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
O60343 UniProt NPD GO	TBCD4_HUMAN	TBC1 domain family member 4 (Akt substrate of 160 kDa) (AS160)	0.98	-	nuc	0					1298
Q8NI27 UniProt NPD GO	THOC2_HUMAN	THO complex subunit 2 (Tho2)	0.98	+	nuc	0	Nucleus (Probable)		300395		1478
Q9UKE5 UniProt NPD GO	TNIK_HUMAN	TRAF2 and NCK-interacting kinase (EC 2.7.11.1)	0.98	+	nuc	0					1360
Q93075 UniProt NPD GO	TATD2_HUMAN	TatD DNase domain-containing deoxyribonuclease 2 (EC 3.1.21.-)	0.98	-	nuc	0	Nucleus (Potential)				761
Q9PU53 UniProt NPD GO	TERF2_CHICK	Telomeric repeat-binding factor 2 (TTAGGG repeat-binding factor 2) (Telomeric DNA-binding protein)	0.98	-	nuc	0	Nucleus (By similarity). Colocalizes with telomeric DNA in interphase cells and is located at chromo ...				718
P63058 UniProt NPD GO	THA_MOUSE	Thyroid hormone receptor alpha (C-erbA-alpha) (c-erbA-1)	0.98	+	nuc	0	Nucleus	nucleus [TAS]			492
P63059 UniProt NPD GO	THA_RAT	Thyroid hormone receptor alpha (C-erbA-alpha) (c-erbA-1)	0.98	+	nuc	0	Nucleus				492
Q9Y2W1 UniProt NPD GO	TR150_HUMAN	Thyroid hormone receptor-associated protein 3 (Thyroid hormone receptor-associated protein complex 1 ...	0.98	+	mit	0	Nucleus (Potential)	mediator complex [IDA] nucleus [IDA]	603809		955
Q569Z6 UniProt NPD GO	TR150_MOUSE	Thyroid hormone receptor-associated protein 3 (Thyroid hormone receptor-associated protein complex 1 ...	0.98	+	mit	0	Nucleus (Potential)	mediator complex [IDA]			951
Q5M7V8 UniProt NPD GO	TR150_RAT	Thyroid hormone receptor-associated protein 3 (Thyroid hormone receptor-associated protein complex 1 ...	0.98	+	mit	0	Nucleus (Potential)				951
Q5BJ39 UniProt NPD GO	TR150_XENLA	Thyroid hormone receptor-associated protein 3 (Thyroid hormone receptor-associated protein complex 1 ...	0.98	+	mit	0	Nucleus (Potential)				951
Q8CB77 UniProt NPD GO	ELOA1_MOUSE	Transcription elongation factor B polypeptide 3 (RNA polymerase II transcription factor SIII subunit ...	0.98	+	nuc	0					773
Q63187 UniProt NPD GO	ELOA1_RAT	Transcription elongation factor B polypeptide 3 (RNA polymerase II transcription factor SIII subunit ...	0.98	+	nuc	0		nucleus [TAS] transcription elongation factor complex [IDA]			773
Q5AAR0 UniProt NPD GO	IWS1_CANAL	Transcription factor IWS1	0.98	+	nuc	0	Nucleus (By similarity)				400
P39679 UniProt NPD GO	MBP1_KLULA	Transcription factor MBP1 (MBF subunit P120)	0.98	+	nuc	0	Nucleus				754
P35269 UniProt NPD GO	T2FA_HUMAN	Transcription initiation factor IIF alpha subunit (EC 2.7.11.1) (TFIIF-alpha) (Transcription initiat ...	0.98	+	nuc	0	Nucleus	transcription factor TFIIF complex [TAS]	189968	1ONV	517
P97302 UniProt NPD GO	BACH1_MOUSE	Transcription regulator protein BACH1 (BTB and CNC homolog 1)	0.98	+	nuc	0	Nucleus (Probable)	nucleus [IDA]			739
O14867 UniProt NPD GO	BACH1_HUMAN	Transcription regulator protein BACH1 (BTB and CNC homolog 1) (HA2303)	0.98	+	nuc	0	Nucleus (By similarity)		602751		736
