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
P21711 UniProt NPD GO	MIX1_XENLA	Homeobox protein MIX.1	0.93	+	nuc	0	Nucleus				377
O70584 UniProt NPD GO	NKX28_MOUSE	Homeobox protein Nkx-2.8 (Homeobox protein NK-2 homolog H) (Homeobox protein Nkx-2.9)	0.93	-	nuc	0	Nucleus (Probable)				235
Q8MID1 UniProt NPD GO	TF2LX_MIOTA	Homeobox protein TGIF2LX (TGFB-induced factor 2-like protein, X-linked) (TGF(beta)induced transcript ...	0.93	+	nuc	0	Nucleus (By similarity)				249
Q8MIC2 UniProt NPD GO	TF2LX_PAPHA	Homeobox protein TGIF2LX (TGFB-induced factor 2-like protein, X-linked) (TGF(beta)induced transcript ...	0.93	+	nuc	0	Nucleus (By similarity)				256
P42587 UniProt NPD GO	HNK2_XENLA	Homeobox protein XENK-2	0.93	+	nuc	0	Nucleus (Probable)				196
Q7TMK6 UniProt NPD GO	HOOK2_MOUSE	Hook homolog 2	0.93	-	nuc	0	Cytoplasm (By similarity). Associates with discrete punctate structure that correspond to neither ea ...				716
Q05043 UniProt NPD GO	YMS0_YEAST	Hypothetical 43.5 kDa protein in TAP42-CYK2 intergenic region	0.93	-	nuc	0		mitochondrion [IDA] nucleus [IDA]			376
P36158 UniProt NPD GO	YK58_YEAST	Hypothetical 68.3 kDa protein in SIS2-MTD1 intergenic region	0.93	+	nuc	0		cytoplasm [IDA]			585
P40523 UniProt NPD GO	YIF5_YEAST	Hypothetical 70.7 kDa protein in SNP1-GPP1 intergenic region	0.93	-	nuc	0					627
Q10932 UniProt NPD GO	YT22_CAEEL	Hypothetical protein B0304.2	0.93	-	nuc	0					218
Q11194 UniProt NPD GO	YX23_CAEEL	Hypothetical protein C04E7.3	0.93	-	nuc	0					518
Q11181 UniProt NPD GO	YPC4_CAEEL	Hypothetical protein C05D10.4	0.93	-	nuc	0					597
Q09458 UniProt NPD GO	YQ37_CAEEL	Hypothetical protein C09F5.7	0.93	-	nuc	0					395
Q09252 UniProt NPD GO	YQ56_CAEEL	Hypothetical protein C16C10.6	0.93	+	nuc	0					392
Q10191 UniProt NPD GO	YAWH_SCHPO	Hypothetical protein C3F10.17 in chromosome I	0.93	+	nuc	0					386
P34447 UniProt NPD GO	YM2A_CAEEL	Hypothetical protein F54F2.2, isoform a	0.93	-	nuc	0	Nucleus (Potential)				867
P34619 UniProt NPD GO	YO83_CAEEL	Hypothetical protein ZK1236.3	0.93	-	nuc	0					1000
Q8T053 UniProt NPD GO	Y678_DROME	Hypothetical zinc finger protein CG2678 in chromosome 3	0.93	-	nuc	0	Nucleus (Potential)	nucleus [NAS]			434
Q04213 UniProt NPD GO	IOC4_YEAST	ISWI one complex protein 4	0.93	+	nuc	0	Nucleus	ISW1 complex [IPI]			475
Q19375 UniProt NPD GO	IWS1_CAEEL	IWS1-like protein	0.93	-	nuc	0	Nucleus (By similarity)				511
P40154 UniProt NPD GO	IES2_YEAST	Ino eighty subunit 2	0.93	+	nuc	0	Nucleus	nucleus [IDA]			320
P46997 UniProt NPD GO	JJJ2_YEAST	J protein type 2	0.93	+	nuc	0		cytoplasm [IDA] nucleus [IDA]			482
Q60V67 UniProt NPD GO	JHD1_CAEBR	JmjC domain-containing histone demethylation protein 1 (EC 1.14.11.-)	0.93	+	nuc	0	Nucleus (By similarity)				1063
O75164 UniProt NPD GO	JHD3A_HUMAN	JmjC domain-containing histone demethylation protein 3A (EC 1.14.11.-) (Jumonji domain-containing pr ...	0.93	+	nuc	0	Nucleus	nucleus [IDA]	609764	2GP5	1064
P21613 UniProt NPD GO	KINH_LOLPE	Kinesin heavy chain	0.93	-	nuc	0					967
Q12840 UniProt NPD GO	KIF5A_HUMAN	Kinesin heavy chain isoform 5A (Neuronal kinesin heavy chain) (NKHC) (Kinesin heavy chain neuron-spe ...	0.93	-	nuc	0	Cytoplasm; perinuclear region. Concentrated in the cell body of the neurons, particularly in the per ...	kinesin complex [TAS] membrane fraction [TAS]	602821		1032
O60282 UniProt NPD GO	KIF5C_HUMAN	Kinesin heavy chain isoform 5C (Kinesin heavy chain neuron-specific 2)	0.93	-	nuc	0		kinesin complex [TAS]	604593		957
