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
Q7TQI3 UniProt NPD GO	OTUB1_MOUSE	Ubiquitin thioesterase protein OTUB1 (EC 3.4.-.-) (Otubain 1) (OTU domain-containing ubiquitin aldeh ...	0.39	-	cyt	0					271
P31254 UniProt NPD GO	UBE1Y_MOUSE	Ubiquitin-activating enzyme E1 Y (Fragment)	0.39	-	cyt	0					442
P52478 UniProt NPD GO	UBC1_CAEEL	Ubiquitin-conjugating enzyme E2 1 (EC 6.3.2.19) (Ubiquitin-protein ligase 1) (Ubiquitin carrier prot ...	0.39	-	nuc	0				1Z3D	192
Q6FR76 UniProt NPD GO	UBC2_CANGA	Ubiquitin-conjugating enzyme E2 2 (EC 6.3.2.19) (Ubiquitin-protein ligase UBC2) (Ubiquitin carrier p ...	0.39	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				167
Q96UP5 UniProt NPD GO	UBC2_EMENI	Ubiquitin-conjugating enzyme E2 2 (EC 6.3.2.19) (Ubiquitin-protein ligase ubc2) (Ubiquitin carrier p ...	0.39	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				151
P49428 UniProt NPD GO	UBCX_PICPA	Ubiquitin-conjugating enzyme E2-24 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.39	-	nuc	0	Peroxisome				204
Q8NCU1 UniProt NPD GO	CN048_HUMAN	Uncharacterized protein C14orf48	0.39	-	nuc	0					140
Q8R1Y2 UniProt NPD GO	CP045_MOUSE	Uncharacterized protein C16orf45 homolog	0.39	-	nuc	0					203
P38162 UniProt NPD GO	YBK7_YEAST	Uncharacterized protein YBL107C	0.39	-	nuc	0		cytoplasm [IDA]			196
P53130 UniProt NPD GO	YGM1_YEAST	Uncharacterized protein YGL121C	0.39	-	cyt	0					126
P38884 UniProt NPD GO	YHZ8_YEAST	Uncharacterized protein YHR198C	0.39	-	mit	0		mitochondrion [IDA]			321
Q12291 UniProt NPD GO	YL063_YEAST	Uncharacterized protein YLR063W	0.39	-	mit	0	Cytoplasm	cytoplasm [IDA]			365
P52623 UniProt NPD GO	UCK1_MOUSE	Uridine-cytidine kinase 1 (EC 2.7.1.48) (UCK 1) (Uridine monophosphokinase 1) (Cytidine monophosphok ...	0.39	+	cyt	0					277
Q94480 UniProt NPD GO	V136_DICDI	VEG136 protein (Fragment)	0.39	-	nuc	0					357
P40157 UniProt NPD GO	VID27_YEAST	Vacuolar import and degradation protein 27	0.39	-	nuc	0	Cytoplasm	cytoplasm [IDA]			782
Q80TY5 UniProt NPD GO	VP13B_MOUSE	Vacuolar protein sorting 13B (Cohen syndrome protein 1 homolog) (Fragment)	0.39	-	nuc	0	Membrane; multi-pass membrane protein (Potential)				1603
Q5TJF0 UniProt NPD GO	VPS52_CANFA	Vacuolar protein sorting protein 52	0.39	-	end	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein (By ...				723
Q9UN37 UniProt NPD GO	VPS4A_HUMAN	Vacuolar sorting protein 4a (SKD2 protein) (hVPS4) (VPS4-1)	0.39	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Membrane-associated in the prevacuolar endosomal c ...	cytoplasm [IDA] perinuclear region [IDA]	609982		437
O35251 UniProt NPD GO	VEGFD_RAT	Vascular endothelial growth factor D precursor (VEGF-D) (c-fos-induced growth factor) (FIGF)	0.39	-	nuc	1 *	Secreted protein (By similarity)				326
P11858 UniProt NPD GO	NEUV_RANES	Vasotocin-neurophysin VT precursor (VT) [Contains: Hydrin-2 (Hydrin II); Vasotocin; Neurophysin VT]	0.39	-	nuc	0	Secreted protein				141
Q3HXY3 UniProt NPD GO	NGFV1_PSEAU	Venom nerve growth factor 1 precursor (vNGF-1)	0.39	-	exc	0	Secreted protein				242
Q3HXY1 UniProt NPD GO	NGFV3_PSEAU	Venom nerve growth factor 3 precursor (vNGF-3)	0.39	-	exc	0	Secreted protein				242
P38362 UniProt NPD GO	YB8J_YEAST	Very hypothetical protein YBR300C	0.39	-	nuc	1 *					165
P53291 UniProt NPD GO	YG3U_YEAST	Very hypothetical protein YGL164W	0.39	-	mit	0					111
O89116 UniProt NPD GO	VTI1A_MOUSE	Vesicle transport through interaction with t-SNAREs homolog 1A (Vesicle transport v-SNARE protein Vt ...	0.39	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein. Mainly associated with the Go ...				217
Q28661 UniProt NPD GO	PROC_RABIT	Vitamin K-dependent protein C precursor (EC 3.4.21.69) (Autoprothrombin IIA) (Anticoagulant protein ...	0.39	-	mit	0		extracellular region [ISS]			458
