Psyllid ID: psy6209

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-----
Protein Sequence
MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGVR
Secondary Structure (PSIPRED)
cccEEEEEcccEEEEEEccccccccEEEEEEcccccccccHHHHHHHHHHHHcccccccccccEEEEEccccEEEEEEEEEccccEEEEccccEEEEcccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccEEEEcccEEEEEccccccccEEEEEEEcccccccEccccEEEEcccHHHHHccccccccEEEEEccccEEEEEEEEEccccEEEEcccEEEEEcccccccHHHHHHHHccc
Coil and Loop (DISEMBL)
msfrlttpcrdlLDRQRDIQIVygkrihvlpiddsvqgltgnlfevylkpyfleayrpvhkddlfivrggmravefkivdtdpapycivaadtvihcegdpikregeenkpngvr
Flexible Loop (DISEMBL)
msfrlttpcrdlldrQRDIQIVYgkrihvlpiddsvqgLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEgdpikregeenkpngvr
Low Complexity Region (SEG)
MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGVR
Disordered region (IsUnstruct)
******TPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEG****************
Disordered Region (DISOPRED)
**FRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGE********
Disordered Region (DISEMBL)
********CRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKRE**********
Disordered Region (DISPRO)
*SFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGE********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGVR
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	115	2.2.26 [Sep-21-2011]
Q6GL04	805	Transitional endoplasmic	yes	N/A	0.817	0.116	0.787	1e-40
Q7ZU99	806	Transitional endoplasmic	yes	N/A	0.817	0.116	0.787	2e-40
P46462	806	Transitional endoplasmic	yes	N/A	0.817	0.116	0.787	2e-40
Q01853	806	Transitional endoplasmic	yes	N/A	0.817	0.116	0.787	2e-40
P55072	806	Transitional endoplasmic	yes	N/A	0.817	0.116	0.787	2e-40
Q3ZBT1	806	Transitional endoplasmic	yes	N/A	0.817	0.116	0.787	2e-40
P03974	806	Transitional endoplasmic	yes	N/A	0.817	0.116	0.787	2e-40
P23787	805	Transitional endoplasmic	N/A	N/A	0.817	0.116	0.776	2e-40
Q9LZF6	810	Cell division control pro	yes	N/A	0.765	0.108	0.715	8e-36
P54609	809	Cell division control pro	yes	N/A	0.765	0.108	0.715	9e-36

>sp|Q6GL04|TERA_XENTR Transitional endoplasmic reticulum ATPase OS=Xenopus tropicalis GN=vcp PE=2 SV=1

 Score =  164 bits (415), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 74/94 (78%), Positives = 85/94 (90%)

Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 108 VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 167

Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 168 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the nuclear envelope and of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process.
Xenopus tropicalis (taxid: 8364)

>sp|Q7ZU99|TERA_DANRE Transitional endoplasmic reticulum ATPase OS=Danio rerio GN=vcp PE=1 SV=1

 Score =  164 bits (415), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 74/94 (78%), Positives = 85/94 (90%)

Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 108 VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 167

Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 168 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process (By similarity). Enhances cell cycle progression and inhibits apoptosis at low temperatures.

Danio rerio (taxid: 7955)

>sp|P46462|TERA_RAT Transitional endoplasmic reticulum ATPase OS=Rattus norvegicus GN=Vcp PE=1 SV=3

 Score =  164 bits (414), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 74/94 (78%), Positives = 85/94 (90%)

Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 108 VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 167

Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 168 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process. 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. Regulates E3 ubiquitin-protein ligase activity of RNF19A (By similarity). Component of the VCP/p97-AMFR/gp78 complex that participates in the final step of the sterol-mediated ubiquitination and endoplasmic reticulum-associated degradation (ERAD) of HMGCR.

Rattus norvegicus (taxid: 10116)

>sp|Q01853|TERA_MOUSE Transitional endoplasmic reticulum ATPase OS=Mus musculus GN=Vcp PE=1 SV=4

 Score =  164 bits (414), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 74/94 (78%), Positives = 85/94 (90%)

Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 108 VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 167

Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 168 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process. 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. Regulates E3 ubiquitin-protein ligase activity of RNF19A (By similarity). Component of the VCP/p97-AMFR/gp78 complex that participates in the final step of the sterol-mediated ubiquitination and endoplasmic reticulum-associated degradation (ERAD) of HMGCR.

Mus musculus (taxid: 10090)

>sp|P55072|TERA_HUMAN Transitional endoplasmic reticulum ATPase OS=Homo sapiens GN=VCP PE=1 SV=4

 Score =  164 bits (414), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 74/94 (78%), Positives = 85/94 (90%)

Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 108 VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 167

Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 168 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process. 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. Regulates E3 ubiquitin-protein ligase activity of RNF19A (By similarity). Component of the VCP/p97-AMFR/gp78 complex that participates in the final step of the sterol-mediated ubiquitination and endoplasmic reticulum-associated degradation (ERAD) of HMGCR.

Homo sapiens (taxid: 9606)

>sp|Q3ZBT1|TERA_BOVIN Transitional endoplasmic reticulum ATPase OS=Bos taurus GN=VCP PE=2 SV=1

 Score =  164 bits (414), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 74/94 (78%), Positives = 85/94 (90%)

Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 108 VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 167

Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 168 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process. 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. Regulates E3 ubiquitin-protein ligase activity of RNF19A (By similarity). Component of the VCP/p97-AMFR/gp78 complex that participates in the final step of the sterol-mediated ubiquitination and endoplasmic reticulum-associated degradation (ERAD) of HMGCR.

Bos taurus (taxid: 9913)

>sp|P03974|TERA_PIG Transitional endoplasmic reticulum ATPase OS=Sus scrofa GN=VCP PE=1 SV=5

 Score =  164 bits (414), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 74/94 (78%), Positives = 85/94 (90%)

Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 108 VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 167

Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 168 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process. 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. Regulates E3 ubiquitin-protein ligase activity of RNF19A (By similarity). Component of the VCP/p97-AMFR/gp78 complex that participates in the final step of the sterol-mediated ubiquitination and endoplasmic reticulum-associated degradation (ERAD) of HMGCR.

Sus scrofa (taxid: 9823)

>sp|P23787|TERA_XENLA Transitional endoplasmic reticulum ATPase OS=Xenopus laevis GN=vcp PE=1 SV=3

 Score =  163 bits (413), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 73/94 (77%), Positives = 85/94 (90%)

Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKR+HVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 108 VKYGKRVHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 167

Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 168 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

Necessary for the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis. Involved in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). The transfer of membranes from the endoplasmic reticulum to the Golgi apparatus occurs via 50-70 nm transition vesicles which derive from part-rough, part-smooth transitional elements of the endoplasmic reticulum (tER). Vesicle budding from the tER is an ATP-dependent process.

Xenopus laevis (taxid: 8355)

>sp|Q9LZF6|CD48E_ARATH Cell division control protein 48 homolog E OS=Arabidopsis thaliana GN=CDC48E PE=1 SV=2

 Score =  148 bits (374), Expect = 8e-36,   Method: Compositional matrix adjust.
 Identities = 63/88 (71%), Positives = 79/88 (89%)

Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKR+H+LP+DD+V+G+TGNLF+ YLKPYFLEAYRPV K DLF+VRGGMR+VEFK+++
Sbjct: 112 VKYGKRVHILPVDDTVEGVTGNLFDAYLKPYFLEAYRPVRKGDLFLVRGGMRSVEFKVIE 171

Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEE 108
           TDPA YC+VA DT I CEG+P+KRE EE
Sbjct: 172 TDPAEYCVVAPDTEIFCEGEPVKREDEE 199

Probably functions in cell division and growth processes. Interacts with certain SNAREs as part of specialized membrane fusion events where vesicles from the same organelle fuse (homotypic fusion).

Arabidopsis thaliana (taxid: 3702)

>sp|P54609|CD48A_ARATH Cell division control protein 48 homolog A OS=Arabidopsis thaliana GN=CDC48A PE=1 SV=1

 Score =  148 bits (374), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 63/88 (71%), Positives = 79/88 (89%)

Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKR+H+LP+DD+V+G+TGNLF+ YLKPYFLEAYRPV K DLF+VRGGMR+VEFK+++
Sbjct: 112 VKYGKRVHILPVDDTVEGVTGNLFDAYLKPYFLEAYRPVRKGDLFLVRGGMRSVEFKVIE 171

Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEE 108
           TDPA YC+VA DT I CEG+P+KRE EE
Sbjct: 172 TDPAEYCVVAPDTEIFCEGEPVKREDEE 199

Probably functions in cell division and growth processes. Interacts with certain SNAREs as part of specialized membrane fusion events where vesicles from the same organelle fuse (homotypic fusion).

Arabidopsis thaliana (taxid: 3702)

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	115
344251788	2171	Transitional endoplasmic reticulum ATPas	0.852	0.045	0.719	2e-41
193617621	804	PREDICTED: transitional endoplasmic reti	0.904	0.129	0.769	3e-41
345486620	801	PREDICTED: transitional endoplasmic reti	0.904	0.129	0.759	6e-41
383861759	811	PREDICTED: transitional endoplasmic reti	0.904	0.128	0.75	1e-40
383861757	801	PREDICTED: transitional endoplasmic reti	0.904	0.129	0.75	2e-40
444729881	1258	Transitional endoplasmic reticulum ATPas	0.904	0.082	0.730	2e-40
322801676	793	hypothetical protein SINV_06607 [Solenop	0.904	0.131	0.759	2e-40
307211146	796	Transitional endoplasmic reticulum ATPas	0.904	0.130	0.75	3e-40
307174120	801	Transitional endoplasmic reticulum ATPas	0.904	0.129	0.75	6e-40
332031336	832	Transitional endoplasmic reticulum ATPas	0.904	0.125	0.75	7e-40

>gi|344251788|gb|EGW07892.1| Transitional endoplasmic reticulum ATPase [Cricetulus griseus]

 Score =  172 bits (437), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 77/107 (71%), Positives = 88/107 (82%), Gaps = 9/107 (8%)

Query: 8    PCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIV 67
            PC D         + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+V
Sbjct: 1447 PCPD---------VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLV 1497

Query: 68   RGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
            RGGMRAVEFK+V+TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 1498 RGGMRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 1544

Source: Cricetulus griseus

Species: Cricetulus griseus

Genus: Cricetulus

Family: Cricetidae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|193617621|ref|XP_001949588.1| PREDICTED: transitional endoplasmic reticulum ATPase TER94-like [Acyrthosiphon pisum]

 Score =  172 bits (435), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 80/104 (76%), Positives = 91/104 (87%)

Query: 11  DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
           D++  Q+   + YGKRIHVLPIDD+V+GLTGNLFEV+LKPYFLEAYRP+HKDD FIVRGG
Sbjct: 96  DIVQIQQCPDVKYGKRIHVLPIDDTVEGLTGNLFEVFLKPYFLEAYRPIHKDDNFIVRGG 155

Query: 71  MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           MRAVEFK+V+TDP+PYCIVA DTVIHCEGDPIKRE EE   N V
Sbjct: 156 MRAVEFKVVETDPSPYCIVAYDTVIHCEGDPIKREEEEEASNTV 199

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345486620|ref|XP_001605497.2| PREDICTED: transitional endoplasmic reticulum ATPase TER94-like [Nasonia vitripennis]

 Score =  171 bits (433), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 79/104 (75%), Positives = 90/104 (86%)

Query: 11  DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
           D++  Q   +I YGKRIHVLPIDD+V+GLTGNLFEVYLKPYFLEAYRP+HKDD FIVRGG
Sbjct: 96  DVVSVQSCPEIKYGKRIHVLPIDDTVEGLTGNLFEVYLKPYFLEAYRPIHKDDTFIVRGG 155

Query: 71  MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           MRAVEFK+V+TDP P+CIVA +TVIHCEGDP+KRE EE   N V
Sbjct: 156 MRAVEFKVVETDPGPFCIVAPETVIHCEGDPVKREEEEEALNAV 199

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383861759|ref|XP_003706352.1| PREDICTED: transitional endoplasmic reticulum ATPase TER94-like isoform 2 [Megachile rotundata]

 Score =  169 bits (429), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 78/104 (75%), Positives = 89/104 (85%)

Query: 11  DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
           D++  Q   ++ YGKRIHVLP+DD++ GLTGNLFEVYLKPYFLEAYRP+HKDD FIVRGG
Sbjct: 95  DVVSVQACPEVKYGKRIHVLPMDDTITGLTGNLFEVYLKPYFLEAYRPIHKDDNFIVRGG 154

Query: 71  MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           MRAVEFK+V+TDP P+CIVA DTVIHCEGDPIKRE EE   N V
Sbjct: 155 MRAVEFKVVETDPGPFCIVAPDTVIHCEGDPIKREEEEESLNAV 198

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383861757|ref|XP_003706351.1| PREDICTED: transitional endoplasmic reticulum ATPase TER94-like isoform 1 [Megachile rotundata]

