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
Q09762 UniProt NPD GO	YA78_SCHPO	Hypothetical protein C24H6.08 in chromosome I	0.32	-	nuc	0					220
Q09700 UniProt NPD GO	YA29_SCHPO	Hypothetical protein C2F7.09c in chromosome I	0.32	-	nuc	0					491
Q09279 UniProt NPD GO	YQI6_CAEEL	Hypothetical protein C45G9.6	0.32	-	exc	0					542
Q10250 UniProt NPD GO	YD22_SCHPO	Hypothetical protein C56F8.02 in chromosome I	0.32	-	mit	0	Membrane; multi-pass membrane protein (Potential)				1517
P34423 UniProt NPD GO	YL32_CAEEL	Hypothetical protein F44B9.2	0.32	-	cyt	0					503
Q9P6S6 UniProt NPD GO	YNL1_SCHPO	Hypothetical protein SPBC27.01c in chromosome II	0.32	-	cyt	0					132
Q22111 UniProt NPD GO	YC5D_CAEEL	Hypothetical protein T02G5.13 in chromosome II	0.32	-	mit	0					399
Q10014 UniProt NPD GO	YR01_CAEEL	Hypothetical protein T25E4.1 precursor	0.32	-	end	0	Membrane; multi-pass membrane protein (Potential)				231
P30652 UniProt NPD GO	YOW6_CAEEL	Hypothetical protein ZK643.6 precursor	0.32	-	nuc	0					180
Q09541 UniProt NPD GO	YQS6_CAEEL	Hypothetical subtilase-type proteinase F21H12.6 in chromosome II (EC 3.4.21.-)	0.32	-	mit	0					1374
O13600 UniProt NPD GO	YNI6_SCHPO	Hypothetical zinc finger SWIM domain-containing protein SPBC11B10.06	0.32	-	nuc	0					209
Q9NWT6 UniProt NPD GO	HIF1N_HUMAN	Hypoxia-inducible factor 1 alpha inhibitor (EC 1.14.11.16) (Hypoxia-inducible factor asparagine hydr ...	0.32	-	cyt	0	Nucleus (Potential)		606615	1YCI	349
Q6BIV1 UniProt NPD GO	ISN1_DEBHA	IMP-specific 5'-nucleotidase 1 (EC 3.1.3.-)	0.32	-	nuc	0					485
P01593 UniProt NPD GO	KV1A_HUMAN	Ig kappa chain V-I region AG	0.32	-	nuc	0		extracellular region [NAS]			108
P04434 UniProt NPD GO	KV3J_HUMAN	Ig kappa chain V-III region VH precursor (Fragment)	0.32	-	nuc	0		extracellular region [NAS]			116
P23108 UniProt NPD GO	IGJ_RABIT	Immunoglobulin J chain	0.32	-	nuc	0					136
P40069 UniProt NPD GO	IMB4_YEAST	Importin beta-4 subunit (Karyopherin beta-4 subunit) (Ran-binding protein YRB4)	0.32	-	cyt	0	Cytoplasm. Nucleus. Nucleus; nuclear envelope; nuclear pore complex	cytoplasm [IDA] nuclear pore [IDA] nucleus [IDA]			1113
Q9LSQ4 UniProt NPD GO	GH36_ARATH	Indole-3-acetic acid-amido synthetase GH3.6 (EC 6.3.2.-) (Auxin-responsive GH3-like protein 6) (AtGH ...	0.32	-	cyt	0					612
Q6CIB3 UniProt NPD GO	LPE10_KLULA	Inner membrane magnesium transporter LPE10, mitochondrial precursor	0.32	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				397
Q95221 UniProt NPD GO	IP6K2_RABIT	Inositol hexakisphosphate kinase 2 (EC 2.7.4.21) (InsP6 kinase 2) (Inositol hexakisphosphate kinase ...	0.32	-	mit	0	Nucleus (By similarity)				425
Q5PXE9 UniProt NPD GO	IPPK_RAT	Inositol-pentakisphosphate 2-kinase (EC 2.7.1.-) (Inositol-1,3,4,5,6-pentakisphosphate 2-kinase) (In ...	0.32	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable)	intracellular [ISS]			489
Q9WTL4 UniProt NPD GO	INSRR_MOUSE	Insulin receptor-related protein precursor (EC 2.7.10.1) (IRR) (IR-related receptor) [Contains: Insu ...	0.32	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				1300
Q02815 UniProt NPD GO	IGF1_ONCMY	Insulin-like growth factor I precursor (IGF-I) (Somatomedin)	0.32	-	nuc	0	Secreted protein				176
P24853 UniProt NPD GO	IBP2_PIG	Insulin-like growth factor-binding protein 2 precursor (IGFBP-2) (IBP-2) (IGF-binding protein 2)	0.32	-	exc	0	Secreted protein				316
O75578 UniProt NPD GO	ITA10_HUMAN	Integrin alpha-10 precursor	0.32	-	end	1	Membrane; single-pass type I membrane protein	integrin complex [TAS]	604042		1167
P06756 UniProt NPD GO	ITAV_HUMAN	Integrin alpha-V precursor (Vitronectin receptor subunit alpha) (CD51 antigen) [Contains: Integrin a ...	0.32	-	nuc	1	Membrane; single-pass type I membrane protein	integrin complex [NAS]	193210	1U8C	1048
P20702 UniProt NPD GO	ITAX_HUMAN	Integrin alpha-X precursor (Leukocyte adhesion glycoprotein p150,95 alpha chain) (Leukocyte adhesion ...	0.32	-	end	1	Membrane; single-pass type I membrane protein	integrin complex [TAS]	151510	1N3Y	1163
