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
Q9BQA6 UniProt NPD GO	TTY8_HUMAN	Transcript Y 8 protein	0.36	-	nuc	0					61
Q8STS7 UniProt NPD GO	ELOF1_ENCCU	Transcription elongation factor 1 homolog	0.36	-	mit	0	Nucleus (By similarity)				80
Q8IYN2 UniProt NPD GO	TCAL8_HUMAN	Transcription elongation factor A protein-like 8 (TCEA-like protein 8) (Transcription elongation fac ...	0.36	-	nuc	0	Nucleus (Probable)				117
Q96WN6 UniProt NPD GO	ACE2_TRIRE	Transcription factor ACEII	0.36	-	nuc	0	Nucleus (Probable)	nucleus [IC]			341
P48512 UniProt NPD GO	TF2B1_ARATH	Transcription initiation factor IIB-1 (General transcription factor TFIIB-1) (AtTFIIB1)	0.36	-	nuc	0	Nucleus				312
Q6PHK6 UniProt NPD GO	PURB_BRARE	Transcriptional activator protein Pur-beta (Purine-rich element-binding protein B)	0.36	-	nuc	0	Nucleus (By similarity)				296
Q9SHI1 UniProt NPD GO	IF2C_ARATH	Translation initiation factor IF-2, chloroplast precursor	0.36	-	mit	0	Plastid; chloroplast				1016
Q5AI21 UniProt NPD GO	SEC62_CANAL	Translocation protein SEC62	0.36	-	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				293
Q9P0I2 UniProt NPD GO	TM111_HUMAN	Transmembrane protein 111	0.36	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				260
Q99KI3 UniProt NPD GO	TM111_MOUSE	Transmembrane protein 111	0.36	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				260
Q5R7C1 UniProt NPD GO	TM111_PONPY	Transmembrane protein 111	0.36	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				260
Q5U2V8 UniProt NPD GO	TM111_RAT	Transmembrane protein 111	0.36	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				260
Q8K4K2 UniProt NPD GO	TRIB3_MOUSE	Tribbles homolog 3 (TRB-3) (Neuronal cell death-inducible putative kinase)	0.36	-	nuc	0	Nucleus	nucleus [IDA]			354
Q9C040 UniProt NPD GO	TRIM2_HUMAN	Tripartite motif-containing protein 2 (RING finger protein 86)	0.36	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [IEP]			744
Q60HH1 UniProt NPD GO	TPP1_MACFA	Tripeptidyl-peptidase 1 precursor (EC 3.4.14.9) (Tripeptidyl-peptidase I) (TPP-I) (Tripeptidyl amino ...	0.36	-	mit	0	Lysosome (By similarity)				563
P31816 UniProt NPD GO	TPM_LOCMI	Tropomyosin	0.36	-	nuc	0					283
Q9GZ69 UniProt NPD GO	TPM_MIMNO	Tropomyosin	0.36	-	nuc	0					284
Q8T6L5 UniProt NPD GO	TPM_PERFU	Tropomyosin	0.36	-	nuc	0					284
Q7SY53 UniProt NPD GO	T23O_BRARE	Tryptophan 2,3-dioxygenase (EC 1.13.11.11) (TO) (Tryptophan pyrrolase) (Tryptophanase) (Tryptophan o ...	0.36	-	cyt	0					407
Q5U4U6 UniProt NPD GO	T23O_XENLA	Tryptophan 2,3-dioxygenase (EC 1.13.11.11) (TO) (Tryptophan pyrrolase) (Tryptophanase) (Tryptophan o ...	0.36	-	cyt	0					406
Q91W27 UniProt NPD GO	TIP39_MOUSE	Tuberoinfundibular peptide of 39 residues precursor (TIP39)	0.36	-	mit	1 *	Secreted protein				100
P0C172 UniProt NPD GO	TIP39_RAT	Tuberoinfundibular peptide of 39 residues precursor (TIP39)	0.36	-	mit	1 *	Secreted protein				100
Q6FNU9 UniProt NPD GO	TBG_CANGA	Tubulin gamma chain (Gamma tubulin)	0.36	-	cyt	0					465
Q9Y4R7 UniProt NPD GO	TTLL3_HUMAN	Tubulin--tyrosine ligase-like protein 3 (HOTTL)	0.36	-	cyt	0					352
Q28205 UniProt NPD GO	TBCD_BOVIN	Tubulin-specific chaperone D (Tubulin-folding cofactor D) (Beta-tubulin cofactor D)	0.36	-	nuc	0					1199
O97557 UniProt NPD GO	TUFT1_PIG	Tuftelin (Fragment)	0.36	-	nuc	0	Secreted protein (By similarity). Secreted at a very early stage of enamel formation, and tightly bo ...	extracellular region [ISS]			188
Q9UNE0 UniProt NPD GO	EDAR_HUMAN	Tumor necrosis factor receptor superfamily member EDAR precursor (Anhidrotic ectodysplasin receptor ...	0.36	-	nuc	1	Membrane; single-pass type I membrane protein (Probable)	integral to membrane [NAS]	604095		448