 Score =  169 bits (429), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 78/104 (75%), Positives = 89/104 (85%)

Query: 11  DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
           D++  Q   ++ YGKRIHVLP+DD++ GLTGNLFEVYLKPYFLEAYRP+HKDD FIVRGG
Sbjct: 96  DVVSVQACPEVKYGKRIHVLPMDDTITGLTGNLFEVYLKPYFLEAYRPIHKDDNFIVRGG 155

Query: 71  MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           MRAVEFK+V+TDP P+CIVA DTVIHCEGDPIKRE EE   N V
Sbjct: 156 MRAVEFKVVETDPGPFCIVAPDTVIHCEGDPIKREEEEESLNAV 199

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|444729881|gb|ELW70284.1| Transitional endoplasmic reticulum ATPase [Tupaia chinensis]

 Score =  169 bits (428), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 76/104 (73%), Positives = 89/104 (85%)

Query: 11  DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
           D++  Q    + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGG
Sbjct: 551 DVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGG 610

Query: 71  MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           MRAVEFK+V+TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 611 MRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 654

Source: Tupaia chinensis

Species: Tupaia chinensis

Genus: Tupaia

Family: Tupaiidae

Order: Scandentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|322801676|gb|EFZ22299.1| hypothetical protein SINV_06607 [Solenopsis invicta]

 Score =  169 bits (427), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 79/104 (75%), Positives = 89/104 (85%)

Query: 11  DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
           D++  Q   ++ YGKRIHVLP+DD+V GLTGNLFEVYLKPYFLEAYRP+HKDD FIVRGG
Sbjct: 88  DVVSVQACPEVKYGKRIHVLPMDDTVDGLTGNLFEVYLKPYFLEAYRPIHKDDNFIVRGG 147

Query: 71  MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           MRAVEFK+V+TDP P+CIVA DTVIHCEGDPIKRE EE   N V
Sbjct: 148 MRAVEFKVVETDPGPFCIVAPDTVIHCEGDPIKREEEEEALNAV 191

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307211146|gb|EFN87364.1| Transitional endoplasmic reticulum ATPase TER94 [Harpegnathos saltator]

 Score =  169 bits (427), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 78/104 (75%), Positives = 89/104 (85%)

Query: 11  DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
           D++  Q   ++ YGKRIHVLP+DD++ GLTGNLFEVYLKPYFLEAYRP+HKDD FIVRGG
Sbjct: 96  DVVSVQACPEVKYGKRIHVLPMDDTIDGLTGNLFEVYLKPYFLEAYRPIHKDDNFIVRGG 155

Query: 71  MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           MRAVEFK+V+TDP P+CIVA DTVIHCEGDPIKRE EE   N V
Sbjct: 156 MRAVEFKVVETDPGPFCIVAPDTVIHCEGDPIKREEEEEALNAV 199

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307174120|gb|EFN64778.1| Transitional endoplasmic reticulum ATPase TER94 [Camponotus floridanus]

 Score =  167 bits (424), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 78/104 (75%), Positives = 89/104 (85%)

Query: 11  DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
           D++  Q   ++ YGKRIHVLP+DD+V GLTGNLFEV+LKPYFLEAYRP+HKDD FIVRGG
Sbjct: 96  DVVSVQACPEVKYGKRIHVLPMDDTVDGLTGNLFEVFLKPYFLEAYRPIHKDDNFIVRGG 155

Query: 71  MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           MRAVEFK+V+TDP P+CIVA DTVIHCEGDPIKRE EE   N V
Sbjct: 156 MRAVEFKVVETDPGPFCIVAPDTVIHCEGDPIKREEEEEALNAV 199

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332031336|gb|EGI70849.1| Transitional endoplasmic reticulum ATPase TER94 [Acromyrmex echinatior]

 Score =  167 bits (423), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 78/104 (75%), Positives = 88/104 (84%)

Query: 11  DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
           D++  Q   ++ YGKRIHVLP+DD+V GL GNLFEVYLKPYFLEAYRP+HKDD FIVRGG
Sbjct: 127 DVVSVQACPEVKYGKRIHVLPMDDTVDGLAGNLFEVYLKPYFLEAYRPIHKDDNFIVRGG 186

Query: 71  MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           MRAVEFK+V+TDP P+CIVA DTVIHCEGDPIKRE EE   N V
Sbjct: 187 MRAVEFKVVETDPGPFCIVAPDTVIHCEGDPIKREEEEEALNAV 230

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

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	115
UNIPROTKB|C9IZA5	160	VCP "Transitional endoplasmic	0.904	0.65	0.730	3.7e-39
UNIPROTKB|E1BTS8	804	LOC426240 "Uncharacterized pro	0.904	0.129	0.730	2.7e-38
UNIPROTKB|Q6GL04	805	vcp "Transitional endoplasmic	0.904	0.129	0.730	2.7e-38
UNIPROTKB|G3X757	806	VCP "Transitional endoplasmic	0.904	0.129	0.730	2.7e-38
UNIPROTKB|Q3ZBT1	806	VCP "Transitional endoplasmic	0.904	0.129	0.730	2.7e-38
UNIPROTKB|P55072	806	VCP "Transitional endoplasmic	0.904	0.129	0.730	2.7e-38
UNIPROTKB|P03974	806	VCP "Transitional endoplasmic	0.904	0.129	0.730	2.7e-38
MGI|MGI:99919	806	Vcp "valosin containing protei	0.904	0.129	0.730	2.7e-38
RGD|621595	806	Vcp "valosin-containing protei	0.904	0.129	0.730	2.7e-38
ZFIN|ZDB-GENE-030131-5408	806	vcp "valosin containing protei	0.904	0.129	0.730	2.7e-38

UNIPROTKB|C9IZA5 VCP "Transitional endoplasmic reticulum ATPase" [Homo sapiens (taxid:9606)]

 Score = 418 (152.2 bits), Expect = 3.7e-39, P = 3.7e-39
 Identities = 76/104 (73%), Positives = 89/104 (85%)

Query:    11 DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
             D++  Q    + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGG
Sbjct:    53 DVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGG 112

Query:    71 MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
             MRAVEFK+V+TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct:   113 MRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 156

GO:0005102 "receptor binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

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

GO:0006888 "ER to Golgi vesicle-mediated transport" evidence=IEA

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

GO:0016887 "ATPase activity" evidence=IEA

GO:0031593 "polyubiquitin binding" evidence=IEA

GO:0032403 "protein complex binding" evidence=IEA

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

GO:0042802 "identical protein binding" evidence=IEA

GO:0043234 "protein complex" evidence=IEA

GO:0051260 "protein homooligomerization" evidence=IEA

GO:0070842 "aggresome assembly" evidence=IEA

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|E1BTS8 LOC426240 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 418 (152.2 bits), Expect = 2.7e-38, P = 2.7e-38
 Identities = 76/104 (73%), Positives = 89/104 (85%)

Query:    11 DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
             D++  Q    + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGG
Sbjct:    98 DVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGG 157

Query:    71 MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
             MRAVEFK+V+TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct:   158 MRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q6GL04 vcp "Transitional endoplasmic reticulum ATPase" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 418 (152.2 bits), Expect = 2.7e-38, P = 2.7e-38
 Identities = 76/104 (73%), Positives = 89/104 (85%)

Query:    11 DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
             D++  Q    + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGG
Sbjct:    98 DVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGG 157

Query:    71 MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
             MRAVEFK+V+TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct:   158 MRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

GO:0000785 "chromatin" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0005737 "cytoplasm" evidence=ISS

GO:0006200 "ATP catabolic process" evidence=ISS

GO:0006302 "double-strand break repair" evidence=ISS

GO:0006974 "response to DNA damage stimulus" evidence=ISS

GO:0016567 "protein ubiquitination" evidence=ISS

GO:0016887 "ATPase activity" evidence=ISS

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISS

GO:0019985 "translesion synthesis" evidence=ISS

GO:0030433 "ER-associated protein catabolic process" evidence=ISS

GO:0032403 "protein complex binding" evidence=ISS

GO:0034214 "protein hexamerization" evidence=ISS

GO:0035861 "site of double-strand break" evidence=ISS

GO:0035101 "FACT complex" evidence=ISS

UNIPROTKB|G3X757 VCP "Transitional endoplasmic reticulum ATPase" [Bos taurus (taxid:9913)]

 Score = 418 (152.2 bits), Expect = 2.7e-38, P = 2.7e-38
 Identities = 76/104 (73%), Positives = 89/104 (85%)

Query:    11 DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
             D++  Q    + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGG
Sbjct:    98 DVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGG 157

Query:    71 MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
             MRAVEFK+V+TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct:   158 MRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

GO:0070842 "aggresome assembly" evidence=IEA

GO:0045732 "positive regulation of protein catabolic process" evidence=IEA

GO:0035861 "site of double-strand break" evidence=IEA

GO:0031593 "polyubiquitin binding" evidence=IEA

GO:0031334 "positive regulation of protein complex assembly" evidence=IEA

GO:0030970 "retrograde protein transport, ER to cytosol" evidence=IEA

GO:0019904 "protein domain specific binding" evidence=IEA

GO:0019903 "protein phosphatase binding" evidence=IEA

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=IEA

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA

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

GO:0006302 "double-strand break repair" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000502 "proteasome complex" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

UNIPROTKB|Q3ZBT1 VCP "Transitional endoplasmic reticulum ATPase" [Bos taurus (taxid:9913)]

 Score = 418 (152.2 bits), Expect = 2.7e-38, P = 2.7e-38
 Identities = 76/104 (73%), Positives = 89/104 (85%)

Query:    11 DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
             D++  Q    + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGG
Sbjct:    98 DVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGG 157

Query:    71 MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
             MRAVEFK+V+TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct:   158 MRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

GO:0019985 "translesion synthesis" evidence=ISS

GO:0016567 "protein ubiquitination" evidence=ISS

GO:0006974 "response to DNA damage stimulus" evidence=ISS

GO:0006302 "double-strand break repair" evidence=ISS

GO:0035861 "site of double-strand break" evidence=ISS

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISS

GO:0030433 "ER-associated protein catabolic process" evidence=ISS

GO:0005829 "cytosol" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008289 "lipid binding" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

UNIPROTKB|P55072 VCP "Transitional endoplasmic reticulum ATPase" [Homo sapiens (taxid:9606)]

 Score = 418 (152.2 bits), Expect = 2.7e-38, P = 2.7e-38
 Identities = 76/104 (73%), Positives = 89/104 (85%)

Query:    11 DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
             D++  Q    + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGG
Sbjct:    98 DVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGG 157

Query:    71 MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
             MRAVEFK+V+TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct:   158 MRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

GO:0008289 "lipid binding" evidence=IEA

GO:0005102 "receptor binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006888 "ER to Golgi vesicle-mediated transport" evidence=IEA

GO:0032403 "protein complex binding" evidence=IEA

GO:0042802 "identical protein binding" evidence=IEA

GO:0051260 "protein homooligomerization" evidence=IEA

GO:0070842 "aggresome assembly" evidence=IEA

GO:0043231 "intracellular membrane-bounded organelle" evidence=ISS

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=ISS

GO:0006281 "DNA repair" evidence=NAS

GO:0006974 "response to DNA damage stimulus" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA;TAS

GO:0005829 "cytosol" evidence=IDA

GO:0006302 "double-strand break repair" evidence=IDA

GO:0019904 "protein domain specific binding" evidence=IPI

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

GO:0030970 "retrograde protein transport, ER to cytosol" evidence=IDA

GO:0030433 "ER-associated protein catabolic process" evidence=IMP;TAS

GO:0030968 "endoplasmic reticulum unfolded protein response" evidence=TAS

GO:0016887 "ATPase activity" evidence=TAS

GO:0005783 "endoplasmic reticulum" evidence=IDA

GO:0016567 "protein ubiquitination" evidence=IDA;NAS

GO:0042981 "regulation of apoptotic process" evidence=TAS

GO:0045184 "establishment of protein localization" evidence=TAS

GO:0019985 "translesion synthesis" evidence=IMP

GO:0035861 "site of double-strand break" evidence=IDA

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=IMP

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=IDA

GO:0000502 "proteasome complex" evidence=IDA

GO:0019903 "protein phosphatase binding" evidence=IPI

GO:0045732 "positive regulation of protein catabolic process" evidence=IDA

GO:0031334 "positive regulation of protein complex assembly" evidence=IDA

GO:0031593 "polyubiquitin binding" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

UNIPROTKB|P03974 VCP "Transitional endoplasmic reticulum ATPase" [Sus scrofa (taxid:9823)]

 Score = 418 (152.2 bits), Expect = 2.7e-38, P = 2.7e-38
 Identities = 76/104 (73%), Positives = 89/104 (85%)

