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
Q02805 UniProt NPD GO	ROD1_YEAST	Protein ROD1	0.99	-	nuc	0	Membrane; peripheral membrane protein. Membrane-associated or associated to a complex that cofractio ...	plasma membrane [IDA]			837
Q03707 UniProt NPD GO	SRC1_YEAST	Protein SRC1	0.99	+	nuc	1					834
P50111 UniProt NPD GO	ZDS1_YEAST	Protein ZDS1 (Protein NRC1) (RT2GS1)	0.99	-	nuc	0		bud neck [IDA] bud tip [IDA] cytoplasm [IPI] nuclear pore [IPI]			915
O60879 UniProt NPD GO	DIAP2_HUMAN	Protein diaphanous homolog 2 (Diaphanous-related formin-2) (DRF2)	0.99	+	nuc	0	Isoform 3: Cytoplasm; cytosol. Isoform 3: Endosome; early endosome. Isoform 3 is cytosolic but when ...		300511		1101
Q9ULU4 UniProt NPD GO	PKCB1_HUMAN	Protein kinase C-binding protein 1 (Rack7) (Cutaneous T-cell lymphoma-associated antigen se14-3) (CT ...	0.99	-	nuc	0					1186
P24583 UniProt NPD GO	KPC1_YEAST	Protein kinase C-like 1 (EC 2.7.11.13) (PKC 1)	0.99	+	nuc	0		cytoplasm [IDA] cytoskeleton [IDA] nucleus [IDA] site of polarized growth [IDA]			1151
P36583 UniProt NPD GO	PCK2_SCHPO	Protein kinase C-like 2 (EC 2.7.11.13)	0.99	-	nuc	0		cell septum [IDA]			1016
P13185 UniProt NPD GO	KIN1_YEAST	Protein kinase KIN1 (EC 2.7.11.1)	0.99	-	nuc	0		membrane fraction [IDA] plasma membrane [IPI]			1064
Q11184 UniProt NPD GO	LE756_CAEEL	Protein let-756 (Lethal protein 756)	0.99	+	nuc	0					425
Q9PU36 UniProt NPD GO	PCLO_CHICK	Protein piccolo (Aczonin) (Fragment)	0.99	-	nuc	0	Concentrated at the presynaptic side of synaptic junctions (By similarity)	synapse [ISS]			5120
Q9QYX7 UniProt NPD GO	PCLO_MOUSE	Protein piccolo (Aczonin) (Multidomain presynaptic cytomatrix protein) (Brain-derived HLMN protein)	0.99	-	nuc	0	Concentrated at the presynaptic side of synaptic junctions	synapse [IDA]			5038
P91620 UniProt NPD GO	SIF2_DROME	Protein still life, isoforms C/SIF type 2	0.99	-	nuc	0	Localizes to the submembranous region of synaptic terminals				2061
P25172 UniProt NPD GO	SUZ2_DROME	Protein suppressor 2 of zeste (Protein posterior sex combs)	0.99	+	nuc	0	Nucleus (Probable)				1368
P59597 UniProt NPD GO	SUUR_DROER	Protein suppressor of underreplication	0.99	+	nuc	0	Nucleus (By similarity). Binds to polytene chromosomes from salivary glands; localized at late-repli ...				962
P20193 UniProt NPD GO	SUV3_DROME	Protein suppressor of variegation 3-7	0.99	-	nuc	0	Nucleus (Probable)				1250
Q7Y667 UniProt NPD GO	YCF2_CALFE	Protein ycf2	0.99	-	end	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2287
Q2L949 UniProt NPD GO	YCF2_GOSHI	Protein ycf2	0.99	-	end	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2298
P61242 UniProt NPD GO	YCF2_LYCES	Protein ycf2	0.99	-	nuc	1	Plastid; chloroplast; chloroplast stroma. Plastid; chromoplast; chromoplast stroma				2278
Q6EVY7 UniProt NPD GO	YCF2_NYMAL	Protein ycf2	0.99	-	end	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2253
Q9MEF2 UniProt NPD GO	YCF2_OENHO	Protein ycf2	0.99	+	nuc	0	Plastid; chloroplast; chloroplast stroma				2280
Q32836 UniProt NPD GO	YCF2_PELHO	Protein ycf2	0.99	-	end	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2109
Q85WV5 UniProt NPD GO	YCF2_PINKO	Protein ycf2	0.99	-	nuc	0	Plastid; chloroplast; chloroplast stroma (By similarity)				1320
P41653 UniProt NPD GO	YCF2_PINTH	Protein ycf2	0.99	-	nuc	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2054
Q2MIC5 UniProt NPD GO	YCF2_SOLBU	Protein ycf2	0.99	-	nuc	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2278
Q27RY7 UniProt NPD GO	YCF2_SOLTU	Protein ycf2	0.99	-	nuc	1	Plastid; chloroplast; chloroplast stroma (By similarity)				2278
Q74Z27 UniProt NPD GO	INO80_ASHGO	Putative DNA helicase INO80 (EC 3.6.1.-)	0.99	+	nuc	0	Nucleus (By similarity)				1414
Q6BGY8 UniProt NPD GO	INO80_DEBHA	Putative DNA helicase INO80 (EC 3.6.1.-)	0.99	+	nuc	0	Nucleus (By similarity)				1364
Q4IL82 UniProt NPD GO	INO80_GIBZE	Putative DNA helicase INO80 (EC 3.6.1.-)	0.99	+	nuc	0	Nucleus (By similarity)				1904
Q4PGL2 UniProt NPD GO	INO80_USTMA	Putative DNA helicase INO80 (EC 3.6.1.-)	0.99	-	nuc	0	Nucleus (By similarity)				1910
