Citrus Sinensis ID: 040719

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-----

MVRFLTERRCVAPLTLDDVDDVGDCYEGNSVRTMPYLKLPQPRIRLSVLKLDGSRFDVYIERNATVGELRQAIEEVFTLSPTEGQGKISWTNVWGHFCLCYDGRKLVNDKTHIRDFRMKDGDELQFSRHMSLDYLHSKRRSKTQNVACQQFSRLSVESDTCEQAVLAKDNLEDQHKRLSPGSDADEEKKHDLADRDSLGNQDDSY

cccccccccccccccccccccccccccccccccccccccccccEEEEEEEEcccEEEEEEcccccHHHHHHHHHHHHcccccccccEEEEcEEcccEEEEEccEEEccccHHHcccccccccEEEEEEEccccccccccccccccccccccccccccccHHHHHHHHcccHHHHHccccccccccHHHHHHHHHHcccccccccc

ccEEEEccccccccccccccccccHHccccHHHcHccccccccEEEEEEEEcccEEEEEEEccccHHHHHHHHHHHHHHcHHccccEEEHHHHHcEEEEEEcccEccccHHHHHHcccccccEEEEEEEEEccccccccccccccEcHccccccccccccccEHEcccccHHHHHccccccccccHccHcccccccccccccccc

mvrflterrcvapltlddvddvgdcyegnsvrtmpylklpqprirlsvlkldgsrfdvyIERNATVGELRQAIEEVftlsptegqgkiswtnvwghfclcydgrklvndkthirdfrmkdgdelqfsRHMSLDYLHSKRRSKTQNVACQqfsrlsvesdtCEQAVLAKDNledqhkrlspgsdadeekkhdladrdslgnqddsy

mvrflterrcvapltlddvddvgDCYEgnsvrtmpylklpqprIRLSVLKLDGSRFDVYIERNATVGELRQAIEEVFTLSPTEGQGKISWTNVWGHFCLCYDGRKLVNDKTHIRDFrmkdgdelqfSRHMSLDYLHSKRRSKTQNVACQQFSRLSVESDTCEQAVLakdnledqhkrlspgsdadeekkhdladrdslgnqddsy

***FLTERRCVAPLTLDDVDDVGDCYEGNSVRTMPYLKLPQPRIRLSVLKLDGSRFDVYIERNATVGELRQAIEEVFTLSPTEGQGKISWTNVWGHFCLCYDGRKLVNDKTHIRDFRMK**************************************************************************************

*******RRCVAPLTLDDVDDVGDCYEGNSVRTMPYLKLPQPRIRLSVLKLDGSRFDVYIERNATVGELRQAIEEVF**********ISWTNVWGHFCLCYDGRKLVNDKTHIRDFRMKDGDELQFS******************************************************************************

MVRFLTERRCVAPLTLDDVDDVGDCYEGNSVRTMPYLKLPQPRIRLSVLKLDGSRFDVYIERNATVGELRQAIEEVFTLSPTEGQGKISWTNVWGHFCLCYDGRKLVNDKTHIRDFRMKDGDELQFSRHMSLDYL**********VA*Q*FSRLSVESDTCEQAVLAKDNLEDQ*K*****************************

ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii

SSSSSSSSSSSSSSSSSSSSSiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo

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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		205	2.2.26 [Sep-21-2011]
Q8VIK1		123	U11/U12 small nuclear rib	yes	no	0.414	0.691	0.333	4e-07
Q3ZBQ4		123	U11/U12 small nuclear rib	yes	no	0.414	0.691	0.333	6e-07
Q9BV90		132	U11/U12 small nuclear rib	yes	no	0.404	0.628	0.329	2e-06

>sp\|Q8VIK1\|SNR25_MOUSE U11/U12 small nuclear ribonucleoprotein 25 kDa protein OS=Mus musculus GN=Snrnp25 PE=1 SV=1	Back alignment and function desciption

 Score = 55.1 bits (131), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 29/87 (33%), Positives = 48/87 (55%), Gaps = 2/87 (2%)

Query: 46  LSVLKLDGSRFDVYIERNATVGELRQAIEEVFTLSPTE--GQGKISWTNVWGHFCLCYDG 103
           + V K+DG    V + +NATV +L++AI+    L      G   ISW+ VW  + L   G
Sbjct: 34  VRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAG 93

Query: 104 RKLVNDKTHIRDFRMKDGDELQFSRHM 130
            KL  D+  +RD+ +++ DE+ F + +
Sbjct: 94  EKLTEDRKKLRDYGIRNRDEVSFIKKL 120

Mus musculus (taxid: 10090)

>sp\|Q3ZBQ4\|SNR25_BOVIN U11/U12 small nuclear ribonucleoprotein 25 kDa protein OS=Bos taurus GN=SNRNP25 PE=2 SV=2	Back alignment and function description

>sp\|Q9BV90\|SNR25_HUMAN U11/U12 small nuclear ribonucleoprotein 25 kDa protein OS=Homo sapiens GN=SNRNP25 PE=1 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		205
255553225		274	conserved hypothetical protein [Ricinus	0.887	0.664	0.464	1e-34
15220048		243	ubiquitin-like domain-containing protein	0.839	0.707	0.423	7e-33
297839931		243	hypothetical protein ARALYDRAFT_895992 [	0.741	0.625	0.462	2e-32
297743473		630	unnamed protein product [Vitis vinifera]	0.570	0.185	0.564	3e-32
225442930		232	PREDICTED: uncharacterized protein LOC10	0.575	0.508	0.559	3e-32
449469242		243	PREDICTED: uncharacterized protein LOC10	0.760	0.641	0.457	2e-30
388501394		226	unknown [Medicago truncatula]	0.648	0.588	0.470	9e-30
449520183		277	PREDICTED: uncharacterized LOC101219460	0.663	0.490	0.485	1e-29
357437001		266	U11/U12 small nuclear ribonucleoprotein	0.648	0.5	0.470	2e-29
15239396		208	ubiquitin-like domain-containing protein	0.560	0.552	0.542	1e-28

>gi\|255553225\|ref\|XP_002517655.1\| conserved hypothetical protein [Ricinus communis] gi\|223543287\|gb\|EEF44819.1\| conserved hypothetical protein [Ricinus communis]	Back alignment and taxonomy information

 Score =  151 bits (382), Expect = 1e-34,   Method: Compositional matrix adjust.
 Identities = 91/196 (46%), Positives = 128/196 (65%), Gaps = 14/196 (7%)

Query: 1   MVRFLTERRC-VAPLTLD-DVDDVGDCYEGNSVRTMPYLKLPQPRIRLSVLKLDGSRFDV 58
           +++ + ERRC ++PL+L  D DD  +   G  VR   YLKLPQ  ++L+VLKLDGS FDV
Sbjct: 29  ILKVIIERRCGLSPLSLKVDEDDAVNGNGGLVVRRYSYLKLPQQLLKLTVLKLDGSSFDV 88

Query: 59  YIERNATVGELRQAIEEVFTLSPTEGQGKISWTNVWGHFCLCYDGRKLVNDKTHIRDFRM 118
            I RNATV EL+QA+EE+F+ SP EG  KISW+ VWGHFCL Y+ +KL+NDK  IR+F +
Sbjct: 89  NIGRNATVAELKQAVEEIFSSSPEEGHDKISWSLVWGHFCLSYENQKLINDKVCIRNFGI 148

Query: 119 KDGDELQFSRHMSLDYLHSKRRSKTQNVACQQFSRLSVESDTCEQAVLAKDNLEDQHKRL 178
           KDGD+LQF RHMS++Y +S R+S +QN   +     S ++           N+E + K  
Sbjct: 149 KDGDQLQFIRHMSINYSNS-RQSTSQNAVRKSLGPPSKDA-----------NVEKEQKTT 196

Query: 179 SPGSDADEEKKHDLAD 194
              +  +E + ++L D
Sbjct: 197 EDHTSMNENQDYNLYD 212

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Class:

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi\|15220048\|ref\|NP_178123.1\| ubiquitin-like domain-containing protein kinase [Arabidopsis thaliana] gi\|54261721\|gb\|AAV31164.1\| At1g80060 [Arabidopsis thaliana] gi\|58331795\|gb\|AAW70395.1\| At1g80060 [Arabidopsis thaliana] gi\|332198231\|gb\|AEE36352.1\| ubiquitin-like domain-containing protein kinase [Arabidopsis thaliana]	Back alignment and taxonomy information

>gi\|297839931\|ref\|XP_002887847.1\| hypothetical protein ARALYDRAFT_895992 [Arabidopsis lyrata subsp. lyrata] gi\|297333688\|gb\|EFH64106.1\| hypothetical protein ARALYDRAFT_895992 [Arabidopsis lyrata subsp. lyrata]	Back alignment and taxonomy information

>gi\|297743473\|emb\|CBI36340.3\| unnamed protein product [Vitis vinifera]	Back alignment and taxonomy information

>gi\|225442930\|ref\|XP_002265295.1\| PREDICTED: uncharacterized protein LOC100262712 [Vitis vinifera]	Back alignment and taxonomy information

>gi\|449469242\|ref\|XP_004152330.1\| PREDICTED: uncharacterized protein LOC101206096 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|388501394\|gb\|AFK38763.1\| unknown [Medicago truncatula]	Back alignment and taxonomy information

>gi\|449520183\|ref\|XP_004167113.1\| PREDICTED: uncharacterized LOC101219460 [Cucumis sativus]	Back alignment and taxonomy information

>gi\|357437001\|ref\|XP_003588776.1\| U11/U12 small nuclear ribonucleoprotein 25 kDa protein [Medicago truncatula] gi\|355477824\|gb\|AES59027.1\| U11/U12 small nuclear ribonucleoprotein 25 kDa protein [Medicago truncatula]	Back alignment and taxonomy information

>gi\|15239396\|ref\|NP_197916.1\| ubiquitin-like domain-containing protein-like protein [Arabidopsis thaliana] gi\|26451503\|dbj\|BAC42849.1\| unknown protein [Arabidopsis thaliana] gi\|28973251\|gb\|AAO63950.1\| unknown protein [Arabidopsis thaliana] gi\|332006045\|gb\|AED93428.1\| ubiquitin-like domain-containing protein-like protein [Arabidopsis thaliana]	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		205
TAIR\|locus:2016244		243	AT1G80060 "AT1G80060" [Arabido	0.765	0.646	0.460	4.6e-34
TAIR\|locus:2145502		208	AT5G25340 "AT5G25340" [Arabido	0.560	0.552	0.542	4.4e-29
TAIR\|locus:2116495		239	AT4G32270 "AT4G32270" [Arabido	0.721	0.619	0.406	5.7e-27
TAIR\|locus:2077447		165	AT3G07860 "AT3G07860" [Arabido	0.473	0.587	0.336	2.5e-10
ZFIN\|ZDB-GENE-050417-179		173	zgc:112000 "zgc:112000" [Danio	0.404	0.479	0.341	7.6e-09
MGI\|MGI:1925622		123	Snrnp25 "small nuclear ribonuc	0.404	0.674	0.341	1.2e-08
UNIPROTKB\|Q3ZBQ4		123	SNRNP25 "U11/U12 small nuclear	0.404	0.674	0.341	1.6e-08
UNIPROTKB\|Q9BV90		132	SNRNP25 "U11/U12 small nuclear	0.404	0.628	0.329	4.4e-08

TAIR\|locus:2016244 AT1G80060 "AT1G80060" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

 Score = 370 (135.3 bits), Expect = 4.6e-34, P = 4.6e-34
 Identities = 76/165 (46%), Positives = 113/165 (68%)