Query:    11 DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
             D++  Q    + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGG
Sbjct:    98 DVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGG 157

Query:    71 MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
             MRAVEFK+V+TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct:   158 MRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

GO:0019985 "translesion synthesis" evidence=ISS

GO:0016567 "protein ubiquitination" evidence=ISS

GO:0006974 "response to DNA damage stimulus" evidence=ISS

GO:0035861 "site of double-strand break" evidence=ISS

GO:0006302 "double-strand break repair" evidence=ISS

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISS

GO:0030433 "ER-associated protein catabolic process" evidence=ISS

GO:0005829 "cytosol" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008289 "lipid binding" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

MGI|MGI:99919 Vcp "valosin containing protein" [Mus musculus (taxid:10090)]

 Score = 418 (152.2 bits), Expect = 2.7e-38, P = 2.7e-38
 Identities = 76/104 (73%), Positives = 89/104 (85%)

Query:    11 DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
             D++  Q    + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGG
Sbjct:    98 DVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGG 157

Query:    71 MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
             MRAVEFK+V+TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct:   158 MRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000502 "proteasome complex" evidence=ISO

GO:0005102 "receptor binding" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005524 "ATP binding" evidence=ISO

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0005783 "endoplasmic reticulum" evidence=ISO

GO:0005829 "cytosol" evidence=ISO

GO:0006200 "ATP catabolic process" evidence=ISO

GO:0006281 "DNA repair" evidence=IEA

GO:0006302 "double-strand break repair" evidence=ISO

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

GO:0006810 "transport" evidence=IEA

GO:0006888 "ER to Golgi vesicle-mediated transport" evidence=ISO

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IDA

GO:0006974 "response to DNA damage stimulus" evidence=ISO

GO:0008289 "lipid binding" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=ISO

GO:0016787 "hydrolase activity" evidence=IEA

GO:0016887 "ATPase activity" evidence=ISO

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISO

GO:0019903 "protein phosphatase binding" evidence=ISO

GO:0019904 "protein domain specific binding" evidence=ISO

GO:0019985 "translesion synthesis" evidence=ISO

GO:0030433 "ER-associated protein catabolic process" evidence=ISO

GO:0030970 "retrograde protein transport, ER to cytosol" evidence=ISO

GO:0031334 "positive regulation of protein complex assembly" evidence=ISO

GO:0031593 "polyubiquitin binding" evidence=ISO;IDA

GO:0032403 "protein complex binding" evidence=ISO

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=ISO

GO:0035861 "site of double-strand break" evidence=ISO

GO:0042802 "identical protein binding" evidence=ISO

GO:0043231 "intracellular membrane-bounded organelle" evidence=ISO

GO:0043234 "protein complex" evidence=IPI

GO:0043531 "ADP binding" evidence=ISO

GO:0045732 "positive regulation of protein catabolic process" evidence=ISO

GO:0051260 "protein homooligomerization" evidence=ISO

GO:0070842 "aggresome assembly" evidence=IGI

RGD|621595 Vcp "valosin-containing protein" [Rattus norvegicus (taxid:10116)]

 Score = 418 (152.2 bits), Expect = 2.7e-38, P = 2.7e-38
 Identities = 76/104 (73%), Positives = 89/104 (85%)

Query:    11 DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
             D++  Q    + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGG
Sbjct:    98 DVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGG 157

Query:    71 MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
             MRAVEFK+V+TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct:   158 MRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

GO:0000502 "proteasome complex" evidence=IEA;ISO

GO:0005102 "receptor binding" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0005524 "ATP binding" evidence=IDA;IMP

GO:0005634 "nucleus" evidence=IEA;ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005783 "endoplasmic reticulum" evidence=ISO;IDA

GO:0005829 "cytosol" evidence=ISO;IDA

GO:0006200 "ATP catabolic process" evidence=IDA

GO:0006302 "double-strand break repair" evidence=ISO;ISS

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

GO:0006888 "ER to Golgi vesicle-mediated transport" evidence=IMP

GO:0006919 "activation of cysteine-type endopeptidase activity involved in apoptotic process" evidence=IEA;ISO

GO:0006974 "response to DNA damage stimulus" evidence=ISO;ISS

GO:0008289 "lipid binding" evidence=IEA

GO:0016567 "protein ubiquitination" evidence=ISO;ISS

GO:0016887 "ATPase activity" evidence=IDA

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISO;ISS

GO:0019903 "protein phosphatase binding" evidence=IEA;ISO

GO:0019904 "protein domain specific binding" evidence=IEA;ISO

GO:0019985 "translesion synthesis" evidence=ISO;ISS

GO:0030433 "ER-associated protein catabolic process" evidence=ISO;ISS

GO:0030970 "retrograde protein transport, ER to cytosol" evidence=IEA;ISO

GO:0031334 "positive regulation of protein complex assembly" evidence=IEA;ISO

GO:0031593 "polyubiquitin binding" evidence=IEA;ISO

GO:0032403 "protein complex binding" evidence=IPI

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=ISO;IMP

GO:0035861 "site of double-strand break" evidence=ISO;ISS

GO:0042802 "identical protein binding" evidence=IDA

GO:0043231 "intracellular membrane-bounded organelle" evidence=IDA

GO:0043234 "protein complex" evidence=ISO

GO:0043531 "ADP binding" evidence=IMP

GO:0045732 "positive regulation of protein catabolic process" evidence=ISO

GO:0051260 "protein homooligomerization" evidence=IDA

GO:0070842 "aggresome assembly" evidence=IEA;ISO

GO:0005730 "nucleolus" evidence=ISO

ZFIN|ZDB-GENE-030131-5408 vcp "valosin containing protein" [Danio rerio (taxid:7955)]

 Score = 418 (152.2 bits), Expect = 2.7e-38, P = 2.7e-38
 Identities = 76/104 (73%), Positives = 89/104 (85%)

Query:    11 DLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG 70
             D++  Q    + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGG
Sbjct:    98 DVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGG 157

Query:    71 MRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
             MRAVEFK+V+TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct:   158 MRAVEFKVVETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

GO:0016787 "hydrolase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0017111 "nucleoside-triphosphatase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

GO:0006974 "response to DNA damage stimulus" evidence=IEA;ISS

GO:0016567 "protein ubiquitination" evidence=ISS

GO:0035861 "site of double-strand break" evidence=ISS

GO:0006302 "double-strand break repair" evidence=ISS

GO:0018279 "protein N-linked glycosylation via asparagine" evidence=ISS

GO:0019985 "translesion synthesis" evidence=ISS

GO:0030433 "ER-associated protein catabolic process" evidence=ISS

GO:0009790 "embryo development" evidence=IMP

GO:2000058 "regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process" evidence=IMP

GO:0005634 "nucleus" evidence=IEA

GO:0006810 "transport" evidence=IEA

GO:0008289 "lipid binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0006281 "DNA repair" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

GO:0005829 "cytosol" 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q7KN62	TERA_DROME	No assigned EC number	0.6346	0.9043	0.1298	yes	N/A
Q9LZF6	CD48E_ARATH	No assigned EC number	0.7159	0.7652	0.1086	yes	N/A
Q3ZBT1	TERA_BOVIN	No assigned EC number	0.7872	0.8173	0.1166	yes	N/A
P54811	TERA1_CAEEL	No assigned EC number	0.6736	0.8260	0.1174	yes	N/A
Q7ZU99	TERA_DANRE	No assigned EC number	0.7872	0.8173	0.1166	yes	N/A
P25694	CDC48_YEAST	No assigned EC number	0.6489	0.8173	0.1125	yes	N/A
Q9P3A7	CDC48_SCHPO	No assigned EC number	0.6333	0.7826	0.1104	yes	N/A
P54609	CD48A_ARATH	No assigned EC number	0.7159	0.7652	0.1087	yes	N/A
P55072	TERA_HUMAN	No assigned EC number	0.7872	0.8173	0.1166	yes	N/A
Q6GL04	TERA_XENTR	No assigned EC number	0.7872	0.8173	0.1167	yes	N/A
P03974	TERA_PIG	No assigned EC number	0.7872	0.8173	0.1166	yes	N/A
Q01853	TERA_MOUSE	No assigned EC number	0.7872	0.8173	0.1166	yes	N/A
Q5AWS6	CDC48_EMENI	No assigned EC number	0.6489	0.8173	0.1142	yes	N/A
P46462	TERA_RAT	No assigned EC number	0.7872	0.8173	0.1166	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	115
smart01072	64	smart01072, CDC48_2, Cell division protein 48 (CDC	6e-12
pfam02933	61	pfam02933, CDC48_2, Cell division protein 48 (CDC4	6e-08

>gnl|CDD|215011 smart01072, CDC48_2, Cell division protein 48 (CDC48) domain 2

 Score = 55.7 bits (135), Expect = 6e-12
 Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 44  FEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIK 103
           F  Y+K   L   RPV K D  +V    +A+ F +V T+P+   IV  DT I     P++
Sbjct: 6   FAEYVKRKLLG--RPVTKGDTIVVPFLGKALPFVVVSTEPSGPVIVTDDTEIEILEKPVE 63

Query: 104 R 104
            
Sbjct: 64  E 64

This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. 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 is a substrate 185-residue recognition domain. Length = 64

>gnl|CDD|202475 pfam02933, CDC48_2, Cell division protein 48 (CDC48), domain 2

 Score = 45.6 bits (109), Expect = 6e-08
 Identities = 15/58 (25%), Positives = 22/58 (37%), Gaps = 2/58 (3%)

Query: 44  FEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDP 101
              Y K  F    +PV K    +     + +   +V T+P+   IV  DT I     P
Sbjct: 6   ELAYFKRQFEG--QPVSKGQTIVFDFLGKLLPLVVVSTEPSGPVIVTEDTEIEIGEKP 61

This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. 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 pfam00004 is a substrate 185-residue recognition domain. Length = 61

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	115
PF02933	64	CDC48_2: Cell division protein 48 (CDC48), domain	99.61
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	99.3
PF03152	176	UFD1: Ubiquitin fusion degradation protein UFD1; I	98.74
KOG0730|consensus	693		98.63
KOG1816|consensus	308		98.19
PLN03086	567	PRLI-interacting factor K; Provisional	98.17
PF09262	80	PEX-1N: Peroxisome biogenesis factor 1, N-terminal	97.22
KOG0735|consensus	952		96.68
COG5140	331	UFD1 Ubiquitin fusion-degradation protein [Posttra	96.6
COG1223	368	Predicted ATPase (AAA+ superfamily) [General funct	95.8
PF01272	77	GreA_GreB: Transcription elongation factor, GreA/G	83.04

>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=99.61  E-value=3e-15  Score=93.50  Aligned_cols=62  Identities=31%  Similarity=0.508  Sum_probs=56.4

Q ss_pred             cccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEecCCCcEEEcCCceEEEcCcccc
Q psy6209          39 LTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEGDPIK  103 (115)
Q Consensus        39 i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~P~~~viVt~~T~I~~~~~pv~  103 (115)
                      +++++.+ |++++|.  +||+++||.|.+...++.++|+|++|+|.++|+|+++|.|++.++|++
T Consensus         2 ~d~d~~~-~~~~~l~--~~pv~~Gd~i~~~~~~~~~~~~V~~~~P~~~v~it~~T~i~i~~~p~~   63 (64)
T PF02933_consen    2 FDGDFMA-YFKRQLE--GRPVTKGDTIVFPFFGQALPFKVVSTEPSGPVIITEDTEIEIKEEPVE   63 (64)
T ss_dssp             ECSHHHH-HHHHHHT--TEEEETT-EEEEEETTEEEEEEEEEECSSSEEEEETTSEEEESSTTBC
T ss_pred             CCccHHH-HHHHHHc--CCCccCCCEEEEEeCCcEEEEEEEEEEcCCCEEECCCcEEEEcccccc
Confidence            4566555 9999999  999999999999999999999999999999999999999999999875

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 ....

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=99.30  E-value=1.4e-11  Score=106.53  Aligned_cols=99  Identities=23%  Similarity=0.389  Sum_probs=86.3

Q ss_pred             CCcccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEE
Q psy6209           1 MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD   80 (115)
Q Consensus         1 ~R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~   80 (115)
                      +|+|+|+++||.|+|+++ ++++|++|+++|+...  .+ +..+.+|++.+|.  ++|+..||.+.+...+...+|.|++
T Consensus        69 ~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~--~~-~~~~~~~~~~~~~--~~~~~~g~~~~~~~~~~~~~~~v~~  142 (733)
T TIGR01243        69 LRANAGVTIGDTVTVERA-EVKEAKKVVLAPTQPI--RF-GRDFVDYVKEFLL--GKPISKGETVIVPVLEGALPFVVVS  142 (733)
T ss_pred             HHhhcCCCCCCeEEEeec-CCCccceEeecccccc--cc-ccchHHHHHHHHc--CCCCCCCCEEEecccCcceeEEEEe
Confidence            589999999999999996 7999999999997532  23 3356789999999  8999999999998777789999999


Q ss_pred             ecCCCcEEEcCCceEEEcCccccCc
Q psy6209          81 TDPAPYCIVAADTVIHCEGDPIKRE  105 (115)
Q Consensus        81 t~P~~~viVt~~T~I~~~~~pv~re  105 (115)
                      +.|.+++.++..|.+.+.+++..+.
T Consensus       143 ~~p~~~~~~~~~t~~~~~~~~~~~~  167 (733)
T TIGR01243       143 TQPAGFVYVTEATEVEIREKPVREE  167 (733)
T ss_pred             cCCCCcEEECCCceEEecCCccccc
Confidence            9999999999999999988887554

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.

