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
P56568 UniProt NPD GO	RIP1_LUFCY	Ribosome-inactivating protein luffin P1 (EC 3.2.2.22) (Arginine/glutamate-rich polypeptide) (AGRP) [ ...	0.40	-	nuc	0					47
P91931 UniProt NPD GO	DCAM_DROME	S-adenosylmethionine decarboxylase proenzyme (EC 4.1.1.50) (AdoMetDC) (SamDC) [Contains: S-adenosylm ...	0.40	-	cyt	0					347
P17840 UniProt NPD GO	SLSG3_BRAOL	S-locus-specific glycoprotein S13 precursor (SLSG-13) (Fragment)	0.40	-	exc	1 *					434
Q99J08 UniProt NPD GO	S14L2_MOUSE	SEC14-like protein 2 (Alpha-tocopherol-associated protein) (TAP)	0.40	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in absence of alpha-tocopherol, and ...	cytoplasm [ISS] nucleus [ISS]			403
Q9BRG2 UniProt NPD GO	SH23A_HUMAN	SH2 domain-containing protein 3A (Novel SH2-containing protein 1)	0.40	-	nuc	0			604721		576
Q9D780 UniProt NPD GO	SLAF9_MOUSE	SLAM family member 9 precursor	0.40	+	exc	1	Membrane; single-pass type I membrane protein				285
Q62249 UniProt NPD GO	SOX19_MOUSE	SOX-19 protein (Fragment)	0.40	-	nuc	0	Nucleus (Potential)				55
P15638 UniProt NPD GO	URT2_DESRO	Salivary plasminogen activator alpha 2 precursor (EC 3.4.21.68) (DSPA alpha-2) (BAT-PA) (T-plasminog ...	0.40	-	exc	0					477
P22814 UniProt NPD GO	RUNT_DROME	Segmentation protein Runt	0.40	-	nuc	0	Nucleus				510
Q9DBC0 UniProt NPD GO	SELO_MOUSE	Selenoprotein O	0.40	-	mit	0					667
Q9BGQ3 UniProt NPD GO	SEPT5_MACFA	Septin-5	0.40	-	cyt	0		plasma membrane [ISS] synaptic vesicle [ISS]			378
O54949 UniProt NPD GO	NLK_MOUSE	Serine/threonine kinase NLK (EC 2.7.11.24) (Nemo-like kinase)	0.40	-	nuc	0	Nucleus. Predominantly. Cytoplasm. A smaller fraction is cytoplasmic	nucleus [IEP]			515
Q76MJ5 UniProt NPD GO	ERN2_HUMAN	Serine/threonine-protein kinase/endoribonuclease IRE2 precursor (Inositol-requiring protein 2) (hIRE ...	0.40	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein		604034		925
Q19552 UniProt NPD GO	SRA29_CAEEL	Serpentine receptor class alpha-29 (Protein sra-29)	0.40	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				348
P58043 UniProt NPD GO	SESN2_MOUSE	Sestrin-2	0.40	-	cyt	0					480
P16255 UniProt NPD GO	SRP14_CANFA	Signal recognition particle 14 kDa protein (SRP14)	0.40	-	nuc	0	Cytoplasm				110
P49969 UniProt NPD GO	SR542_HORVU	Signal recognition particle 54 kDa protein 2 (SRP54)	0.40	-	cyt	0	Cytoplasm				497
Q9Z172 UniProt NPD GO	SUMO3_MOUSE	Small ubiquitin-related modifier 3 precursor (SUMO-3) (Ubiquitin-like protein SMT3A) (SMT3 homolog 1 ...	0.40	-	nuc	0					110
Q01118 UniProt NPD GO	SCN7A_HUMAN	Sodium channel protein type 7 subunit alpha (Sodium channel protein type VII subunit alpha) (Putativ ...	0.40	-	end	21	Membrane; multi-pass membrane protein		182392		1682
Q9WV27 UniProt NPD GO	AT1A4_MOUSE	Sodium/potassium-transporting ATPase alpha-4 chain (EC 3.6.3.9) (Sodium pump 4) (Na+/K+ ATPase 4)	0.40	-	end	10	Membrane; multi-pass membrane protein	sodium:potassium-exchanging ATPase complex [ISS]			1032
Q9H2Y9 UniProt NPD GO	SO5A1_HUMAN	Solute carrier organic anion transporter family member 5A1 (Solute carrier family 21 member 15) (Org ...	0.40	+	end	11	Membrane; multi-pass membrane protein				848
Q9YGH4 UniProt NPD GO	SMS2_CARAU	Somatostatin-2 precursor (Somatostatin II) [Contains: [Tyr21,Gly24]-somatostatin-28; [Tyr7,Gly10]-so ...	0.40	-	exc	0	Secreted protein				120
P48248 UniProt NPD GO	SOMA_MORSA	Somatotropin precursor (Growth hormone)	0.40	-	exc	0	Secreted protein				204
Q9IBE5 UniProt NPD GO	SOMA_SIGGU	Somatotropin precursor (Growth hormone)	0.40	-	exc	0	Secreted protein				196
O93360 UniProt NPD GO	SOMA2_CARAU	Somatotropin-2 precursor (Somatotropin II) (Growth hormone II)	0.40	-	exc	0	Secreted protein				210
Q95LJ2 UniProt NPD GO	SPESP_MACFA	Sperm equatorial segment protein 1 precursor	0.40	-	exc	0	Acrosome (By similarity). Small proacrosomal granules (during the Golgi phase), enlarged acrosomal v ...				352
