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
Q61039 UniProt NPD GO	HAND2_MOUSE	Heart- and neural crest derivatives-expressed protein 2 (Deciduum, heart, autonomic nervous system a ...	0.57	+	nuc	0		transcription factor complex [IDA]			217
Q08277 UniProt NPD GO	HSP82_MAIZE	Heat shock protein 82	0.57	-	cyt	0	Cytoplasm (Potential)				715
P27741 UniProt NPD GO	HSP83_LEIAM	Heat shock protein 83 (HSP 83)	0.57	-	cyt	0	Cytoplasm				701
Q25293 UniProt NPD GO	HSP83_LEIIN	Heat shock protein 83-1 (HSP 83)	0.57	-	cyt	0	Cytoplasm (By similarity)				701
P31540 UniProt NPD GO	HSP98_NEUCR	Heat shock protein HSP98	0.57	-	nuc	0	More concentrated in polyribosomes than in monoribosomes, and preferentially localized in the large ...				927
O60243 UniProt NPD GO	H6ST1_HUMAN	Heparan-sulfate 6-O-sulfotransferase 1 (EC 2.8.2.-) (HS6ST-1)	0.57	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)	integral to plasma membrane [TAS]	604846		410
Q91ZB4 UniProt NPD GO	H6ST1_CRIGR	Heparan-sulfate 6-O-sulfotransferase 1 (EC 2.8.2.-) (HS6ST-1) (Fragment)	0.57	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				403
Q76KB2 UniProt NPD GO	H6ST1_CHICK	Heparan-sulfate 6-O-sulfotransferase 1 (EC 2.8.2.-) (HS6ST-1) (cHS6ST-1)	0.57	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				408
O35479 UniProt NPD GO	HNRPG_MOUSE	Heterogeneous nuclear ribonucleoprotein G (hnRNP G) (RNA-binding motif protein, X chromosome)	0.57	-	nuc	0	Nucleus. Component of ribonucleosomes	nucleus [IDA]			388
P52925 UniProt NPD GO	HMGB2_RAT	High mobility group protein B2 (High mobility group protein 2) (HMG-2)	0.57	-	nuc	0	Nucleus	condensed chromosome [ISS] cytoplasm [ISS] nucleus [ISS] perinuclear region [ISS]			209
Q8K585 UniProt NPD GO	HMGA1_RAT	High mobility group protein HMG-I/HMG-Y (HMG-I(Y)) (High mobility group AT-hook protein 1) (High mob ...	0.57	+	nuc	0	Nucleus				106
O60658 UniProt NPD GO	PDE8A_HUMAN	High-affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8A (EC 3.1.4.17)	0.57	-	nuc	0			602972	1LXX	829
P26568 UniProt NPD GO	H11_ARATH	Histone H1.1	0.57	+	nuc	0	Nucleus				274
Q9LD75 UniProt NPD GO	H2A2_LILLO	Histone H2A.2 (GH2A)	0.57	-	nuc	0	Nucleus (By similarity)				128
P70696 UniProt NPD GO	H2B1A_MOUSE	Histone H2B type 1-A (Histone H2B, testis) (Testis-specific histone H2B)	0.57	-	nuc	0	Nucleus				126
P58876 UniProt NPD GO	H2B1D_HUMAN	Histone H2B type 1-D (H2B.b) (H2B/b) (H2B.1 B) (HIRA-interacting protein 2)	0.57	+	nuc	0	Nucleus	nucleosome [ISS]	602799		125
P10854 UniProt NPD GO	H2B1M_MOUSE	Histone H2B type 1-M (H2B 291B)	0.57	+	nuc	0	Nucleus	nucleosome [ISS]			125
Q9MBF7 UniProt NPD GO	H2B_LILLO	Histone H2B.1 (GH2B)	0.57	+	nuc	0	Nucleus (By similarity)				158
P02288 UniProt NPD GO	H2BE2_PSAMI	Histone H2B.2, embryonic	0.57	-	nuc	0	Nucleus				122
Q06196 UniProt NPD GO	H3_ENTHI	Histone H3	0.57	-	nuc	0	Nucleus				134
Q5DWI3 UniProt NPD GO	H3_MARPO	Histone H3	0.57	-	nuc	0	Nucleus (By similarity)				135
P07041 UniProt NPD GO	H3_NEUCR	Histone H3	0.57	-	nuc	0	Nucleus (By similarity)				135
P61835 UniProt NPD GO	H3_TRIRE	Histone H3	0.57	-	nuc	0	Nucleus (By similarity)				135