>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=98.74  E-value=2e-08  Score=74.35  Aligned_cols=92  Identities=15%  Similarity=0.208  Sum_probs=64.4

Q ss_pred             CCcccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEE
Q psy6209           1 MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD   80 (115)
Q Consensus         1 ~R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~   80 (115)
                      |-+|+++.-||.|.|+-+ ..+.|+.|+|.|-+..--.+.  ....+|...|+ .+--+++||+|.|...+...+|.|++
T Consensus        80 mm~~L~l~~g~~V~v~~~-~LPkgt~vkLqP~~~~F~~i~--n~KavLE~~Lr-~ystLT~Gd~I~i~~~~~~y~l~V~e  155 (176)
T PF03152_consen   80 MMQNLGLQEGDIVRVEYV-SLPKGTFVKLQPQSSDFLDIS--NPKAVLERALR-NYSTLTKGDTISIEYNNKTYELDVVE  155 (176)
T ss_dssp             HHHHHT--TTEEEEEEEE-E----SEEEEEESCHHHHCSS---HHHHHHHHHC-C-SEEETTSEEEEECTTEEEEEEEEE
T ss_pred             HHhhcCCCCCCEEEEEEe-ECCCCCEEEEeECCCcccccc--chHHHHHhhcc-cCceeecCCEEEEEeCCEEEEEEEEE
Confidence            668999999999999985 999999999999743211232  24677888884 46679999999999999999999999


Q ss_pred             ecCCCcEEEcCCceEEE
Q psy6209          81 TDPAPYCIVAADTVIHC   97 (115)
Q Consensus        81 t~P~~~viVt~~T~I~~   97 (115)
                      ++|++.+.|- +|.+++
T Consensus       156 ~kP~~aV~Ii-dTDl~v  171 (176)
T PF03152_consen  156 VKPENAVSII-DTDLEV  171 (176)
T ss_dssp             ECSSSCEE-S-SS-SEE
T ss_pred             EcCCCEEEEE-eCceEE
Confidence            9997754444 454444

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.

>KOG0730|consensus

Probab=98.63  E-value=1.1e-08  Score=87.99  Aligned_cols=102  Identities=40%  Similarity=0.694  Sum_probs=94.2

Q ss_pred             CcccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEe
Q psy6209           2 SFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDT   81 (115)
Q Consensus         2 R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t   81 (115)
                      |.|+.++.|+.+.+.+...++.+.+++++|..++.+++.++.++.+.++|+..+++|+.+|+++   ..+..++|+++.+
T Consensus        77 r~~l~~~~~~~~~~~~~p~v~~~~~i~~l~~~~~~~~i~~~~~d~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~  153 (693)
T KOG0730|consen   77 RSNLRLQLGRLLHSSDCPSVKRPARIAVLPVDDTSEGIAGELFDVLERPFLLEALRPLVKGDTF---AGLNPAEFKVLEL  153 (693)
T ss_pred             ccchhhcccceecccCCCCccccceeeeeehhhccccchhhhhhhhhhhhhhhhhCccccccch---hhhhhhhhhcccc
Confidence            7899999999999998789999999999999999888998889999999999999999999998   4456789999999


Q ss_pred             cCCCcEEEcCCceEEEcCccccCcccc
Q psy6209          82 DPAPYCIVAADTVIHCEGDPIKREGEE  108 (115)
Q Consensus        82 ~P~~~viVt~~T~I~~~~~pv~re~~~  108 (115)
                      .|..  .++++|.+++.++++++++++
T Consensus       154 ~~~~--~v~~~t~~~~~~~~~~~~~~~  178 (693)
T KOG0730|consen  154 DPSP--QVTPDTELSYLGEPAKREEEE  178 (693)
T ss_pred             ccch--hcCccchhhhcCCCccccccc
Confidence            9988  899999999999999998776

>KOG1816|consensus

Probab=98.19  E-value=1.5e-05  Score=63.12  Aligned_cols=97  Identities=22%  Similarity=0.275  Sum_probs=71.8

Q ss_pred             CCcccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEE
Q psy6209           1 MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD   80 (115)
Q Consensus         1 ~R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~   80 (115)
                      |=+|++..-||.|.|+-+ .++.|+-|.|.|-  ++.-++-..-...|..-|+ ++--+++||.|.|..++...+|+|++
T Consensus        92 Mmq~L~le~gdlv~i~~v-~lpkgtyvKLqP~--s~dFLDItNpKAvLE~~LR-n~acLT~gDvi~i~Yn~k~y~i~V~e  167 (308)
T KOG1816|consen   92 MMQNLLLEEGDLVRIRSV-TLPKGTYVKLQPH--SVDFLDITNPKAVLENALR-NYACLTTGDVILINYNEKTYELKVVE  167 (308)
T ss_pred             hhhhccCCCCCeEEEEEe-eccccceeeeccC--CCCccccCChHHHHHHHHh-hccccccCCEEEEecCCeEEEEEEEE
Confidence            678999999999999995 9999999999995  3322221111344444443 24469999999999999999999999


Q ss_pred             ecCCC-cEEEcCCceEEEcCccc
Q psy6209          81 TDPAP-YCIVAADTVIHCEGDPI  102 (115)
Q Consensus        81 t~P~~-~viVt~~T~I~~~~~pv  102 (115)
                      ++|+. ++||--+.++.. ..|+
T Consensus       168 ~kPa~aVsIiEtD~~VDF-~pP~  189 (308)
T KOG1816|consen  168 TKPANAVSIIETDLNVDF-DPPL  189 (308)
T ss_pred             ecCCceeEEEEcceeecc-cCCc
Confidence            99965 455665666665 3454

>PLN03086 PRLI-interacting factor K; Provisional

Probab=98.17  E-value=1.4e-05  Score=68.26  Aligned_cols=93  Identities=14%  Similarity=0.157  Sum_probs=71.6

Q ss_pred             CCcccCCCC---CCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEE
Q psy6209           1 MSFRLTTPC---RDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFK   77 (115)
Q Consensus         1 ~R~Nagv~i---GD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~Fk   77 (115)
                      |.+|+|..-   |+.|+|+.+ .+|.|+.|.|.|-+..-  ++-.....+|..+|.+ +--+++||+|.|..+....+|.
T Consensus       159 m~~~L~~~~~~~~~~v~v~~~-~Lpkgt~vklqP~~~~f--~di~npKavLE~~Lr~-~stLT~Gd~i~i~~~~~~y~~~  234 (567)
T PLN03086        159 VWSNLFPSDPPDVPLVEVRYI-WLPKGTYAKLQPDGVGF--SDLPNHKAVLETALRQ-HATLSEDDVLVVNYGQLTYKLK  234 (567)
T ss_pred             HHhhcCCCCCCCCCeEEEEEe-ecCCCCEEEEeeccCCc--CCcccHHHHHHHHhhc-CccccCCCEEEEecCCEEEEEE
Confidence            678998753   889999995 99999999999975321  1222346788888872 5579999999999888899999


Q ss_pred             EEEecCC-CcEEEcCCceEEE
Q psy6209          78 IVDTDPA-PYCIVAADTVIHC   97 (115)
Q Consensus        78 Vv~t~P~-~~viVt~~T~I~~   97 (115)
                      |++++|+ ++++|.-+=++.+
T Consensus       235 V~ev~P~~aVsiieTDi~VDf  255 (567)
T PLN03086        235 VLELKPASSVSVLETDIEVDI  255 (567)
T ss_pred             EEEEcCCCeeEEEeCceEEEe
Confidence            9999997 5566654444444

>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=97.22  E-value=0.00053  Score=44.80  Aligned_cols=73  Identities=22%  Similarity=0.374  Sum_probs=44.8

Q ss_pred             ccEEEEccCCCC-ccCcccchHHHHhhHhhhhCCCceecCCEEEEcc-CCceEEEEEEEecCCC----cEEEcCCceEEE
Q psy6209          24 GKRIHVLPIDDS-VQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRG-GMRAVEFKIVDTDPAP----YCIVAADTVIHC   97 (115)
Q Consensus        24 A~~V~laP~~d~-i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~-~~~~v~FkVv~t~P~~----~viVt~~T~I~~   97 (115)
                      |+.|.+.|.+.. =+ +-+ +-..|+...|++--|-|..|..|.+.. .+..+.|+|.++.|..    +++++++|+|.+
T Consensus         1 A~~V~veP~T~dDWE-IlE-l~A~~lE~~lL~QiRvv~~~~~~~v~v~~~~~i~~~V~~i~p~~~~~~~~~L~~~TEv~V   78 (80)
T PF09262_consen    1 AKSVEVEPLTSDDWE-ILE-LHAEFLEDQLLSQIRVVFPGQVFPVWVSQNTVIKFKVVSIEPSSSAEGCARLSPDTEVIV   78 (80)
T ss_dssp             -SEEEEEESSHHHHH-HHH-HS-SSHHHHHHHH--EE-TT-EEEEESSSS-EEEEEEEEEES--S---SEE--TT-EEEE
T ss_pred             CcEEEEEcCCccHHH-HHH-HhHHHHHHHHHHhheeecCCCEEEEEEcCCeEEEEEEEEccCCCCceeEEEeCCCcEEEE
Confidence            678999996310 01 111 224667777776678999999999986 4678999999999954    799999999987


Q ss_pred             c
Q psy6209          98 E   98 (115)
Q Consensus        98 ~   98 (115)
                      .
T Consensus        79 a   79 (80)
T PF09262_consen   79 A   79 (80)
T ss_dssp             -
T ss_pred             C
Confidence            4

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.

>KOG0735|consensus

Probab=96.68  E-value=0.012  Score=52.18  Aligned_cols=97  Identities=18%  Similarity=0.194  Sum_probs=76.1

Q ss_pred             ccCCCCCCeEEEEeCCCCCCccEEEEccCC-CCccCcccchHHHHhhHhhhhCCCceecCCEEEEccC-CceEEEEEEEe
Q psy6209           4 RLTTPCRDLLDRQRDIQIVYGKRIHVLPID-DSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG-MRAVEFKIVDT   81 (115)
Q Consensus         4 Nagv~iGD~V~V~k~~~v~~A~~V~laP~~-d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~-~~~v~FkVv~t   81 (115)
                      -+|..-|+.|+++.++.+..|+.|++-|.. |.=+ |-+ +-..++...++.-.|-|+. .+|.|-.. +..+.|+|+++
T Consensus        71 ~l~L~e~~~V~l~~~~~v~~~~~V~VeP~TsdDWE-IiE-lnA~~~e~~lL~Q~RIv~~-~~f~iwl~~~t~i~fqv~rl  147 (952)
T KOG0735|consen   71 TLGLAENQEVKLSIIDHVHEATQVEVEPVTSDDWE-IIE-LNAEWLEENLLVQTRIVTP-EIFIIWLPSGTVIQFQVDRL  147 (952)
T ss_pred             hccCCCCCeEEEEEcCCccceeEEEEeeccCccHH-HHH-hhHHHHhhhhhhheeeccc-ceeEEEEcCccEEEEEEeee
Confidence            368888999999999999999999999963 2222 222 2245666667666788888 77777544 57899999999


Q ss_pred             cC-CCcEEEcCCceEEEcCcccc
Q psy6209          82 DP-APYCIVAADTVIHCEGDPIK  103 (115)
Q Consensus        82 ~P-~~~viVt~~T~I~~~~~pv~  103 (115)
                      .| ..++.+..+|++-+..++-+
T Consensus       148 ~Ps~~~gRl~~~Tev~VaPK~~k  170 (952)
T KOG0735|consen  148 IPSMLYGRLLRGTEVLVAPKPNK  170 (952)
T ss_pred             ecccceeeecCCceEEEecCccc
Confidence            99 68999999999999877664

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

Probab=96.60  E-value=0.015  Score=45.74  Aligned_cols=98  Identities=19%  Similarity=0.235  Sum_probs=62.9

