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
Q9Y5J1 UniProt NPD GO	UTP18_HUMAN	U3 small nucleolar RNA-associated protein 18 homolog (WD repeat protein 50)	0.74	+	nuc	0	Nucleus; nucleolus	nucleus [IDA] small nucleolar ribonucleoprotein complex [ISS]			556
Q5U5C5 UniProt NPD GO	PRP31_XENLA	U4/U6 small nuclear ribonucleoprotein Prp31 (Pre-mRNA-processing factor 31)	0.74	-	nuc	0	Nucleus (By similarity)				498
Q5TJF3 UniProt NPD GO	RING1_CANFA	Ubiquitin ligase protein RING1 (EC 6.3.2.-) (RING finger protein 1) (RING1a)	0.74	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				406
Q9SPL2 UniProt NPD GO	CIP8_ARATH	Ubiquitin-protein ligase CIP8 (EC 6.3.2.-) (COP1-interacting protein 8)	0.74	-	nuc	0	Cytoplasm (Probable)				334
Q9WTV6 UniProt NPD GO	UBP18_MOUSE	Ubl carboxyl-terminal hydrolase 18 (EC 3.1.2.-) (Ubl thioesterase 18) (ISG15-specific-processing pro ...	0.74	-	cyt	0					368
Q96B23 UniProt NPD GO	CR025_HUMAN	Uncharacterized protein C18orf25	0.74	-	nuc	0					404
Q96MY1 UniProt NPD GO	CT112_HUMAN	Uncharacterized protein C20orf112	0.74	-	nuc	0					436
Q5RFT9 UniProt NPD GO	CT112_PONPY	Uncharacterized protein C20orf112 homolog	0.74	-	nuc	0					436
Q96M20 UniProt NPD GO	CT152_HUMAN	Uncharacterized protein C20orf152	0.74	-	mit	0					576
Q12167 UniProt NPD GO	YD065_YEAST	Uncharacterized protein YDR065W	0.74	+	nuc	0	Mitochondrion	mitochondrion [IDA]			365
P43598 UniProt NPD GO	YFI7_YEAST	Uncharacterized protein YFR017C	0.74	-	nuc	0		cytoplasm [IDA]			195
P50091 UniProt NPD GO	YG53_YEAST	Uncharacterized protein YGR239C	0.74	-	nuc	0		cytosol [IDA] peroxisome [IDA]			288
P38757 UniProt NPD GO	YHG4_YEAST	Uncharacterized protein YHR004C	0.74	-	nuc	1		integral to membrane [IDA] mitochondrion [IDA] nuclear envelope-endoplasmic reticulum network [IDA]			446
P39526 UniProt NPD GO	YJU7_YEAST	Uncharacterized protein YJL207C	0.74	+	cyt	0					2014
P53725 UniProt NPD GO	YN8D_YEAST	Uncharacterized protein YNR024W	0.74	-	nuc	0		nucleus [IDA]			186
Q12194 UniProt NPD GO	YP066_YEAST	Uncharacterized protein YPL066W	0.74	-	nuc	0		bud neck [IDA] cytoplasm [IDA]			479
Q12467 UniProt NPD GO	YP168_YEAST	Uncharacterized protein YPL168W	0.74	-	nuc	1	Mitochondrion; mitochondrial membrane; single-pass membrane protein (Potential)	mitochondrion [IDA]			430
Q80T11 UniProt NPD GO	USH1G_MOUSE	Usher syndrome type-1G protein homolog (Scaffold protein containing ankyrin repeats and SAM domain) ...	0.74	-	nuc	0					461
P20795 UniProt NPD GO	VPS33_YEAST	Vacuolar protein sorting 33 (SLP1 protein)	0.74	-	cyt	0		cytosol [IDA] HOPS complex [IPI] vacuolar membrane (sensu Fungi) [IDA]			691
Q8CCB4 UniProt NPD GO	VPS53_MOUSE	Vacuolar protein sorting protein 53	0.74	-	mit	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein (By ...				832
P43585 UniProt NPD GO	VTC2_YEAST	Vacuolar transporter chaperone 2 (Phosphate metabolism protein 1)	0.74	+	nuc	3	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuolar membrane [IDA]			828
Q8IWG1 UniProt NPD GO	WDR63_HUMAN	WD repeat protein 63 (Testis development protein NYD-SP29)	0.74	-	nuc	0					891
Q9ZVF5 UniProt NPD GO	WOX6_ARATH	WUSCHEL-related homeobox 6 (Protein PRETTY FEW SEEDS2)	0.74	-	nuc	0	Nucleus (By similarity)				271
Q5HZF2 UniProt NPD GO	WBP4_RAT	WW domain-binding protein 4 (WBP-4)	0.74	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				374
P42768 UniProt NPD GO	WASP_HUMAN	Wiskott-Aldrich syndrome protein (WASp)	0.74	-	nuc	0		actin cytoskeleton [TAS]	300392	2A3Z	501
P21574 UniProt NPD GO	YBX2A_XENLA	Y-box-binding protein 2-A (Cytoplasmic RNA-binding protein p56) (mRNP4)	0.74	-	nuc	0	Cytoplasm. Either free or associated with ribonucleoprotein particles				336
