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
Q6CWW9 UniProt NPD GO	SPT5_KLULA	Transcription elongation factor SPT5 (Chromatin elongation factor SPT5)	0.78	-	nuc	0	Nucleus (By similarity)				1036
Q99081 UniProt NPD GO	HTF4_HUMAN	Transcription factor 12 (Transcription factor HTF-4) (E-box-binding protein) (DNA-binding protein HT ...	0.78	-	nuc	0	Nucleus		600480		682
O54792 UniProt NPD GO	HES2_MOUSE	Transcription factor HES-2 (Hairy and enhancer of split 2)	0.78	-	nuc	0	Nucleus				157
P51509 UniProt NPD GO	RELB_CHICK	Transcription factor RelB homolog	0.78	-	nuc	0	Nucleus				549
P38889 UniProt NPD GO	SKN7_YEAST	Transcription factor SKN7 (Peroxide sensitivity protein POS9)	0.78	-	nuc	0	Nucleus	nucleus [IDA]			622
P35713 UniProt NPD GO	SOX18_HUMAN	Transcription factor SOX-18	0.78	+	nuc	0	Nucleus (Potential)		607823		384
P06774 UniProt NPD GO	HAP2_YEAST	Transcriptional activator HAP2	0.78	+	nuc	0	Nucleus	CCAAT-binding factor complex [TAS] nucleus [IDA]			265
O42804 UniProt NPD GO	XLNR_ASPNG	Transcriptional activator xlnR	0.78	-	nuc	0	Nucleus				875
Q5ZJF3 UniProt NPD GO	TAD2L_CHICK	Transcriptional adapter 2-like (ADA2-like protein)	0.78	+	nuc	0	Nucleus (By similarity)				446
Q9JHB5 UniProt NPD GO	TSNAX_RAT	Translin-associated protein X (Translin-associated factor X)	0.78	-	nuc	0	Nucleus				290
Q9BYT9 UniProt NPD GO	TM16C_HUMAN	Transmembrane protein 16C	0.78	-	end	8	Membrane; multi-pass membrane protein (Probable)				981
Q80X80 UniProt NPD GO	TMM24_MOUSE	Transmembrane protein 24	0.78	-	nuc	1 *					706
Q9D2H5 UniProt NPD GO	TRI42_MOUSE	Tripartite motif-containing protein 42	0.78	-	nuc	0					723
Q9JLV2 UniProt NPD GO	TP4AP_MOUSE	Trpc4-associated protein (Trp4-associated protein) (Short transient receptor potential channel 4-ass ...	0.78	-	nuc	0		cytosol [ISS] endoplasmic reticulum lumen [ISS]			797
Q9Z273 UniProt NPD GO	TULP1_MOUSE	Tubby-related protein 1 (Tubby-like protein 1)	0.78	+	nuc	0					543
Q09778 UniProt NPD GO	TSC1_SCHPO	Tuberous sclerosis 1 protein homolog	0.78	-	nuc	0					899
O08727 UniProt NPD GO	TR11B_RAT	Tumor necrosis factor receptor superfamily member 11B precursor (Osteoprotegerin)	0.78	-	exc	0	Secreted protein (By similarity)				401
P55025 UniProt NPD GO	TYRO_ORYLA	Tyrosinase precursor (EC 1.14.18.1) (Monophenol monooxygenase)	0.78	+	end	1	Melanosome; melanosomal membrane; single-pass type I membrane protein				540
Q62130 UniProt NPD GO	PTN14_MOUSE	Tyrosine-protein phosphatase non-receptor type 14 (EC 3.1.3.48) (Protein-tyrosine phosphatase PTP36) ...	0.78	-	nuc	0					1189
Q06180 UniProt NPD GO	PTN2_MOUSE	Tyrosine-protein phosphatase non-receptor type 2 (EC 3.1.3.48) (Protein-tyrosine phosphatase PTP-2) ...	0.78	-	nuc	1	Cytoplasm				406
O14048 UniProt NPD GO	UBX2_SCHPO	UBX domain-containing protein 2	0.78	+	nuc	0					427
P53874 UniProt NPD GO	UBP10_YEAST	Ubiquitin carboxyl-terminal hydrolase 10 (EC 3.1.2.15) (Ubiquitin thioesterase 10) (Ubiquitin-specif ...	0.78	-	nuc	0		nucleus [IDA]			792
Q99K46 UniProt NPD GO	UBP11_MOUSE	Ubiquitin carboxyl-terminal hydrolase 11 (EC 3.1.2.15) (Ubiquitin thioesterase 11) (Ubiquitin-specif ...	0.78	-	nuc	0	Nucleus (By similarity)				797
Q01477 UniProt NPD GO	UBP3_YEAST	Ubiquitin carboxyl-terminal hydrolase 3 (EC 3.1.2.15) (Ubiquitin thioesterase 3) (Ubiquitin-specific ...	0.78	-	nuc	0		cytoplasm [IC]			912
Q8NFA0 UniProt NPD GO	UBP32_HUMAN	Ubiquitin carboxyl-terminal hydrolase 32 (EC 3.1.2.15) (Ubiquitin thioesterase 32) (Ubiquitin-specif ...	0.78	-	nuc	0			607740		1604
O22207 UniProt NPD GO	UBP5_ARATH	Ubiquitin carboxyl-terminal hydrolase 5 (EC 3.1.2.15) (Ubiquitin thioesterase 5) (Ubiquitin-specific ...	0.78	-	nuc	0					924