Q ss_pred             CCcccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCc--eEEEEE
Q psy6209           1 MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMR--AVEFKI   78 (115)
Q Consensus         1 ~R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~--~v~FkV   78 (115)
                      |=+-++...||.|.++- .+++-++-|.|.|-  ++.-++-..-...|.+-|+ ++.-+++||.|.|..+++  .|.|.+
T Consensus       100 Mm~tLs~epgdlv~~~~-td~plG~fVKL~Pq--SVdFLdI~dpkavLEn~LR-NfstLt~~D~iei~ynd~v~~Ik~~~  175 (331)
T COG5140         100 MMQTLSMEPGDLVVLRY-TDFPLGKFVKLIPQ--SVDFLDIEDPKAVLENCLR-NFSTLTEGDEIEIQYNDEVGSIKFTV  175 (331)
T ss_pred             HHHhccCCCCcEEEEEe-ccccccceEEeccc--ccceEeccChHHHHHHHHh-hccccccCCEEEEEECCeeeEEEEEE
Confidence            44668889999999998 59999999999995  3422221111234444443 355799999999988764  567777


Q ss_pred             EEecCCCcEEEcCCceEEE-cCccc
Q psy6209          79 VDTDPAPYCIVAADTVIHC-EGDPI  102 (115)
Q Consensus        79 v~t~P~~~viVt~~T~I~~-~~~pv  102 (115)
                      ++.+|+..+|-.-+|.+.+ --.|+
T Consensus       176 v~pe~S~~~i~vveTDLvvDF~pPi  200 (331)
T COG5140         176 VHPEPSANAIYVVETDLVVDFLPPI  200 (331)
T ss_pred             eccCCCcceEEEEecceeeeccCCc
Confidence            7777754433222344333 23455

>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]

Probab=95.80  E-value=0.051  Score=43.65  Aligned_cols=75  Identities=17%  Similarity=0.298  Sum_probs=57.2

Q ss_pred             CCccEEEEccCCCCccC-------c--ccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEecCCCcEEEcCC
Q psy6209          22 VYGKRIHVLPIDDSVQG-------L--TGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAAD   92 (115)
Q Consensus        22 ~~A~~V~laP~~d~i~~-------i--~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~P~~~viVt~~   92 (115)
                      ++++-+.|.|...++..       +  +.++|+-|.+...+  +.-+++||.+.=..+-...-|+|+++.|++..+++..
T Consensus        22 ~~~k~lil~P~GyP~~~~~~e~pvv~dn~~~F~~YArdQW~--Ge~v~eg~ylFD~~~~pdyAfkvI~~~P~~~~i~~st   99 (368)
T COG1223          22 KSSKYLILRPMGYPLRESGMEYPVVDDNPEVFNIYARDQWL--GEVVREGDYLFDTRMFPDYAFKVIRVVPSGGGIITST   99 (368)
T ss_pred             ccceEEEEccCCCccccccCCCceecCCHHHHHHHHHHhhc--ceeeecCceEeecccccccceeEEEEeCCCCceecce
Confidence            45677888886544421       1  12468889999988  9999999998776666778999999999999988866


Q ss_pred             ceEEEc
Q psy6209          93 TVIHCE   98 (115)
Q Consensus        93 T~I~~~   98 (115)
                      |.+.++
T Consensus       100 ~i~vl~  105 (368)
T COG1223         100 TIFVLE  105 (368)
T ss_pred             EEEEec
Confidence            665553

>PF01272 GreA_GreB: Transcription elongation factor, GreA/GreB, C-term; InterPro: IPR001437 Bacterial proteins greA and greB are necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites

Probab=83.04  E-value=9.1  Score=23.97  Aligned_cols=70  Identities=9%  Similarity=-0.015  Sum_probs=40.2

Q ss_pred             CCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccch--HHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEec
Q psy6209           6 TTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNL--FEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTD   82 (115)
Q Consensus         6 gv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~--~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~   82 (115)
                      .|++|.+|+++-. +-..-..++|....+.  ....+.  +..=|-.-|+  +  -+.||.+.+...+...+|+|.+++
T Consensus         5 ~V~~Gs~V~l~~~-~~~~~~~~~lv~~~~~--~~~~~~IS~~SPLG~ALl--G--~~~Gd~v~~~~~~g~~~~~I~~I~   76 (77)
T PF01272_consen    5 VVTIGSTVTLKDL-DDGEEETYTLVGPDEA--DPDNGKISIDSPLGKALL--G--KKVGDEVEVELPGGERKYEILEIE   76 (77)
T ss_dssp             B-STTEEEEEEET-TTTEEEEEEEE-GGG---BSTSTEEETTSHHHHHHT--T---BTT-EEEEEETTBEEEEEEEEEE
T ss_pred             EEEeCCEEEEEEC-CCCCEEEEEEEeEhHh--CCceeEEEecCHHHHHhc--C--CCCCCEEEEEeCCceEEEEEEEEE
Confidence            5889999999874 4455566666633221  111100  0122233333  3  378999999987778889998863

Arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked DNA/RNA/ polymerase ternary complexes. Cleavage of the nascent transcript by cleavage factors, such as greA or greB, allows the resumption of elongation from the new 3' terminus [, ]. Escherichia coli GreA and GreB are sequence homologues and have homologues in every known bacterial genome []. GreA induces cleavage two or three nucleotides behind the terminus and can only prevent the formation of arrested complexes while greB releases longer sequences up to eighteen nucleotides in length and can rescue preexisting arrested complexes. These functional differences correlate with a distinctive structural feature, the distribution of positively charged residues on one face of the N-terminal coiled coil. Remarkably, despite close functional similarity, the prokaryotic Gre factors have no sequence or structural similarity with eukaryotic TFIIS. ; GO: 0003677 DNA binding, 0032784 regulation of transcription elongation, DNA-dependent; PDB: 2P4V_E 2ETN_B 3BMB_B 2PN0_D 1GRJ_A 2EUL_C 3AOH_Y 3AOI_X 2F23_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	115
3hu2_A	489	Structure Of P97 N-D1 R86a Mutant In Complex With A		1e-41
3hu1_A	489	Structure Of P97 N-D1 R95g Mutant In Complex With A		1e-41
1e32_A	458	Structure Of The N-Terminal Domain And The D1 Aaa D		1e-41
1r7r_A	816	The Crystal Structure Of Murine P97VCP AT 3.6A Leng		1e-41
3cf1_A	806	Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Len		1e-41
3hu3_A	489	Structure Of P97 N-D1 R155h Mutant In Complex With		6e-41
2pjh_B	193	Strctural Model Of The P97 N Domain- Npl4 Ubd Compl		9e-41
3qc8_A	178	Crystal Structure Of Faf1 Ubx Domain In Complex Wit		3e-40
3qwz_A	211	Crystal Structure Of Faf1 Ubx-P97n-Domain Complex L		3e-40
3tiw_A	187	Crystal Structure Of P97n In Complex With The C-Ter		1e-36
3qq7_A	186	Crystal Structure Of The P97 N-Terminal Domain Leng		1e-36

>pdb|3HU2|A Chain A, Structure Of P97 N-D1 R86a Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  164 bits (415), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 74/94 (78%), Positives = 85/94 (90%)
Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 108 VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 167
Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 168 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

>pdb|3HU1|A Chain A, Structure Of P97 N-D1 R95g Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  164 bits (415), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 74/94 (78%), Positives = 85/94 (90%)
Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 108 VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 167
Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 168 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

>pdb|1E32|A Chain A, Structure Of The N-Terminal Domain And The D1 Aaa Domain Of Membrane Fusion Atpase P97 Length = 458

Iteration: 1
 Score =  164 bits (414), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 74/94 (78%), Positives = 85/94 (90%)
Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 108 VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 167
Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 168 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A Length = 816

Iteration: 1
 Score =  164 bits (414), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 74/94 (78%), Positives = 85/94 (90%)
Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 108 VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 167
Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 168 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX Length = 806

Iteration: 1
 Score =  164 bits (414), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 74/94 (78%), Positives = 85/94 (90%)
Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 108 VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 167
Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 168 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

>pdb|3HU3|A Chain A, Structure Of P97 N-D1 R155h Mutant In Complex With Atpgs Length = 489

Iteration: 1
 Score =  162 bits (409), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 73/94 (77%), Positives = 84/94 (89%)
Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+V GGMRAVEFK+V+
Sbjct: 108 VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVHGGMRAVEFKVVE 167
Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 168 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201

>pdb|2PJH|B Chain B, Strctural Model Of The P97 N Domain- Npl4 Ubd Complex Length = 193

Iteration: 1
 Score =  161 bits (407), Expect = 9e-41,   Method: Compositional matrix adjust.
 Identities = 74/94 (78%), Positives = 85/94 (90%)
Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 88  VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 147
Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 148 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 181

>pdb|3QC8|A Chain A, Crystal Structure Of Faf1 Ubx Domain In Complex With P97VCP N DOMAIN Reveals The Conserved Fcisp Touch-Turn Motif Of Ubx Domain Suffering Conformational Change Length = 178

Iteration: 1
 Score =  159 bits (403), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 72/88 (81%), Positives = 83/88 (94%)
Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 90  VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 149
Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEE 108
           TDP+PYCIVA DTVIHCEG+PIKRE EE
Sbjct: 150 TDPSPYCIVAPDTVIHCEGEPIKREDEE 177

>pdb|3QWZ|A Chain A, Crystal Structure Of Faf1 Ubx-P97n-Domain Complex Length = 211

Iteration: 1
 Score =  159 bits (403), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 73/94 (77%), Positives = 84/94 (89%)
Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEF +V+
Sbjct: 111 VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFXVVE 170
Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 171 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 204

>pdb|3TIW|A Chain A, Crystal Structure Of P97n In Complex With The C-Terminus Of Gp78 Length = 187

Iteration: 1
 Score =  147 bits (372), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 65/80 (81%), Positives = 76/80 (95%)
Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 108 VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 167
Query: 81  TDPAPYCIVAADTVIHCEGD 100
           TDP+PYCIVA DTVIHCEG+
Sbjct: 168 TDPSPYCIVAPDTVIHCEGE 187

>pdb|3QQ7|A Chain A, Crystal Structure Of The P97 N-Terminal Domain Length = 186

Iteration: 1
 Score =  147 bits (371), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 65/80 (81%), Positives = 76/80 (95%)
Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 107 VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 166
Query: 81  TDPAPYCIVAADTVIHCEGD 100
           TDP+PYCIVA DTVIHCEG+
Sbjct: 167 TDPSPYCIVAPDTVIHCEGE 186

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	115
3qwz_A	211	Transitional endoplasmic reticulum ATPase; UBX, P9	9e-31
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	4e-30
3tiw_A	187	Transitional endoplasmic reticulum ATPase; beta-ba	8e-29
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	1e-26
1cz4_A	185	VCP-like ATPase; double-PSI beta-barrel, beta-CLAM	8e-21
2yuj_A	190	Ubiquitin fusion degradation 1-like; ubiquitin-dep	2e-05

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

 Score =  107 bits (269), Expect = 9e-31
 Identities = 73/95 (76%), Positives = 84/95 (88%)

Query: 20  QIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIV 79
            + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEF +V
Sbjct: 110 DVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFXVV 169

Query: 80  DTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           +TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 170 ETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 204

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A* 2pjh_B Length = 489

 Score =  111 bits (278), Expect = 4e-30
 Identities = 73/96 (76%), Positives = 84/96 (87%)

Query: 20  QIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIV 79
            + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+V GGMRAVEFK+V
Sbjct: 107 DVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVHGGMRAVEFKVV 166

Query: 80  DTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGVR 115
           +TDP+PYCIVA DTVIHCEG+PIKRE EE   N V 
Sbjct: 167 ETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVG 202

>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 =  102 bits (254), Expect = 8e-29
 Identities = 65/78 (83%), Positives = 75/78 (96%)

Query: 23  YGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTD 82
           YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+TD
Sbjct: 110 YGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETD 169

Query: 83  PAPYCIVAADTVIHCEGD 100
           P+PYCIVA DTVIHCEG+
Sbjct: 170 PSPYCIVAPDTVIHCEGE 187

>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 = 81.5 bits (201), Expect = 8e-21
 Identities = 25/98 (25%), Positives = 41/98 (41%), Gaps = 8/98 (8%)

Query: 17  RDIQIVYGKRIHVLPIDDSVQGLT-GNLFEVYLKPYFLEAYRPVHKDDLFIVRG----GM 71
           R ++    K++ + PI    Q L  G   E Y++   +   RP+ + D   V G    G 
Sbjct: 88  RKVRTEIAKKVTLAPIIRKDQRLKFGEGIEEYVQRALI--RRPMLEQDNISVPGLTLAGQ 145

Query: 72  RAVEFKIVDTDPAPYC-IVAADTVIHCEGDPIKREGEE 108
             + FK+V T P+     +  +T I    +P     EE
Sbjct: 146 TGLLFKVVKTLPSKVPVEIGEETKIEIREEPASEVLEE 183

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

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 13/102 (12%), Positives = 32/102 (31%), Gaps = 9/102 (8%)

