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
Q5J3L7 UniProt NPD GO	VN1B5_RAT	Vomeronasal type-1 receptor B5 (Vomeronasal receptor 4) (Pheromone receptor VN4) (M21 pheromone rece ...	0.35	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				310
Q3UGF1 UniProt NPD GO	WDR19_MOUSE	WD repeat protein 19	0.35	-	cyt	0					1341
Q9CX97 UniProt NPD GO	WDR55_MOUSE	WD repeat protein 55	0.35	-	cyt	0					388
Q562E7 UniProt NPD GO	WDR81_HUMAN	WD repeat protein 81	0.35	-	cyt	0					890
Q9NZC7 UniProt NPD GO	WWOX_HUMAN	WW domain-containing oxidoreductase (EC 1.1.1.-) (Fragile site FRA16D oxidoreductase)	0.35	-	cyt	0	Cytoplasm. Nucleus. Mitochondrion. Partially localizes to the mitochondria. Ref.16: Golgi apparatus. ...	cytoplasm [TAS]	133239	1WMV	414
Q94129 UniProt NPD GO	WRT4_CAEEL	Warthog protein 4 precursor (M75 protein) [Contains: Warthog protein 4 N-product; Warthog protein 4 ...	0.35	-	end	0	Warthog protein 4: Secreted protein (By similarity). Cell surface (By similarity). Warthog protein 4 ...	extracellular region [NAS] plasma membrane [NAS]			557
Q5GH66 UniProt NPD GO	XKR5_MOUSE	XK-related protein 5	0.35	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				676
P06676 UniProt NPD GO	ZEA8_MAIZE	Zein-alpha 19C1 precursor (19 kDa zein 19C1)	0.35	-	exc	0					240
P06677 UniProt NPD GO	ZEA9_MAIZE	Zein-alpha 19C2 precursor (19 kDa zein 19C2)	0.35	-	exc	0					240
P04703 UniProt NPD GO	ZEA7_MAIZE	Zein-alpha A20 precursor (19 kDa zein A20)	0.35	-	exc	0					240
P04698 UniProt NPD GO	ZEAZ_MAIZE	Zein-alpha PZ22.3 precursor (22 kDa zein PZ22.3)	0.35	-	exc	0					267
Q8WW36 UniProt NPD GO	ZCH13_HUMAN	Zinc finger CCHC domain-containing protein 13	0.35	+	nuc	0					166
Q9D5Z5 UniProt NPD GO	ZMY17_MOUSE	Zinc finger MYND domain-containing protein 17	0.35	-	mit	0					446
Q15973 UniProt NPD GO	ZN124_HUMAN	Zinc finger protein 124 (HZF-16)	0.35	-	nuc	0	Nucleus (Potential)		194631		351
P52744 UniProt NPD GO	ZN138_HUMAN	Zinc finger protein 138 (Fragment)	0.35	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	604080		239
Q8N7M2 UniProt NPD GO	ZN283_HUMAN	Zinc finger protein 283	0.35	-	nuc	0	Nucleus (Probable)				609
Q95K52 UniProt NPD GO	ZN283_MACFA	Zinc finger protein 283	0.35	-	nuc	0	Nucleus (Probable)				654
P17039 UniProt NPD GO	ZNF30_HUMAN	Zinc finger protein 30 (Zinc finger protein KOX28)	0.35	-	nuc	0	Nucleus (Potential)				542
Q14585 UniProt NPD GO	ZN345_HUMAN	Zinc finger protein 345 (Zinc finger protein HZF10)	0.35	-	nuc	0	Nucleus (Probable)				488
O75123 UniProt NPD GO	ZN623_HUMAN	Zinc finger protein 623	0.35	-	nuc	0	Nucleus (Potential)				536
O17264 UniProt NPD GO	NAS27_CAEEL	Zinc metalloproteinase nas-27 precursor (EC 3.4.24.21) (Nematode astacin 27)	0.35	-	nuc	0	Secreted protein (Potential)				428
P42098 UniProt NPD GO	ZP3_PIG	Zona pellucida sperm-binding protein 3 precursor (Zona pellucida sperm-binding protein C) (Zona pell ...	0.35	-	nuc	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein; extracellular ...				421
O55028 UniProt NPD GO	BCKD_MOUSE	[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial precursor (EC 2.7.11.4) (B ...	0.35	-	nuc	0	Mitochondrion; mitochondrial matrix	alpha-ketoglutarate dehydrogenase complex (... [ISS] mitochondrion [ISS]			412
Q9Y233 UniProt NPD GO	PDE10_HUMAN	cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A (EC 3.1.4.17)	0.35	-	mit	0	Located mostly to soluble cellular fractions			1LRB	779
P31322 UniProt NPD GO	KAP3_BOVIN	cAMP-dependent protein kinase type II-beta regulatory subunit	0.35	-	cyt	0					417
P56211 UniProt NPD GO	ARP19_HUMAN	cAMP-regulated phosphoprotein 19 (ARPP-19)	0.35	-	nuc	0	Cytoplasm (By similarity)		605487		111