P40068 UniProt NPD GO	FLO8_YEAST	Transcriptional activator FLO8 (Protein PDH5)	0.98	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			799
P32494 UniProt NPD GO	ADA3_YEAST	Transcriptional adapter 3 (Protein NGG1)	0.98	+	nuc	0	Nucleus (Potential)	Ada2/Gcn5/Ada3 transcription activator complex [IPI] SAGA complex [IDA] SLIK (SAGA-like) complex [IPI]			702
Q08923 UniProt NPD GO	CTI6_YEAST	Transcriptional regulatory protein CTI6 (CYC8-TUP1-interacting protein 6)	0.98	-	nuc	0	Nucleus	nucleus [IC]			506
Q09306 UniProt NPD GO	TUB1_CAEEL	Tubby protein homolog 1	0.98	+	nuc	0					426
Q5R978 UniProt NPD GO	TTLL5_PONPY	Tubulin--tyrosine ligase-like protein 5	0.98	+	nuc	0					1299
Q6EMB2 UniProt NPD GO	TTLL5_HUMAN	Tubulin--tyrosine ligase-like protein 5 (SRC1 and TIF2-associated modulatory protein)	0.98	+	nuc	0					1277
Q640M1 UniProt NPD GO	UT14A_MOUSE	U3 small nucleolar RNA-associated protein 14 homolog A (Juvenile spermatogonial depletion-like X-lin ...	0.98	+	nuc	0	Nucleus; nucleolus (By similarity)				767
Q6EJB6 UniProt NPD GO	UT14B_MOUSE	U3 small nucleolar RNA-associated protein 14 homolog B (Juvenile spermatogonial depletion protein)	0.98	+	nuc	0	Nucleus; nucleolus (By similarity)				756
P47083 UniProt NPD GO	MPP10_YEAST	U3 small nucleolar ribonucleoprotein protein MPP10	0.98	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA] nucleus [IDA] small nuclear ribonucleoprotein complex [TAS] small nucleolar ribonucleoprotein complex [IPI]			593
O13910 UniProt NPD GO	MPP10_SCHPO	U3 small nucleolar ribonucleoprotein protein mpp10	0.98	-	nuc	0	Nucleus; nucleolus (By similarity)				598
Q9P275 UniProt NPD GO	UBP36_HUMAN	Ubiquitin carboxyl-terminal hydrolase 36 (EC 3.1.2.15) (Ubiquitin thioesterase 36) (Ubiquitin-specif ...	0.98	+	nuc	0	Nucleus; nucleolus				1121
Q9H9J4 UniProt NPD GO	UBP42_HUMAN	Ubiquitin carboxyl-terminal hydrolase 42 (EC 3.1.2.15) (Ubiquitin thioesterase 42) (Ubiquitin-specif ...	0.98	+	nuc	0					1325
P40453 UniProt NPD GO	UBP7_YEAST	Ubiquitin carboxyl-terminal hydrolase 7 (EC 3.1.2.15) (Ubiquitin thioesterase 7) (Ubiquitin-specific ...	0.98	-	nuc	0		cytoplasm [IC]			1071
P40818 UniProt NPD GO	UBP8_HUMAN	Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.1.2.15) (Ubiquitin thioesterase 8) (Ubiquitin-specific ...	0.98	-	nuc	0			603158	2GWF	1118
Q80ZI6 UniProt NPD GO	LRSM1_MOUSE	Ubiquitin ligase protein LRSAM1 (EC 6.3.2.-) (Leucine-rich repeat and sterile alpha motif-containing ...	0.98	-	nuc	0	Cytoplasm (By similarity). Displays a punctuate distribution and localizes to a submembranal ring (B ...				727
Q9NS56 UniProt NPD GO	TOPRS_HUMAN	Ubiquitin-protein E3 ligase Topors (EC 6.3.2.-) (SUMO1-protein E3 ligase Topors) (Topoisomerase I-bi ...	0.98	+	nuc	0	Nucleus. Localizes to discrete nuclear foci which partly overlap with PML nuclear bodies		609507		1045
