Citrus Sinensis ID: 016557

Local Sequence Feature Prediction

Prediction and (Method)	Result

Residue Number Marker

Protein Sequence

Secondary Structure (PSIPRED)

Secondary Structure Prediction (SSPRO)

Coil and Loop (DISEMBL)

Flexible Loop (DISEMBL)

Low Complexity Region (SEG)

Disordered region (IsUnstruct)

Disordered Region (DISOPRED)

Disordered Region (DISEMBL)

Disordered Region (DISPRO)

Transmembrane Helix (TMHMM)

Transmembrane Helix (HMMTOP)

Transmembrane Helix (MEMSAT)

TM Helix, Signal Peptide (MEMSAT_SVM)

TM Helix, Signal Peptide (Phobius)

Signal Peptide (SignalP HMM Mode)

Signal Peptide (SignalP NN Mode)

Coiled Coils (COILS)

Positional Conservation

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------

MTKKRKNNGSADEDRHVKSVKVVEQSSPSPPRLGFENPLLPLANTYDDDDEEEEYGGRGDSGAKVGQNGRTGEDDDEDKDEDEDDLANGYGQGQRSRLVEVRRDCPYLDTVNRQVLDFDFEKFCSVSLSNLNVYACLVCGKYYQGRGQKSHAYTHSLEAGHHVYINLRTEKVYCLPDGYEINDPSLEDIRHVGLNNIKETDFVNVTIQSLMRVTPLRNFFLIPENYRHCKSPLVHRFGDLTRKIWHARNFKGQVSPHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDLRNTKKNTSIIYECFQGELEVVKEIPKNTISGNDQNTEKGSDGGDDHDNITTETSRMPFLMLGLDLPPPPLFKDVMEKNIIPQLQRLSGHMWQG

cccccccccccccccHHHHHHccccccccccccccccccccccccccccHHHHHcccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccEEEEcccccEEEccccccEEcccccccccccccccccccEEEEcccccEEEcccccccccccccccccccccccccccHHHHHHHHHHccHHHHHHHccccccccccHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHccccccccccccHHHHHHHHHHHHHHHHHHccccccccccccccHHHHHHHccccccccccccEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccc

cccEEEccccccccccccHccccccccccccccccccccccccccccccHHHHHHcccccccccccccccccccccccccccccccHHHccccHHccccccccccccHcccccccccccHHHEEEEEEcccEEEEEEEEccEEccccccccEEEEEEccccEEEEEEcccEEEEcccccEEEcccHHHccEEcccccccccHHHHHHHHHHccccHHHHHcccccccccccHHHHHHHHHHHHHHcHHHccccccHHHHHHHHHHHHccccEEEccccHHHHHHHHHHHHHHHHccccccccEEEEHcccEEEEEEEccccccccHHHHHHHHHHcccccccccEEEEEccEEEEEcccccccccccHHHccccccccEEccccccc

mtkkrknngsadedrhvKSVKVVeqsspspprlgfenpllplantyddddeeeeyggrgdsgakvgqngrtgedddedkdededdlangygqgqrsrlvevrrdcpyldtvnrqvldFDFEKFCSvslsnlnvYACLVcgkyyqgrgqkshaythsleAGHHVYINLrtekvyclpdgyeindpsledirhvglnniketdfvNVTIQSLmrvtplrnfflipenyrhcksplvhrfgdLTRKIWHArnfkgqvspHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDLRNTKKNTSIIYECFQGELEvvkeipkntisgndqntekgsdggddhdnittetsrmpflmlgldlpppplfkdvmekniipqlqrlsghmwqg

mtkkrknngsadedrhvksvkvveqsspspprlgfenpllpLANTYDDDDEEEEyggrgdsgakvgqngrtgedddedkdededdlangygqgqrsrlvevrrdcPYLDTVNRQVLDFDFEKFCSVSLSNLNVYACLVCGKYYQGRGQKSHAYTHSLEAGHHVYINLRTEKVYCLPDGYEINDPSLEDIRHVGLNNIKETDFVNVTIQSLMRVTPLRNFFLIPENYRHCKSPLVHRFGDLTRKIWHARNFKGQVSPHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDLRNTKKNTSIIYECFQGELEVVKeipkntisgndqntekgsdggddhDNITTETSRMPFLMLGLDLPPPPLFKDVMEKNIIPQLQRLSGHMWQG

MTKKRKNNGSADEDRHVKSVKVVEQSSPSPPRLGFENPLLPLANTYddddeeeeYGGRGDSGAKVGQNGRTGedddedkdededdLANGYGQGQRSRLVEVRRDCPYLDTVNRQVLDFDFEKFCSVSLSNLNVYACLVCGKYYQGRGQKSHAYTHSLEAGHHVYINLRTEKVYCLPDGYEINDPSLEDIRHVGLNNIKETDFVNVTIQSLMRVTPLRNFFLIPENYRHCKSPLVHRFGDLTRKIWHARNFKGQVSPHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDLRNTKKNTSIIYECFQGELEVVKEIPKNTISGNDQNTEKGSDGGDDHDNITTETSRmpflmlgldlpppplfKDVMEKNIIPQLQRLSGHMWQG

************************************************************************************************RLVEVRRDCPYLDTVNRQVLDFDFEKFCSVSLSNLNVYACLVCGKYYQG******************YINLRTEKVYCLPDGYEINDPSLEDIRHVGLNNIKETDFVNVTIQSLMRVTPLRNFFLIPENYRHCKSPLVHRFGDLTRKIWHARNFKGQVSPHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDLRNTKKNTSIIYECFQGELEVVKEI*********************************FLMLGLDLPPPPLFKDVMEKNII*************

**********************************************************************************************************YLDTVNRQVLDFDFEKFCSVSLSNLNVYACLVCGKYYQGRGQKSHAYTHSLEAGHHVYINLRTEKVYCLPDGYEI**********VGLNNIKETDFVNVTIQSLMRVTPLRNFFLIPENYRHCKSPLVHRFGDLTRKIWHARNFKGQVSPHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDLR*************QGELEVVKEIPKNTISGNDQNTEKGSDGGDDHDNITTETSRMPFLMLGLDLPPPPLFKDVMEKNIIPQLQRLSG*****

******************************PRLGFENPLLPLANTYDD**************************************ANGYGQGQRSRLVEVRRDCPYLDTVNRQVLDFDFEKFCSVSLSNLNVYACLVCGKYYQGRGQKSHAYTHSLEAGHHVYINLRTEKVYCLPDGYEINDPSLEDIRHVGLNNIKETDFVNVTIQSLMRVTPLRNFFLIPENYRHCKSPLVHRFGDLTRKIWHARNFKGQVSPHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDLRNTKKNTSIIYECFQGELEVVKEIPKNTISGNDQNTEKGSDGGDDHDNITTETSRMPFLMLGLDLPPPPLFKDVMEKNIIPQLQRLSGHMWQG

*********************************GFENPLLPLAN*********************************************************RRDCPYLDTVNRQVLDFDFEKFCSVSLSNLNVYACLVCGKYYQGRGQKSHAYTHSLEAGHHVYINLRTEKVYCLPDGYEINDPSLEDIRHVGLNNIKETDFVNVTIQSLMRVTPLRNFFLIPENYRHCKSPLVHRFGDLTRKIWHARNFKGQVSPHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDLRNTKKNTSIIYECFQGELEVVKEIPKNTISGNDQNTEKGSDGGDDHDNITTETSRMPFLMLGLDLPPPPLFKDVMEKNIIPQLQRLSG*****

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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no confident homologs detected

Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Alignment graph	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query		387	2.2.26 [Sep-21-2011]
Q3TIX9		564	U4/U6.U5 tri-snRNP-associ	yes	no	0.770	0.528	0.448	7e-75
Q53GS9		565	U4/U6.U5 tri-snRNP-associ	yes	no	0.770	0.527	0.448	8e-75
Q5R761		565	U4/U6.U5 tri-snRNP-associ	yes	no	0.770	0.527	0.445	1e-73
Q9USR2		502	Probable mRNA-splicing pr	yes	no	0.677	0.521	0.433	4e-65
P43589		448	Pre-mRNA-splicing factor	yes	no	0.630	0.544	0.298	6e-28
Q9SUX7		184	Putative F-box protein At	no	no	0.286	0.603	0.474	7e-13
Q8TEY7		942	Ubiquitin carboxyl-termin	no	no	0.503	0.207	0.248	1e-09
Q8R5K2		909	Ubiquitin carboxyl-termin	no	no	0.501	0.213	0.249	2e-09
Q5REG5		914	Ubiquitin carboxyl-termin	no	no	0.490	0.207	0.252	3e-09
A6QNM7		912	Ubiquitin carboxyl-termin	no	no	0.490	0.208	0.249	9e-09

>sp\|Q3TIX9\|SNUT2_MOUSE U4/U6.U5 tri-snRNP-associated protein 2 OS=Mus musculus GN=Usp39 PE=2 SV=2	Back alignment and function desciption

 Score =  281 bits (718), Expect = 7e-75,   Method: Compositional matrix adjust.
 Identities = 157/350 (44%), Positives = 205/350 (58%), Gaps = 52/350 (14%)

Query: 70  RTGEDDDEDKDEDEDDLANGYGQGQRSRLVEVRRDCPYLDTVNRQVLDFDFEKFCSVSLS 129
           R  E D++ + E E    NG    +  R     R CPYLDT+NR VLDFDFEK CS+SLS
Sbjct: 73  REREADEDSEPEREVRAKNGRVDSEDRR----SRHCPYLDTINRSVLDFDFEKLCSISLS 128