Query:    27 EGNSV--RTMPYLKLP-QPRIRLSVLKLDGSRFDVYIERNATVGELRQAIEEVFTLSPTE 83
             +G S+  R   YLKLP Q RI+LSV+KL+GS FDV + ++ +V EL++A+E+VFT+SP E
Sbjct:    33 DGGSISGRRSSYLKLPPQGRIKLSVVKLNGSLFDVEVAKDCSVAELKRAVEQVFTISPLE 92

Query:    84 GQGKISWTNVWGHFCLCYDGRKLVNDKTHIRDFRMKDGDELQFSRHMSLDYLHSKRRSKT 143
             G G ISW++VWGHFCLCY  ++LVNDKT IR   + DGD+L F RH+S+D+    +RSK+
Sbjct:    93 GHGMISWSHVWGHFCLCYRDQRLVNDKTSIRYLGLNDGDQLHFVRHLSIDHSPMNKRSKS 152

Query:   144 QNVACQQFSRLSVESDTCEQAVLAKDN--LEDQHKRLSPGSDADE 186
              +  C+++  L V S   E  +  ++   ++D  ++  PG+  DE
Sbjct:   153 PS--CKRYLELDVSSIVNEIQIQNQNQNGVDDVAEKCYPGAQ-DE 194

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISM

TAIR\|locus:2145502 AT5G25340 "AT5G25340" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2116495 AT4G32270 "AT4G32270" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

TAIR\|locus:2077447 AT3G07860 "AT3G07860" [Arabidopsis thaliana (taxid:3702)]	Back alignment and assigned GO terms

ZFIN\|ZDB-GENE-050417-179 zgc:112000 "zgc:112000" [Danio rerio (taxid:7955)]	Back alignment and assigned GO terms

MGI\|MGI:1925622 Snrnp25 "small nuclear ribonucleoprotein 25 (U11/U12)" [Mus musculus (taxid:10090)]	Back alignment and assigned GO terms

UNIPROTKB\|Q3ZBQ4 SNRNP25 "U11/U12 small nuclear ribonucleoprotein 25 kDa protein" [Bos taurus (taxid:9913)]	Back alignment and assigned GO terms

UNIPROTKB\|Q9BV90 SNRNP25 "U11/U12 small nuclear ribonucleoprotein 25 kDa protein" [Homo sapiens (taxid:9606)]	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

No EC number assignment, probably not an enzyme!

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Your Input:
	AT1G80060	unknown protein; FUNCTIONS IN- molecular_function unknown; INVOLVED IN- protein modification process; LOCATED IN- cellular_component unknown; EXPRESSED IN- 17 plant structures; EXPRESSED DURING- 7 growth stages; CONTAINS InterPro DOMAIN/s- Ubiquitin (InterPro-IPR000626); BEST Arabidopsis thaliana protein match is- unknown protein (TAIR-AT4G32270.1); Has 97 Blast hits to 97 proteins in 32 species- Archae - 0; Bacteria - 0; Metazoa - 56; Fungi - 0; Plants - 38; Viruses - 0; Other Eukaryotes - 3 (source- NCBI BLink). (243 aa)
		(Arabidopsis thaliana)
Predicted Functional Partners:
		Sorry, there are no predicted associations at the current settings.

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		205
pfam08817		77	pfam08817, YukD, WXG100 protein secretion system (	6e-04
smart00213		72	smart00213, UBQ, Ubiquitin homologues	0.001

>gnl\|CDD\|220030 pfam08817, YukD, WXG100 protein secretion system (Wss), protein YukD	Back alignment and domain information

 Score = 36.8 bits (86), Expect = 6e-04
 Identities = 22/83 (26%), Positives = 35/83 (42%), Gaps = 8/83 (9%)

Query: 43  RIRLSVLKLDGSRFDVYIERNATVGELRQAIEEVFTLSPTEGQGKISWTNVWGHFCLCYD 102
            IR++V    G + D+ +  +  V EL   + E   L  T+  G+  +        L   
Sbjct: 1   LIRVTVDAGHGRQVDLVLPADVPVKELIPLLVEALKLPGTDPSGQGVYR-------LARK 53

Query: 103 GRKLVNDKTHIRDFRMKDGDELQ 125
           G  L +D T + D  + DGD L 
Sbjct: 54  GIPLSDDDT-LADAGVTDGDILV 75

The YukD protein family members participate in the formation of a translocon required for the secretion of WXG100 proteins (pfam06013) in monoderm bacteria, with the WXG100 protein secretion system (Wss). Like the cytoplasmic protein EsaC in Staphylococcus aureus, YukD was hypothesized to play a role of a chaperone. YukD adopts a ubiquitin-like fold. Usually, ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that the classical YukD lacks the capacity for covalent bond formation with other proteins. In contrast to the situation in firmicutes, YukD-like proteins in actinobacteria are often fused to a transporter involved in the ESAT-6/ESX/Wss secretion pathway. Members of the YukD family are also associated in gene neighborhoods with other enzymatic members of the ubiquitin signaling and degradation pathway such as the E1, E2 and E3 trienzyme complex that catalyze ubiquitin transfer to substrates, and the JAB family metallopeptidases that are involved in its release. This suggests that a subset of the YukD family in bacteria are conjugated and released from proteins as in the eukaryotic ubiquitin-mediated signaling and degradation pathway. Length = 77

>gnl\|CDD\|214563 smart00213, UBQ, Ubiquitin homologues	Back alignment and domain information

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Alignment Graph	Length	Definition	Probability
Query		205
cd01804		78	midnolin_N Ubiquitin-like domain of midnolin. midn	99.55
cd01791		73	Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also know	99.53
cd01806		76	Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also kn	99.45
cd01792		80	ISG15_repeat1 ISG15 ubiquitin-like protein, first	99.45
cd01807		74	GDX_N ubiquitin-like domain of GDX. GDX contains a	99.44
cd01803		76	Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40	99.43
cd01805		77	RAD23_N Ubiquitin-like domain of RAD23. RAD23 belo	99.42
cd01809		72	Scythe_N Ubiquitin-like domain of Scythe protein.	99.41
cd01808		71	hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC	99.38
cd01797		78	NIRF_N amino-terminal ubiquitin-like domain of Np9	99.37
cd01810		74	ISG15_repeat2 ISG15 ubiquitin-like protein, second	99.37
PTZ00044		76	ubiquitin; Provisional	99.34
cd01802		103	AN1_N ubiquitin-like domain of AN1. AN1 (also know	99.34
cd01790		79	Herp_N Homocysteine-responsive endoplasmic reticul	99.33
PF00240		69	ubiquitin: Ubiquitin family; InterPro: IPR000626 U	99.32
cd01793		74	Fubi Fubi ubiquitin-like protein. Fubi is a ubiqui	99.31
cd01798		70	parkin_N amino-terminal ubiquitin-like of parkin p	99.31
cd01794		70	DC_UbP_C dendritic cell derived ubiquitin-like pro	99.28
cd01812		71	BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-ter	99.28
cd01813		74	UBP_N UBP ubiquitin processing protease. The UBP (	99.26
cd01796		71	DDI1_N DNA damage inducible protein 1 ubiquitin-li	99.23
KOG0010		493	consensus Ubiquitin-like protein [Posttranslationa	99.18
smart00213		64	UBQ Ubiquitin homologues. Ubiquitin-mediated prote	99.14
cd01800		76	SF3a120_C Ubiquitin-like domain of Mammalian splic	99.12
TIGR00601		378	rad23 UV excision repair protein Rad23. All protei	99.1
cd01763		87	Sumo Small ubiquitin-related modifier (SUMO). Smal	99.03
cd01769		69	UBL Ubiquitin-like domain of UBL. UBLs function by	99.03
PF11976		72	Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; Inter	98.94
cd01815		75	BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC	98.86
cd01799		75	Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HO	98.82
cd01801		77	Tsc13_N Ubiquitin-like domain of Tsc13. Tsc13_N N-	98.81
PLN02560		308	enoyl-CoA reductase	98.73
cd01795		107	USP48_C USP ubiquitin-specific protease. The USP (	98.67
KOG0011		340	consensus Nucleotide excision repair factor NEF2,	98.63
cd01789		84	Alp11_N Ubiquitin-like domain of Alp11 tubulin-fol	98.52
PF14560		87	Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2K	98.4
KOG0004		156	consensus Ubiquitin/40S ribosomal protein S27a fus	98.38
PF11543		80	UN_NPL4: Nuclear pore localisation protein NPL4; I	98.34
cd01814		113	NTGP5 Ubiquitin-like NTGP5 and ATGP4. NTGP5 and AT	98.34
PF13881		111	Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB	98.24
cd00196		69	UBQ Ubiquitin-like proteins. Ubiquitin homologs; I	98.11
KOG0003		128	consensus Ubiquitin/60s ribosomal protein L40 fusi	98.1
PF08817		79	YukD: WXG100 protein secretion system (Wss), prote	98.1
KOG0005		70	consensus Ubiquitin-like protein [Cell cycle contr	98.06
KOG0001		75	consensus Ubiquitin and ubiquitin-like proteins [P	97.65
KOG4248		1143	consensus Ubiquitin-like protein, regulator of apo	97.43
cd01788		119	ElonginB Ubiquitin-like domain of Elongin B. Elong	97.04
cd01770		79	p47_UBX p47-like ubiquitin domain. p47_UBX p47 is	96.73
PF00789		82	UBX: UBX domain; InterPro: IPR001012 The UBX domai	96.53
KOG1639		297	consensus Steroid reductase required for elongatio	96.47
PF10302		97	DUF2407: DUF2407 ubiquitin-like domain; InterPro:	96.21
COG5417		81	Uncharacterized small protein [Function unknown]	96.01
KOG1769		99	consensus Ubiquitin-like proteins [Posttranslation	96.0
PF09379		80	FERM_N: FERM N-terminal domain ; InterPro: IPR0189	95.6
KOG1872		473	consensus Ubiquitin-specific protease [Posttransla	94.98
cd01767		77	UBX UBX (ubiquitin regulatory X) domain. The UBX (	94.63
PF14453		57	ThiS-like: ThiS-like ubiquitin	94.57
cd01811		80	OASL_repeat1 2'-5' oligoadenylate synthetase-like	94.15
smart00166		80	UBX Domain present in ubiquitin-regulatory protein	93.87
KOG3493		73	consensus Ubiquitin-like protein [Posttranslationa	93.82
PF11470		65	TUG-UBL1: GLUT4 regulating protein TUG; InterPro:	93.42
PF15044		76	CLU_N: Mitochondrial function, CLU-N-term	93.37
cd01772		79	SAKS1_UBX SAKS1-like UBX domain. SAKS1 (SAPK-subst	93.19
KOG4495		110	consensus RNA polymerase II transcription elongati	93.03
PLN02799		82	Molybdopterin synthase sulfur carrier subunit	92.79
smart00295		207	B41 Band 4.1 homologues. Also known as ezrin/radix	92.75
PF13019		162	Telomere_Sde2: Telomere stability and silencing	91.62
cd01774		85	Faf1_like2_UBX Faf1 ike-2 UBX domain. Faf1_like2 i	90.95
TIGR01687		88	moaD_arch MoaD family protein, archaeal. Members o	90.88
cd00754		80	MoaD Ubiquitin domain of MoaD-like proteins. MoaD	90.76
TIGR01682		80	moaD molybdopterin converting factor, subunit 1, n	90.28
TIGR02958		452	sec_mycoba_snm4 secretion protein snm4. Members of	89.24
PF02597		77	ThiS: ThiS family; InterPro: IPR003749 ThiS (thiam	88.02
COG5227		103	SMT3 Ubiquitin-like protein (sentrin) [Posttransla	87.68
PRK06488		65	sulfur carrier protein ThiS; Validated	85.1
KOG0006		446	consensus E3 ubiquitin-protein ligase (Parkin prot	84.57
PRK08364		70	sulfur carrier protein ThiS; Provisional	84.12
cd01775		97	CYR1_RA Ubiquitin domain of CYR1 adenylate cyclase	83.26
PF10209		122	DUF2340: Uncharacterized conserved protein (DUF234	82.66
PRK08053		66	sulfur carrier protein ThiS; Provisional	82.29

