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
Q8TED0 UniProt NPD GO	UTP15_HUMAN	U3 small nucleolar RNA-associated protein 15 homolog	0.45	-	cyt	0	Nucleus; nucleolus				518
Q2KIJ6 UniProt NPD GO	UBXD1_BOVIN	UBX domain-containing protein 1	0.45	-	nuc	0					441
Q99PL6 UniProt NPD GO	UBXD1_MOUSE	UBX domain-containing protein 1	0.45	-	nuc	0					442
O18158 UniProt NPD GO	OGT1_CAEEL	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase (EC 2.4.1.-) (O-GlcNAc) (OGT)	0.45	-	nuc	0	Nucleus. Cytoplasm; perinuclear region	nucleus [IDA]			1151
Q08960 UniProt NPD GO	YP207_YEAST	UPF0026 protein YPL207W	0.45	-	mit	1 *		endoplasmic reticulum [IDA]			810
O80832 UniProt NPD GO	YU87_ARATH	UPF0187 protein At2g45870, chloroplast precursor	0.45	-	mit	2	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				410
O74803 UniProt NPD GO	RHP23_SCHPO	UV excision repair protein rhp23 (RAD23 homolog)	0.45	-	nuc	0	Nucleus	nucleus [IDA]			368
P13271 UniProt NPD GO	UCRQ_BOVIN	Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C (EC 1.10.2.2) (Ubiquinol-cy ...	0.45	-	mit	0	Mitochondrion; mitochondrial inner membrane			3BCC	81
P38237 UniProt NPD GO	UBP14_YEAST	Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.1.2.15) (Ubiquitin thioesterase 14) (Ubiquitin-specif ...	0.45	-	nuc	0	Cytoplasm (Potential)	cytoplasm [IC]			803
Q6C093 UniProt NPD GO	UBC2_YARLI	Ubiquitin-conjugating enzyme E2 2 (EC 6.3.2.19) (Ubiquitin-protein ligase UBC2) (Ubiquitin carrier p ...	0.45	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				151
Q9JJZ4 UniProt NPD GO	UB2J1_MOUSE	Ubiquitin-conjugating enzyme E2 J1 (EC 6.3.2.19) (Non-canonical ubiquitin-conjugating enzyme 1) (NCU ...	0.45	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein (By simi ...				318
Q8N5U0 UniProt NPD GO	CK042_HUMAN	Uncharacterized protein C11orf42	0.45	-	nuc	0					333
Q9H6D7 UniProt NPD GO	CN094_HUMAN	Uncharacterized protein C14orf94	0.45	-	cyt	0					363
Q9N0B5 UniProt NPD GO	CO027_MACFA	Uncharacterized protein C15orf27 homolog	0.45	-	nuc	0					347
Q58DG5 UniProt NPD GO	CT055_BOVIN	Uncharacterized protein C20orf55 homolog	0.45	-	nuc	0					295
Q5R458 UniProt NPD GO	CB011_PONPY	Uncharacterized protein C2orf11 homolog	0.45	-	nuc	0					501
Q9H7Y0 UniProt NPD GO	CX036_HUMAN	Uncharacterized protein CXorf36 precursor	0.45	-	nuc	0					182
Q12516 UniProt NPD GO	YD133_YEAST	Uncharacterized protein YDL133W	0.45	-	end	4	Membrane; multi-pass membrane protein (Potential)				437
P40033 UniProt NPD GO	YEO0_YEAST	Uncharacterized protein YER050C	0.45	-	nuc	0		mitochondrial small ribosomal subunit [IDA]			202
Q08416 UniProt NPD GO	YO044_YEAST	Uncharacterized protein YOR044W	0.45	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			157
O95399 UniProt NPD GO	UTS2_HUMAN	Urotensin-2 precursor (Urotensin-II) (U-II) (UII)	0.45	-	exc	0	Secreted protein	extracellular space [TAS]	604097		124
P46202 UniProt NPD GO	UFAP2_PIG	Uteroferrin-associated basic protein 2 precursor (UABP-2)	0.45	-	mit	0	Secreted protein; extracellular space (Potential)				420
P01283 UniProt NPD GO	VIP_RAT	VIP peptides precursor [Contains: Intestinal peptide PHV-42; Intestinal peptide PHI-27 (Peptide hist ...	0.45	-	exc	0	Secreted protein				170
P50518 UniProt NPD GO	VATE_MOUSE	Vacuolar ATP synthase subunit E (EC 3.6.3.14) (V-ATPase E subunit) (Vacuolar proton pump E subunit) ...	0.45	-	cyt	0		cytoplasm [IDA] mitochondrion [IDA]			228
P27801 UniProt NPD GO	PEP3_YEAST	Vacuolar membrane protein PEP3 (Vacuolar protein sorting 18)	0.45	-	cyt	0	Vacuole; vacuolar membrane; peripheral membrane protein; cytoplasmic side	extrinsic to vacuolar membrane [IDA] HOPS complex [IPI] vacuolar membrane (sensu Fungi) [IDA]			918
Q9P7V6 UniProt NPD GO	VPS33_SCHPO	Vacuolar protein sorting 33	0.45	-	nuc	0					592
