQPHTKDFLDISNPKAI-LETTLR-NYSCLTTGDSIMVAYNN  100 (267)
Q Consensus        24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~~-~LPkGt~vkLqP~s~~Fl~isnpKav-LE~~LR-nystLT~Gd~I~I~yn~  100 (267)
                      .|..|-+=.-..+.|+|.+|+.|.++-+ ..+.++-|.+.|.++|=|+|-+--|. ||..|- ++--+|. .++.|+++.
T Consensus        58 se~~ieIn~~~A~~l~L~e~~~V~l~~~~~v~~~~~V~VeP~TsdDWEIiElnA~~~e~~lL~Q~RIv~~-~~f~iwl~~  136 (952)
T KOG0735|consen   58 SENVIEINRVYAHTLGLAENQEVKLSIIDHVHEATQVEVEPVTSDDWEIIELNAEWLEENLLVQTRIVTP-EIFIIWLPS  136 (952)
T ss_pred             ccceEEeehhhHhhccCCCCCeEEEEEcCCccceeEEEEeeccCccHHHHHhhHHHHhhhhhhheeeccc-ceeEEEEcC
Confidence            4666777788899999999999999976 79999999999999998898777666 677665 6888999 888899987


Q ss_pred             EEE-EEEEEEecCCCeeEEEeCceeeeecCC
Q 024476          101 KKY-YIDIIETKPSNAISIIETDCEVDFAPP  130 (267)
Q Consensus       101 ~~y-~l~V~e~kP~~aVsIIeTDleVDf~pP  130 (267)
                      .+| .|.|..+.|+..+.=++++-+|=++|-
T Consensus       137 ~t~i~fqv~rl~Ps~~~gRl~~~Tev~VaPK  167 (952)
T KOG0735|consen  137 GTVIQFQVDRLIPSMLYGRLLRGTEVLVAPK  167 (952)
T ss_pred             ccEEEEEEeeeecccceeeecCCceEEEecC
Confidence            655 788999999999999999999999883

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=94.46  E-value=0.23  Score=51.74  Aligned_cols=104  Identities=17%  Similarity=0.182  Sum_probs=75.5

Q ss_pred             cEEEEEeee-ee--eCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhhccccceec
Q 024476           12 RVSHCGVLE-FI--AEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCL   88 (267)
Q Consensus        12 r~th~GVLE-F~--A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRnystL   88 (267)
                      +.+.|-|+. ..  ...|.|.|..-+.+++++..||.|.|+.+.++.+..|.+.|.. ....-.+...++-..|.+ ..|
T Consensus        44 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~-~~~  121 (733)
T TIGR01243        44 RSVVAIVWPLRPDDEGRGIIRMDGYLRANAGVTIGDTVTVERAEVKEAKKVVLAPTQ-PIRFGRDFVDYVKEFLLG-KPI  121 (733)
T ss_pred             CceeEEEEecCccccCCCEEeecHHHHhhcCCCCCCeEEEeecCCCccceEeecccc-ccccccchHHHHHHHHcC-CCC
Confidence            445566654 22  2468999999999999999999999999999999999999953 111001222333333333 458


Q ss_pred             ccCCEEEEEECCEEEEEEEEEecCCCeeE
Q 024476           89 TTGDSIMVAYNNKKYYIDIIETKPSNAIS  117 (267)
Q Consensus        89 T~Gd~I~I~yn~~~y~l~V~e~kP~~aVs  117 (267)
                      ++||.|.+.+....+.+.|+++.|...+.
T Consensus       122 ~~g~~~~~~~~~~~~~~~v~~~~p~~~~~  150 (733)
T TIGR01243       122 SKGETVIVPVLEGALPFVVVSTQPAGFVY  150 (733)
T ss_pred             CCCCEEEecccCcceeEEEEecCCCCcEE
Confidence            99999999988878889999999965443

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=93.13  E-value=0.095  Score=40.86  Aligned_cols=74  Identities=24%  Similarity=0.314  Sum_probs=49.3

Q ss_pred             cceEEEeeCCcCcCCc-cCchHHHhhccc-cceecccCCEEEEEE-CCEEEEEEEEEecCCCe---eEEEeCceeeeecC
Q 024476           56 GTYVKLQPHTKDFLDI-SNPKAILETTLR-NYSCLTTGDSIMVAY-NNKKYYIDIIETKPSNA---ISIIETDCEVDFAP  129 (267)
Q Consensus        56 Gt~vkLqP~s~~Fl~i-snpKavLE~~LR-nystLT~Gd~I~I~y-n~~~y~l~V~e~kP~~a---VsIIeTDleVDf~p  129 (267)
                      ++.|.+.|.+.|=++| ...-..||..|- +-.+++.|.++.++- ++..-.|.|..+.|...   ...+..|.||=++|
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            4678999999887764 555666777766 589999999999998 56777999999999866   78899999887765

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=87.53  E-value=2.7  Score=27.54  Aligned_cols=39  Identities=33%  Similarity=0.461  Sum_probs=31.3

Q ss_pred             eCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeC
Q 024476           23 AEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPH   64 (267)
Q Consensus        23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~   64 (267)
                      .+.|.|.||.-+.+.|++.+||.+.|...  +. .-+.|.|.
T Consensus         4 ~~kgri~iP~~~r~~l~~~~gd~~~i~~~--~~-~~l~l~p~   42 (43)
T TIGR01439         4 DKKGQIVIPKEIREKLGLKEGDRLEVIRV--ED-GEIILRPA   42 (43)
T ss_pred             CcCCeEEecHHHHHHcCcCCCCEEEEEEe--CC-CEEEEEEC
Confidence            46799999999999999999999988753  33 35666664

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.

>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=85.68  E-value=1.1  Score=34.57  Aligned_cols=69  Identities=23%  Similarity=0.235  Sum_probs=46.9

Q ss_pred             CCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhhccccceecccCCEEEEE
Q 024476           24 EEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVA   97 (267)
Q Consensus        24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRnystLT~Gd~I~I~   97 (267)
                      ..|.++|..-.|+.|++.+||.|.|...   +-|.+.+.|...+  +...=.--|-...|+..-+..||.|.|.
T Consensus        14 ~~n~v~v~~~~m~~l~l~~gd~v~i~g~---~~tv~~v~~~~~~--~~~~g~I~l~~~~R~n~~v~igd~V~V~   82 (87)
T PF02359_consen   14 GTNCVRVSPEDMEELGLFPGDVVLISGK---RKTVAFVFPDRPD--DSPPGVIRLSGIQRKNAGVSIGDRVTVR   82 (87)
T ss_dssp             CTTEEEEEHHHHHCTTT-TTEEEEEETT---TEEEEEEEEECCS--TTCTTEEEE-HHHHHHCT--TTSEEEEE
T ss_pred             CCCEEEEcHHHHHHcCCCCccEEEEeCC---ceEEEEEEECCCC--CCCCCEEEECHHHHhhCCcCCCCEEEEE
Confidence            5689999999999999999999999872   2266777665322  1111111256677888889999999986

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 ....

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

Probab=84.63  E-value=2.1  Score=29.39  Aligned_cols=39  Identities=26%  Similarity=0.418  Sum_probs=30.4

Q ss_pred             CCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCC
Q 024476           24 EEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHT   65 (267)
Q Consensus        24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s   65 (267)
                      ..+.|.||.-+++.|+|++||.|.|...  ..| -+.|.|..
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  233 66666653

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 ....

