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
P50087 UniProt NPD GO	YG4Y_YEAST	Hypothetical 26.9 kDa protein in YHB1-PFK1 intergenic region	0.37	-	nuc	1		mitochondrion [IDA]			233
Q04746 UniProt NPD GO	YMV5_YEAST	Hypothetical 58.4 kDa protein in NCA1-HMS1 intergenic region	0.37	-	cyt	0		endoplasmic reticulum membrane [IDA] mitochondrion [IDA]			504
P38849 UniProt NPD GO	YHV1_YEAST	Hypothetical 59.8 kDa protein in IMP3-SPO12 intergenic region	0.37	-	nuc	1					526
P78797 UniProt NPD GO	YJ4A_SCHPO	Hypothetical proline-rich protein C70.10 precursor	0.37	-	nuc	1 *					155
Q17439 UniProt NPD GO	YQVW_CAEEL	Hypothetical protein B0035.15	0.37	-	nuc	0					283
Q10919 UniProt NPD GO	YT16_CAEEL	Hypothetical protein B0252.6	0.37	-	nuc	0					188
Q11086 UniProt NPD GO	YT72_CAEEL	Hypothetical protein C01C10.2	0.37	-	cyt	0					204
Q11089 UniProt NPD GO	YWY2_CAEEL	Hypothetical protein C01C4.2	0.37	-	nuc	0					244
O94728 UniProt NPD GO	YG0G_SCHPO	Hypothetical protein C1604.16c in chromosome II	0.37	-	nuc	0					199
O74466 UniProt NPD GO	YQC4_SCHPO	Hypothetical protein C1739.04c in chromosome III	0.37	-	nuc	1					288
Q10296 UniProt NPD GO	YD42_SCHPO	Hypothetical protein C22H10.02 in chromosome I	0.37	-	nuc	0					158
Q10495 UniProt NPD GO	YDG8_SCHPO	Hypothetical protein C26F1.08c in chromosome I	0.37	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				977
Q8SWH6 UniProt NPD GO	Y206_ENCCU	Hypothetical protein ECU02_0060	0.37	+	cyt	0					602
Q09302 UniProt NPD GO	YQP1_CAEEL	Hypothetical protein F07F6.1	0.37	-	mit	0					428
Q9C0W0 UniProt NPD GO	YHI9_SCHPO	Hypothetical protein P22H7.09c in chromosome II	0.37	-	nuc	0		Mis6-Sim4 complex [TAS]			411
Q09351 UniProt NPD GO	YRU5_CAEEL	Hypothetical protein T09B9.5	0.37	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				363
Q09367 UniProt NPD GO	YS2A_CAEEL	Hypothetical protein ZK1320.10	0.37	-	nuc	0					134
P34665 UniProt NPD GO	YOY8_CAEEL	Hypothetical protein ZK652.8	0.37	-	nuc	0					171
P01599 UniProt NPD GO	KV1G_HUMAN	Ig kappa chain V-I region Gal	0.37	-	nuc	0		extracellular region [NAS]			108
P04431 UniProt NPD GO	KV1W_HUMAN	Ig kappa chain V-I region Walker precursor	0.37	-	exc	0		extracellular region [NAS]			129
P01647 UniProt NPD GO	KV5N_MOUSE	Ig kappa chain V-V region HP 124E1	0.37	-	nuc	0				1EZV	108
P01648 UniProt NPD GO	KV5O_MOUSE	Ig kappa chain V-V region HP 91A3	0.37	-	nuc	0					108
P01644 UniProt NPD GO	KV5K_MOUSE	Ig kappa chain V-V region HP R16.7	0.37	-	nuc	0					108
Q9D880 UniProt NPD GO	TIM50_MOUSE	Import inner membrane translocase subunit TIM50, mitochondrial precursor	0.37	-	mit	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)	mitochondrial inner membrane presequence tr... [ISS]			353
P17490 UniProt NPD GO	INHA_RAT	Inhibin alpha chain precursor	0.37	-	exc	0	Secreted protein	extracellular region [ISS]			366
Q90660 UniProt NPD GO	BIR_CHICK	Inhibitor of apoptosis protein (IAP) (Inhibitor of T-cell apoptosis protein)	0.37	-	nuc	0	Nucleus. Predominantly. Ref.2: Cytoplasm				611
Q6FV22 UniProt NPD GO	MRS2_CANGA	Inner membrane magnesium transporter MRS2, mitochondrial precursor (RNA-splicing protein MRS2)	0.37	-	nuc	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				456
Q03412 UniProt NPD GO	UNC7_CAEEL	Innexin unc-7 (Uncoordinated protein 7)	0.37	-	end	3	Membrane; multi-pass membrane protein	gap junction [IMP] integral to membrane [NAS] plasma membrane [IDA]			522
Q23157 UniProt NPD GO	INX11_CAEEL	Innexin-11	0.37	-	nuc	2 *	Membrane; multi-pass membrane protein				465
