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
P98118 UniProt NPD GO	PROS_RABIT	Vitamin K-dependent protein S precursor (Fragment)	0.33	-	nuc	0	Secreted protein				646
P02843 UniProt NPD GO	VIT1_DROME	Vitellogenin-1 precursor (Vitellogenin I) (Yolk protein 1)	0.33	-	exc	0	Secreted protein	extracellular region [TAS]			439
Q98893 UniProt NPD GO	VIT2_FUNHE	Vitellogenin-2 precursor (Vitellogenin II) (VTG II) [Contains: Lipovitellin-1 (LV1); Phosvitin (PV); ...	0.33	-	exc	0					1687
P40338 UniProt NPD GO	VHL_MOUSE	Von Hippel-Lindau disease tumor suppressor (pVHL)	0.33	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Nucleus (By simila ...				181
Q8IUA0 UniProt NPD GO	WFDC8_HUMAN	WAP four-disulfide core domain protein 8 precursor (Putative protease inhibitor WAP8)	0.33	-	exc	0	Secreted protein (Potential)				241
P61480 UniProt NPD GO	WDR12_RAT	WD repeat protein 12	0.33	-	nuc	0	Nucleus; nucleolus (By similarity)				423
Q8IZU2 UniProt NPD GO	WDR17_HUMAN	WD repeat protein 17	0.33	-	cyt	0			609005		1322
Q8C6G8 UniProt NPD GO	WDR26_MOUSE	WD repeat protein 26	0.33	-	cyt	0					514
Q9BUR4 UniProt NPD GO	WDR79_HUMAN	WD repeat protein 79	0.33	-	nuc	0					548
Q96G27 UniProt NPD GO	WBP1_HUMAN	WW domain-binding protein 1 (WBP-1)	0.33	-	nuc	1			606961		269
Q91WL8 UniProt NPD GO	WWOX_MOUSE	WW domain-containing oxidoreductase (EC 1.1.1.-)	0.33	-	cyt	0	Cytoplasm. Nucleus. Mitochondrion (By similarity). Partially localizes to the mitochondria (By simil ...	mitochondrion [IDA] nucleus [IDA]			414
Q5R9W5 UniProt NPD GO	WWOX_PONPY	WW domain-containing oxidoreductase (EC 1.1.1.-)	0.33	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Mitochondrion (By similarity). Partially localiz ...				414
P38315 UniProt NPD GO	YBP1_YEAST	YAP1-binding protein 1 (Activator of YAP1)	0.33	-	cyt	0	Cytoplasm	cytoplasm [IDA]			674
P02859 UniProt NPD GO	ZEA1_MAIZE	Zein-alpha A30 precursor (19 kDa zein A30)	0.33	-	exc	0					234
P04705 UniProt NPD GO	ZEAB_MAIZE	Zein-alpha PZ19.1 precursor (19 kDa zein PZ19.1) (Fragment)	0.33	-	exc	0					186
P04701 UniProt NPD GO	ZEAL_MAIZE	Zein-alpha Z4 precursor	0.33	-	exc	0					267
Q6UIM2 UniProt NPD GO	ZNHI3_PANTR	Zinc finger HIT domain-containing protein 3 (Thyroid receptor-interacting protein 3) (TRIP-3) (Thyro ...	0.33	-	nuc	0					141
Q6JLC9 UniProt NPD GO	ZN331_CANFA	Zinc finger protein 331	0.33	-	nuc	0	Nucleus (Potential)				490
Q8NA42 UniProt NPD GO	ZN383_HUMAN	Zinc finger protein 383	0.33	-	nuc	0	Nucleus. Cytoplasm. Shuttling between the nucleus and cytoplasm may occur under different stimulatio ...				475
Q14592 UniProt NPD GO	ZN460_HUMAN	Zinc finger protein 460 (Zinc finger protein 272) (Zinc finger protein HZF8)	0.33	-	nuc	0	Nucleus (Probable)		604755		562
Q8WV37 UniProt NPD GO	ZN480_HUMAN	Zinc finger protein 480	0.33	-	nuc	0	Nucleus				516
Q96SK3 UniProt NPD GO	ZN607_HUMAN	Zinc finger protein 607	0.33	-	nuc	0	Nucleus (Potential)				371
Q8IW36 UniProt NPD GO	ZN695_HUMAN	Zinc finger protein 695 (Zinc finger protein SBZF3)	0.33	-	nuc	0	Nucleus (Potential)				172
P31320 UniProt NPD GO	KAPR_BLAEM	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.33	+	cyt	0					403
P00516 UniProt NPD GO	KGP1A_BOVIN	cGMP-dependent protein kinase 1, alpha isozyme (EC 2.7.11.12) (CGK 1 alpha) (cGKI-alpha)	0.33	-	cyt	0					670
Q59T36 UniProt NPD GO	YTH1_CANAL	mRNA 3'-end-processing protein YTH1	0.33	-	nuc	0	Nucleus (By similarity)				215
O14134 UniProt NPD GO	ELF1_SCHPO	mRNA export factor elf1	0.33	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA]			1057