Query: 1   MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTG--NLFEVYLKPYFLEAYRP 58
           M   L      L+ +   + +         P       +T    + E  L+ +       
Sbjct: 95  MMQNLLLEEGGLV-QVESVNLQVATYSKFQPQSPDFLDITNPKAVLENALRNFAC----- 148

Query: 59  VHKDDLFIVRGGMRAVEFKIVDTDPAPY-CIVAADTVIHCEG 99
           +   D+  +    +  E ++++T P     I+  D  +  + 
Sbjct: 149 LTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDFDA 190

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	115
3qwz_A	211	Transitional endoplasmic reticulum ATPase; UBX, P9	100.0
3tiw_A	187	Transitional endoplasmic reticulum ATPase; beta-ba	99.97
1cz4_A	185	VCP-like ATPase; double-PSI beta-barrel, beta-CLAM	99.94
1wlf_A	179	PEX1, peroxisome biogenesis factor 1; N-terminal d	99.86
3cf2_A	806	TER ATPase, transitional endoplasmic reticulum ATP	99.86
2jv2_A	83	Putative uncharacterized protein PH1500; AAA ATPas	99.85
1ypw_A	806	Transitional endoplasmic reticulum ATPase; AAA, P9	99.84
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	99.68
2yuj_A	190	Ubiquitin fusion degradation 1-like; ubiquitin-dep	98.75
1zc1_A	208	Ubiquitin fusion degradation protein 1; UFD1, doub	98.63
1cr5_A	189	SEC18P (residues 22 - 210); double-PSI beta barrel	96.94
1qcs_A	211	N-ethylmaleimide sensitive factor (NSF-N); double-	96.84

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

Probab=100.00  E-value=3.4e-34  Score=215.33  Aligned_cols=114  Identities=67%  Similarity=1.147  Sum_probs=104.2

Q ss_pred             CCcccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEE
Q psy6209           1 MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD   80 (115)
Q Consensus         1 ~R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~   80 (115)
                      ||+||||++||+|+|+|+.++++|++|+|||+++++.++.+++|..||++||++.+|||++||+|.+..+++.++|+|++
T Consensus        91 ~R~N~gV~iGD~V~V~~~~~v~~A~~V~LaP~~~~i~~i~~~~~~~~lk~~l~~~~rPV~~GD~i~v~~~~~~v~f~Vv~  170 (211)
T 3qwz_A           91 VRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFXVVE  170 (211)
T ss_dssp             HHHHTTCCTTCEEEEEECTTCCBCSEEEEEEBGGGCTTCCSCHHHHTTHHHHTTCCEEEETTCEEECCCTTSCCEEEEEE
T ss_pred             HHhhcCCCCCCEEEEEECCCCCCceEEEEeccCcchhccCchhHHHHHHHHHhhCCceeecCCEEEEccCCcEEEEEEEe
Confidence            69999999999999999658999999999999888866888888999999998789999999999999889999999999


Q ss_pred             ecCCCcEEEcCCceEEEcCccccCccccCCCCCC
Q psy6209          81 TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV  114 (115)
Q Consensus        81 t~P~~~viVt~~T~I~~~~~pv~re~~~~~~~~~  114 (115)
                      |+|+++|+|+++|+|+|+++|++||++|+.+++|
T Consensus       171 t~P~g~viV~~~T~I~~~~~pv~~~~~e~~~~~V  204 (211)
T 3qwz_A          171 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV  204 (211)
T ss_dssp             EESSSEEEECTTCEEECCSCCBCCCGGGSCCC--
T ss_pred             ecCCCCEEECCCcEEEEcCcccccccccccCCCc
Confidence            9999999999999999999999999876566554

>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=99.97  E-value=1.1e-31  Score=198.37  Aligned_cols=100  Identities=68%  Similarity=1.202  Sum_probs=89.5

Q ss_pred             CCcccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEE
Q psy6209           1 MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD   80 (115)
Q Consensus         1 ~R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~   80 (115)
                      ||+||||++||+|+|+++.++++|++|+|+|+++++.++.+++|..||++||++++|||++||+|.+..+++.++|+|++
T Consensus        88 ~R~N~gV~iGD~V~V~~~~~v~~A~~V~LaP~~~~i~~i~~~~~~~~lk~~l~~~~rpV~~GD~i~v~~~~~~v~f~Vv~  167 (187)
T 3tiw_A           88 VRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE  167 (187)
T ss_dssp             HHHHTTCCTTCEEEEEECTTCEECSEEEEEECCCC-----CCHHHHTHHHHHTTTCCEEETTCEEEEECSSSEEEEEEEE
T ss_pred             HHhhcCCCCCCEEEEEECCCCCCceEEEEeccccchhhccchhHHHHHHHHhccCCceeeCCCEEEEccCCCEEEEEEEE
Confidence            59999999999999999658999999999999888866888888999999999778999999999999989999999999


Q ss_pred             ecCCCcEEEcCCceEEEcCc
Q psy6209          81 TDPAPYCIVAADTVIHCEGD  100 (115)
Q Consensus        81 t~P~~~viVt~~T~I~~~~~  100 (115)
                      |+|+++|+|+++|+|+|+|+
T Consensus       168 t~P~~~v~V~~~T~I~~eg~  187 (187)
T 3tiw_A          168 TDPSPYCIVAPDTVIHCEGE  187 (187)
T ss_dssp             EESSSEEECCTTCEEECCC-
T ss_pred             ecCCCCEEECCCcEEEecCC
Confidence            99999999999999999875

>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=99.94  E-value=3.7e-27  Score=173.66  Aligned_cols=103  Identities=21%  Similarity=0.321  Sum_probs=92.9

Q ss_pred             CCcccCCCCCCeEEEEeCCCCCCccEEEEccCC---CCccCcccchHHHHhhHhhhhCCCceecCCEEEEcc---CCc-e
Q psy6209           1 MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPID---DSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRG---GMR-A   73 (115)
Q Consensus         1 ~R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~---d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~---~~~-~   73 (115)
                      ||+|+|+++||+|+|+|+ ++++|++|+|+|++   +++. +.+++ ..||++||.  +|||++||+|.+..   .|+ .
T Consensus        73 ~R~N~gv~iGD~V~V~~~-~~~~A~~V~l~P~~~~~~~~~-~~~~~-~~~l~~~l~--~rpv~~Gd~v~v~~~~~~g~~~  147 (185)
T 1cz4_A           73 MRNNCGASIGDKVKVRKV-RTEIAKKVTLAPIIRKDQRLK-FGEGI-EEYVQRALI--RRPMLEQDNISVPGLTLAGQTG  147 (185)
T ss_dssp             HHHHHTCCTTCEEEEEEE-CCCBCSEEEEEEECSTTCCSC-CCSSH-HHHHHHHHT--TCEECTTCEECCSSCCCSSCCC
T ss_pred             HHhccCCCCCCEEEEEEC-CCCCccEEEEecccccccccc-cccch-HHHHHHHHC--CCcccCCCEEEEeeeccCCCeE
Confidence            599999999999999995 99999999999996   6674 76654 799999999  89999999999986   778 9


Q ss_pred             EEEEEEEecCCC-cEEEcCCceEEEcCccccCcccc
Q psy6209          74 VEFKIVDTDPAP-YCIVAADTVIHCEGDPIKREGEE  108 (115)
Q Consensus        74 v~FkVv~t~P~~-~viVt~~T~I~~~~~pv~re~~~  108 (115)
                      ++|+|++|+|++ +|+|+++|+|+|+++|+++.-+|
T Consensus       148 ~~f~Vv~t~P~~~~v~Vt~~T~I~i~~~p~~~~~~~  183 (185)
T 1cz4_A          148 LLFKVVKTLPSKVPVEIGEETKIEIREEPASEVLEE  183 (185)
T ss_dssp             CEEEEEEESSSSSCEECCTTCEEEECSCCSTTCCCS
T ss_pred             EEEEEEEEcCCCceEEEcCCeEEEECCccchHhhhc
Confidence            999999999999 99999999999999999855443

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

Probab=99.86  E-value=1.6e-22  Score=148.15  Aligned_cols=99  Identities=17%  Similarity=0.222  Sum_probs=84.7

Q ss_pred             CCcccCCCCCCeEEEEeCCCCCCccEEEEccCCC-CccCcccchHHHHhhHhhhhCCCceecCCEEEEccCC-ceEEEEE
Q psy6209           1 MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDD-SVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGM-RAVEFKI   78 (115)
Q Consensus         1 ~R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d-~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~-~~v~FkV   78 (115)
                      +|+|||+++||+|+|++..++++|++|+|+|.+. ..+ +.+ ++.+||+++|++-.|||.+||+|.+...+ ..++|+|
T Consensus        78 ~r~n~gv~~Gd~V~V~~~~~~~~A~~V~laP~~~dD~e-i~e-~~a~~le~~Ll~QiR~v~~G~~i~v~~~g~~~i~f~V  155 (179)
T 1wlf_A           78 VGQKLGLSSGDQVFLRPCSHVVSCQQVEVEPLSADDWE-ILE-LHAISLEQHLLDQIRIVFPKAVVPIWVDQQTYIFIQI  155 (179)
T ss_dssp             HHHHTTCCTTCEEEEEECSCCEECSEEEEEESSHHHHH-HHH-HSCSSHHHHHHHHCCEECTTCEEEEESSSSCEEEEEE
T ss_pred             HHhHCCCCCCCEEEEEECCCCccceEEEEEcCCcCCeE-Eeh-hHHHHHHHHHhcCceeccCCCEEEEEecCCeEEEEEE
Confidence            4899999999999999966999999999999842 143 544 34799999999444999999999998766 8999999


Q ss_pred             EEecC-CCcEEEcCCceEEEcCcc
Q psy6209          79 VDTDP-APYCIVAADTVIHCEGDP  101 (115)
Q Consensus        79 v~t~P-~~~viVt~~T~I~~~~~p  101 (115)
                      ++|+| .++|+|+++|+|.+.++|
T Consensus       156 ~~~~P~~~~v~It~~TeI~v~pk~  179 (179)
T 1wlf_A          156 VTLMPAAPYGRLETNTKLLIQPKT  179 (179)
T ss_dssp             EEEESCCSSEECCTTCEEEECC--
T ss_pred             EEeeCCCCeEEECCCcEEEEecCC
Confidence            99999 999999999999998775

>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=99.86  E-value=1.4e-21  Score=169.17  Aligned_cols=114  Identities=68%  Similarity=1.158  Sum_probs=104.9

Q ss_pred             CCcccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEE
Q psy6209           1 MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD   80 (115)
Q Consensus         1 ~R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~   80 (115)
                      +|+|||+++||.|+|+++.++++|++|+|+|+++++..+.++.+..|+++||...+|||.+||+|.+...++.++|+|++
T Consensus        88 ~r~n~~v~~gd~V~v~~~~~~~~a~~v~l~p~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~gd~~~v~~~~~~~~f~V~~  167 (806)
T 3cf2_A           88 VRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE  167 (806)
T ss_dssp             HHHTTTCCTTCEEEEEECCCCCBCSBEEEEEBTTTSTTCCSCHHHHTHHHHHTTTCCEEETTCEEEECCTTSCEEEEEEE
T ss_pred             HHHhcCCCCCCEEEEEECCCCCcCCEEEEeccccchhccchhHHHHHHHHHHHhcCCcccCCCEEEEecCCcEEEEEEEE
Confidence            48999999999999999878999999999999988877888888999999998889999999999999999999999999


Q ss_pred             ecCCCcEEEcCCceEEEcCccccCccccCCCCCC
Q psy6209          81 TDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV  114 (115)
Q Consensus        81 t~P~~~viVt~~T~I~~~~~pv~re~~~~~~~~~  114 (115)
                      |+|.++|+|+++|.|.+.++|+.+++++...++|
T Consensus       168 ~~P~~~~~v~~~T~i~~~~~~~~~~~~~~~~~~v  201 (806)
T 3cf2_A          168 TDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV  201 (806)
T ss_dssp             ESSSSEEECCTTSBCCBCSCCBCCCTTSCCSSSC
T ss_pred             EeCCCCeEECCCcEEEEeccccCcccccccCCCC
Confidence            9999999999999999999999988776555544

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

Probab=99.85  E-value=2.6e-21  Score=126.47  Aligned_cols=75  Identities=20%  Similarity=0.206  Sum_probs=67.9