>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=80.12  E-value=0.88  Score=35.50  Aligned_cols=26  Identities=19%  Similarity=0.286  Sum_probs=19.1

Q ss_pred             CCeEeccHHHHHHcCCCCCCeEEEEE
Q 024476           25 EGMIYMPYWMMENLLLQEGDIVRVKN   50 (267)
Q Consensus        25 EG~i~LP~Wmm~~L~l~~gd~V~I~~   50 (267)
                      +.-||+|.++.+.++|+.||.|.=.-
T Consensus        28 ~~DvYVs~~qIrrf~LR~GD~V~G~v   53 (78)
T PF07497_consen   28 PDDVYVSPSQIRRFGLRTGDLVEGQV   53 (78)
T ss_dssp             TTSEEE-CCCCCCTT--TTEEEEEEE
T ss_pred             CCCEEECHHHHHHcCCCCCCEEEEEE
Confidence            45689999999999999999887543

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	267
2yuj_A	190	Solution Structure Of Human Ubiquitin Fusion Degrad		3e-43
1zc1_A	208	Ufd1 Exhibits The Aaa-Atpase Fold With Two Distinct		5e-39

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

Iteration: 1
 Score =  171 bits (434), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 74/127 (58%), Positives = 100/127 (78%)
Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLF+L N  ++R++HCGVLEF+A+EG+ Y+P+WMM+NLLL+EG +V+V++V L   TY K
Sbjct: 62  MLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSK 121
Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
            QP + DFLDI+NPKA+LE  LRN++CLTTGD I + YN K Y + ++ETKP  A+SIIE
Sbjct: 122 FQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIE 181
Query: 121 TDCEVDF 127
            D  VDF
Sbjct: 182 CDMNVDF 188

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

Iteration: 1
 Score =  157 bits (397), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 74/140 (52%), Positives = 99/140 (70%), Gaps = 3/140 (2%)
Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLF+L  N   RV+H GVLEFIAEEG +Y+P WMME L +Q G ++++ +  +P G +VK
Sbjct: 67  MLFKLTANETGRVTHGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVK 126
Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKP---SNAIS 117
           L+P + DFLDIS+PKA+LE  LRN+S LT  D I ++YN K + I I+E KP   S +I 
Sbjct: 127 LEPQSVDFLDISDPKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSIC 186
Query: 118 IIETDCEVDFAPPLDYKEPE 137
           +IETD   DFAPP+ Y EP+
Sbjct: 187 VIETDLVTDFAPPVGYVEPD 206

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	267
1zc1_A	208	Ubiquitin fusion degradation protein 1; UFD1, doub	2e-69
2yuj_A	190	Ubiquitin fusion degradation 1-like; ubiquitin-dep	2e-65
3tiw_A	187	Transitional endoplasmic reticulum ATPase; beta-ba	1e-08
1wlf_A	179	PEX1, peroxisome biogenesis factor 1; N-terminal d	3e-08
3qwz_A	211	Transitional endoplasmic reticulum ATPase; UBX, P9	8e-05
1cz4_A	185	VCP-like ATPase; double-PSI beta-barrel, beta-CLAM	1e-04
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	8e-04

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

 Score =  212 bits (541), Expect = 2e-69
 Identities = 74/141 (52%), Positives = 99/141 (70%), Gaps = 3/141 (2%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLF+L  N   RV+H GVLEFIAEEG +Y+P WMME L +Q G ++++ +  +P G +VK
Sbjct: 67  MLFKLTANETGRVTHGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVK 126

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKP---SNAIS 117
           L+P + DFLDIS+PKA+LE  LRN+S LT  D I ++YN K + I I+E KP   S +I 
Sbjct: 127 LEPQSVDFLDISDPKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSIC 186

Query: 118 IIETDCEVDFAPPLDYKEPEK 138
           +IETD   DFAPP+ Y EP+ 
Sbjct: 187 VIETDLVTDFAPPVGYVEPDY 207

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

 Score =  201 bits (512), Expect = 2e-65
 Identities = 74/128 (57%), Positives = 100/128 (78%)

Query: 1   MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVK 60
           MLF+L N  ++R++HCGVLEF+A+EG+ Y+P+WMM+NLLL+EG +V+V++V L   TY K
Sbjct: 62  MLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSK 121

Query: 61  LQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE 120
            QP + DFLDI+NPKA+LE  LRN++CLTTGD I + YN K Y + ++ETKP  A+SIIE
Sbjct: 122 FQPQSPDFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIE 181

Query: 121 TDCEVDFA 128
            D  VDF 
Sbjct: 182 CDMNVDFD 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 = 52.4 bits (125), Expect = 1e-08
 Identities = 19/109 (17%), Positives = 40/109 (36%), Gaps = 5/109 (4%)

Query: 23  AEEGMIYMPYWMMENLLLQEGDIVRVKNVT-LPKGTYVKLQPHTKDFLDISNP--KAILE 79
             +  I M   +  NL ++ GD++ ++    +  G  + + P       I+    +  L+
Sbjct: 77  CSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLK 136

Query: 80  TTLR-NYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE-TDCEVD 126
                 Y  +  GD  +V    +     ++ET PS    +   T    +
Sbjct: 137 PYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCE 185

>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 Length = 179

 Score = 51.1 bits (122), Expect = 3e-08
 Identities = 18/110 (16%), Positives = 47/110 (42%), Gaps = 4/110 (3%)

Query: 24  EEGMIYMPYWMMENLLLQEGDIVRVKNVT-LPKGTYVKLQPHTKDFLDI--SNPKAILET 80
            E +  +   + + L L  GD V ++  + +     V+++P + D  +I   +  ++ + 
Sbjct: 68  SENVAEINRQVGQKLGLSSGDQVFLRPCSHVVSCQQVEVEPLSADDWEILELHAISLEQH 127

Query: 81  TLRNYSCLTTGDSIMVAYNNKKY-YIDIIETKPSNAISIIETDCEVDFAP 129
            L     +     + +  + + Y +I I+   P+     +ET+ ++   P
Sbjct: 128 LLDQIRIVFPKAVVPIWVDQQTYIFIQIVTLMPAAPYGRLETNTKLLIQP 177

>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 = 19/112 (16%), Positives = 40/112 (35%), Gaps = 5/112 (4%)

Query: 23  AEEGMIYMPYWMMENLLLQEGDIVRVKNVT-LPKGTYVKLQPHTKDFLDISNP--KAILE 79
             +  I M   +  NL ++ GD++ ++    +  G  + + P       I+    +  L+
Sbjct: 80  CSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLK 139

Query: 80  TTLRNYSC-LTTGDSIMVAYNNKKYYIDIIETKPSNAISIIE-TDCEVDFAP 129
                    +  GD  +V    +     ++ET PS    +   T    +  P
Sbjct: 140 PYFLEAYRPIRKGDIFLVRGGMRAVEFXVVETDPSPYCIVAPDTVIHCEGEP 191

>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 Length = 185

 Score = 41.1 bits (96), Expect = 1e-04
 Identities = 28/130 (21%), Positives = 44/130 (33%), Gaps = 11/130 (8%)

Query: 11  ERVSHCGVLEFIAE---EGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKD 67
            R +   V     E   +G++ +   M  N     GD V+V+ V       V L P  + 
Sbjct: 47  VRKTVGRVYRARPEDENKGIVRIDSVMRNNCGASIGDKVKVRKVRTEIAKKVTLAPIIRK 106

Query: 68  FLDISNPKAILETTLRNYSC--LTTGDSIMV----AYNNKKYYIDIIETKPSNAISII-- 119
              +   + I E   R      +   D+I V              +++T PS     I  
Sbjct: 107 DQRLKFGEGIEEYVQRALIRRPMLEQDNISVPGLTLAGQTGLLFKVVKTLPSKVPVEIGE 166