>cd01804 midnolin_N Ubiquitin-like domain of midnolin	Back alignment and domain information

Probab=99.55  E-value=2.7e-14  Score=104.22  Aligned_cols=76  Identities=18%  Similarity=0.379  Sum_probs=66.4

Q ss_pred             CeEEEEEecCCcEEEEEeCCCCcHHHHHHHHHHHhccCCCCCCCcccccccccceEEeeCCeeecCCcchhcccCCCCCC
Q 040719           43 RIRLSVLKLDGSRFDVYIERNATVGELRQAIEEVFTLSPTEGQGKISWTNVWGHFCLCYDGRKLVNDKTHIRDFRMKDGD  122 (205)
Q Consensus        43 aMkLtVrkldGs~f~V~V~~sATV~DLKkAI~~~f~~~pe~g~qkISW~~VWk~fcLi~~G~KLldD~ktLsdyGIkDGd  122 (205)
                      +|+|+|+...|+.++|+|+.++||+|||+.|++.+..++++             .+|+|.|+ +++|+ +|.+|||++|+
T Consensus         1 ~m~I~Vk~~~G~~~~l~v~~~~TV~~LK~~I~~~~~~~~~~-------------qrL~~~Gk-~L~d~-~L~~~gi~~~~   65 (78)
T cd01804           1 PMNLNIHSTTGTRFDLSVPPDETVEGLKKRISQRLKVPKER-------------LALLHRET-RLSSG-KLQDLGLGDGS   65 (78)
T ss_pred             CeEEEEEECCCCEEEEEECCcCHHHHHHHHHHHHhCCChHH-------------EEEEECCc-CCCCC-cHHHcCCCCCC
Confidence            59999999999999999999999999999999998666654             36999995 55677 99999999999


Q ss_pred             EEEEEEecccc
Q 040719          123 ELQFSRHMSLD  133 (205)
Q Consensus       123 ~L~Fk~rl~~~  133 (205)
                      +|+++..+...
T Consensus        66 ~i~l~~~~~~~   76 (78)
T cd01804          66 KLTLVPTVEAG   76 (78)
T ss_pred             EEEEEeecccc
Confidence            99999887543

midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.

>cd01791 Ubl5 UBL5 ubiquitin-like modifier	Back alignment and domain information

>cd01806 Nedd8 Nebb8-like ubiquitin protein	Back alignment and domain information

>cd01792 ISG15_repeat1 ISG15 ubiquitin-like protein, first repeat of 2	Back alignment and domain information

>cd01807 GDX_N ubiquitin-like domain of GDX	Back alignment and domain information

>cd01803 Ubiquitin Ubiquitin	Back alignment and domain information

>cd01805 RAD23_N Ubiquitin-like domain of RAD23	Back alignment and domain information

>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein	Back alignment and domain information

>cd01808 hPLIC_N Ubiquitin-like domain of hPLIC-1 and hPLIC2	Back alignment and domain information

>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF	Back alignment and domain information

>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2	Back alignment and domain information

>PTZ00044 ubiquitin; Provisional	Back alignment and domain information

>cd01802 AN1_N ubiquitin-like domain of AN1	Back alignment and domain information

>cd01790 Herp_N Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain protein	Back alignment and domain information

>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade	Back alignment and domain information

>cd01793 Fubi Fubi ubiquitin-like protein	Back alignment and domain information

>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein	Back alignment and domain information

>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein	Back alignment and domain information

>cd01812 BAG1_N Ubiquitin-like domain of BAG1	Back alignment and domain information

>cd01813 UBP_N UBP ubiquitin processing protease	Back alignment and domain information

>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain	Back alignment and domain information

>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]	Back alignment and domain information

>smart00213 UBQ Ubiquitin homologues	Back alignment and domain information

>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120	Back alignment and domain information

>TIGR00601 rad23 UV excision repair protein Rad23	Back alignment and domain information

>cd01763 Sumo Small ubiquitin-related modifier (SUMO)	Back alignment and domain information

>cd01769 UBL Ubiquitin-like domain of UBL	Back alignment and domain information

>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins	Back alignment and domain information

>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP	Back alignment and domain information

>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1	Back alignment and domain information

>cd01801 Tsc13_N Ubiquitin-like domain of Tsc13	Back alignment and domain information

>PLN02560 enoyl-CoA reductase	Back alignment and domain information

>cd01795 USP48_C USP ubiquitin-specific protease	Back alignment and domain information

>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]	Back alignment and domain information

>cd01789 Alp11_N Ubiquitin-like domain of Alp11 tubulin-folding cofactor B	Back alignment and domain information

>PF14560 Ubiquitin_2: Ubiquitin-like domain; PDB: 1WJN_A 2KJ6_A 2KJR_A 1V6E_A 1T0Y_A	Back alignment and domain information

>KOG0004 consensus Ubiquitin/40S ribosomal protein S27a fusion [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PF11543 UN_NPL4: Nuclear pore localisation protein NPL4; InterPro: IPR024682 Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway	Back alignment and domain information

>cd01814 NTGP5 Ubiquitin-like NTGP5 and ATGP4	Back alignment and domain information

>PF13881 Rad60-SLD_2: Ubiquitin-2 like Rad60 SUMO-like; PDB: 1SE9_A 1WGH_A 2GOW_A	Back alignment and domain information

>cd00196 UBQ Ubiquitin-like proteins	Back alignment and domain information

>KOG0003 consensus Ubiquitin/60s ribosomal protein L40 fusion [Translation, ribosomal structure and biogenesis]	Back alignment and domain information

>PF08817 YukD: WXG100 protein secretion system (Wss), protein YukD; InterPro: IPR014921 YukD is a bacterial protein that adopts a ubiquitin-like fold []	Back alignment and domain information

>KOG0005 consensus Ubiquitin-like protein [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>KOG0001 consensus Ubiquitin and ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones; General function prediction only]	Back alignment and domain information

>KOG4248 consensus Ubiquitin-like protein, regulator of apoptosis [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>cd01788 ElonginB Ubiquitin-like domain of Elongin B	Back alignment and domain information

>cd01770 p47_UBX p47-like ubiquitin domain	Back alignment and domain information

>PF00789 UBX: UBX domain; InterPro: IPR001012 The UBX domain is found in ubiquitin-regulatory proteins, which are members of the ubiquitination pathway, as well as a number of other proteins including FAF-1 (FAS-associated factor 1), the human Rep-8 reproduction protein and several hypothetical proteins from yeast	Back alignment and domain information

>KOG1639 consensus Steroid reductase required for elongation of the very long chain fatty acids [Lipid transport and metabolism]	Back alignment and domain information

>PF10302 DUF2407: DUF2407 ubiquitin-like domain; InterPro: IPR019413 This entry represents a family of proteins of unknown function found in fungi	Back alignment and domain information

>COG5417 Uncharacterized small protein [Function unknown]	Back alignment and domain information

>KOG1769 consensus Ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain	Back alignment and domain information

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

>cd01767 UBX UBX (ubiquitin regulatory X) domain	Back alignment and domain information

>PF14453 ThiS-like: ThiS-like ubiquitin	Back alignment and domain information

>cd01811 OASL_repeat1 2'-5' oligoadenylate synthetase-like protein, repeat 1 of 2	Back alignment and domain information

>smart00166 UBX Domain present in ubiquitin-regulatory proteins	Back alignment and domain information

>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly	Back alignment and domain information

>PF15044 CLU_N: Mitochondrial function, CLU-N-term	Back alignment and domain information

>cd01772 SAKS1_UBX SAKS1-like UBX domain	Back alignment and domain information

>KOG4495 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin B [Transcription]	Back alignment and domain information

>PLN02799 Molybdopterin synthase sulfur carrier subunit	Back alignment and domain information

>smart00295 B41 Band 4	Back alignment and domain information

>PF13019 Telomere_Sde2: Telomere stability and silencing	Back alignment and domain information

>cd01774 Faf1_like2_UBX Faf1 ike-2 UBX domain	Back alignment and domain information

>TIGR01687 moaD_arch MoaD family protein, archaeal	Back alignment and domain information

>cd00754 MoaD Ubiquitin domain of MoaD-like proteins	Back alignment and domain information

>TIGR01682 moaD molybdopterin converting factor, subunit 1, non-archaeal	Back alignment and domain information

>TIGR02958 sec_mycoba_snm4 secretion protein snm4	Back alignment and domain information

>PF02597 ThiS: ThiS family; InterPro: IPR003749 ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer	Back alignment and domain information

>COG5227 SMT3 Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PRK06488 sulfur carrier protein ThiS; Validated	Back alignment and domain information

>KOG0006 consensus E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones]	Back alignment and domain information

>PRK08364 sulfur carrier protein ThiS; Provisional	Back alignment and domain information

>cd01775 CYR1_RA Ubiquitin domain of CYR1 adenylate cyclase	Back alignment and domain information

>PF10209 DUF2340: Uncharacterized conserved protein (DUF2340); InterPro: IPR018794 This entry consists of small proteins of approximately 150 amino acids whose function is unknown	Back alignment and domain information

>PRK08053 sulfur carrier protein ThiS; Provisional	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		205
1v2y_A		105	Solution Structure Of Mouse Hypothetical Gene (Rike		8e-08

>pdb|1V2Y|A Chain A, Solution Structure Of Mouse Hypothetical Gene (Riken Cdna 3300001g02) Product Homologous To Ubiquitin Fold Length = 105

Back alignment and structure

Iteration: 1
 Score = 53.5 bits (127), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 29/86 (33%), Positives = 47/86 (54%), Gaps = 2/86 (2%)
Query: 48  VLKLDGSRFDVYIERNATVGELRQAIEEVFTLSPTEGQG--KISWTNVWGHFCLCYDGRK 105
           V K+DG    V + +NATV +L++AI+    L      G   ISW+ VW  + L   G K
Sbjct: 12  VCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEK 71
Query: 106 LVNDKTHIRDFRMKDGDELQFSRHMS 131
           L  D+  +RD+ +++ DE+ F + + 
Sbjct: 72  LTEDRKKLRDYGIRNRDEVSFIKKLG 97

PyMOL of 1v2y

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Alignment Graph	Length	Definition	E-value
Query		205
1v2y_A		105	3300001G02RIK protein; hypothetical protein, ubiqu	3e-36
1oqy_A		368	HHR23A, UV excision repair protein RAD23 homolog A	6e-04
1v86_A		95	DNA segment, CHR 7, wayne state university 128, ex	7e-04

>1v2y_A 3300001G02RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 Length = 105	Back alignment and structure

 Score =  121 bits (306), Expect = 3e-36
 Identities = 29/99 (29%), Positives = 49/99 (49%), Gaps = 2/99 (2%)

Query: 38  KLPQPRIRLSVLKLDGSRFDVYIERNATVGELRQAIEEVFTLSPTE--GQGKISWTNVWG 95
                 + + V K+DG    V + +NATV +L++AI+    L      G   ISW+ VW 
Sbjct: 2   SSGSSGMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWR 61

