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
O14108 UniProt NPD GO	ETA2_SCHPO	DNA-binding protein eta2	0.98	+	nuc	0	Nucleus (By similarity)				569
Q7PCJ6 UniProt NPD GO	RPOC2_CHLRE	DNA-directed RNA polymerase beta'' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta'' s ...	0.98	+	nuc	0	Plastid; chloroplast				3120
P07276 UniProt NPD GO	RAD2_YEAST	DNA-repair protein RAD2	0.98	+	nuc	0	Nucleus	nucleotide-excision repair factor 3 complex [TAS]			1031
Q24595 UniProt NPD GO	XPC_DROME	DNA-repair protein complementing XP-C cells homolog (Xeroderma pigmentosum group C-complementing pro ...	0.98	-	nuc	0	Nucleus (Probable)				1293
P28715 UniProt NPD GO	ERCC5_HUMAN	DNA-repair protein complementing XP-G cells (Xeroderma pigmentosum group G-complementing protein) (D ...	0.98	+	nuc	0	Nucleus		278780		1186
P35689 UniProt NPD GO	ERCC5_MOUSE	DNA-repair protein complementing XP-G cells homolog (Xeroderma pigmentosum group G-complementing pro ...	0.98	+	nuc	0	Nucleus (By similarity)				1170
Q96NX9 UniProt NPD GO	DACH2_HUMAN	Dachshund homolog 2 (Dach2)	0.98	-	nuc	0	Nucleus (Probable)				599
Q9BTC0 UniProt NPD GO	DIDO1_HUMAN	Death-inducer obliterator 1 (DIO-1) (Death-associated transcription factor 1) (DATF-1) (hDido1)	0.98	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocates to the nucleus after pro-apoptotic ...		604140		2240
P32350 UniProt NPD GO	KNS1_YEAST	Dual specificity protein kinase KNS1 (EC 2.7.12.1)	0.98	-	nuc	0					737
O97592 UniProt NPD GO	DMD_CANFA	Dystrophin	0.98	-	nuc	0					3680
Q09472 UniProt NPD GO	EP300_HUMAN	E1A-associated protein p300 (EC 2.3.1.48)	0.98	+	nuc	0	Nucleus	nucleus [IDA]	602700	1P4Q	2414
Q9NWF9 UniProt NPD GO	UB7I1_HUMAN	E3 ubiquitin ligase TRIAD3 (EC 6.3.2.-) (Ubiquitin-conjugating enzyme 7-interacting protein 1) (Zinc ...	0.98	-	nuc	0	Cytoplasm		609948		866
Q07139 UniProt NPD GO	ECT2_MOUSE	ECT2 protein (Epithelial cell-transforming sequence 2 oncogene)	0.98	+	nuc	0				2COU	738
P57679 UniProt NPD GO	EVC_HUMAN	Ellis-van Creveld syndrome protein (DWF-1)	0.98	-	nuc	1 *			604831		992
Q8C9X6 UniProt NPD GO	EPC1_MOUSE	Enhancer of polycomb homolog 1	0.98	+	nuc	0	Nucleus (By similarity)				813
Q52LR7 UniProt NPD GO	EPC2_HUMAN	Enhancer of polycomb homolog 2	0.98	+	nuc	0	Nucleus (By similarity)				807
Q8C0I4 UniProt NPD GO	EPC2_MOUSE	Enhancer of polycomb homolog 2	0.98	+	nuc	0	Nucleus (By similarity)				808
Q6DJR9 UniProt NPD GO	EPC2_XENTR	Enhancer of polycomb homolog 2	0.98	+	nuc	0	Nucleus (By similarity)				804
P70351 UniProt NPD GO	EZH1_MOUSE	Enhancer of zeste homolog 1 (ENX-2)	0.98	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			747
Q15910 UniProt NPD GO	EZH2_HUMAN	Enhancer of zeste homolog 2 (ENX-1)	0.98	-	nuc	0	Nucleus (Probable)		601573		746
Q9P2K8 UniProt NPD GO	E2AK4_HUMAN	Eukaryotic translation initiation factor 2-alpha kinase 4 (EC 2.7.11.1) (GCN2-like protein)	0.98	-	nuc	0		cytosolic ribosome (sensu Eukaryota) [ISS] intracellular [NAS]			1649
Q9XHR2 UniProt NPD GO	IF3A_MAIZE	Eukaryotic translation initiation factor 3 subunit 10 (eIF-3 theta) (Eukaryotic translation initiati ...	0.98	-	nuc	0					962
P39875 UniProt NPD GO	EXO1_YEAST	Exodeoxyribonuclease 1 (EC 3.1.-.-) (Exodeoxyribonuclease I) (Exonuclease I) (EXO I) (Protein DHS1)	0.98	+	nuc	0	Nucleus (Potential)	nucleus [IPI]			702
Q24558 UniProt NPD GO	EXO1_DROME	Exonuclease 1 (EC 3.1.-.-) (Exonuclease I) (Protein tosca)	0.98	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]			732
Q9QZM9 UniProt NPD GO	FBX16_MOUSE	F-box only protein 16	0.98	-	nuc	0					334
Q8CDI2 UniProt NPD GO	FBX43_MOUSE	F-box only protein 43 (Endogenous meiotic inhibitor 2)	0.98	-	nuc	0					640
Q9Y2L6 UniProt NPD GO	FRM4B_HUMAN	FERM domain-containing protein 4B (GRP1-binding protein GRSP1)	0.98	+	nuc	0	Cytoplasm (By similarity)				980
