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
Q9UNH7 UniProt NPD GO	SNX6_HUMAN	Sorting nexin-6 (TRAF4-associated factor 2)	0.34	-	cyt	0		intracellular [NAS]	606098		406
O55034 UniProt NPD GO	SPAG4_RAT	Sperm-associated antigen 4 protein (Outer dense fiber-associated protein SPAG4)	0.34	-	mit	2	Membrane; multi-pass membrane protein (Potential). Axoneme. In spermatids, it is localized in the tr ...	microtubule [IDA]			444
P28290 UniProt NPD GO	SSFA2_HUMAN	Sperm-specific antigen 2 (Cleavage signal-1 protein) (CS-1)	0.34	-	nuc	0	Cell surface. Surface of sperm	plasma membrane [NAS]	118990		267
Q09176 UniProt NPD GO	U2AF1_SCHPO	Splicing factor U2AF 23 kDa subunit (U2 auxiliary factor 23 kDa subunit) (U2 snRNP auxiliary factor ...	0.34	-	nuc	0	Nucleus	commitment complex [IDA] snRNP U2 [TAS]			216
O48651 UniProt NPD GO	ERG1_PANGI	Squalene monooxygenase (EC 1.14.99.7) (Squalene epoxidase) (SE)	0.34	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				539
Q14247 UniProt NPD GO	SRC8_HUMAN	Src substrate cortactin (Amplaxin) (Oncogene EMS1)	0.34	-	cyt	0	Cytoplasm (By similarity). Associated with membrane ruffles and lamellipodia (By similarity)	cell cortex [ISS] cytoplasm [ISS] cytoskeleton [TAS] lamellipodium [ISS] ruffle [ISS] soluble fraction [TAS]	164765	2D1X	550
O35501 UniProt NPD GO	GRP75_CRIGR	Stress-70 protein, mitochondrial precursor (75 kDa glucose-regulated protein) (GRP 75)	0.34	-	mit	0	Mitochondrion				679
P48721 UniProt NPD GO	GRP75_RAT	Stress-70 protein, mitochondrial precursor (75 kDa glucose-regulated protein) (GRP 75) (Peptide-bind ...	0.34	-	mit	0	Mitochondrion				679
P38646 UniProt NPD GO	GRP75_HUMAN	Stress-70 protein, mitochondrial precursor (75 kDa glucose-regulated protein) (GRP 75) (Peptide-bind ...	0.34	-	mit	0	Mitochondrion	cell surface [IEP] cytoplasm [TAS] mitochondrion [TAS]	600548		679
P28863 UniProt NPD GO	MMP3_RABIT	Stromelysin-1 precursor (EC 3.4.24.17) (Matrix metalloproteinase-3) (MMP-3) (Transin-1) (SL-1)	0.34	-	exc	0					478
P50237 UniProt NPD GO	ST1C1_RAT	Sulfotransferase 1C1 (EC 2.8.2.-) (N-hydroxyarylamine sulfotransferase) (HAST-I)	0.34	-	cyt	0	Cytoplasm (By similarity)	cytosol [NAS]			304
Q9CZU3 UniProt NPD GO	SK2L2_MOUSE	Superkiller viralicidic activity 2-like 2 (EC 3.6.1.-) (ATP-dependent helicase SKIV2L2)	0.34	-	nuc	0	Nucleus; nucleolus (By similarity)				1040
P18489 UniProt NPD GO	SYB_DROME	Synaptobrevin	0.34	-	nuc	1	Synaptic vesicle; synaptic vesicle membrane; single-pass type IV membrane protein. Neuronal synaptic ...	plasma membrane [NAS] synaptic vesicle [NAS]			152
Q03322 UniProt NPD GO	TLG1_YEAST	T-SNARE affecting a late Golgi compartment protein 1 (Syntaxin TLG1)	0.34	-	nuc	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type IV membrane pro ...	early endosome [TAS] Golgi trans cisterna [TAS] Golgi trans face [TAS]		2C5K	224