Query: 96  HFCLCYDGRKLVNDKTHIRDFRMKDGDELQFSRHMSLDY 134
            + L   G KL  D+  +RD+ +++ DE+ F + +    
Sbjct: 62  TYHLTSAGEKLTEDRKKLRDYGIRNRDEVSFIKKLGQKS 100

PyMOL of 1v2y

>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} SCOP: a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A Length = 368	Back alignment and structure

>1v86_A DNA segment, CHR 7, wayne state university 128, expressed; ubiquitin fold, structural genomics, D7WSU128E protein; HET: DNA; NMR {Mus musculus} SCOP: d.15.1.1 Length = 95	Back alignment and structure

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Alignment Graph	Length	Definition	Probability
Query		205
1v2y_A		105	3300001G02RIK protein; hypothetical protein, ubiqu	99.96
3phx_B		79	Ubiquitin-like protein ISG15; OTU domain, DE-ubiqu	99.57
3v6c_B		91	Ubiquitin; structural genomics, structural genomic	99.56
3dbh_I		88	NEDD8; cell cycle, activating enzyme, apoptosis, m	99.55
3mtn_B		85	UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquit	99.54
3n3k_B		85	Ubiquitin; hydrolase, protease, thiol protease, DU	99.54
1ndd_A		76	NEDD8, protein (ubiquitin-like protein NEDD8); pro	99.53
3a9j_A		76	Ubiquitin; protein complex, cytoplasm, isopeptide	99.53
4fbj_B		88	NEDD8; effector-HOST target complex, glutamine dea	99.53
3k9o_B		96	Ubiquitin, UBB+1; E2-25K, complex structure, ATP-b	99.52
4hcn_B		98	Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidas	99.52
2dzi_A		81	Ubiquitin-like protein 4A; GDX, structural genomic	99.52
2faz_A		78	Ubiquitin-like containing PHD and ring finger DOM	99.51
1wh3_A		87	59 kDa 2'-5'-oligoadenylate synthetase like protei	99.51
4eew_A		88	Large proline-rich protein BAG6; ubiquitin-like fo	99.5
4dwf_A		90	HLA-B-associated transcript 3; ubiquitin-like doma	99.48
2bwf_A		77	Ubiquitin-like protein DSK2; signaling protein, UB	99.47
1sif_A		88	Ubiquitin; hydrophobic mutants, folding, stability	99.47
2kk8_A		84	Uncharacterized protein AT4G05270; solution arabid	99.47
2wyq_A		85	HHR23A, UV excision repair protein RAD23 homolog A	99.47
1wy8_A		89	NP95-like ring finger protein, isoform A; ubiquiti	99.47
2ojr_A		111	Ubiquitin; lanthide-binding TAG, terbium, TB, SAD	99.46
1uel_A		95	HHR23B, UV excision repair protein RAD23 homolog B	99.46
3rt3_B		159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.45
1wx8_A		96	Riken cDNA 4931431F19; ubiquitin-like domain, ubiq	99.44
1yx5_B		98	Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo s	99.44
2hj8_A		88	Interferon-induced 17 kDa protein; HR2873B, human	99.44
3vdz_A		111	Ubiquitin-40S ribosomal protein S27A; gadolinium,	99.44
2uyz_B		79	Small ubiquitin-related modifier 1; sumoylation, c	99.43
2klc_A		101	Ubiquilin-1; ubiquitin-like, structural genomics,	99.42
3m62_B		106	UV excision repair protein RAD23; armadillo-like r	99.4
1ttn_A		106	DC-UBP, dendritic cell-derived ubiquitin-like prot	99.39
3b1l_X		76	E3 ubiquitin-protein ligase parkin; proteasome, AL	99.1
1wyw_B		97	Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Ho	99.39
3b08_A		152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.39
1wgd_A		93	Homocysteine-responsive endoplasmic reticulum- res	99.38
1yqb_A		100	Ubiquilin 3; structural genomics consortium, ubiqu	99.38
2daf_A		118	FLJ35834 protein; hypothetical protein FLJ35834, u	99.38
2kan_A		94	Uncharacterized protein AR3433A; ubiquitin fold, a	99.37
1v5o_A		102	1700011N24RIK protein; hypothetical protein, ubiqu	99.37
2l7r_A		93	Ubiquitin-like protein FUBI; structural genomics,	99.36
1j8c_A		125	Ubiquitin-like protein hplic-2; ubiquitin-like dom	99.36
1uh6_A		100	Ubiquitin-like 5; beta-grAsp fold, structural geno	99.36
1wia_A		95	Hypothetical ubiquitin-like protein (riken cDNA 20	99.35
1wx7_A		106	Ubiquilin 3; ubiquitin-like domain, structural gen	99.35
4a20_A		98	Ubiquitin-like protein MDY2; protein binding, GET-	99.35
1x1m_A		107	Ubiquitin-like protein SB132; structural genomics,	99.34
2kdi_A		114	Ubiquitin, vacuolar protein sorting-associated pro	99.33
1we6_A		111	Splicing factor, putative; structural genomics, ub	99.33
3l0w_B		169	Monoubiquitinated proliferating cell nuclear antig	99.32
3b08_A		152	Polyubiquitin-C, ubiquitin; protein complex, signa	99.32
3u30_A		172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.3
1wxv_A		92	BAG-family molecular chaperone regulator-1; struct	99.3
3u30_A		172	Ubiquitin, linear DI-ubiquitin; immune system; 2.4	99.29
1wju_A		100	NEDD8 ultimate buster-1; ubiquitin-like domain, st	99.28
3u5c_f		152	40S ribosomal protein S31; translation, ribosome,	99.27
2kd0_A		85	LRR repeats and ubiquitin-like domain-containing p	99.27
3m63_B		101	Ubiquitin domain-containing protein DSK2; armadill	99.27
2dzj_A		88	Synaptic glycoprotein SC2; ubiquitin-like fold, st	99.26
2kdb_A		99	Homocysteine-responsive endoplasmic reticulum- res	99.26
3q3f_A		189	Ribonuclease/ubiquitin chimeric protein; domain SW	99.26
3u5e_m		128	60S ribosomal protein L40; translation, ribosome,	99.26
3plu_A		93	Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-	99.26
3rt3_B		159	Ubiquitin-like protein ISG15; ubiquitin-like domai	99.25
1v5t_A		90	8430435I17RIK protein; hypothetical protein, ubiqu	99.25
2lxa_A		87	Ubiquitin-like protein MDY2; ubiquitin-like domain	99.25
1we7_A		115	SF3A1 protein; structural genomics, ubiquitin-like	99.25
1wgh_A		116	Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fo	99.23
1v86_A		95	DNA segment, CHR 7, wayne state university 128, ex	99.22
2gow_A		125	HCG-1 protein, ubiquitin-like protein 3; BC059385,	99.22
1wgg_A		96	Ubiquitin carboxyl-terminal hydrolase 14; ubiquiti	99.2
1wf9_A		107	NPL4 family protein; beta-grAsp fold like domain,	99.16
4dbg_A		105	Ranbp-type and C3HC4-type zinc finger-containing;	99.15
1se9_A		126	Ubiquitin family; ubiquitin-like, cell-free, wheat	99.15
3ai5_A		307	Yeast enhanced green fluorescent protein, ubiquit;	99.09
2kzr_A		86	Ubiquitin thioesterase OTU1; structural genomics,	99.08
2kjr_A		95	CG11242; UBL, ubiquitin, ubiquitin-like, structura	99.07
1v6e_A		95	Cytoskeleton-associated protein 1; tubulin-specifi	99.04
1oqy_A		368	HHR23A, UV excision repair protein RAD23 homolog A	99.01
4ajy_B		118	Transcription elongation factor B polypeptide 2; E	98.99
2fnj_B		118	Transcription elongation factor B polypeptide 2; b	98.93
3shq_A		320	UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila	98.92
2kj6_A		97	Tubulin folding cofactor B; methods development, N	98.92
2io1_B		94	Small ubiquitin-related modifier 3 precursor; SUMO	98.92
2io0_B		91	Small ubiquitin-related modifier 2 precursor; SUMO	98.91
4b6w_A		86	Tubulin-specific chaperone; CAP-Gly, ubiquitin-lik	98.9
1t0y_A		122	Tubulin folding cofactor B; ubiquitin-like, cytosk	98.9
2dzm_A		100	FAS-associated factor 1; ubiquitin-like domain, HF	98.88
1wjn_A		97	Tubulin-folding protein TBCE; ubiquitin-like domai	98.86
1wm3_A		72	Ubiquitin-like protein SMT3B; ubiquitin fold, half	98.76
3a4r_A		79	Nfatc2-interacting protein; ubiquitin fold, coiled	98.75
2d07_B		93	Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Ho	98.7
1wz0_A		104	Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-li	98.66
2k8h_A		110	Small ubiquitin protein; SUMO, post-translational	98.61
2xzm_9		189	RPS31E; ribosome, translation; 3.93A {Tetrahymena	98.56
2eke_C		106	Ubiquitin-like protein SMT3; UBC9, SUMO binding mo	98.49
2pjh_A		80	Protein NPL4, nuclear protein localization protein	98.29
3kyd_D		115	Small ubiquitin-related modifier 1; SUMO, thioeste	98.17
3goe_A		82	DNA repair protein RAD60; SUMO-like domain, sumoyl	97.97
2bps_A		81	YUKD protein; ubiquitin-like protein, ubiquitin; 2	97.94
3pge_A		200	SUMO-modified proliferating cell nuclear antigen;	97.87
3tix_A		207	Ubiquitin-like protein SMT3, RNA-induced transcri	97.72
2jxx_A		97	Nfatc2-interacting protein; nuclear factor of acti	97.54
3v7o_A		227	Minor nucleoprotein VP30; ssgcid, seattle structur	97.31
2kc2_A		128	Talin-1, F1; FERM, adhesion, cell membrane, cell p	97.23
2al3_A		90	TUG long isoform; TUG UBL1 insulin, endocytosis/ex	97.12
3uf8_A		209	Ubiquitin-like protein SMT3, peptidyl-prolyl CIS-	96.23
3ix6_A		360	TS, tsase, thymidylate synthase; niaid, ssgcid, se	96.12
3qx1_A		84	FAS-associated factor 1; UBX, protein binding, P97	95.98
4da1_A		389	Protein phosphatase 1K, mitochondrial; metal-ION-a	95.73
2l76_A		95	Nfatc2-interacting protein; ubiquitin-like domain,	95.49
4a3p_A		217	Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {H	94.92
2dzk_A		109	UBX domain-containing protein 2; ubiquitin-like fo	94.88
3jyu_A		231	Ubiquitin carboxyl-terminal hydrolase; domain in u	94.87
1vjk_A		98	Molybdopterin converting factor, subunit 1; struct	94.84
1wj4_A		124	KIAA0794 protein; UBX domain, beta-grAsp fold, str	94.62
2r2o_A		138	Plexin-B1; effector domain, structural genomics, s	94.37
3ivf_A		371	Talin-1; FERM domain, cell membrane, cell projecti	94.14
1s3s_G		127	P47 protein; AAA ATPase, protein-protein complex,	93.63
4e71_A		111	Plexin-B2, MM1; transmembrane, signaling, RBD, str	93.26
1ryj_A		70	Unknown; beta/alpha protein, structural genomics,	92.77
1h4r_A		314	Merlin; FERM, neurofibromatosis, NF2, structural p	92.59
2cr5_A		109	Reproduction 8; UBX domain, D0H8S2298E protein, st	92.52
1wgk_A		114	Riken cDNA 2900073H19 protein; THis domain, ubiqut	92.3
2qjl_A		99	URM1, ubiquitin-related modifier 1; ubiquitin-like	92.02
2daj_A		91	KIAA0977 protein, COBL-like 1; ubiquitin-like doma	91.34
3po0_A		89	Small archaeal modifier protein 1; ubiquitin-like	90.73
3ivf_A		371	Talin-1; FERM domain, cell membrane, cell projecti	90.61
1tyg_B		87	YJBS; alpha beta barrel, protein-protein complex,	90.37
4e74_A		117	Plexin-A4; RBD, structural genomics, structural ge	89.59
3qij_A		296	Protein 4.1; cytoskeleton, structural genomics, st	89.33
1f0z_A		66	THis protein; ubiquitin fold, transport protein; N	89.33
1ef1_A		294	Moesin; membrane, FERM domain, tail domain, membra	89.29
3rpf_C		74	Molybdopterin converting factor, subunit 1 (MOAD);	87.07
3h6n_A		127	Plexin-D1; structural genomics consortium, SGC, me	86.46
3dwg_C		93	9.5 kDa culture filtrate antigen CFP10A; sulfur ca	86.28
3hm6_X		644	Plexin-B1; structural genomics consortium, SGC, me	85.83
2ns5_A		85	Partitioning-defective 3 homolog; cell polarity, N	85.2
3ig3_A		627	Plxna3 protein; plexin intracellular GAP RBD inact	84.43
1vd2_A		89	Protein kinase C, IOTA type; PB1 domain, OPCA moti	83.69
2i1j_A		575	Moesin; FERM, coiled-coil, C-ermad, ERM, radixin,	81.3