P49901 UniProt NPD GO	MCSP_HUMAN	Sperm mitochondrial-associated cysteine-rich protein	0.40	-	nuc	0	Cytoplasm. Becomes associated with the spermatid mitochondrion capsule at step 16 of spermatogenesis ...	cytoplasm [ISS] mitochondrion [ISS]	601148		116
P37268 UniProt NPD GO	FDFT_HUMAN	Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl-diphosphate farnesyltransferase) (FPP:FPP far ...	0.40	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to membrane [TAS]	184420	1EZF	417
Q9DG09 UniProt NPD GO	STAR_CHICK	Steroidogenic acute regulatory protein, mitochondrial precursor (StAR) (StARD1)	0.40	-	mit	0	Mitochondrion (By similarity)				281
P48933 UniProt NPD GO	DHSB_CYACA	Succinate dehydrogenase [ubiquinone] iron-sulfur protein (EC 1.3.5.1) (IP)	0.40	-	nuc	0	Mitochondrion; mitochondrial inner membrane				262
Q9BT88 UniProt NPD GO	SYT11_HUMAN	Synaptotagmin-11 (Synaptotagmin XI) (SytXI)	0.40	+	nuc	1 *	Membrane; single-pass membrane protein. In substantia nigra, observed in neuronal cell bodies and ne ...		608741		431
Q9R0N6 UniProt NPD GO	SYT8_MOUSE	Synaptotagmin-8 (Synaptotagmin VIII) (SytVIII)	0.40	-	nuc	1 *	Cell membrane; single-pass type III membrane protein. Acrosome				395
Q94KK7 UniProt NPD GO	SYP52_ARATH	Syntaxin-52 (AtSYP52)	0.40	-	nuc	1	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type IV membrane pro ...				233
O75333 UniProt NPD GO	TBX10_HUMAN	T-box transcription factor TBX10 (T-box protein 10)	0.40	-	nuc	0	Nucleus (Potential)		604648		385
P17982 UniProt NPD GO	NAR2A_RAT	T-cell ecto-ADP-ribosyltransferase 1 precursor (EC 2.4.2.31) (T-cell NAD(P)(+)--arginine ADP-ribosyl ...	0.40	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				275
P97473 UniProt NPD GO	TRBP2_MOUSE	TAR RNA-binding protein 2 (Protamine-1 RNA-binding protein) (PRM-1 RNA-binding protein)	0.40	-	nuc	0	Cytoplasm. Nucleus				365
Q15633 UniProt NPD GO	TRBP2_HUMAN	TAR RNA-binding protein 2 (Trans-activation-responsive RNA-binding protein)	0.40	-	nuc	0	Nucleus	nucleus [TAS]	605053	2CPN	366
Q8N5T2 UniProt NPD GO	TBC19_HUMAN	TBC1 domain family member 19	0.40	-	cyt	2					526
Q99PW4 UniProt NPD GO	PRPK_MOUSE	TP53-regulating kinase (EC 2.7.11.1) (p53-related protein kinase) (Nori-2)	0.40	-	cyt	0	Nucleus (By similarity)	nucleus [ISS]			244
Q06183 UniProt NPD GO	TEBH_EUPCR	Telomere-binding protein homolog	0.40	-	mit	0	Nucleus (Probable)				460
Q90502 UniProt NPD GO	TBFG_EPTST	Thread biopolymer filament subunit gamma	0.40	-	cyt	0	Secreted protein; extracellular space				603
P26639 UniProt NPD GO	SYTC_HUMAN	Threonyl-tRNA synthetase, cytoplasmic (EC 6.1.1.3) (Threonine--tRNA ligase) (ThrRS)	0.40	-	cyt	0	Cytoplasm	cytoplasm [TAS] soluble fraction [TAS]	187790	1WWT	723
P07236 UniProt NPD GO	SYTM_YEAST	Threonyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.3) (Threonine--tRNA ligase) (ThrRS)	0.40	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]			462
P01150 UniProt NPD GO	TRH_RAT	Thyroliberin precursor [Contains: Prothyroliberin; Thyroliberin (Thyrotropin-releasing hormone) (TRH ...	0.40	-	exc	0	Secreted protein				255
Q8SPE9 UniProt NPD GO	TLR4_PONPY	Toll-like receptor 4 precursor (CD284 antigen)	0.40	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	lipopolysaccharide receptor complex [ISS]			828
P40689 UniProt NPD GO	TSL_DROME	Torso-like protein precursor	0.40	-	exc	0	Secreted protein. Is a component of the vitelline membrane (VM, the inner layer of the eggshell)	extracellular region [IDA]			353
Q8LEF3 UniProt NPD GO	ELOF1_ARATH	Transcription elongation factor 1 homolog	0.40	-	mit	0	Nucleus (By similarity)				120
Q3SY56 UniProt NPD GO	SP6_HUMAN	Transcription factor Sp6 (Krueppel-like factor 14)	0.40	-	nuc	0	Nucleus (By similarity)		608613		376
P62915 UniProt NPD GO	TF2B_MOUSE	Transcription initiation factor IIB (General transcription factor TFIIB) (RNA polymerase II alpha in ...	0.40	-	nuc	0	Nucleus (By similarity)				316
P62916 UniProt NPD GO	TF2B_RAT	Transcription initiation factor IIB (General transcription factor TFIIB) (RNA polymerase II alpha in ...	0.40	-	nuc	0	Nucleus				316

You are viewing entries 32201 to 32250 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.