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
Q9USP9 UniProt NPD GO	YHP4_SCHPO	Probable RNA-binding protein C902.04	0.73	-	nuc	0	Nucleus	nucleus [IDA]			589
O14014 UniProt NPD GO	RGA3_SCHPO	Probable Rho-type GTPase-activating protein 3	0.73	-	nuc	0	Cell poles and septum	barrier septum [IDA] cell cortex of cell tip [IDA]			969
Q9SVB7 UniProt NPD GO	WRK13_ARATH	Probable WRKY transcription factor 13 (WRKY DNA-binding protein 13)	0.73	-	nuc	0	Nucleus (Probable)				304
Q9SAH7 UniProt NPD GO	WRK40_ARATH	Probable WRKY transcription factor 40 (WRKY DNA-binding protein 40)	0.73	-	nuc	0	Nucleus (Potential)				302
Q9V7G5 UniProt NPD GO	C4AA1_DROME	Probable cytochrome P450 4aa1 (EC 1.14.-.-) (CYPIVAA1)	0.73	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				514
Q96U60 UniProt NPD GO	NDC80_NEUCR	Probable kinetochore protein ndc-80	0.73	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				743
Q09388 UniProt NPD GO	ACM2_CAEEL	Probable muscarinic acetylcholine receptor gar-2 (G-protein linked acetylcholine receptor 2)	0.73	-	end	7 *	Membrane; multi-pass membrane protein				627
P58223 UniProt NPD GO	Y4837_ARATH	Probable nucleic acid-binding protein At4g18375	0.73	-	nuc	0	Nucleus (Potential)				606
Q12204 UniProt NPD GO	YOR22_YEAST	Probable phospholipase YOR022C, mitochondrial precursor (EC 3.1.1.-)	0.73	-	mit	0	Mitochondrion	mitochondrion [IDA]			715
P40527 UniProt NPD GO	ATC7_YEAST	Probable phospholipid-transporting ATPase NEO1 (EC 3.6.3.1)	0.73	-	end	5	Membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IDA] endosome [IDA] Golgi apparatus [IDA] Golgi membrane [IDA]			1151
Q17606 UniProt NPD GO	RLP24_CAEEL	Probable ribosome biogenesis protein RLP24	0.73	-	nuc	0	Nucleus; nucleolus (By similarity)				162
Q91185 UniProt NPD GO	PRT_ORYLA	Protamine	0.73	+	nuc	0	Nucleus				32
Q24735 UniProt NPD GO	60A_DROVI	Protein 60A precursor (Protein glass bottom boat)	0.73	-	exc	1 *	Secreted protein (By similarity)				436
O22892 UniProt NPD GO	GSR2_ARATH	Protein At2g40430	0.73	-	nuc	0					442
Q9M160 UniProt NPD GO	Y4095_ARATH	Protein At4g00950	0.73	+	nuc	0					291
Q9V7A7 UniProt NPD GO	BAT4_DROME	Protein BAT4 homolog	0.73	-	nuc	0					336
Q53FD0 UniProt NPD GO	CN140_HUMAN	Protein C14orf140	0.73	-	nuc	0					275
Q9Y426 UniProt NPD GO	CU025_HUMAN	Protein C21orf25 precursor	0.73	-	nuc	1 *					696
P58468 UniProt NPD GO	CU070_MOUSE	Protein C21orf70 homolog	0.73	-	nuc	0					219
Q96E09 UniProt NPD GO	CI042_HUMAN	Protein C9orf42	0.73	-	nuc	0					287
O16207 UniProt NPD GO	YF26_CAEEL	Protein F29A7.6	0.73	-	nuc	0					189
Q5U4F3 UniProt NPD GO	F107B_RAT	Protein FAM107B	0.73	-	nuc	0					131
Q3UEN2 UniProt NPD GO	FA35A_MOUSE	Protein FAM35A	0.73	-	nuc	0					898
Q9NWZ8 UniProt NPD GO	F51A1_HUMAN	Protein FAM51A1	0.73	-	mit	0					242
Q04934 UniProt NPD GO	IVY1_YEAST	Protein IVY1 (Interaction with VPS33 and YPT7 protein 1)	0.73	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein. Binds to various phospholipids	vacuolar membrane (sensu Fungi) [IDA]			453
Q8BKS9 UniProt NPD GO	K0020_MOUSE	Protein KIAA0020	0.73	+	nuc	0	Nucleus; nucleolus (By similarity)				647