P01346 UniProt NPD GO	IGF2_RAT	Insulin-like growth factor II precursor (IGF-II) (Multiplication-stimulating polypeptide) (Multiplic ...	0.37	-	exc	0	Secreted protein	extracellular space [TAS]			180
Q61702 UniProt NPD GO	ITIH1_MOUSE	Inter-alpha-trypsin inhibitor heavy chain H1 precursor (ITI heavy chain H1) (Inter-alpha-inhibitor h ...	0.37	-	exc	0					907
P97279 UniProt NPD GO	ITIH2_MESAU	Inter-alpha-trypsin inhibitor heavy chain H2 precursor (ITI heavy chain H2) (Inter-alpha-inhibitor h ...	0.37	-	cyt	0					946
P05004 UniProt NPD GO	IFNA2_HORSE	Interferon alpha-2 precursor	0.37	-	exc	0	Secreted protein				184
P05006 UniProt NPD GO	IFNA4_HORSE	Interferon alpha-4 precursor	0.37	-	exc	0	Secreted protein				184
P37290 UniProt NPD GO	IFND1_HUMAN	Interferon delta-1 precursor	0.37	-	vac	0	Secreted protein				195
P05000 UniProt NPD GO	IFNW1_HUMAN	Interferon omega-1 precursor (Interferon alpha-II-1)	0.37	-	mit	0	Secreted protein		147553		195
P56477 UniProt NPD GO	IRF5_MOUSE	Interferon regulatory factor 5 (IRF-5)	0.37	-	nuc	0	Nucleus				497
Q95187 UniProt NPD GO	IFNT_GIRCA	Interferon tau precursor (IFN-tau) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolysin) ( ...	0.37	-	nuc	1 *	Secreted protein. Secreted into the uterine lumen				195
Q08053 UniProt NPD GO	IFNTA_SHEEP	Interferon tau-10 precursor (IFN-tau10) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolys ...	0.37	-	mit	1 *	Secreted protein. Secreted into the uterine lumen				195
Q6R2X3 UniProt NPD GO	IL1B_EUMJU	Interleukin-1 beta precursor (IL-1 beta)	0.37	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				270
P41687 UniProt NPD GO	IL1B_FELCA	Interleukin-1 beta precursor (IL-1 beta)	0.37	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				267
P20808 UniProt NPD GO	IL11_MACFA	Interleukin-11 precursor (IL-11)	0.37	-	exc	0	Secreted protein	extracellular region [ISS]			199
Q08867 UniProt NPD GO	IL2_MUSSP	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.37	-	exc	0	Secreted protein				166
Q865Y0 UniProt NPD GO	IL4_PAPAN	Interleukin-4 precursor (IL-4) (B-cell stimulatory factor 1) (BSF-1) (Lymphocyte stimulatory factor ...	0.37	-	exc	0	Secreted protein	extracellular space [ISS]			153
P24394 UniProt NPD GO	IL4RA_HUMAN	Interleukin-4 receptor alpha chain precursor (IL-4R-alpha) (CD124 antigen) [Contains: Soluble interl ...	0.37	-	exc	0	Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein	integral to plasma membrane [TAS]	147781	1ITE	825
Q28540 UniProt NPD GO	IL7_SHEEP	Interleukin-7 precursor (IL-7)	0.37	-	exc	0	Secreted protein	extracellular region [ISS]			176
O89109 UniProt NPD GO	KCNN4_MOUSE	Intermediate conductance calcium-activated potassium channel protein 4 (SK4) (KCa4) (IK1)	0.37	+	end	5 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IC]			425
P14708 UniProt NPD GO	INVO_PONPY	Involucrin	0.37	-	nuc	0	Cytoplasm. Constituent of the scaffolding of the cornified envelope	cornified envelope [ISS] cytoplasm [ISS]			835
Q90Y57 UniProt NPD GO	JAG1A_BRARE	Jagged-1a precursor (Jagged1a) (Jagged1)	0.37	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)	integral to membrane [NAS]			1242
Q07666 UniProt NPD GO	SAM68_HUMAN	KH domain-containing, RNA-binding, signal transduction-associated protein 1 (p21 Ras GTPase-activati ...	0.37	-	nuc	0	Nucleus. Membrane	membrane [IDA] nucleus [IDA]	602489		443

You are viewing entries 34251 to 34300 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.