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
Q8SQ40 UniProt NPD GO	CCL5_FELCA	Small inducible cytokine A5 precursor (CCL5) (T-cell-specific RANTES protein)	0.41	-	exc	0	Secreted protein				92
Q68AY9 UniProt NPD GO	CCL8_CANFA	Small inducible cytokine A8 precursor (CCL8) (Monocyte chemotactic protein 2) (MCP-2) (Monocyte chem ...	0.41	-	exc	0	Secreted protein (By similarity)				99
Q6NRT3 UniProt NPD GO	SMU1_XENLA	Smu-1 suppressor of mec-8 and unc-52 protein homolog	0.41	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				513
Q8WRY4 UniProt NPD GO	SCX9_CENLL	Sodium-channel modifier neurotoxin Cll9 precursor	0.41	-	nuc	1 *	Secreted protein				84
Q14940 UniProt NPD GO	SL9A5_HUMAN	Sodium/hydrogen exchanger 5 (Na(+)/H(+) exchanger 5) (NHE-5) (Solute carrier family 9 member 5)	0.41	+	end	10 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]	600477		896
Q9IAL8 UniProt NPD GO	NCKX1_CHICK	Sodium/potassium/calcium exchanger 1 precursor (Na(+)/K(+)/Ca(2+)-exchange protein 1) (Retinal rod N ...	0.41	-	end	11 *	Membrane; multi-pass membrane protein				663
P34746 UniProt NPD GO	SOMA_OREMO	Somatotropin precursor (Growth hormone)	0.41	-	exc	0	Secreted protein				204
P13391 UniProt NPD GO	SOMA_ORENI	Somatotropin precursor (Growth hormone)	0.41	-	exc	0	Secreted protein				204
P87391 UniProt NPD GO	SOMA_SEBSC	Somatotropin precursor (Growth hormone)	0.41	-	exc	0	Secreted protein				204
Q8C080 UniProt NPD GO	SNX16_MOUSE	Sorting nexin-16	0.41	-	mit	0					344
Q9NPE6 UniProt NPD GO	SPAG4_HUMAN	Sperm-associated antigen 4 protein (Outer dense fiber-associated protein SPAG4)	0.41	-	mit	1	Membrane; multi-pass membrane protein (Potential). Axoneme (By similarity). In spermatids, it is loc ...		603038		437
Q27022 UniProt NPD GO	SP23_TENMO	Spermatophorin SP23 precursor	0.41	-	nuc	0	Secreted protein				182
Q8BLI4 UniProt NPD GO	SART2_MOUSE	Squamous cell carcinoma antigen recognized by T-cells 2 precursor (SART-2)	0.41	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				958
Q6SZW1 UniProt NPD GO	SARM1_HUMAN	Sterile alpha and TIR motif-containing protein 1 (Sterile alpha and Armadillo repeat protein) (Tir-1 ...	0.41	-	cyt	0	Cytoplasm (By similarity)		607732		724
Q12770 UniProt NPD GO	SCAP_HUMAN	Sterol regulatory element-binding protein cleavage-activating protein (SREBP cleavage-activating pro ...	0.41	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...	endoplasmic reticulum [NAS] Golgi apparatus [NAS] integral to membrane [NAS]	601510		1278
O35985 UniProt NPD GO	SMR2C_MOUSE	Submaxillary gland androgen-regulated protein 2, isoform gamma precursor (Salivary protein MSG2, iso ...	0.41	-	exc	0	Secreted protein				143
P23739 UniProt NPD GO	SUIS_RAT	Sucrase-isomaltase, intestinal [Contains: Sucrase (EC 3.2.1.48); Isomaltase (EC 3.2.1.10)]	0.41	-	mit	1 *	Cell membrane; single-pass type II membrane protein. Brush border				1840
P39692 UniProt NPD GO	MET10_YEAST	Sulfite reductase [NADPH] flavoprotein component (EC 1.8.1.2)	0.41	-	cyt	0		cytoplasm [TAS] sulfite reductase complex (NADPH) [IDA]			1035
Q62276 UniProt NPD GO	SURF5_MOUSE	Surfeit locus protein 5	0.41	-	nuc	0					140
Q64375 UniProt NPD GO	SC65_RAT	Synaptonemal complex protein SC65	0.41	-	cyt	0	Nucleus. Located in the pairing zone of the synaptonemal complex	synaptonemal complex [IDA]			431
Q9ERB0 UniProt NPD GO	SNP29_MOUSE	Synaptosomal-associated protein 29 (SNAP-29) (Vesicle-membrane fusion protein SNAP-29) (Soluble 29 k ...	0.41	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. Appears to be mostly membrane-bound, probably via ...				260
Q9Z2P6 UniProt NPD GO	SNP29_RAT	Synaptosomal-associated protein 29 (SNAP-29) (Vesicle-membrane fusion protein SNAP-29) (Soluble 29 k ...	0.41	-	nuc	0					257
Q60770 UniProt NPD GO	STXB3_MOUSE	Syntaxin-binding protein 3 (UNC-18 homolog 3) (UNC-18C) (MUNC-18-3)	0.41	-	nuc	0		cytosol [IDA] plasma membrane [IDA]			592
P90971 UniProt NPD GO	TBX12_CAEEL	T-box protein 12 (Protein male abnormal 9)	0.41	-	nuc	0	Nucleus (Potential)				346