>1v2y_A 3300001G02RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1	Back alignment and structure

Probab=99.96  E-value=2.1e-29  Score=194.37  Aligned_cols=97  Identities=31%  Similarity=0.565  Sum_probs=90.8

Q ss_pred             CCCeEEEEEecCCcEEEEEeCCCCcHHHHHHHHHHHhccCC--CCCCCcccccccccceEEeeCCeeecCCcchhcccCC
Q 040719           41 QPRIRLSVLKLDGSRFDVYIERNATVGELRQAIEEVFTLSP--TEGQGKISWTNVWGHFCLCYDGRKLVNDKTHIRDFRM  118 (205)
Q Consensus        41 ~~aMkLtVrkldGs~f~V~V~~sATV~DLKkAI~~~f~~~p--e~g~qkISW~~VWk~fcLi~~G~KLldD~ktLsdyGI  118 (205)
                      +.+|+|+|++++|+.|+|+|++++||+|||++|++++..++  ++|+++|||+|+|.+|||+|+|++|.+|+++|++|||
T Consensus         5 ~~~M~I~Vk~l~g~~~~v~V~~~~TV~dLK~~I~~~~~i~~~~q~g~~~isw~~~w~q~~Li~~Gk~L~dD~~tL~dygI   84 (105)
T 1v2y_A            5 SSGMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGI   84 (105)
T ss_dssp             CCSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHTC
T ss_pred             CCcEEEEEEecCCCEEEEEECCCChHHHHHHHHHHHhCCCcccccCcceeeeeecceeEEEEeCCcCccCCcCCHHHcCC
Confidence            46899999999999999999999999999999999987655  5688999999999999999999888888999999999


Q ss_pred             CCCCEEEEEEecccccccc
Q 040719          119 KDGDELQFSRHMSLDYLHS  137 (205)
Q Consensus       119 kDGd~L~Fk~rl~~~~~~~  137 (205)
                      ++|++|||+.|+...|.|.
T Consensus        85 ~~g~~l~lv~~lr~~~~~~  103 (105)
T 1v2y_A           85 RNRDEVSFIKKLGQKSGPS  103 (105)
T ss_dssp             CSSEEEEEEECSCSCCCCC
T ss_pred             CCCCEEEEEehhccCCCCC
Confidence            9999999999999998875

PyMOL of 1v2y

>3phx_B Ubiquitin-like protein ISG15; OTU domain, DE-ubiquitinase, DE-isgylase, hydrolase-protein complex; 1.60A {Homo sapiens}	Back alignment and structure

>3v6c_B Ubiquitin; structural genomics, structural genomics consortium, SGC, UB protease, hydrolase-signaling protein complex; 1.70A {Homo sapiens} PDB: 3v6e_B	Back alignment and structure

>3dbh_I NEDD8; cell cycle, activating enzyme, apoptosis, membrane, UBL conjugation pathway, ATP-binding, ligase, nucleotide- binding, polymorphism; 2.85A {Homo sapiens} SCOP: d.15.1.1 PDB: 3dbr_I 3dbl_I	Back alignment and structure

>3mtn_B UBA80, ubcep1, ubiquitin variant UBV.21.4; ubiquitin-specific protease activity, hydrolase, ubiquitin B structural genomics consortium, SGC; 2.70A {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>3n3k_B Ubiquitin; hydrolase, protease, thiol protease, DUB, zinc ribbon, inhibitor, ubiqu acetylation, cytoplasm, isopeptide bond, nucleus; 2.60A {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>1ndd_A NEDD8, protein (ubiquitin-like protein NEDD8); proteolysis, signaling protei; 1.60A {Homo sapiens} SCOP: d.15.1.1 PDB: 1r4m_I 1r4n_I* 1xt9_B 2ko3_A 3gzn_I* 2bkr_B 2nvu_I* 3dqv_A 1bt0_A	Back alignment and structure

>3a9j_A Ubiquitin; protein complex, cytoplasm, isopeptide bond, metal-binding, zinc; 1.18A {Mus musculus} PDB: 3a1q_B 2znv_B 3a9k_A 3h7p_A 3jsv_A 3dvg_Y 3dvn_Y 3nob_A 2o6v_D* 3jw0_X 3jvz_X 3nhe_B* 1aar_A 1d3z_A 1f9j_A 1fxt_B 1g6j_A 1nbf_C 1cmx_B 1q5w_B ...	Back alignment and structure

>4fbj_B NEDD8; effector-HOST target complex, glutamine deamidase, deamidati bacterial effector, cell cycle-protein binding complex; 1.60A {Homo sapiens} PDB: 4f8c_B	Back alignment and structure

>3k9o_B Ubiquitin, UBB+1; E2-25K, complex structure, ATP-binding, isopeptide BO ligase, nucleotide-binding, UBL conjugation pathway; 1.80A {Homo sapiens} PDB: 2k25_A 2kx0_A	Back alignment and structure

>4hcn_B Polyubiquitin, ubiquitin; ubiquitin/NEDD8 deamidase, NEDD8, protein binding; 2.60A {Saccharomyces cerevisiae}	Back alignment and structure

>2dzi_A Ubiquitin-like protein 4A; GDX, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2faz_A Ubiquitin-like containing PHD and ring finger DOM protein 1; cell cycle, DNA damage, DNA repair, DNA-binding, ligase, Met binding, nuclear protein; 2.00A {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>1wh3_A 59 kDa 2'-5'-oligoadenylate synthetase like protein; P59 OASL, ubiquitin family, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>4eew_A Large proline-rich protein BAG6; ubiquitin-like fold, GP78-binding, chaperone; 1.30A {Homo sapiens}	Back alignment and structure

>4dwf_A HLA-B-associated transcript 3; ubiquitin-like domain, BAT3 protein, PF00240, structural GEN joint center for structural genomics, JCSG; 1.80A {Homo sapiens} PDB: 1wx9_A	Back alignment and structure

>2bwf_A Ubiquitin-like protein DSK2; signaling protein, UBA, signaling proteins; 1.15A {Saccharomyces cerevisiae} SCOP: d.15.1.1 PDB: 2bwe_S	Back alignment and structure

>1sif_A Ubiquitin; hydrophobic mutants, folding, stability, structural protein; 2.18A {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>2kk8_A Uncharacterized protein AT4G05270; solution arabidopsis thaliana, uncharacterized putative protein, NESG, structural genomics; NMR {Arabidopsis thaliana}	Back alignment and structure

>2wyq_A HHR23A, UV excision repair protein RAD23 homolog A; DNA binding protein, DNA excision repair, proteasomal degrad polyubiquitin; 1.65A {Homo sapiens} PDB: 1p98_A 1p9d_U 1p1a_A	Back alignment and structure

>1wy8_A NP95-like ring finger protein, isoform A; ubiquitin-like domain, NP95/ICBP90-like ring finger (NIRF), ubiquitin ligase, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>2ojr_A Ubiquitin; lanthide-binding TAG, terbium, TB, SAD phasing, protein binding; 2.60A {Homo sapiens}	Back alignment and structure

>1uel_A HHR23B, UV excision repair protein RAD23 homolog B; UBL, UIM, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A	Back alignment and structure

>1wx8_A Riken cDNA 4931431F19; ubiquitin-like domain, ubiquilin 1-like, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1	Back alignment and structure

>1yx5_B Ubiquitin; proteasome, UIM, hydrolase; NMR {Homo sapiens} SCOP: d.15.1.1 PDB: 1yx6_B	Back alignment and structure

>2hj8_A Interferon-induced 17 kDa protein; HR2873B, human ISG15, structure, northeast structural genomics consortium, protein structure initiative, NESG; NMR {Homo sapiens}	Back alignment and structure

>3vdz_A Ubiquitin-40S ribosomal protein S27A; gadolinium, MRI contrast agent, peptide-based contrast agent lanthanide binding TAG; 2.40A {Synthetic construct} PDB: 2ojr_A	Back alignment and structure

>2uyz_B Small ubiquitin-related modifier 1; sumoylation, cell division, nuclear protein, ubiquitin-like modifier, UBL conjugation pathway; 1.4A {Homo sapiens} SCOP: d.15.1.1 PDB: 2vrr_B 2iy0_B 2iy1_B 2g4d_B 2las_A 2io2_B 1z5s_B 3uip_B* 1tgz_B* 2bf8_B	Back alignment and structure

>2klc_A Ubiquilin-1; ubiquitin-like, structural genomics, PSI-2, protein structur initiative, northeast structural genomics consortium, NESG; NMR {Homo sapiens}	Back alignment and structure

>3m62_B UV excision repair protein RAD23; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}	Back alignment and structure

>1ttn_A DC-UBP, dendritic cell-derived ubiquitin-like protein; ubiquitin-like domain, solution structure, signaling protein; NMR {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>3b1l_X E3 ubiquitin-protein ligase parkin; proteasome, ALFA-beta-protein; 1.85A {Mus musculus} PDB: 1mg8_A 2zeq_A 2knb_A 1iyf_A	Back alignment and structure

>1wyw_B Ubiquitin-like protein SMT3C; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 1y8r_C* 2asq_A 2pe6_B 1a5r_A 2kqs_A 3kyc_D* 3rzw_C	Back alignment and structure

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B	Back alignment and structure

>1wgd_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; ENDPLASMIC reticulum stress, UBL domain; NMR {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>1yqb_A Ubiquilin 3; structural genomics consortium, ubiquitin, ubiquitin-like domain, structural genomics, signaling protein SGC; 2.00A {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>2daf_A FLJ35834 protein; hypothetical protein FLJ35834, ubiquitin-like domain, structural genomics, NPPSFA; NMR {Homo sapiens}	Back alignment and structure

>2kan_A Uncharacterized protein AR3433A; ubiquitin fold, alpha+beta, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}	Back alignment and structure

>1v5o_A 1700011N24RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1	Back alignment and structure

>2l7r_A Ubiquitin-like protein FUBI; structural genomics, PSI-biology, protein structure initiati northeast structural genomics consortium, NESG; NMR {Homo sapiens}	Back alignment and structure

>1j8c_A Ubiquitin-like protein hplic-2; ubiquitin-like domain, structural genomics; NMR {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>1uh6_A Ubiquitin-like 5; beta-grAsp fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1	Back alignment and structure

