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
Q69Z69 UniProt NPD GO	ESCO1_MOUSE	N-acetyltransferase ESCO1 (EC 2.3.1.-) (Establishment of cohesion 1 homolog 1) (ECO1 homolog 1)	0.99	-	nuc	0	Nucleus (By similarity)				843
P30414 UniProt NPD GO	NKTR_HUMAN	NK-tumor recognition protein (Natural-killer cells cyclophilin-related protein) (NK-TR protein)	0.99	+	nuc	0	Membrane; peripheral membrane protein. Attached to the membrane via its N-terminus		161565		1462
Q6T4R5 UniProt NPD GO	NHS_HUMAN	Nance-Horan syndrome protein (Congenital cataracts and dental anomalies protein)	0.99	+	nuc	0	Nucleus (Potential)		302350		1630
Q86NP2 UniProt NPD GO	NELFA_DROME	Negative elongation factor A homolog	0.99	+	nuc	0	Nucleus (By similarity)	transcriptional repressor complex [ISS]			1251
Q7PLI2 UniProt NPD GO	NIPB_DROME	Nipped-B protein (SCC2 homolog)	0.99	+	nuc	0	Nucleus	nucleus [IDA]			2077
Q23064 UniProt NPD GO	UNC83_CAEEL	Nuclear migration protein unc-83 (Uncoordinated protein 83)	0.99	-	nuc	1	Nucleus; nuclear membrane; single-pass type IV membrane protein (Potential). The transmembrane domai ...				1041
O75376 UniProt NPD GO	NCOR1_HUMAN	Nuclear receptor corepressor 1 (N-CoR1) (N-CoR)	0.99	-	nuc	0	Nucleus (By similarity)		600849		2440
Q60974 UniProt NPD GO	NCOR1_MOUSE	Nuclear receptor corepressor 1 (N-CoR1) (N-CoR) (Retinoid X receptor-interacting protein 13) (RIP13) ...	0.99	+	nuc	0	Nucleus	nucleus [IC]			2453
Q8QG78 UniProt NPD GO	NCOR1_XENLA	Nuclear receptor corepressor 1 (N-CoR1) (N-CoR) (xN-CoR)	0.99	+	nuc	0	Nucleus (By similarity)				2498
Q9WU42 UniProt NPD GO	NCOR2_MOUSE	Nuclear receptor corepressor 2 (N-CoR2) (Silencing mediator of retinoic acid and thyroid hormone rec ...	0.99	+	nuc	0	Nucleus	nucleus [IC]			2472
Q66H99 UniProt NPD GO	NOL10_RAT	Nucleolar protein 10	0.99	-	nuc	0	Nucleus; nucleolus (By similarity)				688
P25980 UniProt NPD GO	UBF1B_XENLA	Nucleolar transcription factor 1-B (Upstream-binding factor 1-B) (UBF-1-B) (xUBF-2)	0.99	+	nuc	0	Nucleus				701
P32833 UniProt NPD GO	ORC2_YEAST	Origin recognition complex subunit 2 (Origin recognition complex 71 kDa subunit)	0.99	+	nuc	0	Nucleus	nuclear origin of replication recognition c... [TAS] pre-replicative complex [TAS]			620
Q8MJ04 UniProt NPD GO	RP1_CANFA	Oxygen-regulated protein 1 (Retinitis pigmentosa RP1 protein homolog)	0.99	-	nuc	0					2141
Q8MJG1 UniProt NPD GO	PSIP1_BOVIN	PC4 and SFRS1-interacting protein (Lens epithelium-derived growth factor) (Fragment)	0.99	+	nuc	0	Nucleus (By similarity)				483
Q5SPL2 UniProt NPD GO	PHF12_MOUSE	PHD finger protein 12 (PHD factor 1) (Pf1)	0.99	-	nuc	0	Nucleus (Probable)	nucleus [ISS] transcriptional repressor complex [ISS]			1003
O94880 UniProt NPD GO	PHF14_HUMAN	PHD finger protein 14	0.99	+	nuc	0					888
Q9D4H9 UniProt NPD GO	PHF14_MOUSE	PHD finger protein 14	0.99	+	nuc	0					881
Q8BLG0 UniProt NPD GO	PHF20_MOUSE	PHD finger protein 20 (Hepatocellular carcinoma-associated antigen 58 homolog)	0.99	+	nuc	0	Nucleus (Probable)				1010
P21127 UniProt NPD GO	CD2L1_HUMAN	PITSLRE serine/threonine-protein kinase CDC2L1 (EC 2.7.11.22) (Galactosyltransferase-associated prot ...	0.99	+	nuc	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleus [IEP]	176873		795
Q9NQV6 UniProt NPD GO	PRD10_HUMAN	PR domain zinc finger protein 10 (PR domain-containing protein 10)	0.99	-	nuc	0	Nucleus (Potential)				1061
Q63755 UniProt NPD GO	PRDM2_RAT	PR domain zinc finger protein 2 (PR domain-containing protein 2) (Retinoblastoma protein-interacting ...	0.99	+	nuc	0	Nucleus (By similarity)				1706
Q13029 UniProt NPD GO	PRDM2_HUMAN	PR domain zinc finger protein 2 (PR domain-containing protein 2) (Retinoblastoma protein-interacting ...	0.99	-	nuc	0	Nucleus	nucleus [NAS]	601196		1718
P48785 UniProt NPD GO	PRH_ARATH	Pathogenesis-related homeodomain protein (PRHA)	0.99	+	nuc	0	Nucleus				796
Q27450 UniProt NPD GO	CYP1_BRUMA	Peptidyl-prolyl cis-trans isomerase 1 (EC 5.2.1.8) (PPIase 1) (Cyclophilin) (BmCYP-1)	0.99	+	nuc	0				1C5F	843