Q5FVR0 UniProt NPD GO	TIMD2_RAT	T-cell immunoglobulin and mucin domain-containing protein 2 precursor (TIMD-2) (T-cell membrane prot ...	0.34	-	exc	1 *	Membrane; single-pass type I membrane protein (Potential)				349
Q5PXD3 UniProt NPD GO	CD3G_PIG	T-cell surface glycoprotein CD3 gamma chain precursor (T-cell receptor T3 gamma chain)	0.34	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				182
P79336 UniProt NPD GO	CD8B_FELCA	T-cell surface glycoprotein CD8 beta chain precursor (CD8b antigen)	0.34	-	end	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			210
O17488 UniProt NPD GO	TBP_ARTSF	TATA-box-binding protein (TATA-box factor) (TATA-binding factor) (TATA sequence-binding protein) (TB ...	0.34	-	nuc	0	Nucleus				275
Q8R4I4 UniProt NPD GO	TF2AY_MOUSE	TFIIA-alpha and beta-like factor (General transcription factor II A, 1-like factor)	0.34	-	nuc	0	Nucleus				468
Q5REP2 UniProt NPD GO	TI21L_PONPY	TIM21-like protein, mitochondrial precursor	0.34	-	nuc	1	Mitochondrion; mitochondrial membrane; single-pass membrane protein (Potential)				172
Q12933 UniProt NPD GO	TRAF2_HUMAN	TNF receptor-associated factor 2 (Tumor necrosis factor type 2 receptor-associated protein 3)	0.34	-	nuc	0	Cytoplasm		601895	1QSC	501
Q96S44 UniProt NPD GO	PRPK_HUMAN	TP53-regulating kinase (EC 2.7.11.1) (p53-related protein kinase) (Nori-2)	0.34	-	cyt	0	Nucleus				253
P38254 UniProt NPD GO	YBU4_YEAST	TTL domain-containing protein YBR094W	0.34	-	cyt	0		cytoplasm [IDA]			753
Q645Y5 UniProt NPD GO	TA2R3_GORGO	Taste receptor type 2 member 3 (T2R3)	0.34	-	end	7 *	Membrane; multi-pass membrane protein				315
Q9NYW6 UniProt NPD GO	TA2R3_HUMAN	Taste receptor type 2 member 3 (T2R3)	0.34	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [IC]	604868		315
Q646D2 UniProt NPD GO	TA2R3_PANPA	Taste receptor type 2 member 3 (T2R3)	0.34	-	end	7 *	Membrane; multi-pass membrane protein				315
Q646A7 UniProt NPD GO	TA2R3_PANTR	Taste receptor type 2 member 3 (T2R3)	0.34	-	end	7 *	Membrane; multi-pass membrane protein				315
Q646A2 UniProt NPD GO	TA2R7_GORGO	Taste receptor type 2 member 7 (T2R7)	0.34	-	end	7 *	Membrane; multi-pass membrane protein				318
Q9NYW3 UniProt NPD GO	TA2R7_HUMAN	Taste receptor type 2 member 7 (T2R7) (Taste receptor family B member 4) (TRB4)	0.34	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	604793		318
Q6NUS6 UniProt NPD GO	TECT3_HUMAN	Tectonic 3 precursor	0.34	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				607
Q92752 UniProt NPD GO	TENR_HUMAN	Tenascin-R precursor (TN-R) (Restrictin) (Janusin)	0.34	-	cyt	0	Secreted protein; extracellular space; extracellular matrix		601995		1358
Q8VBT0 UniProt NPD GO	TXND1_MOUSE	Thioredoxin domain-containing protein 1 precursor	0.34	-	end	3 *	Membrane; single-pass type I membrane protein (Potential). Predominantly found in the endoplasmic re ...				278
Q86VQ3 UniProt NPD GO	TXND2_HUMAN	Thioredoxin domain-containing protein 2 (Spermatid-specific thioredoxin-1) (Sptrx-1)	0.34	-	nuc	0	Cytoplasm. In ejaculated spermatozoa, it localizes in the caudal region of the head to the end of th ...	cytoplasm [ISS]			553