Q04437 UniProt NPD GO	KU80_YEAST	Yeast Ku80 protein (High affinity DNA-binding factor subunit 2)	0.74	-	nuc	0	Nucleus	nuclear chromatin [TAS] nuclear telomeric heterochromatin [TAS]			629
Q8N5P1 UniProt NPD GO	ZC3H8_HUMAN	Zinc finger CCCH domain-containing protein 8	0.74	-	nuc	0	Nucleus (By similarity)				291
Q6IR42 UniProt NPD GO	ZCPW1_MOUSE	Zinc finger CW-type PWWP domain protein 1 homolog	0.74	-	nuc	0					630
Q9DAZ9 UniProt NPD GO	ZFY19_MOUSE	Zinc finger FYVE domain-containing protein 19	0.74	-	nuc	0				1WFK	389
Q7TQG0 UniProt NPD GO	ZBTB5_MOUSE	Zinc finger and BTB domain-containing protein 5 (Transcription factor ZNF-POZ)	0.74	+	nuc	0	Nucleus (Potential)				670
O15156 UniProt NPD GO	ZBT7B_HUMAN	Zinc finger and BTB domain-containing protein 7B (Zinc finger protein 67 homolog) (Zfp-67) (Zinc fin ...	0.74	+	nuc	0	Nucleus		607646		539
Q96NC0 UniProt NPD GO	ZMAT2_HUMAN	Zinc finger matrin type 2	0.74	-	nuc	0	Nucleus (Potential)				199
Q9CPW7 UniProt NPD GO	ZMAT2_MOUSE	Zinc finger matrin type 2	0.74	-	nuc	0	Nucleus (Potential)				199
Q06732 UniProt NPD GO	ZN11B_HUMAN	Zinc finger protein 11B	0.74	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	194522		778
Q15928 UniProt NPD GO	ZN141_HUMAN	Zinc finger protein 141	0.74	-	nuc	0	Nucleus (Potential)		194648		474
O75820 UniProt NPD GO	ZN189_HUMAN	Zinc finger protein 189	0.74	-	nuc	0	Nucleus (Probable)		603132		626
Q91VN1 UniProt NPD GO	ZNF24_MOUSE	Zinc finger protein 24 (Zinc finger protein 191) (Zfp-191) (Zinc finger protein ZF-12)	0.74	-	nuc	0	Nucleus (Potential)				368
Q60585 UniProt NPD GO	ZFP30_MOUSE	Zinc finger protein 30 (Zfp-30)	0.74	-	nuc	0	Nucleus (Potential)				533
Q96PQ6 UniProt NPD GO	ZN317_HUMAN	Zinc finger protein 317	0.74	-	nuc	0	Nucleus (Probable)				595
Q8JZL0 UniProt NPD GO	ZN467_MOUSE	Zinc finger protein 467 (Endothelial cell-derived zinc finger protein) (EZI)	0.74	-	nuc	0	Nucleus	nucleus [IDA]			594
Q8BI67 UniProt NPD GO	ZN473_MOUSE	Zinc finger protein 473 homolog (Zinc finger protein 100) (Zfp-100)	0.74	-	nuc	0	Nucleus (By similarity)				892
Q9UKT9 UniProt NPD GO	AIOL_HUMAN	Zinc finger protein Aiolos	0.74	-	nuc	0	Nucleus (Probable)		606221		509
Q9C7E8 UniProt NPD GO	COL15_ARATH	Zinc finger protein CONSTANS-LIKE 15	0.74	-	nuc	0	Nucleus (Potential)				433
Q22398 UniProt NPD GO	NAS22_CAEEL	Zinc metalloproteinase nas-22 precursor (EC 3.4.24.21) (Nematode astacin 22)	0.74	-	nuc	0	Secreted protein (Potential)				595
P27815 UniProt NPD GO	PDE4A_HUMAN	cAMP-specific 3',5'-cyclic phosphodiesterase 4A (EC 3.1.4.17) (DPDE2) (PDE46)	0.74	-	nuc	0	Isoform 4: Membrane; peripheral membrane protein. Isoform 4 has propensity for association with memb ...	insoluble fraction [TAS] membrane fraction [TAS] soluble fraction [TAS]	600126		886
Q6BY20 UniProt NPD GO	PALF_DEBHA	pH-response regulator protein palF/RIM8	0.74	-	nuc	0					782
Q4WY67 UniProt NPD GO	PACC_ASPFU	pH-response transcription factor pacC/RIM101	0.74	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				676
P58871 UniProt NPD GO	TB182_MOUSE	182 kDa tankyrase 1-binding protein (Fragment)	0.73	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Colocalizes with chromosomes during mitosis, and ...				909
P02365 UniProt NPD GO	RS6_YEAST	40S ribosomal protein S6 (S10) (YS4) (RP9)	0.73	-	nuc	0		cytoplasm [IDA] cytosolic small ribosomal subunit (sensu Eu... [TAS] small nucleolar ribonucleoprotein complex [IPI]			236

You are viewing entries 12151 to 12200 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.