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
Q5PPZ9 UniProt NPD GO	GDS1B_XENLA	Rap1 GTPase-GDP dissociation stimulator 1-B (RalB-binding protein-B) (Rap1gds1-B protein) (smgGDS-B) ...	0.17	-	end	0					607
P34729 UniProt NPD GO	RAS1_PHYPO	Ras-like protein 1	0.17	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side. Inner surface of plasma membrane				189
P08647 UniProt NPD GO	RAS_SCHPO	Ras-like protein 1	0.17	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				219
P61106 UniProt NPD GO	RAB14_HUMAN	Ras-related protein Rab-14	0.17	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	cytosol [ISS] early endosome [ISS] Golgi stack [ISS] late endosome [ISS] lysosome [ISS] membrane fraction [ISS] nuclear envelope-endoplasmic reticulum network [ISS] perinuclear region [ISS] plasma membrane [ISS] rough endoplasmic reticulum [ISS] trans-Golgi network transport vesicle [ISS]		2AED	214
Q91V41 UniProt NPD GO	RAB14_MOUSE	Ras-related protein Rab-14	0.17	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				214
P61107 UniProt NPD GO	RAB14_RAT	Ras-related protein Rab-14	0.17	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	cytosol [IDA] early endosome [IDA] Golgi stack [IDA] late endosome [IDA] lysosome [IDA] membrane fraction [IDA] nuclear envelope-endoplasmic reticulum network [IDA] perinuclear region [IDA] plasma membrane [IDA] rough endoplasmic reticulum [IDA] trans-Golgi network transport vesicle [IDA]			214
P35294 UniProt NPD GO	RAB19_MOUSE	Ras-related protein Rab-19	0.17	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				217
O00194 UniProt NPD GO	RB27B_HUMAN	Ras-related protein Rab-27B (C25KG)	0.17	-	cyt	0	Membrane; lipid-anchor		603869	2F7S	217
Q8CG50 UniProt NPD GO	RAB43_MOUSE	Ras-related protein Rab-43	0.17	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				210
Q53B90 UniProt NPD GO	RAB43_RAT	Ras-related protein Rab-43	0.17	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				210
Q6PHI9 UniProt NPD GO	RAB4A_BRARE	Ras-related protein Rab-4A	0.17	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				213
P18066 UniProt NPD GO	RAB5A_CANFA	Ras-related protein Rab-5A	0.17	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Endosome; early endosome; early endos ...				215
P61271 UniProt NPD GO	RAB5A_MACFA	Ras-related protein Rab-5A	0.17	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Endosome; early endosome; early endos ...				215
Q96283 UniProt NPD GO	RB11A_ARATH	Ras-related protein Rab11A	0.17	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				217
O24461 UniProt NPD GO	RAB7_PRUAR	Ras-related protein Rab7	0.17	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				207
Q06141 UniProt NPD GO	REG3A_HUMAN	Regenerating islet-derived protein 3 alpha precursor (Reg III-alpha) (Pancreatitis-associated protei ...	0.17	-	exc	0	Secreted protein. Found in the apical region of pancreatic acinar cells	cytoplasm [TAS] extracellular space [TAS] soluble fraction [TAS]	167805	1UV0	175
Q15293 UniProt NPD GO	RCN1_HUMAN	Reticulocalbin-1 precursor	0.17	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum lumen [TAS]	602735		331
Q2KJ39 UniProt NPD GO	RCN3_BOVIN	Reticulocalbin-3 precursor	0.17	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				328
Q04947 UniProt NPD GO	RTN1_YEAST	Reticulon-like protein 1	0.17	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA] endoplasmic reticulum membrane [IDA] Golgi apparatus [IDA] mitochondrion [IDA]			295
Q9Z1L4 UniProt NPD GO	XLRS1_MOUSE	Retinoschisin precursor (X-linked juvenile retinoschisis protein homolog)	0.17	-	exc	0	Secreted protein (By similarity)				224
Q94915 UniProt NPD GO	REG2_DROME	Rhythmically expressed gene 2 protein (dREG-2)	0.17	-	nuc	0					260
Q5BK46 UniProt NPD GO	RNH1_RAT	Ribonuclease H1 (EC 3.1.26.4) (RNase H1)	0.17	+	mit	0	Cytoplasm (Potential)				285
O46534 UniProt NPD GO	RNAS6_CERAE	Ribonuclease K6 precursor (EC 3.1.27.-) (RNase K6)	0.17	-	nuc	1 *	Secreted protein				150
