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
O43031 UniProt NPD GO	SPP2_SCHPO	Pre-mRNA-splicing factor spp2 (Complexed with cdc5 protein 28) (Cell cycle control protein cwf28)	0.94	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				381
P40328 UniProt NPD GO	TBP6_YEAST	Probable 26S protease subunit YTA6 (TAT-binding homolog 6)	0.94	-	nuc	0		cell cortex [IDA]			754
P38760 UniProt NPD GO	YHH5_YEAST	Probable RNA-binding protein YHR015W	0.94	-	nuc	0		nuclear pore [IPI]			659
Q8S1Z1 UniProt NPD GO	UTP11_ORYSA	Probable U3 small nucleolar RNA-associated protein 11 (U3 snoRNA-associated protein 11)	0.94	-	nuc	0	Nucleus; nucleolus (By similarity)				229
Q9FLX8 UniProt NPD GO	WRK27_ARATH	Probable WRKY transcription factor 27 (WRKY DNA-binding protein 27)	0.94	-	nuc	0	Nucleus (Probable)				348
Q9XI90 UniProt NPD GO	WRKY4_ARATH	Probable WRKY transcription factor 4 (WRKY DNA-binding protein 4)	0.94	-	nuc	0	Nucleus (Probable)			1WJ2	514
Q4WXP0 UniProt NPD GO	NDC80_ASPFU	Probable kinetochore protein ndc80	0.94	-	mit	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				736
Q09530 UniProt NPD GO	MOG5_CAEEL	Probable pre-mRNA-splicing factor ATP-dependent RNA helicase mog-5 (EC 3.6.1.-) (Sex determination p ...	0.94	+	nuc	0	Nucleus (Probable)				1200
Q09353 UniProt NPD GO	SENT_CAEEL	Probable sentrin-specific protease (EC 3.4.22.-)	0.94	-	nuc	0	Nucleus (Potential)				697
P39529 UniProt NPD GO	YJU6_YEAST	Probable transcriptional regulatory protein YJL206C	0.94	-	nuc	0	Nucleus (Probable)				758
O94269 UniProt NPD GO	UBP3_SCHPO	Probable ubiquitin carboxyl-terminal hydrolase 3 (EC 3.1.2.15) (Ubiquitin thioesterase 3) (Ubiquitin ...	0.94	-	nuc	0					512
Q63647 UniProt NPD GO	PNRC1_RAT	Proline-rich nuclear receptor coactivator 1 (Proline-rich protein 2)	0.94	+	nuc	0	Nucleus (By similarity)				296
P17502 UniProt NPD GO	PRT_ANTGR	Protamine	0.94	+	nuc	0	Nucleus				132
Q5ZIM6 UniProt NPD GO	AATF_CHICK	Protein AATF (Apoptosis-antagonizing transcription factor)	0.94	+	nuc	0	Nucleus; nucleolus (By similarity)				574
Q9JKX4 UniProt NPD GO	AATF_MOUSE	Protein AATF (Apoptosis-antagonizing transcription factor) (Rb-binding protein Che-1) (Traube protei ...	0.94	-	nuc	0	Nucleus; nucleolus	cytoplasm [IDA] nucleolus [IDA] nucleus [IDA]			526
P42568 UniProt NPD GO	AF9_HUMAN	Protein AF-9 (ALL1 fused gene from chromosome 9 protein) (Myeloid/lymphoid or mixed-lineage leukemia ...	0.94	+	nuc	0	Nucleus (By similarity)	nucleus [TAS]	159558		568
Q5VXU9 UniProt NPD GO	CI084_HUMAN	Protein C9orf84	0.94	+	nuc	0					1444
Q8BND4 UniProt NPD GO	DX26B_MOUSE	Protein DDX26B	0.94	-	nuc	0					861
Q5R724 UniProt NPD GO	FA48A_PONPY	Protein FAM48A	0.94	-	nuc	0					522
Q8NEM7 UniProt NPD GO	FA48A_HUMAN	Protein FAM48A (p38-interacting protein) (p38IP)	0.94	-	nuc	0					779
Q9FDW0 UniProt NPD GO	FRIGI_ARATH	Protein FRIGIDA	0.94	-	nuc	0	Nucleus (Probable)				609
P39520 UniProt NPD GO	IFH1_YEAST	Protein IFH1 (Protein RRP3)	0.94	+	nuc	0	Nucleus (Probable)	nucleolus [IDA] nucleus [IDA]			1085
Q767M0 UniProt NPD GO	K1949_PIG	Protein KIAA1949 homolog	0.94	-	nuc	0					618
Q86UE4 UniProt NPD GO	LYRIC_HUMAN	Protein LYRIC (Lysine-rich CEACAM1 co-isolated protein) (3D3/lyric) (Metastasis adhesion protein) (M ...	0.94	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				582
Q4I0C5 UniProt NPD GO	RDR1_GIBZE	Protein RDR1	0.94	-	nuc	0	Nucleus (Probable)				544
P14291 UniProt NPD GO	RED1_YEAST	Protein RED1	0.94	-	nuc	0	Nucleus	synaptonemal complex [IDA]			827
