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
Q02852 UniProt NPD GO	ATPX_ANTSP	ATP synthase B' chain (EC 3.6.3.14) (Subunit II)	0.45	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				159
Q99758 UniProt NPD GO	ABCA3_HUMAN	ATP-binding cassette sub-family A member 3 (ATP-binding cassette transporter 3) (ATP-binding cassett ...	0.45	-	end	11 *		integral to membrane [TAS] lamellar body [IDA] membrane fraction [TAS] plasma membrane [IDA]	601615		1704
Q755A5 UniProt NPD GO	DBP3_ASHGO	ATP-dependent RNA helicase DBP3 (EC 3.6.1.-)	0.45	+	nuc	0	Nucleus; nucleolus (By similarity)				535
Q6C0X2 UniProt NPD GO	DHH1_YARLI	ATP-dependent RNA helicase DHH1 (EC 3.6.1.-)	0.45	-	nuc	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				522
Q6CTN7 UniProt NPD GO	MAK5_KLULA	ATP-dependent RNA helicase MAK5 (EC 3.6.1.-)	0.45	-	nuc	0	Nucleus; nucleolus (By similarity)				796
Q6C3J3 UniProt NPD GO	MRH4_YARLI	ATP-dependent RNA helicase MRH4, mitochondrial precursor (EC 3.6.1.-)	0.45	-	mit	0	Mitochondrion (By similarity)				514
Q5AUL4 UniProt NPD GO	FAL1_EMENI	ATP-dependent RNA helicase fal1 (EC 3.6.1.-)	0.45	-	cyt	0	Nucleus; nucleolus (By similarity)				399
P33311 UniProt NPD GO	MDL2_YEAST	ATP-dependent permease MDL2, mitochondrial precursor (Multidrug resistance-like protein 2)	0.45	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			773
Q9NYB9 UniProt NPD GO	ABI2_HUMAN	Abl interactor 2 (Abelson interactor 2) (Abi-2) (Abl-binding protein 3) (AblBP3) (Arg-binding protei ...	0.45	-	nuc	0	Cytoplasm (By similarity). Isoform 1 but not isoform 3 is localized to protruding lamellipodia and f ...	cytoplasm [TAS] filopodium [NAS] lamellipodium [NAS]	606442		513
Q4IN52 UniProt NPD GO	ACN9_GIBZE	Acetate non-utilizing protein 9, mitochondrial precursor	0.45	-	mit	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				130
Q9EST6 UniProt NPD GO	AN32B_RAT	Acidic leucine-rich nuclear phosphoprotein 32 family member B (Proliferation-related acidic leucine- ...	0.45	-	nuc	0	Nucleus. Accumulates in the nuclei at the S phase				272
Q5XIE0 UniProt NPD GO	AN32E_RAT	Acidic leucine-rich nuclear phosphoprotein 32 family member E	0.45	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				258
P46251 UniProt NPD GO	ADF1_MAIZE	Actin-depolymerizing factor 1 (ADF 1) (ZmABP1) (ZmADF1)	0.45	-	nuc	0					139
O00198 UniProt NPD GO	HRK_HUMAN	Activator of apoptosis harakiri (Neuronal death protein DP5) (BH3-interacting domain protein 3)	0.45	-	mit	1			603447		91
Q8VHH7 UniProt NPD GO	ADCY3_MOUSE	Adenylate cyclase type 3 (EC 4.6.1.1) (Adenylate cyclase type III) (Adenylate cyclase, olfactive typ ...	0.45	-	end	12	Membrane; multi-pass membrane protein	plasma membrane [TAS]			1145
P17555 UniProt NPD GO	CAP_YEAST	Adenylyl cyclase-associated protein (CAP)	0.45	-	nuc	0	Actin patch. Cortical actin patches	actin cortical patch [TAS]		1KQ5	526
Q09328 UniProt NPD GO	MGAT5_HUMAN	Alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase V (EC 2.4.1.155) (Mannoside ac ...	0.45	+	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	Golgi membrane [NAS] integral to membrane [NAS]	601774		741