Query: 120 ETDCEVDFAP 129
           ET  E+   P
Sbjct: 167 ETKIEIREEP 176

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	267
1zc1_A	208	Ubiquitin fusion degradation protein 1; UFD1, doub	100.0
2yuj_A	190	Ubiquitin fusion degradation 1-like; ubiquitin-dep	100.0
3qwz_A	211	Transitional endoplasmic reticulum ATPase; UBX, P9	99.37
3tiw_A	187	Transitional endoplasmic reticulum ATPase; beta-ba	99.34
1cz4_A	185	VCP-like ATPase; double-PSI beta-barrel, beta-CLAM	99.31
1wlf_A	179	PEX1, peroxisome biogenesis factor 1; N-terminal d	98.96
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	97.57
2jv2_A	83	Putative uncharacterized protein PH1500; AAA ATPas	97.32
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	96.78
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	95.77
1yfb_A	59	Transition state regulatory protein ABRB; , homodi	91.88
1cz4_A	185	VCP-like ATPase; double-PSI beta-barrel, beta-CLAM	91.57
3tiw_A	187	Transitional endoplasmic reticulum ATPase; beta-ba	90.66
2glw_A	92	PHS018, 92AA long hypothetical protein; RIFT barre	90.61
1qcs_A	211	N-ethylmaleimide sensitive factor (NSF-N); double-	89.7
3qwz_A	211	Transitional endoplasmic reticulum ATPase; UBX, P9	88.32
2l66_A	53	SSO7C4, transcriptional regulator, ABRB family; DN	87.99
1cr5_A	189	SEC18P (residues 22 - 210); double-PSI beta barrel	87.23
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	82.18

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

Probab=100.00  E-value=2.4e-62  Score=434.38  Aligned_cols=139  Identities=53%  Similarity=0.937  Sum_probs=137.1

Q ss_pred             CeEEEEeCCCCcEEEEEeeeeeeCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhh
Q 024476            1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILET   80 (267)
Q Consensus         1 MlF~l~N~~~~r~th~GVLEF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~   80 (267)
                      |+|+|+|..++++||||||||+|+||+||||+|||++|+|++||+|+|++++||+|+|||||||+.+|++|+|||||||+
T Consensus        67 m~F~l~n~~~~~~th~GVlEF~A~EG~v~lP~wmm~~L~l~~gd~V~i~~~~LPkgt~vklqP~~~~Fldi~npKavLE~  146 (208)
T 1zc1_A           67 MLFKLTANETGRVTHGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFLDISDPKAVLEN  146 (208)
T ss_dssp             CCEEEECTTTCCEEEEEEEEECCSSCEEEECHHHHHHHTCCTTCEEEEEEEECCCCSEEEEECCHHHHHTSSCHHHHHHH
T ss_pred             EEEEEEeCCCCCEEEEEEEEEEcCCCeEEcCHHHHHhcCCCCCCEEEEEEeEcCCCCEEEEeECccccccccCHHHHHHH
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccceecccCCEEEEEECCEEEEEEEEEecCCC---eeEEEeCceeeeecCCCCCCCCCCc
Q 024476           81 TLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSN---AISIIETDCEVDFAPPLDYKEPEKP  139 (267)
Q Consensus        81 ~LRnystLT~Gd~I~I~yn~~~y~l~V~e~kP~~---aVsIIeTDleVDf~pPldy~Epe~~  139 (267)
                      +||||+|||+||+|.|+||++.|+|+|+|++|++   |||||||||+|||+||+||+||+++
T Consensus       147 ~LRnfstLT~Gd~I~i~~~~~~y~l~V~e~kP~~~~~aV~IidTDleVDf~~p~~y~ep~~~  208 (208)
T 1zc1_A          147 VLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSICVIETDLVTDFAPPVGYVEPDYK  208 (208)
T ss_dssp             HHHHCSCEESSSEEEEEETTEEEEEEEEEEECSSTTCEECCSSSCSEEEECCCCCCCCCCCC
T ss_pred             HhhcCccccCCCEEEEEeCCEEEEEEEEEEcCCCCCceEEEEeCceEEEecCCCCCcCCCCC
Confidence            9999999999999999999999999999999998   9999999999999999999999874

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

Probab=100.00  E-value=4.7e-58  Score=402.20  Aligned_cols=129  Identities=57%  Similarity=1.050  Sum_probs=127.9

Q ss_pred             CeEEEEeCCCCcEEEEEeeeeeeCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhh
Q 024476            1 MLFELRNNAAERVSHCGVLEFIAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILET   80 (267)
Q Consensus         1 MlF~l~N~~~~r~th~GVLEF~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~   80 (267)
                      |+|+|+|..++|+||||||||+|+||+||||+|||++|+|++||.|+|++++||+|+|||||||+++|++|+|||||||+
T Consensus        62 m~F~l~n~~~~r~th~GVlEFsA~EG~i~lP~wmm~~L~l~~gd~V~v~~~~LPkgt~vklqP~~~~Fl~i~npKavLE~  141 (190)
T 2yuj_A           62 MLFKLTNKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSPDFLDITNPKAVLEN  141 (190)
T ss_dssp             CEEEEEETTTTEEEEEEEEECCCBTTBEECCSHHHHHHTCCTTEEEEEEEECCCCCSEEEEEESSHHHHHSSCHHHHHHH
T ss_pred             eEEEEecCCCCceEEEEEEEEecCCCeEEeCHHHHHhcCCCCCCEEEEEEeecCCCcEEEEEECCccccccccHHHHHHH
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccceecccCCEEEEEECCEEEEEEEEEecCCCeeEEEeCceeeeecC
Q 024476           81 TLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFAP  129 (267)
Q Consensus        81 ~LRnystLT~Gd~I~I~yn~~~y~l~V~e~kP~~aVsIIeTDleVDf~p  129 (267)
                      +||||+|||+||+|.|+||++.|+|+|+|++|++|||||||||+|||+|
T Consensus       142 ~LrnfstLT~Gd~I~I~~~~~~y~l~V~e~kP~~aV~IidTDl~vDf~p  190 (190)
T 2yuj_A          142 ALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDFDA  190 (190)
T ss_dssp             HHTTCCEECTTCEEEEESSSCEEEEEEEEESSSSSEECSSCCCEEEECC
T ss_pred             HHhcCcccccCCEEEEEeCCEEEEEEEEEEcCCCeEEEEeCCEEEEecC
Confidence            9999999999999999999999999999999999999999999999986

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

Probab=99.37  E-value=4.6e-12  Score=112.20  Aligned_cols=124  Identities=20%  Similarity=0.309  Sum_probs=105.1

Q ss_pred             EEEEeCCCCcEEEEEeeee-eeCCCeEeccHHHHHHcCCCCCCeEEEEEe-ecCCcceEEEeeCCcCcCCccC--chHHH
Q 024476            3 FELRNNAAERVSHCGVLEF-IAEEGMIYMPYWMMENLLLQEGDIVRVKNV-TLPKGTYVKLQPHTKDFLDISN--PKAIL   78 (267)
Q Consensus         3 F~l~N~~~~r~th~GVLEF-~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~-~LPkGt~vkLqP~s~~Fl~isn--pKavL   78 (267)
                      .+|+. ...+.|+|-|+.. ..+.|.|.|..||++||++..||.|.|+.+ .++.|+.|.|.|.+..+-.|+.  ...+|
T Consensus        60 V~I~G-kr~k~Tva~v~~~~~~~~g~Irid~~~R~N~gV~iGD~V~V~~~~~v~~A~~V~LaP~~~~i~~i~~~~~~~~l  138 (211)
T 3qwz_A           60 VLLKG-XKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYL  138 (211)
T ss_dssp             EEEEC-STTCEEEEEEEECTTSCTTEEEECHHHHHHTTCCTTCEEEEEECTTCCBCSEEEEEEBGGGCTTCCSCHHHHTT
T ss_pred             EEEeC-CCCCcEEEEEEeCCCCCCCEEEeCHHHHhhcCCCCCCEEEEEECCCCCCceEEEEeccCcchhccCchhHHHHH
Confidence            45663 3345899999865 457899999999999999999999999999 8999999999998655544543  36778


