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
O35353 UniProt NPD GO	GBB4_RAT	Guanine nucleotide-binding protein subunit beta 4 (Transducin beta chain 4)	0.36	-	cyt	0					339
Q6CSZ0 UniProt NPD GO	NOP10_KLULA	H/ACA ribonucleoprotein complex subunit 3 (Nucleolar protein family A member 3) (snoRNP protein NOP1 ...	0.36	-	nuc	0	Nucleus; nucleolus (By similarity)				57
Q86Y56 UniProt NPD GO	HEAT2_HUMAN	HEAT repeat-containing protein 2	0.36	-	end	0					855
O35387 UniProt NPD GO	HAX1_MOUSE	HS1-associating protein X-1 (HAX-1) (HS1-binding protein)	0.36	-	nuc	0	Mitochondrion (By similarity). Endoplasmic reticulum (By similarity). Nucleus; nuclear membrane (By ...	mitochondrion [IDA]			280
P34930 UniProt NPD GO	HS70A_PIG	Heat shock 70 kDa protein 1A (HSP70.1)	0.36	-	cyt	0					641
P34932 UniProt NPD GO	HSP74_HUMAN	Heat shock 70 kDa protein 4 (Heat shock 70-related protein APG-2) (HSP70RY)	0.36	-	nuc	0	Cytoplasm (Probable)	cytoplasm [NAS]	601113		840
Q9N1U2 UniProt NPD GO	HSP76_SAGOE	Heat shock 70 kDa protein 6 (Hsp-70-related intracellular vitamin D-binding protein)	0.36	-	cyt	0					643
Q91055 UniProt NPD GO	HELO_HELHO	Helothermine precursor (HLTx)	0.36	-	exc	0	Secreted protein				242
P09601 UniProt NPD GO	HMOX1_HUMAN	Heme oxygenase 1 (EC 1.14.99.3) (HO-1)	0.36	-	cyt	1	Microsome	endoplasmic reticulum [TAS] membrane fraction [TAS]	141250	1XK3	288
P42665 UniProt NPD GO	HGLB_SCHJA	Hemoglobinase precursor (EC 3.4.22.34) (Antigen Sj32)	0.36	-	mit	0					423
O17645 UniProt NPD GO	HST2_CAEEL	Heparan sulfate 2-O-sulfotransferase hst-2 (EC 2.8.2.-) (Heparan sulfotransferase 2) (HS2ST1 homolog ...	0.36	+	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				324
P12226 UniProt NPD GO	FGF2_XENLA	Heparin-binding growth factor 2 precursor (HBGF-2) (Basic fibroblast growth factor) (BFGF)	0.36	-	nuc	0					155
O35799 UniProt NPD GO	HFE_RAT	Hereditary hemochromatosis protein homolog precursor (RT1-CAFE)	0.36	-	end	2 *	Membrane; single-pass type I membrane protein				360
Q91VB4 UniProt NPD GO	HPS3_MOUSE	Hermansky-Pudlak syndrome 3 protein homolog (Cocoa protein)	0.36	-	mit	0	Cytoplasm	cytoplasm [IDA]			1002
P48809 UniProt NPD GO	RB27C_DROME	Heterogeneous nuclear ribonucleoprotein 27C (Hrb27-C) (hnRNP 48) (HRP48.1)	0.36	-	nuc	0	Nucleus. Cytoplasm. Nuclear and/or cytoplasmic	nucleoplasm [IDA] ribonucleoprotein complex [IDA]			421
P07156 UniProt NPD GO	HMGB1_CRIGR	High mobility group protein B1 (High mobility group protein 1) (HMG-1) (Fragment)	0.36	-	nuc	0	Nucleus	condensed chromosome [ISS]		1NHN	180
P43276 UniProt NPD GO	H15_MOUSE	Histone H1.5 (H1 VAR.5) (H1b)	0.36	+	nuc	0	Nucleus				222
P82887 UniProt NPD GO	H2B_OLILU	Histone H2B	0.36	-	nuc	0	Nucleus				113
P02280 UniProt NPD GO	H2B_CRONI	Histone H2B (Fragment)	0.36	-	cyt	0	Nucleus				92
