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
P55090 UniProt NPD GO	UCN1_RAT	Urocortin precursor (Corticotensin)	0.43	-	exc	0	Secreted protein				122
Q8HYC2 UniProt NPD GO	UTS2_MACMU	Urotensin-2 precursor (Urotensin-II) (U-II) (UII)	0.43	-	exc	0	Secreted protein (By similarity)				125
Q9NDR5 UniProt NPD GO	VATC_ASCSS	Vacuolar ATP synthase subunit C (EC 3.6.3.14) (V-ATPase C subunit) (Vacuolar proton pump C subunit)	0.43	+	cyt	0					384
Q9N2P6 UniProt NPD GO	VEPD_DROME	Ventrally expressed gene D protein	0.43	-	nuc	0					81
Q91VU6 UniProt NPD GO	WDR23_MOUSE	WD repeat protein 23	0.43	-	nuc	0					549
Q7ZX22 UniProt NPD GO	WDR24_XENLA	WD repeat protein 24	0.43	-	mit	0					780
Q8TC44 UniProt NPD GO	WD51B_HUMAN	WD repeat protein 51B	0.43	-	cyt	0					478
Q5ND34 UniProt NPD GO	WDR81_MOUSE	WD repeat protein 81	0.43	-	mit	0					887
Q6IN36 UniProt NPD GO	WASIP_RAT	Wiskott-Aldrich syndrome protein-interacting protein (WASP-interacting protein)	0.43	-	nuc	0	Vesicle surfaces and along actin tails. Co-localized with actin stress fibers. When co-expressed wit ...				487
Q5QQ54 UniProt NPD GO	XYLT_CIOSA	Xylosyltransferase (EC 2.4.2.26) (Peptide O-xylosyltransferase)	0.43	-	mit	1 *	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...				843
Q5QQ51 UniProt NPD GO	XYLT2_PANTR	Xylosyltransferase 2 (EC 2.4.2.26) (Xylosyltransferase II) (Peptide O-xylosyltransferase 2)	0.43	-	mit	1 *	Or: Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By ...				865
Q5ZLS2 UniProt NPD GO	YJDC_CHICK	YjeF domain-containing protein 1	0.43	-	nuc	0					506
Q6FIF0 UniProt NPD GO	Z20D3_HUMAN	Zinc finger A20 domain-containing protein 3 (Associated with PRK1 protein)	0.43	-	nuc	0					208
O75800 UniProt NPD GO	ZMY10_HUMAN	Zinc finger MYND domain-containing protein 10 (BLu protein)	0.43	-	cyt	0			607070	2DAN	440
Q01611 UniProt NPD GO	ZFY1_XENLA	Zinc finger Y-chromosomal protein 1 (ZFY-1)	0.43	+	nuc	0	Nucleus (Probable)				794
Q6J212 UniProt NPD GO	ZN313_PANTR	Zinc finger protein 313	0.43	-	nuc	0					228
Q80V23 UniProt NPD GO	ZNF32_MOUSE	Zinc finger protein 32 (Zinc finger protein 637)	0.43	-	nuc	0	Nucleus (Potential)				272
Q9H8G1 UniProt NPD GO	ZN430_HUMAN	Zinc finger protein 430	0.43	-	nuc	0	Nucleus (Potential)				570
Q03309 UniProt NPD GO	ZFP46_MOUSE	Zinc finger protein 46 (Zfp-46) (Zinc finger protein MLZ-4)	0.43	-	nuc	0	Nucleus (Probable)				393
Q8NCK3 UniProt NPD GO	ZN485_HUMAN	Zinc finger protein 485	0.43	-	nuc	0	Nucleus (Potential)				441
Q5RF70 UniProt NPD GO	ZN501_PONPY	Zinc finger protein 501	0.43	-	nuc	0	Nucleus (Potential)				262
Q96CX3 UniProt NPD GO	ZN501_HUMAN	Zinc finger protein 501 (Zinc finger protein 52)	0.43	-	nuc	0	Nucleus (Potential)				262
Q8N587 UniProt NPD GO	ZN561_HUMAN	Zinc finger protein 561	0.43	-	nuc	0	Nucleus (Potential)				486
Q5DWN0 UniProt NPD GO	GFI1_CANFA	Zinc finger protein Gfi-1 (Growth factor independence 1)	0.43	-	nuc	0	Nucleus (By similarity)				422
P46684 UniProt NPD GO	ZIC1_MOUSE	Zinc finger protein ZIC 1 (Zinc finger protein of the cerebellum 1)	0.43	-	nuc	0	Nucleus				447
Q62523 UniProt NPD GO	ZYX_MOUSE	Zyxin	0.43	-	nuc	0	Cytoplasm. Cytoskeleton. Associates with the actin cytoskeleton near the adhesion plaques				564
