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
Q02953 UniProt NPD GO	HSF_SCHPO	Heat shock factor protein (HSF) (Heat shock transcription factor) (HSTF)	0.91	+	nuc	0	Nucleus				609
Q6CA87 UniProt NPD GO	SWR1_YARLI	Helicase SWR1 (EC 3.6.1.-)	0.91	+	nuc	0	Nucleus (By similarity)				1772
Q8BW74 UniProt NPD GO	HLF_MOUSE	Hepatic leukemia factor	0.91	+	nuc	0	Nucleus (Probable)				295
Q6CKE9 UniProt NPD GO	ESA1_KLULA	Histone acetyltransferase ESA1 (EC 2.3.1.48)	0.91	+	nuc	0	Nucleus (By similarity)				439
Q960X4 UniProt NPD GO	TIP60_DROME	Histone acetyltransferase Tip60 (EC 2.3.1.48)	0.91	-	nuc	0	Nucleus (Probable)	TIP60 histone acetyltransferase complex [IDA]			541
O94446 UniProt NPD GO	ESA1_SCHPO	Histone acetyltransferase mst1 (EC 2.3.1.48)	0.91	+	nuc	0	Nucleus	nuclear chromatin [IDA] nucleus [IDA]			463
Q00401 UniProt NPD GO	HMH2_DUGTI	Homeobox protein DTH-2	0.91	-	nuc	0	Nucleus (Probable)				363
P46607 UniProt NPD GO	HGL2_ARATH	Homeobox protein GLABRA2 (Homeobox-leucine zipper protein ATHB-10) (HD-ZIP protein ATHB-10)	0.91	+	nuc	0	Nucleus (Probable)				745
O95096 UniProt NPD GO	NKX22_HUMAN	Homeobox protein Nkx-2.2 (Homeobox protein NK-2 homolog B)	0.91	+	nuc	0	Nucleus (By similarity)		604612		273
P42586 UniProt NPD GO	NKX22_MOUSE	Homeobox protein Nkx-2.2 (Homeobox protein NK-2 homolog B)	0.91	+	nuc	0	Nucleus	nucleus [IDA]			273
Q90481 UniProt NPD GO	NX22A_BRARE	Homeobox protein Nkx-2.2a (Homeobox protein NK-2 homolog B)	0.91	+	nuc	0	Nucleus (By similarity)				269
Q8C0Y1 UniProt NPD GO	TGIF2_MOUSE	Homeobox protein TGIF2 (TGFB-induced factor 2) (5'-TG-3'-interacting factor 2) (TGF(beta)-induced tr ...	0.91	-	nuc	0	Nucleus (By similarity). Excluded from nucleoli (By similarity)				237
Q8MID8 UniProt NPD GO	TF2LX_MACFA	Homeobox protein TGIF2LX (TGFB-induced factor 2-like protein, X-linked) (TGF(beta)induced transcript ...	0.91	+	nuc	0	Nucleus (By similarity)				249
Q8MID6 UniProt NPD GO	TF2LX_MACMU	Homeobox protein TGIF2LX (TGFB-induced factor 2-like protein, X-linked) (TGF(beta)induced transcript ...	0.91	-	nuc	0	Nucleus (By similarity)				249
Q8MIB7 UniProt NPD GO	TF2LX_PANTR	Homeobox protein TGIF2LX (TGFB-induced factor 2-like protein, X-linked) (TGF(beta)induced transcript ...	0.91	-	nuc	0	Nucleus (By similarity)				241
P40427 UniProt NPD GO	EXD_DROME	Homeobox protein extradenticle	0.91	-	nuc	0	Nucleus (Probable)	cytoplasm [TAS] nucleus [IDA]		1B8I	376
P54366 UniProt NPD GO	GSC_DROME	Homeobox protein goosecoid	0.91	+	nuc	0	Nucleus				419
P46639 UniProt NPD GO	KNAT1_ARATH	Homeobox protein knotted-1-like 1 (KNAT1)	0.91	-	nuc	0	Nucleus (Probable)				398
P35736 UniProt NPD GO	YKF0_YEAST	Hypothetical 103.1 kDa protein in NUP120-CSE4 intergenic region	0.91	-	nuc	0					922
P38201 UniProt NPD GO	YBC9_YEAST	Hypothetical 42.6 kDa protein in AAC2-RPL19B intergenic region	0.91	+	nuc	0		cytoplasm [IDA] nucleus [IDA]			376
Q04472 UniProt NPD GO	YM05_YEAST	Hypothetical 58.0 kDa protein in ILV2-ADE17 intergenic region	0.91	-	nuc	1		mitochondrion [IDA]			501
Q03153 UniProt NPD GO	YMY8_YEAST	Hypothetical 70.4 kDa protein in SNZ1-YPK2 intergenic region	0.91	-	nuc	0		mitochondrion [IDA]			612
P53137 UniProt NPD GO	YGL0_YEAST	Hypothetical 72.0 kDa protein in TAF60-MLC1 intergenic region	0.91	-	nuc	0		cytoplasm [IDA]			624
P47156 UniProt NPD GO	YJ89_YEAST	Hypothetical 85.0 kDa protein in STE24-ATP2 intergenic region	0.91	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			728
