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
Q9H4Z3 UniProt NPD GO	PCIF1_HUMAN	Phosphorylated CTD-interacting factor 1	0.88	-	nuc	0	Nucleus				704
P14760 UniProt NPD GO	RR7_ASTLO	Plastid 30S ribosomal protein S7	0.88	+	nuc	0	Plastid				178
Q9Y2H5 UniProt NPD GO	PKHA6_HUMAN	Pleckstrin homology domain-containing family A member 6 (Phosphoinositol 3-phosphate-binding protein ...	0.88	-	nuc	0			607771		1048
Q9BWT3 UniProt NPD GO	PAPOG_HUMAN	Poly(A) polymerase gamma (EC 2.7.7.19) (PAP gamma) (Polynucleotide adenylyltransferase gamma) (SRP R ...	0.88	+	nuc	0	Nucleus (Probable)				736
Q90ZA1 UniProt NPD GO	PARN_XENLA	Poly(A)-specific ribonuclease PARN (EC 3.1.13.4) (Polyadenylate-specific ribonuclease) (Deadenylatin ...	0.88	-	nuc	0	Cytoplasm. Nucleus				631
P26017 UniProt NPD GO	PC_DROME	Polycomb group protein Pc (Protein polycomb)	0.88	-	nuc	0	Nucleus (By similarity)	PRC1 complex [TAS]		1PFB	390
Q9NS91 UniProt NPD GO	RAD18_HUMAN	Postreplication repair protein RAD18 (hRAD18) (hHR18) (RING finger protein 73)	0.88	-	nuc	0	Nucleus (By similarity)	nucleus [NAS]	605256		495
Q10065 UniProt NPD GO	TRK2_SCHPO	Potassium transport protein 2	0.88	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				880
Q754U8 UniProt NPD GO	PRP5_ASHGO	Pre-mRNA-processing ATP-dependent RNA helicase PRP5 (EC 3.6.1.-)	0.88	+	nuc	0	Nucleus (By similarity)				816
Q4WT99 UniProt NPD GO	PRP5_ASPFU	Pre-mRNA-processing ATP-dependent RNA helicase prp5 (EC 3.6.1.-)	0.88	+	nuc	0	Nucleus (By similarity)				1211
O14176 UniProt NPD GO	PRP40_SCHPO	Pre-mRNA-processing protein prp40	0.88	+	nuc	0	Nucleus (By similarity)				695
Q4P0G6 UniProt NPD GO	CWC21_USTMA	Pre-mRNA-splicing factor CWC21	0.88	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				348
Q4PCY0 UniProt NPD GO	CWC22_USTMA	Pre-mRNA-splicing factor CWC22	0.88	+	end	2	Cytoplasm (By similarity). Nucleus (By similarity)				886
Q6BU18 UniProt NPD GO	CWC26_DEBHA	Pre-mRNA-splicing factor CWC26	0.88	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				268
Q7SAF6 UniProt NPD GO	CEF1_NEUCR	Pre-mRNA-splicing factor cef-1	0.88	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				779
O94417 UniProt NPD GO	CWC26_SCHPO	Pre-mRNA-splicing factor cwc26 (Complexed with cdc5 protein 26) (Cell cycle control protein cwf26)	0.88	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				305
O59733 UniProt NPD GO	SYF2_SCHPO	Pre-mRNA-splicing factor syf2	0.88	+	nuc	0	Nucleus (By similarity)				229
Q06344 UniProt NPD GO	ESF1_YEAST	Pre-rRNA-processing protein ESF1 (18S rRNA factor 1)	0.88	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA] nucleus [IDA]			628
Q9SQV1 UniProt NPD GO	RH40_ARATH	Probable DEAD-box ATP-dependent RNA helicase 40 (EC 3.6.1.-)	0.88	+	nuc	0	Nucleus (By similarity)				1088
P10581 UniProt NPD GO	RPOP_MAIZE	Probable DNA-directed RNA polymerase (EC 2.7.7.6) (S-2 DNA ORF1)	0.88	+	nuc	0					1098
Q9U178 UniProt NPD GO	UTP11_LEIMA	Probable U3 small nucleolar RNA-associated protein 11 (U3 snoRNA-associated protein 11)	0.88	+	nuc	0	Nucleus; nucleolus (By similarity)				361
Q7G8Y3 UniProt NPD GO	ISW2_ORYSA	Probable chromatin remodelling complex ATPase chain (EC 3.6.1.-) (ISW2-like) (Sucrose nonfermenting ...	0.88	+	nuc	0	Nucleus (By similarity)				1107