Q96H15 UniProt NPD GO	TIMD4_HUMAN	T-cell immunoglobulin and mucin domain-containing protein 4 precursor (TIMD-4) (T-cell membrane prot ...	0.41	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)				378
P01732 UniProt NPD GO	CD8A_HUMAN	T-cell surface glycoprotein CD8 alpha chain precursor (T-lymphocyte differentiation antigen T8/Leu-2 ...	0.41	-	exc	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein	integral to plasma membrane [NAS] T cell receptor complex [NAS]	186910	1Q69	235
Q04364 UniProt NPD GO	YMP8_YEAST	TPR repeat-containing protein YMR018W	0.41	-	nuc	0					514
Q06510 UniProt NPD GO	TAZ1_YEAST	Tafazzin homolog	0.41	-	mit	0	Mitochondrion	mitochondrion [IDA]			381
Q646F6 UniProt NPD GO	TA2R7_PAPHA	Taste receptor type 2 member 7 (T2R7)	0.41	-	end	7 *	Membrane; multi-pass membrane protein				317
O70548 UniProt NPD GO	TELT_MOUSE	Telethonin (Titin cap protein)	0.41	-	nuc	0	Sarcomeric				167
P68305 UniProt NPD GO	THB_CAIMO	Thyroid hormone receptor beta	0.41	+	cyt	0	Nucleus				369
P68306 UniProt NPD GO	THB_CHICK	Thyroid hormone receptor beta	0.41	+	cyt	0	Nucleus				369
Q8NFQ8 UniProt NPD GO	TOIP2_HUMAN	Torsin-1A-interacting protein 2 (Lumenal domain-like LAP1)	0.41	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein				470
Q9XVZ8 UniProt NPD GO	ELOF1_CAEEL	Transcription elongation factor 1 homolog	0.41	-	nuc	0	Nucleus (By similarity)				84
Q13892 UniProt NPD GO	BT3L3_HUMAN	Transcription factor BTF3 homolog 3 (Basic transcription factor 3-like 3)	0.41	-	mit	0	Nucleus (Potential)	nucleus [NAS]	603739		214
P93417 UniProt NPD GO	GAM1_ORYSA	Transcription factor GAMYB (OsGAMyb)	0.41	-	nuc	0	Nucleus (Probable)				553
P24488 UniProt NPD GO	HAP2_SCHPO	Transcriptional activator hap2	0.41	+	nuc	0	Nucleus				334
Q6FJC7 UniProt NPD GO	LGE1_CANGA	Transcriptional regulatory protein LGE1	0.41	-	nuc	0	Nucleus (By similarity)				313
P78706 UniProt NPD GO	RCO1_NEUCR	Transcriptional repressor rco-1	0.41	-	nuc	0					604
Q18297 UniProt NPD GO	TRPA1_CAEEL	Transient receptor potential cation channel subfamily A member 1 homolog	0.41	-	end	5	Membrane; multi-pass membrane protein (Probable)				1193
Q9H295 UniProt NPD GO	TM7S4_HUMAN	Transmembrane 7 superfamily member 4 (Dendritic cell-specific transmembrane protein) (DC-STAMP) (IL- ...	0.41	-	end	6 *	Cell membrane; multi-pass membrane protein (Potential). Localized to the cell surface	cell surface [IDA] integral to membrane [NAS]	605933		470
Q7YU24 UniProt NPD GO	MARF_DROME	Transmembrane GTPase Marf (EC 3.6.5.-) (Mitochondrial assembly regulatory factor) (Mitofusin)	0.41	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)	mitochondrial envelope [ISS]			810
Q8IU68 UniProt NPD GO	TMC8_HUMAN	Transmembrane channel-like protein 8 (Epidermodysplasia verruciformis protein 2)	0.41	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein		605829		726
Q9DBI0 UniProt NPD GO	TMPS6_MOUSE	Transmembrane protease, serine 6 (EC 3.4.21.-) (Matriptase-2)	0.41	-	gol	1 *	Membrane; single-pass type II membrane protein	integral to membrane [ISS] plasma membrane [IDA]			799
O14787 UniProt NPD GO	TNPO2_HUMAN	Transportin-2 (Karyopherin beta-2b)	0.41	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [TAS] nucleus [TAS]	603002		897
Q96F44 UniProt NPD GO	TRI11_HUMAN	Tripartite motif-containing protein 11 (EC 6.3.2.-) (RING finger protein 92) (Protein BIA1)	0.41	-	nuc	0	Cytoplasm. Nucleus		607868		468
Q14142 UniProt NPD GO	TRI14_HUMAN	Tripartite motif-containing protein 14	0.41	-	mit	0		cytoplasm [IDA]	606556		442
Q7YR33 UniProt NPD GO	TRI15_PANTR	Tripartite motif-containing protein 15 (Zinc finger protein B7)	0.41	-	cyt	0					465
Q6QA27 UniProt NPD GO	TRI44_RAT	Tripartite motif-containing protein 44 (Protein DIPB)	0.41	-	nuc	0					344
Q7Z4K8 UniProt NPD GO	TRI46_HUMAN	Tripartite motif-containing protein 46 (Tripartite, fibronectin type-III and C-terminal SPRY motif p ...	0.41	-	cyt	0					759

You are viewing entries 31451 to 31500 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.