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
P01831 UniProt NPD GO	THY1_MOUSE	Thy-1 membrane glycoprotein precursor (Thy-1 antigen) (CD90 antigen) (CDw90 antigen)	0.46	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	cytosol [ISS] external side of plasma membrane [IDA] growth cone [ISS] lipid raft [ISS] plasma membrane [ISS]			162
P11214 UniProt NPD GO	TPA_MOUSE	Tissue-type plasminogen activator precursor (EC 3.4.21.68) (tPA) (t-PA) (t-plasminogen activator) [C ...	0.46	-	end	0	Secreted protein; extracellular space	apical part of cell [IDA] cytoplasm [IDA] extracellular space [IDA] secretory granule [IDA]			559
Q14106 UniProt NPD GO	TOB2_HUMAN	Tob2 protein (Transducer of erbB-2 2)	0.46	-	nuc	0	Cytoplasm	nucleus [TAS]	607396		344
Q9JM55 UniProt NPD GO	TOB2_MOUSE	Tob2 protein (Transducer of erbB-2 2)	0.46	-	nuc	0					345
Q9EPQ1 UniProt NPD GO	TLR1_MOUSE	Toll-like receptor 1 precursor (Toll/interleukin-1 receptor-like protein) (TIL) (CD281 antigen)	0.46	-	end	2 *	Cell membrane; single-pass type I membrane protein. Phagosome; phagosomal membrane; single-pass type ...	membrane [NAS] phagocytic vesicle [NAS]			795
Q5I2M3 UniProt NPD GO	TLR9_PIG	Toll-like receptor 9 precursor (CD289 antigen)	0.46	-	end	0	Membrane; single-pass type I membrane protein (By similarity)				1030
P58911 UniProt NPD GO	TX60A_PHYSE	Toxin PsTX-60A precursor	0.46	-	exc	0	Secreted protein. Found in nematocyst				501
Q58DF3 UniProt NPD GO	TRABD_BOVIN	TraB domain-containing protein	0.46	-	cyt	0					377
Q9SMH4 UniProt NPD GO	RAA2_CHLRE	Trans-splicing factor Raa2, chloroplast precursor	0.46	-	mit	0	Plastid; chloroplast. Associated with low density membranes				410
Q99990 UniProt NPD GO	VGLL1_HUMAN	Transcription cofactor vestigial-like protein 1 (Vgl-1) (Protein TONDU)	0.46	-	nuc	0	Nucleus	nucleus [NAS]			258
P40647 UniProt NPD GO	SOX5_XENLA	Transcription factor SOX-5 (xSOX-5) (Fragment)	0.46	-	nuc	0	Nucleus (Potential)				54
Q62441 UniProt NPD GO	TLE4_MOUSE	Transducin-like enhancer protein 4 (Groucho-related protein 4) (Grg-4)	0.46	-	nuc	0	Nucleus (Probable)	nucleus [IC]			766
Q9JJ11 UniProt NPD GO	TACC3_MOUSE	Transforming acidic coiled-coil-containing protein 3 (ARNT-interacting protein)	0.46	-	nuc	0	Cytoplasm	centrosome [IDA] cytoplasm [IDA]			631
Q8BLA8 UniProt NPD GO	TRPA1_MOUSE	Transient receptor potential cation channel subfamily A member 1 (Ankyrin-like with transmembrane do ...	0.46	-	end	5	Membrane; multi-pass membrane protein (Probable)				1125
Q7TN58 UniProt NPD GO	TMC8_MOUSE	Transmembrane channel-like protein 8 (Epidermodysplasia verruciformis protein 2 homolog)	0.46	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				722
Q8BIK6 UniProt NPD GO	TMPS7_MOUSE	Transmembrane protease, serine 7 precursor (EC 3.4.21.-)	0.46	-	nuc	0					572
Q5E9G4 UniProt NPD GO	TRI10_BOVIN	Tripartite motif-containing protein 10	0.46	-	cyt	0	Cytoplasm (By similarity)				489
O19085 UniProt NPD GO	TRI10_PIG	Tripartite motif-containing protein 10 (RING finger protein 9) (B30-RING finger protein)	0.46	-	cyt	0					482
Q96DX7 UniProt NPD GO	TRI44_HUMAN	Tripartite motif-containing protein 44 (Protein DIPB)	0.46	-	nuc	0					344
Q58D15 UniProt NPD GO	TRI54_BOVIN	Tripartite motif-containing protein 54	0.46	-	nuc	0	Cytoplasm (By similarity). Associates with microtubules. Localizes to the Z-lines in skeletal muscle ...				366
Q29RQ5 UniProt NPD GO	TRIM9_BOVIN	Tripartite motif-containing protein 9	0.46	-	nuc	0					710
Q91ZY8 UniProt NPD GO	TRIM9_RAT	Tripartite motif-containing protein 9 (SNAP-25-interacting RING finger protein)	0.46	-	nuc	0	Enriched at synaptic terminals where it exists in a soluble form and a synaptic vesicle-associated f ...	synaptic vesicle [IDA]			710
Q6S9E0 UniProt NPD GO	TTP_SHEEP	Tristetraproline (TTP) (Zinc finger protein 36 homolog) (Zfp-36)	0.46	-	nuc	0	Nucleus (By similarity)				325
P28289 UniProt NPD GO	TMOD1_HUMAN	Tropomodulin-1 (Erythrocyte tropomodulin) (E-Tmod)	0.46	-	nuc	0			190930		359
P13413 UniProt NPD GO	TNNI1_RAT	Troponin I, slow skeletal muscle (Troponin I, slow-twitch isoform)	0.46	-	nuc	0					186
