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
Q9ULL5 UniProt NPD GO	PRR12_HUMAN	Proline-rich protein 12	0.92	+	nuc	0					1215
P35313 UniProt NPD GO	PRM2_GORGO	Protamine-2 (Protamine-P2) (Sperm histone P2)	0.92	+	nuc	0	Nucleus				102
P07978 UniProt NPD GO	PRM2_MOUSE	Protamine-2 (Protamine-P2) (Sperm histone P2) [Contains: PP2-A; PP2-C; PP2-D; PP2-B (Protamine MP2)] ...	0.92	+	nuc	0	Nucleus	nucleus [IDA]			107
Q9NY61 UniProt NPD GO	AATF_HUMAN	Protein AATF (Apoptosis-antagonizing transcription factor) (Rb-binding protein Che-1)	0.92	-	nuc	0	Nucleus; nucleolus	nucleus [IDA]	608463		560
Q6CTS8 UniProt NPD GO	BFR2_KLULA	Protein BFR2	0.92	-	nuc	0	Nucleus; nucleolus (By similarity)				526
P53286 UniProt NPD GO	BTN2_YEAST	Protein BTN2	0.92	-	nuc	0	Cytoplasm	cytosol [IDA]			410
Q99MU0 UniProt NPD GO	DBF4_CRIGR	Protein DBF4 homolog (ChDBF4)	0.92	+	nuc	0	Nucleus				676
P36041 UniProt NPD GO	EAP1_YEAST	Protein EAP1 (eIF4E-associated protein 1)	0.92	-	nuc	0	Cytoplasm	mRNA cap complex [IPI]			632
Q7Z589 UniProt NPD GO	EMSY_HUMAN	Protein EMSY	0.92	+	nuc	0	Nucleus. Localizes to DNA damage markers in irradiated cells; suggesting that it participates in DNA ...		608574	2FMM	1322
Q8BMB0 UniProt NPD GO	EMSY_MOUSE	Protein EMSY	0.92	+	nuc	0	Nucleus. Localizes to DNA damage markers in irradiated cells; suggesting that it participates in DNA ...				1264
Q969W3 UniProt NPD GO	F104A_HUMAN	Protein FAM104A	0.92	+	nuc	0					120
Q7TT00 UniProt NPD GO	FA48A_MOUSE	Protein FAM48A (p38-interacting protein) (p38IP)	0.92	-	nuc	0					530
Q6C4R3 UniProt NPD GO	FYV7_YARLI	Protein FYV7	0.92	-	nuc	0	Nucleus; nucleolus (By similarity)				229
O43310 UniProt NPD GO	K0427_HUMAN	Protein KIAA0427	0.92	+	nuc	0					598
Q5TM66 UniProt NPD GO	K1949_MACMU	Protein KIAA1949 homolog	0.92	-	nuc	0					613
Q7ZX37 UniProt NPD GO	PTSRB_XENLA	Protein PTDSR-B	0.92	+	nuc	0	Nucleus (By similarity)				403
P33750 UniProt NPD GO	SOF1_YEAST	Protein SOF1	0.92	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA] small nuclear ribonucleoprotein complex [TAS] small nucleolar ribonucleoprotein complex [IPI]			489
P40317 UniProt NPD GO	SOK1_YEAST	Protein SOK1	0.92	-	nuc	0	Nucleus	nucleus [IDA]			901
P35210 UniProt NPD GO	SPT23_YEAST	Protein SPT23	0.92	-	nuc	1		endoplasmic reticulum membrane [IDA] nucleus [IC]			1082
Q9VC45 UniProt NPD GO	ASP_DROME	Protein abnormal spindle	0.92	+	nuc	0	Cytoplasm. Nucleus. During interphase in syncytial embryos distribution is cytoplasmic. On entering ...	microtubule associated complex [IDA] microtubule organizing center [IDA]			1954
Q5AW04 UniProt NPD GO	BFR2_EMENI	Protein bfr2	0.92	+	nuc	0	Nucleus; nucleolus (By similarity)				576
P39572 UniProt NPD GO	GIANT_DROME	Protein giant	0.92	-	nuc	0	Nucleus				448
P87253 UniProt NPD GO	KPC1_NEUCR	Protein kinase C-like (EC 2.7.11.13)	0.92	-	nuc	0					1142
Q02099 UniProt NPD GO	RAD3_SCHPO	Protein kinase rad3 (EC 2.7.11.1) (DNA-repair protein rad3)	0.92	-	end	1	Nucleus	nuclear chromosome [IDA]			2386
P18431 UniProt NPD GO	SGG_DROME	Protein kinase shaggy (EC 2.7.11.1) (Protein zeste-white 3)	0.92	+	nuc	0					1067
Q24371 UniProt NPD GO	L2DTL_DROME	Protein lethal(2)denticleless (Protein DTL83)	0.92	+	nuc	0	Cytoplasm (Potential)				769
Q9W4E2 UniProt NPD GO	NBEA_DROME	Protein neurobeachin (Protein rugose) (A-kinase anchor protein 550) (AKAP 550) (dAKAP550)	0.92	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	cytoplasm [IDA] integral to membrane [IDA]			3584
P16554 UniProt NPD GO	NUMB_DROME	Protein numb	0.92	-	nuc	0	Nucleus	basal cortex [NAS] cytoplasm [TAS]		2NMB	556