Q7SEM8 UniProt NPD GO	PALC_NEUCR	pH-response regulator protein palC	0.33	-	mit	0					490
O75971 UniProt NPD GO	SNPC5_HUMAN	snRNA-activating protein complex subunit 5 (SNAPc subunit 5) (snRNA-activating protein complex 19 kD ...	0.33	-	nuc	0	Nucleus	nucleus [TAS]	605979		98
P53759 UniProt NPD GO	DUS1_YEAST	tRNA-dihydrouridine synthase 1 (EC 1.-.-.-)	0.33	-	cyt	0		nucleus [IDA]			423
Q04675 UniProt NPD GO	SEN15_YEAST	tRNA-splicing endonuclease subunit SEN15 (tRNA-intron endonuclease SEN15) (Splicing endonuclease of ...	0.33	-	nuc	0	Nucleus. Intracellular membrane; peripheral membrane protein. Mitochondrion; mitochondrial outer mem ...	mitochondrial outer membrane [IDA] nuclear inner membrane [TAS] tRNA-intron endonuclease complex [TAS]			128
O81192 UniProt NPD GO	BPPS_SALOF	(+)-bornyl diphosphate synthase, chloroplast precursor (EC 5.5.1.8) (SBS) (BPPS)	0.32	-	cyt	0	Plastid; chloroplast			1N24	598
P93212 UniProt NPD GO	14337_LYCES	14-3-3 protein 7	0.32	-	nuc	0					252
Q4R572 UniProt NPD GO	1433B_MACFA	14-3-3 protein beta/alpha	0.32	-	nuc	0	Cytoplasm (By similarity)				245
P68250 UniProt NPD GO	1433B_BOVIN	14-3-3 protein beta/alpha (Protein kinase C inhibitor protein 1) (KCIP-1)	0.32	-	nuc	0	Cytoplasm				245
P31946 UniProt NPD GO	1433B_HUMAN	14-3-3 protein beta/alpha (Protein kinase C inhibitor protein 1) (KCIP-1) (Protein 1054)	0.32	-	nuc	0	Cytoplasm	cytoplasm [IDA] perinuclear region [IDA]	601289	2C23	245
P61982 UniProt NPD GO	1433G_MOUSE	14-3-3 protein gamma	0.32	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			246
Q5RC20 UniProt NPD GO	1433G_PONPY	14-3-3 protein gamma	0.32	-	nuc	0	Cytoplasm (By similarity)				246
P61983 UniProt NPD GO	1433G_RAT	14-3-3 protein gamma	0.32	-	nuc	0	Cytoplasm	cytoplasm [ISS]			246
P68252 UniProt NPD GO	1433G_BOVIN	14-3-3 protein gamma (Protein kinase C inhibitor protein 1) (KCIP-1)	0.32	-	nuc	0	Cytoplasm	cytoplasm [ISS]			246
P61981 UniProt NPD GO	1433G_HUMAN	14-3-3 protein gamma (Protein kinase C inhibitor protein 1) (KCIP-1)	0.32	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]	605356	2B05	246
Q6UFZ2 UniProt NPD GO	143G2_ONCMY	14-3-3 protein gamma-2 (Protein 14-3-3G2)	0.32	-	nuc	0	Cytoplasm (By similarity)				248
Q26537 UniProt NPD GO	14332_SCHMA	14-3-3 protein homolog 2 (14-3-3-2) (Fragment)	0.32	-	nuc	0					214
P93259 UniProt NPD GO	1433_MESCR	14-3-3-like protein (G-box-binding factor)	0.32	-	nuc	0					264
P13233 UniProt NPD GO	CN37_RAT	2',3'-cyclic-nucleotide 3'-phosphodiesterase (EC 3.1.4.37) (CNP) (CNPase)	0.32	-	mit	0	Membrane. Firmly bound to membrane structures of brain white matter	intrinsic to membrane [IMP]		1N4T	420
O35084 UniProt NPD GO	CP27B_MOUSE	25-hydroxyvitamin D-1 alpha hydroxylase, mitochondrial precursor (EC 1.14.13.13) (Cytochrome P450 su ...	0.32	-	mit	0	Mitochondrion				507
O35132 UniProt NPD GO	CP27B_RAT	25-hydroxyvitamin D-1 alpha hydroxylase, mitochondrial precursor (EC 1.14.13.13) (Cytochrome P450 su ...	0.32	-	mit	0	Mitochondrion				501
P33298 UniProt NPD GO	PRS6B_YEAST	26S protease regulatory subunit 6B homolog (Protein YNT1) (TAT-binding homolog 2)	0.32	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)	proteasome regulatory particle, base subcom... [IDA]			428
Q99871 UniProt NPD GO	S1769_HUMAN	26S proteasome-associated UCH37-interacting protein 1 (X-linked protein STS1769)	0.32	-	nuc	0			300540		358
O35680 UniProt NPD GO	RT12_MOUSE	28S ribosomal protein S12, mitochondrial precursor (S12mt) (MRP-S12) (MT-RPS12)	0.32	-	mit	0	Mitochondrion				139

You are viewing entries 38151 to 38200 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.