P22844 UniProt NPD GO	H5A_XENLA	Histone H5A (XLH5A) (H1D) (H1-SA)	0.57	+	nuc	0	Nucleus				196
Q6V9I6 UniProt NPD GO	HD2A_SOLCH	Histone deacetylase 2a (HD2a) (ScHD2a)	0.57	-	nuc	0	Nucleus; nucleolus (By similarity)				269
Q99626 UniProt NPD GO	CDX2_HUMAN	Homeobox protein CDX-2 (Caudal-type homeobox protein 2) (CDX-3)	0.57	+	nuc	0	Nucleus		600297		313
P56177 UniProt NPD GO	DLX1_HUMAN	Homeobox protein DLX-1	0.57	+	nuc	0	Nucleus (Potential)	nucleus [NAS]	600029		255
Q64317 UniProt NPD GO	DLX1_MOUSE	Homeobox protein DLX-1	0.57	+	nuc	0	Nucleus (Potential)	nucleus [IDA]			255
Q07687 UniProt NPD GO	DLX2_HUMAN	Homeobox protein DLX-2	0.57	+	nuc	0	Nucleus (Potential)		126255		328
Q64205 UniProt NPD GO	DLX3_MOUSE	Homeobox protein DLX-3	0.57	+	nuc	0	Nucleus (Potential)				287
P50574 UniProt NPD GO	DLX2A_BRARE	Homeobox protein Dlx2a (DLX-2) (Distal-less homeobox gene 2a)	0.57	+	nuc	0	Nucleus (Potential)				270
P09637 UniProt NPD GO	HXA5_SALSA	Homeobox protein Hox-A5 (S12-B) (Fragment)	0.57	+	nuc	0	Nucleus				78
P31268 UniProt NPD GO	HXA7_HUMAN	Homeobox protein Hox-A7 (Hox-1A) (Hox 1.1)	0.57	+	nuc	0	Nucleus		142950		230
Q9PWD5 UniProt NPD GO	HXA9_MORSA	Homeobox protein Hox-A9	0.57	+	nuc	0	Nucleus (By similarity)				269
P14652 UniProt NPD GO	HXB2_HUMAN	Homeobox protein Hox-B2 (Hox-2H) (Hox-2.8) (K8)	0.57	+	nuc	0	Nucleus		142967		356
P23682 UniProt NPD GO	HXB3_CHICK	Homeobox protein Hox-B3 (Chox-2.7)	0.57	+	nuc	0	Nucleus				399
P31313 UniProt NPD GO	HXC12_MOUSE	Homeobox protein Hox-C12 (Hox-3.8) (Fragment)	0.57	+	nuc	0	Nucleus				60
Q98SH9 UniProt NPD GO	HXC1A_BRARE	Homeobox protein Hox-C1a	0.57	+	nuc	0	Nucleus (By similarity)				302
Q22910 UniProt NPD GO	HM31_CAEEL	Homeobox protein ceh-31	0.57	-	nuc	0	Nucleus (Probable)				244
P20269 UniProt NPD GO	HM05_CAEEL	Homeobox protein ceh-5	0.57	+	nuc	0	Nucleus (Potential)				148
O15499 UniProt NPD GO	GSCL_HUMAN	Homeobox protein goosecoid-like (GSC-2)	0.57	-	nuc	0	Nucleus (By similarity)		601845		205
P56664 UniProt NPD GO	KNOX6_MAIZE	Homeobox protein knotted-1-like 6 (Fragment)	0.57	-	nuc	0	Nucleus (Probable)				85
P56665 UniProt NPD GO	KNOX7_MAIZE	Homeobox protein knotted-1-like 7 (Fragment)	0.57	-	nuc	0	Nucleus (Probable)				85
Q8T940 UniProt NPD GO	UBX_JUNCO	Homeotic protein ultrabithorax (JcUbx)	0.57	+	nuc	0	Nucleus	nucleus [IDA]			253
P54257 UniProt NPD GO	HAP1_HUMAN	Huntingtin-associated protein 1 (HAP-1) (Neuroan 1)	0.57	-	mit	0		actin cytoskeleton [TAS]	600947		671
P25657 UniProt NPD GO	YCY9_YEAST	Hypothetical 18.0 kDa protein in GIT1-PAU3 intergenic region	0.57	-	nuc	0					155
P09754 UniProt NPD GO	YCX2_CHLMO	Hypothetical 35.9 kDa protein in psbA intron 2	0.57	-	nuc	0	Plastid; chloroplast				312
P18634 UniProt NPD GO	YL392_YEAST	Hypothetical 59.8 kDa protein in SSR1-ATP10 intergenic region	0.57	-	nuc	0		cytoplasm [IDA]			518
Q09202 UniProt NPD GO	YP23_CAEEL	Hypothetical protein AH6.3	0.57	-	nuc	1 *					230
P34338 UniProt NPD GO	YK14_CAEEL	Hypothetical protein C15H7.4	0.57	-	nuc	0					327

You are viewing entries 20751 to 20800 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.