Query: 130 NLNVYACLVCGKYYQGRGQKSHAYTHSLEAGHHVYINLRTEKVYCLPDGYEINDPSLEDI 189
           ++N YACLVCGKY+QGRG KSHAY HS++  HHV++NL T K YCLPD YEI D SLEDI
Sbjct: 129 HINAYACLVCGKYFQGRGLKSHAYIHSVQFSHHVFLNLHTLKFYCLPDNYEIIDSSLEDI 188

Query: 190 RHV---------------------------------GLNNIKETDFVNVTIQSLMRVTPL 216
            +V                                 GLNNIK  D+ N  +Q+L  V PL
Sbjct: 189 TYVLKPTFTKQQIANLDKQAKLSRAYDGTTYLPGIVGLNNIKANDYANAVLQALSNVPPL 248

Query: 217 RNFFLIPENYRHCKSP-------LVHRFGDLTRKIWHARNFKGQVSPHEFLQAVMKASKK 269
           RN+FL  +NY++ K P       LV RFG+L RK+W+ RNFK  VSPHE LQAV+  SKK
Sbjct: 249 RNYFLEEDNYKNIKRPPGDIMFLLVQRFGELMRKLWNPRNFKAHVSPHEMLQAVVLCSKK 308

Query: 270 RFRIGVQSNPVEFMSWLLNTLHSDL-RNTKKNTSIIYECFQGELEV-VKEIPKNTISGND 327
            F+I  Q + V+F+SW LN LHS L    KK  +I+ + FQG + +  K++P   +   +
Sbjct: 309 TFQITKQGDGVDFLSWFLNALHSALGGTKKKKKTIVNDVFQGSMRIFTKKLPHPDLPAEE 368

Query: 328 QNTEKGSDGGDDHDNITTETSRMPFLMLGLDLPPPPLFKDVMEKNIIPQL 377
           +   +     D++     E++   F+ L LDLP  PL+KD  E+ IIPQ+
Sbjct: 369 K---EQLLHNDEYQETMVEST---FMYLTLDLPTAPLYKDEKEQLIIPQV 412

May play a role in mRNA splicing. It is unsure if the protein really exhibits hydrolase activity. Could be a competitor of ubiquitin C-terminal hydrolases (UCHs).
Mus musculus (taxid: 10090)

>sp\|Q53GS9\|SNUT2_HUMAN U4/U6.U5 tri-snRNP-associated protein 2 OS=Homo sapiens GN=USP39 PE=1 SV=2	Back alignment and function description

>sp\|Q5R761\|SNUT2_PONAB U4/U6.U5 tri-snRNP-associated protein 2 OS=Pongo abelii GN=USP39 PE=2 SV=1	Back alignment and function description

>sp\|Q9USR2\|UBP10_SCHPO Probable mRNA-splicing protein ubp10 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=ubp10 PE=3 SV=1	Back alignment and function description

>sp\|P43589\|SAD1_YEAST Pre-mRNA-splicing factor SAD1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SAD1 PE=1 SV=1	Back alignment and function description

>sp\|Q9SUX7\|FB245_ARATH Putative F-box protein At4g22420 OS=Arabidopsis thaliana GN=At4g22420 PE=4 SV=1	Back alignment and function description

>sp\|Q8TEY7\|UBP33_HUMAN Ubiquitin carboxyl-terminal hydrolase 33 OS=Homo sapiens GN=USP33 PE=1 SV=2	Back alignment and function description

>sp\|Q8R5K2\|UBP33_MOUSE Ubiquitin carboxyl-terminal hydrolase 33 OS=Mus musculus GN=Usp33 PE=1 SV=2	Back alignment and function description

>sp\|Q5REG5\|UBP33_PONAB Ubiquitin carboxyl-terminal hydrolase 33 OS=Pongo abelii GN=USP33 PE=2 SV=1	Back alignment and function description

>sp\|A6QNM7\|UBP33_BOVIN Ubiquitin carboxyl-terminal hydrolase 33 OS=Bos taurus GN=USP33 PE=2 SV=1	Back alignment and function description

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Alignment Graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		387
147862940		566	hypothetical protein VITISV_019937 [Viti	0.966	0.660	0.675	1e-139
356546089		563	PREDICTED: U4/U6.U5 tri-snRNP-associated	0.868	0.596	0.704	1e-136
356534252		569	PREDICTED: U4/U6.U5 tri-snRNP-associated	0.852	0.579	0.681	1e-136
255559080		557	ubiquitin specific protease 39 and snrnp	0.958	0.666	0.658	1e-134
145333717		541	ubiquitin carboxyl-terminal hydrolase-li	0.901	0.645	0.659	1e-134
334186810		539	U4/U6.U5 tri-snRNP-associated protein 2	0.901	0.647	0.662	1e-133
449443550		550	PREDICTED: U4/U6.U5 tri-snRNP-associated	0.948	0.667	0.668	1e-133
449520261		550	PREDICTED: U4/U6.U5 tri-snRNP-associated	0.948	0.667	0.665	1e-132
357474209		544	U4/U6.U5 tri-snRNP-associated protein [M	0.891	0.634	0.658	1e-132
224089613		557	predicted protein [Populus trichocarpa]	0.950	0.660	0.644	1e-127

>gi\|147862940\|emb\|CAN83206.1\| hypothetical protein VITISV_019937 [Vitis vinifera]	Back alignment and taxonomy information

 Score =  501 bits (1291), Expect = e-139,   Method: Compositional matrix adjust.
 Identities = 287/425 (67%), Positives = 315/425 (74%), Gaps = 51/425 (12%)

Query: 1   MTKKRKNNGSADEDRH---VKSVKVVEQSSPSPPRLGFENPLLPLANTYDDDDEEEEYGG 57
           M  KR++N   DE R    +K  K +++SSP P  L FEN L  LA+  DDDDE+EE   
Sbjct: 1   MKTKREDNSDEDEGREFPDLKRQKKLDESSPPPASLAFENALHTLASYDDDDDEKEEEEM 60

Query: 58  RGDSGAKVGQNGRTGEDDDEDKDEDEDDLANGY-------GQGQRSRLVEVRRDCPYLDT 110
           +  SG +  ++ R  E +     E+ DD  +          Q +RSRLVEVRRDCPYLDT
Sbjct: 61  KEASGLRGREDNRRAERNGHRDGEEYDDDDDDDDDPHQEANQVKRSRLVEVRRDCPYLDT 120

Query: 111 VNRQVLDFDFEKFCSVSLSNLNVYACLVCGKYYQGRGQKSHAYTHSLEAGHHVYINLRTE 170
           VNRQVLDFDFEKFCSVSLSNLNVYACLVCGKYYQGRGQKSHAYTHSLEAGHHVYINLRTE
Sbjct: 121 VNRQVLDFDFEKFCSVSLSNLNVYACLVCGKYYQGRGQKSHAYTHSLEAGHHVYINLRTE 180

Query: 171 KVYCLPDGYEINDPSLEDIRHV---------------------------------GLNNI 197
           KVYCLPDGYEINDPSL+DIRHV                                 GLNNI
Sbjct: 181 KVYCLPDGYEINDPSLDDIRHVLNPRFTREQVDQLDKNKQWSRALDGSDYLPGMVGLNNI 240

Query: 198 KETDFVNVTIQSLMRVTPLRNFFLIPENYRHCKSPLVHRFGDLTRKIWHARNFKGQVSPH 257
           KETDFVNVTIQSLMRVTPLRNFFLIPENYRHCKSPLVHRFG+LTRKIWHARNFKGQVSPH
Sbjct: 241 KETDFVNVTIQSLMRVTPLRNFFLIPENYRHCKSPLVHRFGELTRKIWHARNFKGQVSPH 300

Query: 258 EFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDLRNTKKNTSIIYECFQGELEVVKE 317
           EFLQAVMKASKKRFRIG QS+PVEFMSWLLNTLH DLR +KKN+SIIY CFQGELEVVKE
Sbjct: 301 EFLQAVMKASKKRFRIGAQSDPVEFMSWLLNTLHGDLRTSKKNSSIIYNCFQGELEVVKE 360

Query: 318 IPKNTI-----SGNDQNTEKGSDGGDDHDNITTETSRMPFLMLGLDLPPPPLFKDVMEKN 372
           IP         +G+DQN    +   D+H ++  ET RMPFLMLGLDLPPPPLFKDVMEKN
Sbjct: 361 IPNKGFFEKRENGDDQNK---ATTADEHADVILETCRMPFLMLGLDLPPPPLFKDVMEKN 417

Query: 373 IIPQL 377
           IIPQ+
Sbjct: 418 IIPQV 422

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|356546089\|ref\|XP_003541464.1\| PREDICTED: U4/U6.U5 tri-snRNP-associated protein 2-like [Glycine max]	Back alignment and taxonomy information

>gi\|356534252\|ref\|XP_003535671.1\| PREDICTED: U4/U6.U5 tri-snRNP-associated protein 2-like [Glycine max]	Back alignment and taxonomy information

>gi\|255559080\|ref\|XP_002520562.1\| ubiquitin specific protease 39 and snrnp assembly factor, putative [Ricinus communis] gi\|223540222\|gb\|EEF41795.1\| ubiquitin specific protease 39 and snrnp assembly factor, putative [Ricinus communis]	Back alignment and taxonomy information

