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
Q8CGF7 UniProt NPD GO	TCRG1_MOUSE	Transcription elongation regulator 1 (TATA box-binding protein-associated factor 2S) (Transcription ...	0.90	-	nuc	0	Nucleus (By similarity)			1E0L	1100
Q8R3L2 UniProt NPD GO	TCF25_MOUSE	Transcription factor 25 (Nuclear localized protein 1)	0.90	+	nuc	0	Nucleus	nucleus [IDA]			676
Q64163 UniProt NPD GO	TDP2_MOUSE	Transcription factor Dp-2 (E2F dimerization partner 2) (Dp-3)	0.90	-	nuc	0	Nucleus	nuclear envelope [TAS] transcription factor complex [IC]			446
Q64092 UniProt NPD GO	TFE3_MOUSE	Transcription factor E3 (Fragment)	0.90	+	exc	0	Nucleus	transcription factor complex [IC]			446
P46070 UniProt NPD GO	TF3B_KLULA	Transcription factor IIIB 70 kDa subunit (TFIIIB) (B-related factor) (BRF1)	0.90	-	nuc	0	Nucleus				556
P52955 UniProt NPD GO	LBX1_MOUSE	Transcription factor LBX1	0.90	+	nuc	0	Nucleus (Probable)	transcription factor complex [IDA]			280
P55863 UniProt NPD GO	SOX3_XENLA	Transcription factor SOX-3 (xSOX3) (xSOX-11)	0.90	+	nuc	0	Nucleus				309
Q6IZ48 UniProt NPD GO	SOX8_TETNG	Transcription factor SOX-8	0.90	+	nuc	0	Nucleus (Potential)				462
P47792 UniProt NPD GO	SX19A_BRARE	Transcription factor Sox-19a	0.90	-	nuc	0	Nucleus				297
Q8I7Z8 UniProt NPD GO	HAM_DROME	Transcription factor hamlet	0.90	-	nuc	0	Nucleus	nucleus [IDA]			990
Q05913 UniProt NPD GO	T2FA_DROME	Transcription initiation factor IIF alpha subunit (EC 2.7.11.1) (TFIIF-alpha) (Transcription factor ...	0.90	+	nuc	0	Nucleus				577
P47825 UniProt NPD GO	TAF4_DROME	Transcription initiation factor TFIID subunit 4 (Transcription initiation factor TFIID 110 kDa subun ...	0.90	-	nuc	0	Nucleus	transcription factor TFIID complex [IPI]			921
Q15545 UniProt NPD GO	TAF7_HUMAN	Transcription initiation factor TFIID subunit 7 (Transcription initiation factor TFIID 55 kDa subuni ...	0.90	-	nuc	0	Nucleus	transcription factor TFIID complex [IDA]	600573		349
P18480 UniProt NPD GO	SNF5_YEAST	Transcription regulatory protein SNF5 (SWI/SNF complex component SNF5) (Transcription factor TYE4)	0.90	+	mit	0	Nucleus	SWI/SNF complex [TAS]			905
P26370 UniProt NPD GO	UGA3_YEAST	Transcriptional activator protein UGA3	0.90	+	nuc	0	Nucleus	nucleus [IC]			528
O75478 UniProt NPD GO	TAD2L_HUMAN	Transcriptional adapter 2-like (ADA2-like protein)	0.90	+	nuc	0	Nucleus	nucleus [TAS]	602276	1X41	443
O75528 UniProt NPD GO	TAD3L_HUMAN	Transcriptional adapter 3-like (ADA3-like protein) (ADA3 homolog) (hADA3)	0.90	-	nuc	0	Nucleus	nucleus [TAS]	602945		432
Q8R0L9 UniProt NPD GO	TAD3L_MOUSE	Transcriptional adapter 3-like (ADA3-like protein) (ADA3 homolog) (mADA3)	0.90	-	nuc	0	Nucleus (By similarity)				432
P22579 UniProt NPD GO	SIN3_YEAST	Transcriptional regulatory protein SIN3	0.90	-	nuc	0	Nucleus	Sin3 complex [IPI]			1536
P15203 UniProt NPD GO	TGFB3_PIG	Transforming growth factor beta-3 precursor (TGF-beta-3)	0.90	+	mit	0	Secreted protein				409
Q9BX84 UniProt NPD GO	TRPM6_HUMAN	Transient receptor potential cation channel subfamily M member 6 (EC 2.7.11.1) (Channel kinase 2) (M ...	0.90	-	end	6	Membrane; multi-pass membrane protein		607009		2022
P48994 UniProt NPD GO	TRPL_DROME	Transient-receptor-potential-like protein	0.90	-	end	4	Integral membrane protein; in the dark, there is 20 fold more rhabdomeral trpl protein forming plasm ...	inaD signaling complex [IPI] integral to membrane [NAS] intracellular [IDA] plasma membrane [IDA]			1124
P13805 UniProt NPD GO	TNNT1_HUMAN	Troponin T, slow skeletal muscle (TnTs) (Slow skeletal muscle troponin T) (sTnT)	0.90	-	nuc	0			605355		277
O00294 UniProt NPD GO	TULP1_HUMAN	Tubby-related protein 1 (Tubby-like protein 1)	0.90	+	nuc	0			600132	2FIM	542
Q9LVG4 UniProt NPD GO	APRR3_ARATH	Two-component response regulator-like APRR3 (Pseudo-response regulator 3)	0.90	-	nuc	0	Nucleus (Probable)				495
P23458 UniProt NPD GO	JAK1_HUMAN	Tyrosine-protein kinase JAK1 (EC 2.7.10.2) (Janus kinase 1) (JAK-1)	0.90	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein. Wholly intracellular, possibly membrane asso ...		147795		1142
