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
P70314 UniProt NPD GO	PITX1_MOUSE	Pituitary homeobox 1 (Homeobox protein P-OTX) (Pituitary OTX-related factor) (Hindlimb expressed hom ...	0.85	+	nuc	0	Nucleus				315
Q86W56 UniProt NPD GO	PARG_HUMAN	Poly(ADP-ribose) glycohydrolase (EC 3.2.1.143)	0.85	-	nuc	0	Isoform 1: Nucleus. Isoform 2, isoform 3: Cytoplasm	cytoplasm [TAS]	603501		976
O88622 UniProt NPD GO	PARG_MOUSE	Poly(ADP-ribose) glycohydrolase (EC 3.2.1.143)	0.85	-	nuc	0	Nucleus (By similarity)	cytosol [IMP] nucleus [IDA]			969
P25916 UniProt NPD GO	PCGF4_MOUSE	Polycomb group RING finger protein 4 (Polycomb complex protein BMI-1)	0.85	-	nuc	0	Nucleus	nuclear body [IDA]		2CKL	324
Q8S4P6 UniProt NPD GO	EZ1_MAIZE	Polycomb protein EZ1 (Enhancer of zeste protein 1)	0.85	-	nuc	0	Nucleus (Probable)				931
Q4V7W5 UniProt NPD GO	PHC2_XENLA	Polyhomeotic-like protein 2	0.85	-	nuc	0	Nucleus (Probable)				344
P41778 UniProt NPD GO	PBX1_MOUSE	Pre-B-cell leukemia transcription factor 1 (Homeobox protein PBX1)	0.85	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]		1LFU	430
P40424 UniProt NPD GO	PBX1_HUMAN	Pre-B-cell leukemia transcription factor 1 (Homeobox protein PBX1) (Homeobox protein PRL)	0.85	-	nuc	0	Nucleus (Probable)	nucleus [ISS]	176310	1PUF	430
P40426 UniProt NPD GO	PBX3_HUMAN	Pre-B-cell leukemia transcription factor 3 (Homeobox protein PBX3)	0.85	-	nuc	0	Nucleus (Probable)	nucleus [ISS]	176312		434
O35317 UniProt NPD GO	PBX3_MOUSE	Pre-B-cell leukemia transcription factor 3 (Homeobox protein PBX3)	0.85	-	nuc	0	Nucleus (By similarity)	nucleus [IDA] transcription factor complex [IDA]			434
Q4I7F9 UniProt NPD GO	PRP28_GIBZE	Pre-mRNA-splicing ATP-dependent RNA helicase PRP28 (EC 3.6.1.-)	0.85	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				721
Q7SEL0 UniProt NPD GO	PRP28_NEUCR	Pre-mRNA-splicing ATP-dependent RNA helicase prp-28 (EC 3.6.1.-)	0.85	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				728
Q6BSP7 UniProt NPD GO	CLF1_DEBHA	Pre-mRNA-splicing factor CLF1	0.85	+	cyt	0	Nucleus (By similarity)				714
Q4PB37 UniProt NPD GO	CLF1_USTMA	Pre-mRNA-splicing factor CLF1	0.85	-	mit	0	Nucleus (By similarity)				781
Q4P400 UniProt NPD GO	CWC24_USTMA	Pre-mRNA-splicing factor CWC24	0.85	+	nuc	0	Nucleus (By similarity)				355
Q06091 UniProt NPD GO	SN309_YEAST	Pre-mRNA-splicing factor SNT309 (Synergistic to PRP19 mutation protein 309) (PRP19-associated comple ...	0.85	-	nuc	0	Nucleus	spliceosome complex [IDA]			175
Q521C0 UniProt NPD GO	SYF2_MAGGR	Pre-mRNA-splicing factor SYF2	0.85	-	nuc	0	Nucleus (By similarity)				340
Q5AVC5 UniProt NPD GO	CWC24_EMENI	Pre-mRNA-splicing factor cwc24	0.85	-	nuc	0	Nucleus (By similarity)				332
Q96MT3 UniProt NPD GO	PRIC1_HUMAN	Prickle-like protein 1 (REST/NRSF-interacting LIM domain protein 1)	0.85	+	nuc	0	Nucleus; nuclear membrane. Cytoplasm; cytosol. A smaller amount is detected in the cytosol		608500		831
Q71QF9 UniProt NPD GO	PRIC1_RAT	Prickle-like protein 1 (REST/NRSF-interacting LIM domain protein 1)	0.85	-	nuc	0	Nucleus; nuclear membrane (By similarity). Cytoplasm; cytosol (By similarity). A smaller amount is d ...				831
O18696 UniProt NPD GO	PDE1_CAEEL	Probable 3',5'-cyclic phosphodiesterase pde-1 (EC 3.1.4.17)	0.85	-	nuc	0					664