Q68FV8 UniProt NPD GO	UBTD1_RAT	Ubiquitin domain-containing protein 1	0.78	+	nuc	0					227
Q96T88 UniProt NPD GO	UHRF1_HUMAN	Ubiquitin-like PHD and RING finger domain-containing protein 1 (EC 6.3.2.-) (Ubiquitin-like-containi ...	0.78	-	nuc	0	Nucleus		607990	2FAZ	793
Q96EP1 UniProt NPD GO	CHFR_HUMAN	Ubiquitin-protein ligase CHFR (EC 6.3.2.-) (Checkpoint with forkhead and RING finger domains protein ...	0.78	-	nuc	0	Nucleus		605209	1LGQ	664
O70481 UniProt NPD GO	UBR1_MOUSE	Ubiquitin-protein ligase E3 component N-recognin-1 (EC 6.-.-.-) (Ubiquitin-protein ligase E3-alpha-1 ...	0.78	+	end	0	Cytoplasm; cytosol (By similarity)	proteasome complex (sensu Eukaryota) [IGI] ubiquitin ligase complex [IGI]			1757
O74563 UniProt NPD GO	BRE1_SCHPO	Ubiquitin-protein ligase bre1 (EC 6.3.2.-)	0.78	-	nuc	0	Nucleus (By similarity)				680
O13863 UniProt NPD GO	YDU2_SCHPO	Uncharacterized kinase C1B1.02c (EC 2.7.1.-)	0.78	-	nuc	0					537
Q9NX31 UniProt NPD GO	CT111_HUMAN	Uncharacterized protein C20orf111	0.78	-	nuc	0					292
Q5RD08 UniProt NPD GO	CT111_PONPY	Uncharacterized protein C20orf111 homolog	0.78	-	nuc	0					292
Q9CYC5 UniProt NPD GO	CT172_MOUSE	Uncharacterized protein C20orf172 homolog	0.78	-	nuc	0	Nucleus (By similarity). Associated with the kinetochore (By similarity)				348
Q8IW19 UniProt NPD GO	CB013_HUMAN	Uncharacterized protein C2orf13	0.78	-	nuc	0					511
Q07555 UniProt NPD GO	YD129_YEAST	Uncharacterized protein YDL129W	0.78	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			291
Q07684 UniProt NPD GO	YD233_YEAST	Uncharacterized protein YDL233W	0.78	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			458
P53061 UniProt NPD GO	YGZ9_YEAST	Uncharacterized protein YGL249W	0.78	-	nuc	0		synaptonemal complex [IDA]			704
Q06251 UniProt NPD GO	YL177_YEAST	Uncharacterized protein YLR177W	0.78	-	nuc	0	Cytoplasm	cytoplasm [IDA]			628
Q5WR09 UniProt NPD GO	VATG1_CANFA	Vacuolar ATP synthase subunit G 1 (EC 3.6.3.14) (V-ATPase G subunit 1) (Vacuolar proton pump G subun ...	0.78	-	nuc	0					117
Q9CR51 UniProt NPD GO	VATG1_MOUSE	Vacuolar ATP synthase subunit G 1 (EC 3.6.3.14) (V-ATPase G subunit 1) (Vacuolar proton pump G subun ...	0.78	-	nuc	0		hydrogen-translocating V-type ATPase complex [IPI] intracellular [IDA] lysosomal membrane [IDA]			117
P87295 UniProt NPD GO	PEP5_SCHPO	Vacuolar membrane protein pep5 (Vacuolar protein sorting 11)	0.78	-	cyt	0					860
Q05919 UniProt NPD GO	VPS38_YEAST	Vacuolar protein sorting protein 38	0.78	-	nuc	0	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; peripheral membrane protein. End ...				439
Q92331 UniProt NPD GO	VPS5_YEAST	Vacuolar protein sorting-associated protein VPS5	0.78	-	nuc	0	Cytoplasm	cytosol [IDA] endosome [IDA] retromer complex [TAS]			675
Q9NNX9 UniProt NPD GO	VCX3_HUMAN	Variable charge X-linked protein 3 (VCX-A protein) (Variably charged protein X-A) (Variable charge p ...	0.78	-	nuc	0		nucleolus [ISS] nucleus [ISS]	300229		186
P34374 UniProt NPD GO	UNC36_CAEEL	Voltage-dependent calcium channel unc-36 precursor (Uncoordinated protein 36)	0.78	-	exc	0					1249
Q6EE22 UniProt NPD GO	ZC3H5_CANFA	Zinc finger CCCH domain-containing protein 5	0.78	-	nuc	0					810
Q8BL48 UniProt NPD GO	ZC3H5_MOUSE	Zinc finger CCCH domain-containing protein 5	0.78	-	nuc	0	Nucleus (Probable)				810
Q9UGI0 UniProt NPD GO	ZRAN1_HUMAN	Zinc finger Ran-binding domain-containing protein 1 (Protein TRABID)	0.78	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			708

You are viewing entries 10151 to 10200 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.