Q10946 UniProt NPD GO	YMP2_CAEEL	Hypothetical protein B0361.2	0.91	+	nuc	0					460
Q10451 UniProt NPD GO	YLE1_SCHPO	Hypothetical protein C1093.01 in chromosome I	0.91	-	nuc	0					1261
Q10200 UniProt NPD GO	YBY1_SCHPO	Hypothetical protein C11C11.01 in chromosome II	0.91	-	nuc	0					493
O59783 UniProt NPD GO	YCN6_SCHPO	Hypothetical protein C320.06 in chromosome III	0.91	-	nuc	0					289
O14174 UniProt NPD GO	YE5A_SCHPO	Hypothetical protein C4D7.10c in chromosome I	0.91	+	nuc	0					473
O36021 UniProt NPD GO	YEK9_SCHPO	Hypothetical protein C4F10.09c in chromosome I	0.91	+	nuc	0					860
Q10210 UniProt NPD GO	YAY2_SCHPO	Hypothetical protein C4H3.02c in chromosome I	0.91	-	nuc	0					391
P34367 UniProt NPD GO	YLJ2_CAEEL	Hypothetical protein C50C3.2 in chromosome III	0.91	-	nuc	0					2107
O74560 UniProt NPD GO	YCZ7_SCHPO	Hypothetical protein C970.07c in chromosome III	0.91	-	nuc	0		cytoplasm [IDA] mating-type region heterochromatin [TAS] nucleus [IDA] Rik1-E3 ubiquitin ligase complex [IDA]			636
P41880 UniProt NPD GO	YPT2_CAEEL	Hypothetical protein F37A4.2	0.91	+	nuc	0					189
P34531 UniProt NPD GO	YM92_CAEEL	Hypothetical protein M01A8.2 in chromosome III	0.91	-	nuc	0					937
Q8BP00 UniProt NPD GO	IQCB1_MOUSE	IQ calmodulin-binding motif-containing protein 1	0.91	-	nuc	0					598
Q6BVY9 UniProt NPD GO	TIM50_DEBHA	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.91	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				471
O35594 UniProt NPD GO	IFT81_MOUSE	Intraflagellar transport 81 (Carnitine deficiency-associated protein expressed in ventricle 1) (CDV- ...	0.91	-	nuc	0					676
P41230 UniProt NPD GO	JAD1C_MOUSE	Jumonji/ARID domain-containing protein 1C (SmcX protein) (Xe169 protein)	0.91	-	nuc	0					1554
Q09285 UniProt NPD GO	YQK1_CAEEL	KH domain-containing protein C56G2.1	0.91	+	end	1					867
P35978 UniProt NPD GO	KINH_STRPU	Kinesin heavy chain	0.91	-	nuc	0					1031
P33176 UniProt NPD GO	KINH_HUMAN	Kinesin heavy chain (Ubiquitous kinesin heavy chain) (UKHC)	0.91	-	nuc	0	Uniformly distributed between soma and neurites in hippocampal neurons (By similarity)	kinesin complex [TAS]	602809	1MKJ	963
Q2PQA9 UniProt NPD GO	KINH_RAT	Kinesin heavy chain (Ubiquitous kinesin heavy chain) (UKHC)	0.91	-	nuc	0	Uniformly distributed between soma and neurites in hippocampal neurons				963
Q9H1H9 UniProt NPD GO	KI13A_HUMAN	Kinesin-like protein KIF13A (Kinesin-like protein RBKIN)	0.91	-	nuc	0			605433		1805
Q95LP1 UniProt NPD GO	KIF2C_MACFA	Kinesin-like protein KIF2C (Mitotic centromere-associated kinesin) (MCAK)	0.91	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				671
O43900 UniProt NPD GO	LMO6_HUMAN	LIM domain only protein 6 (Triple LIM domain protein 6)	0.91	-	nuc	0			300111		615
Q80VL3 UniProt NPD GO	LMO6_MOUSE	LIM domain only protein 6 (Triple LIM domain protein 6)	0.91	-	nuc	0					624
P11048 UniProt NPD GO	LMNA_XENLA	Lamin-A	0.91	+	nuc	0	Nucleus				665
Q03252 UniProt NPD GO	LMNB2_HUMAN	Lamin-B2	0.91	-	nuc	0	Nucleus; nuclear inner membrane; lipid-anchor; nucleoplasmic side	nuclear lamina [NAS]	150341		600
Q8BLB7 UniProt NPD GO	LMBL3_MOUSE	Lethal(3)malignant brain tumor-like 3 protein (L(3)mbt-like 3 protein)	0.91	-	nuc	0	Nucleus (Potential)				883

You are viewing entries 3701 to 3750 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.