Q9Z1T6 UniProt NPD GO	FYV1_MOUSE	FYVE finger-containing phosphoinositide kinase (EC 2.7.1.68) (1-phosphatidylinositol-4-phosphate 5-k ...	0.98	-	nuc	0	Cytoplasmic vesicle; cytoplasmic vesicle membrane; peripheral membrane protein. Associated with vesi ...	vesicle membrane [IDA]			2052
Q9Y2I7 UniProt NPD GO	FYV1_HUMAN	FYVE finger-containing phosphoinositide kinase (EC 2.7.1.68) (1-phosphatidylinositol-4-phosphate 5-k ...	0.98	-	nuc	0	Endosome; endosomal membrane. Mainly associated with membranes of the late endocytic pathway	lipid raft [IDA]	609414		2098
Q6ZV73 UniProt NPD GO	FGD6_HUMAN	FYVE, RhoGEF and PH domain-containing protein 6 (Zinc finger FYVE domain-containing protein 24)	0.98	+	nuc	0	Cytoplasm (Probable)	cytoplasm [ISS] Golgi apparatus [ISS] lamellipodium [ISS] ruffle [ISS]			1430
P97691 UniProt NPD GO	FOXM1_RAT	Forkhead box protein M1 (Winged helix factor from INS-1 cells) (INS-1 winged helix)	0.98	+	nuc	0	Nucleus (By similarity)				759
Q5W1J6 UniProt NPD GO	FOXM1_XENLA	Forkhead box protein M1 (XlFoxM1)	0.98	-	nuc	0	Nucleus (Potential)				759
Q01115 UniProt NPD GO	FRQ_LEPAU	Frequency clock protein	0.98	-	nuc	0					992
P19970 UniProt NPD GO	FRQ_NEUCR	Frequency clock protein	0.98	+	nuc	0					989
Q13227 UniProt NPD GO	GPS2_HUMAN	G protein pathway suppressor 2 (Protein GPS2)	0.98	+	nuc	0			601935		327
Q03016 UniProt NPD GO	GIP3_YEAST	GLC7-interacting protein 3	0.98	-	nuc	0	Cytoplasm. Endoplasmic reticulum	cytoplasm [IDA] endoplasmic reticulum [IDA] mitochondrion [IDA]			1276
Q9DB00 UniProt NPD GO	GON4L_MOUSE	GON-4-like protein (GON-4 homolog)	0.98	+	nuc	0	Nucleus (Potential)			1UG2	2260
P48423 UniProt NPD GO	GAP1_DROME	GTPase-activating protein (Ras GTPase-activating protein)	0.98	+	nuc	0		plasma membrane [IDA]			1163
P17121 UniProt NPD GO	SAC7_YEAST	GTPase-activating protein SAC7	0.98	-	nuc	0		intracellular [TAS]			654
Q8K284 UniProt NPD GO	TF3C1_MOUSE	General transcription factor 3C polypeptide 1 (Transcription factor IIIC-subunit alpha) (TF3C-alpha) ...	0.98	+	nuc	0	Nucleus (By similarity)				2101
Q63505 UniProt NPD GO	TF3C1_RAT	General transcription factor 3C polypeptide 1 (Transcription factor IIIC-subunit alpha) (TF3C-alpha) ...	0.98	+	nuc	0	Nucleus				2148
Q91VW5 UniProt NPD GO	GOGA4_MOUSE	Golgin subfamily A member 4 (tGolgin-1)	0.98	-	nuc	0	Cytoplasm. Golgi apparatus; Golgi membrane; peripheral membrane protein	Golgi apparatus [IDA]			2238
Q9BVP2 UniProt NPD GO	GNL3_HUMAN	Guanine nucleotide-binding protein-like 3 (Nucleolar GTP-binding protein 3) (Nucleostemin) (E2-induc ...	0.98	+	nuc	0	Nucleus (By similarity). Nucleus; nucleolus (By similarity). Shuttles between the nucleus and nucleo ...	nucleolus [ISS] nucleus [ISS]	608011		549
Q12180 UniProt NPD GO	HAL9_YEAST	Halotolerance protein 9	0.98	+	nuc	0	Cytoplasm. Nucleus	mitochondrion [IDA]			1030
Q05471 UniProt NPD GO	SWR1_YEAST	Helicase SWR1 (EC 3.6.1.-) (Swi2/Snf2-related 1)	0.98	+	nuc	0	Nucleus	nucleus [IDA] SWR1 complex [IPI]			1514
P12685 UniProt NPD GO	TRK1_YEAST	High-affinity potassium transport protein	0.98	+	nuc	8 *	Membrane; multi-pass membrane protein	plasma membrane [TAS]			1235
Q8WML3 UniProt NPD GO	MYST4_MACFA	Histone acetyltransferase MYST4 (EC 2.3.1.48) (EC 2.3.1.-) (MYST protein 4) (MOZ, YBF2/SAS3, SAS2 an ...	0.98	+	nuc	0	Nucleus (Probable)	nucleosome [ISS]			1784
Q8WYB5 UniProt NPD GO	MYST4_HUMAN	Histone acetyltransferase MYST4 (EC 2.3.1.48) (EC 2.3.1.-) (MYST protein 4) (MOZ, YBF2/SAS3, SAS2 an ...	0.98	+	nuc	0	Nucleus (Probable)	nucleosome [ISS]	605880		2073
Q8BRB7 UniProt NPD GO	MYST4_MOUSE	Histone acetyltransferase MYST4 (EC 2.3.1.48) (EC 2.3.1.-) (MYST protein 4) (MOZ, YBF2/SAS3, SAS2 an ...	0.98	+	nuc	0	Nucleus (Probable)	nucleosome [ISS]			1872
O88491 UniProt NPD GO	NSD1_MOUSE	Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific (EC 2.1.1.43) (H3-K36-HMT ...	0.98	+	nuc	0	Nucleus	histone methyltransferase complex [IC] nucleus [IC]			2588

You are viewing entries 601 to 650 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.