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
Q7TSH8 UniProt NPD GO	K0195_MOUSE	Protein KIAA0195	0.85	+	end	10	Membrane; multi-pass membrane protein (Potential)				1360
Q8VDP4 UniProt NPD GO	K1967_MOUSE	Protein KIAA1967 homolog	0.85	-	nuc	0					922
Q8CJ19 UniProt NPD GO	MICA3_MOUSE	Protein MICAL-3	0.85	+	mit	0	Cytoplasm (By similarity)				864
Q07807 UniProt NPD GO	PUF3_YEAST	Protein PUF3	0.85	-	nuc	0		cytoplasm [IDA]			879
P38634 UniProt NPD GO	SIC1_YEAST	Protein SIC1 (CDK inhibitor p40)	0.85	-	mit	0		cytoplasm [IDA] nucleus [IDA]			284
Q9U969 UniProt NPD GO	SWS_DROME	Protein Swiss cheese	0.85	-	nuc	1 *					1425
Q26263 UniProt NPD GO	DPN_DROME	Protein deadpan	0.85	-	nuc	0	Nucleus (Probable)				435
Q8T4F7 UniProt NPD GO	ENA_DROME	Protein enabled	0.85	-	nuc	0	Expressed at the leading edge of lamellipodia. Co-localizes with Chic at the periphery of cells	lamellipodium [IDA]			829
P14585 UniProt NPD GO	LIN12_CAEEL	Protein lin-12 precursor (Abnormal cell lineage protein 12)	0.85	+	exc	1	Membrane; single-pass type I membrane protein	apical plasma membrane [IDA] plasma membrane [IDA]		2FO1	1429
Q10573 UniProt NPD GO	LIN25_CAEEL	Protein lin-25 (Abnormal cell lineage protein 25)	0.85	-	nuc	0	Nucleus (Probable)				1139
Q8WYL5 UniProt NPD GO	SSH1_HUMAN	Protein phosphatase Slingshot homolog 1 (EC 3.1.3.48) (EC 3.1.3.16) (SSH-1L) (hSSH-1L)	0.85	-	nuc	0	Cytoplasm. Also recruited to actin rich membrane protrusions such as lamellipodia, which may allow l ...	cytoplasm [IDA] plasma membrane [IDA]	606778		1049
P41236 UniProt NPD GO	IPP2_HUMAN	Protein phosphatase inhibitor 2 (IPP-2)	0.85	-	nuc	0			601792		204
O74454 UniProt NPD GO	STS5_SCHPO	Protein sts5	0.85	-	nuc	0	Cytoplasm	cytoplasm [IDA]			1066
Q9U9I5 UniProt NPD GO	SWA_DROPS	Protein swallow	0.85	-	nuc	0	Uniformly distributed in eggs, becomes localized to the nuclei during early mitotic divisions in ear ...				530
P22265 UniProt NPD GO	TSH_DROME	Protein teashirt	0.85	-	nuc	0	Nucleus. Cytoplasm. Initially localized in the cytoplasm soon after the blastoderm stage, and become ...	cytoplasm [IDA] nucleus [IDA]			954
P37398 UniProt NPD GO	VIV_ORYSA	Protein viviparous homolog	0.85	-	nuc	0		nucleus [IEP]			726
P00520 UniProt NPD GO	ABL1_MOUSE	Proto-oncogene tyrosine-protein kinase ABL1 (EC 2.7.10.2) (p150) (c-ABL) (Abelson murine leukemia vi ...	0.85	-	nuc	0	Cytoplasm. Nucleus. The myristoylated c-ABL protein was reported to be nuclear	cytoplasm [TAS] nucleus [TAS]		1OPK	1123
Q6PGC1 UniProt NPD GO	DHX29_MOUSE	Putative ATP-dependent RNA helicase DHX29 (EC 3.6.1.-) (DEAH box protein 29)	0.85	-	nuc	0					1365
P43610 UniProt NPD GO	YFK8_YEAST	Putative ATP-dependent helicase YFR038W (EC 3.6.1.-)	0.85	-	nuc	0	Nucleus (Potential)				853
P83102 UniProt NPD GO	DYRK3_DROME	Putative dual specificity tyrosine-phosphorylation-regulated kinase 3 homolog (EC 2.7.12.1)	0.85	-	nuc	0					828
Q9V9A8 UniProt NPD GO	PHTF_DROME	Putative homeodomain transcription factor	0.85	-	end	7	Nucleus (Potential)				880
Q6U949 UniProt NPD GO	IG2AS_HUMAN	Putative insulin-like growth factor 2 antisense gene protein (IGF2-AS) (PEG8/IGF2AS protein)	0.85	-	nuc	0					168
Q9VJB6 UniProt NPD GO	CADN2_DROME	Putative neural-cadherin 2 precursor (Cadherin-N2 protein) (DN2-cadherin)	0.85	+	nuc	2	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]			2215
P40656 UniProt NPD GO	SOX14_DROME	Putative transcription factor SOX-14	0.85	-	nuc	0	Nucleus (Potential)				669
Q07978 UniProt NPD GO	YL031_YEAST	Putative uncharacterized protein YLR031W	0.85	-	nuc	0					186
