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
P17038 UniProt NPD GO	ZNF43_HUMAN	Zinc finger protein 43 (Zinc protein HTF6) (Zinc finger protein KOX27)	0.38	-	nuc	0	Nucleus (Probable)		603972		803
Q5ZMM5 UniProt NPD GO	ZN706_CHICK	Zinc finger protein 706	0.38	-	nuc	0					76
P98061 UniProt NPD GO	NAS28_CAEEL	Zinc metalloproteinase nas-28 precursor (EC 3.4.24.21) (Nematode astacin 28)	0.38	-	exc	0	Secreted protein (Potential)				497
P30625 UniProt NPD GO	KAPR_CAEEL	cAMP-dependent protein kinase regulatory subunit	0.38	-	cyt	0	Cytoplasm; cytosol				366
Q86ZN7 UniProt NPD GO	KAPR_TRIAT	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit)	0.38	-	cyt	0					462
Q9HEW1 UniProt NPD GO	KAPR_CANAL	cAMP-dependent protein kinase regulatory subunit (PKA regulatory subunit) (PKA-R)	0.38	-	nuc	0					459
Q00194 UniProt NPD GO	CNGA1_BOVIN	cGMP-gated cation channel alpha 1 (CNG channel alpha 1) (CNG-1) (CNG1) (Cyclic nucleotide-gated chan ...	0.38	+	end	2	Membrane; multi-pass membrane protein				690
Q17607 UniProt NPD GO	MCE1_CAEEL	mRNA capping enzyme [Includes: Polynucleotide 5'-triphosphatase (EC 3.1.3.33) (mRNA 5'-triphosphatas ...	0.38	-	cyt	0	Nucleus (By similarity)				623
P84148 UniProt NPD GO	MTR2_CANAL	mRNA transport regulator MTR2	0.38	-	nuc	0	Nucleus			1Q42	181
Q8NF37 UniProt NPD GO	PCAT1_HUMAN	1-acylglycerophosphocholine O-acyltransferase 1 (EC 2.3.1.23) (Lung-type acyl-coa:lysophosphatidylch ...	0.37	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...				534
Q9M2Y8 UniProt NPD GO	1A19_ARATH	1-aminocyclopropane-1-carboxylate synthase 9 (EC 4.4.1.14) (ACC synthase 9) (S-adenosyl-L-methionine ...	0.37	-	mit	0					470
Q9XHP0 UniProt NPD GO	11S2_SESIN	11S globulin seed storage protein 2 precursor (11S globulin seed storage protein II) (alpha-globulin ...	0.37	-	mit	0		protein body [NAS]			459
P13744 UniProt NPD GO	11SB_CUCMA	11S globulin subunit beta precursor [Contains: 11S globulin gamma chain (11S globulin acidic chain); ...	0.37	-	exc	0					480
P42649 UniProt NPD GO	14332_ENTHI	14-3-3 protein 2 (14-3-3-2)	0.37	-	cyt	0					238
Q02218 UniProt NPD GO	ODO1_HUMAN	2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor (EC 1.2.4.2) (Alpha-ketoglutarate ...	0.37	-	mit	0	Mitochondrion; mitochondrial matrix		203740		1002
P46466 UniProt NPD GO	PRS4_ORYSA	26S protease regulatory subunit 4 homolog (TAT-binding protein homolog 2)	0.37	-	nuc	0	Cytoplasm (Potential). Nucleus (Potential)				448
Q9SEI4 UniProt NPD GO	PRS6B_ARATH	26S protease regulatory subunit 6B homolog (26S proteasome AAA-ATPase subunit RPT3) (Regulatory part ...	0.37	-	nuc	0	Cytoplasm (Potential). Nucleus (Potential)				408
P46471 UniProt NPD GO	PRS7_MOUSE	26S protease regulatory subunit 7 (Protein MSS1)	0.37	-	nuc	0	Cytoplasm. Nucleus				432
Q9CX56 UniProt NPD GO	PSD8_MOUSE	26S proteasome non-ATPase regulatory subunit 8 (26S proteasome regulatory subunit S14)	0.37	-	cyt	0					257
Q39649 UniProt NPD GO	2SS_CUCMA	2S albumin precursor [Contains: 2S albumin small chain; 2S albumin large chain]	0.37	-	exc	0	Protein body. Vacuole. Cotyledonary membrane-bound vacuolar protein bodies	storage vacuole [IDA]			141
