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
Q8IWT3 UniProt NPD GO	PARC_HUMAN	p53-associated parkin-like cytoplasmic protein (UbcH7-associated protein 1)	0.82	-	nuc	0	Cytoplasm		607489		2517
Q6BLT2 UniProt NPD GO	PALA_DEBHA	pH-response regulator protein palA/RIM20	0.82	-	nuc	0					766
Q00202 UniProt NPD GO	PACC_EMENI	pH-response transcription factor pacC/RIM101	0.82	-	nuc	0	Cytoplasm. Nucleus. Cytoplasmic at acidic ambient pH, and nuclear in its processed form at alkaline ...				678
Q4R6W9 UniProt NPD GO	SNPC1_MACFA	snRNA-activating protein complex subunit 1 (SNAPc subunit 1) (snRNA-activating protein complex 43 kD ...	0.82	-	nuc	0	Nucleus (By similarity)				367
Q4U9M9 UniProt NPD GO	104K_THEAN	104 kDa microneme-rhoptry antigen precursor (p104)	0.81	+	nuc	1	Cell membrane; lipid-anchor; GPI-anchor (Potential). In microneme/rhoptry complexes (By similarity)				893
Q9Z2Q5 UniProt NPD GO	RM40_MOUSE	39S ribosomal protein L40, mitochondrial precursor (L40mt) (MRP-40) (Nuclear localization signal-con ...	0.81	+	nuc	0	Mitochondrion (By similarity)	mitochondrial ribosome [ISS]			206
Q9U762 UniProt NPD GO	RS6_AEDAL	40S ribosomal protein S6	0.81	+	nuc	0					349
Q5E958 UniProt NPD GO	RS8_BOVIN	40S ribosomal protein S8	0.81	+	nuc	0					207
P62241 UniProt NPD GO	RS8_HUMAN	40S ribosomal protein S8	0.81	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	600357		207
Q4R6P8 UniProt NPD GO	RS8_MACFA	40S ribosomal protein S8	0.81	+	nuc	0					207
P62242 UniProt NPD GO	RS8_MOUSE	40S ribosomal protein S8	0.81	+	nuc	0					207
P62243 UniProt NPD GO	RS8_RAT	40S ribosomal protein S8	0.81	+	nuc	0					207
Q9P7B2 UniProt NPD GO	RS8B_SCHPO	40S ribosomal protein S8-B	0.81	-	nuc	0					200
Q02792 UniProt NPD GO	XRN2_YEAST	5'-3' exoribonuclease 2 (EC 3.1.11.-) (Ribonucleic acid-trafficking protein 1) (p116)	0.81	-	nuc	0	Nucleus	mitochondrion [IDA] nucleus [IDA]			1006
Q9UGJ0 UniProt NPD GO	AAKG2_HUMAN	5'-AMP-activated protein kinase subunit gamma-2 (AMPK gamma-2 chain) (AMPK gamma2) (H91620p)	0.81	-	nuc	0			602743		569
Q00013 UniProt NPD GO	EM55_HUMAN	55 kDa erythrocyte membrane protein (p55) (Membrane protein, palmitoylated 1)	0.81	-	nuc	0	Membrane; peripheral membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	305360		466
P41125 UniProt NPD GO	RL13_CHICK	60S ribosomal protein L13 (Breast basic conserved protein 1)	0.81	-	nuc	0					210
Q6BNC2 UniProt NPD GO	RL24_DEBHA	60S ribosomal protein L24	0.81	-	nuc	0					156
P41098 UniProt NPD GO	RL34_TOBAC	60S ribosomal protein L34	0.81	-	mit	0					120
O44125 UniProt NPD GO	RL37_SCHMA	60S ribosomal protein L37	0.81	-	nuc	0					87
Q9NRR6 UniProt NPD GO	INP5E_HUMAN	72 kDa inositol polyphosphate 5-phosphatase (EC 3.1.3.36) (Phosphatidylinositol-4,5-bisphosphate 5-p ...	0.81	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein; cytoplasmic side (B ...				644
P50998 UniProt NPD GO	AMPD_SCHPO	AMP deaminase (EC 3.5.4.6) (Myoadenylate deaminase)	0.81	+	exc	0					846
P10759 UniProt NPD GO	AMPD1_RAT	AMP deaminase 1 (EC 3.5.4.6) (Myoadenylate deaminase) (AMP deaminase isoform M)	0.81	-	cyt	0					747
Q4KLG9 UniProt NPD GO	ZFN2B_RAT	AN1-type zinc finger protein 2B	0.81	-	nuc	0					257
Q99856 UniProt NPD GO	ARI3A_HUMAN	AT-rich interactive domain-containing protein 3A (ARID domain-containing protein 3A) (B-cell regulat ...	0.81	-	nuc	0	Nucleus (By similarity)	nucleus [NAS]	603265		593
Q7S6F3 UniProt NPD GO	DBP9_NEUCR	ATP-dependent RNA helicase dbp-9 (EC 3.6.1.-)	0.81	+	nuc	0	Nucleus; nucleolus (By similarity)				676
Q59KF3 UniProt NPD GO	SPB1_CANAL	AdoMet-dependent rRNA methyltransferase SPB1 (EC 2.1.1.-) (2'-O-ribose RNA methyltransferase) (S-ade ...	0.81	+	nuc	0	Nucleus; nucleolus (By similarity)				845
O82743 UniProt NPD GO	AGL19_ARATH	Agamous-like MADS-box protein AGL19	0.81	-	nuc	0	Nucleus (By similarity)				219