Q ss_pred             hhccc-cceecccCCEEEEEECCEEEEEEEEEecCCCeeEEEeCceeeeec
Q 024476           79 ETTLR-NYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFA  128 (267)
Q Consensus        79 E~~LR-nystLT~Gd~I~I~yn~~~y~l~V~e~kP~~aVsIIeTDleVDf~  128 (267)
                      ...|. +|-.|++||+|.|.+.++.++|.|++++|. .+|+|..|-+|++.
T Consensus       139 k~~l~~~~rPV~~GD~i~v~~~~~~v~f~Vv~t~P~-g~viV~~~T~I~~~  188 (211)
T 3qwz_A          139 KPYFLEAYRPIRKGDIFLVRGGMRAVEFXVVETDPS-PYCIVAPDTVIHCE  188 (211)
T ss_dssp             HHHHTTCCEEEETTCEEECCCTTSCCEEEEEEEESS-SEEEECTTCEEECC
T ss_pred             HHHHhhCCceeecCCEEEEccCCcEEEEEEEeecCC-CCEEECCCcEEEEc
Confidence            88888 499999999999999999999999999997 68999988888884

>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=99.34  E-value=1.2e-11  Score=107.62  Aligned_cols=123  Identities=20%  Similarity=0.312  Sum_probs=99.5

Q ss_pred             EEEEeCCCCcEEEEEeeee-eeCCCeEeccHHHHHHcCCCCCCeEEEEEe-ecCCcceEEEeeCCcCcCCccC--chHHH
Q 024476            3 FELRNNAAERVSHCGVLEF-IAEEGMIYMPYWMMENLLLQEGDIVRVKNV-TLPKGTYVKLQPHTKDFLDISN--PKAIL   78 (267)
Q Consensus         3 F~l~N~~~~r~th~GVLEF-~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~-~LPkGt~vkLqP~s~~Fl~isn--pKavL   78 (267)
                      .+|+. ...+.|+|-|+.. ..++|.|.|..|+++||++..||.|.|+.+ .++.|+.|.|.|.+...-.|+.  ...+|
T Consensus        57 V~I~G-kr~k~Tva~v~~~~~~~~g~Irid~~~R~N~gV~iGD~V~V~~~~~v~~A~~V~LaP~~~~i~~i~~~~~~~~l  135 (187)
T 3tiw_A           57 VLLKG-KKRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYL  135 (187)
T ss_dssp             EEEEC-STTCEEEEEEEECTTSCTTEEEECHHHHHHTTCCTTCEEEEEECTTCEECSEEEEEECCCC-----CCHHHHTH
T ss_pred             EEEEC-CCCCeEEEEEEECCCCCCCEEEeCHHHHhhcCCCCCCEEEEEECCCCCCceEEEEeccccchhhccchhHHHHH
Confidence            35553 3345899999875 447899999999999999999999999999 8999999999998644323442  36778


Q ss_pred             hhccc-cceecccCCEEEEEECCEEEEEEEEEecCCCeeEEEeCceeeee
Q 024476           79 ETTLR-NYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDF  127 (267)
Q Consensus        79 E~~LR-nystLT~Gd~I~I~yn~~~y~l~V~e~kP~~aVsIIeTDleVDf  127 (267)
                      ...|. +|-.+++||+|.|.+.++.++|.|++++|. .+|+|..|-+|.+
T Consensus       136 k~~l~~~~rpV~~GD~i~v~~~~~~v~f~Vv~t~P~-~~v~V~~~T~I~~  184 (187)
T 3tiw_A          136 KPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPS-PYCIVAPDTVIHC  184 (187)
T ss_dssp             HHHHTTTCCEEETTCEEEEECSSSEEEEEEEEEESS-SEEECCTTCEEEC
T ss_pred             HHHhccCCceeeCCCEEEEccCCCEEEEEEEEecCC-CCEEECCCcEEEe
Confidence            88888 499999999999999999999999999997 6778876666654

>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=99.31  E-value=1.4e-11  Score=106.75  Aligned_cols=118  Identities=18%  Similarity=0.190  Sum_probs=101.5

Q ss_pred             CcEEEEEeee-eeeC--CCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCC---cCcCCccCchHHHhhcccc
Q 024476           11 ERVSHCGVLE-FIAE--EGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHT---KDFLDISNPKAILETTLRN   84 (267)
Q Consensus        11 ~r~th~GVLE-F~A~--EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s---~~Fl~isnpKavLE~~LRn   84 (267)
                      .|.|+|-|+. +..+  .|.|.|..|+++|+++..||.|.|+.+.++.|+.|.|.|.+   ..+.-..|....|...|++
T Consensus        47 ~r~t~a~v~~~~~ed~~~g~Irid~~~R~N~gv~iGD~V~V~~~~~~~A~~V~l~P~~~~~~~~~~~~~~~~~l~~~l~~  126 (185)
T 1cz4_A           47 VRKTVGRVYRARPEDENKGIVRIDSVMRNNCGASIGDKVKVRKVRTEIAKKVTLAPIIRKDQRLKFGEGIEEYVQRALIR  126 (185)
T ss_dssp             SSEEEEEEEECSSTTTTTSEEECCHHHHHHHTCCTTCEEEEEEECCCBCSEEEEEEECSTTCCSCCCSSHHHHHHHHHTT
T ss_pred             CCeEEEEEEEcCcCcCCCCEEEeCHHHHhccCCCCCCEEEEEECCCCCccEEEEecccccccccccccchHHHHHHHHCC
Confidence            5689999986 3333  68999999999999999999999999999999999999985   4443235778889999999


Q ss_pred             ceecccCCEEEEEE---CCE-EEEEEEEEecCCCeeEEEeCceeeeecC
Q 024476           85 YSCLTTGDSIMVAY---NNK-KYYIDIIETKPSNAISIIETDCEVDFAP  129 (267)
Q Consensus        85 ystLT~Gd~I~I~y---n~~-~y~l~V~e~kP~~aVsIIeTDleVDf~p  129 (267)
                      +. |++||+|.+.+   .++ ...|.|++++|..++|+|..|-+|++..
T Consensus       127 rp-v~~Gd~v~v~~~~~~g~~~~~f~Vv~t~P~~~~v~Vt~~T~I~i~~  174 (185)
T 1cz4_A          127 RP-MLEQDNISVPGLTLAGQTGLLFKVVKTLPSKVPVEIGEETKIEIRE  174 (185)
T ss_dssp             CE-ECTTCEECCSSCCCSSCCCCEEEEEEESSSSSCEECCTTCEEEECS
T ss_pred             Cc-ccCCCEEEEeeeccCCCeEEEEEEEEEcCCCceEEEcCCeEEEECC
Confidence            75 99999999986   667 8999999999988789999999998853

>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=98.96  E-value=1.3e-09  Score=93.88  Aligned_cols=125  Identities=17%  Similarity=0.188  Sum_probs=104.4

Q ss_pred             EEEEeCCCCcEEEEEeeeeee----CCCeEeccHHHHHHcCCCCCCeEEEEE-eecCCcceEEEeeCCcCcCCc-cCchH
Q 024476            3 FELRNNAAERVSHCGVLEFIA----EEGMIYMPYWMMENLLLQEGDIVRVKN-VTLPKGTYVKLQPHTKDFLDI-SNPKA   76 (267)
Q Consensus         3 F~l~N~~~~r~th~GVLEF~A----~EG~i~LP~Wmm~~L~l~~gd~V~I~~-~~LPkGt~vkLqP~s~~Fl~i-snpKa   76 (267)
                      -+|+-  ..++.++|...+..    ..+.|-|..-+.+||++..||.|.|+- ...+.++-|.|.|.+.|-++| .+.-.
T Consensus        45 VeI~g--~~~t~~~~w~~~~~~~d~~~~~I~Id~~~r~n~gv~~Gd~V~V~~~~~~~~A~~V~laP~~~dD~ei~e~~a~  122 (179)
T 1wlf_A           45 IEVAS--DHQPTYLSWVEGRHFNDQSENVAEINRQVGQKLGLSSGDQVFLRPCSHVVSCQQVEVEPLSADDWEILELHAI  122 (179)
T ss_dssp             EEEES--SSCCEEECEEECSSCC---CCEEEEEHHHHHHTTCCTTCEEEEEECSCCEECSEEEEEESSHHHHHHHHHSCS
T ss_pred             EEEEe--CCeeEEEEEECCCCcccCCCCEEEECHHHHhHCCCCCCCEEEEEECCCCccceEEEEEcCCcCCeEEehhHHH
Confidence            35553  23567788877754    467999999999999999999999998 799999999999998765554 55567