Q ss_pred             CCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEecCCCcEEEcCCceEEEcC
Q psy6209          20 QIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEG   99 (115)
Q Consensus        20 ~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~P~~~viVt~~T~I~~~~   99 (115)
                      +--.|++|+|||++ +++ ++++ +.+|||++|.  +|||++||+|.+...|++++|+|++|+|+ +|+|+++|+|+|++
T Consensus         8 ~~~~A~kVvLAP~~-~i~-~~~~-~~~~lk~~L~--grPV~~GD~I~i~~~G~~i~F~Vv~t~P~-~V~Vt~~T~I~i~~   81 (83)
T 2jv2_A            8 EGVIMSELKLKPLP-KVE-LPPD-FVDVIRIKLQ--GKTVRTGDVIGISILGKEVKFKVVQAYPS-PLRVEDRTKITLVT   81 (83)
T ss_dssp             CCCCCCEEEEEESS-SCC-CCHH-HHHHHHHHHT--TSEECTTCEEEEEETTEEEEEEEEEEESS-SEECCTTSEEEECC
T ss_pred             cceEEEEEEEcCCC-cee-cCcc-HHHHHHHHHC--CCCccCCCEEEEeeCCCEEEEEEEEecCc-cEEECCCcEEEEEe
Confidence            44589999999995 674 8775 4899999999  99999999999998899999999999999 99999999999976


Q ss_pred             c
Q psy6209         100 D  100 (115)
Q Consensus       100 ~  100 (115)
                      +
T Consensus        82 e   82 (83)
T 2jv2_A           82 H   82 (83)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.68  E-value=1.4e-16  Score=130.94  Aligned_cols=106  Identities=68%  Similarity=1.194  Sum_probs=97.4

Q ss_pred             CCcccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEE
Q psy6209           1 MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD   80 (115)
Q Consensus         1 ~R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~   80 (115)
                      ||+|+|+++||+|+|+++.++++|++|+|+|+++.++.+..+.|+.+.||++....+|+.+||.+.+...++.++|++++
T Consensus        88 ~r~n~~~~~gd~v~v~~~~~~~~a~~v~~~~~~~av~a~~~ga~d~~~Kp~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~  167 (489)
T 3hu3_A           88 VRNNLRVRLGDVISIQPCPDVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVHGGMRAVEFKVVE  167 (489)
T ss_dssp             HHHHTTCCTTCEEEEEECTTCCBCSEEEEEEBGGGSSSCCSCHHHHTHHHHHTTTCEEEETTCEEEEEETTEEEEEEEEE
T ss_pred             HHhhcCCCCCCEEEEEECCCCCccCEEEEcCCCcccccccchhHHHHhHHHHhhcCcccccCCEEEecCCCceEEEEEEe
Confidence            58999999999999999779999999999999887776776678889999998778999999999999989999999999


Q ss_pred             ecCCCcEEEcCCceEEEcCccccCcc
Q psy6209          81 TDPAPYCIVAADTVIHCEGDPIKREG  106 (115)
Q Consensus        81 t~P~~~viVt~~T~I~~~~~pv~re~  106 (115)
                      ++|.+.++++++|.+.+.++|+.+++
T Consensus       168 ~~~~~~~~~~~~t~~~~~~~~~~~~~  193 (489)
T 3hu3_A          168 TDPSPYCIVAPDTVIHCEGEPIKRED  193 (489)
T ss_dssp             EESSSEEEECTTCEEECCSSCBCHHH
T ss_pred             ecCCCceEEcCCeEEEEccCcccccc
Confidence            99999999999999999999987653

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

Probab=98.75  E-value=1.7e-08  Score=74.50  Aligned_cols=92  Identities=12%  Similarity=0.164  Sum_probs=71.0

Q ss_pred             CCcccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEE
Q psy6209           1 MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD   80 (115)
Q Consensus         1 ~R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~   80 (115)
                      |.+|+++.-||.|.|+-+ ..+.|+.|+|.|-+..--.+. | ...+|...|+ ++--+++||+|.|...+...+|.|++
T Consensus        95 mm~~L~l~~gd~V~v~~~-~LPkgt~vklqP~~~~Fl~i~-n-pKavLE~~Lr-nfstLT~Gd~I~I~~~~~~y~l~V~e  170 (190)
T 2yuj_A           95 MMQNLLLEEGGLVQVESV-NLQVATYSKFQPQSPDFLDIT-N-PKAVLENALR-NFACLTTGDVIAINYNEKIYELRVME  170 (190)
T ss_dssp             HHHHHTCCTTEEEEEEEE-CCCCCSEEEEEESSHHHHHSS-C-HHHHHHHHHT-TCCEECTTCEEEEESSSCEEEEEEEE
T ss_pred             HHHhcCCCCCCEEEEEEe-ecCCCcEEEEEECCccccccc-c-HHHHHHHHHh-cCcccccCCEEEEEeCCEEEEEEEEE
Confidence            678999999999999985 999999999999642111132 2 4677888887 35569999999999988999999999


Q ss_pred             ecCCCcEEEcCCceEEE
Q psy6209          81 TDPAPYCIVAADTVIHC   97 (115)
Q Consensus        81 t~P~~~viVt~~T~I~~   97 (115)
                      ++|+..+.|- +|.+++
T Consensus       171 ~kP~~aV~Ii-dTDl~v  186 (190)
T 2yuj_A          171 TKPDKAVSII-ECDMNV  186 (190)
T ss_dssp             ESSSSSEECS-SCCCEE
T ss_pred             EcCCCeEEEE-eCCEEE
Confidence            9997544433 444443

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

Probab=98.63  E-value=7.1e-08  Score=72.04  Aligned_cols=97  Identities=16%  Similarity=0.316  Sum_probs=75.3

Q ss_pred             CCcccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEE
Q psy6209           1 MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD   80 (115)
Q Consensus         1 ~R~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~   80 (115)
                      |.+|+++.-||.|.|+-+ +.+.|+.|+|.|-+..--.+. | ...+|...|+ ++--+++||+|.|...++..+|.|++
T Consensus       100 mm~~L~l~~gd~V~i~~~-~LPkgt~vklqP~~~~Fldi~-n-pKavLE~~LR-nfstLT~Gd~I~i~~~~~~y~l~V~e  175 (208)
T 1zc1_A          100 MMETLGIQPGSLLQISST-DVPLGQFVKLEPQSVDFLDIS-D-PKAVLENVLR-NFSTLTVDDVIEISYNGKTFKIKILE  175 (208)
T ss_dssp             HHHHHTCCTTCEEEEEEE-ECCCCSEEEEECCHHHHHTSS-C-HHHHHHHHHH-HCSCEESSSEEEEEETTEEEEEEEEE
T ss_pred             HHHhcCCCCCCEEEEEEe-EcCCCCEEEEeECcccccccc-C-HHHHHHHHhh-cCccccCCCEEEEEeCCEEEEEEEEE
Confidence            678999999999999985 999999999999532111132 2 3567788887 36689999999999989999999999


Q ss_pred             ecCCC----cEEEcCCceEEEcCccc
Q psy6209          81 TDPAP----YCIVAADTVIHCEGDPI  102 (115)
Q Consensus        81 t~P~~----~viVt~~T~I~~~~~pv  102 (115)
                      ++|+.    +|+|.-+=++.+ ..|+
T Consensus       176 ~kP~~~~~aV~IidTDleVDf-~~p~  200 (208)
T 1zc1_A          176 VKPESSSKSICVIETDLVTDF-APPV  200 (208)
T ss_dssp             EECSSTTCEECCSSSCSEEEE-CCCC
T ss_pred             EcCCCCCceEEEEeCceEEEe-cCCC
Confidence            99984    666665555555 3444

>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=96.94  E-value=0.0055  Score=44.48  Aligned_cols=94  Identities=9%  Similarity=-0.034  Sum_probs=65.1

Q ss_pred             CcccCCCCCCeEEEEeCCCC-------CCccEEEEc--cCC--CC-ccCcccchHHHHhhHhhhhCCCceecCCEEEEcc
Q psy6209           2 SFRLTTPCRDLLDRQRDIQI-------VYGKRIHVL--PID--DS-VQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRG   69 (115)
Q Consensus         2 R~Nagv~iGD~V~V~k~~~v-------~~A~~V~la--P~~--d~-i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~   69 (115)
                      |+-|++++||.|.|++. +.       .++-.+.|.  ...  .. -..++.+.+...++..|.  +.+++.|+.+.+..
T Consensus        65 R~wa~lsl~~~v~V~~y-~p~~~~~~~~~l~si~lEidf~~k~~~~~~~~D~dela~~f~~~F~--~Qift~gQ~l~f~~  141 (189)
T 1cr5_A           65 RTWGGWSLNQDVQAKAF-DLFKYSGKQSYLGSIDIDISFRARGKAVSTVFDQDELAKQFVRCYE--SQIFSPTQYLIMEF  141 (189)
T ss_dssp             HHHHTCCTTCEEEEEEC-CHHHHHTTCCEEEEEEEEEEECC-------CCCHHHHHHHHHHHHT--TCEECTTCEEEEEE
T ss_pred             HHhhcccCCCeEEEEEe-CCccCCCCcceEEEEEEEEEehhcCCCCCCccCHHHHHHHHHHHHc--CCCCCCCCEEEEEE
Confidence            78899999999999996 32       234444442  221  10 123665555666777777  99999999999988


Q ss_pred             CCceEEEEEEEec----------------CCCcEEEcCCceEEEc
Q psy6209          70 GMRAVEFKIVDTD----------------PAPYCIVAADTVIHCE   98 (115)
Q Consensus        70 ~~~~v~FkVv~t~----------------P~~~viVt~~T~I~~~   98 (115)
                      .+..+.+.|.++.                +...++++++|.|...
T Consensus       142 ~g~~l~l~V~~i~~~d~~~~~~~~~~~~~~~~~GiL~~~T~i~F~  186 (189)
T 1cr5_A          142 QGHFFDLKIRNVQAIDLGDIEPTSAVATGIETKGILTKQTQINFF  186 (189)
T ss_dssp             TTEEEEEEEEEEEEECTTSSSCSSCCBCSTTCCEECCTTCEEEEE
T ss_pred             CCcEEEEEEEEEEEeccccccccCcCCCCccceEEEcCCcEEEEE
Confidence            7777777776642                2347999999998763

>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=96.84  E-value=0.0075  Score=44.44  Aligned_cols=94  Identities=3%  Similarity=-0.065  Sum_probs=64.7

Q ss_pred             CcccCCCCCCeEEEEeCCCC---CCccEEEEc--cCC--C-CccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCce
Q psy6209           2 SFRLTTPCRDLLDRQRDIQI---VYGKRIHVL--PID--D-SVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRA   73 (115)
Q Consensus         2 R~Nagv~iGD~V~V~k~~~v---~~A~~V~la--P~~--d-~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~   73 (115)
                      |+-|++++||.|.|++...-   .++-.++|-  ...  . +-..++.+.+...++..|.  +++++.|+.+.+...+..
T Consensus        71 R~wa~lsl~~~v~V~~y~~~~~~~~l~si~lEidf~~k~~~~~~~~D~dela~~f~~~F~--~Qift~gQ~l~f~~~g~~  148 (211)
T 1qcs_A           71 RKWAGLSIGQEIEVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKMAAEFIQQFN--NQAFSVGQQLVFSFNDKL  148 (211)
T ss_dssp             HHHHTCCTTCEEEEEEECCCHHHHBEEEEEEEEEESCGGGCCCCEEEHHHHHHHHHHHHT--TCEEETTCEEEEEETTEE
T ss_pred             HhhhcccCCCcEEEEEecCCCCCceEEEEEEEEEehhcCCCCCcccCHHHHHHHHHHHHc--CCCCCCCCEEEEEECCcE
Confidence            78899999999999997221   123334442  221  1 1123655445566677777  999999999999877777


Q ss_pred             EEEEEEEe-----------------cCCCcEEEcCCceEEE
Q psy6209          74 VEFKIVDT-----------------DPAPYCIVAADTVIHC   97 (115)
Q Consensus        74 v~FkVv~t-----------------~P~~~viVt~~T~I~~   97 (115)
                      +.+.|.++                 +|...++++++|.|..
T Consensus       149 l~l~V~~v~~~d~~~~~~~~~~~~~~~~~~GiL~~~T~i~F  189 (211)
T 1qcs_A          149 FGLLVKDIEAMDPSILKGEPASGKRQKIEVGLVVGNSQVAF  189 (211)
T ss_dssp             EEEEEEEEEECCCCTTC-------CCBCSEEECCTTCEEEE
T ss_pred             EEEEEeEEEEecccccccCcccccCCCcceeEEcCCcEEEE
Confidence            77777663                 2245799999999876

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	115
d1e32a3	94	d.31.1.1 (A:107-200) Membrane fusion atpase p97 do	6e-50
d1cz5a2	94	d.31.1.1 (A:92-185) C-terminal domain of VAT-N, VA	6e-20

>d1e32a3 d.31.1.1 (A:107-200) Membrane fusion atpase p97 domain 2, P97-Nc {Mouse (Mus musculus) [TaxId: 10090]} Length = 94

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]

 Score =  151 bits (383), Expect = 6e-50
 Identities = 73/92 (79%), Positives = 84/92 (91%)