>1wia_A Hypothetical ubiquitin-like protein (riken cDNA 2010008E23); 'structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1	Back alignment and structure

>1wx7_A Ubiquilin 3; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>4a20_A Ubiquitin-like protein MDY2; protein binding, GET-pathway, tail-anchored proteins; 1.78A {Saccharomyces cerevisiae} PDB: 2lxc_A 4goc_A	Back alignment and structure

>1x1m_A Ubiquitin-like protein SB132; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.1	Back alignment and structure

>2kdi_A Ubiquitin, vacuolar protein sorting-associated protein 27 fusion protein; ubiquitin interacting motif, UIM, protein domain interface; NMR {Saccharomyces cerevisiae}	Back alignment and structure

>1we6_A Splicing factor, putative; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: d.15.1.1	Back alignment and structure

>3l0w_B Monoubiquitinated proliferating cell nuclear antigen, proliferating cell nuclear antigen; replication, DNA damage, DNA repair; 2.80A {Saccharomyces cerevisiae} PDB: 3l10_B	Back alignment and structure

>3b08_A Polyubiquitin-C, ubiquitin; protein complex, signaling protein-metal binding protein COM; HET: TRE; 1.70A {Homo sapiens} PDB: 2w9n_A* 3b0a_A* 3axc_A 2zvn_A 2zvo_A 2y5b_B	Back alignment and structure

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}	Back alignment and structure

>1wxv_A BAG-family molecular chaperone regulator-1; structural genomics, apoptosis, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>3u30_A Ubiquitin, linear DI-ubiquitin; immune system; 2.43A {Homo sapiens}	Back alignment and structure

>1wju_A NEDD8 ultimate buster-1; ubiquitin-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, protein binding; NMR {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>3u5c_f 40S ribosomal protein S31; translation, ribosome, ribosomal, ribosomal R ribosomal protein, eukaryotic ribosome, RNA-protein C; 3.00A {Saccharomyces cerevisiae} PDB: 3u5g_f	Back alignment and structure

>2kd0_A LRR repeats and ubiquitin-like domain-containing protein AT2G30105; ubiquitin-like protein, NESG, leucine-rich repeat, structural genomics; NMR {Arabidopsis thaliana}	Back alignment and structure

>3m63_B Ubiquitin domain-containing protein DSK2; armadillo-like repeats, UBL conjugation pathway, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae}	Back alignment and structure

>2dzj_A Synaptic glycoprotein SC2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>2kdb_A Homocysteine-responsive endoplasmic reticulum- resident ubiquitin-like domain member...; UBL domain, membrane, polymorphism, transmembrane; NMR {Homo sapiens}	Back alignment and structure

>3q3f_A Ribonuclease/ubiquitin chimeric protein; domain SWAP, oligomerization, ubiquitin insertion, hydrolase binding; 2.17A {Bacillus amyloliquefaciens}	Back alignment and structure

>3u5e_m 60S ribosomal protein L40; translation, ribosome, ribosomal R ribosomal protein, STM1, eukaryotic ribosome; 3.00A {Saccharomyces cerevisiae} PDB: 3u5i_m 4b6a_m 4a18_K 4a19_K 4a1b_K 4a1d_K 4adx_5 3izc_p 3izs_p 3iz5_p 3izr_p	Back alignment and structure

>3plu_A Ubiquitin-like modifier HUB1; ubiquitin-like, HUB-1, SNU66, peptide binding protein; 1.40A {Saccharomyces cerevisiae} PDB: 3plv_A 1m94_A 1p0r_A	Back alignment and structure

>3rt3_B Ubiquitin-like protein ISG15; ubiquitin-like domain, isgylation, antiviral protein-viral P complex; 2.01A {Homo sapiens} PDB: 3sdl_C 3r66_C 3pse_B 1z2m_A	Back alignment and structure

>1v5t_A 8430435I17RIK protein; hypothetical protein, ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 2kx3_A	Back alignment and structure

>2lxa_A Ubiquitin-like protein MDY2; ubiquitin-like domain, protein-protein interaction, SGT2 BIN domain, GET pathway, protein binding; NMR {Saccharomyces cerevisiae}	Back alignment and structure

>1we7_A SF3A1 protein; structural genomics, ubiquitin-like domain, riken structural genomics/proteomics initiative, RSGI, gene regulation; NMR {Mus musculus} SCOP: d.15.1.1 PDB: 1zkh_A	Back alignment and structure

>1wgh_A Ubiquitin-like 3, HCG-1 protein; ubiquitin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Mus musculus} SCOP: d.15.1.1	Back alignment and structure

>1v86_A DNA segment, CHR 7, wayne state university 128, expressed; ubiquitin fold, structural genomics, D7WSU128E protein; HET: DNA; NMR {Mus musculus} SCOP: d.15.1.1	Back alignment and structure

>2gow_A HCG-1 protein, ubiquitin-like protein 3; BC059385, structural genomics, protein structure initiative, PSI; NMR {Homo sapiens}	Back alignment and structure

>1wgg_A Ubiquitin carboxyl-terminal hydrolase 14; ubiquitin specific protease 14, USP14, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1	Back alignment and structure

>1wf9_A NPL4 family protein; beta-grAsp fold like domain, hypothetical protein, structural genomics, NPPSFA; NMR {Arabidopsis thaliana} SCOP: d.15.1.1	Back alignment and structure

>4dbg_A Ranbp-type and C3HC4-type zinc finger-containing; ubiquitin fold, ubiquitination, ligase; 2.71A {Homo sapiens} PDB: 2lgy_A	Back alignment and structure

>1se9_A Ubiquitin family; ubiquitin-like, cell-free, wheat GERM, structural genomics, protein structure initiative, CESG; NMR {Arabidopsis thaliana} SCOP: d.15.1.1	Back alignment and structure

>3ai5_A Yeast enhanced green fluorescent protein, ubiquit; ubiquitin, fusion protein, fluore protein, transcription; HET: CR2; 1.40A {Aequorea victoria} PDB: 3ako_B*	Back alignment and structure

>2kzr_A Ubiquitin thioesterase OTU1; structural genomics, northeast structural genomics consortiu PSI-2, protein structure initiative, hydrolase; NMR {Mus musculus}	Back alignment and structure

>2kjr_A CG11242; UBL, ubiquitin, ubiquitin-like, structural genomics, PSI-2, protein structure initiative; NMR {Drosophila melanogaster}	Back alignment and structure

>1v6e_A Cytoskeleton-associated protein 1; tubulin-specific chaperone B, tubulin folding cofactor B, microtubule, ubiquitin-like fold, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1	Back alignment and structure

>1oqy_A HHR23A, UV excision repair protein RAD23 homolog A; DNA repair, proteasome-mediated degradation, protein- protein interaction, replication; NMR {Homo sapiens} SCOP: a.5.2.1 a.5.2.1 a.189.1.1 d.15.1.1 PDB: 1qze_A 1tp4_A	Back alignment and structure

>4ajy_B Transcription elongation factor B polypeptide 2; E3 ubiquitin ligase, transcription factor, hypoxic signaling transcription; 1.73A {Homo sapiens} PDB: 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A 3ztc_A* 3ztd_A* 3zun_A* 1lm8_B 4b95_A* 2fnj_B 4b9k_A* 4awj_A*	Back alignment and structure

>2fnj_B Transcription elongation factor B polypeptide 2; beta-sandwich, lectin-like, SPRY, protein transport/signaling protein complex; 1.80A {Mus musculus} SCOP: d.15.1.1 PDB: 1lm8_B 1lqb_A 1vcb_A 2c9w_B 2izv_B 2jz3_B 2xai_C 3dcg_A 3zrc_A* 3zrf_A	Back alignment and structure

>3shq_A UBLCP1; phosphatase, hydrolase; 1.96A {Drosophila melanogaster}	Back alignment and structure

>2kj6_A Tubulin folding cofactor B; methods development, NESG, solution PSI-2, structural genomics, protein structure initiative; NMR {Arabidopsis thaliana}	Back alignment and structure

>2io1_B Small ubiquitin-related modifier 3 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.60A {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>2io0_B Small ubiquitin-related modifier 2 precursor; SUMO, SENP, ULP, complex, protein binding, hydrolase; 2.30A {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>4b6w_A Tubulin-specific chaperone; CAP-Gly, ubiquitin-like; HET: MSE; 2.35A {Trypanosoma brucei brucei strain 927}	Back alignment and structure

>1t0y_A Tubulin folding cofactor B; ubiquitin-like, cytoskeleton, microtubule, CESG, structural genomics, protein structure initiative, PSI; NMR {Caenorhabditis elegans} SCOP: d.15.1.1	Back alignment and structure

>2dzm_A FAS-associated factor 1; ubiquitin-like domain, HFAF1, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>1wjn_A Tubulin-folding protein TBCE; ubiquitin-like domain, progressive motor neuropathy, structural genomics; NMR {Mus musculus} SCOP: d.15.1.1	Back alignment and structure

>1wm3_A Ubiquitin-like protein SMT3B; ubiquitin fold, half-open barrel, two helices, protein transport; 1.20A {Homo sapiens} SCOP: d.15.1.1 PDB: 1wm2_A 3uin_B 3uio_B 2ckh_B	Back alignment and structure

>3a4r_A Nfatc2-interacting protein; ubiquitin fold, coiled coil, cytoplasm, methylation, nucleus, transcription; 1.00A {Mus musculus} PDB: 3a4s_C 3rd2_A	Back alignment and structure

>2d07_B Ubiquitin-like protein SMT3B; hydrolase; 2.10A {Homo sapiens} SCOP: d.15.1.1 PDB: 2rpq_A 2awt_A 2io3_B 2iyd_B 1u4a_A 2k1f_A	Back alignment and structure

>1wz0_A Ubiquitin-like protein SMT3B; SUMO-2, ubiquitin-like molecule, structural genomics, sentrin2, NPPFSA; NMR {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>2k8h_A Small ubiquitin protein; SUMO, post-translational modifier, signaling protein; NMR {Trypanosoma brucei}	Back alignment and structure

>2xzm_9 RPS31E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB: 2xzn_9	Back alignment and structure

>2eke_C Ubiquitin-like protein SMT3; UBC9, SUMO binding motif, SBM, ligase/protein binding complex; 1.90A {Saccharomyces cerevisiae} SCOP: d.15.1.1	Back alignment and structure

>2pjh_A Protein NPL4, nuclear protein localization protein 4 homolog; UFD1, NPL4, AAA, protein binding, transport protein; NMR {Mus musculus}	Back alignment and structure

>3kyd_D Small ubiquitin-related modifier 1; SUMO, thioester, adenylation, inhibitor, TETR intermediate, ligase, nucleus, phosphoprotein; HET: VMX; 2.61A {Homo sapiens} SCOP: d.15.1.1	Back alignment and structure

>3goe_A DNA repair protein RAD60; SUMO-like domain, sumoylation, SUMO, genome stability, DNA damage, DNA recombination, nucleus; HET: DNA; 0.97A {Schizosaccharomyces pombe} PDB: 3rcz_A*	Back alignment and structure

>2bps_A YUKD protein; ubiquitin-like protein, ubiquitin; 2.7A {Bacillus subtilis}	Back alignment and structure

>3pge_A SUMO-modified proliferating cell nuclear antigen; DNA replication, DNA binding protein; 2.80A {Saccharomyces cerevisiae}	Back alignment and structure

>3tix_A Ubiquitin-like protein SMT3, RNA-induced transcri silencing complex protein TAS3; PIN, rossmann fold, SPOC, alpha-helical hairpin, heterochrom silencing, RITS, RNAI, argonaute; 2.90A {Saccharomyces cerevisiae}	Back alignment and structure

