NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
O12990 UniProt NPD GO	JAK1_BRARE	Tyrosine-protein kinase Jak1 (EC 2.7.10.2) (Janus kinase 1) (Jak-1)	0.65	-	cyt	0	Intracytoplasmic membrane; peripheral membrane protein. Wholly intracellular, possibly membrane asso ...				1153
P34138 UniProt NPD GO	PTP2_DICDI	Tyrosine-protein phosphatase 2 (EC 3.1.3.48) (Protein-tyrosine-phosphate phosphohydrolase 2) (PTPA)	0.65	+	nuc	0					377
Q9NYH9 UniProt NPD GO	UTP6_HUMAN	U3 small nucleolar RNA-associated protein 6 homolog (Multiple hat domains protein) (Hepatocellular c ...	0.65	-	cyt	0	Nucleus; nucleolus				597
O22212 UniProt NPD GO	PRP4_ARATH	U4/U6 small nuclear ribonucleoprotein PRP4-like protein	0.65	-	nuc	0					554
P34223 UniProt NPD GO	UBX1_YEAST	UBX domain-containing protein 1 (Suppressor of high-copy PP1 protein)	0.65	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]			423
Q12229 UniProt NPD GO	UBX3_YEAST	UBX domain-containing protein 3	0.65	-	nuc	1	Cytoplasm	cytoplasm [IDA]			455
Q6P7A2 UniProt NPD GO	UBE4A_RAT	Ubiquitin conjugation factor E4 A	0.65	-	cyt	0					1066
Q8TBB1 UniProt NPD GO	LNX1_HUMAN	Ubiquitin ligase LNX (EC 6.3.2.-) (Numb-binding protein 1) (Ligand of Numb-protein X 1)	0.65	-	nuc	0	Cytoplasm (By similarity)		609732		728
P25865 UniProt NPD GO	UBC1_ARATH	Ubiquitin-conjugating enzyme E2-17 kDa 1 (EC 6.3.2.19) (Ubiquitin-protein ligase 1) (Ubiquitin carri ...	0.65	-	nuc	0				2AAK	152
P42745 UniProt NPD GO	UBC2_ARATH	Ubiquitin-conjugating enzyme E2-17 kDa 2 (EC 6.3.2.19) (Ubiquitin-protein ligase 2) (Ubiquitin carri ...	0.65	-	nuc	0					152
Q7TMI3 UniProt NPD GO	UHRF2_MOUSE	Ubiquitin-like PHD and RING finger domain-containing protein 2 (EC 6.3.2.-) (Ubiquitin-like-containi ...	0.65	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			803
Q8K1B8 UniProt NPD GO	URP2_MOUSE	Unc-112-related protein 2 (Kindlin-3)	0.65	-	cyt	0	Cytoplasm (Probable)				665
Q8IXX5 UniProt NPD GO	CA037_HUMAN	Uncharacterized protein C1orf37	0.65	-	nuc	1					376
Q95JR6 UniProt NPD GO	CT152_MACFA	Uncharacterized protein C20orf152 homolog	0.65	-	mit	0					585
P38202 UniProt NPD GO	YBC8_YEAST	Uncharacterized protein YBL028C	0.65	-	nuc	0		nucleolus [IDA] nucleus [IDA]			106
P25586 UniProt NPD GO	YCF9_YEAST	Uncharacterized protein YCL059C	0.65	-	nuc	0		nucleolus [IDA] small nucleolar ribonucleoprotein complex [IPI]			316
P25591 UniProt NPD GO	YCG3_YEAST	Uncharacterized protein YCL063W	0.65	-	nuc	0		vacuolar membrane [IDA]			423
P40052 UniProt NPD GO	YEQ9_YEAST	Uncharacterized protein YER079W	0.65	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			210
P40063 UniProt NPD GO	YET4_YEAST	Uncharacterized protein YER104W	0.65	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			208
P42947 UniProt NPD GO	YJK7_YEAST	Uncharacterized protein YJL107C	0.65	+	nuc	0					387
P42842 UniProt NPD GO	YN53_YEAST	Uncharacterized protein YNL313C	0.65	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			904
P48970 UniProt NPD GO	UNIV_STRPU	Univin precursor	0.65	-	exc	0	Secreted protein (By similarity)				395
P38263 UniProt NPD GO	VID24_YEAST	Vacuolar import and degradation protein 24 (Glucose-induced degradation protein 4)	0.65	-	nuc	0	Cytoplasmic vesicle; cytoplasmic vesicle membrane; peripheral membrane protein. FBPase-containing ve ...	cytoplasmic membrane-bound vesicle [IDA] extrinsic to membrane [IDA]			362
Q9H270 UniProt NPD GO	VPS11_HUMAN	Vacuolar protein sorting 11 (hVPS11) (RING finger protein 108)	0.65	-	cyt	0	Late endosome; late endosomal membrane; peripheral membrane protein. Lysosome; lysosomal membrane; p ...		608549		941
P32609 UniProt NPD GO	PEP7_YEAST	Vacuolar segregation protein PEP7 (Protein VAC1) (Vacuolar protein sorting 19)	0.65	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein; cytoplasmic side	cytoplasm [IDA] external side of endosome membrane [IDA]			515