Q9D2N9 UniProt NPD GO	VP33A_MOUSE	Vacuolar protein sorting 33A	0.45	-	cyt	0	Late endosome; late endosomal membrane; peripheral membrane protein (By similarity). Lysosome; lysos ...				598
P47142 UniProt NPD GO	VPS25_YEAST	Vacuolar protein sorting protein 25	0.45	-	nuc	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein	ESCRT II complex [IDA]		1XB4	202
O75351 UniProt NPD GO	VPS4B_HUMAN	Vacuolar sorting protein 4b (SKD1 protein)	0.45	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Membrane-associated in the prevacuolar endosomal c ...	endosome [IDA]		2CPT	444
P46467 UniProt NPD GO	VPS4B_MOUSE	Vacuolar sorting protein 4b (SKD1 protein)	0.45	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Membrane-associated in the prevacuolar endosomal c ...				444
P39929 UniProt NPD GO	SNF7_YEAST	Vacuolar sorting protein SNF7 (DOA4-independent degradation protein 1) (Vacuolar protein sorting-ass ...	0.45	-	nuc	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein	cytoplasm [IDA] ESCRT III complex [IDA]			240
P47901 UniProt NPD GO	V1BR_HUMAN	Vasopressin V1b receptor (V1bR) (AVPR V1b) (Vasopressin V3 receptor) (AVPR V3) (Antidiuretic hormone ...	0.45	-	end	7 *	Membrane; multi-pass membrane protein	endosome [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	600264		424
P40162 UniProt NPD GO	YNU5_YEAST	Very hypothetical protein YNL205C	0.45	-	mit	0					140
P98155 UniProt NPD GO	VLDLR_HUMAN	Very low-density lipoprotein receptor precursor (VLDL receptor) (VLDL-R)	0.45	-	exc	1	Membrane; single-pass type I membrane protein	membrane fraction [IDA] plasma membrane [TAS]	192977	1V9U	873
Q8VIC9 UniProt NPD GO	VN1A5_MOUSE	Vomeronasal type-1 receptor A5 (Vomeronasal type-1 receptor A2)	0.45	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				329
Q7Z5U6 UniProt NPD GO	WDR53_HUMAN	WD repeat protein 53	0.45	-	nuc	0					358
Q3SWZ7 UniProt NPD GO	WDR79_BOVIN	WD repeat protein 79	0.45	-	nuc	0					540
Q9ZUT0 UniProt NPD GO	WBC2_ARATH	White-brown complex homolog protein 2	0.45	-	end	6	Membrane; multi-pass membrane protein (By similarity)				755
Q9Y5A9 UniProt NPD GO	YTHD2_HUMAN	YTH domain protein 2 (High-glucose-regulated protein 8) (NY-REN-2 antigen) (CLL-associated antigen K ...	0.45	-	nuc	0					579
Q96F86 UniProt NPD GO	YJDC_HUMAN	YjeF domain-containing protein 1 (Edc3)	0.45	-	nuc	0	Cytoplasm. Processing bodies (PB)		609842		508
Q03924 UniProt NPD GO	ZN117_HUMAN	Zinc finger protein 117 (Zinc finger protein HPF9) (Fragment)	0.45	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	194624		418
Q62981 UniProt NPD GO	ZF260_RAT	Zinc finger protein 260 (Zfp-260) (POZF-1) (Pancreas-only zinc finger protein 1)	0.45	-	nuc	0	Nucleus				407
O43296 UniProt NPD GO	ZN264_HUMAN	Zinc finger protein 264	0.45	-	nuc	0	Nucleus (Probable)		604668		627
Q39262 UniProt NPD GO	ZFP3_ARATH	Zinc finger protein 3	0.45	-	nuc	0					235
Q9NQX6 UniProt NPD GO	ZN331_HUMAN	Zinc finger protein 331 (Zinc finger protein 463) (C2H2-like zinc finger protein rearranged in thyro ...	0.45	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	606043		463
Q9D0C1 UniProt NPD GO	ZN364_MOUSE	Zinc finger protein 364 (Rabring 7)	0.45	-	nuc	0					305
Q9P255 UniProt NPD GO	ZN492_HUMAN	Zinc finger protein 492 (Fragment)	0.45	-	nuc	0	Nucleus (Probable)				574
Q96K62 UniProt NPD GO	ZN499_HUMAN	Zinc finger protein 499	0.45	-	nuc	0	Nucleus (Potential)				511
Q8TAW3 UniProt NPD GO	ZN671_HUMAN	Zinc finger protein 671	0.45	-	nuc	0	Nucleus (Probable)				556
O89085 UniProt NPD GO	PDE4A_CAVPO	cAMP-dependent 3',5'-cyclic phosphodiesterase 4A (EC 3.1.4.17) (Fragment)	0.45	-	nuc	0					117

You are viewing entries 28701 to 28750 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.