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
Q9UMQ3 UniProt NPD GO	BARX2_HUMAN	Homeobox protein BarH-like 2	0.56	+	nuc	0	Nucleus		604823		254
P40764 UniProt NPD GO	DLX2_MOUSE	Homeobox protein DLX-2 (Homeobox protein TES-1)	0.56	+	nuc	0	Nucleus (Probable)	nucleus [IDA]			332
Q62424 UniProt NPD GO	HXA13_MOUSE	Homeobox protein Hox-A13 (Hox-1.10)	0.56	+	nuc	0	Nucleus	nucleus [IDA]			386
P18865 UniProt NPD GO	HXC4_RAT	Homeobox protein Hox-C4 (R3) (Fragment)	0.56	+	nuc	0	Nucleus				76
P52953 UniProt NPD GO	MSX2_RAT	Homeobox protein MSX-2 (Hox-8.1) (Fragment)	0.56	+	nuc	0	Nucleus				139
P56916 UniProt NPD GO	GSCL_MOUSE	Homeobox protein goosecoid-like (GSC-2)	0.56	-	nuc	0	Nucleus (By similarity)				198
P46603 UniProt NPD GO	HAT9_ARATH	Homeobox-leucine zipper protein HAT9 (Homeodomain-leucine zipper protein HAT9) (Homeodomain transcri ...	0.56	+	nuc	0	Nucleus (Potential)				274
Q8VHD8 UniProt NPD GO	HORN_MOUSE	Hornerin	0.56	-	nuc	0	Found in keratohyalin granules of the granular cells of the epidermis	cornified envelope [IDA]			2496
P36097 UniProt NPD GO	YKD3_YEAST	Hypothetical 118.9 kDa protein in PTM1-IXR1 intergenic region	0.56	-	end	0	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA]			1038
P53232 UniProt NPD GO	YG1Y_YEAST	Hypothetical 12.1 kDa protein in SCM4-MUP1 intergenic region	0.56	+	nuc	0					107
O20173 UniProt NPD GO	YCX9_CHLVU	Hypothetical 27.9 kDa protein in trnR-minE intergenic region (ORF249)	0.56	-	nuc	1 *	Plastid; chloroplast				249
P38722 UniProt NPD GO	YHE9_YEAST	Hypothetical 31.5 kDa protein in CBP2 5'region	0.56	-	mit	0					271
P32792 UniProt NPD GO	YHH7_YEAST	Hypothetical 44.2 kDa protein in SPO13-ARG4 intergenic region	0.56	-	cyt	0		mitochondrial outer membrane [IDA] mitochondrion [IDA]			385
Q02203 UniProt NPD GO	YKY5_YEAST	Hypothetical 50.3 kDa protein in PAP1-MRPL13 intergenic region	0.56	-	nuc	1					447
P38770 UniProt NPD GO	YHJ6_YEAST	Hypothetical 53.4 kDa protein in SLT2-PUT2 intergenic region	0.56	-	nuc	2	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA] nuclear envelope [IDA]			471
P92526 UniProt NPD GO	M890_ARATH	Hypothetical mitochondrial protein AtMg00890 (ORF106d)	0.56	+	nuc	0	Mitochondrion (Potential)				106
Q10906 UniProt NPD GO	YWO3_CAEEL	Hypothetical protein AH9.3	0.56	-	nuc	0					165
Q10918 UniProt NPD GO	YT15_CAEEL	Hypothetical protein B0252.5	0.56	-	nuc	0					301
Q10928 UniProt NPD GO	YWR5_CAEEL	Hypothetical protein B0302.5	0.56	-	nuc	0					165
P34294 UniProt NPD GO	YKO6_CAEEL	Hypothetical protein C05B5.6	0.56	-	nuc	0					408
Q17667 UniProt NPD GO	YANI_CAEEL	Hypothetical protein C05E11.1	0.56	-	nuc	2 *					342
Q09873 UniProt NPD GO	YAGA_SCHPO	Hypothetical protein C12G12.10 in chromosome I	0.56	-	nuc	0					420
P87293 UniProt NPD GO	YDN1_SCHPO	Hypothetical protein C16A10.01 in chromosome I	0.56	-	nuc	9	Membrane; multi-pass membrane protein (Potential)				830
O74463 UniProt NPD GO	YQC1_SCHPO	Hypothetical protein C1739.01 in chromosome III	0.56	-	nuc	0					547
Q10496 UniProt NPD GO	YDG9_SCHPO	Hypothetical protein C26F1.09 in chromosome I	0.56	-	nuc	0					1031
Q92363 UniProt NPD GO	YEJL_SCHPO	Hypothetical protein C31G5.21 in chromosome I	0.56	-	nuc	0					118
Q10141 UniProt NPD GO	YAS5_SCHPO	Hypothetical protein C3H8.05c precursor	0.56	-	mit	0					1073
Q10239 UniProt NPD GO	YD16_SCHPO	Hypothetical protein C4G9.06c in chromosome I	0.56	-	nuc	0					113