Q ss_pred             HHhhcccc-ceecccCCEEEEEECC-EEEEEEEEEecCCCeeEEEeCceeeeecC
Q 024476           77 ILETTLRN-YSCLTTGDSIMVAYNN-KKYYIDIIETKPSNAISIIETDCEVDFAP  129 (267)
Q Consensus        77 vLE~~LRn-ystLT~Gd~I~I~yn~-~~y~l~V~e~kP~~aVsIIeTDleVDf~p  129 (267)
                      .||..|.+ +-.+++||+|.|+..+ ....|.|+.+.|...+++|..|-+|.++|
T Consensus       123 ~le~~Ll~QiR~v~~G~~i~v~~~g~~~i~f~V~~~~P~~~~v~It~~TeI~v~p  177 (179)
T 1wlf_A          123 SLEQHLLDQIRIVFPKAVVPIWVDQQTYIFIQIVTLMPAAPYGRLETNTKLLIQP  177 (179)
T ss_dssp             SHHHHHHHHCCEECTTCEEEEESSSSCEEEEEEEEEESCCSSEECCTTCEEEECC
T ss_pred             HHHHHHhcCceeccCCCEEEEEecCCeEEEEEEEEeeCCCCeEEECCCcEEEEec
Confidence            78888885 8999999999999766 88899999999977889999999998866

>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=97.57  E-value=0.00028  Score=72.86  Aligned_cols=102  Identities=20%  Similarity=0.279  Sum_probs=79.9

Q ss_pred             eCCCeEeccHHHHHHcCCCCCCeEEEEEe-ecCCcceEEEeeCCcCcCCc--cCchHHHhhccc-cceecccCCEEEEEE
Q 024476           23 AEEGMIYMPYWMMENLLLQEGDIVRVKNV-TLPKGTYVKLQPHTKDFLDI--SNPKAILETTLR-NYSCLTTGDSIMVAY   98 (267)
Q Consensus        23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~-~LPkGt~vkLqP~s~~Fl~i--snpKavLE~~LR-nystLT~Gd~I~I~y   98 (267)
                      .+.|.|.|..-+.+||++..||.|.|+-+ .++.++.|.|.|.+...-.+  ......|...|. .+-.+++||+|.|.+
T Consensus        77 ~~~~~i~~~~~~r~n~~v~~gd~V~v~~~~~~~~a~~v~l~p~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~gd~~~v~~  156 (806)
T 3cf2_A           77 CSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRG  156 (806)
T ss_dssp             SBTTBCEECHHHHHTTTCCTTCEEEEEECCCCCBCSBEEEEEBTTTSTTCCSCHHHHTHHHHHTTTCCEEETTCEEEECC
T ss_pred             CCCCEEEeCHHHHHhcCCCCCCEEEEEECCCCCcCCEEEEeccccchhccchhHHHHHHHHHHHhcCCcccCCCEEEEec
Confidence            36799999999999999999999999988 79999999999975332222  223444555554 367899999999999


Q ss_pred             CCEEEEEEEEEecCCCeeEEEe--Cceee
Q 024476           99 NNKKYYIDIIETKPSNAISIIE--TDCEV  125 (267)
Q Consensus        99 n~~~y~l~V~e~kP~~aVsIIe--TDleV  125 (267)
                      .+....|.|++++|...+ +|.  |.+.+
T Consensus       157 ~~~~~~f~V~~~~P~~~~-~v~~~T~i~~  184 (806)
T 3cf2_A          157 GMRAVEFKVVETDPSPYC-IVAPDTVIHC  184 (806)
T ss_dssp             TTSCEEEEEEEESSSSEE-ECCTTSBCCB
T ss_pred             CCcEEEEEEEEEeCCCCe-EECCCcEEEE
Confidence            999999999999998654 444  44444

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

Probab=97.32  E-value=0.00076  Score=51.72  Aligned_cols=68  Identities=18%  Similarity=0.301  Sum_probs=53.9

Q ss_pred             CcceEEEeeCCcCcCCc-cCchHHHhhccccceecccCCEEEEEECCEEEEEEEEEecCCCeeEEEeCceeeee
Q 024476           55 KGTYVKLQPHTKDFLDI-SNPKAILETTLRNYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDF  127 (267)
Q Consensus        55 kGt~vkLqP~s~~Fl~i-snpKavLE~~LRnystLT~Gd~I~I~yn~~~y~l~V~e~kP~~aVsIIeTDleVDf  127 (267)
                      -|+-|.|.|.+  -+.+ .|.-..|-+.|++.. +++||+|.|..-++...|.|++++|.  +++|.-|-++++
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 IMSELKLKPLP--KVELPPDFVDVIRIKLQGKT-VRTGDVIGISILGKEVKFKVVQAYPS--PLRVEDRTKITL   79 (83)
T ss_dssp             CCCEEEEEESS--SCCCCHHHHHHHHHHHTTSE-ECTTCEEEEEETTEEEEEEEEEEESS--SEECCTTSEEEE
T ss_pred             EEEEEEEcCCC--ceecCccHHHHHHHHHCCCC-ccCCCEEEEeeCCCEEEEEEEEecCc--cEEECCCcEEEE
Confidence            47889999984  2334 344566777777755 99999999998889999999999997  888887777766

>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=95.77  E-value=0.15  Score=49.21  Aligned_cols=115  Identities=20%  Similarity=0.297  Sum_probs=83.5

Q ss_pred             CCcEEEEEeee-eeeCCCeEeccHHHHHHcCCCCCCeEEEEEe-ecCCcceEEEeeCCcCcCCccCc-hHHHhhcc-c-c
Q 024476           10 AERVSHCGVLE-FIAEEGMIYMPYWMMENLLLQEGDIVRVKNV-TLPKGTYVKLQPHTKDFLDISNP-KAILETTL-R-N   84 (267)
Q Consensus        10 ~~r~th~GVLE-F~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~-~LPkGt~vkLqP~s~~Fl~isnp-KavLE~~L-R-n   84 (267)
                      ..+.|.|.|+- -.-+.|.|-|..-+.+|+++.-||.|.|+-+ .+|.|+-|.|.|-+..--.+..- -..|+.-+ . .
T Consensus        63 ~~~~~~~~~~~~~~~~~~~i~~~~~~r~n~~~~~gd~v~v~~~~~~~~a~~v~~~~~~~av~a~~~ga~d~~~Kp~~~~~  142 (489)
T 3hu3_A           63 KRREAVCIVLSDDTCSDEKIRMNRVVRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEA  142 (489)
T ss_dssp             TTCEEEEEEEECTTSCTTEEECCHHHHHHTTCCTTCEEEEEECTTCCBCSEEEEEEBGGGSSSCCSCHHHHTHHHHHTTT
T ss_pred             ccCcEEEEEeeCCCCCCCEEEecHHHHhhcCCCCCCEEEEEECCCCCccCEEEEcCCCcccccccchhHHHHhHHHHhhc
Confidence            34578899862 2235789999999999999999999999999 99999999999976543323221 11222222 2 3