>gi\|145333717\|ref\|NP_001078426.1\| ubiquitin carboxyl-terminal hydrolase-like protein [Arabidopsis thaliana] gi\|23397271\|gb\|AAN31917.1\| unknown protein [Arabidopsis thaliana] gi\|110741459\|dbj\|BAE98689.1\| hypothetical protein [Arabidopsis thaliana] gi\|332659187\|gb\|AEE84587.1\| ubiquitin carboxyl-terminal hydrolase-like protein [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|334186810\|ref\|NP_001190799.1\| U4/U6.U5 tri-snRNP-associated protein 2 [Arabidopsis thaliana] gi\|332659199\|gb\|AEE84599.1\| U4/U6.U5 tri-snRNP-associated protein 2 [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|449443550\|ref\|XP_004139540.1\| PREDICTED: U4/U6.U5 tri-snRNP-associated protein 2-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|449520261\|ref\|XP_004167152.1\| PREDICTED: U4/U6.U5 tri-snRNP-associated protein 2-like [Cucumis sativus]	Back alignment and taxonomy information

>gi\|357474209\|ref\|XP_003607389.1\| U4/U6.U5 tri-snRNP-associated protein [Medicago truncatula] gi\|355508444\|gb\|AES89586.1\| U4/U6.U5 tri-snRNP-associated protein [Medicago truncatula]	Back alignment and taxonomy information

>gi\|224089613\|ref\|XP_002308779.1\| predicted protein [Populus trichocarpa] gi\|222854755\|gb\|EEE92302.1\| predicted protein [Populus trichocarpa]	Back alignment and taxonomy information

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Alignment graph	Length	Definition	Q cover	H cover	Identity	E-value
Query		387
TAIR\|locus:4010713900		541	AT4G22285 [Arabidopsis thalian	0.496	0.354	0.626	3.1e-124
TAIR\|locus:2127490		340	AT4G22410 [Arabidopsis thalian	0.335	0.382	0.846	3.4e-101
DICTYBASE\|DDB_G0278929		718	usp39 "putative ubiquitin carb	0.472	0.254	0.442	1.4e-72
ZFIN\|ZDB-GENE-030131-966		497	usp39 "ubiquitin specific pept	0.260	0.203	0.654	1.6e-71
UNIPROTKB\|B9A018		536	USP39 "U4/U6.U5 tri-snRNP-asso	0.232	0.167	0.722	1.8e-68
UNIPROTKB\|G5E9H0		488	USP39 "U4/U6.U5 tri-snRNP-asso	0.232	0.184	0.722	1.8e-68
UNIPROTKB\|I3LFS1		428	USP39 "Uncharacterized protein	0.232	0.210	0.722	1.8e-68
UNIPROTKB\|B8ZZD1		502	USP39 "U4/U6.U5 tri-snRNP-asso	0.232	0.179	0.722	2.3e-68
UNIPROTKB\|E2QZF6		561	USP39 "Uncharacterized protein	0.232	0.160	0.722	4.9e-68
MGI\|MGI:107622		564	Usp39 "ubiquitin specific pept	0.232	0.159	0.722	5.4e-68

TAIR\|locus:4010713900 AT4G22285 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 604 (217.7 bits), Expect = 3.1e-124, Sum P(3) = 3.1e-124
 Identities = 124/198 (62%), Positives = 138/198 (69%)

Query:     3 KKRKNNGSADEDRHVKSVKVVEQSSPSPPRLGFENPLLPLANTYXXXXXXXXYG-----G 57
             ++   NG ++E+R VK  +V+E+S   PP LGF NPLLPLANTY                
Sbjct:     4 EREVKNGVSEEEREVKRKRVMERSDSPPPPLGFNNPLLPLANTYDDDDEEEENEQKKSQA 63

Query:    58 RGDSGAKVGQNGRTGXXXXXXXXXXXXXLANGYGQGQRSRLVEVRRDCPYLDTVNRQVLD 117
             RG+  AK   NG                     G+G+ SR VEVRRDCPYLDTVNRQVLD
Sbjct:    64 RGNGVAKGEGNGNKVKGEAQEEVDDDEDDDVSKGKGKHSRHVEVRRDCPYLDTVNRQVLD 123

Query:   118 FDFEKFCSVSLSNLNVYACLVCGKYYQGRGQKSHAYTHSLEAGHHVYINLRTEKVYCLPD 177
             FDFE+FCSVSLSNLNVYACLVCGKY+QGR QKSHAYTHSLEAGHHVYINL TEKVYCLPD
Sbjct:   124 FDFERFCSVSLSNLNVYACLVCGKYFQGRSQKSHAYTHSLEAGHHVYINLLTEKVYCLPD 183

Query:   178 GYEINDPSLEDIRHVGLN 195
              YEINDPSL+DIRHV LN
Sbjct:   184 SYEINDPSLDDIRHV-LN 200

GO:0004221 "ubiquitin thiolesterase activity" evidence=IEA

GO:0005622 "intracellular" evidence=IEA

GO:0005634 "nucleus" evidence=ISM

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005829 "cytosol" evidence=RCA

TAIR\|locus:2127490 AT4G22410 [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

DICTYBASE\|DDB_G0278929 usp39 "putative ubiquitin carboxyl-terminal hydrolase (UCH)" [Dictyostelium discoideum (taxid:44689)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-030131-966 usp39 "ubiquitin specific peptidase 39" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

UNIPROTKB\|B9A018 USP39 "U4/U6.U5 tri-snRNP-associated protein 2" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|G5E9H0 USP39 "U4/U6.U5 tri-snRNP-associated protein 2" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|I3LFS1 USP39 "Uncharacterized protein" [Sus scrofa (taxid:9823)]	Back alignment and assigned GO terms

UNIPROTKB\|B8ZZD1 USP39 "U4/U6.U5 tri-snRNP-associated protein 2" [Homo sapiens (taxid:9606)]	Back alignment and assigned GO terms

UNIPROTKB\|E2QZF6 USP39 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]	Back alignment and assigned GO terms

MGI\|MGI:107622 Usp39 "ubiquitin specific peptidase 39" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

Prediction Level	EC number	Confidence of Prediction
3rd Layer	3.4.19	LOW CONFIDENCE prediction!
3rd Layer	3.4.19.12	LOW CONFIDENCE prediction!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	GSVIVG00010886001	SubName- Full=Chromosome undetermined scaffold_292, whole genome shotgun sequence; (513 aa)
		(Vitis vinifera)
Predicted Functional Partners:
	GSVIVG00028845001	SubName- Full=Chromosome chr1 scaffold_46, whole genome shotgun sequence; (504 aa)	•	•	•	0.729
	GSVIVG00031353001	SubName- Full=Chromosome chr11 scaffold_56, whole genome shotgun sequence; (202 aa)		•	•	0.538
	GSVIVG00025837001	SubName- Full=Chromosome chr12 scaffold_36, whole genome shotgun sequence; (1007 aa)	•	•	•	0.535
	GSVIVG00037110001	SubName- Full=Chromosome chr16 scaffold_86, whole genome shotgun sequence; (512 aa)	•		•	0.476
	GSVIVG00027571001	RecName- Full=Ubiquitin carboxyl-terminal hydrolase; EC=3.1.2.15; (808 aa)	•		•	0.452
	GSVIVG00024530001	SubName- Full=Chromosome chr6 scaffold_3, whole genome shotgun sequence; (454 aa)	•			0.436
	GSVIVG00013856001	SubName- Full=Chromosome chr16 scaffold_10, whole genome shotgun sequence; (98 aa)	•	•		0.436
	GSVIVG00005644001	SubName- Full=Putative uncharacterized protein (Chromosome undetermined scaffold_155, whole gen [...] (988 aa)	•	•		0.435
	GSVIVG00025475001	SubName- Full=Chromosome chr8 scaffold_34, whole genome shotgun sequence; (188 aa)	•	•		0.425
	GSVIVG00005967001	SubName- Full=Chromosome chr4 scaffold_162, whole genome shotgun sequence; (321 aa)	•		•	0.424

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Alignment Graph	Length	Definition	E-value
Query		387
cd02669		440	cd02669, Peptidase_C19M, A subfamily of Peptidase	1e-153
pfam02148		63	pfam02148, zf-UBP, Zn-finger in ubiquitin-hydrolas	3e-23
smart00290		50	smart00290, ZnF_UBP, Ubiquitin Carboxyl-terminal H	2e-17
pfam00443		313	pfam00443, UCH, Ubiquitin carboxyl-terminal hydrol	4e-14
cd02661		304	cd02661, Peptidase_C19E, A subfamily of Peptidase	3e-08
cd02660		328	cd02660, Peptidase_C19D, A subfamily of Peptidase	4e-05
COG5560		823	COG5560, UBP12, Ubiquitin C-terminal hydrolase [Po	3e-04

>gnl\|CDD\|239134 cd02669, Peptidase_C19M, A subfamily of Peptidase C19	Back alignment and domain information

 Score =  439 bits (1132), Expect = e-153
 Identities = 173/309 (55%), Positives = 205/309 (66%), Gaps = 43/309 (13%)

Query: 106 PYLDTVNRQVLDFDFEKFCSVSLSNLNVYACLVCGKYYQGRGQKSHAYTHSLEAGHHVYI 165
           PYLDT+NR VLDFDFEK CSVSLSNLNVYACLVCGKY+QGRG+ SHAYTHSLE  HHV++
Sbjct: 1   PYLDTINRSVLDFDFEKVCSVSLSNLNVYACLVCGKYFQGRGKGSHAYTHSLEDNHHVFL 60