P69110 UniProt NPD GO	H32_TETAM	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69111 UniProt NPD GO	H32_TETAU	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69112 UniProt NPD GO	H32_TETCA	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69113 UniProt NPD GO	H32_TETCU	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69114 UniProt NPD GO	H32_TETEL	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69115 UniProt NPD GO	H32_TETFU	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69116 UniProt NPD GO	H32_TETHY	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69117 UniProt NPD GO	H32_TETLE	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69118 UniProt NPD GO	H32_TETMA	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69119 UniProt NPD GO	H32_TETMI	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69120 UniProt NPD GO	H32_TETNA	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69121 UniProt NPD GO	H32_TETNI	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69123 UniProt NPD GO	H32_TETPA	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69124 UniProt NPD GO	H32_TETPI	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69122 UniProt NPD GO	H32_TETPR	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69125 UniProt NPD GO	H32_TETRO	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69126 UniProt NPD GO	H32_TETSO	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P69127 UniProt NPD GO	H32_TETTR	Histone H3.2 (Fragment)	0.36	-	nuc	0	Nucleus (By similarity)				40
P02301 UniProt NPD GO	H34_MOUSE	Histone H3.4 (Embryonic)	0.36	-	nuc	0	Nucleus (By similarity)				134
Q8NIG3 UniProt NPD GO	H4_CANGA	Histone H4	0.36	-	cyt	0	Nucleus (By similarity)				102
Q757K0 UniProt NPD GO	H41_ASHGO	Histone H4.1	0.36	-	cyt	0	Nucleus (By similarity)				102
Q03330 UniProt NPD GO	GCN5_YEAST	Histone acetyltransferase GCN5 (EC 2.3.1.48)	0.36	+	nuc	0	Nucleus	Ada2/Gcn5/Ada3 transcription activator complex [IPI] SAGA complex [IDA] SLIK (SAGA-like) complex [IPI]		1YGH	439
Q6CSI1 UniProt NPD GO	HAT2_KLULA	Histone acetyltransferase type B subunit 2 (EC 2.3.1.48)	0.36	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				408
Q9ER42 UniProt NPD GO	BARX1_MOUSE	Homeobox protein BarH-like 1	0.36	+	nuc	0	Nucleus (Probable)				254
Q9N0M2 UniProt NPD GO	BARX2_SHEEP	Homeobox protein BarH-like 2 (Fragment)	0.36	+	nuc	0	Nucleus (By similarity)				133
P81193 UniProt NPD GO	CDX_LINSA	Homeobox protein CDX (Caudal-type homeobox protein) (LSCDX) (Fragment)	0.36	+	nuc	0	Nucleus (By similarity)				70
Q9BZM3 UniProt NPD GO	GSH2_HUMAN	Homeobox protein GSH-2	0.36	+	nuc	0	Nucleus (By similarity)				304
P14158 UniProt NPD GO	HXD3_SHEEP	Homeobox protein Hox-D3 (Homeobox protein Hox-7.1) (OHox-7.1) (Fragment)	0.36	-	nuc	0	Nucleus (Potential)				46
P52651 UniProt NPD GO	RHOX5_MOUSE	Homeobox protein Rhox5 (Reproductive homeobox on chromosome X 5) (Homeobox protein Pem) (Placenta an ...	0.36	-	cyt	0	Nucleus (Potential)	cytoplasm [IDA] nucleus [IDA]			210
P31537 UniProt NPD GO	HME1A_XENLA	Homeobox protein engrailed-1-A (En-1A) (Fragment)	0.36	+	nuc	0	Nucleus (Potential)				60
O60062 UniProt NPD GO	MET2_SCHPO	Homoserine O-acetyltransferase (EC 2.3.1.31) (Homoserine O-trans-acetylase)	0.36	-	nuc	0					489

You are viewing entries 35001 to 35050 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.