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
Q9D9C7 UniProt NPD GO	CC062_MOUSE	Protein C3orf62 homolog	0.74	-	nuc	0					252
Q5R4W4 UniProt NPD GO	CF062_PONPY	Protein C6orf62 homolog	0.74	+	nuc	0					229
Q6AYM0 UniProt NPD GO	CG031_RAT	Protein C7orf31 homolog	0.74	-	nuc	0					588
Q8VCE4 UniProt NPD GO	CI040_MOUSE	Protein C9orf40 homolog	0.74	-	mit	0					163
Q5RCP1 UniProt NPD GO	CI097_PONPY	Protein C9orf97 homolog	0.74	-	nuc	0					516
P53280 UniProt NPD GO	CF130_YEAST	Protein CAF130 (130 kDa CCR4-associated factor)	0.74	-	nuc	1	Cytoplasm (Probable). Nucleus (Probable)	CCR4-NOT complex [IPI]			1122
Q07897 UniProt NPD GO	CMS1_YEAST	Protein CMS1 (Complementation of MCM10 suppressor protein 1)	0.74	+	nuc	0	Nucleus	nucleus [IDA]			291
P38637 UniProt NPD GO	DBF8_YEAST	Protein DBF8	0.74	-	nuc	0		nucleus [IDA]			319
Q52LJ0 UniProt NPD GO	FA98B_HUMAN	Protein FAM98B	0.74	-	nuc	0					330
Q15018 UniProt NPD GO	K0157_HUMAN	Protein KIAA0157	0.74	-	nuc	0					415
Q96RT1 UniProt NPD GO	LAP2_HUMAN	Protein LAP2 (Erbb2-interacting protein) (Erbin) (Densin-180-like protein)	0.74	-	nuc	0	Cell membrane; cell-cell junction; hemidesmosome. Found in hemidesmosomes, which are cell-substrate ...	cytoplasm [IDA] hemidesmosome [IDA] nucleus [IDA]	606944	1N7T	1412
Q5AI80 UniProt NPD GO	VTS1_CANAL	Protein VTS1	0.74	-	nuc	0	Cytoplasm (By similarity)				679
Q4P965 UniProt NPD GO	VTS1_USTMA	Protein VTS1	0.74	-	mit	0	Cytoplasm (By similarity)				728
Q6CHK0 UniProt NPD GO	VTS1_YARLI	Protein VTS1	0.74	-	nuc	0	Cytoplasm (By similarity)				437
Q32N19 UniProt NPD GO	ZN750_XENLA	Protein ZNF750	0.74	-	nuc	0					674
O04379 UniProt NPD GO	AGO1_ARATH	Protein argonaute	0.74	+	nuc	0	Cytoplasm (Potential)				1048
P19102 UniProt NPD GO	ETS2A_XENLA	Protein c-ets-2-A (C-ets-2A)	0.74	+	nuc	0	Nucleus				472
Q96RT6 UniProt NPD GO	CTGE2_HUMAN	Protein cTAGE-2	0.74	-	nuc	1 *			608856		754
Q03921 UniProt NPD GO	DOP1_YEAST	Protein dopey	0.74	+	nuc	0	Golgi apparatus; Golgi membrane; single-pass membrane protein. Early Golgi	cytoplasm [IDA] Golgi membrane [IDA] mitochondrion [IDA]			1698
O62537 UniProt NPD GO	HUNB_DROOR	Protein hunchback	0.74	-	nuc	0	Nucleus (By similarity)				767
O62538 UniProt NPD GO	HUNB_DROSE	Protein hunchback	0.74	-	nuc	0	Nucleus (By similarity)				757
O62541 UniProt NPD GO	HUNB_DROYA	Protein hunchback	0.74	-	nuc	0	Nucleus (By similarity)				759
Q01791 UniProt NPD GO	HUNB_TRICA	Protein hunchback	0.74	-	nuc	0	Nucleus (Probable)				524
Q6DDH0 UniProt NPD GO	PP1RB_XENLA	Protein phosphatase 1 regulatory subunit 11	0.74	+	nuc	0					119
Q96I34 UniProt NPD GO	PP16A_HUMAN	Protein phosphatase 1 regulatory subunit 16A (Myosin phosphatase-targeting subunit 3)	0.74	-	nuc	0	Cell membrane; lipid-anchor (By similarity)		609172		528
P36872 UniProt NPD GO	2ABA_DROME	Protein phosphatase PP2A 55 kDa regulatory subunit (Protein phosphatase PP2A regulatory subunit B) ( ...	0.74	-	nuc	0		cytoplasm [IDA] protein phosphatase type 2A complex [IDA]			499
Q9N3X8 UniProt NPD GO	SDK_CAEEL	Protein sidekick homolog precursor (Neuronal IgCAM protein 4)	0.74	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				2325
P32033 UniProt NPD GO	YCF2_CUSRE	Protein ycf2	0.74	-	nuc	0	Plastid; plastid stroma (By similarity)				740
Q9H6R0 UniProt NPD GO	DHX33_HUMAN	Putative ATP-dependent RNA helicase DHX33 (EC 3.6.1.-) (DEAH box protein 33)	0.74	+	mit	0	Nucleus; nucleolus				707