P20806 UniProt NPD GO	7LESS_DROVI	Protein sevenless (EC 2.7.10.1)	0.92	+	nuc	1					2594
P34707 UniProt NPD GO	SKN1_CAEEL	Protein skinhead-1	0.92	-	nuc	0	Nucleus	nucleus [NAS]		1SKN	623
Q8MQW8 UniProt NPD GO	SPRI_DROME	Protein sprint (SH2 poly-proline-containing Ras-interactor protein)	0.92	-	nuc	0					1790
Q08876 UniProt NPD GO	SUHW_DROVI	Protein suppressor of hairy wing	0.92	-	nuc	0	Nucleus				899
P40688 UniProt NPD GO	SWA_DROME	Protein swallow	0.92	-	nuc	0	Uniformly distributed in eggs, becomes localized to the nuclei during early mitotic divisions in ear ...				548
Q9TX44 UniProt NPD GO	TWIST_DROVI	Protein twist	0.92	+	nuc	0	Nucleus (By similarity)	nucleus [ISS]			519
Q92954 UniProt NPD GO	PRG4_HUMAN	Proteoglycan-4 precursor (Lubricin) (Megakaryocyte-stimulating factor) (Superficial zone proteoglyca ...	0.92	+	nuc	0	Secreted protein		604283		1404
Q7X7E9 UniProt NPD GO	DNL4_ORYSA	Putative DNA ligase 4 (EC 6.5.1.1) (DNA ligase IV) (Polydeoxyribonucleotide synthase [ATP] 4)	0.92	-	end	0	Nucleus (By similarity)				1322
Q8IXJ9 UniProt NPD GO	ASXL1_HUMAN	Putative Polycomb group protein ASXL1 (Additional sex combs-like protein 1)	0.92	-	nuc	0	Nucleus (Probable)				1541
Q21376 UniProt NPD GO	SULF1_CAEEL	Putative extracellular sulfatase Sulf-1 homolog precursor (EC 3.1.6.-) (CeSulf-1)	0.92	+	nuc	1 *	Endoplasmic reticulum (By similarity). Golgi apparatus; Golgi stack (By similarity). Cell surface (B ...	cell surface [ISS] endoplasmic reticulum [ISS] Golgi stack [ISS]			709
P40017 UniProt NPD GO	YEL4_YEAST	Putative uncharacterized O-acetyltransferase YER024W (EC 2.3.1.-)	0.92	-	nuc	0		cytoplasm [IDA]			923
Q9LSW9 UniProt NPD GO	ATL5K_ARATH	RING-H2 finger protein ATL5K (RING-H2 finger protein ATL16)	0.92	-	nuc	1 *					375
Q5ZLY0 UniProt NPD GO	RNUXA_CHICK	RNA U small nuclear RNA export adapter protein	0.92	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)				399
Q6CFE7 UniProt NPD GO	REXO3_YARLI	RNA exonuclease 3 (EC 3.1.-.-)	0.92	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				757
Q9Y5B0 UniProt NPD GO	CTDP1_HUMAN	RNA polymerase II subunit A C-terminal domain phosphatase (EC 3.1.3.16) (TFIIF-associating CTD phosp ...	0.92	-	nuc	0	Nucleus		604927	1ONV	961
Q3B7T9 UniProt NPD GO	RFIP1_RAT	Rab11 family-interacting protein 1 (Rab11-FIP1) (Rab-coupling protein)	0.92	-	nuc	0	Membrane-bound. RAB11A rather than RAB4A mediates RAB11FIP1 localization in the endocytic recycling ...				648
Q15311 UniProt NPD GO	RBP1_HUMAN	RalA-binding protein 1 (RalBP1) (Ral-interacting protein 1) (76 kDa Ral-interacting protein) (Dinitr ...	0.92	+	nuc	0	Membrane; peripheral membrane protein	membrane [IDA]	605801		654
Q8TB24 UniProt NPD GO	RIN3_HUMAN	Ras and Rab interactor 3 (Ras interaction/interference protein 3)	0.92	-	nuc	0					984
Q09820 UniProt NPD GO	RENT1_SCHPO	Regulator of nonsense transcripts 1 homolog (EC 3.6.1.-) (ATP-dependent helicase SPAC16C9.06c)	0.92	+	nuc	0	Cytoplasm (Potential)				925
Q9H1J1 UniProt NPD GO	REN3A_HUMAN	Regulator of nonsense transcripts 3A (Nonsense mRNA reducing factor 3A) (Up-frameshift suppressor 3 ...	0.92	+	nuc	0	Nucleus. Cytoplasm. Shuttling between the nucleus and the cytoplasm	cytoplasm [NAS] nucleus [NAS]			476
Q9Y7G2 UniProt NPD GO	MIG1_CANAL	Regulatory protein MIG1	0.92	-	nuc	0	Nucleus (By similarity)				574
P52288 UniProt NPD GO	MIG1_KLUMA	Regulatory protein MIG1	0.92	-	nuc	0	Nucleus				543

You are viewing entries 3401 to 3450 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.