P56212 UniProt NPD GO	ARP19_MOUSE	cAMP-regulated phosphoprotein 19 (ARPP-19)	0.35	-	nuc	0	Cytoplasm (By similarity)				111
Q712U6 UniProt NPD GO	ARP19_PIG	cAMP-regulated phosphoprotein 19 (ARPP-19)	0.35	-	nuc	0	Cytoplasm (By similarity)				111
Q712U5 UniProt NPD GO	ARP19_RAT	cAMP-regulated phosphoprotein 19 (ARPP-19)	0.35	-	nuc	0	Cytoplasm				111
P25299 UniProt NPD GO	RNA15_YEAST	mRNA 3'-end-processing protein RNA15	0.35	-	nuc	0	Nucleus	mRNA cleavage factor complex [IPI]			296
Q5REQ8 UniProt NPD GO	DCP2_PONPY	mRNA decapping enzyme 2 (EC 3.-.-.-)	0.35	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Predominantly cytoplasmic, in processing bodies ...				385
P68251 UniProt NPD GO	1433B_SHEEP	14-3-3 protein beta/alpha (Protein kinase C inhibitor protein 1) (KCIP-1) (Fragments)	0.34	-	nuc	0	Cytoplasm				192
P29310 UniProt NPD GO	1433Z_DROME	14-3-3-like protein (Leonardo protein) (14-3-3 protein zeta)	0.34	-	nuc	0		nucleus [NAS] ring canal (sensu Insecta) [IDA]			248
P23502 UniProt NPD GO	SL17_ENTHI	170 kDa surface lectin precursor	0.34	-	exc	1	Membrane; single-pass type I membrane protein				1285
P29681 UniProt NPD GO	IMPE2_DROME	20-hydroxyecdysone protein precursor (20-HE)	0.34	-	exc	0	Secreted protein. Secreted from the apical cell surface	cytoplasm [IDA] extracellular region [IDA] extrinsic to membrane [TAS]			466
O42586 UniProt NPD GO	PR6AB_XENLA	26S protease regulatory subunit 6A-B (TAT-binding protein 10) (TBP-10)	0.34	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				404
P54775 UniProt NPD GO	PRS6B_MOUSE	26S protease regulatory subunit 6B (MIP224) (MB67-interacting protein) (TAT-binding protein 7) (TBP- ...	0.34	-	cyt	0	Cytoplasm. Nucleus				418
Q8SQI9 UniProt NPD GO	PRS6B_ENCCU	26S protease regulatory subunit 6B homolog	0.34	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				387
Q9CPX7 UniProt NPD GO	RT16_MOUSE	28S ribosomal protein S16, mitochondrial precursor (S16mt) (MRP-S16)	0.34	+	cyt	0	Mitochondrion (By similarity)				135
Q5ADT9 UniProt NPD GO	RT10_CANAL	30S ribosomal protein S10, mitochondrial precursor (Mitochondrial ribosomal small subunit protein 10 ...	0.34	-	nuc	0	Mitochondrion (By similarity)				234
Q7RYL4 UniProt NPD GO	RT10_NEUCR	30S ribosomal protein S10, mitochondrial precursor (Mitochondrial ribosomal small subunit protein 10 ...	0.34	-	mit	0	Mitochondrion (By similarity)				257
Q3SYS1 UniProt NPD GO	RM13_BOVIN	39S ribosomal protein L13, mitochondrial (L13mt) (MRP-L13)	0.34	-	cyt	0	Mitochondrion (By similarity)				178
Q6PDW6 UniProt NPD GO	RM17_RAT	39S ribosomal protein L17, mitochondrial precursor (L17mt) (MRP-L17)	0.34	-	nuc	0	Mitochondrion (Potential)				176
Q921S7 UniProt NPD GO	RM37_MOUSE	39S ribosomal protein L37, mitochondrial precursor (L37mt) (MRP-L37)	0.34	-	cyt	0	Mitochondrion (By similarity)				423
Q9VF89 UniProt NPD GO	RM09_DROME	39S ribosomal protein L9, mitochondrial precursor (L9mt)	0.34	-	mit	0	Mitochondrion (By similarity)	mitochondrial large ribosomal subunit [TAS]			248
P19950 UniProt NPD GO	RS141_MAIZE	40S ribosomal protein S14 (Clone MCH1)	0.34	-	mit	0					149
P62847 UniProt NPD GO	RS24_HUMAN	40S ribosomal protein S24	0.34	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	602412		133
P62849 UniProt NPD GO	RS24_MOUSE	40S ribosomal protein S24	0.34	-	nuc	0					133
P62850 UniProt NPD GO	RS24_RAT	40S ribosomal protein S24	0.34	-	nuc	0		small ribosomal subunit [ISS]			133
P62848 UniProt NPD GO	RS24_MESAU	40S ribosomal protein S24 (Ribosomal protein S19)	0.34	-	nuc	0		small ribosomal subunit [ISS]			133

You are viewing entries 36351 to 36400 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.