Query: 166 NLRTEKVYCLPDGYEINDPSLEDIRH---------------------------------V 192
           NL T K YCLPD YEI D SL+DI++                                 V
Sbjct: 61  NLETLKFYCLPDNYEIIDSSLDDIKYVLNPTYTKEQISDLDRDPKLSRDLDGKPYLPGFV 120

Query: 193 GLNNIKETDFVNVTIQSLMRVTPLRNFFLIPENYR---HCKSPLVHRFGDLTRKIWHARN 249
           GLNNIK  D+ NV IQ+L  V P+RNFFL+ ENY      KS LV R  +L RKIW+ RN
Sbjct: 121 GLNNIKNNDYANVIIQALSHVKPIRNFFLLYENYENIKDRKSELVKRLSELIRKIWNPRN 180

Query: 250 FKGQVSPHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDL-RNTKKNTSIIYECF 308
           FKG VSPHE LQAV K SKK+F I  QS+PVEF+SWLLNTLH DL  + K N+SII++CF
Sbjct: 181 FKGHVSPHELLQAVSKVSKKKFSITEQSDPVEFLSWLLNTLHKDLGGSKKPNSSIIHDCF 240

Query: 309 QGELEVVKEIPKNTISGNDQNTEKGSDGGDDHDNITTETSRMPFLMLGLDLPPPPLFKDV 368
           QG++++  +  K          E+GS      D+   +TS  PFL+L LDLPPPPLFKD 
Sbjct: 241 QGKVQIETQKIKPHAE------EEGSKDKFFKDSRVKKTSVSPFLLLTLDLPPPPLFKDG 294

Query: 369 MEKNIIPQL 377
            E+NIIPQ+
Sbjct: 295 NEENIIPQV 303

Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. Length = 440

>gnl\|CDD\|216903 pfam02148, zf-UBP, Zn-finger in ubiquitin-hydrolases and other protein	Back alignment and domain information

>gnl\|CDD\|197632 smart00290, ZnF_UBP, Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger	Back alignment and domain information

>gnl\|CDD\|215922 pfam00443, UCH, Ubiquitin carboxyl-terminal hydrolase	Back alignment and domain information

>gnl\|CDD\|239126 cd02661, Peptidase_C19E, A subfamily of Peptidase C19	Back alignment and domain information

>gnl\|CDD\|239125 cd02660, Peptidase_C19D, A subfamily of Peptidase C19	Back alignment and domain information

>gnl\|CDD\|227847 COG5560, UBP12, Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		387
cd02669		440	Peptidase_C19M A subfamily of Peptidase C19. Pepti	100.0
KOG2026		442	consensus Spindle pole body protein - Sad1p [Cytos	100.0
KOG0944		763	consensus Ubiquitin-specific protease UBP14 [Postt	100.0
KOG1873		877	consensus Ubiquitin-specific protease [Posttransla	100.0
COG5207		749	UBP14 Isopeptidase T [Posttranslational modificati	100.0
cd02658		311	Peptidase_C19B A subfamily of Peptidase C19. Pepti	99.96
cd02663		300	Peptidase_C19G A subfamily of Peptidase C19. Pepti	99.96
cd02660		328	Peptidase_C19D A subfamily of Peptidase C19. Pepti	99.96
cd02668		324	Peptidase_C19L A subfamily of Peptidase C19. Pepti	99.96
COG5560		823	UBP12 Ubiquitin C-terminal hydrolase [Posttranslat	99.96
cd02657		305	Peptidase_C19A A subfamily of Peptidase C19. Pepti	99.96
cd02671		332	Peptidase_C19O A subfamily of Peptidase C19. Pepti	99.95
cd02661		304	Peptidase_C19E A subfamily of Peptidase C19. Pepti	99.94
cd02666		343	Peptidase_C19J A subfamily of Peptidase C19. Pepti	99.93
cd02659		334	peptidase_C19C A subfamily of Peptidase C19. Pepti	99.93
cd02664		327	Peptidase_C19H A subfamily of Peptidase C19. Pepti	99.93
cd02667		279	Peptidase_C19K A subfamily of Peptidase C19. Pepti	99.92
KOG1865		545	consensus Ubiquitin carboxyl-terminal hydrolase [P	99.92
KOG1867		492	consensus Ubiquitin-specific protease [Posttransla	99.91
COG5533		415	UBP5 Ubiquitin C-terminal hydrolase [Posttranslati	99.87
cd02662		240	Peptidase_C19F A subfamily of Peptidase C19. Pepti	99.86
PF00443		269	UCH: Ubiquitin carboxyl-terminal hydrolase; InterP	99.85
KOG1868		653	consensus Ubiquitin C-terminal hydrolase [Posttran	99.78
cd02674		230	Peptidase_C19R A subfamily of peptidase C19. Pepti	99.71
COG5077		1089	Ubiquitin carboxyl-terminal hydrolase [Posttransla	99.69
KOG1863		1093	consensus Ubiquitin carboxyl-terminal hydrolase [P	99.67
KOG1870		842	consensus Ubiquitin C-terminal hydrolase [Posttran	99.67
PF02148		63	zf-UBP: Zn-finger in ubiquitin-hydrolases and othe	99.62
cd02673		245	Peptidase_C19Q A subfamily of Peptidase C19. Pepti	99.61
cd02665		228	Peptidase_C19I A subfamily of Peptidase C19. Pepti	99.61
cd02257		255	Peptidase_C19 Peptidase C19 contains ubiquitinyl h	99.58
KOG1866		944	consensus Ubiquitin carboxyl-terminal hydrolase [P	99.52
PF13423		295	UCH_1: Ubiquitin carboxyl-terminal hydrolase	99.49
KOG1871		420	consensus Ubiquitin-specific protease [Posttransla	99.31
KOG2026		442	consensus Spindle pole body protein - Sad1p [Cytos	99.1
cd02672		268	Peptidase_C19P A subfamily of Peptidase C19. Pepti	99.1
smart00290		50	ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like	99.03
KOG0804		493	consensus Cytoplasmic Zn-finger protein BRAP2 (BRC	98.95
KOG4598		1203	consensus Putative ubiquitin-specific protease [Po	98.94
KOG1872		473	consensus Ubiquitin-specific protease [Posttransla	98.93
KOG1864		587	consensus Ubiquitin-specific protease [Posttransla	98.88
cd02670		241	Peptidase_C19N A subfamily of Peptidase C19. Pepti	97.06
KOG1864		587	consensus Ubiquitin-specific protease [Posttransla	97.0
KOG1275		1118	consensus PAB-dependent poly(A) ribonuclease, subu	96.97
PF09416		152	UPF1_Zn_bind: RNA helicase (UPF2 interacting domai	92.66
PF05408		193	Peptidase_C28: Foot-and-mouth virus L-proteinase;	84.26

>cd02669 Peptidase_C19M A subfamily of Peptidase C19	Back alignment and domain information

Probab=100.00  E-value=1.6e-65  Score=526.17  Aligned_cols=270  Identities=64%  Similarity=1.034  Sum_probs=242.0

Q ss_pred             CchhhhcccccCCCCCccccccCCCCceEEecccCcccccCCCCCcccccccccCCceEEecCCCceeecCCCcccCCCC
Q 016557          106 PYLDTVNRQVLDFDFEKFCSVSLSNLNVYACLVCGKYYQGRGQKSHAYTHSLEAGHHVYINLRTEKVYCLPDGYEINDPS  185 (387)
Q Consensus       106 ~~l~ti~~~~Ldfd~ek~Cs~c~s~~nl~~CL~CG~~~cGr~~~sHa~~H~~~~~H~v~inl~t~~vyC~~c~~eV~D~s  185 (387)
                      |||+||||.+|||||||+|++|+++.|+|+||+||+|||||+.++||+.|+.+++|++||++.|++||||||+++|.|++
T Consensus         1 ~yl~ti~r~~ldfd~e~~C~~~~~~~n~~~CL~cg~~~~g~~~~~ha~~H~~~~~H~~~v~l~t~~~yc~~~~~~v~d~~   80 (440)
T cd02669           1 PYLDTINRSVLDFDFEKVCSVSLSNLNVYACLVCGKYFQGRGKGSHAYTHSLEDNHHVFLNLETLKFYCLPDNYEIIDSS   80 (440)
T ss_pred             CchhhhhhhhccccccccccccCCCCcEEEEcccCCeecCCCCCcHHHHHhhccCCCEEEECCCCCEEEeCCCCEEeCcc
Confidence            79999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             cchhcc---------------------------------cccccCCCCcchhhHhhHhhccchhhhhhccCCCcC---CC
Q 016557          186 LEDIRH---------------------------------VGLNNIKETDFVNVTIQSLMRVTPLRNFFLIPENYR---HC  229 (387)
Q Consensus       186 L~~i~~---------------------------------vGL~NlGNTCYmNSVLQ~L~~ip~fr~~~l~~~~~~---~~  229 (387)
                      |++|++                                 +||+|+|||||||||||+|+|+|+||++|+...+..   ..
T Consensus        81 l~~i~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~G~vGL~NlGnTCYmNsvLQ~L~~~p~lr~~~l~~~~~~~~~~~  160 (440)
T cd02669          81 LDDIKYVLNPTYTKEQISDLDRDPKLSRDLDGKPYLPGFVGLNNIKNNDYANVIIQALSHVKPIRNFFLLYENYENIKDR  160 (440)
T ss_pred             HHHHHHHhcCCCCHHHHHHhhhccccccccCCCCccCCccCccCCCCchHHHHHHHHHHCCHHHHHHHhhccccccccCC
Confidence            877652                                 399999999999999999999999999999765432   24