Q5BAZ5 UniProt NPD GO	INO80_EMENI	Putative DNA helicase ino80 (EC 3.6.1.-)	0.99	+	nuc	0	Nucleus (By similarity)				1612
O94603 UniProt NPD GO	JHD1_SCHPO	Putative JmjC domain-containing histone demethylation protein 1 (EC 1.14.11.-) (Heterochromatin-dest ...	0.99	-	nuc	0	Nucleus	nucleus [IDA]			948
P46551 UniProt NPD GO	CD2L7_CAEEL	Putative cell division cycle 2-related protein kinase 7 (EC 2.7.11.22)	0.99	+	nuc	0					730
O00472 UniProt NPD GO	ELL2_HUMAN	RNA polymerase II elongation factor ELL2	0.99	+	nuc	0	Nucleus	transcription elongation factor complex [TAS]	601874		640
Q80Y56 UniProt NPD GO	RBNS5_MOUSE	Rabenosyn-5 (FYVE finger-containing Rab5 effector protein rabenosyn-5) (Zinc finger FYVE domain-cont ...	0.99	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Endosome; early endosome; early endos ...				783
Q9H1K0 UniProt NPD GO	RBNS5_HUMAN	Rabenosyn-5 (FYVE finger-containing Rab5 effector protein rabenosyn-5) (Zinc finger FYVE domain-cont ...	0.99	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side. Endosome; early endosome; early endosome membrane; li ...	endosome [NAS]	609511	1Z0K	784
Q8MLZ5 UniProt NPD GO	GAP2_CAEEL	Ras GTPase-activating protein gap-2 (GTPase-activating protein 2)	0.99	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [NAS]			1207
Q86UR5 UniProt NPD GO	RIMS1_HUMAN	Regulating synaptic membrane exocytosis protein 1 (Rab3-interacting molecule 1) (RIM 1)	0.99	+	nuc	0		presynaptic membrane [NAS]	603649	2CSS	1692
Q9JIR4 UniProt NPD GO	RIMS1_RAT	Regulating synaptic membrane exocytosis protein 1 (Rab3-interacting molecule 1) (RIM 1)	0.99	+	nuc	0	Cell membrane; peripheral membrane protein. Associated with plasma membranes from synaptic junctions ...	presynaptic membrane [IDA]		1ZUB	1615
Q9JIS1 UniProt NPD GO	RIMS2_RAT	Regulating synaptic membrane exocytosis protein 2 (Rab3-interacting molecule 2) (RIM 2)	0.99	+	nuc	0				2CJS	1555
O60182 UniProt NPD GO	RFC1_SCHPO	Replication factor C subunit 1 (Replication factor C1)	0.99	-	nuc	0	Nucleus; nucleolus	Ctf18 RFC-like complex [TAS] DNA replication factor C complex [TAS] Elg1 RFC-like complex [IDA] Rad17 RFC-like complex [TAS]			934
P97868 UniProt NPD GO	RBBP6_MOUSE	Retinoblastoma-binding protein 6 (p53-associated cellular protein of testis) (Proliferation potentia ...	0.99	+	nuc	0	Nucleus; nucleolus. Colocalizes with mitotic chromosomes				1790
Q7Z6E9 UniProt NPD GO	RBBP6_HUMAN	Retinoblastoma-binding protein 6 (p53-associated cellular protein of testis) (Proliferation potentia ...	0.99	+	nuc	0	Nucleus; nucleolus. Colocalizes with mitotic chromosomes		600938	2C7H	1792
Q08999 UniProt NPD GO	RBL2_HUMAN	Retinoblastoma-like protein 2 (130 kDa retinoblastoma-associated protein) (PRB2) (P130) (RBR-2)	0.99	+	nuc	0	Nucleus		180203		1139
Q7Z5J4 UniProt NPD GO	RAI1_HUMAN	Retinoic acid-induced protein 1	0.99	+	nuc	0	Cytoplasm. Nucleus. In neurons, localized to neurites (By similarity)		607642		1906
Q9NRR4 UniProt NPD GO	RNC_HUMAN	Ribonuclease III (EC 3.1.26.3) (RNase III) (Drosha) (p241)	0.99	+	nuc	0	Nucleus. A fraction is translocated to the nucleolus during the S phase of the cell cycle		608828		1374
Q5RCE6 UniProt NPD GO	RL1D1_PONPY	Ribosomal L1 domain-containing protein 1	0.99	+	nuc	0	Nucleus; nucleolus (By similarity)				490
O76021 UniProt NPD GO	RL1D1_HUMAN	Ribosomal L1 domain-containing protein 1 (Cellular senescence-inhibited gene protein) (Protein PBK1) ...	0.99	+	nuc	0	Nucleus; nucleolus				490
P36124 UniProt NPD GO	SET3_YEAST	SET domain protein 3	0.99	-	nuc	0		histone deacetylase complex [IPI]			751
Q9Y6X0 UniProt NPD GO	SETBP_HUMAN	SET-binding protein (SEB)	0.99	+	nuc	0	Nucleus				1542
Q99590 UniProt NPD GO	SFRIP_HUMAN	SFRS2-interacting protein (Splicing factor, arginine/serine-rich 2-interacting protein) (SC35-intera ...	0.99	+	nuc	0	Nucleus	DNA-directed RNA polymerase II, core complex [TAS]	603668		1148

You are viewing entries 401 to 450 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.