P53767 UniProt NPD GO	VGFR1_RAT	Vascular endothelial growth factor receptor 1 precursor (EC 2.7.10.1) (VEGFR-1) (Tyrosine-protein ki ...	0.65	-	end	0	Membrane; single-pass type I membrane protein				1336
Q6DF55 UniProt NPD GO	VASN_XENTR	Vasorin precursor	0.65	-	exc	1	Membrane; single-pass type I membrane protein (Probable)				661
Q3HXX7 UniProt NPD GO	NGFV2_TROCA	Venom nerve growth factor 2 precursor (vNGF-2)	0.65	-	exc	0	Secreted protein				244
P13918 UniProt NPD GO	VCLC_PEA	Vicilin precursor	0.65	-	nuc	0	Protein body. Vacuole. Cotyledonary membrane-bound vacuolar protein bodies				459
Q00341 UniProt NPD GO	VIGLN_HUMAN	Vigilin (High density lipoprotein-binding protein) (HDL-binding protein)	0.65	-	cyt	0	Cytoplasm. Nucleus	plasma membrane [TAS]	142695	2CTM	1268
Q9Z1A6 UniProt NPD GO	VIGLN_RAT	Vigilin (High density lipoprotein-binding protein) (HDL-binding protein)	0.65	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				1268
O65570 UniProt NPD GO	VILI4_ARATH	Villin-4	0.65	-	nuc	0					974
Q05808 UniProt NPD GO	VIT_ANTGR	Vitellogenin precursor [Contains: YP47; YP160]	0.65	-	nuc	0	Secreted protein				1790
Q8R0S4 UniProt NPD GO	CACB4_MOUSE	Voltage-dependent L-type calcium channel subunit beta-4 (CAB4) (Calcium channel voltage-dependent su ...	0.65	-	nuc	0		voltage-gated calcium channel complex [TAS]			486
Q02294 UniProt NPD GO	CAC1B_RAT	Voltage-dependent N-type calcium channel subunit alpha-1B (Voltage-gated calcium channel subunit alp ...	0.65	-	end	19	Membrane; multi-pass membrane protein	plasma membrane [IDA]			2336
P49659 UniProt NPD GO	CTK1_RABIT	Voltage-independent pH-sensitive potassium channel (RACTK1)	0.65	-	mit	0	Membrane; multi-pass membrane protein				284
Q9P7C0 UniProt NPD GO	YKU5_SCHPO	WD repeat protein C2E1P5.05 in chromosome I	0.65	-	cyt	0	Nucleus				524
Q9GZV5 UniProt NPD GO	WWTR1_HUMAN	WW domain-containing transcription regulator protein 1 (Transcriptional coactivator with PDZ-binding ...	0.65	-	nuc	0	Nucleus. Cytoplasm. Concentrates along specific portions of the plasma membrane, and accumulates in ...	nucleus [NAS]	607392		400
P22561 UniProt NPD GO	WT1_MOUSE	Wilms' tumor protein homolog	0.65	+	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			449
P49952 UniProt NPD GO	WT1_RAT	Wilms' tumor protein homolog	0.65	+	nuc	0	Nucleus				448
O36027 UniProt NPD GO	WSP1_SCHPO	Wiskott-Aldrich syndrome homolog protein 1	0.65	-	nuc	0		cell tip [TAS] contractile ring (sensu Fungi) [TAS]			574
Q9N1T2 UniProt NPD GO	RPGR_CANFA	X-linked retinitis pigmentosa GTPase regulator	0.65	+	nuc	0	Golgi apparatus (By similarity)	Golgi apparatus [ISS]			1003
P41824 UniProt NPD GO	YBOXH_APLCA	Y-box factor homolog (APY1)	0.65	-	nuc	0	Nucleus (Probable)				253
Q8VDM1 UniProt NPD GO	ZGPAT_MOUSE	Zinc finger CCCH-type with G patch domain protein	0.65	-	nuc	0					511
Q96K21 UniProt NPD GO	ZFY19_HUMAN	Zinc finger FYVE domain-containing protein 19 (MLL partner containing FYVE domain)	0.65	-	nuc	0					471
Q24JY4 UniProt NPD GO	ZNHI1_BOVIN	Zinc finger HIT domain-containing protein 1	0.65	-	nuc	0					154
O43257 UniProt NPD GO	ZNHI1_HUMAN	Zinc finger HIT domain-containing protein 1 (Cyclin-G1-binding protein 1)	0.65	-	nuc	0					154
P98168 UniProt NPD GO	ZXDA_HUMAN	Zinc finger X-linked protein ZXDA	0.65	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	300235		799
Q9P2Y4 UniProt NPD GO	ZN219_HUMAN	Zinc finger protein 219	0.65	-	nuc	0	Nucleus	nucleus [TAS]	605036		722
Q9NZL3 UniProt NPD GO	ZN224_HUMAN	Zinc finger protein 224 (Zinc finger protein 255) (Bone marrow zinc finger 2) (BMZF-2)	0.65	-	nuc	0	Nucleus		606955		707

You are viewing entries 16651 to 16700 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.