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
Q6IS24 UniProt NPD GO	GLTL3_HUMAN	Putative polypeptide N-acetylgalactosaminyltransferase-like protein 3 (EC 2.4.1.41) (Protein-UDP ace ...	0.39	-	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				598
O24585 UniProt NPD GO	CRI4_MAIZE	Putative receptor protein kinase CRINKLY4 precursor (EC 2.7.11.1)	0.39	-	end	2 *	Membrane; single-pass type I membrane protein				901
Q8QZS5 UniProt NPD GO	RN183_MOUSE	RING finger protein 183	0.39	-	nuc	1	Membrane; single-pass membrane protein (Potential)				190
Q9LZJ6 UniProt NPD GO	ATL3L_ARATH	RING-H2 finger protein ATL3L (RING-H2 finger protein ATL5)	0.39	-	nuc	1 *					257
Q75B93 UniProt NPD GO	TFB4_ASHGO	RNA polymerase II transcription factor B subunit 4 (RNA polymerase II transcription factor B p34 sub ...	0.39	+	cyt	0	Nucleus (By similarity)				341
O97556 UniProt NPD GO	GDIB_CANFA	Rab GDP dissociation inhibitor beta (Rab GDI beta) (Guanosine diphosphate dissociation inhibitor 2) ...	0.39	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				445
Q61598 UniProt NPD GO	GDIB_MOUSE	Rab GDP dissociation inhibitor beta (Rab GDI beta) (Guanosine diphosphate dissociation inhibitor 2) ...	0.39	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)	Golgi apparatus [IPI]			445
Q9H2M9 UniProt NPD GO	RBGPR_HUMAN	Rab3 GTPase-activating protein non-catalytic subunit (Rab3 GTPase-activating protein 150 kDa subunit ...	0.39	-	cyt	0	Cytoplasm. In neurons, it is enriched in the synaptic soluble fraction	soluble fraction [ISS]			1393
P48820 UniProt NPD GO	RBP2_BOVIN	Ran-binding protein 2 (RanBP2) (Nuclear pore complex protein Nup358) (Nucleoporin Nup358) (358 kDa n ...	0.39	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex (By similarity). Cytoplasmic filaments (By similarit ...				1085
O43374 UniProt NPD GO	RASL2_HUMAN	Ras GTPase-activating protein 4 (RasGAP-activating-like protein 2) (Calcium-promoted Ras inactivator ...	0.39	-	cyt	0	Cytoplasm; cytosol. Cell membrane; peripheral membrane protein. Localized to the cytosol as a result ...		607943		803
Q9UQX7 UniProt NPD GO	RAS1_CANAL	Ras-like protein 1 (Ras homolog type B)	0.39	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				290
Q80X95 UniProt NPD GO	RRAGA_MOUSE	Ras-related GTP-binding protein A (Rag A) (RagA)	0.39	-	mit	0	Cytoplasm (By similarity). Predominantly cytoplasmic. Nucleus (By similarity). May shuttle between t ...	cytoplasm [ISS] nucleus [ISS]			313
Q63486 UniProt NPD GO	RRAGA_RAT	Ras-related GTP-binding protein A (Rag A) (RagA)	0.39	-	mit	0	Cytoplasm (By similarity). Predominantly cytoplasmic. Nucleus (By similarity). May shuttle between t ...	cytoplasm [ISS] nucleus [ISS]			313
Q7L523 UniProt NPD GO	RRAGA_HUMAN	Ras-related GTP-binding protein A (Rag A) (RagA) (Adenovirus E3 14.7 kDa-interacting protein 1) (FIP ...	0.39	-	mit	0	Cytoplasm. Predominantly cytoplasmic. Nucleus. May shuttle between the cytoplasm and nucleus, depend ...	cytoplasm [IDA] nucleus [IDA]			313
P22128 UniProt NPD GO	RAB8_DISOM	Ras-related protein Rab-8 (ORA2)	0.39	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				210
Q9H426 UniProt NPD GO	RIMS4_HUMAN	Regulating synaptic membrane exocytosis protein 4 (Rab3-interacting molecule 4) (RIM 4) (RIM4 gamma) ...	0.39	-	mit	0					269
P60191 UniProt NPD GO	RIMS4_MOUSE	Regulating synaptic membrane exocytosis protein 4 (Rab3-interacting molecule 4) (RIM 4) (RIM4 gamma) ...	0.39	-	mit	0					269
Q9HBX9 UniProt NPD GO	RXFP1_HUMAN	Relaxin receptor 1 (Relaxin family peptide receptor 1) (Leucine-rich repeat-containing G-protein cou ...	0.39	-	end	7	Membrane; multi-pass membrane protein		606654		757
Q12443 UniProt NPD GO	RTN2_YEAST	Reticulon-like protein 2	0.39	-	mit	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA]			393
P20829 UniProt NPD GO	ENV2_DROME	Retrovirus-related Env polyprotein from transposon 297	0.39	-	end	1 *					471
Q92730 UniProt NPD GO	RND1_HUMAN	Rho-related GTP-binding protein Rho6 (Rho family GTPase 1) (Rnd1)	0.39	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	adherens junction [IDA]	609038	2CLS	232
Q15835 UniProt NPD GO	RK_HUMAN	Rhodopsin kinase precursor (EC 2.7.11.14) (RK) (G protein-coupled receptor kinase 1)	0.39	+	cyt	0	Membrane; lipid-anchor		258100		563
