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
Q9Y663 UniProt NPD GO	OST3A_HUMAN	Heparan sulfate glucosamine 3-O-sulfotransferase 3A1 (EC 2.8.2.30) (Heparan sulfate D-glucosaminyl 3 ...	0.65	+	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)	integral to membrane [TAS]	604057	1T8U	406
Q56UJ5 UniProt NPD GO	H6ST1_BRARE	Heparan-sulfate 6-O-sulfotransferase 1 (EC 2.8.2.-) (HS6ST-1)	0.65	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				405
Q8IZP7 UniProt NPD GO	H6ST3_HUMAN	Heparan-sulfate 6-O-sulfotransferase 3 (EC 2.8.2.-) (HS6ST-3)	0.65	+	mit	1 *	Membrane; single-pass type II membrane protein (Potential)		609401		471
Q9Y251 UniProt NPD GO	HPSE_HUMAN	Heparanase precursor (EC 3.2.-.-) (Heparanase-1) (Hpa1) (Endo-glucoronidase) [Contains: Heparanase 8 ...	0.65	-	exc	0	Lysosome; lysosomal membrane; peripheral membrane protein. Secreted protein. Secreted, internalised ...		604724		543
Q92902 UniProt NPD GO	HPS1_HUMAN	Hermansky-Pudlak syndrome 1 protein	0.65	-	cyt	0		cytoplasm [TAS] cytoplasmic membrane-bound vesicle [IDA] integral to plasma membrane [TAS] lysosome [TAS] membrane fraction [TAS] soluble fraction [TAS]	604982		700
Q5R715 UniProt NPD GO	HMGN3_PONPY	High mobility group nucleosome-binding domain-containing protein 3	0.65	-	nuc	0	Nucleus (By similarity)				99
P33778 UniProt NPD GO	H2B1B_HUMAN	Histone H2B type 1-B (H2B.f) (H2B/f) (H2B.1)	0.65	+	nuc	0	Nucleus	nucleosome [NAS]	602803		125
Q8SVT3 UniProt NPD GO	HD5_ENCCU	Homeobox protein HD-5 (EcHD-5)	0.65	-	nuc	0	Nucleus				133
P42581 UniProt NPD GO	HMX3_MOUSE	Homeobox protein HMX3 (Homeobox protein Nkx-5.1)	0.65	+	nuc	0	Nucleus (Probable)				458
Q9IA19 UniProt NPD GO	HXA1_HETFR	Homeobox protein Hox-A1	0.65	+	nuc	0	Nucleus (By similarity)				326
Q9IA20 UniProt NPD GO	HXA2_HETFR	Homeobox protein Hox-A2	0.65	+	nuc	0	Nucleus (By similarity)				363
P31357 UniProt NPD GO	HXB1_AMBME	Homeobox protein Hox-B1 (AHox1) (Fragment)	0.65	+	nuc	1	Nucleus				184
P17919 UniProt NPD GO	HXB1_MOUSE	Homeobox protein Hox-B1 (Hox-2.9)	0.65	+	nuc	0	Nucleus				297
P50207 UniProt NPD GO	HXC13_MOUSE	Homeobox protein Hox-C13	0.65	+	nuc	0	Nucleus				328
P09020 UniProt NPD GO	HXC5_XENLA	Homeobox protein Hox-C5 (XlHbox-5) (Fragment)	0.65	+	nuc	0	Nucleus				87
Q28601 UniProt NPD GO	HXC9_SHEEP	Homeobox protein Hox-C9 (Fragment)	0.65	+	nuc	0	Nucleus				96
O00470 UniProt NPD GO	MEIS1_HUMAN	Homeobox protein Meis1	0.65	-	nuc	0	Nucleus (By similarity)		601739		390
P97367 UniProt NPD GO	MEIS2_MOUSE	Homeobox protein Meis2 (Meis1-related protein 1)	0.65	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			477
Q90267 UniProt NPD GO	OTX1L_BRARE	Homeobox protein Otx1l (ZOTX3)	0.65	-	nuc	0	Nucleus (Probable)				338
Q9QZ28 UniProt NPD GO	SIX6_MOUSE	Homeobox protein SIX6 (Sine oculis homeobox homolog 6) (Optic homeobox 2) (Six9 protein)	0.65	-	nuc	0	Nucleus (By similarity)				246
Q26605 UniProt NPD GO	SMOX6_SCHMA	Homeobox protein SMOX-6 (Fragment)	0.65	+	nuc	0	Nucleus (Potential)				204
P50476 UniProt NPD GO	HOX3_XENLA	Homeobox protein XHOX-3	0.65	+	nuc	0	Nucleus				388
Q04281 UniProt NPD GO	HOX71_XENLA	Homeobox protein XHOX-7.1 (Fragment)	0.65	+	nuc	0	Nucleus (Probable)				295
