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
Q8VDS8 UniProt NPD GO	STX18_MOUSE	Syntaxin-18	0.74	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein (By simi ...				334
Q8K400 UniProt NPD GO	STXB5_MOUSE	Syntaxin-binding protein 5 (Tomosyn-1) (Lethal(2) giant larvae protein homolog 3)	0.74	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein. Membrane; peripheral membrane protein. Cytopl ...	nicotinic acetylcholine-gated receptor-chan... [IDA]			1152
Q5I2P1 UniProt NPD GO	TBX5_RAT	T-box transcription factor TBX5 (T-box protein 5)	0.74	-	nuc	0	Nucleus (Potential)				517
Q3SYX1 UniProt NPD GO	TRAT1_BOVIN	T-cell receptor-associated transmembrane adapter 1 (T-cell receptor-interacting molecule) (TRIM)	0.74	-	nuc	1 *	Cell membrane; single-pass type III membrane protein (By similarity)				193
P08920 UniProt NPD GO	CD2_MOUSE	T-cell surface antigen CD2 precursor (T-cell surface antigen T11/Leu-5) (LFA-2) (LFA-3 receptor) (Ly ...	0.74	+	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS]			344
Q8TC07 UniProt NPD GO	TBC15_HUMAN	TBC1 domain family member 15	0.74	-	cyt	0					691
Q92609 UniProt NPD GO	TBCD5_HUMAN	TBC1 domain family member 5	0.74	-	nuc	0					795
Q5U208 UniProt NPD GO	THAP1_RAT	THAP domain-containing protein 1	0.74	+	nuc	0	Nucleus; nucleoplasm (By similarity). And PML nuclear bodies (By similarity)				210
Q20255 UniProt NPD GO	YSY1_CAEEL	TPR repeat-containing protein ZK328.7	0.74	-	nuc	0					1332
Q71LX4 UniProt NPD GO	TLN2_MOUSE	Talin-2	0.74	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion (By similarity). Synapse (By similarity). Focal ...				2375
Q3UVR3 UniProt NPD GO	TTBK2_MOUSE	Tau-tubulin kinase 2	0.74	-	nuc	0					1243
O70372 UniProt NPD GO	TERT_MOUSE	Telomerase reverse transcriptase (EC 2.7.7.49) (Telomerase catalytic subunit)	0.74	-	nuc	0	Nucleus				1122
Q9CRD2 UniProt NPD GO	K0103_MOUSE	Tetratricopeptide repeat protein KIAA0103	0.74	-	nuc	0	Nucleus				297
Q9PUA8 UniProt NPD GO	THA_ELECQ	Thyroid hormone receptor alpha (Fragment)	0.74	+	nuc	0	Nucleus				71
Q95LA9 UniProt NPD GO	TLR2_BOVIN	Toll-like receptor 2 precursor (CD282 antigen)	0.74	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				784
Q5R7A3 UniProt NPD GO	TOIP1_PONPY	Torsin-1A-interacting protein 1	0.74	-	nuc	0	Nucleus; nuclear inner membrane; single-pass membrane protein (By similarity)				598
Q14135 UniProt NPD GO	VGLL4_HUMAN	Transcription cofactor vestigial-like protein 4 (Vgl-4)	0.74	-	nuc	0	Nucleus (By similarity)				290
Q969E4 UniProt NPD GO	TCAL3_HUMAN	Transcription elongation factor A protein-like 3 (TCEA-like protein 3) (Transcription elongation fac ...	0.74	-	nuc	0	Nucleus (Probable)				200
Q96EI5 UniProt NPD GO	TCAL4_HUMAN	Transcription elongation factor A protein-like 4 (TCEA-like protein 4) (Transcription elongation fac ...	0.74	-	nuc	0	Nucleus (Probable)				215
Q5R6B4 UniProt NPD GO	TCAL4_PONPY	Transcription elongation factor A protein-like 4 (TCEA-like protein 4) (Transcription elongation fac ...	0.74	-	nuc	0	Nucleus (Probable)				209
Q4PIC4 UniProt NPD GO	SPT5_USTMA	Transcription elongation factor SPT5 (Chromatin elongation factor SPT5)	0.74	+	mit	0	Nucleus (By similarity)				1057
P30985 UniProt NPD GO	HTF4_CHICK	Transcription factor 12 (Transcription factor HTF-4) (E-box-binding protein) (Class A helix-loop-hel ...	0.74	-	nuc	0	Nucleus				657
Q99KJ5 UniProt NPD GO	TCF19_MOUSE	Transcription factor 19-like protein (SC1 protein homolog)	0.74	-	nuc	0	Nucleus (Potential)				263
P15881 UniProt NPD GO	ITF2_CANFA	Transcription factor 4 (Immunoglobulin transcription factor 2) (ITF-2) (Thyroglobulin promoter trans ...	0.74	-	nuc	0	Nucleus				642
Q04930 UniProt NPD GO	CRF1_YEAST	Transcription factor CRF1 (Corepressor with FHL1 protein 1)	0.74	+	nuc	0	Cytoplasm. Nucleus. The nuclear location is negatively regulated by the TOR pathway	cytoplasm [IDA] nucleus [IDA]			467