Query: 21  IVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVD 80
           + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+
Sbjct: 2   VKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVE 61

Query: 81  TDPAPYCIVAADTVIHCEGDPIKREGEENKPN 112
           TDP+PYCIVA DTVIHCEG+PIKRE EE   N
Sbjct: 62  TDPSPYCIVAPDTVIHCEGEPIKREDEEESLN 93

>d1cz5a2 d.31.1.1 (A:92-185) C-terminal domain of VAT-N, VAT-Nc {Archaeon Thermoplasma acidophilum [TaxId: 2303]} Length = 94

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]

 Score = 75.6 bits (186), Expect = 6e-20
 Identities = 24/90 (26%), Positives = 38/90 (42%), Gaps = 8/90 (8%)

Query: 25  KRIHVLPIDDSVQGLT-GNLFEVYLKPYFLEAYRPVHKDDLFIVRG----GMRAVEFKIV 79
           K++ + PI    Q L  G   E Y++   +   RP+ + D   V G    G   + FK+V
Sbjct: 5   KKVTLAPIIRKDQRLKFGEGIEEYVQRALIR--RPMLEQDNISVPGLTLAGQTGLLFKVV 62

Query: 80  DTDPAPYC-IVAADTVIHCEGDPIKREGEE 108
            T P+     +  +T I    +P     EE
Sbjct: 63  KTLPSKVPVEIGEETKIEIREEPASEVLEE 92

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	115
d1e32a3	94	Membrane fusion atpase p97 domain 2, P97-Nc {Mouse	100.0
d1cz5a2	94	C-terminal domain of VAT-N, VAT-Nc {Archaeon Therm	99.89
d1wlfa1	80	Peroxisome biogenesis factor 1 (PEX-1), domain 2 {	96.96
d1cr5a2	103	C-terminal domain of NSF-N, NSF-Nc {Baker's yeast	89.86
d1qcsa2	116	C-terminal domain of NSF-N, NSF-Nc {Hamster (Crice	83.81
d1e32a1	86	Membrane fusion ATPase p97 N-terminal domain , P97	80.05

>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=100.00  E-value=1.2e-35  Score=196.37  Aligned_cols=94  Identities=78%  Similarity=1.384  Sum_probs=91.5

Q ss_pred             CCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEecCCCcEEEcCCceEEEcC
Q psy6209          20 QIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTDPAPYCIVAADTVIHCEG   99 (115)
Q Consensus        20 ~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~P~~~viVt~~T~I~~~~   99 (115)
                      ++|+|++|+++|++||++++++++|+.||+|||++++|||++||+|.+.++++.|||||++|+|+++|+|+++|.|+|+|
T Consensus         1 di~~~krV~vlP~~DTieglsgnlf~~ylkPYf~~~yrPv~~gD~f~v~g~~r~VEFKVv~~dp~~~~iV~~~T~I~~eG   80 (94)
T d1e32a3           1 DVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETDPSPYCIVAPDTVIHCEG   80 (94)
T ss_dssp             TCCBCSCEEEEEBGGGTTTCBSCHHHHTHHHHHTTSCEEEETTCEEEEEETTEEEEEEEEEESSSSEEEECTTCCCBCCS
T ss_pred             CCCcccEEEEEecccccCCCCccHHHHHHhHHHhhcCccccCCCEEEEccCCeeEEEEEEeecCCCceEEcCCCEEEeCC
Confidence            47999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccccCccccCCCCC
Q psy6209         100 DPIKREGEENKPNG  113 (115)
Q Consensus       100 ~pv~re~~~~~~~~  113 (115)
                      +|++|||+|+++|+
T Consensus        81 epi~Red~e~~~~~   94 (94)
T d1e32a3          81 EPIKREDEEESLNE   94 (94)
T ss_dssp             CCBCCCTTSCCTTS
T ss_pred             cccchhhhhhhhcC
Confidence            99999999998885

>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=99.89  E-value=1.8e-23  Score=137.94  Aligned_cols=84  Identities=25%  Similarity=0.339  Sum_probs=72.2

Q ss_pred             CCccEEEEccCCCCccC--cccchHHHHhhHhhhhCCCceecCCEEEEccCC----ceEEEEEEEecCCC-cEEEcCCce
Q psy6209          22 VYGKRIHVLPIDDSVQG--LTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGM----RAVEFKIVDTDPAP-YCIVAADTV   94 (115)
Q Consensus        22 ~~A~~V~laP~~d~i~~--i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~----~~v~FkVv~t~P~~-~viVt~~T~   94 (115)
                      ..|+||+|||+.+.-..  +.++ +.+||+++|.  +|||++||.|.+..++    +.++|+|++|+|++ +|+|+++|+
T Consensus         2 ~~A~kVvLAP~~~~~~~i~~~~~-~~~ylk~~L~--grPV~~GD~i~v~~~~~~g~~~i~F~Vv~t~P~g~~ViIt~~Te   78 (94)
T d1cz5a2           2 EIAKKVTLAPIIRKDQRLKFGEG-IEEYVQRALI--RRPMLEQDNISVPGLTLAGQTGLLFKVVKTLPSKVPVEIGEETK   78 (94)
T ss_dssp             CBCSEEEEEECSCTTTTCCCCSS-HHHHHHHHHS--SCEECTTCEECCSSCCCSSCCCCSEEEEEESSSSSCEECCTTCE
T ss_pred             ccccEEEECcCCCccceEEEcCC-HHHHHHHHHc--CCCCcCCCEEEEeeccccCCceEeEEEEEEeCCCCeEEECCCeE
Confidence            47999999998553222  4453 6899999999  9999999999997654    78999999999999 599999999


Q ss_pred             EEEcCccccCcccc
Q psy6209          95 IHCEGDPIKREGEE  108 (115)
Q Consensus        95 I~~~~~pv~re~~~  108 (115)
                      |+++++|+++++++
T Consensus        79 I~i~~~Pv~e~~e~   92 (94)
T d1cz5a2          79 IEIREEPASEVLEE   92 (94)
T ss_dssp             EEECSCCSSSCSCC
T ss_pred             EEEecCcCcccccc
Confidence            99999999999776

>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=96.96  E-value=0.00039  Score=43.02  Aligned_cols=75  Identities=20%  Similarity=0.291  Sum_probs=55.9

Q ss_pred             CCccEEEEccCCCC-ccCcccchHHHHhhHhhhhCCCceecCCEEEEccC-CceEEEEEEEecC-CCcEEEcCCceEEEc
Q psy6209          22 VYGKRIHVLPIDDS-VQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGG-MRAVEFKIVDTDP-APYCIVAADTVIHCE   98 (115)
Q Consensus        22 ~~A~~V~laP~~d~-i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~-~~~v~FkVv~t~P-~~~viVt~~T~I~~~   98 (115)
                      ..|++|.+.|.+.. =+ +-+ +-..++...|++--|-|..|.++.+... +..+.|+|.+++| ..++++.++|++.+.
T Consensus         2 ~~~~~V~veP~T~dDWE-IiE-l~a~~lE~~LL~QiRiV~~~~~~~v~v~~~~~~~~~V~~i~P~~~~~~L~~~TEv~Va   79 (80)
T d1wlfa1           2 VSCQQVEVEPLSADDWE-ILE-LHAISLEQHLLDQIRIVFPKAVVPIWVDQQTYIFIQIVTLMPAAPYGRLETNTKLLIQ   79 (80)
T ss_dssp             EECSEEEEEESSHHHHH-HHH-HSCSSHHHHHHHHCCEECTTCEEEEESSSSCEEEEEEEEEESCCSSEECCTTCEEEEC
T ss_pred             cceEEEEEecCChhhHH-HHH-HHHHHHHHHHHhheeeccCCCEEEEEECCCcEEEEEEEEecCCCeeEEecCCCEEEeC
Confidence            35788999996310 11 111 2235667777766899999999999765 5689999999999 589999999999874

>d1cr5a2 d.31.1.1 (A:108-210) C-terminal domain of NSF-N, NSF-Nc {Baker's yeast (Saccharomyces cerevisiae), sec18p [TaxId: 4932]}

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 NSF-N, NSF-Nc
species: Baker's yeast (Saccharomyces cerevisiae), sec18p [TaxId: 4932]

Probab=89.86  E-value=0.49  Score=29.59  Aligned_cols=57  Identities=11%  Similarity=0.077  Sum_probs=41.3

Q ss_pred             cccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEec----------------CCCcEEEcCCceEEE
Q psy6209          39 LTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTD----------------PAPYCIVAADTVIHC   97 (115)
Q Consensus        39 i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~----------------P~~~viVt~~T~I~~   97 (115)
                      ++.|.........|.  +.+++.|+.+.....+..+.|.|.++.                |..-++.+.+|.|..
T Consensus        27 ~D~Dela~~F~~~F~--~Q~ft~gQ~l~f~f~~~~l~l~Vk~v~~~Dl~~~~~~~~~~~~~~~~GiL~~~T~V~F   99 (103)
T d1cr5a2          27 FDQDELAKQFVRCYE--SQIFSPTQYLIMEFQGHFFDLKIRNVQAIDLGDIEPTSAVATGIETKGILTKQTQINF   99 (103)
T ss_dssp             CCHHHHHHHHHHHHT--TCEECTTCEEEEEETTEEEEEEEEEEEEECTTSSSCSSCCBCSTTCCEECCTTCEEEE
T ss_pred             ccHHHHHHHHHHHhc--CCCCCCCcEEEEEECCcEEEEEEEEEEEEccccccCCcccccCcccceEEecCcEEEE
Confidence            443333444555666  999999999999988888888886643                233588999998865

>d1qcsa2 d.31.1.1 (A:86-201) C-terminal domain of NSF-N, NSF-Nc {Hamster (Cricetulus griseus) [TaxId: 10029]}

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 NSF-N, NSF-Nc
species: Hamster (Cricetulus griseus) [TaxId: 10029]

Probab=83.81  E-value=1.6  Score=27.64  Aligned_cols=58  Identities=7%  Similarity=0.078  Sum_probs=42.6

Q ss_pred             cccchHHHHhhHhhhhCCCceecCCEEEEccCCceEEEEEEEec-----------------CCCcEEEcCCceEEEc
Q psy6209          39 LTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTD-----------------PAPYCIVAADTVIHCE   98 (115)
Q Consensus        39 i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~~~~~~v~FkVv~t~-----------------P~~~viVt~~T~I~~~   98 (115)
                      ++.|.........|.  +.+++.|+.+.+...+..+.+.|.++.                 |...++.+.+|.|...
T Consensus        27 ~D~Dela~~F~~~F~--~Qift~gQ~l~f~f~~~~l~l~Vk~v~~~D~~~~~~~~~~~~~~~~~~GiL~~~T~V~F~  101 (116)
T d1qcsa2          27 YDTDKMAAEFIQQFN--NQAFSVGQQLVFSFNDKLFGLLVKDIEAMDPSILKGEPASGKRQKIEVGLVVGNSQVAFE  101 (116)
T ss_dssp             EEHHHHHHHHHHHHT--TCEEETTCEEEEEETTEEEEEEEEEEEECCCCTTC-------CCBCSEEECCTTCEEEEE
T ss_pred             cCHHHHHHHHHHHhC--CCCcCCCcEEEEEeCCcEEEEEEEEEEEecchhccCCccccccCcccceEEcCCceEEEE
Confidence            443333445556666  999999999999988888888885542                 2356889999999874

>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=80.05  E-value=1.9  Score=25.72  Aligned_cols=57  Identities=12%  Similarity=-0.009  Sum_probs=33.8

Q ss_pred             cccCCCCCCeEEEEeCCCCCCccEEEEccCCCCccCcccchHHHHhhHhhhhCCCceecCCEEEEc
Q psy6209           3 FRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVR   68 (115)
Q Consensus         3 ~Nagv~iGD~V~V~k~~~v~~A~~V~laP~~d~i~~i~~~~~~~~lk~~l~~~~rPV~~Gd~i~v~   68 (115)
                      +-||+..||.|.|+-  .-..+..+..++.++.=.++-.  .+.+++..+.     |..||.+.|.
T Consensus        27 ~~Lgl~~GD~V~I~G--kr~t~av~~~~~~~d~~~g~Ir--id~~~R~Nag-----v~iGD~V~V~   83 (86)
T d1e32a1          27 DELQLFRGDTVLLKG--KKRREAVCIVLSDDTCSDEKIR--MNRVVRNNLR-----VRLGDVISIQ   83 (86)
T ss_dssp             HHTTCCTTCEEEEEC--STTCEEEEEEEECTTSCSSEEE--ECHHHHHHTT-----CCTTCEEEEE
T ss_pred             HHcCCCCCCEEEEEc--CCceeEEEEEeccCCCCCCEEE--ecHHHHhhcC-----cCCCCEEEEE
Confidence            358999999999985  3233334444444331111111  2356666555     8899998875