>2jxx_A Nfatc2-interacting protein; nuclear factor of activated T-cells, cytoplasmic 2- interacting protein, ubiquitin like homologue; NMR {Homo sapiens}	Back alignment and structure

>3v7o_A Minor nucleoprotein VP30; ssgcid, seattle structural genomics center for infectious disease, SMT, transcription; 2.25A {Reston ebolavirus}	Back alignment and structure

>2kc2_A Talin-1, F1; FERM, adhesion, cell membrane, cell projection, cytoplasm, cytoskeleton, membrane, phosphoprotein, structural protein; NMR {Mus musculus}	Back alignment and structure

>2al3_A TUG long isoform; TUG UBL1 insulin, endocytosis/exocytosis complex; NMR {Mus musculus} SCOP: d.15.1.2	Back alignment and structure

>3uf8_A Ubiquitin-like protein SMT3, peptidyl-prolyl CIS- isomerase; ssgcid, seattle structural genomics center for in disease; HET: FK5; 1.50A {Burkholderia pseudomallei} PDB: 4ggq_C* 3vaw_A* 3uqa_A* 4g50_A* 4fn2_A* 3uqb_A* 4giv_A* 1euv_B 3v60_A 3v61_A 3v62_A*	Back alignment and structure

>3ix6_A TS, tsase, thymidylate synthase; niaid, ssgcid, seattle structural center for infectious DISE brucellosis, orchitis, epididymitis, mastitis; 2.20A {Brucella melitensis}	Back alignment and structure

>3qx1_A FAS-associated factor 1; UBX, protein binding, P97 binding; 1.60A {Homo sapiens} PDB: 3qwz_B* 3qc8_B 3qca_A 3qq8_B 3r3m_B 1h8c_A	Back alignment and structure

>4da1_A Protein phosphatase 1K, mitochondrial; metal-ION-assisted catalysis, dehydrogenase phosphatase, hydrolase; 2.38A {Homo sapiens} PDB: 3qht_A 1l2n_A	Back alignment and structure

>2l76_A Nfatc2-interacting protein; ubiquitin-like domain, structural genomics, PSI-biology, Pro structure initiative; NMR {Homo sapiens}	Back alignment and structure

>4a3p_A Ubiquitin carboxyl-terminal hydrolase 15; 1.40A {Homo sapiens} PDB: 4a3o_A 3pv1_A 3ppa_A* 3t9l_A 3lmn_A	Back alignment and structure

>2dzk_A UBX domain-containing protein 2; ubiquitin-like fold, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} PDB: 2kxj_A	Back alignment and structure

>3jyu_A Ubiquitin carboxyl-terminal hydrolase; domain in ubiquitin-specific peptidases (DUSP), proto- oncogene, ubiquitin-fold, UBL, protease, thioesterase; HET: 1PS; 2.37A {Mus musculus}	Back alignment and structure

>1vjk_A Molybdopterin converting factor, subunit 1; structural genomics, PSI, protein structure INI southeast collaboratory for structural genomics; 1.51A {Pyrococcus furiosus} SCOP: d.15.3.1	Back alignment and structure

>1wj4_A KIAA0794 protein; UBX domain, beta-grAsp fold, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Homo sapiens} SCOP: d.15.1.2	Back alignment and structure

>2r2o_A Plexin-B1; effector domain, structural genomics, structural GEN consortium, SGC, glycoprotein, membrane, phosphorylation, R secreted, transmembrane; 2.00A {Homo sapiens} PDB: 2rex_A* 2jph_A	Back alignment and structure

>3ivf_A Talin-1; FERM domain, cell membrane, cell projection, cytoskeleton, M phosphoprotein, cell adhesion, structural protein; 1.94A {Mus musculus} PDB: 2kma_A 2kc1_A	Back alignment and structure

>1s3s_G P47 protein; AAA ATPase, protein-protein complex, UBX domain, protein binding; HET: ADP; 2.90A {Rattus norvegicus} SCOP: d.15.1.2 PDB: 1i42_A 1jru_A	Back alignment and structure

>4e71_A Plexin-B2, MM1; transmembrane, signaling, RBD, structural genomics consortium, SGC, signaling protein; 2.26A {Homo sapiens}	Back alignment and structure

>1ryj_A Unknown; beta/alpha protein, structural genomics, protein structure initiative, OCSP, NESG, PSI; NMR {Methanothermococcusthermolithotrophicus} SCOP: d.15.3.2	Back alignment and structure

>1h4r_A Merlin; FERM, neurofibromatosis, NF2, structural protein, cytoskeleton, anti-oncogene; 1.8A {Homo sapiens} SCOP: a.11.2.1 b.55.1.5 d.15.1.4 PDB: 1isn_A 3u8z_A	Back alignment and structure

>2cr5_A Reproduction 8; UBX domain, D0H8S2298E protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: d.15.1.2	Back alignment and structure

>1wgk_A Riken cDNA 2900073H19 protein; THis domain, ubiqutin-like fold, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.15.3.3 PDB: 1xo3_A	Back alignment and structure

>2qjl_A URM1, ubiquitin-related modifier 1; ubiquitin-like protein, signaling protein; 1.44A {Saccharomyces cerevisiae} PDB: 2pko_A 2ax5_A	Back alignment and structure

>2daj_A KIAA0977 protein, COBL-like 1; ubiquitin-like domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}	Back alignment and structure

>3po0_A Small archaeal modifier protein 1; ubiquitin-like protein, protein binding; 1.55A {Haloferax volcanii} PDB: 2l83_A	Back alignment and structure

>3ivf_A Talin-1; FERM domain, cell membrane, cell projection, cytoskeleton, M phosphoprotein, cell adhesion, structural protein; 1.94A {Mus musculus} PDB: 2kma_A 2kc1_A	Back alignment and structure

>1tyg_B YJBS; alpha beta barrel, protein-protein complex, THis, BIOS protein; 3.15A {Bacillus subtilis} SCOP: d.15.3.2	Back alignment and structure

>4e74_A Plexin-A4; RBD, structural genomics, structural genomics consor SGC, signaling protein; 1.58A {Homo sapiens} PDB: 3q3j_A*	Back alignment and structure

>3qij_A Protein 4.1; cytoskeleton, structural genomics, structural genomics conso SGC; 1.80A {Homo sapiens} PDB: 1gg3_A 3bin_A 2he7_A 2rq1_A	Back alignment and structure

>1f0z_A THis protein; ubiquitin fold, transport protein; NMR {Escherichia coli} SCOP: d.15.3.2 PDB: 1zud_2	Back alignment and structure

>1ef1_A Moesin; membrane, FERM domain, tail domain, membrane protein; 1.90A {Homo sapiens} SCOP: a.11.2.1 b.55.1.5 d.15.1.4 PDB: 1sgh_A 1j19_A 2emt_A 2ems_A 2d10_A 2d11_A 2yvc_A 2d2q_A 2zpy_A 1gc7_A 1gc6_A 1ni2_A	Back alignment and structure

>3rpf_C Molybdopterin converting factor, subunit 1 (MOAD); MCSG, PSI-biology, structural genomics, midwest center for S genomics, transferase; 1.90A {Helicobacter pylori}	Back alignment and structure

>3h6n_A Plexin-D1; structural genomics consortium, SGC, membrane, transmembrane, receptor, alternative splicing, cell membrane, glycoprotein, polymorphism; 2.00A {Homo sapiens}	Back alignment and structure

>3dwg_C 9.5 kDa culture filtrate antigen CFP10A; sulfur carrier protein complex, beta-grAsp fold, amino-acid biosynthesis; HET: PLP; 1.53A {Mycobacterium tuberculosis} PDB: 3dwm_A	Back alignment and structure

>3hm6_X Plexin-B1; structural genomics consortium, SGC, membrane, transmembrane receptor, cell membrane, glycoprotein, phosphoprotein; 2.40A {Homo sapiens} PDB: 3sua_D* 3su8_X*	Back alignment and structure

>2ns5_A Partitioning-defective 3 homolog; cell polarity, N-terminal domain, PB1 domain, asymmetric membrane localization, signaling protein; NMR {Rattus norvegicus}	Back alignment and structure

>3ig3_A Plxna3 protein; plexin intracellular GAP RBD inactive, membrane, transmembra membrane protein, signaling protein; 1.99A {Mus musculus} PDB: 3ryt_A*	Back alignment and structure

>1vd2_A Protein kinase C, IOTA type; PB1 domain, OPCA motif, APKC, ZIP/P62, MEK5, molecular recognition, transferase; NMR {Homo sapiens} SCOP: d.15.2.2 PDB: 1wmh_A	Back alignment and structure

>2i1j_A Moesin; FERM, coiled-coil, C-ermad, ERM, radixin, ezrin, MER actin binding, masking, regulation, SELF-inhibition, cell A membrane protein; 2.10A {Spodoptera frugiperda} PDB: 2i1k_A 1e5w_A	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		205
d1v2ya_		105	d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik	9e-18
d2uyzb1		77	d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human	2e-04
d1oqya4		77	d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 h	6e-04
d2bwfa1		73	d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyc	6e-04
d1zkha1		86	d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-t	0.002
d1wiaa_		95	d.15.1.1 (A:) Ubiquitin-like protein bab25500 (201	0.003
d1se9a_		101	d.15.1.1 (A:) Hypothetical protein At3g01050 {Thal	0.003

>d1v2ya_ d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik {Mouse (Mus musculus) [TaxId: 10090]} Length = 105	Back information, alignment and structure


class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3300001g02rik
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 73.2 bits (179), Expect = 9e-18
 Identities = 29/90 (32%), Positives = 49/90 (54%), Gaps = 2/90 (2%)

Query: 44  IRLSVLKLDGSRFDVYIERNATVGELRQAIEEVFTLSPTE--GQGKISWTNVWGHFCLCY 101
           + + V K+DG    V + +NATV +L++AI+    L      G   ISW+ VW  + L  
Sbjct: 8   MTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTS 67

Query: 102 DGRKLVNDKTHIRDFRMKDGDELQFSRHMS 131
            G KL  D+  +RD+ +++ DE+ F + + 
Sbjct: 68  AGEKLTEDRKKLRDYGIRNRDEVSFIKKLG 97

PyMOL of d1v2ya_

>d2uyzb1 d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human (Homo sapiens) [TaxId: 9606]} Length = 77	Back information, alignment and structure

>d1oqya4 d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 homolog A (Hhr23a) {Human (Homo sapiens) [TaxId: 9606]} Length = 77	Back information, alignment and structure

>d2bwfa1 d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 73	Back information, alignment and structure

>d1zkha1 d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]} Length = 86	Back information, alignment and structure

>d1wiaa_ d.15.1.1 (A:) Ubiquitin-like protein bab25500 (2010008E23Rik) {Mouse (Mus musculus) [TaxId: 10090]} Length = 95	Back information, alignment and structure