P35368 UniProt NPD GO	ADA1B_HUMAN	Alpha-1B adrenergic receptor (Alpha 1B-adrenoceptor) (Alpha 1B-adrenoreceptor)	0.45	+	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	104220		519
P18825 UniProt NPD GO	ADA2C_HUMAN	Alpha-2C adrenergic receptor (Alpha-2C adrenoceptor) (Alpha-2C adrenoreceptor) (Alpha-2 adrenergic r ...	0.45	+	end	7 *	Membrane; multi-pass membrane protein	endosome [TAS] integral to plasma membrane [TAS]	104250		462
Q9EPC1 UniProt NPD GO	PARVA_MOUSE	Alpha-parvin (Actopaxin)	0.45	+	nuc	0	Cell membrane; cell-matrix junction; focal adhesion; cytoplasmic side. Constituent of focal adhesion ...	cytoplasm [IDA] focal adhesion [IDA] lamellipodium [IDA] nucleus [IDA]			372
P04726 UniProt NPD GO	GDA6_WHEAT	Alpha/beta-gliadin clone PW1215 precursor (Prolamin)	0.45	-	exc	0					296
P04727 UniProt NPD GO	GDA7_WHEAT	Alpha/beta-gliadin clone PW8142 precursor (Prolamin)	0.45	-	exc	0					313
P37090 UniProt NPD GO	SCNNB_RAT	Amiloride-sensitive sodium channel subunit beta (Epithelial Na+ channel subunit beta) (Beta ENaC) (N ...	0.45	-	mit	1	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...			1I5H	638
P22966 UniProt NPD GO	ACET_HUMAN	Angiotensin-converting enzyme, testis-specific isoform precursor (EC 3.4.15.1) (EC 3.2.1.-) (ACE-T) ...	0.45	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein. A soluble form ...	integral to membrane [NAS]	106180	1UZF	732
P97429 UniProt NPD GO	ANXA4_MOUSE	Annexin A4 (Annexin IV)	0.45	-	cyt	0					318
P41990 UniProt NPD GO	APX1_CAEEL	Anterior pharynx in excess protein 1 precursor	0.45	-	nuc	1 *	Membrane; single-pass type I membrane protein	integral to membrane [NAS]			515
P06727 UniProt NPD GO	APOA4_HUMAN	Apolipoprotein A-IV precursor (Apo-AIV) (ApoA-IV)	0.45	-	exc	0	Secreted protein	extracellular region [NAS]	107690		396
P33621 UniProt NPD GO	APOA4_MACFA	Apolipoprotein A-IV precursor (Apo-AIV) (ApoA-IV)	0.45	-	exc	0	Secreted protein				429
Q9GLC0 UniProt NPD GO	APOE_TUPGL	Apolipoprotein E precursor (Apo-E)	0.45	-	exc	0	Secreted protein (By similarity)	cytoplasm [ISS] extracellular region [ISS]			313
O70582 UniProt NPD GO	LX12B_MOUSE	Arachidonate 12-lipoxygenase, 12R type (EC 1.13.11.-) (Epidermis-type lipoxygenase 12) (12R-lipoxyge ...	0.45	-	cyt	0					701
Q86W34 UniProt NPD GO	AMZ2_HUMAN	Archaemetzincin-2 (EC 3.-.-.-) (Archeobacterial metalloproteinase-like protein 2)	0.45	-	cyt	0					360
Q9D0I9 UniProt NPD GO	SYR_MOUSE	Arginyl-tRNA synthetase (EC 6.1.1.19) (Arginine--tRNA ligase) (ArgRS)	0.45	-	nuc	0	Cytoplasm				660
P38840 UniProt NPD GO	ARO9_YEAST	Aromatic amino acid aminotransferase 2 (EC 2.6.1.-) (Aromatic amino acid aminotransferase II)	0.45	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			513
Q5T4W7 UniProt NPD GO	ARTN_HUMAN	Artemin precursor (Enovin) (Neublastin)	0.45	-	nuc	0	Secreted protein (By similarity)		603886	2GYZ	220