Q40966 UniProt NPD GO	RNS4_PYRPY	Ribonuclease S-4 precursor (EC 3.1.27.1) (S4-RNase)	0.17	-	nuc	1 *	Secreted protein; extracellular space				228
P00660 UniProt NPD GO	RNAS1_CONTA	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.17	-	nuc	0	Secreted protein				124
P00666 UniProt NPD GO	RNAS1_RANTA	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.17	-	nuc	0	Secreted protein				124
P19644 UniProt NPD GO	RNAS1_SEMEN	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.17	-	nuc	0	Secreted protein				128
Q60561 UniProt NPD GO	RIR2_MESAU	Ribonucleoside-diphosphate reductase M2 subunit (EC 1.17.4.1) (Ribonucleotide reductase small subuni ...	0.17	-	cyt	0	Cytoplasm				386
Q9SJ20 UniProt NPD GO	RIR1_ARATH	Ribonucleoside-diphosphate reductase large subunit (EC 1.17.4.1) (Ribonucleoside-diphosphate reducta ...	0.17	-	cyt	0	Cytoplasm (By similarity)				816
P50651 UniProt NPD GO	RIR2_ARATH	Ribonucleoside-diphosphate reductase small chain (EC 1.17.4.1) (Ribonucleotide reductase small subun ...	0.17	-	mit	1	Cytoplasm (By similarity)				341
Q9D7G0 UniProt NPD GO	PRPS1_MOUSE	Ribose-phosphate pyrophosphokinase I (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase I) (PRS-I ...	0.17	-	cyt	0					317
P60892 UniProt NPD GO	PRPS1_RAT	Ribose-phosphate pyrophosphokinase I (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase I) (PRS-I ...	0.17	-	cyt	0					317
Q2HJ58 UniProt NPD GO	PRPS1_BOVIN	Ribose-phosphate pyrophosphokinase I (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase I) (PRS-I ...	0.17	-	cyt	0					317
P60891 UniProt NPD GO	PRPS1_HUMAN	Ribose-phosphate pyrophosphokinase I (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase I) (PRS-I ...	0.17	-	cyt	0			311850		317
Q9D7S7 UniProt NPD GO	RL22L_MOUSE	Ribosomal protein L22-like 1	0.17	-	nuc	0					122
P37394 UniProt NPD GO	RBS_CYACA	Ribulose bisphosphate carboxylase small chain (EC 4.1.1.39) (RuBisCO small subunit)	0.17	-	cyt	0	Plastid; chloroplast				138
Q42516 UniProt NPD GO	RBS1_AMAHP	Ribulose bisphosphate carboxylase small chain 1, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.17	-	mit	0	Plastid; chloroplast				183
P16130 UniProt NPD GO	RBS2_ACECL	Ribulose bisphosphate carboxylase small chain 2 (EC 4.1.1.39) (RuBisCO small subunit 2) (Fragment)	0.17	-	cyt	0	Plastid; chloroplast				86
Q38692 UniProt NPD GO	RBS6_ACECL	Ribulose bisphosphate carboxylase small chain 6, chloroplast precursor (EC 4.1.1.39) (RuBisCO small ...	0.17	-	mit	0	Plastid; chloroplast				182
Q9FWT5 UniProt NPD GO	RIP3_ORYSA	Ripening-related protein 3 precursor	0.17	-	exc	1 *	Secreted protein (Potential)				213
P35913 UniProt NPD GO	PDE6B_HUMAN	Rod cGMP-specific 3',5'-cyclic phosphodiesterase beta-subunit precursor (EC 3.1.4.35) (GMP-PDE beta) ...	0.17	-	cyt	0	Membrane; lipid-anchor		268000		854
Q9C0X6 UniProt NPD GO	RUVB1_SCHPO	RuvB-like helicase 1 (EC 3.6.1.-)	0.17	-	nuc	0	Nucleus (By similarity)				456
Q9S7T9 UniProt NPD GO	DCAM2_ARATH	S-adenosylmethionine decarboxylase proenzyme 2 (EC 4.1.1.50) (AdoMetDC 2) (SamDC 2) [Contains: S-ade ...	0.17	-	nuc	0					362
Q03400 UniProt NPD GO	SANT_PLAF7	S-antigen protein precursor	0.17	-	nuc	0	Parasitophorous vacuole				585
P04927 UniProt NPD GO	SANT_PLAFF	S-antigen protein precursor	0.17	-	exc	0	Parasitophorous vacuole				265
O75368 UniProt NPD GO	SH3L1_HUMAN	SH3 domain-binding glutamic acid-rich-like protein	0.17	-	mit	0		cytoplasm [TAS] nucleus [TAS]	300190	1U6T	114
P19965 UniProt NPD GO	SP15_TORCA	SITS-binding protein (SP105)	0.17	-	nuc	1 *	Membrane; multi-pass membrane protein (Potential)				696
P15464 UniProt NPD GO	HB21_SPAEH	SMH class II histocompatibility antigen, beta-1 chain precursor	0.17	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				258
Q8LBB2 UniProt NPD GO	KING1_ARATH	SNF1-related protein kinase regulatory subunit gamma 1 (AKIN gamma1) (AKING1)	0.17	-	cyt	0					424
Q96A44 UniProt NPD GO	SSB4_HUMAN	SPRY domain-containing SOCS box protein 4 (SSB-4)	0.17	-	nuc	0	Cytoplasm (Probable)				273

You are viewing entries 54901 to 54950 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.