P49869 UniProt NPD GO	HR38_DROME	Probable nuclear hormone receptor HR38 (dHR38)	0.88	-	nuc	0	Nucleus			1PDU	1073
O54827 UniProt NPD GO	AT10A_MOUSE	Probable phospholipid-transporting ATPase VA (EC 3.6.3.1) (P-locus fat-associated ATPase)	0.88	+	end	8	Membrane; multi-pass membrane protein	integral to membrane [ISS]			1508
O45244 UniProt NPD GO	DHX16_CAEEL	Probable pre-mRNA-splicing factor ATP-dependent RNA helicase mog-4 (EC 3.6.1.-) (Sex determination p ...	0.88	+	cyt	0	Nucleus (Probable)				1008
Q10435 UniProt NPD GO	YDE1_SCHPO	Probable ubiquitin fusion degradation protein C12B10.01c	0.88	-	nuc	0					1647
Q9M3A3 UniProt NPD GO	ABIL2_ARATH	Protein ABIL2 (Abl interactor-like protein 2) (AtABIL2)	0.88	+	nuc	0					312
Q6NMC6 UniProt NPD GO	ABIL3_ARATH	Protein ABIL3 (Abl interactor-like protein 3) (AtABIL3)	0.88	+	nuc	0					321
O95872 UniProt NPD GO	BAT4_HUMAN	Protein BAT4 (HLA-B-associated transcript 4) (G5 protein)	0.88	+	nuc	0			142610		356
Q75EZ2 UniProt NPD GO	BFR2_ASHGO	Protein BFR2	0.88	-	nuc	0	Nucleus; nucleolus (By similarity)				528
Q6FQG3 UniProt NPD GO	BSP1_CANGA	Protein BSP1	0.88	+	nuc	0	Cell membrane; peripheral membrane protein (By similarity). Actin patches				525
Q9H943 UniProt NPD GO	CJ068_HUMAN	Protein C10orf68	0.88	-	nuc	0					628
Q9H8W3 UniProt NPD GO	CJ084_HUMAN	Protein C10orf84	0.88	+	nuc	0					233
O74338 UniProt NPD GO	YH25_SCHPO	Protein C1A4.05 in chromosome II	0.88	-	nuc	0	Septum				700
Q9Y3R5 UniProt NPD GO	CU005_HUMAN	Protein C21orf5	0.88	-	end	0		Golgi membrane [ISS]	604803		2298
Q9Y7V2 UniProt NPD GO	YCHD_SCHPO	Protein C645.13 in chromosome III	0.88	-	nuc	0	Nucleus				721
Q6ZUB1 UniProt NPD GO	CI079_HUMAN	Protein C9orf79	0.88	-	nuc	0					1445
Q06455 UniProt NPD GO	MTG8_HUMAN	Protein CBFA2T1 (Protein MTG8) (Protein ETO) (Eight twenty one protein) (Cyclin-D-related protein) ( ...	0.88	-	nuc	0	Nucleus (Potential)		133435	1WQ6	604
Q8TDJ6 UniProt NPD GO	DMXL2_HUMAN	Protein DmX-like 2 (Rabconnectin-3)	0.88	-	nuc	0	Synaptic vesicle; synaptic vesicle membrane; peripheral membrane protein	synaptic vesicle [IDA]			3036
Q7Z4H7 UniProt NPD GO	FA29A_HUMAN	Protein FAM29A	0.88	-	nuc	0					955
P13902 UniProt NPD GO	INO4_YEAST	Protein INO4	0.88	+	nuc	0	Nucleus (Probable)	nucleus [IC]			151
Q6ZU52 UniProt NPD GO	K0408_HUMAN	Protein KIAA0408	0.88	-	nuc	0					694
Q6NXI6 UniProt NPD GO	K0460_MOUSE	Protein KIAA0460	0.88	+	nuc	0					1469
Q96AA8 UniProt NPD GO	K0555_HUMAN	Protein KIAA0555	0.88	-	nuc	0					810
Q8CCJ3 UniProt NPD GO	K0776_MOUSE	Protein KIAA0776	0.88	+	cyt	0					793
Q9P2G4 UniProt NPD GO	K1383_HUMAN	Protein KIAA1383	0.88	-	nuc	0					905
Q8N163 UniProt NPD GO	K1967_HUMAN	Protein KIAA1967 (Deleted in breast cancer gene 1 protein) (DBC.1) (DBC-1) (p30 DBC)	0.88	-	nuc	0		cytoplasm [IDA] mitochondrial matrix [IDA] nucleus [IDA]	607359		923
Q7RTP6 UniProt NPD GO	MICA3_HUMAN	Protein MICAL-3	0.88	+	nuc	0	Cytoplasm (By similarity)		608882		976
P37304 UniProt NPD GO	PAM1_YEAST	Protein PAM1	0.88	+	nuc	0		bud neck [IDA]			830
P50896 UniProt NPD GO	PSP1_YEAST	Protein PSP1 (Protein GIN5)	0.88	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA]			841

You are viewing entries 5251 to 5300 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.