Q8WXS5 UniProt NPD GO	CCG8_HUMAN	Voltage-dependent calcium channel gamma-8 subunit (Neuronal voltage-gated calcium channel gamma-8 su ...	0.39	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)	voltage-gated calcium channel complex [NAS]	606900		425
Q8VIC7 UniProt NPD GO	VN1A2_MOUSE	Vomeronasal type-1 receptor A2 (Pheromone receptor 2) (Vomeronasal type-1 receptor A9) (mV1R2)	0.39	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				318
Q9SW08 UniProt NPD GO	WBC4_ARATH	White-brown complex homolog protein 4	0.39	-	end	7	Membrane; multi-pass membrane protein (By similarity)				577
Q9FNB5 UniProt NPD GO	WBC6_ARATH	White-brown complex homolog protein 6	0.39	-	end	6	Membrane; multi-pass membrane protein (By similarity)				727
Q5QQ49 UniProt NPD GO	XYLT2_BOVIN	Xylosyltransferase 2 (EC 2.4.2.26) (Xylosyltransferase II) (Peptide O-xylosyltransferase 2)	0.39	-	mit	1 *	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...				867
Q9EPL0 UniProt NPD GO	XYLT2_MOUSE	Xylosyltransferase 2 (EC 2.4.2.26) (Xylosyltransferase II) (Peptide O-xylosyltransferase 2)	0.39	-	mit	1 *	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...				865
Q9H1B5 UniProt NPD GO	XYLT2_HUMAN	Xylosyltransferase 2 (EC 2.4.2.26) (Xylosyltransferase II) (xylT-II) (XT-II) (Peptide O-xylosyltrans ...	0.39	-	mit	1 *	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...		608125		865
P13675 UniProt NPD GO	SMY_MOUSE	Y-linked testis-specific protein	0.39	+	mit	0					232
Q5JLB5 UniProt NPD GO	ZFNL2_ORYSA	Zinc finger CCCH domain-containing protein ZFN-like 2	0.39	-	nuc	0	Nucleus (By similarity)				439
Q60821 UniProt NPD GO	ZBT17_MOUSE	Zinc finger and BTB domain-containing protein 17 (Zinc finger protein 151) (Zinc finger protein 100) ...	0.39	-	nuc	0	Nucleus (By similarity)				794
Q6P560 UniProt NPD GO	ZN182_MOUSE	Zinc finger protein 182 (Zinc finger protein 21)	0.39	-	nuc	0	Nucleus (Potential)				627
Q9UJW7 UniProt NPD GO	ZN229_HUMAN	Zinc finger protein 229 (Fragment)	0.39	-	nuc	0	Nucleus (Probable)				420
P24399 UniProt NPD GO	ZN239_MOUSE	Zinc finger protein 239 (Zfp-239) (Zinc finger protein MOK-2)	0.39	-	nuc	0	Nucleus (Potential)				201
Q96NJ6 UniProt NPD GO	ZFP3_HUMAN	Zinc finger protein 3 homolog (Zfp-3)	0.39	-	nuc	0	Nucleus (Potential)		194480		502
Q9Y4L5 UniProt NPD GO	ZN364_HUMAN	Zinc finger protein 364 (Rabring 7) (RING finger protein 115)	0.39	-	nuc	0					304
Q8N0Y2 UniProt NPD GO	ZN444_HUMAN	Zinc finger protein 444 (Endothelial zinc finger protein 2) (EZF-2) (Zinc finger and SCAN domain-con ...	0.39	-	nuc	0	Nucleus (Potential)		607874		327
Q6V9R5 UniProt NPD GO	ZN562_HUMAN	Zinc finger protein 562	0.39	-	nuc	0	Nucleus (Potential)				426
Q7Z3V5 UniProt NPD GO	ZN571_HUMAN	Zinc finger protein 571	0.39	-	nuc	0	Nucleus (Potential)				609
Q5R5Q6 UniProt NPD GO	ZN571_PONPY	Zinc finger protein 571	0.39	-	nuc	0	Nucleus (Probable)				608
Q9Y5V0 UniProt NPD GO	ZN706_HUMAN	Zinc finger protein 706	0.39	-	nuc	0					76
Q9D115 UniProt NPD GO	ZN706_MOUSE	Zinc finger protein 706	0.39	-	nuc	0					76
P36508 UniProt NPD GO	ZNF76_HUMAN	Zinc finger protein 76	0.39	-	nuc	0	Nucleus (Potential)		194549		570
O75312 UniProt NPD GO	ZPR1_HUMAN	Zinc-finger protein ZPR1 (Zinc finger protein 259)	0.39	-	nuc	0	Cytoplasm. Nucleus. Translocates to the nucleus after treatment with mitogens	cytoplasm [TAS] nucleolus [TAS] nucleus [TAS]	603901		459
Q60736 UniProt NPD GO	ZP3R_MOUSE	Zona pellucida sperm-binding protein 3 receptor precursor (Sperm fertilization protein 56) (sp56)	0.39	-	nuc	0	Acrosome; acrosomal lumen. Sperm acrosomal matrix	acrosomal matrix [IDA]			579

You are viewing entries 33101 to 33150 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.