O59922 UniProt NPD GO	KAPR_EMENI	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.43	-	nuc	0					412
Q5ZLY8 UniProt NPD GO	ARP19_CHICK	cAMP-regulated phosphoprotein 19 (ARPP-19)	0.43	-	nuc	0	Cytoplasm (By similarity)				111
P29973 UniProt NPD GO	CNGA1_HUMAN	cGMP-gated cation channel alpha 1 (CNG channel alpha 1) (CNG-1) (CNG1) (Cyclic nucleotide-gated chan ...	0.43	+	end	2	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	268000		686
Q99189 UniProt NPD GO	MTR10_YEAST	mRNA transport regulator MTR10	0.43	-	nuc	0	Nucleus (Potential)	cytoplasm [IDA] nucleus [IDA]			972
Q85G85 UniProt NPD GO	TILS_CYAME	tRNA(Ile)-lysidine synthase (EC 6.3.4.-) (tRNA(Ile)-lysidine synthetase) (tRNA(Ile)-2-lysyl-cytidine ...	0.43	-	mit	0	Plastid; chloroplast				290
Q6P1R4 UniProt NPD GO	DUS1L_HUMAN	tRNA-dihydrouridine synthase 1-like (EC 1.-.-.-)	0.43	-	cyt	0					473
Q754T3 UniProt NPD GO	SEN34_ASHGO	tRNA-splicing endonuclease subunit SEN34 (EC 3.1.27.9) (tRNA-intron endonuclease SEN34)	0.43	+	mit	0					292
P80012 UniProt NPD GO	VWF_BOVIN	von Willebrand factor precursor (vWF) (Fragment)	0.43	-	exc	0	Secreted protein (By similarity). Localized to storage granules (By similarity)				937
Q5XGC8 UniProt NPD GO	1433B_XENTR	14-3-3 protein beta/alpha	0.42	-	nuc	0	Cytoplasm (By similarity)				244
O42766 UniProt NPD GO	1433_CANAL	14-3-3 protein homolog	0.42	-	nuc	0					264
Q06464 UniProt NPD GO	GPMI_ANTSP	2,3-bisphosphoglycerate-independent phosphoglycerate mutase (EC 5.4.2.1) (Phosphoglyceromutase) (BPG ...	0.42	-	nuc	0	Plastid; chloroplast				510
O74894 UniProt NPD GO	PRS6B_SCHPO	26S protease regulatory subunit 6B homolog	0.42	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				389
P84576 UniProt NPD GO	2SS_CUCMO	2S albumin [Contains: 2S albumin small chain (Moschin A); 2S albumin large chain (Moschin B)] (Fragm ...	0.42	-	nuc	0					61
P15460 UniProt NPD GO	2SS4_ARATH	2S seed storage protein 4 precursor (2S albumin storage protein) (NWMU2-2S albumin 4) [Contains: 2S ...	0.42	-	exc	1 *					166
Q05761 UniProt NPD GO	RS13_MAIZE	40S ribosomal protein S13	0.42	-	nuc	0					151
O65059 UniProt NPD GO	RS15_PICMA	40S ribosomal protein S15	0.42	-	cyt	0					151
P48588 UniProt NPD GO	RS25_DROME	40S ribosomal protein S25	0.42	+	nuc	0					117
Q6Q312 UniProt NPD GO	RS26_SHEEP	40S ribosomal protein S26	0.42	-	nuc	0					114
P49216 UniProt NPD GO	RS26_ORYSA	40S ribosomal protein S26 (S31)	0.42	-	nuc	0					133
Q9M2F1 UniProt NPD GO	RS27B_ARATH	40S ribosomal protein S27-2	0.42	-	nuc	0					86
P14797 UniProt NPD GO	RS27A_DICDI	40S ribosomal protein S27a	0.42	+	nuc	0					78
P68202 UniProt NPD GO	RS27A_PLUXY	40S ribosomal protein S27a	0.42	+	nuc	0					79
Q10101 UniProt NPD GO	RS7_SCHPO	40S ribosomal protein S7	0.42	+	mit	0					195
O13516 UniProt NPD GO	RS9A_YEAST	40S ribosomal protein S9-A (S13) (YS11) (RP21) (YP28)	0.42	-	nuc	0		cytoplasm [IDA] cytosolic small ribosomal subunit (sensu Eu... [TAS] small nucleolar ribonucleoprotein complex [IPI]		1K5X	196

You are viewing entries 30101 to 30150 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.