Q9XJ27 UniProt NPD GO	RR9_ARATH	30S ribosomal protein S9, chloroplast precursor	0.37	-	mit	0	Plastid; chloroplast				208
Q9D1P0 UniProt NPD GO	RM13_MOUSE	39S ribosomal protein L13, mitochondrial (L13mt) (MRP-L13)	0.37	-	cyt	0	Mitochondrion (By similarity)	mitochondrial large ribosomal subunit [IDA]			178
P59480 UniProt NPD GO	RM45_XENLA	39S ribosomal protein L45, mitochondrial precursor (L45mt) (MRP-L45)	0.37	-	mit	0	Mitochondrion (By similarity)	mitochondrion [ISS]			309
Q11004 UniProt NPD GO	PPID_SCHPO	40 kDa peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-40) (CYP-40 ...	0.37	-	cyt	0	Cytoplasm (By similarity)				356
P46298 UniProt NPD GO	RS13_PEA	40S ribosomal protein S13	0.37	-	nuc	0					151
P49205 UniProt NPD GO	RS17A_ARATH	40S ribosomal protein S17-1	0.37	-	nuc	0					140
Q94613 UniProt NPD GO	RS19_MYAAR	40S ribosomal protein S19	0.37	-	nuc	0					149
Q962Q6 UniProt NPD GO	RS24_SPOFR	40S ribosomal protein S24	0.37	-	nuc	0					132
Q962Q5 UniProt NPD GO	RS25_SPOFR	40S ribosomal protein S25	0.37	+	nuc	0					119
P41692 UniProt NPD GO	RS26_MUSVI	40S ribosomal protein S26 (Fragment)	0.37	-	nuc	0					40
Q96564 UniProt NPD GO	RS27_HORVU	40S ribosomal protein S27 (Manganese efficiency-related protein 1)	0.37	-	nuc	0					86
P22277 UniProt NPD GO	RS27A_HORVU	40S ribosomal protein S27a	0.37	+	nuc	0					79
P47905 UniProt NPD GO	RS27A_LUPAL	40S ribosomal protein S27a	0.37	+	nuc	0					79
P59271 UniProt NPD GO	R27AA_ARATH	40S ribosomal protein S27a-1	0.37	+	nuc	0					80
P59232 UniProt NPD GO	R27AB_ARATH	40S ribosomal protein S27a-2	0.37	+	nuc	0					81
P49689 UniProt NPD GO	RS30_ARATH	40S ribosomal protein S30	0.37	+	nuc	0					62
Q4T8S6 UniProt NPD GO	RS3A_TETNG	40S ribosomal protein S3a	0.37	+	nuc	0					265
P13196 UniProt NPD GO	HEM1_HUMAN	5-aminolevulinate synthase, nonspecific, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic aci ...	0.37	-	mit	0	Mitochondrion; mitochondrial matrix		125290		640
P78985 UniProt NPD GO	K6PF_ASPNG	6-phosphofructokinase (EC 2.7.1.11) (Phosphofructokinase) (Phosphohexokinase) (6PF-1-K)	0.37	+	cyt	0	Cytoplasm (By similarity)				783
Q6FTK4 UniProt NPD GO	RL11_CANGA	60S ribosomal protein L11	0.37	-	cyt	0					174
P46222 UniProt NPD GO	RL11_DROME	60S ribosomal protein L11	0.37	-	nuc	0					184
P36521 UniProt NPD GO	RM11_YEAST	60S ribosomal protein L11, mitochondrial precursor (YmL11)	0.37	-	nuc	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			249
Q7ZWJ4 UniProt NPD GO	RL18A_BRARE	60S ribosomal protein L18a	0.37	-	mit	0					176
P62717 UniProt NPD GO	RL18A_MOUSE	60S ribosomal protein L18a	0.37	-	mit	0					176
P62718 UniProt NPD GO	RL18A_RAT	60S ribosomal protein L18a	0.37	-	mit	0					176
Q43291 UniProt NPD GO	RL211_ARATH	60S ribosomal protein L21-1	0.37	-	nuc	0					164
P52865 UniProt NPD GO	RL22_GADMO	60S ribosomal protein L22 (Fragment)	0.37	-	nuc	0					124
P51997 UniProt NPD GO	RL25_PUCGR	60S ribosomal protein L25	0.37	-	mit	0					158
P41092 UniProt NPD GO	RL27A_DROME	60S ribosomal protein L27a	0.37	+	mit	0					149
Q56JX3 UniProt NPD GO	RL31_BOVIN	60S ribosomal protein L31	0.37	-	nuc	0					125

You are viewing entries 33901 to 33950 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.