Q9ESK9 UniProt NPD GO	RBCC1_MOUSE	RB1-inducible coiled-coil protein 1 (Coiled-coil-forming protein 1) (LaXp180 protein)	0.85	-	nuc	0	Nucleus	nucleus [IDA]			1588
Q80U40 UniProt NPD GO	RIMB2_MOUSE	RIM-binding protein 2 (RIM-BP2)	0.85	-	nuc	0	Synaptic plasma membrane (By similarity)				1072
P78317 UniProt NPD GO	RNF4_HUMAN	RING finger protein 4	0.85	-	nuc	0	Cytoplasm. Nucleus	nucleus [TAS]	602850		190
Q7TT28 UniProt NPD GO	REXO1_MOUSE	RNA exonuclease 1 homolog (EC 3.1.-.-) (Transcription elongation factor B polypeptide 3-binding prot ...	0.85	+	nuc	0	Nucleus (By similarity)				1213
Q7S9B7 UniProt NPD GO	REXO4_NEUCR	RNA exonuclease 4 (EC 3.1.-.-)	0.85	+	nuc	0	Nucleus (By similarity)				406
Q5XJE5 UniProt NPD GO	LEO1_MOUSE	RNA polymerase-associated protein LEO1	0.85	-	nuc	0	Nucleus (By similarity)				667
Q8R0F5 UniProt NPD GO	RBMX2_MOUSE	RNA-binding motif protein, X-linked 2	0.85	+	nuc	0					326
Q9W4D2 UniProt NPD GO	RNP4F_DROME	RNA-binding protein 4F	0.85	-	nuc	0	Cytoplasm (Probable)	cytoplasm [NAS]			941
Q4VSN1 UniProt NPD GO	RIPK5_BRARE	Receptor-interacting serine/threonine-protein kinase 5 (EC 2.7.11.1) (Dusty protein kinase) (Dusty P ...	0.85	-	nuc	0	Cytoplasm (Probable)				885
O02626 UniProt NPD GO	AEX3_CAEEL	Regulator of presynaptic activity aex-3 (Aboc, expulsion defective protein 3)	0.85	-	nuc	0		cell [IDA]			1409
Q9W2Q1 UniProt NPD GO	RX_DROME	Retinal homeobox protein Rx (DRx1) (DRx)	0.85	+	nuc	0	Nucleus (By similarity)				873
P22448 UniProt NPD GO	RARB_CHICK	Retinoic acid receptor beta (RAR-beta)	0.85	+	exc	0	Nucleus				455
Q9W6B3 UniProt NPD GO	RARB_COTJA	Retinoic acid receptor beta (RAR-beta)	0.85	+	exc	0	Nucleus				455
P22605 UniProt NPD GO	RARB_MOUSE	Retinoic acid receptor beta (RAR-beta)	0.85	+	nuc	0	Nucleus			1XDK	482
P11369 UniProt NPD GO	POL2_MOUSE	Retrovirus-related Pol polyprotein LINE-1 (Long interspersed element-1) (L1) [Includes: Reverse tran ...	0.85	+	nuc	0					1281
O15085 UniProt NPD GO	ARHGB_HUMAN	Rho guanine nucleotide exchange factor 11 (PDZ-RhoGEF)	0.85	-	nuc	0	Cytoplasm. Membrane. Translocated to the membrane upon stimulation	intracellular [IC]	605708	1XCG	1522
Q9ES67 UniProt NPD GO	ARHGB_RAT	Rho guanine nucleotide exchange factor 11 (RhoGEF glutamate transport modulator GTRAP48)	0.85	-	nuc	0	Cytoplasm (By similarity). Membrane (By similarity). Translocated to the membrane upon stimulation ( ...				1527
Q13464 UniProt NPD GO	ROCK1_HUMAN	Rho-associated protein kinase 1 (EC 2.7.11.1) (Rho-associated, coiled-coil-containing protein kinase ...	0.85	-	nuc	0	Cytoplasm. Associated with the mother centriole and an intercentriolar linker (By similarity). Golgi ...		601702	2ETR	1354
Q2KIB9 UniProt NPD GO	RPP29_BOVIN	Ribonuclease P protein subunit p29 (EC 3.1.26.5)	0.85	-	nuc	0	Nucleus; nucleolus (By similarity)				220
O95707 UniProt NPD GO	RPP29_HUMAN	Ribonuclease P protein subunit p29 (EC 3.1.26.5) (hPOP4)	0.85	+	nuc	0	Nucleus; nucleolus	ribonuclease MRP complex [TAS]	606114		220
O74777 UniProt NPD GO	MIS3_SCHPO	Ribosomal RNA assembly protein mis3	0.85	+	nuc	0	Nucleus; nucleolus				327
Q91WF7 UniProt NPD GO	SAC3_MOUSE	SAC domain-containing protein 3	0.85	-	cyt	1					907
Q8BSD5 UniProt NPD GO	SHE_MOUSE	SH2 domain-containing adapter protein E	0.85	-	mit	0					492
Q9D7V1 UniProt NPD GO	SH24A_MOUSE	SH2 domain-containing protein 4A	0.85	-	nuc	0					421
Q810B7 UniProt NPD GO	SLIK5_MOUSE	SLIT and NTRK-like protein 5 precursor	0.85	-	nuc	1	Membrane; single-pass membrane protein (Potential)				957

You are viewing entries 6701 to 6750 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.