>d1se9a_ d.15.1.1 (A:) Hypothetical protein At3g01050 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]} Length = 101	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		205
d1v2ya_		105	Ubiquitin-like protein 3300001g02rik {Mouse (Mus m	99.89
d1bt0a_		73	Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxI	99.61
d1z2ma2		76	Interferon-induced 15 kDa protein {Human (Homo sap	99.58
d1ogwa_		76	Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	99.57
d1wh3a_		87	2'-5'-oligoadenylate synthetase-like protein, OASL	99.54
d2zeqa1		78	Ubiquitin-like domain of parkin {Mouse (Mus muscul	99.54
d2faza1		76	Ubiquitin-like PHD and RING finger domain-containi	99.54
d1ttna1		80	Dendritic cell-derived ubiquitin-like protein {Hum	99.53
d1uela_		95	Ubiquitin-like domain of Rad23 homolog B (Hhr23B)	99.53
d1m94a_		73	Ubiquitin-like modifier protein hub1 {Baker's yeas	99.51
d2bwfa1		73	DSK2 {Baker's yeast (Saccharomyces cerevisiae) [Ta	99.5
d1oqya4		77	Ubiquitin-like domain of Rad23 homolog A (Hhr23a)	99.5
d1wy8a1		76	Ubiquitin-like PHD and RING finger domain-containi	99.5
d1v5oa_		102	1700011n24rik protein {Mouse (Mus musculus) [TaxId	99.49
d1wx9a1		73	Large proline-rich protein BAT3 {Human (Homo sapie	99.47
d1yqba1		84	Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	99.45
d1z2ma1		76	Interferon-induced 15 kDa protein {Human (Homo sap	99.45
d1j8ca_		103	Ubiquitin-like N-terminal domain of PLIC-2 {Human	99.44
d1wx8a1		83	4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]	99.43
d1zkha1		86	Splicing factor 3 subunit 1, C-terminal domain {Hu	99.42
d1wxva1		81	Bag-family molecular chaperone regulator-1 {Human	99.39
d1wiaa_		95	Ubiquitin-like protein bab25500 (2010008E23Rik) {M	99.38
d1uh6a_		100	Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculu	99.34
d1se9a_		101	Hypothetical protein At3g01050 {Thale cress (Arabi	99.28
d1wgga_		96	Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (M	99.27
d1v86a_		95	hypothetical D7wsu128e protein {Mouse (Mus musculu	99.24
d1v5ta_		90	8430435i17rik protein {Mouse (Mus musculus) [TaxId	99.24
d1wjua_		100	NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens	99.21
d1wgha_		116	Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculu	99.21
d1we6a_		111	Splicing factor 3 subunit 1, C-terminal domain {Th	99.14
d1wgda_		93	Homocysteine-responsive endoplasmic reticulum-resi	99.13
d1euvb_		79	SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomy	99.06
d1wjna_		97	Tubulin-folding protein TbcE {Mouse (Mus musculus)	98.97
d1v6ea_		95	Ubiquitin-like domain of tubulin folding cofactor	98.96
d1x1ma1		94	Ubiquitin-like protein 7 {Mouse (Mus musculus) [Ta	98.92
d2uyzb1		77	SUMO-1 (smt3 homologue) {Human (Homo sapiens) [Tax	98.9
d2c9wb1		103	Elongin B {Human (Homo sapiens) [TaxId: 9606]}	98.75
d1t0ya_		90	Ubiquitin-like domain of tubulin folding cofactor	98.74
d1wm3a_		72	SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	98.06
d1wf9a1		94	NPL4-like protein 1 {Thale cress (Arabidopsis thal	98.06
d1i42a_		89	p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	96.91
d1vjka_		88	Molybdopterin synthase subunit MoaD {Pyrococcus fu	95.92
d2al3a1		76	Tether containing UBX domain for GLUT4 (Tug) {Mous	95.49
d2cr5a1		96	UBX domain-containing protein 6 (Reproduction 8) {	95.13
d1h8ca_		82	Fas-associated factor 1, Faf1 {Human (Homo sapiens	94.54
d1xo3a_		101	C9orf74 homolog {Mouse (Mus musculus) [TaxId: 1009	93.84
d1ef1a3		84	Moesin {Human (Homo sapiens) [TaxId: 9606]}	91.36
d1wj4a_		124	Hypothetical protein KIAA0794 {Human (Homo sapiens	90.82
d1h4ra3		84	Merlin {Human (Homo sapiens) [TaxId: 9606]}	83.89
d1ip9a_		85	Bud emergence mediator Bemp1 {Baker's yeast (Sacch	82.7

>d1v2ya_ d.15.1.1 (A:) Ubiquitin-like protein 3300001g02rik {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

class: Alpha and beta proteins (a+b)
fold: beta-Grasp (ubiquitin-like)
superfamily: Ubiquitin-like
family: Ubiquitin-related
domain: Ubiquitin-like protein 3300001g02rik
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.89  E-value=4.8e-24  Score=161.26  Aligned_cols=97  Identities=31%  Similarity=0.565  Sum_probs=87.1

Q ss_pred             CCCeEEEEEecCCcEEEEEeCCCCcHHHHHHHHHHHhccCCC--CCCCcccccccccceEEeeCCeeecCCcchhcccCC
Q 040719           41 QPRIRLSVLKLDGSRFDVYIERNATVGELRQAIEEVFTLSPT--EGQGKISWTNVWGHFCLCYDGRKLVNDKTHIRDFRM  118 (205)
Q Consensus        41 ~~aMkLtVrkldGs~f~V~V~~sATV~DLKkAI~~~f~~~pe--~g~qkISW~~VWk~fcLi~~G~KLldD~ktLsdyGI  118 (205)
                      +..|+|+|++.+|+.|+|+|+.++||+|||++|+..+..+++  ++.+.|||+|+|++|||+|.|+.|.+|..+|.+|||
T Consensus         5 ss~M~v~Vk~~~G~~~~v~V~~~~TV~~LK~~I~~~~~ip~~~Qr~~~~~~~~~~~~~~~Li~~G~~L~d~~~tL~~~gI   84 (105)
T d1v2ya_           5 SSGMTVRVCKMDGEVMPVVVVQNATVLDLKKAIQRYVQLKQEREGGVQHISWSYVWRTYHLTSAGEKLTEDRKKLRDYGI   84 (105)
T ss_dssp             CCSEEEEEECSSSCEEEEEECTTCBHHHHHHHHHHHHHHHHHHTTCCCCCCHHHHHTTEEEESSSCEECCSSSBHHHHTC
T ss_pred             CCcEEEEEEeCCCCEEEEEECCCChHHHHHHHHHHHHCcCHHHhcccccccccccccceEEEECCEECcccCCCHHHcCC
Confidence            358999999999999999999999999999999999876654  356889999999999999999888788889999999


Q ss_pred             CCCCEEEEEEecccccccc
Q 040719          119 KDGDELQFSRHMSLDYLHS  137 (205)
Q Consensus       119 kDGd~L~Fk~rl~~~~~~~  137 (205)
                      ++|++|||+.|+...-.|.
T Consensus        85 ~~g~~l~lv~r~~~~~gps  103 (105)
T d1v2ya_          85 RNRDEVSFIKKLGQKSGPS  103 (105)
T ss_dssp             CSSEEEEEEECSCSCCCCC
T ss_pred             CCCCEEEEEEecCCCCCCC
Confidence            9999999999987665553

PyMOL of d1v2ya_

>d1bt0a_ d.15.1.1 (A:) Rub1 {Mouse-ear cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1z2ma2 d.15.1.1 (A:79-154) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ogwa_ d.15.1.1 (A:) Ubiquitin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wh3a_ d.15.1.1 (A:) 2'-5'-oligoadenylate synthetase-like protein, OASL {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2zeqa1 d.15.1.1 (A:1-78) Ubiquitin-like domain of parkin {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2faza1 d.15.1.1 (A:1-76) Ubiquitin-like PHD and RING finger domain-containing protein 1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ttna1 d.15.1.1 (A:21-100) Dendritic cell-derived ubiquitin-like protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1uela_ d.15.1.1 (A:) Ubiquitin-like domain of Rad23 homolog B (Hhr23B) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1m94a_ d.15.1.1 (A:) Ubiquitin-like modifier protein hub1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d2bwfa1 d.15.1.1 (A:2-74) DSK2 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure

>d1oqya4 d.15.1.1 (A:1-77) Ubiquitin-like domain of Rad23 homolog A (Hhr23a) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wy8a1 d.15.1.1 (A:8-83) Ubiquitin-like PHD and RING finger domain-containing protein 2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1v5oa_ d.15.1.1 (A:) 1700011n24rik protein {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1wx9a1 d.15.1.1 (A:8-80) Large proline-rich protein BAT3 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1yqba1 d.15.1.1 (A:15-98) Ubiquilin-3 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1z2ma1 d.15.1.1 (A:3-78) Interferon-induced 15 kDa protein {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1j8ca_ d.15.1.1 (A:) Ubiquitin-like N-terminal domain of PLIC-2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wx8a1 d.15.1.1 (A:8-90) 4931431F19Rik {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1zkha1 d.15.1.1 (A:1-86) Splicing factor 3 subunit 1, C-terminal domain {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wxva1 d.15.1.1 (A:7-87) Bag-family molecular chaperone regulator-1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wiaa_ d.15.1.1 (A:) Ubiquitin-like protein bab25500 (2010008E23Rik) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1uh6a_ d.15.1.1 (A:) Ubiquitin-like protein 5, ubl5 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1se9a_ d.15.1.1 (A:) Hypothetical protein At3g01050 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1wgga_ d.15.1.1 (A:) Ubiquitin carboxyl-terminal hydrolase 14 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1v86a_ d.15.1.1 (A:) hypothetical D7wsu128e protein {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1v5ta_ d.15.1.1 (A:) 8430435i17rik protein {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1wjua_ d.15.1.1 (A:) NEDD8 ultimate buster-1, NUB1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wgha_ d.15.1.1 (A:) Ubiquitin-like protein 3, Ubl3 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1we6a_ d.15.1.1 (A:) Splicing factor 3 subunit 1, C-terminal domain {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1wgda_ d.15.1.1 (A:) Homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein, HERPUD1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1euvb_ d.15.1.1 (B:) SUMO-1 (smt3 homologue) {Baker's yeast (Saccharomyces cerevisiae), smt3 [TaxId: 4932]}	Back information, alignment and structure

>d1wjna_ d.15.1.1 (A:) Tubulin-folding protein TbcE {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1v6ea_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1x1ma1 d.15.1.1 (A:8-101) Ubiquitin-like protein 7 {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2uyzb1 d.15.1.1 (B:20-96) SUMO-1 (smt3 homologue) {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d2c9wb1 d.15.1.1 (B:2-104) Elongin B {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1t0ya_ d.15.1.1 (A:) Ubiquitin-like domain of tubulin folding cofactor B {Nematode (Caenorhabditis elegans) [TaxId: 6239]}	Back information, alignment and structure

>d1wm3a_ d.15.1.1 (A:) SUMO-2 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wf9a1 d.15.1.1 (A:8-101) NPL4-like protein 1 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}	Back information, alignment and structure

>d1i42a_ d.15.1.2 (A:) p47 {Rat (Rattus norvegicus) [TaxId: 10116]}	Back information, alignment and structure

>d1vjka_ d.15.3.1 (A:) Molybdopterin synthase subunit MoaD {Pyrococcus furiosus [TaxId: 2261]}	Back information, alignment and structure

>d2al3a1 d.15.1.2 (A:10-85) Tether containing UBX domain for GLUT4 (Tug) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d2cr5a1 d.15.1.2 (A:8-103) UBX domain-containing protein 6 (Reproduction 8) {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1h8ca_ d.15.1.2 (A:) Fas-associated factor 1, Faf1 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1xo3a_ d.15.3.3 (A:) C9orf74 homolog {Mouse (Mus musculus) [TaxId: 10090]}	Back information, alignment and structure

>d1ef1a3 d.15.1.4 (A:4-87) Moesin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1wj4a_ d.15.1.2 (A:) Hypothetical protein KIAA0794 {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1h4ra3 d.15.1.4 (A:20-103) Merlin {Human (Homo sapiens) [TaxId: 9606]}	Back information, alignment and structure

>d1ip9a_ d.15.2.2 (A:) Bud emergence mediator Bemp1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}	Back information, alignment and structure