Q ss_pred             CChHHHHHHHHHHHHHhccCCCCCCchHHHHHHHHHhhcCCCCCCCccCHHHHHHHHHHHHHHHhhcC-CCCCccccccc
Q 016557          230 KSPLVHRFGDLTRKIWHARNFKGQVSPHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDLRNT-KKNTSIIYECF  308 (387)
Q Consensus       230 ~~~l~~~L~~L~~~l~s~~~~~~~vsP~~ll~~l~~~s~~~F~~~~QqDA~EFL~~LLn~L~~el~~~-~~~~siI~~~F  308 (387)
                      ..+++++|..+++++|+++.++.+++|.+|+++++..+++.|.++.||||||||+||||.||+++... +...++|+++|
T Consensus       161 ~~~l~~~l~~l~~kl~~~~~~~~~isP~~fl~~l~~~~~~~f~~~~QqDA~EFl~~LLd~L~~~l~~~~~~~~~ii~~~F  240 (440)
T cd02669         161 KSELVKRLSELIRKIWNPRNFKGHVSPHELLQAVSKVSKKKFSITEQSDPVEFLSWLLNTLHKDLGGSKKPNSSIIHDCF  240 (440)
T ss_pred             CcHHHHHHHHHHHHHhccccCCCccCHHHHHHHHHhhcccccCCcccCCHHHHHHHHHHHHHHHhccCCCCCCCcceecc
Confidence            56899999999999999887888999999999999886678999999999999999999999998753 45689999999


Q ss_pred             ceEEEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCccceeeecceeeeecCCCCCChhHHhhhcCccccccCC
Q 016557          309 QGELEVVKEIPKNTISGNDQNTEKGSDGGDDHDNITTETSRMPFLMLGLDLPPPPLFKDVMEKNIIPQLQRLS  381 (387)
Q Consensus       309 ~G~l~~~~~C~~c~~~~~~~~~~~~~~~~~~~~~~~~s~~~epFl~LSLdLP~~p~fkd~le~n~iPqv~l~~  381 (387)
                      +|+++++++|..|....      ..+...|..|+...+++.+|||+|||+||+.|+|+|+...++|||++|.+
T Consensus       241 ~G~l~~~~~c~~~~~~~------~~~~~~~~~c~~~~s~~~~pF~~LsLdip~~~~~~~~~~~~~l~~~~l~e  307 (440)
T cd02669         241 QGKVQIETQKIKPHAEE------EGSKDKFFKDSRVKKTSVSPFLLLTLDLPPPPLFKDGNEENIIPQVPLKQ  307 (440)
T ss_pred             CceEEEEEEeecccccc------cccccccccccccceeeeccceEEEecCCCCccccccccccccCcccHHH
Confidence            99999999999886221      11122456677678899999999999999999999999999999998753

>KOG2026 consensus Spindle pole body protein - Sad1p [Cytoskeleton]	Back alignment and domain information

>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1873 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>cd02658 Peptidase_C19B A subfamily of Peptidase C19	Back alignment and domain information

>cd02663 Peptidase_C19G A subfamily of Peptidase C19	Back alignment and domain information

>cd02660 Peptidase_C19D A subfamily of Peptidase C19	Back alignment and domain information

>cd02668 Peptidase_C19L A subfamily of Peptidase C19	Back alignment and domain information

>COG5560 UBP12 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>cd02657 Peptidase_C19A A subfamily of Peptidase C19	Back alignment and domain information

>cd02671 Peptidase_C19O A subfamily of Peptidase C19	Back alignment and domain information

>cd02661 Peptidase_C19E A subfamily of Peptidase C19	Back alignment and domain information

>cd02666 Peptidase_C19J A subfamily of Peptidase C19	Back alignment and domain information

>cd02659 peptidase_C19C A subfamily of Peptidase C19	Back alignment and domain information

>cd02664 Peptidase_C19H A subfamily of Peptidase C19	Back alignment and domain information

>cd02667 Peptidase_C19K A subfamily of Peptidase C19	Back alignment and domain information

>KOG1865 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1867 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>cd02662 Peptidase_C19F A subfamily of Peptidase C19	Back alignment and domain information

>PF00443 UCH: Ubiquitin carboxyl-terminal hydrolase; InterPro: IPR001394 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families	Back alignment and domain information

>KOG1868 consensus Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>cd02674 Peptidase_C19R A subfamily of peptidase C19	Back alignment and domain information

>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1863 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1870 consensus Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule	Back alignment and domain information

>cd02673 Peptidase_C19Q A subfamily of Peptidase C19	Back alignment and domain information

>cd02665 Peptidase_C19I A subfamily of Peptidase C19	Back alignment and domain information

>cd02257 Peptidase_C19 Peptidase C19 contains ubiquitinyl hydrolases	Back alignment and domain information

>KOG1866 consensus Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF13423 UCH_1: Ubiquitin carboxyl-terminal hydrolase	Back alignment and domain information

>KOG1871 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG2026 consensus Spindle pole body protein - Sad1p [Cytoskeleton]	Back alignment and domain information

>cd02672 Peptidase_C19P A subfamily of Peptidase C19	Back alignment and domain information

>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger	Back alignment and domain information

>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]	Back alignment and domain information

>KOG4598 consensus Putative ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1872 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1864 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>cd02670 Peptidase_C19N A subfamily of Peptidase C19	Back alignment and domain information

>KOG1864 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG1275 consensus PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair]	Back alignment and domain information

>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation	Back alignment and domain information

>PF05408 Peptidase_C28: Foot-and-mouth virus L-proteinase; InterPro: IPR008739 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families	Back alignment and domain information

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Alignment Graph	Length	Definition	E-value
Query		387
3mtn_A		373	Usp21 In Complex With A Ubiquitin-based, Usp21-spec		3e-06
2y5b_A		370	Structure Of Usp21 In Complex With Linear Diubiquit		4e-06
3i3t_A		355	Crystal Structure Of Covalent Ubiquitin-usp21 Compl		4e-06
2y6e_A		367	Ubiquitin Specific Protease 4 Is Inhibited By Its U		4e-06

>pdb|3MTN|A Chain A, Usp21 In Complex With A Ubiquitin-based, Usp21-specific Inhibitor Length = 373

Back alignment and structure

Iteration: 1

Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust. Identities = 36/122 (29%), Positives = 56/122 (45%), Gaps = 12/122 (9%) Query: 191 HVGLNNIKETDFVNVTIQSLMRVTPLRNFFL-------IPENYRHCKSPLVHRFGDLTRK 243 HVGL N+ T F+N +Q L PLR+F L +P R L F D+ Sbjct: 22 HVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGR--AQELTEAFADVIGA 79 Query: 244 IWHARNFKGQVSPHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDL-RNTKKNTS 302 +WH + + V+P F +AV + F Q + EF+ L+ LH ++ R ++ Sbjct: 80 LWHPDSCEA-VNPTRF-RAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPP 137 Query: 303 II 304 I+ Sbjct: 138 IL 139

PyMOL of 3mtn

>pdb|2Y5B|A Chain A, Structure Of Usp21 In Complex With Linear Diubiquitin-Aldehyde Length = 370

Back alignment and structure

>pdb|3I3T|A Chain A, Crystal Structure Of Covalent Ubiquitin-usp21 Complex Length = 355

Back alignment and structure

>pdb|2Y6E|A Chain A, Ubiquitin Specific Protease 4 Is Inhibited By Its Ubiquitin- Like Domain Length = 367

Back alignment and structure

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		387
3ihp_A		854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	2e-35
3c5k_A		109	HD6, histone deacetylase 6; HDAC6, zinc finger, ac	1e-23
2uzg_A		97	Ubiquitin carboxyl-terminal hydrolase 33; UBL conj	3e-19
3mhs_A		476	Ubiquitin carboxyl-terminal hydrolase 8; multi-pro	5e-18
3nhe_A		348	Ubiquitin carboxyl-terminal hydrolase 2; cysteine	1e-15
2gfo_A		396	Ubiquitin carboxyl-terminal hydrolase 8; protease,	5e-15
2g45_A		129	Ubiquitin carboxyl-terminal hydrolase 5; zinc fing	9e-15
2y6e_A		367	Ubiquitin carboxyl-terminal hydrolase 4; HET: CME;	2e-14
2ayn_A		404	Ubiquitin carboxyl-terminal hydrolase 14; deubiqui	5e-13
3i3t_A		355	Ubiquitin carboxyl-terminal hydrolase 21; hydrolas	1e-12
2i50_A		126	Ubiquitin carboxyl-terminal hydrolase 16; alpha/be	3e-11
1nb8_A		353	Ubiquitin carboxyl-terminal hydrolase 7; UBP, deub	5e-09
2f1z_A		522	Ubiquitin carboxyl-terminal hydrolase 7; hausp, US	1e-08
2ida_A		102	Hypothetical protein; zinc binding protein, struct	1e-04
1vt4_I		1221	APAF-1 related killer DARK; drosophila apoptosome,	3e-04
1vjv_A		415	Ubiquitin carboxyl-terminal hydrolase 6; YFR010W,	7e-04

>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {Homo sapiens} Length = 854	Back alignment and structure