Q ss_pred             ceecccCCEEEEEECCEEEEEEEEEecCCCeeEEEeCceee
Q 024476           85 YSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEV  125 (267)
Q Consensus        85 ystLT~Gd~I~I~yn~~~y~l~V~e~kP~~aVsIIeTDleV  125 (267)
                      +-.+..||.+.+....+.+.+.+++.+|... +++..+-.+
T Consensus       143 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~t~~  182 (489)
T 3hu3_A          143 YRPIRKGDIFLVHGGMRAVEFKVVETDPSPY-CIVAPDTVI  182 (489)
T ss_dssp             CEEEETTCEEEEEETTEEEEEEEEEEESSSE-EEECTTCEE
T ss_pred             CcccccCCEEEecCCCceEEEEEEeecCCCc-eEEcCCeEE
Confidence            6677889999999999999999999988644 333333333

>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=91.88  E-value=0.44  Score=33.99  Aligned_cols=39  Identities=18%  Similarity=0.198  Sum_probs=32.6

Q ss_pred             eCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCC
Q 024476           23 AEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHT   65 (267)
Q Consensus        23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s   65 (267)
                      ...|.|.+|.=+.+.|+|++||.|.|...    +.-+.|+|..
T Consensus        19 ~~kGqItIPkeiR~~Lgi~~Gd~l~i~~~----~~~IiL~p~~   57 (59)
T 1yfb_A           19 DELGRVVIPIELRRTLGIAEKDALEIYVD----DEKIILKKYK   57 (59)
T ss_dssp             CTTCEEECCHHHHHHTTCCTTCEEEEEEE----TTEEEEEECC
T ss_pred             CCCCEEEeCHHHHHHcCCCCCCEEEEEEE----CCEEEEEECC
Confidence            47899999999999999999999988764    2358888864

>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=91.57  E-value=0.2  Score=42.87  Aligned_cols=90  Identities=16%  Similarity=0.187  Sum_probs=63.5

Q ss_pred             eeeeeeC---CCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhhccccceecccCCEE
Q 024476           18 VLEFIAE---EGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSI   94 (267)
Q Consensus        18 VLEF~A~---EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRnystLT~Gd~I   94 (267)
                      |.|-.+.   -|.|+|+.=.|+.|+|.+||.|.|+.   .+.+.++.-|...+  ++.+-.--|-..+|+-.-+..||.+
T Consensus        11 V~~a~~~D~gr~ivrl~p~~m~~Lgl~~GD~V~I~G---~r~t~a~v~~~~~e--d~~~g~Irid~~~R~N~gv~iGD~V   85 (185)
T 1cz4_A           11 VAEANSTDPGMSRVRLDESSRRLLDAEIGDVVEIEK---VRKTVGRVYRARPE--DENKGIVRIDSVMRNNCGASIGDKV   85 (185)
T ss_dssp             EECCSSCCCCSSEEEECHHHHHTTCCCTTCEEEEES---SSEEEEEEEECSST--TTTTSEEECCHHHHHHHTCCTTCEE
T ss_pred             EecCcccccCCCEEEECHHHHHHcCCCCCCEEEEEc---CCeEEEEEEEcCcC--cCCCCEEEeCHHHHhccCCCCCCEE
Confidence            5554433   37799999999999999999999975   56788888886322  2222222344566766789999999


Q ss_pred             EEEECCEEEEEEEEEecCCCeeEEEeC
Q 024476           95 MVAYNNKKYYIDIIETKPSNAISIIET  121 (267)
Q Consensus        95 ~I~yn~~~y~l~V~e~kP~~aVsIIeT  121 (267)
                      .|.-         .+++++..|.+--+
T Consensus        86 ~V~~---------~~~~~A~~V~l~P~  103 (185)
T 1cz4_A           86 KVRK---------VRTEIAKKVTLAPI  103 (185)
T ss_dssp             EEEE---------ECCCBCSEEEEEEE
T ss_pred             EEEE---------CCCCCccEEEEecc
Confidence            9873         35677777766533

>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=90.66  E-value=0.24  Score=42.65  Aligned_cols=71  Identities=20%  Similarity=0.242  Sum_probs=54.1

Q ss_pred             CCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhhccccceecccCCEEEEEEC
Q 024476           24 EEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYN   99 (267)
Q Consensus        24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRnystLT~Gd~I~I~yn   99 (267)
                      +.|.|.|+.-.|+.|+|.+||.|.|+..+ -+-|.+...|..    +...-.--|-..+|+-..+..||.+.|.--
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----TCSDEKIRMNRVVRNNLRVRLGDVISIQPC  105 (187)
T ss_dssp             CTTEEEECHHHHHHHTCCTTCEEEEECST-TCEEEEEEEECT----TSCTTEEEECHHHHHHTTCCTTCEEEEEEC
T ss_pred             CCcEEEECHHHHHHcCCCCCCEEEEECCC-CCeEEEEEEECC----CCCCCEEEeCHHHHhhcCCCCCCEEEEEEC
Confidence            57899999999999999999999999742 124777777763    233333345677788888999999998744

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

Probab=90.61  E-value=0.87  Score=35.04  Aligned_cols=68  Identities=22%  Similarity=0.250  Sum_probs=47.4

Q ss_pred             CCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcce----EEEeeCCcCcCCccCchHHHhhccccceecccCCEEEEEE
Q 024476           24 EEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTY----VKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAY   98 (267)
Q Consensus        24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~----vkLqP~s~~Fl~isnpKavLE~~LRnystLT~Gd~I~I~y   98 (267)
                      ..|+|-+|..+-+.|++.+||.|.++.+.+..|.-    ....=  ..-.+|.=||.+     |..--|..||.+.|..
T Consensus        13 ~~gqvtiP~~iR~~LgI~~GD~V~v~~i~~~~g~~~~~~~~~~v--~~kGqitIPkei-----R~~lgi~~Gd~l~~~~   84 (92)
T 2glw_A           13 RIGRIIIPAGTRKFYGIEQGDFVEIKIVKYEGEEPKEGTFTARV--GEQGSVIIPKAL-----RDVIGIKPGEVIEVLL   84 (92)
T ss_dssp             GGGEEECCHHHHHHHTCCTTCEEEEEEEEEETTEEEEEEEEEEC--CGGGEEECCHHH-----HHHHTCCTTCEEEEEE
T ss_pred             CCCEEEecHHHHHHcCCCCCCEEEEEEEEecCCccceeEEEEEE--CcCceEECcHHH-----HHHcCCCCCCEEEEEE
Confidence            57999999999999999999999998766666651    11100  112244556554     4445788999998864

>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=89.70  E-value=1.2  Score=38.61  Aligned_cols=88  Identities=13%  Similarity=0.219  Sum_probs=62.2

Q ss_pred             CCCeEeccHHHHHHcCCCCCCeEEEEEeecCCc-ceEEEeeCCcCcCC--c-----cCchHHHhhccccc--eecccCCE
Q 024476           24 EEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKG-TYVKLQPHTKDFLD--I-----SNPKAILETTLRNY--SCLTTGDS   93 (267)
Q Consensus        24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkG-t~vkLqP~s~~Fl~--i-----snpKavLE~~LRny--stLT~Gd~   93 (267)
                      +.|+|.|-.-.-+.+++.-|+.|.|+.-..+.. .|+-.-=.+.||+.  -     -|-..+-..-+++|  ..||.|..
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            789999998888888999999999987654421 23333334455652  1     23344444455566  45999999


Q ss_pred             EEEEECCEEEEEEEEEec
Q 024476           94 IMVAYNNKKYYIDIIETK  111 (267)
Q Consensus        94 I~I~yn~~~y~l~V~e~k  111 (267)
                      |.+.|++..|.|.|.+++
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            999999999998887754

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

Probab=88.32  E-value=0.42  Score=41.95  Aligned_cols=91  Identities=21%  Similarity=0.253  Sum_probs=63.3

