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
P50616 UniProt NPD GO	TOB1_HUMAN	Tob1 protein (Transducer of erbB-2 1)	0.58	-	nuc	0			605523		345
Q8R5K6 UniProt NPD GO	TOB1_RAT	Tob1 protein (Transducer of erbB-2 1)	0.58	-	nuc	0					365
Q9JLF7 UniProt NPD GO	TLR5_MOUSE	Toll-like receptor 5 precursor	0.58	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				859
Q61312 UniProt NPD GO	AP2C_MOUSE	Transcription factor AP-2 gamma (AP2-gamma) (Activating enhancer-binding protein 2 gamma) (AP-2.2)	0.58	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			449
P97360 UniProt NPD GO	ETV6_MOUSE	Transcription factor ETV6 (ETS-related protein Tel1) (Tel) (ETS translocation variant 6)	0.58	-	nuc	0	Nucleus (By similarity)				485
Q61169 UniProt NPD GO	GATA6_MOUSE	Transcription factor GATA-6 (GATA-binding factor 6)	0.58	-	nuc	0	Nucleus	nucleus [IDA]			444
Q95JA5 UniProt NPD GO	GATA6_PIG	Transcription factor GATA-6 (GATA-binding factor 6)	0.58	-	nuc	0	Nucleus (By similarity)				446
Q9W7R5 UniProt NPD GO	SOX21_CHICK	Transcription factor SOX-21	0.58	+	mit	0	Nucleus (Potential)				280
O70494 UniProt NPD GO	SP3_MOUSE	Transcription factor Sp3	0.58	-	nuc	0	Nucleus	nucleus [IDA]			783
P70210 UniProt NPD GO	TEAD3_MOUSE	Transcriptional enhancer factor TEF-5 (TEA domain family member 3) (TEAD-3) (ETF-related factor 1) ( ...	0.58	-	nuc	0	Nucleus	transcription factor complex [IGI]			439
Q9ULS5 UniProt NPD GO	TMCC3_HUMAN	Transmembrane and coiled-coil domains protein 3	0.58	-	end	2	Membrane; multi-pass membrane protein (Potential)				477
Q6P9J9 UniProt NPD GO	TM16F_MOUSE	Transmembrane protein 16F	0.58	-	end	8	Membrane; multi-pass membrane protein (Probable)				911
Q99LG1 UniProt NPD GO	TMM51_MOUSE	Transmembrane protein 51	0.58	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				249
Q03337 UniProt NPD GO	TRS31_YEAST	Transport protein particle 31 kDa subunit (TRAPP 31 kDa subunit)	0.58	-	nuc	0		TRAPP complex [IDA]			283
Q28820 UniProt NPD GO	TRDN_RABIT	Triadin	0.58	-	nuc	1 *	Sarcoplasmic reticulum; sarcoplasmic reticulum membrane; single-pass type II membrane protein				705
Q9WV59 UniProt NPD GO	TRI17_RAT	Tripartite motif-containing protein 17 (Testis RING finger protein)	0.58	+	nuc	0					477
Q8R2Q0 UniProt NPD GO	TRI29_MOUSE	Tripartite motif-containing protein 29	0.58	+	nuc	0	Cytoplasm (By similarity). Colocalizes with intermediate filaments (By similarity)	cytoplasm [IDA]			587
Q8WV44 UniProt NPD GO	TRI41_HUMAN	Tripartite motif-containing protein 41	0.58	-	nuc	0					630
Q99PJ2 UniProt NPD GO	TRIM8_MOUSE	Tripartite motif-containing protein 8 (RING finger protein 27) (Glioblastoma-expressed RING finger p ...	0.58	-	nuc	0		nucleus [IDA]			551
P54401 UniProt NPD GO	TBG_ENTHI	Tubulin gamma chain (Gamma tubulin)	0.58	-	cyt	0					451
P25119 UniProt NPD GO	TNR1B_MOUSE	Tumor necrosis factor receptor superfamily member 1B precursor (Tumor necrosis factor receptor 2) (T ...	0.58	-	nuc	1	Membrane; single-pass type I membrane protein				474
Q80WY6 UniProt NPD GO	TNR1B_RAT	Tumor necrosis factor receptor superfamily member 1B precursor (Tumor necrosis factor receptor 2) (T ...	0.58	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				474
Q9FXD6 UniProt NPD GO	ARR11_ARATH	Two-component response regulator ARR11 (Receiver-like protein 3)	0.58	-	nuc	0	Nucleus				521
Q9BDE0 UniProt NPD GO	TYRO_GORGO	Tyrosinase precursor (EC 1.14.18.1) (Monophenol monooxygenase)	0.58	-	end	1	Melanosome; melanosomal membrane; single-pass type I membrane protein (By similarity)	integral to membrane [ISS] melanosome [ISS]			529
P14679 UniProt NPD GO	TYRO_HUMAN	Tyrosinase precursor (EC 1.14.18.1) (Monophenol monooxygenase) (Tumor rejection antigen AB) (SK29-AB ...	0.58	-	end	1	Melanosome; melanosomal membrane; single-pass type I membrane protein	Golgi-associated vesicle [TAS] integral to membrane [ISS] melanosome [ISS]	606952		529
Q03526 UniProt NPD GO	ITK_MOUSE	Tyrosine-protein kinase ITK/TSK (EC 2.7.10.2) (T-cell-specific kinase) (IL-2-inducible T-cell kinase ...	0.58	-	cyt	0	Cell membrane. Localizes to cell surface receptors in the plasma membrane after stimulation with res ...			2EU0	625