Q9SSM9 UniProt NPD GO	LBD7_ARATH	Putative LOB domain-containing protein 7	0.74	-	nuc	0					214
Q9NA56 UniProt NPD GO	TBX39_CAEEL	Putative T-box protein 39	0.74	-	nuc	0	Nucleus (Potential)				396
Q9NA55 UniProt NPD GO	TBX40_CAEEL	Putative T-box protein 40	0.74	-	nuc	0	Nucleus (Potential)				380
Q9FX25 UniProt NPD GO	ARFM_ARATH	Putative auxin response factor 13	0.74	-	nuc	0	Nucleus				623
Q9LRR5 UniProt NPD GO	DRL21_ARATH	Putative disease resistance protein At3g14460	0.74	-	nuc	0					1424
Q10328 UniProt NPD GO	YD73_SCHPO	Putative homeobox protein C32A11.03c in chromosome I	0.74	-	nuc	0	Nucleus (Potential)				942
Q25410 UniProt NPD GO	MIPR_LYMST	Putative molluscan insulin-related peptide(s) receptor precursor (EC 2.7.10.1) [Contains: Putative m ...	0.74	-	nuc	3 *	Membrane; single-pass type I membrane protein (By similarity)				1607
Q9D4M9 UniProt NPD GO	GLTL5_MOUSE	Putative polypeptide N-acetylgalactosaminyltransferase-like protein 5 (EC 2.4.1.-) (Protein-UDP acet ...	0.74	+	end	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				431
Q6DK85 UniProt NPD GO	KCNRG_XENTR	Putative potassium channel regulatory protein	0.74	-	mit	0					279
Q05999 UniProt NPD GO	KPK7_ARATH	Putative serine/threonine-protein kinase PK7 (EC 2.7.11.1)	0.74	-	nuc	0					578
P52652 UniProt NPD GO	TFS2_CAEEL	Putative transcription elongation factor S-II (TFIIS)	0.74	-	nuc	0	Nucleus (By similarity)				308
Q5UE90 UniProt NPD GO	RSPO2_XENLA	R-spondin-2 precursor (Roof plate-specific spondin-2) (XRspo2)	0.74	+	nuc	0	Secreted protein				243
Q8NHY2 UniProt NPD GO	RFWD2_HUMAN	RING finger and WD repeat domain protein 2 (EC 6.3.2.-) (Ubiquitin-protein ligase COP1) (Constitutiv ...	0.74	-	mit	0	Nucleus; nucleoplasm; nuclear speckle. Cytoplasm. In the nucleus, it forms nuclear speckles		608067		731
O94941 UniProt NPD GO	RNF37_HUMAN	RING finger protein 37 (Ubiquitin-conjugating enzyme 7-interacting protein 5) (U-box domain-containi ...	0.74	-	nuc	0	Nucleus (By similarity)				541
Q5KJQ4 UniProt NPD GO	REXO4_CRYNE	RNA exonuclease 4 (EC 3.1.-.-)	0.74	-	nuc	0	Nucleus (By similarity)				408
Q9H5N1 UniProt NPD GO	RABE2_HUMAN	Rab GTPase-binding effector protein 2 (Rabaptin-5beta)	0.74	-	nuc	0	Cytoplasm. Endosome; early endosome				569
P47708 UniProt NPD GO	RP3A_MOUSE	Rabphilin-3A (Exophilin-1)	0.74	-	nuc	0					681
P47709 UniProt NPD GO	RP3A_RAT	Rabphilin-3A (Exophilin-1)	0.74	-	nuc	0		extrinsic to membrane [IDA] synaptic vesicle membrane [IDA]		3RPB	684
Q921Q7 UniProt NPD GO	RIN1_MOUSE	Ras and Rab interactor 1 (Ras interaction/interference protein 1)	0.74	-	nuc	0	Cytoplasm (By similarity). Membrane (By similarity). Some amount is membrane-associated (By similari ...				763
P97680 UniProt NPD GO	RIN1_RAT	Ras and Rab interactor 1 (Ras interaction/interference protein 1)	0.74	-	nuc	0	Cytoplasm (By similarity). Membrane (By similarity). Some amount is membrane-associated (By similari ...				774
Q9D0V7 UniProt NPD GO	RCAS1_MOUSE	Receptor-binding cancer antigen expressed on SiSo cells (Cancer-associated surface antigen RCAS1) (E ...	0.74	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type III membrane protein. Predominantly located in the ...				213

You are viewing entries 12001 to 12050 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.