Q09936 UniProt NPD GO	YSE2_CAEEL	Hypothetical protein C53C9.2 in chromosome X	0.56	-	nuc	0					397
O14200 UniProt NPD GO	YDQ7_SCHPO	Hypothetical protein C5D6.07c in chromosome I	0.56	-	nuc	1	Membrane; multi-pass membrane protein (Potential)				495
O45435 UniProt NPD GO	YV4Q_CAEEL	Hypothetical protein F32B6.9 in chromosome IV	0.56	-	mit	4 *					413
Q09601 UniProt NPD GO	YRM5_CAEEL	Hypothetical protein R06F6.5	0.56	-	nuc	0					378
Q09355 UniProt NPD GO	YRY5_CAEEL	Hypothetical protein T15H9.5	0.56	+	nuc	0					173
Q09622 UniProt NPD GO	YS83_CAEEL	Hypothetical protein ZK945.3 in chromosome II	0.56	+	nuc	0					766
P33307 UniProt NPD GO	CSE1_YEAST	Importin alpha re-exporter (Chromosome segregation protein CSE1)	0.56	-	cyt	0	Cytoplasm. Nucleus	nuclear envelope [IDA]		1Z3H	960
Q9UI26 UniProt NPD GO	IPO11_HUMAN	Importin-11 (Imp11) (Ran-binding protein 11) (RanBP11)	0.56	-	mit	0	Cytoplasm. Nucleus				975
O14300 UniProt NPD GO	OXA11_SCHPO	Inner membrane protein oxa1-1, mitochondrial precursor (Cytochrome oxidase biogenesis protein 1-1) ( ...	0.56	-	end	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrial inner membrane [TAS]			374
Q4JL91 UniProt NPD GO	IPPK_BRARE	Inositol-pentakisphosphate 2-kinase (EC 2.7.1.-) (Inositol-1,3,4,5,6-pentakisphosphate 2-kinase) (In ...	0.56	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				483
Q93105 UniProt NPD GO	INSR_AEDAE	Insulin-like receptor precursor (EC 2.7.10.1) (MIR) [Contains: Insulin-like receptor alpha chain; In ...	0.56	+	end	1	Membrane; single-pass type I membrane protein (By similarity)	integral to plasma membrane [ISS]			1390
P23229 UniProt NPD GO	ITA6_HUMAN	Integrin alpha-6 precursor (VLA-6) (CD49f antigen) [Contains: Integrin alpha-6 heavy chain; Integrin ...	0.56	-	end	1	Membrane; single-pass type I membrane protein		226730		1130
P01567 UniProt NPD GO	IFNA7_HUMAN	Interferon alpha-7 precursor (Interferon alpha-J1) (IFN-alpha-J1) (Interferon alpha-J) (LeIF J)	0.56	-	mit	0	Secreted protein	extracellular region [TAS]	147567		189
P49877 UniProt NPD GO	IFNAG_BOVIN	Interferon alpha-G precursor	0.56	-	exc	1 *	Secreted protein				189
P18590 UniProt NPD GO	MX3_RAT	Interferon-induced GTP-binding protein Mx3	0.56	-	nuc	0	Cytoplasm				659
P46647 UniProt NPD GO	IL1A_CERTO	Interleukin-1 alpha precursor (IL-1 alpha)	0.56	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				271
P26897 UniProt NPD GO	IL2RA_RAT	Interleukin-2 receptor alpha chain precursor (IL-2 receptor alpha subunit) (IL-2-RA) (IL2-RA) (CD25 ...	0.56	-	nuc	1	Membrane; single-pass type I membrane protein				267
P52191 UniProt NPD GO	IRK16_RAT	Inward rectifier potassium channel 16 (Potassium channel, inwardly rectifying subfamily J member 16) ...	0.56	+	end	2	Membrane; multi-pass membrane protein				419
Q9P2K6 UniProt NPD GO	KLDC5_HUMAN	Kelch domain-containing protein 5	0.56	-	cyt	0					505
Q5K2P4 UniProt NPD GO	K1C13_PROAT	Keratin, type I cytoskeletal 13 (Cytokeratin-13) (CK-13) (Keratin-13) (K13)	0.56	-	nuc	0					465
Q28810 UniProt NPD GO	K2C8_POTTR	Keratin, type II cytoskeletal 8 (Cytokeratin-8) (CK-8) (Keratin-8) (K8) (Fragment)	0.56	-	mit	0					310
Q60682 UniProt NPD GO	KLRA8_MOUSE	Killer cell lectin-like receptor 8 (T-cell surface glycoprotein Ly-49H) (Ly49-H antigen) (Lymphocyte ...	0.56	-	nuc	1 *	Membrane; single-pass type II membrane protein	plasma membrane [TAS]			266

You are viewing entries 21401 to 21450 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.