P07228 UniProt NPD GO	ITB1_CHICK	Integrin beta-1 precursor (CSAT antigen) (JG22 antigen) (RGD-receptor)	0.32	-	nuc	1	Membrane; single-pass type I membrane protein				803
Q5R5S7 UniProt NPD GO	ITBP1_PONPY	Integrin beta-1-binding protein 1	0.32	-	mit	0	Cytoplasm (By similarity)				200
P18084 UniProt NPD GO	ITB5_HUMAN	Integrin beta-5 precursor	0.32	-	exc	1	Membrane; single-pass type I membrane protein		147561		799
P19823 UniProt NPD GO	ITIH2_HUMAN	Inter-alpha-trypsin inhibitor heavy chain H2 precursor (ITI heavy chain H2) (Inter-alpha-inhibitor h ...	0.32	-	vac	0		extracellular region [NAS]	146640		946
P01574 UniProt NPD GO	IFNB_HUMAN	Interferon beta precursor (IFN-beta) (Fibroblast interferon)	0.32	-	exc	1 *	Secreted protein	extracellular region [IC]	147640	1AU1	187
P27930 UniProt NPD GO	IL1R2_HUMAN	Interleukin-1 receptor type II precursor (IL-1R-2) (IL-1R-beta) (CD121b antigen) (CDw121b)	0.32	+	nuc	1	Membrane; single-pass type I membrane protein		147811		398
P47873 UniProt NPD GO	IL11_MOUSE	Interleukin-11 precursor (IL-11)	0.32	-	end	0	Secreted protein	extracellular region [ISS]			199
Q29615 UniProt NPD GO	IL2_MACFA	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.32	-	exc	0	Secreted protein	extracellular space [ISS]			154
P48050 UniProt NPD GO	IRK4_HUMAN	Inward rectifier potassium channel 4 (Potassium channel, inwardly rectifying subfamily J member 4) ( ...	0.32	-	mit	3	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	600504		445
Q64198 UniProt NPD GO	IRK4_MESAU	Inward rectifier potassium channel 4 (Potassium channel, inwardly rectifying subfamily J member 4) ( ...	0.32	-	mit	3	Membrane; multi-pass membrane protein				444
P52189 UniProt NPD GO	IRK4_MOUSE	Inward rectifier potassium channel 4 (Potassium channel, inwardly rectifying subfamily J member 4) ( ...	0.32	-	mit	3	Membrane; multi-pass membrane protein				445
Q5BK17 UniProt NPD GO	IYD1_RAT	Iodotyrosine dehalogenase 1 precursor (EC 1.-.-.-) (IYD-1)	0.32	-	mit	1 *	Membrane; single-pass membrane protein (By similarity)				285
P15479 UniProt NPD GO	ACEA_RICCO	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.32	-	cyt	0	Glyoxysome				576
O75564 UniProt NPD GO	JERKY_HUMAN	Jerky protein homolog	0.32	-	cyt	0	Nucleus (Potential)		603210		520
Q9UBX7 UniProt NPD GO	KLK11_HUMAN	Kallikrein-11 precursor (EC 3.4.21.-) (Hippostasin) (Trypsin-like protease)	0.32	-	mit	0	Secreted protein		604434		282
Q8BGY4 UniProt NPD GO	KLH26_MOUSE	Kelch-like protein 26	0.32	-	nuc	0					606
P06394 UniProt NPD GO	K1C10_BOVIN	Keratin, type I cytoskeletal 10 (Cytokeratin-10) (CK-10) (Keratin-10) (K10) (Cytokeratin-6B) (Cytoke ...	0.32	-	nuc	0					526
P35527 UniProt NPD GO	K1C9_HUMAN	Keratin, type I cytoskeletal 9 (Cytokeratin-9) (CK-9) (Keratin-9) (K9)	0.32	+	nuc	0			607606		623
Q96J84 UniProt NPD GO	KIRR1_HUMAN	Kin of IRRE-like protein 1 precursor (Kin of irregular chiasm-like protein 1) (Nephrin-like protein ...	0.32	-	end	1	Membrane; single-pass type I membrane protein (Potential). Predominantly located at podocyte slit di ...		607428		757
Q8BR86 UniProt NPD GO	KIRR3_MOUSE	Kin of IRRE-like protein 3 precursor (Kin of irregular chiasm-like protein 3)	0.32	-	end	1	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein	extracellular region [IDA] integral to membrane [IDA] plasma membrane [IDA]			778
Q8IZU9 UniProt NPD GO	KIRR3_HUMAN	Kin of IRRE-like protein 3 precursor (Kin of irregular chiasm-like protein 3) (Nephrin-like 2)	0.32	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)	extracellular region [ISS] integral to membrane [ISS]	607761	2CRY	778
Q25298 UniProt NPD GO	KM11C_LEIIN	Kinetoplastid membrane protein 11C	0.32	-	nuc	0	Cytoplasm. Associated with microtubules. Flagellum. Associated with the flagellum and flagellar pock ...	microtubule cytoskeleton [ISS]			92
Q9BXK1 UniProt NPD GO	KLF16_HUMAN	Krueppel-like factor 16 (Transcription factor BTEB4) (Basic transcription element-binding protein 4) ...	0.32	-	nuc	0	Nucleus (By similarity)		606139		252

You are viewing entries 38601 to 38650 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.