P46667 UniProt NPD GO	ATHB5_ARATH	Homeobox-leucine zipper protein ATHB-5 (HD-ZIP protein ATHB-5)	0.65	+	nuc	0	Nucleus				312
P15304 UniProt NPD GO	LIPS_RAT	Hormone-sensitive lipase (EC 3.1.1.79) (HSL)	0.65	-	nuc	0					1068
P53329 UniProt NPD GO	YG5Q_YEAST	Hypothetical 20.0 kDa protein in YTA7-TAF145 intergenic region	0.65	-	nuc	0					174
P36038 UniProt NPD GO	YKU8_YEAST	Hypothetical 31.2 kDa protein in STE6-LOS1 intergenic region	0.65	-	nuc	0		mitochondrion [IDA]			271
P36144 UniProt NPD GO	YK40_YEAST	Hypothetical 31.6 kDa protein in TIF1-KTR2 intergenic region	0.65	-	nuc	0		nucleolus [IDA] nucleus [IDA]			274
P40534 UniProt NPD GO	YID7_YEAST	Hypothetical 75.0 kDa protein in NOT3-CKA1 intergenic region	0.65	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				656
P36122 UniProt NPD GO	YK07_YEAST	Hypothetical 88.0 kDa protein in GCN3-SAP190 intergenic region	0.65	-	cyt	0		mitochondrion [IDA]			765
Q09623 UniProt NPD GO	YS85_CAEEL	Hypothetical RING finger protein ZK945.5 in chromosome II	0.65	-	nuc	0					250
P92563 UniProt NPD GO	M1330_ARATH	Hypothetical mitochondrial protein AtMg01330 (ORF107h)	0.65	-	nuc	0	Mitochondrion (Potential)				127
O82368 UniProt NPD GO	Y2988_ARATH	Hypothetical protein At2g29880	0.65	-	nuc	0					308
P34256 UniProt NPD GO	YKA4_CAEEL	Hypothetical protein B0303.4	0.65	-	end	4 *					616
Q10440 UniProt NPD GO	YDE6_SCHPO	Hypothetical protein C12B10.06c in chromosome I	0.65	-	mit	0					139
Q10267 UniProt NPD GO	YD33_SCHPO	Hypothetical protein C13G7.03 in chromosome I	0.65	+	nuc	0					278
P87299 UniProt NPD GO	YDN8_SCHPO	Hypothetical protein C16A10.08c in chromosome I	0.65	-	nuc	0					285
Q9UTG5 UniProt NPD GO	YKEA_SCHPO	Hypothetical protein C1805.10 in chromosome I	0.65	-	nuc	0					527
O42962 UniProt NPD GO	YGME_SCHPO	Hypothetical protein C19G7.14c in chromosome II	0.65	-	nuc	0					411
Q09894 UniProt NPD GO	YAI7_SCHPO	Hypothetical protein C24B11.07c in chromosome I	0.65	-	nuc	0					561
Q09890 UniProt NPD GO	YC9G_SCHPO	Hypothetical protein C584.16c in chromosome III	0.65	-	nuc	0					231
O14204 UniProt NPD GO	YDQC_SCHPO	Hypothetical protein C5D6.12 in chromosome I	0.65	-	mit	0					314
Q9Y7L4 UniProt NPD GO	YGJ2_SCHPO	Hypothetical protein C685.02 in chromosome II	0.65	-	nuc	0					409
Q8SV63 UniProt NPD GO	Y6G2_ENCCU	Hypothetical protein ECU06_1620	0.65	-	end	0					579
Q10017 UniProt NPD GO	YSW1_CAEEL	Hypothetical protein T25D10.1	0.65	-	nuc	1 *					327
P34623 UniProt NPD GO	YO87_CAEEL	Hypothetical protein ZK1236.7	0.65	+	nuc	1 *					324
P34672 UniProt NPD GO	YO22_CAEEL	Hypothetical protein ZK688.2 in chromosome III	0.65	+	end	4 *					632
O15397 UniProt NPD GO	IPO8_HUMAN	Importin-8 (Imp8) (Ran-binding protein 8) (RanBP8)	0.65	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)		605600		1037
P07250 UniProt NPD GO	IPMK_YEAST	Inositol polyphosphate multikinase (EC 2.7.1.151) (IPMK) (Arginine metabolism regulation protein III ...	0.65	-	nuc	0		nucleus [IDA]			355
P50480 UniProt NPD GO	ISL2_RAT	Insulin gene enhancer protein ISL-2 (Islet-2)	0.65	+	nuc	0	Nucleus			1BW5	360

You are viewing entries 16351 to 16400 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.