P01830 UniProt NPD GO	THY1_RAT	Thy-1 membrane glycoprotein precursor (Thy-1 antigen) (CD90 antigen) (CDw90 antigen)	0.34	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	cytosol [IDA] external side of plasma membrane [ISS] growth cone [IDA] lipid raft [ISS] plasma membrane [IDA]			161
Q9CQI9 UniProt NPD GO	TR25_MOUSE	Thyroid hormone receptor-associated protein 6 (Thyroid hormone receptor-associated protein complex 2 ...	0.34	-	nuc	0	Nucleus (Potential)				178
Q7YRQ8 UniProt NPD GO	TFPI2_BOVIN	Tissue factor pathway inhibitor 2 precursor (TFPI-2)	0.34	+	nuc	0	Secreted protein				234
O02482 UniProt NPD GO	UNC37_CAEEL	Transcription factor unc-37 (Uncoordinated protein 37)	0.34	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			612
Q9NHP7 UniProt NPD GO	TF2B_DROVI	Transcription initiation factor IIB (General transcription factor TFIIB)	0.34	-	nuc	0	Nucleus (By similarity)				293
O94436 UniProt NPD GO	TAF14_SCHPO	Transcription initiation factor TFIID subunit 14 (TBP-associated factor 14) (TBP-associated factor 3 ...	0.34	-	cyt	0	Nucleus; nucleoplasm	transcription factor TFIID complex [IDA] transcription factor TFIIF complex [IDA]			241
Q12206 UniProt NPD GO	WTM2_YEAST	Transcriptional modulator WTM2	0.34	-	mit	0		nucleus [IDA]			467
Q01414 UniProt NPD GO	ERG_LYTVA	Transcriptional regulator ERG homolog (Fragment)	0.34	-	nuc	0	Nucleus				173
Q75A59 UniProt NPD GO	LGE1_ASHGO	Transcriptional regulatory protein LGE1	0.34	-	nuc	0	Nucleus (By similarity)				244
P18341 UniProt NPD GO	TGFB1_BOVIN	Transforming growth factor beta-1 precursor (TGF-beta-1) [Contains: Latency-associated peptide (LAP) ...	0.34	-	nuc	0	Secreted protein	extracellular matrix (sensu Metazoa) [ISS] extracellular space [ISS]			315
P37802 UniProt NPD GO	TAGL2_HUMAN	Transgelin-2 (SM22-alpha homolog)	0.34	-	nuc	0		nuclear membrane [IDA] plasma membrane [IDA]	604634	1WYM	198
Q6FRU9 UniProt NPD GO	SEC62_CANGA	Translocation protein SEC62	0.34	-	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				257
Q811U4 UniProt NPD GO	MFN1_MOUSE	Transmembrane GTPase MFN1 (EC 3.6.5.-) (Mitofusin-1)	0.34	-	nuc	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)			1T3J	741
Q99394 UniProt NPD GO	TRS33_YEAST	Transport protein particle 33 kDa subunit (TRAPP 33 kDa subunit)	0.34	-	nuc	0	Golgi apparatus; cis-Golgi network	TRAPP complex [IDA]			268
Q8K4K3 UniProt NPD GO	TRIB2_MOUSE	Tribbles homolog 2 (TRB-2)	0.34	-	mit	0	Cytoplasm (By similarity). May associate with the cytoskeleton (By similarity)	cytoplasm [ISS]			343
O59947 UniProt NPD GO	TRI5_STACH	Trichodiene synthase (EC 4.2.3.6) (Sesquiterpene cyclase) (TS)	0.34	-	cyt	0					383
P34163 UniProt NPD GO	TGL1_YEAST	Triglyceride lipase-cholesterol esterase (EC 3.1.1.-)	0.34	-	cyt	0		integral to membrane [IDA] lipid particle [IDA]			548

You are viewing entries 37151 to 37200 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.