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
P01730 UniProt NPD GO	CD4_HUMAN	T-cell surface glycoprotein CD4 precursor (T-cell surface antigen T4/Leu-3)	0.59	-	end	1	Cell membrane; single-pass type I membrane protein. Localizes to lipid rafts. Removed from plasma me ...	plasma membrane [IDA] T cell receptor complex [NAS]	186940	3CD4	458
Q9CR47 UniProt NPD GO	TIP1_MOUSE	TGF-beta-inducible nuclear protein 1 (L-name-related protein 42) (LNR42)	0.59	+	nuc	0	Nucleus; nucleolus (By similarity)				260
Q96AY4 UniProt NPD GO	K1043_HUMAN	TPR repeat-containing protein KIAA1043	0.59	-	nuc	0					1716
Q92844 UniProt NPD GO	TANK_HUMAN	TRAF family member-associated NF-kappa-B activator (TRAF-interacting protein) (I-TRAF)	0.59	-	nuc	0	Cytoplasm		603893	1L0A	425
Q9EQN3 UniProt NPD GO	T22D4_MOUSE	TSC22 domain family protein 4 (TSC22-related-inducible leucine zipper protein 2)	0.59	-	nuc	0	Nucleus (Potential)				387
Q5R4U3 UniProt NPD GO	TAXB1_PONPY	Tax1-binding protein 1 homolog	0.59	-	nuc	0					813
Q26648 UniProt NPD GO	TKB1_STRPU	Tektin-B1	0.59	-	nuc	0	Cytoplasm. Microtubule-associated				400
Q6PKC3 UniProt NPD GO	TXD11_HUMAN	Thioredoxin domain-containing protein 11 (EF-hand-binding protein 1)	0.59	-	mit	0	Endoplasmic reticulum				985
Q9D0R2 UniProt NPD GO	SYTC_MOUSE	Threonyl-tRNA synthetase, cytoplasmic (EC 6.1.1.3) (Threonine--tRNA ligase) (ThrRS)	0.59	-	cyt	0	Cytoplasm				722
Q15399 UniProt NPD GO	TLR1_HUMAN	Toll-like receptor 1 precursor (Toll/interleukin-1 receptor-like protein) (TIL) (CD281 antigen)	0.59	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Phagosome; phagosomal membrane; ...	integral to plasma membrane [TAS] phagocytic vesicle [ISS] plasma membrane [TAS]	601194	1FYV	786
P36053 UniProt NPD GO	ELF1_YEAST	Transcription elongation factor 1	0.59	-	nuc	0	Nucleus	nucleus [IDA]			145
Q21338 UniProt NPD GO	SPT5H_CAEEL	Transcription elongation factor SPT5 (DRB sensitivity-inducing factor large subunit) (DSIF large sub ...	0.59	+	nuc	0	Nucleus (By similarity)				1208
Q19849 UniProt NPD GO	EGL44_CAEEL	Transcription enhancer factor-like protein egl-44 (Egg-laying defective protein 44)	0.59	-	nuc	0	Nucleus	nucleus [IDA]			465
Q5TM48 UniProt NPD GO	TCF19_MACMU	Transcription factor 19	0.59	+	nuc	0	Nucleus (Potential)				345
O43680 UniProt NPD GO	TCF21_HUMAN	Transcription factor 21 (Podocyte-expressed 1) (Pod-1) (Epicardin) (Capsulin)	0.59	-	nuc	0	Nucleus		603306		179
Q9N0N3 UniProt NPD GO	AP2A_SHEEP	Transcription factor AP-2 alpha (AP2-alpha) (Activating enhancer-binding protein 2 alpha) (Activator ...	0.59	-	nuc	0	Nucleus (Probable)				491
O93375 UniProt NPD GO	COE2_BRARE	Transcription factor COE2	0.59	-	nuc	0	Nucleus (Potential)				579
Q9FT54 UniProt NPD GO	GTE6_ARATH	Transcription factor GTE6 (GENERAL TRANSCRIPTION FACTOR GROUP E6)	0.59	+	cyt	0	Nucleus				369
P23923 UniProt NPD GO	HBP1B_WHEAT	Transcription factor HBP-1b(c38)	0.59	-	nuc	0	Nucleus				332
Q90889 UniProt NPD GO	MAFG_CHICK	Transcription factor MafG (V-maf musculoaponeurotic fibrosarcoma oncogene homolog G)	0.59	-	nuc	0	Nucleus				162
Q8CIV7 UniProt NPD GO	OVOL2_MOUSE	Transcription factor Ovo-like 2 (mOvo2) (Zinc finger protein 339) (Zinc finger OVO2) (Zinc finger pr ...	0.59	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			274
Q6S4P4 UniProt NPD GO	RF2B_ORYSA	Transcription factor RF2b	0.59	-	nuc	0	Nucleus				329
P51510 UniProt NPD GO	RELB_XENLA	Transcription factor RelB homolog	0.59	-	nuc	0	Nucleus				497
Q02447 UniProt NPD GO	SP3_HUMAN	Transcription factor Sp3 (SPR-2)	0.59	-	nuc	0	Nucleus	nucleus [NAS]	601804		781
Q39163 UniProt NPD GO	TGA5_ARATH	Transcription factor TGA5 (Ocs element-binding factor 5) (OBF5) (AtbZIP26)	0.59	-	nuc	0	Nucleus				330
P79007 UniProt NPD GO	HAP5_SCHPO	Transcriptional activator hap5	0.59	+	nuc	0	Nucleus	CCAAT-binding factor complex [TAS]			415