 Score =  137 bits (345), Expect = 2e-35
 Identities = 47/363 (12%), Positives = 107/363 (29%), Gaps = 94/363 (25%)

Query: 100 EVRRDCPY---LDTVNRQVLDFDFEKFCSVSLSNLNVYACLVCG------KYYQGRGQKS 150
           EVR+   +   L  ++           CS      N++  L  G      +Y+ G G  +
Sbjct: 191 EVRQVSKHAFSLKQLDNPARIPPCGWKCSKCDMRENLWLNLTDGSILCGRRYFDGSGGNN 250

Query: 151 HAYTHSLEAGHHVYINLRTEK-----VYCLPDGYEINDPSLEDIRH-------------- 191
           HA  H  E G+ + + L T       VY   +   + DPSL +                 
Sbjct: 251 HAVEHYRETGYPLAVKLGTITPDGADVYSYDEDDMVLDPSLAEHLSHFGIDMLKMQKTDK 310

Query: 192 ----------------------------------VGLNNIKETDFVNVTIQSLMRVTPLR 217
                                              G+ N+  + ++N  +Q L  +   +
Sbjct: 311 TMTELEIDMNQRIGEWELIQESGVPLKPLFGPGYTGIRNLGNSCYLNSVVQVLFSIPDFQ 370

Query: 218 NFFL--IPENYRHCKSPLVHRFGDLTRKIWHA----------------------RNFKGQ 253
             ++  + + +++  +     F     K+ H                       +  +  
Sbjct: 371 RKYVDKLEKIFQNAPTDPTQDFSTQVAKLGHGLLSGEYSKPVPESGDGERVPEQKEVQDG 430

Query: 254 VSPHEFLQAVMKASKKRFRIGVQSNPVEFMSWLLNTLHSDLRNTKKNTSIIYECFQGELE 313
           ++P  F   + K     F    Q +  EF   L+N +  + R+++    +     + +++
Sbjct: 431 IAPRMFKALIGK-GHPEFSTNRQQDAQEFFLHLINMVERNCRSSENPNEVFRFLVEEKIK 489

Query: 314 VVKEIPKNTISGNDQNTEKGSDGGDDHDNITTETSRMPFLMLGLDLPPPPLFKDVMEKNI 373
            +        +   + T++          +    ++   L            K  + + +
Sbjct: 490 CLA-------TEKVKYTQRVDYIMQLPVPMDAALNKEELLEYEEKKRQAEEEKMALPELV 542

Query: 374 IPQ 376
             Q
Sbjct: 543 RAQ 545

PyMOL of 3ihp

>3c5k_A HD6, histone deacetylase 6; HDAC6, zinc finger, actin-binding, chromatin regulator, cytoplasm, hydrolase, metal-binding, nucleus, phosphoprotein; 1.55A {Homo sapiens} PDB: 3gv4_A 3phd_A Length = 109	Back alignment and structure

>3mhs_A Ubiquitin carboxyl-terminal hydrolase 8; multi-protein complex, hydrolase-transcription regulator-Pro binding complex, acetylation, cytoplasm; 1.89A {Saccharomyces cerevisiae} PDB: 3mhh_A 3m99_A Length = 476	Back alignment and structure

>3nhe_A Ubiquitin carboxyl-terminal hydrolase 2; cysteine protease, substrate ENZY complex, hydrolase-protein binding complex; HET: CME; 1.26A {Homo sapiens} PDB: 2hd5_A 2ibi_A Length = 348	Back alignment and structure

>2gfo_A Ubiquitin carboxyl-terminal hydrolase 8; protease, thiol protease, UBL conjugation pathway deubiquitinating enzyme, DUB, zinc ribbon; 2.00A {Homo sapiens} SCOP: d.3.1.9 PDB: 3n3k_A Length = 396	Back alignment and structure

>2g45_A Ubiquitin carboxyl-terminal hydrolase 5; zinc finger, hydrolase; 1.99A {Homo sapiens} SCOP: g.44.1.5 PDB: 2g43_A 2l80_A Length = 129	Back alignment and structure

>2y6e_A Ubiquitin carboxyl-terminal hydrolase 4; HET: CME; 2.40A {Homo sapiens} Length = 367	Back alignment and structure

>2ayn_A Ubiquitin carboxyl-terminal hydrolase 14; deubiquitinating enzymes, DUB, USP14, proteasome, enzyme mechanism; 3.20A {Homo sapiens} SCOP: d.3.1.9 PDB: 2ayo_A Length = 404	Back alignment and structure

>3i3t_A Ubiquitin carboxyl-terminal hydrolase 21; hydrolase, structural genomics consortium, SGC, activator, alternative splicing, chromatin regulator, nucleus, polymorphism, protease; 2.59A {Homo sapiens} PDB: 2y5b_A 3mtn_A Length = 355	Back alignment and structure

>2i50_A Ubiquitin carboxyl-terminal hydrolase 16; alpha/beta zinc-finger, ring-finger, ZNF-UBP, metalloprotein, ubiquitin-binding protein, USP; NMR {Homo sapiens} Length = 126	Back alignment and structure

>1nb8_A Ubiquitin carboxyl-terminal hydrolase 7; UBP, deubiquitination, hausp, P53 binding; 2.30A {Homo sapiens} SCOP: d.3.1.9 PDB: 1nbf_A Length = 353	Back alignment and structure

>2f1z_A Ubiquitin carboxyl-terminal hydrolase 7; hausp, USP7, UBP, deubiquitinating enzyme, substrate recognition; 3.20A {Homo sapiens} Length = 522	Back alignment and structure

>2ida_A Hypothetical protein; zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Rhodopseudomonas palustris} SCOP: g.44.1.5 Length = 102	Back alignment and structure

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221	Back alignment and structure

>1vjv_A Ubiquitin carboxyl-terminal hydrolase 6; YFR010W, structural genomics, JCSG, PSI, protein structure initiative; HET: MSE; 1.74A {Saccharomyces cerevisiae} SCOP: d.3.1.9 Length = 415	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		387
3mhs_A		476	Ubiquitin carboxyl-terminal hydrolase 8; multi-pro	100.0
3ihp_A		854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	100.0
2y6e_A		367	Ubiquitin carboxyl-terminal hydrolase 4; HET: CME;	99.98
2gfo_A		396	Ubiquitin carboxyl-terminal hydrolase 8; protease,	99.97
3i3t_A		355	Ubiquitin carboxyl-terminal hydrolase 21; hydrolas	99.97
3nhe_A		348	Ubiquitin carboxyl-terminal hydrolase 2; cysteine	99.97
1nb8_A		353	Ubiquitin carboxyl-terminal hydrolase 7; UBP, deub	99.96
2ayn_A		404	Ubiquitin carboxyl-terminal hydrolase 14; deubiqui	99.96
1vjv_A		415	Ubiquitin carboxyl-terminal hydrolase 6; YFR010W,	99.95
2f1z_A		522	Ubiquitin carboxyl-terminal hydrolase 7; hausp, US	99.95
3c5k_A		109	HD6, histone deacetylase 6; HDAC6, zinc finger, ac	99.86
2uzg_A		97	Ubiquitin carboxyl-terminal hydrolase 33; UBL conj	99.79
2g45_A		129	Ubiquitin carboxyl-terminal hydrolase 5; zinc fing	99.75
2ida_A		102	Hypothetical protein; zinc binding protein, struct	99.53
2i50_A		126	Ubiquitin carboxyl-terminal hydrolase 16; alpha/be	99.49
2vhf_A		374	Ubiquitin carboxyl-terminal hydrolase CYLD; cytoki	99.43
2xzl_A		802	ATP-dependent helicase NAM7; hydrolase-RNA complex	83.96
3mp2_A		211	Non-structural protein 3; papain-like protease, TG	81.71
3ihp_A		854	Ubiquitin carboxyl-terminal hydrolase 5; hydrolase	81.16

>3mhs_A Ubiquitin carboxyl-terminal hydrolase 8; multi-protein complex, hydrolase-transcription regulator-Pro binding complex, acetylation, cytoplasm; 1.89A {Saccharomyces cerevisiae} PDB: 3mhh_A 4fjc_A 4fk5_A 4fip_A 3m99_A	Back alignment and structure

Probab=100.00  E-value=1.4e-46  Score=385.76  Aligned_cols=231  Identities=21%  Similarity=0.286  Sum_probs=194.1

Q ss_pred             cccccCCC--CceEEecccCcccccCCCCCcccccccccCCceEEecCCCceeecCCCcccCCCCcchh-----------
Q 016557          123 FCSVSLSN--LNVYACLVCGKYYQGRGQKSHAYTHSLEAGHHVYINLRTEKVYCLPDGYEINDPSLEDI-----------  189 (387)
Q Consensus       123 ~Cs~c~s~--~nl~~CL~CG~~~cGr~~~sHa~~H~~~~~H~v~inl~t~~vyC~~c~~eV~D~sL~~i-----------  189 (387)
                      .|+.|...  .++|+||+||  ++||+.++||+.|+.+++|+++|++.++.||||+|+++|+|+.|...           
T Consensus        50 ~C~~c~~~~~~~~~~cl~cg--~~~c~~~~h~~~H~~~~~h~~~~~~~~~~~~c~~~~~~v~d~~l~~~~~~~~~~~~~~  127 (476)
T 3mhs_A           50 KCGTCHEINSGATFMCLQCG--FCGCWNHSHFLSHSKQIGHIFGINSNNGLLFCFKCEDYIGNIDLINDAILAKYWDDVC  127 (476)
T ss_dssp             BCTTTCCBCSSSEEEESSSS--CEEETTTTHHHHHHHHHCCCEEEETTTCCEEETTTTEEECSCHHHHTGGGGGGHHHHH
T ss_pred             CcccccCCCCCCceEeCCCC--CCccCCchHHHHHhcccCCcEEEECCCCcEEeCCCCCCcccHHHHHHHHhhhccchhh
Confidence            59999876  8999999999  66666799999999999999999999999999999999999865320           