Q5R7N2 UniProt NPD GO	TWF1_PONPY	Twinfilin-1	0.46	-	nuc	0	Cytoplasm. Diffuse cytoplasmic localization with perinuclear and G-actin-rich cortical actin structu ...				350
O82798 UniProt NPD GO	ARR4_ARATH	Two-component response regulator ARR4 (Response regulator 1)	0.46	-	nuc	0	Nucleus (Probable)				259
Q6QN11 UniProt NPD GO	IOD3_PIG	Type III iodothyronine deiodinase (EC 1.97.1.11) (Type-III 5'deiodinase) (DIOIII) (Type 3 DI) (5DIII ...	0.46	-	end	0	Cell membrane; single-pass type II membrane protein (By similarity). Endosome; endosomal membrane; s ...				278
P25911 UniProt NPD GO	LYN_MOUSE	Tyrosine-protein kinase Lyn (EC 2.7.10.2)	0.46	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			511
Q9BZV1 UniProt NPD GO	UBXD1_HUMAN	UBX domain-containing protein 1	0.46	-	cyt	0					441
Q5RJV0 UniProt NPD GO	COQ9_XENTR	Ubiquinone biosynthesis protein COQ9, mitochondrial precursor	0.46	+	mit	0	Mitochondrion (By similarity)				317
Q5XIS7 UniProt NPD GO	UBAP1_RAT	Ubiquitin-associated protein 1 (UBAP)	0.46	-	nuc	0					502
Q91W67 UniProt NPD GO	UBL7_MOUSE	Ubiquitin-like protein 7	0.46	-	nuc	0				1X1M	380
Q7Z3Z2 UniProt NPD GO	CA036_HUMAN	Uncharacterized protein C1orf36	0.46	-	nuc	0					195
Q5XII8 UniProt NPD GO	CA043_RAT	Uncharacterized protein C1orf43 homolog	0.46	-	nuc	1 *					235
Q08187 UniProt NPD GO	YO029_YEAST	Uncharacterized protein YOL029C	0.46	-	nuc	0					201
Q969E3 UniProt NPD GO	UCN3_HUMAN	Urocortin-3 precursor (Urocortin III) (Ucn III) (Stresscopin)	0.46	-	nuc	0	Secreted protein		605901		161
Q8BVE3 UniProt NPD GO	VATH_MOUSE	Vacuolar ATP synthase subunit H (EC 3.6.3.14) (V-ATPase H subunit) (Vacuolar proton pump subunit H)	0.46	-	cyt	0					483
O74981 UniProt NPD GO	YJZ2_SCHPO	Very hypothetical protein C338.02 in chromosome III	0.46	-	nuc	0					125
O88384 UniProt NPD GO	VTI1B_MOUSE	Vesicle transport through interaction with t-SNAREs homolog 1B (Vesicle transport v-SNARE protein Vt ...	0.46	-	nuc	1	Membrane; single-pass type IV membrane protein (By similarity)	Golgi apparatus [IDA]		1GL2	232
O81645 UniProt NPD GO	VILI3_ARATH	Villin-3	0.46	-	cyt	0					966
P12003 UniProt NPD GO	VINC_CHICK	Vinculin (Metavinculin)	0.46	-	nuc	0	Cytoskeleton. Cell membrane; cell-cell junction; adherens junction; cytoplasmic side. Cell membrane; ...	adherens junction [ISS] costamere [ISS] focal adhesion [ISS] intercellular junction [ISS]		1ZW3	1134
P18206 UniProt NPD GO	VINC_HUMAN	Vinculin (Metavinculin)	0.46	-	nuc	0	Cytoskeleton. Cell membrane; cell-cell junction; adherens junction; cytoplasmic side. Cell membrane; ...	adherens junction [ISS] cell-matrix junction [NAS] costamere [ISS] cytoskeleton [TAS] focal adhesion [ISS] intercellular junction [ISS] protein complex [IDA]	193065	1TR2	1133
P33587 UniProt NPD GO	PROC_MOUSE	Vitamin K-dependent protein C precursor (EC 3.4.21.69) (Autoprothrombin IIA) (Anticoagulant protein ...	0.46	-	end	0		extracellular region [ISS]			460
Q99244 UniProt NPD GO	CAC1D_MESAU	Voltage-dependent L-type calcium channel subunit alpha-1D (Voltage-gated calcium channel subunit alp ...	0.46	-	end	19	Membrane; multi-pass membrane protein				1610
O60840 UniProt NPD GO	CAC1F_HUMAN	Voltage-dependent L-type calcium channel subunit alpha-1F (Voltage-gated calcium channel subunit alp ...	0.46	+	end	19	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]	300110		1966
Q9JIS7 UniProt NPD GO	CAC1F_MOUSE	Voltage-dependent L-type calcium channel subunit alpha-1F (Voltage-gated calcium channel subunit alp ...	0.46	+	end	19	Membrane; multi-pass membrane protein				1985
Q5J3K9 UniProt NPD GO	V1A14_RAT	Vomeronasal type-1 receptor A14	0.46	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				339
Q2HJH6 UniProt NPD GO	WDR57_BOVIN	WD repeat protein 57	0.46	-	mit	0	Nucleus (By similarity)				358
O22607 UniProt NPD GO	MSI4_ARATH	WD-40 repeat protein MSI4 (Altered cold-responsive gene 1 protein)	0.46	-	nuc	0	Nucleus				507

You are viewing entries 28001 to 28050 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.