P11308 UniProt NPD GO	ERG_HUMAN	Transcriptional regulator ERG (Transforming protein ERG)	0.59	-	nuc	0	Nucleus	nucleus [TAS]	133450	1SXE	462
Q90837 UniProt NPD GO	ERG_CHICK	Transcriptional regulator Erg	0.59	-	nuc	0	Nucleus				478
Q8BN78 UniProt NPD GO	KAISO_MOUSE	Transcriptional regulator Kaiso (Zinc finger and BTB domain-containing protein 33)	0.59	-	nuc	0	Nucleus	nucleus [IDA]			671
P15062 UniProt NPD GO	ETS1B_CHICK	Transforming protein p68/c-ets-1	0.59	+	nuc	0					485
P32501 UniProt NPD GO	EI2BE_YEAST	Translation initiation factor eIF-2B subunit epsilon (eIF-2B GDP-GTP exchange factor subunit epsilon ...	0.59	-	cyt	0		eukaryotic translation initiation factor 2B... [IDA] multi-eIF complex [IDA] ribosome [TAS]		1PAQ	712
P33892 UniProt NPD GO	GCN1_YEAST	Translational activator GCN1	0.59	-	nuc	0		cytosol [IDA] cytosolic ribosome (sensu Eukaryota) [IDA] mitochondrion [IDA]			2672
Q9D7R2 UniProt NPD GO	TMEPA_MOUSE	Transmembrane prostate androgen-induced protein (NEDD4 WW domain-binding protein 4)	0.59	-	nuc	1 *	Cell membrane; single-pass membrane protein (Potential)	integral to membrane [ISS]			260
Q12226 UniProt NPD GO	AYT1_YEAST	Trichothecene 3-O-acetyltransferase (EC 2.3.1.-)	0.59	-	nuc	0					474
Q12815 UniProt NPD GO	TROAP_HUMAN	Trophinin-associated protein (Tastin) (Trophinin-assisting protein)	0.59	-	mit	0	Cytoplasm	cytoplasm [TAS]	603872		778
P20351 UniProt NPD GO	T23O_DROME	Tryptophan 2,3-dioxygenase (EC 1.13.11.11) (TO) (Tryptophan pyrrolase) (Protein vermilion)	0.59	-	cyt	0					379
P70080 UniProt NPD GO	TPH1_CHICK	Tryptophan 5-hydroxylase 1 (EC 1.14.16.4) (Tryptophan 5-monooxygenase 1)	0.59	-	cyt	0					445
O14836 UniProt NPD GO	TR13B_HUMAN	Tumor necrosis factor receptor superfamily member 13B (Transmembrane activator and CAML interactor) ...	0.59	-	nuc	1	Membrane; single-pass type III membrane protein	integral to plasma membrane [TAS]	240500	1XUT	293
Q8IXH6 UniProt NPD GO	T53I2_HUMAN	Tumor protein p53-inducible nuclear protein 2 (p53-inducible protein U) (PIG-U)	0.59	-	nuc	0	Nucleus				220
P23729 UniProt NPD GO	IF3T_TORCA	Type III intermediate filament	0.59	-	nuc	0					458
Q9VBW3 UniProt NPD GO	CAD96_DROME	Tyrosine kinase receptor Cad96Ca precursor (EC 2.7.10.1) (Cadherin 96Ca) (Tyrosine kinase receptor H ...	0.59	-	nuc	2 *	Membrane; single-pass type I membrane protein (Potential)				773
P29074 UniProt NPD GO	PTN4_HUMAN	Tyrosine-protein phosphatase non-receptor type 4 (EC 3.1.3.48) (Protein-tyrosine phosphatase MEG1) ( ...	0.59	-	nuc	0		cytoplasm [TAS]	176878	2CS5	926
Q91WM3 UniProt NPD GO	U3IP2_MOUSE	U3 small nucleolar RNA-interacting protein 2 (U3 small nucleolar ribonucleoprotein-associated 55 kDa ...	0.59	+	mit	0	Nucleus; nucleolus				475
Q6BYD9 UniProt NPD GO	IMP4_DEBHA	U3 small nucleolar ribonucleoprotein protein IMP4 (U3 snoRNP protein IMP4)	0.59	-	nuc	0	Nucleus; nucleolus (By similarity)				284
Q9JMA1 UniProt NPD GO	UBP14_MOUSE	Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.1.2.15) (Ubiquitin thioesterase 14) (Ubiquitin-specif ...	0.59	-	nuc	0		soluble fraction [IDA] synaptosome [IDA]		1WGG	492
Q8BW70 UniProt NPD GO	UBP38_MOUSE	Ubiquitin carboxyl-terminal hydrolase 38 (EC 3.1.2.15) (Ubiquitin thioesterase 38) (Ubiquitin-specif ...	0.59	-	cyt	0					1042
Q5R9G3 UniProt NPD GO	UBE4A_PONPY	Ubiquitin conjugation factor E4 A	0.59	-	cyt	0					1066
P31253 UniProt NPD GO	UBE1X_MOUSE	Ubiquitin-activating enzyme E1 X (Fragment)	0.59	-	mit	0					450
P51965 UniProt NPD GO	UB2E1_HUMAN	Ubiquitin-conjugating enzyme E2 E1 (EC 6.3.2.19) (Ubiquitin-protein ligase E1) (Ubiquitin carrier pr ...	0.59	-	nuc	0			602916	1XR9	193
P52482 UniProt NPD GO	UB2E1_MOUSE	Ubiquitin-conjugating enzyme E2 E1 (EC 6.3.2.19) (Ubiquitin-protein ligase E1) (Ubiquitin carrier pr ...	0.59	-	nuc	0					193

You are viewing entries 19901 to 19950 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.