Q ss_pred             ------------cccccccCCCCcchhhHhhHhhccchhhhhhccCCC-----cCCCCChHHHHHHHHHHHHHhccCC--
Q 016557          190 ------------RHVGLNNIKETDFVNVTIQSLMRVTPLRNFFLIPEN-----YRHCKSPLVHRFGDLTRKIWHARNF--  250 (387)
Q Consensus       190 ------------~~vGL~NlGNTCYmNSVLQ~L~~ip~fr~~~l~~~~-----~~~~~~~l~~~L~~L~~~l~s~~~~--  250 (387)
                                  +++||.|+|||||||||||+|+|+|+||++|+...+     ......++.++|..+++++|+....  
T Consensus       128 ~~~~~~~~~~~~G~~GL~NlGNTCYmNSvLQ~L~~~p~fr~~~l~~~~~~~~~~~~~~~~l~~~l~~l~~~l~~~~~~~~  207 (476)
T 3mhs_A          128 TKTMVPSMERRDGLSGLINMGSTCFMSSILQCLIHNPYFIRHSMSQIHSNNCKVRSPDKCFSCALDKIVHELYGALNTKQ  207 (476)
T ss_dssp             HHEECCCGGGTTCCCCCCCSSSTHHHHHHHHHHHTCHHHHHHHHTTHHHHHCSSCCTTTCHHHHHHHHHHHHHSCCCC--
T ss_pred             hcccCCCccCCCCCCCCCcCCccHHHHHHHHHHhCCHHHHHHHHhcchhhhccCCCcccchHHHHHHHHHHHhhcccccc
Confidence                        135999999999999999999999999999986432     1233567999999999999985432  


Q ss_pred             -----CCCCchHHHHHH---HHHhhcCCCCCCCccCHHHHHHHHHHHHHHHhhcC------------CCCCcccccccce
Q 016557          251 -----KGQVSPHEFLQA---VMKASKKRFRIGVQSNPVEFMSWLLNTLHSDLRNT------------KKNTSIIYECFQG  310 (387)
Q Consensus       251 -----~~~vsP~~ll~~---l~~~s~~~F~~~~QqDA~EFL~~LLn~L~~el~~~------------~~~~siI~~~F~G  310 (387)
                           ...+.|..++..   +++. .+.|.++.||||||||++||+.||+++...            ....++|+++|+|
T Consensus       208 ~~~~~~~~~~~~~~~~~l~~~~~~-~~~f~~~~QqDA~EFl~~LLd~L~~~~~~~~~~~~~~~~~~~~~~~s~i~~~F~G  286 (476)
T 3mhs_A          208 ASSSSTSTNRQTGFIYLLTCAWKI-NQNLAGYSQQDAHEFWQFIINQIHQSYVLDLPNAKEVSRANNKQCECIVHTVFEG  286 (476)
T ss_dssp             ------CCCSCHHHHHHHHHHHHH-CGGGSSSSCEEHHHHHHHHHHHHHHHHHHHCCC-------CCCSCCSHHHHHSCE
T ss_pred             cccccccccCcchHHHHHHHHHHh-ccccCCCCCcCHHHHHHHHHHHHHHHHhhcccccccccccccccCCCcceeecce
Confidence                 124566665554   4455 589999999999999999999999987531            2346799999999


Q ss_pred             EEEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCccc-eeeecceeeeecCCCCCChhHHhhhcCcccc
Q 016557          311 ELEVVKEIPKNTISGNDQNTEKGSDGGDDHDNITTE-TSRMPFLMLGLDLPPPPLFKDVMEKNIIPQL  377 (387)
Q Consensus       311 ~l~~~~~C~~c~~~~~~~~~~~~~~~~~~~~~~~~s-~~~epFl~LSLdLP~~p~fkd~le~n~iPqv  377 (387)
                      +++++++|..|+                     ..+ ++.+||++|+|+||+...+.++++....|++
T Consensus       287 ~l~~~~~C~~C~---------------------~~s~~~~e~f~~LsL~i~~~~sl~~~L~~~~~~E~  333 (476)
T 3mhs_A          287 SLESSIVCPGCQ---------------------NNSKTTIDPFLDLSLDIKDKKKLYECLDSFHKKEQ  333 (476)
T ss_dssp             EEEEEEECTTTC---------------------CCCEEEEEEESCEEECCTTCCBHHHHHHHHHCCEE
T ss_pred             EEEEEEEECCCC---------------------CeeCCcccchhhhccchhhhhHHHHHHHHhcChhh
Confidence            999999999997                     454 5689999999999999999999999888887

PyMOL of 3mhs

>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {Homo sapiens}	Back alignment and structure

>2y6e_A Ubiquitin carboxyl-terminal hydrolase 4; HET: CME; 2.40A {Homo sapiens}	Back alignment and structure

>2gfo_A Ubiquitin carboxyl-terminal hydrolase 8; protease, thiol protease, UBL conjugation pathway deubiquitinating enzyme, DUB, zinc ribbon; 2.00A {Homo sapiens} SCOP: d.3.1.9 PDB: 3n3k_A	Back alignment and structure

>3i3t_A Ubiquitin carboxyl-terminal hydrolase 21; hydrolase, structural genomics consortium, SGC, activator, alternative splicing, chromatin regulator, nucleus, polymorphism, protease; 2.59A {Homo sapiens} SCOP: d.3.1.0 PDB: 2y5b_A 3mtn_A	Back alignment and structure

>3nhe_A Ubiquitin carboxyl-terminal hydrolase 2; cysteine protease, substrate ENZY complex, hydrolase-protein binding complex; HET: CME; 1.26A {Homo sapiens} SCOP: d.3.1.9 PDB: 2hd5_A 3v6c_A 3v6e_A 2ibi_A	Back alignment and structure

>1nb8_A Ubiquitin carboxyl-terminal hydrolase 7; UBP, deubiquitination, hausp, P53 binding; 2.30A {Homo sapiens} SCOP: d.3.1.9 PDB: 1nbf_A	Back alignment and structure

>2ayn_A Ubiquitin carboxyl-terminal hydrolase 14; deubiquitinating enzymes, DUB, USP14, proteasome, enzyme mechanism; 3.20A {Homo sapiens} SCOP: d.3.1.9 PDB: 2ayo_A	Back alignment and structure

>1vjv_A Ubiquitin carboxyl-terminal hydrolase 6; YFR010W, structural genomics, JCSG, PSI, protein structure initiative; HET: MSE; 1.74A {Saccharomyces cerevisiae} SCOP: d.3.1.9	Back alignment and structure

>2f1z_A Ubiquitin carboxyl-terminal hydrolase 7; hausp, USP7, UBP, deubiquitinating enzyme, substrate recognition; 3.20A {Homo sapiens}	Back alignment and structure

>3c5k_A HD6, histone deacetylase 6; HDAC6, zinc finger, actin-binding, chromatin regulator, cytoplasm, hydrolase, metal-binding, nucleus, phosphoprotein; 1.55A {Homo sapiens} PDB: 3gv4_A 3phd_A	Back alignment and structure

>2g45_A Ubiquitin carboxyl-terminal hydrolase 5; zinc finger, hydrolase; 1.99A {Homo sapiens} SCOP: g.44.1.5 PDB: 2g43_A 2l80_A	Back alignment and structure

>2ida_A Hypothetical protein; zinc binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Rhodopseudomonas palustris} SCOP: g.44.1.5	Back alignment and structure

>2i50_A Ubiquitin carboxyl-terminal hydrolase 16; alpha/beta zinc-finger, ring-finger, ZNF-UBP, metalloprotein, ubiquitin-binding protein, USP; NMR {Homo sapiens}	Back alignment and structure

>2vhf_A Ubiquitin carboxyl-terminal hydrolase CYLD; cytokine signalling, linkage specificity, deubiquitinating enzyme, Lys63- linked, anti-oncogene; 2.8A {Homo sapiens}	Back alignment and structure

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}	Back alignment and structure

>3mp2_A Non-structural protein 3; papain-like protease, TGEV, hydrolase; 2.50A {Porcine transmissible gastroenteritiscoronavirus}	Back alignment and structure

>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol protease, UBL conjugation pathway, metal-binding, zinc-finger,structural genomics; 2.80A {Homo sapiens}	Back alignment and structure

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Alignment Graph	Length	Definition	E-value
Query		387
d2uzga1		95	g.44.1.5 (A:36-130) Ubiquitin carboxyl-terminal hy	3e-24
d2g45a1		113	g.44.1.5 (A:173-285) Ubiquitin carboxyl-terminal h	5e-17
d2hd5a1		336	d.3.1.9 (A:211-521) Ubiquitin carboxyl-terminal hy	3e-13
d2ayna1		383	d.3.1.9 (A:100-482) Ubiquitin carboxyl-terminal hy	3e-12
d2gfoa1		348	d.3.1.9 (A:762-1109) Ubiquitin carboxyl-terminal h	9e-11
d1vjva_		397	d.3.1.9 (A:) Ubiquitin carboxyl-terminal hydrolase	2e-08
d1nbfa_		347	d.3.1.9 (A:) Ubiquitin carboxyl-terminal hydrolase	3e-08
d2idaa1		102	g.44.1.5 (A:1-102) Hypothetical protein RPA1320 {R	6e-06