P00673 UniProt NPD GO	RNAS1_BALAC	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.39	-	nuc	0	Secreted protein				124
Q9Y6S9 UniProt NPD GO	RPKL1_HUMAN	Ribosomal protein S6 kinase-like 1 (EC 2.7.11.1)	0.39	-	nuc	0					549
Q5RA67 UniProt NPD GO	RPKL1_PONPY	Ribosomal protein S6 kinase-like 1 (EC 2.7.11.1)	0.39	-	nuc	0					549
O02655 UniProt NPD GO	DCAM_CAEEL	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.39	-	cyt	0					368
P79888 UniProt NPD GO	DCAM_XENLA	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.39	-	cyt	0					335
Q03067 UniProt NPD GO	SGF11_YEAST	SAGA-associated factor 11 (11 kDa SAGA-associated factor)	0.39	-	nuc	0	Nucleus (Probable)	nucleus [IDA] SAGA complex [IDA]			99
Q99963 UniProt NPD GO	SH3G3_HUMAN	SH3-containing GRB2-like protein 3 (SH3 domain protein 2C) (EEN-B2)	0.39	+	cyt	0			603362		347
Q6GPE9 UniProt NPD GO	SHCBA_XENLA	SHC SH2 domain-binding protein 1 homolog A	0.39	-	mit	0					699
Q6BUX9 UniProt NPD GO	HSV2_DEBHA	SVP1-like protein 2	0.39	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Cytoplasmic vesicle; cytopl ...				432
P25375 UniProt NPD GO	PRTD_YEAST	Saccharolysin (EC 3.4.24.37) (Protease D) (Proteinase yscD) (Oligopeptidase YSCD)	0.39	-	mit	0	Cytoplasm	cytoplasm [IDA] mitochondrial intermembrane space [IDA]			712
Q2VLG4 UniProt NPD GO	C163A_CERAE	Scavenger receptor cysteine-rich type 1 protein M130 precursor (CD163 antigen) [Contains: Soluble CD ...	0.39	-	end	2 *	Cell membrane; single-pass type I membrane protein (By similarity). Soluble CD163: Secreted protein ...				1151
Q62740 UniProt NPD GO	SPP24_RAT	Secreted phosphoprotein 24 precursor (Spp-24) (Secreted phosphoprotein 2)	0.39	-	nuc	0	Secreted protein (By similarity)				203
P63298 UniProt NPD GO	SECR_PIG	Secretin precursor (Fragment)	0.39	-	exc	0	Secreted protein				131
Q80Z70 UniProt NPD GO	SEL1L_RAT	Sel-1 homolog precursor (Suppressor of lin-12-like protein) (Sel-1L)	0.39	-	end	0	Membrane; single-pass type I membrane protein (Potential)				794
P59798 UniProt NPD GO	SELK_RAT	Selenoprotein K	0.39	-	nuc	1 *					94
Q8R4G1 UniProt NPD GO	SNSR1_RAT	Sensory neuron-specific G-protein coupled receptor 1	0.39	-	end	7 *	Membrane; multi-pass membrane protein				323
P14519 UniProt NPD GO	GLYM_RABIT	Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1) (Serine methylase) (Glycine hy ...	0.39	-	mit	0	Mitochondrion				504
P25045 UniProt NPD GO	LCB1_YEAST	Serine palmitoyltransferase 1 (EC 2.3.1.50) (Long chain base biosynthesis protein 1) (SPT 1) (SPT1)	0.39	-	cyt	0	Membrane; multi-pass membrane protein (Potential)	membrane fraction [IDA] microsome [IPI] serine C-palmitoyltransferase complex [IMP]			558
Q91YA2 UniProt NPD GO	KPSH1_MOUSE	Serine/threonine-protein kinase H1 (EC 2.7.11.1) (PSK-H1)	0.39	-	nuc	0	Localized in the Brefeldin A-sensitive Golgi compartment, at centrosomes, in the nucleus with a some ...				423
P38615 UniProt NPD GO	MDS1_YEAST	Serine/threonine-protein kinase MDS1/RIM11 (EC 2.7.11.1)	0.39	-	nuc	0		cytoplasm [IDA]			370
Q8BHI9 UniProt NPD GO	NIM1_MOUSE	Serine/threonine-protein kinase NIM1 (EC 2.7.11.1)	0.39	-	nuc	0					436
Q7ZZC8 UniProt NPD GO	NEK9_XENLA	Serine/threonine-protein kinase Nek9 (EC 2.7.11.1) (NimA-related protein kinase 9) (XNek9) (Nercc1 k ...	0.39	-	nuc	0	Cytoplasm (By similarity)				944
Q20845 UniProt NPD GO	PLK3_CAEEL	Serine/threonine-protein kinase plk-3 (EC 2.7.11.21) (Polo-like kinase 3)	0.39	-	nuc	0	Nucleus (By similarity)				615
Q4P4W3 UniProt NPD GO	PTPA1_USTMA	Serine/threonine-protein phosphatase 2A activator 1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.39	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				487
Q2UCL6 UniProt NPD GO	PTPA2_ASPOR	Serine/threonine-protein phosphatase 2A activator 2 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.39	-	cyt	0	Cytoplasm (By similarity)				422
Q27889 UniProt NPD GO	PP2B2_DROME	Serine/threonine-protein phosphatase 2B catalytic subunit 2, (EC 3.1.3.16) (Calmodulin-dependent cal ...	0.39	-	nuc	0					570
Q39010 UniProt NPD GO	KSG6_ARATH	Shaggy-related protein kinase dzeta (EC 2.7.11.1) (ASK-dzeta)	0.39	-	nuc	0					412
O04160 UniProt NPD GO	KSGT_BRANA	Shaggy-related protein kinase theta (EC 2.7.11.1) (ASK-theta)	0.39	-	mit	0					468

You are viewing entries 32951 to 33000 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.