P28738 UniProt NPD GO	KIF5C_MOUSE	Kinesin heavy chain isoform 5C (Kinesin heavy chain neuron-specific 2)	0.93	-	nuc	0		ciliary rootlet [IDA] cytoplasm [IDA] kinesin complex [TAS] neuron projection [IDA]		1VFZ	956
Q9EQW7 UniProt NPD GO	KI13A_MOUSE	Kinesin-like protein KIF13A	0.93	-	nuc	0					1749
Q9NQT8 UniProt NPD GO	KI13B_HUMAN	Kinesin-like protein KIF13B (Kinesin-like protein GAKIN)	0.93	-	nuc	0		cytoplasm [IDA]	607350	2COW	1826
P70096 UniProt NPD GO	KIF2C_CRIGR	Kinesin-like protein KIF2C (Mitotic centromere-associated kinesin) (MCAK) (Kinesin-like protein 6)	0.93	-	nuc	0	Cytoplasm. Nucleus				718
Q99661 UniProt NPD GO	KIF2C_HUMAN	Kinesin-like protein KIF2C (Mitotic centromere-associated kinesin) (MCAK) (Kinesin-like protein 6)	0.93	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	kinesin complex [TAS]	604538		725
Q62909 UniProt NPD GO	KIF2C_RAT	Kinesin-like protein KIF2C (Mitotic centromere-associated kinesin) (MCAK) (Kinesin-related protein 2 ...	0.93	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				671
Q9Y496 UniProt NPD GO	KIF3A_HUMAN	Kinesin-like protein KIF3A (Microtubule plus end-directed kinesin motor 3A)	0.93	+	nuc	0			604683		702
Q61771 UniProt NPD GO	KIF3B_MOUSE	Kinesin-like protein KIF3B (Microtubule plus end-directed kinesin motor 3B)	0.93	+	nuc	0					747
P12524 UniProt NPD GO	MYCL1_HUMAN	L-myc-1 proto-oncogene protein	0.93	-	nuc	0	Nucleus		164850		364
P12525 UniProt NPD GO	MYCL2_HUMAN	L-myc-2 protein	0.93	-	nuc	0	Nucleus (Potential)		310310		357
P08547 UniProt NPD GO	LIN1_HUMAN	LINE-1 reverse transcriptase homolog	0.93	-	nuc	0					1259
Q3ZD69 UniProt NPD GO	LMNA_PIG	Lamin-A/C	0.93	-	nuc	0	Nucleus (By similarity)				664
P02545 UniProt NPD GO	LMNA_HUMAN	Lamin-A/C (70 kDa lamin) (NY-REN-32 antigen)	0.93	-	nuc	0	Nucleus		115200	1X8Y	664
Q9C0I9 UniProt NPD GO	LRC27_HUMAN	Leucine-rich repeat-containing protein 27	0.93	-	nuc	0					530
Q86X45 UniProt NPD GO	LRRC6_HUMAN	Leucine-rich repeat-containing protein 6 (Leucine-rich testis-specific protein) (Testis-specific leu ...	0.93	-	nuc	0	Cytoplasm (By similarity)				466
P53150 UniProt NPD GO	LIF1_YEAST	Ligase-interacting factor 1	0.93	-	nuc	0	Cytoplasm. Nucleus	nucleus [TAS]		1Z56	421
O75145 UniProt NPD GO	LIPA3_HUMAN	Liprin-alpha-3 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-3 ...	0.93	-	nuc	0	Cytoplasm (By similarity). Cell surface (By similarity). Colocalizes with PTPRF at the cell surface ...		603144		1194
Q86W92 UniProt NPD GO	LIPB1_HUMAN	Liprin-beta-1 (Protein tyrosine phosphatase receptor type f polypeptide-interacting protein-binding ...	0.93	-	nuc	0		plasma membrane [NAS]	603141		1011
Q9V5M6 UniProt NPD GO	LOLA5_DROME	Longitudinals lacking protein, isoforms J/P/Q/S/Z	0.93	-	nuc	0	Nucleus	nucleus [IDA]			963
P30304 UniProt NPD GO	MPIP1_HUMAN	M-phase inducer phosphatase 1 (EC 3.1.3.48) (Dual specificity phosphatase Cdc25A)	0.93	-	nuc	0			116947	1C25	524
P48964 UniProt NPD GO	MPIP1_MOUSE	M-phase inducer phosphatase 1 (EC 3.1.3.48) (Dual specificity phosphatase Cdc25A)	0.93	-	nuc	0					514
P30305 UniProt NPD GO	MPIP2_HUMAN	M-phase inducer phosphatase 2 (EC 3.1.3.48) (Dual specificity phosphatase Cdc25B)	0.93	-	nuc	0	Centrosome	intracellular [NAS]	116949	2A2K	580
Q9BYG3 UniProt NPD GO	MK67I_HUMAN	MKI67 FHA domain-interacting nucleolar phosphoprotein (Nucleolar protein interacting with the FHA do ...	0.93	+	nuc	0	Nucleus; nucleolus. Localizes to mitotic chromosomes in conjunction with MKI67	condensed nuclear chromosome [IDA] cytoplasm [IDA] nucleolus [IDA] nucleoplasm [IDA]		2AFF	293

You are viewing entries 2801 to 2850 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.