P97489 UniProt NPD GO	GATA5_MOUSE	Transcription factor GATA-5 (GATA-binding factor 5)	0.74	-	nuc	0	Nucleus				404
Q92664 UniProt NPD GO	TF3A_HUMAN	Transcription factor IIIA (Factor A) (TFIIIA)	0.74	-	nuc	0	Nucleus		600860		423
Q04863 UniProt NPD GO	RELB_MOUSE	Transcription factor RelB	0.74	+	mit	0	Nucleus			1ZKA	558
O95416 UniProt NPD GO	SOX14_HUMAN	Transcription factor SOX-14	0.74	+	nuc	0	Nucleus (Potential)		604747		240
P61259 UniProt NPD GO	SOX14_MACFA	Transcription factor SOX-14	0.74	+	nuc	0	Nucleus (Potential)				240
Q04892 UniProt NPD GO	SOX14_MOUSE	Transcription factor SOX-14	0.74	+	nuc	0	Nucleus (Potential)				240
P78962 UniProt NPD GO	ATF21_SCHPO	Transcription factor atf21	0.74	+	nuc	0	Nucleus (Potential)				355
Q8UVQ4 UniProt NPD GO	KAISO_XENLA	Transcriptional regulator Kaiso (Zinc finger and BTB domain-containing protein 33) (xKaiso)	0.74	-	nuc	0	Nucleus				701
O02008 UniProt NPD GO	TRA2_DROVI	Transformer-2 sex-determining protein	0.74	-	nuc	0					272
Q9Z1Y6 UniProt NPD GO	TGFB1_CAVPO	Transforming growth factor beta-1 precursor (TGF-beta-1) [Contains: Latency-associated peptide (LAP) ...	0.74	-	exc	0	Secreted protein				390
P04202 UniProt NPD GO	TGFB1_MOUSE	Transforming growth factor beta-1 precursor (TGF-beta-1) [Contains: Latency-associated peptide (LAP) ...	0.74	-	exc	0	Secreted protein	extracellular matrix (sensu Metazoa) [IDA]			390
P17125 UniProt NPD GO	TGFB3_MOUSE	Transforming growth factor beta-3 precursor (TGF-beta-3)	0.74	-	mit	0	Secreted protein				410
P51257 UniProt NPD GO	IF2C_PORPU	Translation initiation factor IF-2, chloroplast	0.74	-	nuc	0	Plastid; chloroplast				763
Q14258 UniProt NPD GO	TRI25_HUMAN	Tripartite motif-containing protein 25 (Zinc finger protein 147) (Estrogen-responsive finger protein ...	0.74	-	nuc	0			600453		630
Q8BGE7 UniProt NPD GO	TRIM6_MOUSE	Tripartite motif-containing protein 6	0.74	-	nuc	0		cytoplasm [IDA]			488
P19429 UniProt NPD GO	TNNI3_HUMAN	Troponin I, cardiac muscle (Cardiac troponin I)	0.74	-	nuc	0		troponin complex [TAS]	115210	1MXL	209
P23693 UniProt NPD GO	TNNI3_RAT	Troponin I, cardiac muscle (Cardiac troponin I)	0.74	-	nuc	0		cytoplasm [IDA] sarcomere [IDA] troponin complex [TAS]			210
Q16206 UniProt NPD GO	COVA1_HUMAN	Tumor-associated hydroquinone oxidase (tNOX) (Cytosolic ovarian carcinoma antigen 1) (APK1 antigen) ...	0.74	-	nuc	0	Cell membrane. Secreted protein; extracellular space. Extracellular and plasma membrane-associated	cytosol [TAS] external side of plasma membrane [IDA]	300282		610
Q84MA2 UniProt NPD GO	IP5P1_ARATH	Type I inositol-1,4,5-trisphosphate 5-phosphatase 1 (EC 3.1.3.56) (At5PTase1)	0.74	-	nuc	0					590
P42682 UniProt NPD GO	TXK_MOUSE	Tyrosine-protein kinase TXK (EC 2.7.10.2) (PTK-RL-18) (Resting lymphocyte kinase)	0.74	-	mit	0	Cytoplasm (Probable)				527
Q24592 UniProt NPD GO	JAK_DROME	Tyrosine-protein kinase hopscotch (EC 2.7.10.2)	0.74	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein. Wholly intracellular, possibly membrane asso ...	cytoplasm [TAS]			1177
P29461 UniProt NPD GO	PTP2_YEAST	Tyrosine-protein phosphatase 2 (EC 3.1.3.48) (Protein-tyrosine phosphatase 2) (PTPase 2)	0.74	-	nuc	0	Cytoplasm	nucleus [IDA]			750
Q8ISC9 UniProt NPD GO	CSW_DROSI	Tyrosine-protein phosphatase corkscrew (EC 3.1.3.48) (Fragment)	0.74	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			555
Q24708 UniProt NPD GO	CSW_DROVI	Tyrosine-protein phosphatase corkscrew (EC 3.1.3.48) (Fragment)	0.74	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			764
P32605 UniProt NPD GO	RU1A_YEAST	U1 small nuclear ribonucleoprotein A (U1 snRNP protein A) (U1-A)	0.74	+	nuc	0		snRNP U1 [IDA]			298

You are viewing entries 12101 to 12150 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.