Q9P7L9 UniProt NPD GO	RM34_SCHPO	Probable 60S ribosomal protein L34, mitochondrial precursor (L34mt)	0.85	+	nuc	0	Mitochondrion (Potential)				108
Q9Y2R4 UniProt NPD GO	DDX52_HUMAN	Probable ATP-dependent RNA helicase DDX52 (EC 3.6.1.-) (DEAD box protein 52) (ATP-dependent RNA heli ...	0.85	-	cyt	0	Nucleus; nucleolus				599
Q6PRD1 UniProt NPD GO	GP179_HUMAN	Probable G-protein coupled receptor 179 precursor (Probable G-protein coupled receptor 158-like 1)	0.85	-	nuc	6 *	Membrane; multi-pass membrane protein				2367
O59742 UniProt NPD GO	IF3X_SCHPO	Probable eukaryotic translation initiation factor 3 135 kDa subunit (eIF3 p135) (Translation initiat ...	0.85	-	nuc	0					1173
Q6FW62 UniProt NPD GO	NDC80_CANGA	Probable kinetochore protein NDC80	0.85	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				706
Q9V9Z9 UniProt NPD GO	EBP2_DROME	Probable rRNA-processing protein EBP2 homolog	0.85	+	nuc	0	Nucleus; nucleolus (By similarity)				307
Q9VKB4 UniProt NPD GO	RPF1_DROME	Probable ribosome production factor 1 (Ribosome biogenesis protein RPF1)	0.85	-	nuc	0	Nucleus; nucleolus (By similarity)	nucleolus [ISS]			394
Q9HFF4 UniProt NPD GO	KK31_SCHPO	Probable serine/threonine-protein kinase C110.01 (EC 2.7.11.1)	0.85	-	nuc	0					1023
Q8WXW3 UniProt NPD GO	PIBF1_HUMAN	Progesterone-induced-blocking factor 1	0.85	-	nuc	0			607532		757
P25502 UniProt NPD GO	PUT3_YEAST	Proline utilization trans-activator	0.85	-	nuc	2	Nucleus	nucleus [IC]		1ZME	979
P51455 UniProt NPD GO	REL2_PANTR	Prorelaxin H2 precursor [Contains: Relaxin B chain; Relaxin A chain] (Fragment)	0.85	-	nuc	0	Secreted protein				166
P55197 UniProt NPD GO	AF10_HUMAN	Protein AF-10	0.85	+	nuc	0	Nucleus (Potential)		602409		1027
Q5T6M2 UniProt NPD GO	CF122_HUMAN	Protein C6orf122	0.85	-	mit	0					205
Q53H80 UniProt NPD GO	CF166_HUMAN	Protein C6orf166	0.85	-	nuc	0					203
Q3TQI7 UniProt NPD GO	CI078_MOUSE	Protein C9orf78 homolog	0.85	-	nuc	0					289
Q13948 UniProt NPD GO	CASP_HUMAN	Protein CASP	0.85	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein		116896		678
P70403 UniProt NPD GO	CASP_MOUSE	Protein CASP	0.85	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)	nucleus [IDA]			678
Q5R8V1 UniProt NPD GO	CASP_PONPY	Protein CASP	0.85	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				678
Q08729 UniProt NPD GO	DSE3_YEAST	Protein DSE3 (Daughter specific expression protein 3)	0.85	-	nuc	0	Bud neck	bud neck [IDA]			430
Q9Y485 UniProt NPD GO	DMXL1_HUMAN	Protein DmX-like 1 (X-like 1 protein)	0.85	-	nuc	0			605671		3027
Q8NE31 UniProt NPD GO	FA13C_HUMAN	Protein FAM13C1	0.85	-	nuc	0					585
Q5JRC9 UniProt NPD GO	FA47A_HUMAN	Protein FAM47A	0.85	-	nuc	0					778
Q9WTJ8 UniProt NPD GO	FA50B_MOUSE	Protein FAM50B (XAP-5-like protein)	0.85	+	nuc	0					334
Q14153 UniProt NPD GO	FA53B_HUMAN	Protein FAM53B	0.85	-	nuc	0					422
Q8BGR5 UniProt NPD GO	FA53B_MOUSE	Protein FAM53B	0.85	-	nuc	0					422
Q5HYJ3 UniProt NPD GO	FA76B_HUMAN	Protein FAM76B	0.85	-	nuc	0					339
Q8IZU0 UniProt NPD GO	FAM9B_HUMAN	Protein FAM9B	0.85	+	nuc	0	Nucleus		300478		186
Q59NQ9 UniProt NPD GO	FYV7_CANAL	Protein FYV7	0.85	-	nuc	0	Nucleus; nucleolus (By similarity)				142
Q6BPI5 UniProt NPD GO	FYV7_DEBHA	Protein FYV7	0.85	-	nuc	0	Nucleus; nucleolus (By similarity)				157

You are viewing entries 6651 to 6700 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.