Q9I7F7 UniProt NPD GO	PR2_DROME	Tyrosine-protein kinase PR2 (EC 2.7.10.2)	0.90	-	nuc	0					1337
Q62376 UniProt NPD GO	RU17_MOUSE	U1 small nuclear ribonucleoprotein 70 kDa (U1 SNRNP 70 kDa) (snRNP70)	0.90	+	nuc	0					448
Q6GLZ8 UniProt NPD GO	SNUT3_XENLA	U4/U6.U5 tri-snRNP-associated protein 3	0.90	+	nuc	0	Nucleus (Potential)				158
Q02331 UniProt NPD GO	YOL4_CAEEL	UPF0028 protein ZK370.4	0.90	+	mit	3 *					1353
P57080 UniProt NPD GO	UBP25_MOUSE	Ubiquitin carboxyl-terminal hydrolase 25 (EC 3.1.2.15) (Ubiquitin thioesterase 25) (Ubiquitin-specif ...	0.90	-	nuc	0				1VDL	1055
P93471 UniProt NPD GO	COP1_PEA	Ubiquitin ligase protein COP1 (EC 6.3.2.-) (Constitutive photomorphogenesis protein 1)	0.90	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Localizes to the nucleus in darkness but is grad ...				672
Q7ZWM8 UniProt NPD GO	RNG2B_XENLA	Ubiquitin ligase protein RING2-B (EC 6.3.2.-) (RING finger protein 2-B) (RING finger protein 1B-B) ( ...	0.90	-	nuc	0	Nucleus (By similarity)				343
Q5RAU7 UniProt NPD GO	BRE1B_PONPY	Ubiquitin-protein ligase BRE1B (EC 6.3.2.-) (BRE1-B) (RING finger protein 40)	0.90	+	nuc	0	Nucleus (By similarity)				1001
O75150 UniProt NPD GO	BRE1B_HUMAN	Ubiquitin-protein ligase BRE1B (EC 6.3.2.-) (BRE1-B) (RING finger protein 40) (95 kDa retinoblastoma ...	0.90	+	nuc	0	Nucleus		607700		1001
Q8IWV8 UniProt NPD GO	UBR2_HUMAN	Ubiquitin-protein ligase E3 component N-recognin-2 (EC 6.-.-.-) (Ubiquitin-protein ligase E3-alpha-2 ...	0.90	-	nuc	0	Nucleus (By similarity)		609134		1755
Q6WKZ8 UniProt NPD GO	UBR2_MOUSE	Ubiquitin-protein ligase E3 component N-recognin-2 (EC 6.-.-.-) (Ubiquitin-protein ligase E3-alpha-2 ...	0.90	-	nuc	0	Nucleus	ubiquitin ligase complex [IGI]			1755
Q62768 UniProt NPD GO	UN13A_RAT	Unc-13 homolog A (Munc13-1)	0.90	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Cell membrane. Localized to the active zone of pre ...			2CJT	1735
Q6NXP0 UniProt NPD GO	CC025_HUMAN	Uncharacterized protein C3orf25	0.90	-	nuc	0					572
P38308 UniProt NPD GO	YB53_YEAST	Uncharacterized protein YBR203W	0.90	+	nuc	0					924
P36134 UniProt NPD GO	YK21_YEAST	Uncharacterized protein YKR041W	0.90	+	nuc	0		cytoplasm [IDA] nucleus [IDA]			250
P50942 UniProt NPD GO	YNK6_YEAST	Uncharacterized protein YNL106C (EC 3.1.3.-)	0.90	-	nuc	0		actin cortical patch [IDA] membrane fraction [IDA]			1183
Q8HYY4 UniProt NPD GO	UACA_BOVIN	Uveal autoantigen with coiled-coil domains and ankyrin repeats protein (Beta-actin-binding protein) ...	0.90	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Expressed diffusely in cytoplasm (By similarity) ...				1401
Q5R5V9 UniProt NPD GO	VPS72_PONPY	Vacuolar protein sorting protein 72 homolog (Transcription factor-like 1)	0.90	-	nuc	0	Nucleus (By similarity)				364
Q15906 UniProt NPD GO	VPS72_HUMAN	Vacuolar protein sorting protein 72 homolog (Transcription factor-like 1) (Protein YL-1)	0.90	-	nuc	0	Nucleus	nucleus [TAS]	600607		364
Q62481 UniProt NPD GO	VPS72_MOUSE	Vacuolar protein sorting protein 72 homolog (Transcription factor-like 1) (Protein YL-1)	0.90	-	nuc	0	Nucleus				368
P67860 UniProt NPD GO	VEGFA_TRIFL	Vascular endothelial growth factor A precursor (VEGF-A) (Vascular permeability factor) (VPF)	0.90	+	nuc	0	Secreted protein				216
O42477 UniProt NPD GO	VSX2_BRARE	Visual system homeobox 2 (Transcription factor VSX2) (Homeobox protein ALX)	0.90	+	nuc	0	Nucleus (By similarity)				395
O13124 UniProt NPD GO	VDR_XENLA	Vitamin D3 receptor (VDR) (1,25-dihydroxyvitamin D3 receptor)	0.90	+	nuc	0	Nucleus				422
P54288 UniProt NPD GO	CACB2_RABIT	Voltage-dependent L-type calcium channel subunit beta-2 (CAB2) (Calcium channel voltage-dependent su ...	0.90	-	nuc	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein; cytoplasmic side (By similarity)			1T3S	632

You are viewing entries 4451 to 4500 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.