P34758 UniProt NPD GO	SCD5_YEAST	Protein SCD5 (Protein FTB1)	0.94	-	nuc	0	Membrane; peripheral membrane protein	actin cortical patch [IDA] peripheral to membrane of membrane fraction [IDA]			872
Q6ZPY2 UniProt NPD GO	SMG5_MOUSE	Protein SMG5 (SMG-5 homolog) (EST1-like protein B)	0.94	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			1017
Q750U1 UniProt NPD GO	STB3_ASHGO	Protein STB3	0.94	-	nuc	0	Cytoplasm (By similarity)				511
Q04635 UniProt NPD GO	ESC1_SCHPO	Protein esc1	0.94	+	mit	0	Nucleus (Probable)				413
Q02645 UniProt NPD GO	HTS_DROME	Protein hu-li tai shao (Adducin-like protein)	0.94	-	nuc	0		fusome [IDA] ring canal inner rim [TAS] spectrosome [IDA]			1156
Q20318 UniProt NPD GO	LIN49_CAEEL	Protein lin-49 (Abnormal cell lineage protein 49)	0.94	-	nuc	0	Nucleus (Probable)				1042
O18214 UniProt NPD GO	MAB3_CAEEL	Protein male abnormal 3	0.94	+	nuc	0	Nucleus (Potential)				290
P51521 UniProt NPD GO	OVO_DROME	Protein ovo (Protein shaven baby)	0.94	-	nuc	0	Cytoplasm. Nucleus	nucleus [IC]			1351
Q9DBR7 UniProt NPD GO	MYPT1_MOUSE	Protein phosphatase 1 regulatory subunit 12A (Myosin phosphatase-targeting subunit 1) (Myosin phosph ...	0.94	-	nuc	0	Cytoplasm (By similarity). Along actomyosin filaments and stress fibers (By similarity)				1004
Q10728 UniProt NPD GO	MYPT1_RAT	Protein phosphatase 1 regulatory subunit 12A (Myosin phosphatase-targeting subunit 1) (Myosin phosph ...	0.94	-	nuc	0	Cytoplasm (By similarity). Along actomyosin filaments and stress fibers (By similarity)				1032
Q10666 UniProt NPD GO	POP1_CAEEL	Protein pop-1 (Posterior pharynx defect protein 1)	0.94	+	nuc	0	Nucleus				438
Q9U3V5 UniProt NPD GO	TIPT_DROME	Protein tiptop	0.94	-	nuc	0	Nucleus (Potential)	nucleus [NAS]			1024
P38073 UniProt NPD GO	YBO3_YEAST	Putative 103.4 kDa transcriptional regulatory protein in RPL4A-HMT1 intergenic region	0.94	+	nuc	0	Nucleus (Probable)				919
Q08964 UniProt NPD GO	YP216_YEAST	Putative ISWI chromatin remodeling complex subunit YPL216W	0.94	-	nuc	0	Nucleus (By similarity)				1102
P59598 UniProt NPD GO	ASXL1_MOUSE	Putative Polycomb group protein ASXL1 (Additional sex combs-like protein 1)	0.94	-	nuc	0	Nucleus (Probable)				1514
Q9Y383 UniProt NPD GO	LC7L2_HUMAN	Putative RNA-binding protein Luc7-like 2	0.94	+	nuc	0					392
Q7TNC4 UniProt NPD GO	LC7L2_MOUSE	Putative RNA-binding protein Luc7-like 2 (CGI-74 homolog)	0.94	+	nuc	0					392
P40923 UniProt NPD GO	YHZ3_SCHPO	Putative homeobox protein C21B10.13c in chromosome II	0.94	+	nuc	0	Nucleus (Potential)				201
Q9P6I9 UniProt NPD GO	YHDD_SCHPO	Putative transcriptional regulatory protein C1683.13c	0.94	-	mit	0	Nucleus				618
Q9ZVD3 UniProt NPD GO	ARR13_ARATH	Putative two-component response regulator ARR13	0.94	+	nuc	0	Nucleus				572
Q10127 UniProt NPD GO	YSO1_CAEEL	Putative zinc finger protein F56D1.1	0.94	-	nuc	0	Nucleus (Potential)				468
Q9JJ25 UniProt NPD GO	MEFV_RAT	Pyrin (Marenostrin)	0.94	-	nuc	0	Cytoplasm. Associated with microtubules and with the filamentous actin of perinuclear filaments and ...	microtubule associated complex [ISS]			750
Q9BXY4 UniProt NPD GO	RSPO3_HUMAN	R-spondin-3 precursor (Roof plate-specific spondin-3) (hRspo3) (Thrombospondin type I domain-contain ...	0.94	+	nuc	0	Secreted protein (By similarity)				272
Q03601 UniProt NPD GO	NHL1_CAEEL	RING finger protein nhl-1	0.94	-	nuc	0					974

You are viewing entries 2451 to 2500 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.