Q62689 UniProt NPD GO	JAK2_RAT	Tyrosine-protein kinase JAK2 (EC 2.7.10.2) (Janus kinase 2) (JAK-2)	0.58	-	cyt	0	Intracytoplasmic membrane; peripheral membrane protein. Wholly intracellular, possibly membrane asso ...				1132
Q09178 UniProt NPD GO	JAK1_CYPCA	Tyrosine-protein kinase Jak1 (EC 2.7.10.2) (Janus kinase 1) (Jak-1)	0.58	-	cyt	0	Intracytoplasmic membrane; peripheral membrane protein. Wholly intracellular, possibly membrane asso ...				1156
Q9V7P1 UniProt NPD GO	UTP18_DROME	U3 small nucleolar RNA-associated protein 18 homolog (WD repeat protein l(2)k07824)	0.58	-	nuc	0	Nucleus; nucleolus (By similarity)				506
P53276 UniProt NPD GO	UTP8_YEAST	U3 small nucleolar RNA-associated protein 8 (U3 snoRNA-associated protein 8)	0.58	-	nuc	0	Nucleus; nucleolus	small nucleolar ribonucleoprotein complex [IPI]			713
Q61JN8 UniProt NPD GO	UGTAP_CAEBR	UGA suppressor tRNA-associated protein homolog	0.58	+	nuc	0	Cytoplasm (By similarity)				482
Q03649 UniProt NPD GO	YM60_YEAST	UPF0017 protein YMR210W	0.58	-	cyt	0					449
P40826 UniProt NPD GO	UBP14_RABIT	Ubiquitin carboxyl-terminal hydrolase 14 (EC 3.1.2.15) (Ubiquitin thioesterase 14) (Ubiquitin-specif ...	0.58	-	mit	0					492
Q9QZL6 UniProt NPD GO	UBP21_MOUSE	Ubiquitin carboxyl-terminal hydrolase 21 (EC 3.1.2.15) (Ubiquitin thioesterase 21) (Ubiquitin-specif ...	0.58	-	nuc	0					566
Q9UK80 UniProt NPD GO	UBP21_HUMAN	Ubiquitin carboxyl-terminal hydrolase 21 (EC 3.1.2.15) (Ubiquitin thioesterase 21) (Ubiquitin-specif ...	0.58	-	nuc	0			604729		565
Q4V8W7 UniProt NPD GO	UBTD1_BRARE	Ubiquitin domain-containing protein 1	0.58	-	nuc	0					227
O70263 UniProt NPD GO	LNX1_MOUSE	Ubiquitin ligase LNX (EC 6.3.2.-) (Numb-binding protein 1) (Ligand of Numb-binding protein 1) (Ligan ...	0.58	-	nuc	0	Cytoplasm	cytoplasm [IDA]			728
O74201 UniProt NPD GO	UBC2_CANAL	Ubiquitin-conjugating enzyme E2 2 (EC 6.3.2.19) (Ubiquitin-protein ligase UBC2) (Ubiquitin carrier p ...	0.58	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				179
Q2T9X7 UniProt NPD GO	UB2E3_BOVIN	Ubiquitin-conjugating enzyme E2 E3 (EC 6.3.2.19) (Ubiquitin-protein ligase E3) (Ubiquitin carrier pr ...	0.58	-	nuc	0	Nucleus. Cytoplasm. Shuttles between the nucleus and cytoplasm in a IPO11-dependent manner (By simil ...				207
Q969T4 UniProt NPD GO	UB2E3_HUMAN	Ubiquitin-conjugating enzyme E2 E3 (EC 6.3.2.19) (Ubiquitin-protein ligase E3) (Ubiquitin carrier pr ...	0.58	-	nuc	0	Nucleus. Cytoplasm. Shuttles between the nucleus and cytoplasm in a IPO11-dependent manner		604151		207
P52483 UniProt NPD GO	UB2E3_MOUSE	Ubiquitin-conjugating enzyme E2 E3 (EC 6.3.2.19) (Ubiquitin-protein ligase E3) (Ubiquitin carrier pr ...	0.58	-	nuc	0	Nucleus. Cytoplasm. Shuttles between the nucleus and cytoplasm in a IPO11-dependent manner	nucleus [IDA]			207
P25866 UniProt NPD GO	UBC2_WHEAT	Ubiquitin-conjugating enzyme E2-17 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.58	-	nuc	0					152
Q7TT23 UniProt NPD GO	CT194_MOUSE	Uncharacterized protein C20orf194 homolog	0.58	-	nuc	0					1179
P38083 UniProt NPD GO	YBR3_YEAST	Uncharacterized protein YBR063C	0.58	-	nuc	0	Membrane; multi-pass membrane protein (Potential)				404
O13577 UniProt NPD GO	YL437_YEAST	Uncharacterized protein YLR437C	0.58	-	nuc	0		cytoplasm [IDA]			133
Q12179 UniProt NPD GO	YP245_YEAST	Uncharacterized protein YPL245W	0.58	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			454
P45644 UniProt NPD GO	VIP_MELGA	VIP peptides precursor [Contains: Intestinal peptide PHI-27-like; Vasoactive intestinal peptide (VIP ...	0.58	-	exc	0	Secreted protein				200
Q2HJ18 UniProt NPD GO	VP33B_BOVIN	Vacuolar protein sorting 33B	0.58	-	cyt	0	Late endosome; late endosomal membrane; peripheral membrane protein (By similarity). Lysosome; lysos ...				617
Q9VLC0 UniProt NPD GO	VPS54_DROME	Vacuolar protein sorting protein 54 (Protein scattered)	0.58	-	cyt	0		Golgi apparatus [ISS] mitochondrion [ISS]			940
O74552 UniProt NPD GO	VPS35_SCHPO	Vacuolar protein sorting-associated protein vps35	0.58	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				785

You are viewing entries 20501 to 20550 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.