Q99816 UniProt NPD GO	TS101_HUMAN	Tumor susceptibility gene 101 protein	0.36	-	nuc	0	Cytoplasm. Mainly. Membrane; peripheral membrane protein. Membrane-associated when active and solubl ...		601387	2F0R	390
Q9ZWS7 UniProt NPD GO	ARR7_ARATH	Two-component response regulator ARR7	0.36	-	nuc	0	Nucleus (Probable)				206
P18161 UniProt NPD GO	KYK2_DICDI	Tyrosine-protein kinase 2 (EC 2.7.10.2) (Fragment)	0.36	-	nuc	0					410
P55144 UniProt NPD GO	TYRO3_MOUSE	Tyrosine-protein kinase receptor TYRO3 precursor (EC 2.7.10.1) (Tyrosine-protein kinase RSE) (Tyrosi ...	0.36	+	end	2 *	Membrane; single-pass type I membrane protein				880
Q06418 UniProt NPD GO	TYRO3_HUMAN	Tyrosine-protein kinase receptor TYRO3 precursor (EC 2.7.10.1) (Tyrosine-protein kinase RSE) (Tyrosi ...	0.36	+	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	600341	1RHF	890
P30530 UniProt NPD GO	UFO_HUMAN	Tyrosine-protein kinase receptor UFO precursor (EC 2.7.10.1) (AXL oncogene)	0.36	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	109135	2C5D	887
P54829 UniProt NPD GO	PTN5_HUMAN	Tyrosine-protein phosphatase non-receptor type 5 (EC 3.1.3.48) (Protein-tyrosine phosphatase striatu ...	0.36	-	mit	1		integral to membrane [TAS]	176879	2CJZ	541
Q96G21 UniProt NPD GO	IMP4_HUMAN	U3 small nucleolar ribonucleoprotein protein IMP4 (U3 snoRNP protein IMP4) (Brix domain-containing p ...	0.36	-	mit	0	Nucleus; nucleolus	nucleolus [IDA]			291
Q9PTQ4 UniProt NPD GO	UTS1_CARAU	UI precursor [Contains: Urophysin; Urotensin-1 (Urotensin I)]	0.36	-	exc	0	Secreted protein				145
Q22915 UniProt NPD GO	YC4P_CAEEL	UPF0103 protein C37C3.8	0.36	-	mit	0					350
P54727 UniProt NPD GO	RD23B_HUMAN	UV excision repair protein RAD23 homolog B (hHR23B) (XP-C repair-complementing complex 58 kDa protei ...	0.36	-	nuc	0	Nucleus (Probable)	nucleus [TAS]	600062	1UEL	409
Q5R597 UniProt NPD GO	UCRQ_PONPY	Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C (EC 1.10.2.2) (Ubiquinol-cy ...	0.36	-	cyt	0	Mitochondrion; mitochondrial inner membrane				81
P54201 UniProt NPD GO	UBPA_DICDI	Ubiquitin carboxyl-terminal hydrolase A (EC 3.1.2.15) (Ubiquitin thioesterase A) (Ubiquitin-specific ...	0.36	-	nuc	0					837
Q5EAE3 UniProt NPD GO	UBTD2_BOVIN	Ubiquitin domain-containing protein 2	0.36	-	nuc	0	Cytoplasm (By similarity)				234
Q6TEM9 UniProt NPD GO	MYLIP_BRARE	Ubiquitin ligase MYLIP (EC 6.3.2.-) (Myosin regulatory light chain-interacting protein) (MIR)	0.36	-	nuc	0	Cytoplasm (Probable)	cytoplasm [IDA]			472
Q38HM4 UniProt NPD GO	TRI63_MOUSE	Ubiquitin ligase TRIM63 (EC 6.3.2.-) (Tripartite motif-containing protein 63) (Muscle-specific RING ...	0.36	-	nuc	0	Cytoplasm. Nucleus. Localizes to the M- and Z-lines in skeletal muscle (By similarity). Colocalizes ...				350
Q9Y3Y2 UniProt NPD GO	CA077_HUMAN	Uncharacterized protein C1orf77	0.36	+	nuc	0					248
Q3SYW9 UniProt NPD GO	CA077_BOVIN	Uncharacterized protein C1orf77 homolog	0.36	+	nuc	0					248
Q9CY57 UniProt NPD GO	CA077_MOUSE	Uncharacterized protein C1orf77 homolog	0.36	+	nuc	0					249
Q498T2 UniProt NPD GO	CA077_RAT	Uncharacterized protein C1orf77 homolog	0.36	+	nuc	0					248
Q80YU0 UniProt NPD GO	CT135_MOUSE	Uncharacterized protein C20orf135 homolog	0.36	-	mit	0					474
Q5R4U5 UniProt NPD GO	CB024_PONPY	Uncharacterized protein C2orf24 homolog	0.36	-	nuc	0					410
Q8TB03 UniProt NPD GO	CX038_HUMAN	Uncharacterized protein CXorf38	0.36	-	mit	0					319

You are viewing entries 35451 to 35500 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.