Q ss_pred             eeeeee-CCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhhccccceecccCCEEEE
Q 024476           18 VLEFIA-EEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMV   96 (267)
Q Consensus        18 VLEF~A-~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRnystLT~Gd~I~I   96 (267)
                      |-|=.. +.|.|.|+.-.|+.|+|.+||.|.|+..+ -+-|.+...|..    +...-+--|-..+|+-..+..||.+.|
T Consensus        31 V~ea~~~Drgivrl~p~~m~~Lgl~~GD~V~I~Gkr-~k~Tva~v~~~~----~~~~g~Irid~~~R~N~gV~iGD~V~V  105 (211)
T 3qwz_A           31 VDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGXK-RREAVCIVLSDD----TCSDEKIRMNRVVRNNLRVRLGDVISI  105 (211)
T ss_dssp             EEECSCCCTTEEEECHHHHHHHTCCBTCEEEEECST-TCEEEEEEEECT----TSCTTEEEECHHHHHHTTCCTTCEEEE
T ss_pred             EcccccCCCcEEEECHHHHHHcCCCCCCEEEEeCCC-CCcEEEEEEeCC----CCCCCEEEeCHHHHhhcCCCCCCEEEE
Confidence            444433 58899999999999999999999999742 224777777753    222223335667777888999999998


Q ss_pred             EECCEEEEEEEEEecCCCeeEEEeC
Q 024476           97 AYNNKKYYIDIIETKPSNAISIIET  121 (267)
Q Consensus        97 ~yn~~~y~l~V~e~kP~~aVsIIeT  121 (267)
                      .--.        +++++.-|.+.=+
T Consensus       106 ~~~~--------~v~~A~~V~LaP~  122 (211)
T 3qwz_A          106 QPCP--------DVKYGKRIHVLPI  122 (211)
T ss_dssp             EECT--------TCCBCSEEEEEEB
T ss_pred             EECC--------CCCCceEEEEecc
Confidence            6321        4556666666544

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

Probab=87.99  E-value=0.41  Score=32.89  Aligned_cols=38  Identities=16%  Similarity=0.263  Sum_probs=30.6

Q ss_pred             eCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeC
Q 024476           23 AEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPH   64 (267)
Q Consensus        23 A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~   64 (267)
                      ...|.|.+|.=+.+.|+|++||.|.+...   .+. +.|+|.
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 666664

>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=87.23  E-value=3  Score=35.55  Aligned_cols=88  Identities=13%  Similarity=0.102  Sum_probs=61.8

Q ss_pred             CCCeEeccHHHHHHcCCCCCCeEEEEEeecC----CcceEEEeeCCcCcCC------c-cCchHHHhhccccc--eeccc
Q 024476           24 EEGMIYMPYWMMENLLLQEGDIVRVKNVTLP----KGTYVKLQPHTKDFLD------I-SNPKAILETTLRNY--SCLTT   90 (267)
Q Consensus        24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LP----kGt~vkLqP~s~~Fl~------i-snpKavLE~~LRny--stLT~   90 (267)
                      +.|+|.|-.-.-+.+++.-|+.|.|+.-..|    ...++-.-=.+.+|+.      . -|-..+-..-+++|  ..||.
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            7899999888888889999999999977542    1233332223445542      1 24444455555566  45999


Q ss_pred             CCEEEEEECCEEEEEEEEEec
Q 024476           91 GDSIMVAYNNKKYYIDIIETK  111 (267)
Q Consensus        91 Gd~I~I~yn~~~y~l~V~e~k  111 (267)
                      |..|.+.|++..|.|.|.++.
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            999999999999998887754

>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=82.18  E-value=1.7  Score=44.92  Aligned_cols=86  Identities=21%  Similarity=0.270  Sum_probs=57.5

Q ss_pred             CCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhhccccceecccCCEEEEEECCEEE
Q 024476           24 EEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMVAYNNKKY  103 (267)
Q Consensus        24 ~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRnystLT~Gd~I~I~yn~~~y  103 (267)
                      +.+.|+|..-.|+.|+|.+||+|.|+..+--.+.-+.+.+.     ++.+-..-|-..+|.-..+..||.|.|.--    
T Consensus        35 d~~~~~~~~~~~~~l~~~~gd~v~i~g~~~~~~~~~~~~~~-----~~~~~~i~~~~~~r~n~~v~~gd~V~v~~~----  105 (806)
T 3cf2_A           35 DNSVVSLSQPKMDELQLFRGDTVLLKGKKRREAVCIVLSDD-----TCSDEKIRMNRVVRNNLRVRLGDVISIQPC----  105 (806)
T ss_dssp             CTTEEEECHHHHHHTTCCSSCEEEEECGGGCBCCEEEEECT-----TSBTTBCEECHHHHHTTTCCTTCEEEEEEC----
T ss_pred             CCCEEEECHHHHHHcCCCCCCEEEEEcCCCceEEEEEcCCC-----CCCCCEEEeCHHHHHhcCCCCCCEEEEEEC----
Confidence            56789999999999999999999998765322222223332     233333345566777778899999998632    


Q ss_pred             EEEEEEecCCCeeEEEeCc
Q 024476          104 YIDIIETKPSNAISIIETD  122 (267)
Q Consensus       104 ~l~V~e~kP~~aVsIIeTD  122 (267)
                          .+++++..|.|..++
T Consensus       106 ----~~~~~a~~v~l~p~~  120 (806)
T 3cf2_A          106 ----PDVKYGKRIHVLPID  120 (806)
T ss_dssp             ----CCCCBCSBEEEEEBT
T ss_pred             ----CCCCcCCEEEEeccc
Confidence                245566666665544

---

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	267
d1e32a3	94	Membrane fusion atpase p97 domain 2, P97-Nc {Mouse	96.59
d1cz5a2	94	C-terminal domain of VAT-N, VAT-Nc {Archaeon Therm	94.19
d1wlfa1	80	Peroxisome biogenesis factor 1 (PEX-1), domain 2 {	93.9
d1e32a1	86	Membrane fusion ATPase p97 N-terminal domain , P97	91.99
d1cz5a1	91	N-terminal domain of VAT-N, VAT-Nn {Archaeon Therm	85.77

>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=96.59  E-value=0.0056  Score=46.32  Aligned_cols=76  Identities=20%  Similarity=0.313  Sum_probs=56.6

Q ss_pred             ecCCcceEEEeeCCcCcCCcc-C-chHHHhhccc-cceecccCCEEEEEECCEEEEEEEEEecCCCeeEEEeCceeeeec
Q 024476           52 TLPKGTYVKLQPHTKDFLDIS-N-PKAILETTLR-NYSCLTTGDSIMVAYNNKKYYIDIIETKPSNAISIIETDCEVDFA  128 (267)
Q Consensus        52 ~LPkGt~vkLqP~s~~Fl~is-n-pKavLE~~LR-nystLT~Gd~I~I~yn~~~y~l~V~e~kP~~aVsIIeTDleVDf~  128 (267)
                      ++|-|+.|.+-|-+..--.|+ | .+.+|.-.+. +|--|++||++.|....+.-+++|++++|++ .|||-.|-.+...
T Consensus         1 di~~~krV~vlP~~DTieglsgnlf~~ylkPYf~~~yrPv~~gD~f~v~g~~r~VEFKVv~~dp~~-~~iV~~~T~I~~e   79 (94)
T d1e32a3           1 DVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSP-YCIVAPDTVIHCE   79 (94)
T ss_dssp             TCCBCSCEEEEEBGGGTTTCBSCHHHHTHHHHHTTSCEEEETTCEEEEEETTEEEEEEEEEESSSS-EEEECTTCCCBCC
T ss_pred             CCCcccEEEEEecccccCCCCccHHHHHHhHHHhhcCccccCCCEEEEccCCeeEEEEEEeecCCC-ceEEcCCCEEEeC
Confidence            368889999999764443333 1 2445555555 5889999999999999999999999999987 5777666555443

>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=94.19  E-value=0.035  Score=41.39  Aligned_cols=73  Identities=15%  Similarity=0.195  Sum_probs=51.6