Q3TCJ1 UniProt NPD GO	K0157_MOUSE	Protein KIAA0157	0.73	-	nuc	0					415
P23999 UniProt NPD GO	MYCS_RAT	Protein S-myc	0.73	+	nuc	0	Nucleus (Potential)				429
Q8GWZ6 UniProt NPD GO	SRR1_ARATH	Protein SENSITIVITY TO RED LIGHT REDUCED 1	0.73	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			275
Q9EQU5 UniProt NPD GO	SET_MOUSE	Protein SET (Phosphatase 2A inhibitor I2PP2A) (I-2PP2A) (Template-activating factor I) (TAF-I)	0.73	-	nuc	0	Cytoplasm; cytosol (By similarity). Endoplasmic reticulum (By similarity). Nucleus; nucleoplasm (By ...	nucleus [IDA]			289
Q12034 UniProt NPD GO	SLF1_YEAST	Protein SLF1	0.73	-	nuc	0		cytoplasm [IDA] polysome [IDA]			447
Q6FM94 UniProt NPD GO	VTS1_CANGA	Protein VTS1	0.73	-	nuc	0	Cytoplasm (By similarity)				549
O95376 UniProt NPD GO	ARI2_HUMAN	Protein ariadne-2 homolog (ARI-2) (Triad1 protein)	0.73	-	nuc	0	Nucleus	nucleus [TAS]	605615		493
P38937 UniProt NPD GO	CUT8_SCHPO	Protein cut8 (Cell untimely torn protein 8)	0.73	-	nuc	0		nucleus [IDA]			262
O61493 UniProt NPD GO	HOOK_DROVI	Protein hook	0.73	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity). Localizes to endosomes. Enriched at neuromuscul ...	endosome [ISS]			678
P05084 UniProt NPD GO	HUNB_DROME	Protein hunchback	0.73	-	nuc	0	Nucleus				758
Q01778 UniProt NPD GO	HUNB_MUSDO	Protein hunchback	0.73	-	nuc	0	Nucleus (Probable)				817
Q04047 UniProt NPD GO	NONA_DROME	Protein no-on-transient A (Puff-specific protein Bj6)	0.73	-	nuc	0					700
Q00756 UniProt NPD GO	PPR3A_RABIT	Protein phosphatase 1 regulatory subunit 3A (Protein phosphatase 1 glycogen-associated regulatory su ...	0.73	-	nuc	1	Membrane; single-pass membrane protein (Potential)				1109
Q9VKM1 UniProt NPD GO	PIWI_DROME	Protein piwi	0.73	-	nuc	0	Nucleus; nucleoplasm. Nurse cells, follicle cells and oocytes in developing egg chambers	nucleoplasm [TAS] nucleus [TAS]			843
Q9W1A4 UniProt NPD GO	TAMO_DROME	Protein tamozhennic	0.73	-	nuc	0	Cytoplasm	cytoplasm [IDA]			797
O15736 UniProt NPD GO	TIPD_DICDI	Protein tipD	0.73	-	nuc	0					612
P82804 UniProt NPD GO	WIBG_DROME	Protein within the bgcn gene intron	0.73	+	nuc	0				1RK8	207
P14238 UniProt NPD GO	FES_FELCA	Proto-oncogene tyrosine-protein kinase Fes/Fps (EC 2.7.10.2) (C-Fes)	0.73	-	cyt	0					820
Q9HCL0 UniProt NPD GO	PCD18_HUMAN	Protocadherin-18 precursor	0.73	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [ISS]	608287		1128
P36418 UniProt NPD GO	VILI_DICDI	Protovillin (100 kDa actin-binding protein)	0.73	-	nuc	0					959
Q21086 UniProt NPD GO	GNL3_CAEEL	Putative guanine nucleotide-binding protein-like 3 homolog (Nucleostemin-1)	0.73	+	nuc	0	Nucleus (By similarity)	nucleolus [ISS] nucleus [ISS]			556
Q09475 UniProt NPD GO	YP93_CAEEL	Putative helicase C28H8.3 (EC 3.6.1.-)	0.73	+	vac	0	Nucleus (Potential)				1714
Q10938 UniProt NPD GO	YWS2_CAEEL	Putative zinc finger protein B0310.2	0.73	-	nuc	0	Nucleus (Probable)				413
Q9WTV7 UniProt NPD GO	RNF12_MOUSE	RING finger protein 12 (LIM domain-interacting RING finger protein) (RING finger LIM domain-binding ...	0.73	-	nuc	0					600

You are viewing entries 12451 to 12500 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.