Q9JI91 UniProt NPD GO	ACTN2_MOUSE	Alpha-actinin-2 (Alpha actinin skeletal muscle isoform 2) (F-actin cross linking protein)	0.81	-	cyt	0	Colocalizes with MYOZ1 and FLNC at the Z-lines of skeletal muscle (By similarity)	striated muscle thin filament [TAS] Z disc [IDA]			894
O35430 UniProt NPD GO	APBA1_RAT	Amyloid beta A4 precursor protein-binding family A member 1 (Neuron-specific X11 protein) (Neuronal ...	0.81	-	nuc	0		plasma membrane [IDA]			839
O97952 UniProt NPD GO	ANDR_MACFA	Androgen receptor (Dihydrotestosterone receptor)	0.81	+	nuc	0	Nucleus				895
Q5M9H0 UniProt NPD GO	ANKS3_RAT	Ankyrin repeat and SAM domain-containing protein 3	0.81	-	nuc	0					663
Q28C34 UniProt NPD GO	AN13C_XENTR	Ankyrin repeat domain-containing protein 13C	0.81	-	nuc	0					509
Q86YR6 UniProt NPD GO	ANR21_HUMAN	Ankyrin repeat domain-containing protein 21 (Protein POTE) (Prostate, ovary, testis-expressed protei ...	0.81	-	nuc	0	Cell membrane; peripheral membrane protein		607549		584
Q5I0B9 UniProt NPD GO	ATG16_XENTR	Autophagy-related protein 16 (APG16-like 1)	0.81	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				537
Q6FP05 UniProt NPD GO	ATG2_CANGA	Autophagy-related protein 2	0.81	-	nuc	0	Perivacuolar compartment (By similarity)				1587
Q9ZV88 UniProt NPD GO	BEH4_ARATH	BES1/BZR1 homolog protein 4	0.81	-	nuc	0					325
Q8S307 UniProt NPD GO	BZR1_ARATH	BRASSINAZOLE-RESISTANT 1 protein (BIN2 SUBSTRATE 2 protein)	0.81	+	nuc	0	Nucleus				336
Q9LN63 UniProt NPD GO	BZR2_ARATH	BRASSINAZOLE-RESISTANT 2 protein (BRI1-EMS-SUPPRESSOR 1 protein) (BIN2 SUBSTRATE 1 protein) (107 pro ...	0.81	+	nuc	0	Nucleus. Cytoplasm. Brassinosteroid treatment triggers nuclear accumulation				335
O70318 UniProt NPD GO	E41L2_MOUSE	Band 4.1-like protein 2 (Generally expressed protein 4.1) (4.1G)	0.81	-	nuc	0					988
Q804S2 UniProt NPD GO	BMP2_TETNG	Bone morphogenetic protein 2 precursor (BMP-2)	0.81	-	exc	0	Secreted protein (By similarity)				420
P25703 UniProt NPD GO	BMP2A_XENLA	Bone morphogenetic protein 2-A precursor (BMP-2-I)	0.81	+	exc	0	Secreted protein (By similarity)				398
P22004 UniProt NPD GO	BMP6_HUMAN	Bone morphogenetic protein 6 precursor (BMP-6)	0.81	-	exc	0	Secreted protein (By similarity)		112266		513
O14514 UniProt NPD GO	BAI1_HUMAN	Brain-specific angiogenesis inhibitor 1 precursor	0.81	-	end	7 *	Cell membrane; multi-pass membrane protein. Likely to be concentrated at cell-cell adhesion sites	integral to plasma membrane [TAS] intercellular junction [TAS] plasma membrane [TAS]	602682		1584
Q9VZE6 UniProt NPD GO	BXDC2_DROME	Brix domain-containing protein 2 homolog (Ribosome biogenesis protein Brix homolog)	0.81	+	nuc	0	Nucleus; nucleolus (By similarity)				359
O60271 UniProt NPD GO	JIP4_HUMAN	C-jun-amino-terminal kinase-interacting protein 4 (JNK-interacting protein 4) (JIP-4) (JNK-associate ...	0.81	-	nuc	0	Cytoplasm. Cytoplasm; perinuclear region. Perinuclear distribution in response to stress signals suc ...		605430		1321
Q9VEU1 UniProt NPD GO	CAD89_DROME	Cadherin 89D precursor	0.81	+	end	2 *	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]			2240
Q63421 UniProt NPD GO	PDE1C_RAT	Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C (EC 3.1.4.17) (Cam-PDE 1C) ...	0.81	+	nuc	0					768
O88831 UniProt NPD GO	KKCC2_RAT	Calcium/calmodulin-dependent protein kinase kinase 2 (EC 2.7.11.17) (Calcium/calmodulin-dependent pr ...	0.81	-	nuc	0	Cytoplasm	intracellular [ISS]			587
P32458 UniProt NPD GO	CDC11_YEAST	Cell division control protein 11	0.81	-	nuc	0	Membrane. Bud neck. Present at the bud neck during cell division. Interacts with phosphatidylinosito ...	mating projection base [IDA] prospore membrane [TAS] septin ring (sensu Saccharomyces) [TAS] spore wall (sensu Fungi) [TAS]			415

You are viewing entries 8201 to 8250 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.