>d2uzga1 g.44.1.5 (A:36-130) Ubiquitin carboxyl-terminal hydrolase 33, UBP33 {Human (Homo sapiens) [TaxId: 9606]} Length = 95	Back information, alignment and structure


class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Zf-UBP
domain: Ubiquitin carboxyl-terminal hydrolase 33, UBP33
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 93.5 bits (232), Expect = 3e-24
 Identities = 25/92 (27%), Positives = 38/92 (41%), Gaps = 7/92 (7%)

Query: 102 RRDCPYLDTVNR----QVLDFDFEKFCSVSLSNLNVYACL--VCGKYYQGRGQKSHAYTH 155
           R  CP+LD+V       ++           +   N++ACL   C     G  Q  H+  H
Sbjct: 1   RNHCPHLDSVGEITKEDLIQKSLGTCQDCKVQGPNLWACLENRCSYVGCGESQVDHSTIH 60

Query: 156 SLEAGHHVYINLRTEKVYC-LPDGYEINDPSL 186
           S E  H++ +NL T +V+C         D  L
Sbjct: 61  SQETKHYLTVNLTTLRVWCYACSKEVFLDRKL 92

PyMOL of d2uzga1

>d2g45a1 g.44.1.5 (A:173-285) Ubiquitin carboxyl-terminal hydrolase 5, UBP5 {Human (Homo sapiens) [TaxId: 9606]} Length = 113	Back information, alignment and structure

>d2hd5a1 d.3.1.9 (A:211-521) Ubiquitin carboxyl-terminal hydrolase 2, USP2 {Human (Homo sapiens) [TaxId: 9606]} Length = 336	Back information, alignment and structure

>d2ayna1 d.3.1.9 (A:100-482) Ubiquitin carboxyl-terminal hydrolase 14 {Human (Homo sapiens) [TaxId: 9606]} Length = 383	Back information, alignment and structure

>d2gfoa1 d.3.1.9 (A:762-1109) Ubiquitin carboxyl-terminal hydrolase 8 {Human (Homo sapiens) [TaxId: 9606]} Length = 348	Back information, alignment and structure

>d1vjva_ d.3.1.9 (A:) Ubiquitin carboxyl-terminal hydrolase 6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 397	Back information, alignment and structure

>d1nbfa_ d.3.1.9 (A:) Ubiquitin carboxyl-terminal hydrolase 7 (USP7, HAUSP) {Human (Homo sapiens) [TaxId: 9606]} Length = 347	Back information, alignment and structure

>d2idaa1 g.44.1.5 (A:1-102) Hypothetical protein RPA1320 {Rhodopseudomonas palustris [TaxId: 1076]} Length = 102	Back information, alignment and structure

Homologous Domains Detected by HHsearch

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

ID	Alignment Graph	Length	Definition	Probability
Query		387
d1nbfa_		347	Ubiquitin carboxyl-terminal hydrolase 7 (USP7, HAU	99.94
d2ayna1		383	Ubiquitin carboxyl-terminal hydrolase 14 {Human (H	99.91
d2gfoa1		348	Ubiquitin carboxyl-terminal hydrolase 8 {Human (Ho	99.9
d2hd5a1		336	Ubiquitin carboxyl-terminal hydrolase 2, USP2 {Hum	99.9
d1vjva_		397	Ubiquitin carboxyl-terminal hydrolase 6 {Baker's y	99.85
d2uzga1		95	Ubiquitin carboxyl-terminal hydrolase 33, UBP33 {H	99.72
d2g45a1		113	Ubiquitin carboxyl-terminal hydrolase 5, UBP5 {Hum	99.66
d2idaa1		102	Hypothetical protein RPA1320 {Rhodopseudomonas pal	99.39

>d1nbfa_ d.3.1.9 (A:) Ubiquitin carboxyl-terminal hydrolase 7 (USP7, HAUSP) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: Cysteine proteinases
superfamily: Cysteine proteinases
family: Ubiquitin carboxyl-terminal hydrolase, UCH
domain: Ubiquitin carboxyl-terminal hydrolase 7 (USP7, HAUSP)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.94  E-value=2.4e-27  Score=230.07  Aligned_cols=160  Identities=14%  Similarity=0.156  Sum_probs=138.5

Q ss_pred             cccccccCCCCcchhhHhhHhhccchhhhhhccCCCc-CCCCChHHHHHHHHHHHHHhccCCCCCCchHHHHHHHHHhhc
Q 016557          190 RHVGLNNIKETDFVNVTIQSLMRVTPLRNFFLIPENY-RHCKSPLVHRFGDLTRKIWHARNFKGQVSPHEFLQAVMKASK  268 (387)
Q Consensus       190 ~~vGL~NlGNTCYmNSVLQ~L~~ip~fr~~~l~~~~~-~~~~~~l~~~L~~L~~~l~s~~~~~~~vsP~~ll~~l~~~s~  268 (387)
                      +++||.|+|||||||||||+|+++|+||++++..... .....++..+|..||..|+.+.   ..+.|..++..+.   .
T Consensus         5 G~vGL~NlGNTCy~NSvLQ~L~~~~~f~~~i~~~~~~~~~~~~~~~~~l~~lf~~l~~~~---~~~~~~~~~~~~~---~   78 (347)
T d1nbfa_           5 GYVGLKNQGATCYMNSLLQTLFFTNQLRKAVYMMPTEGDDSSKSVPLALQRVFYELQHSD---KPVGTKKLTKSFG---W   78 (347)
T ss_dssp             SCCCBCCCSSCHHHHHHHHHHHTSHHHHHHHHTSCCTTCCTTTCHHHHHHHHHHHHHHCS---SCBCCHHHHHHTT---C
T ss_pred             CCcCCeeCCcchHHHHHHHHHHcCHHHHHHHHhCCccCCcccchHHHHHHHHHHHHhcCC---CCcChHHHHHhhc---h
Confidence            4689999999999999999999999999999865422 2344678999999999999863   5789999988773   3


Q ss_pred             CCCCCCCccCHHHHHHHHHHHHHHHhhcCCCCCcccccccceEEEEEEEccCCCCCCCCCCCCCCCCCCCCCCCCcccee
Q 016557          269 KRFRIGVQSNPVEFMSWLLNTLHSDLRNTKKNTSIIYECFQGELEVVKEIPKNTISGNDQNTEKGSDGGDDHDNITTETS  348 (387)
Q Consensus       269 ~~F~~~~QqDA~EFL~~LLn~L~~el~~~~~~~siI~~~F~G~l~~~~~C~~c~~~~~~~~~~~~~~~~~~~~~~~~s~~  348 (387)
                      +.|..+.||||+|||.+||+.|++++... ...++|.++|+|++.+.++|..|+                     ..+.+
T Consensus        79 ~~~~~~~qqDa~Ef~~~ll~~l~~~~~~~-~~~~~i~~lF~g~~~~~~~C~~C~---------------------~~s~~  136 (347)
T d1nbfa_          79 ETLDSFMQHDVQELCRVLLDNVENKMKGT-CVEGTIPKLFRGKMVSYIQCKEVD---------------------YRSDR  136 (347)
T ss_dssp             CGGGGGSCBCHHHHHHHHHHHHHHHHTTS-TTTTHHHHHHCEEEEEEEEESSSC---------------------CEEEE
T ss_pred             hhcchHHHHHHHHHHHHHHHHHHHHHhhc-cccccccceeceEEEEeEEeCCcc---------------------ceeee
Confidence            56888999999999999999999998543 345789999999999999999998                     78889


Q ss_pred             eecceeeeecCCCCCChhHHhhhcCcccc
Q 016557          349 RMPFLMLGLDLPPPPLFKDVMEKNIIPQL  377 (387)
Q Consensus       349 ~epFl~LSLdLP~~p~fkd~le~n~iPqv  377 (387)
                      .++|+.|+|++|....+.++++..+.|+.
T Consensus       137 ~e~f~~l~L~i~~~~~~~~~l~~~~~~e~  165 (347)
T d1nbfa_         137 REDYYDIQLSIKGKKNIFESFVDYVAVEQ  165 (347)
T ss_dssp             EEEESSEEEECTTCCBHHHHHHHHTCCEE
T ss_pred             eccccccccccccccchhhhHHhhcchhe
Confidence            99999999999999999999988877765

PyMOL of d1nbfa_

>d2ayna1 d.3.1.9 (A:100-482) Ubiquitin carboxyl-terminal hydrolase 14 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2gfoa1 d.3.1.9 (A:762-1109) Ubiquitin carboxyl-terminal hydrolase 8 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2hd5a1 d.3.1.9 (A:211-521) Ubiquitin carboxyl-terminal hydrolase 2, USP2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1vjva_ d.3.1.9 (A:) Ubiquitin carboxyl-terminal hydrolase 6 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2uzga1 g.44.1.5 (A:36-130) Ubiquitin carboxyl-terminal hydrolase 33, UBP33 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2g45a1 g.44.1.5 (A:173-285) Ubiquitin carboxyl-terminal hydrolase 5, UBP5 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2idaa1 g.44.1.5 (A:1-102) Hypothetical protein RPA1320 {Rhodopseudomonas palustris [TaxId: 1076]}	Back information, alignment and structure