Q13427 UniProt NPD GO	PPIG_HUMAN	Peptidyl-prolyl cis-trans isomerase G (EC 5.2.1.8) (Peptidyl-prolyl isomerase G) (PPIase G) (Rotamas ...	0.99	+	nuc	0	Nucleus; nucleoplasm; nuclear matrix. Colocalizes with RNA splicing factors at nuclear speckles	nucleoplasm [TAS] nucleus [TAS]	606093		754
O55035 UniProt NPD GO	PPIG_RAT	Peptidyl-prolyl cis-trans isomerase G (EC 5.2.1.8) (Peptidyl-prolyl isomerase G) (PPIase G) (Rotamas ...	0.99	+	nuc	0	Nucleus; nucleoplasm; nuclear matrix. Colocalizes with splicing factors at nuclear speckles	nuclear matrix [IDA]			752
P0C1J2 UniProt NPD GO	CWC27_RHIOR	Peptidyl-prolyl isomerase cwc27 (EC 5.2.1.8)	0.99	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				524
Q8BYK5 UniProt NPD GO	PHAR3_MOUSE	Phosphatase and actin regulator 3 (Scapinin) (Scaffold-associated PP1-inhibiting protein)	0.99	-	nuc	0	Nucleus; nuclear matrix (By similarity). Localized to the nuclear matrix-intermediate filament scaff ...				558
Q8K1N2 UniProt NPD GO	PHLB2_MOUSE	Pleckstrin homology-like domain family B member 2 (Protein LL5-beta)	0.99	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Translocates to th ...				1249
P35820 UniProt NPD GO	PSC_DROME	Polycomb group protein Psc (Protein posterior sex combs)	0.99	-	nuc	0	Nucleus (Probable)				1601
Q9R1C7 UniProt NPD GO	PRP40_MOUSE	Pre-mRNA-processing factor 40 homolog A (Formin-binding protein 3) (Formin-binding protein 11) (FBP ...	0.99	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle				953
Q6FUG1 UniProt NPD GO	CEF1_CANGA	Pre-mRNA-splicing factor CEF1	0.99	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				541
P51531 UniProt NPD GO	SMCA2_HUMAN	Probable global transcription activator SNF2L2 (EC 3.6.1.-) (ATP-dependent helicase SMARCA2) (SNF2-a ...	0.99	+	nuc	0	Nucleus	nucleoplasm [TAS]	600014		1586
P51532 UniProt NPD GO	SMCA4_HUMAN	Probable global transcription activator SNF2L4 (EC 3.6.1.-) (ATP-dependent helicase SMARCA4) (SNF2-b ...	0.99	+	nuc	0	Nucleus	nucleoplasm [TAS] nucleus [TAS]	603254		1647
Q7Z333 UniProt NPD GO	SETX_HUMAN	Probable helicase senataxin (EC 3.6.1.-) (SEN1 homolog)	0.99	-	nuc	0	Nucleus (Probable)		608465		2677
P42950 UniProt NPD GO	YJK3_YEAST	Probable transcriptional regulatory protein YJL103C	0.99	-	nuc	0	Nucleus (Probable)				618
Q05854 UniProt NPD GO	YL278_YEAST	Probable transcriptional regulatory protein YLR278C	0.99	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			1341
P33306 UniProt NPD GO	BCK2_YEAST	Protein BCK2 (Bypass of kinase C protein)	0.99	+	nuc	0		cytoplasm [IDA] nucleus [IDA]			851
Q8C9S4 UniProt NPD GO	CJ118_MOUSE	Protein C10orf118 homolog (Oocyte-testis gene 1 protein)	0.99	-	nuc	0					917
Q8IX21 UniProt NPD GO	CJ006_HUMAN	Protein C10orf6	0.99	-	nuc	0					1173
Q5REF4 UniProt NPD GO	CJ006_PONPY	Protein C10orf6 homolog	0.99	-	nuc	0					1174
P32354 UniProt NPD GO	DNA43_YEAST	Protein DNA43	0.99	+	nuc	0	Nucleus (Potential)	nucleus [IDA]			571
O94988 UniProt NPD GO	FA13A_HUMAN	Protein FAM13A1	0.99	+	nuc	0					697
Q8HYW0 UniProt NPD GO	FA13A_BOVIN	Protein FAM13A1 (Protein Precm1)	0.99	+	nuc	0					697
P40480 UniProt NPD GO	HOS4_YEAST	Protein HOS4	0.99	+	nuc	0		histone deacetylase complex [IPI]			1083
Q7Z3B3 UniProt NPD GO	K1267_HUMAN	Protein KIAA1267	0.99	-	nuc	0					1105
Q9P1Y5 UniProt NPD GO	K1543_HUMAN	Protein KIAA1543	0.99	-	mit	0					1249
P40457 UniProt NPD GO	MLP2_YEAST	Protein MLP2 (Myosin-like protein 2)	0.99	+	nuc	0	Nucleus. Nuclear periphery, excluded from nuclear envelope adjacent to nucleolus	mitochondrion [IDA] nuclear envelope [IDA] nucleoplasm [IDA]			1679
P29539 UniProt NPD GO	RIF1_YEAST	Protein RIF1 (RAP1-interacting factor 1)	0.99	+	nuc	0	Nucleus. Localizes to telomeres. Telomere association begins in G1/S, attains a peak during late G2/ ...	nuclear telomere cap complex [IDA]			1916

You are viewing entries 351 to 400 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.