P50295 UniProt NPD GO	ARY2_MOUSE	Arylamine N-acetyltransferase 2 (EC 2.3.1.5) (Arylamide acetylase 2) (N-acetyltransferase type 2) (N ...	0.45	-	cyt	0	Cytoplasm				290
Q03818 UniProt NPD GO	ATG16_YEAST	Autophagy protein 16 (Cytoplasm to vacuole targeting protein 11) (SAP18 homolog)	0.45	-	nuc	0	Vacuole (Potential). Cytoplasmic vesicle (Potential). Vesicular and vacuolar (Potential). Found in p ...	membrane fraction [IDA]			150
P38270 UniProt NPD GO	ATG14_YEAST	Autophagy-related protein 14 (Cytoplasm to vacuole targeting protein 12)	0.45	-	nuc	0	Membrane; peripheral membrane protein	membrane fraction [IDA]			344
Q4X0B0 UniProt NPD GO	ATG17_ASPFU	Autophagy-related protein 17	0.45	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Cytoplasmic and pu ...				551
P43601 UniProt NPD GO	ATG18_YEAST	Autophagy-related protein 18 (Cytoplasm to vacuole targeting protein 18) (Swollen vacuole phenotype ...	0.45	-	nuc	0	Membrane-associated. Peripheral membrane protein found in pre-autophagosomal structure (PAS) and vac ...	cytosol [IDA] vacuolar membrane (sensu Fungi) [IDA]			500
P35193 UniProt NPD GO	ATG19_YEAST	Autophagy-related protein 19 (Cytoplasm-to-vacuole targeting protein 19)	0.45	-	nuc	0	Membrane-associated. Found in pre-autophagosomal structure and other perivacuolar punctate structure ...	cytoplasm [IDA] peripheral to membrane of membrane fraction [IDA] vacuole [IDA]			415
Q5QFG1 UniProt NPD GO	ATG8_PICAN	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier ATG8)	0.45	-	cyt	0	Membrane; lipid-anchor (By similarity). Perivacuolar punctate structures				125
Q7S4D7 UniProt NPD GO	ATG9_NEUCR	Autophagy-related protein 9	0.45	-	vac	2	Membrane; multi-pass membrane protein. Pre-autophagosomal and other perivacuolar punctate structures ...				908
O24543 UniProt NPD GO	AX22E_PHAAU	Auxin-induced protein 22E (Indole-3-acetic acid-induced protein ARG14)	0.45	-	nuc	0	Nucleus (By similarity)				203
O24408 UniProt NPD GO	IAA18_ARATH	Auxin-responsive protein IAA18 (Indoleacetic acid-induced protein 18)	0.45	-	nuc	0	Nucleus (By similarity)				267
Q08695 UniProt NPD GO	MST1_DROHY	Axoneme-associated protein mst101(1)	0.45	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [IDA]			344
Q8N143 UniProt NPD GO	BCL6B_HUMAN	B-cell CLL/lymphoma 6 member B protein (Bcl6-associated zinc finger protein) (Zinc finger protein 62 ...	0.45	-	nuc	0	Nucleus (By similarity)		608992		480
Q9BQE9 UniProt NPD GO	BCL7B_HUMAN	B-cell CLL/lymphoma 7 protein family member B	0.45	-	nuc	0			605846		202
Q5R9U7 UniProt NPD GO	BAP29_PONPY	B-cell receptor-associated protein 29 (BCR-associated protein Bap29)	0.45	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				241
Q8N8U9 UniProt NPD GO	BMPER_HUMAN	BMP-binding endothelial regulator protein precursor (Bone morphogenetic protein-binding endothelial ...	0.45	-	exc	0	Secreted protein		608699		685
Q8CEZ0 UniProt NPD GO	KCTD2_MOUSE	BTB/POZ domain-containing protein KCTD2	0.45	-	nuc	0					266

You are viewing entries 28101 to 28150 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.