Q ss_pred             CcceEEEeeCCcCcCCc---cCchHHHhhccccceecccCCEEEEEE----CCEEEEEEEEEecCCCeeEEEeCceeeee
Q 024476           55 KGTYVKLQPHTKDFLDI---SNPKAILETTLRNYSCLTTGDSIMVAY----NNKKYYIDIIETKPSNAISIIETDCEVDF  127 (267)
Q Consensus        55 kGt~vkLqP~s~~Fl~i---snpKavLE~~LRnystLT~Gd~I~I~y----n~~~y~l~V~e~kP~~aVsIIeTDleVDf  127 (267)
                      .|+-|.|.|-...-..|   .|.-.+|-+.|..+ -+++||+|.|..    .++...|.|++++|....++|.-|-++++
T Consensus         3 ~A~kVvLAP~~~~~~~i~~~~~~~~ylk~~L~gr-PV~~GD~i~v~~~~~~g~~~i~F~Vv~t~P~g~~ViIt~~TeI~i   81 (94)
T d1cz5a2           3 IAKKVTLAPIIRKDQRLKFGEGIEEYVQRALIRR-PMLEQDNISVPGLTLAGQTGLLFKVVKTLPSKVPVEIGEETKIEI   81 (94)
T ss_dssp             BCSEEEEEECSCTTTTCCCCSSHHHHHHHHHSSC-EECTTCEECCSSCCCSSCCCCSEEEEEESSSSSCEECCTTCEEEE
T ss_pred             cccEEEECcCCCccceEEEcCCHHHHHHHHHcCC-CCcCCCEEEEeeccccCCceEeEEEEEEeCCCCeEEECCCeEEEE
Confidence            47889999964332233   35566677777764 689999999954    34778899999999986566655555555


Q ss_pred             c
Q 024476          128 A  128 (267)
Q Consensus       128 ~  128 (267)
                      .
T Consensus        82 ~   82 (94)
T d1cz5a2          82 R   82 (94)
T ss_dssp             C
T ss_pred             e
Confidence            3

>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=93.90  E-value=0.014  Score=42.72  Aligned_cols=75  Identities=17%  Similarity=0.239  Sum_probs=62.5

Q ss_pred             CcceEEEeeCCcCcCCc-cCchHHHhhccc-cceecccCCEEEEEEC-CEEEEEEEEEecCCCeeEEEeCceeeeecC
Q 024476           55 KGTYVKLQPHTKDFLDI-SNPKAILETTLR-NYSCLTTGDSIMVAYN-NKKYYIDIIETKPSNAISIIETDCEVDFAP  129 (267)
Q Consensus        55 kGt~vkLqP~s~~Fl~i-snpKavLE~~LR-nystLT~Gd~I~I~yn-~~~y~l~V~e~kP~~aVsIIeTDleVDf~p  129 (267)
                      .++.|-+.|.+.|=++| .-.-..||..|- +..+++.|.+|.+.-+ +..-+|.|..+.|......+..|-||=++|
T Consensus         3 ~~~~V~veP~T~dDWEIiEl~a~~lE~~LL~QiRiV~~~~~~~v~v~~~~~~~~~V~~i~P~~~~~~L~~~TEv~VaP   80 (80)
T d1wlfa1           3 SCQQVEVEPLSADDWEILELHAISLEQHLLDQIRIVFPKAVVPIWVDQQTYIFIQIVTLMPAAPYGRLETNTKLLIQP   80 (80)
T ss_dssp             ECSEEEEEESSHHHHHHHHHSCSSHHHHHHHHCCEECTTCEEEEESSSSCEEEEEEEEEESCCSSEECCTTCEEEECC
T ss_pred             ceEEEEEecCChhhHHHHHHHHHHHHHHHHhheeeccCCCEEEEEECCCcEEEEEEEEecCCCeeEEecCCCEEEeCC
Confidence            57889999999887764 555566787776 4899999999999987 467789999999998888899999988765

>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=91.99  E-value=0.092  Score=38.37  Aligned_cols=75  Identities=24%  Similarity=0.232  Sum_probs=50.9

Q ss_pred             eeee-eeCCCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCcCcCCccCchHHHhhccccceecccCCEEEE
Q 024476           18 VLEF-IAEEGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTKDFLDISNPKAILETTLRNYSCLTTGDSIMV   96 (267)
Q Consensus        18 VLEF-~A~EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~~Fl~isnpKavLE~~LRnystLT~Gd~I~I   96 (267)
                      |.|- ..+.|.+.|..-.|+.|+|.+||.|.|+-.   +.+-...-|...+  +...=.--|-...|+=..++.||++.|
T Consensus         8 V~ea~~~D~~iarl~p~~m~~Lgl~~GD~V~I~Gk---r~t~av~~~~~~~--d~~~g~Irid~~~R~Nagv~iGD~V~V   82 (86)
T d1e32a1           8 VDEAINEDNSVVSLSQPKMDELQLFRGDTVLLKGK---KRREAVCIVLSDD--TCSDEKIRMNRVVRNNLRVRLGDVISI   82 (86)
T ss_dssp             EECCSSCCTTEEEECHHHHHHTTCCTTCEEEEECS---TTCEEEEEEEECT--TSCSSEEEECHHHHHHTTCCTTCEEEE
T ss_pred             EeecccCCCCEEEECHHHHHHcCCCCCCEEEEEcC---CceeEEEEEeccC--CCCCCEEEecHHHHhhcCcCCCCEEEE
Confidence            4453 346789999999999999999999999876   3444444443211  111112235566777778899999988


Q ss_pred             E
Q 024476           97 A   97 (267)
Q Consensus        97 ~   97 (267)
                      .
T Consensus        83 ~   83 (86)
T d1e32a1          83 Q   83 (86)
T ss_dssp             E
T ss_pred             E
Confidence            5

>d1cz5a1 b.52.2.3 (A:1-91) N-terminal domain of VAT-N, VAT-Nn {Archaeon Thermoplasma acidophilum [TaxId: 2303]}

class: All beta proteins
fold: Double psi beta-barrel
superfamily: ADC-like
family: Cdc48 N-terminal domain-like
domain: N-terminal domain of VAT-N, VAT-Nn
species: Archaeon Thermoplasma acidophilum [TaxId: 2303]

Probab=85.77  E-value=0.33  Score=35.75  Aligned_cols=67  Identities=18%  Similarity=0.182  Sum_probs=48.0

Q ss_pred             CCeEeccHHHHHHcCCCCCCeEEEEEeecCCcceEEEeeCCc-CcCCccCchHHHhhccccceecccCCEEEEE
Q 024476           25 EGMIYMPYWMMENLLLQEGDIVRVKNVTLPKGTYVKLQPHTK-DFLDISNPKAILETTLRNYSCLTTGDSIMVA   97 (267)
Q Consensus        25 EG~i~LP~Wmm~~L~l~~gd~V~I~~~~LPkGt~vkLqP~s~-~Fl~isnpKavLE~~LRnystLT~Gd~I~I~   97 (267)
                      -|.+.|+.-.|+.|+|.+||.|.|+..   +-|.++.-|... |.-   .-.--|-..+|+=.-...||.+.|.
T Consensus        21 rgiari~~~~m~~Lgl~~GD~V~I~Gk---r~t~a~v~~~~~~d~~---~g~IriDg~~R~Nagv~iGD~V~V~   88 (91)
T d1cz5a1          21 MSRVRLDESSRRLLDAEIGDVVEIEKV---RKTVGRVYRARPEDEN---KGIVRIDSVMRNNCGASIGDKVKVR   88 (91)
T ss_dssp             SSEEEECHHHHHTTSCCTTCEEEEESS---SEEEEEEEECSSTTTT---TSEEECCHHHHHHHTCCTTCCEEEE
T ss_pred             CcEEEECHHHHHHcCCCCCCEEEEEcC---ceEEEEEEecCcccCC---CCEEEEcHHHHHhCCCCCCCEEEEE
Confidence            489999999999999999999999975   357788877543 332   1111133455555667888888875