Q80Z37 UniProt NPD GO	TOPRS_MOUSE	Ubiquitin-protein E3 ligase Topors (EC 6.3.2.-) (SUMO1-protein E3 ligase Topors) (Topoisomerase I-bi ...	0.98	+	nuc	0	Nucleus. Localizes to discrete nuclear foci which probably overlap in part with PML nuclear bodies	nucleus [IDA]			1033
Q9V8P9 UniProt NPD GO	TOPRS_DROME	Ubiquitin-protein E3 ligase Topors (EC 6.3.2.-) (SUMO1-protein E3 ligase Topors) (Topoisomerase I-bi ...	0.98	+	nuc	0	Nucleus. Colocalizes with the gypsy chromatin insulator complex on polytene chromosomes and to nucle ...	nuclear lamina [IDA] polytene chromosome [IDA]			1038
P56273 UniProt NPD GO	MDM2_XENLA	Ubiquitin-protein ligase E3 Mdm2 (EC 6.3.2.-) (p53-binding protein Mdm2) (Double minute 2 protein) ( ...	0.98	-	nuc	0	Nucleus; nucleolus (By similarity)			1YCQ	473
P23804 UniProt NPD GO	MDM2_MOUSE	Ubiquitin-protein ligase E3 Mdm2 (EC 6.3.2.-) (p53-binding protein Mdm2) (Oncoprotein Mdm2) (Double ...	0.98	+	nuc	0	Nucleus; nucleoplasm. Cytoplasm. Expressed predominantly in the nucleoplasm. Nucleus; nucleolus. Int ...	cytoplasm [IDA] nucleolus [IDA] nucleus [IDA]			489
Q60YN5 UniProt NPD GO	BRE1_CAEBR	Ubiquitin-protein ligase bre-1 (EC 6.3.2.-) (RING finger protein rfp-1)	0.98	+	nuc	0	Nucleus (By similarity)				828
Q62770 UniProt NPD GO	UN13C_RAT	Unc-13 homolog C (Munc13-3)	0.98	-	nuc	0	Cytoplasm (Probable). Membrane; peripheral membrane protein (Probable). Localized to presynaptic str ...				2204
Q6PE65 UniProt NPD GO	CN118_MOUSE	Uncharacterized protein C14orf118 homolog	0.98	+	nuc	0					482
Q8CB59 UniProt NPD GO	CN044_MOUSE	Uncharacterized protein C14orf44 homolog	0.98	-	nuc	0					589
Q8CDV0 UniProt NPD GO	CR034_MOUSE	Uncharacterized protein C18orf34 homolog	0.98	+	nuc	0					866
Q12532 UniProt NPD GO	YP009_YEAST	Uncharacterized protein YPL009C	0.98	-	nuc	0	Cytoplasm	cytoplasm [IDA]			1038
Q6P0D5 UniProt NPD GO	WBP11_BRARE	WW domain-binding protein 11 (WBP-11)	0.98	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				640
Q923D5 UniProt NPD GO	WBP11_MOUSE	WW domain-binding protein 11 (WBP-11)	0.98	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Predominantly located in the nucleus with granul ...	cytoplasm [IDA] nuclear speck [IDA] nucleus [IDA]			641
Q5PQQ2 UniProt NPD GO	WBP11_RAT	WW domain-binding protein 11 (Wbp-11)	0.98	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Predominantly located in the nucleus with granul ...				641
P34600 UniProt NPD GO	YO61_CAEEL	WW domain-containing protein ZK1098.1	0.98	+	nuc	0					724
Q3B725 UniProt NPD GO	ZBT24_RAT	Zinc finger and BTB domain-containing protein 24 (Zinc finger protein 450) (Bone morphogenetic prote ...	0.98	-	nuc	0	Nucleus (Potential)	nucleus [IC]			705
O60281 UniProt NPD GO	ZN292_HUMAN	Zinc finger protein 292	0.98	+	nuc	0	Nucleus (Probable)			1X3C	1969

You are viewing entries 851 to 900 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.