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
Q9TZM2 UniProt NPD GO	MO25L_CAEEL	Hypothetical MO25-like protein T27C10.3 in chromosome I	0.38	-	cyt	0					339
O74910 UniProt NPD GO	YCSB_SCHPO	Hypothetical WD repeat protein C613.12c in chromosome III	0.38	-	nuc	0		mating-type region heterochromatin [TAS] nucleus [IDA] Rik1-E3 ubiquitin ligase complex [IDA]			638
P22190 UniProt NPD GO	YMC2_SCHPO	Hypothetical cox1 intron-2 37.2 kDa protein (Probable maturase)	0.38	-	nuc	0					323
P92519 UniProt NPD GO	M810_ARATH	Hypothetical mitochondrial protein AtMg00810 (ORF240b)	0.38	-	nuc	0	Mitochondrion (Potential)				240
O13772 UniProt NPD GO	YE9A_SCHPO	Hypothetical proline/serine-rich protein C17A5.10 in chromosome I	0.38	-	nuc	0					224
Q09215 UniProt NPD GO	YP66_CAEEL	Hypothetical protein B0495.6	0.38	-	nuc	0					87
P34316 UniProt NPD GO	YKT5_CAEEL	Hypothetical protein C07A9.5 in chromosome III	0.38	-	nuc	0					358
Q9USZ2 UniProt NPD GO	YNR7_SCHPO	Hypothetical protein C11G11.07 in chromosome II	0.38	-	cyt	0					955
O13717 UniProt NPD GO	YDZA_SCHPO	Hypothetical protein C14C4.10c in chromosome I	0.38	-	end	1	Membrane; multi-pass membrane protein (Potential)				329
Q10367 UniProt NPD GO	YDBH_SCHPO	Hypothetical protein C22E12.17c in chromosome I	0.38	-	nuc	0					486
Q09240 UniProt NPD GO	YQA2_CAEEL	Hypothetical protein C28F5.2	0.38	-	nuc	0					194
Q18473 UniProt NPD GO	YE15_CAEEL	Hypothetical protein C35A5.5	0.38	-	cyt	1 *					520
P87178 UniProt NPD GO	YB1D_SCHPO	Hypothetical protein C3D6.13c in chromosome II	0.38	-	end	1 *					726
Q09526 UniProt NPD GO	YQN5_CAEEL	Hypothetical protein E02H1.5	0.38	-	nuc	0					253
Q8SVP3 UniProt NPD GO	Y4G6_ENCCU	Hypothetical protein ECU04_1660	0.38	+	cyt	0					269
Q20593 UniProt NPD GO	YE25_CAEEL	Hypothetical protein F49C12.5	0.38	+	mit	1 *					507
Q09348 UniProt NPD GO	YRS4_CAEEL	Hypothetical protein T05H10.4	0.38	-	nuc	0					436
Q10009 UniProt NPD GO	YSV3_CAEEL	Hypothetical protein T19C3.3	0.38	-	nuc	0					92
P51342 UniProt NPD GO	YCF28_PORPU	Hypothetical transcriptional regulator ycf28	0.38	-	nuc	1	Plastid; chloroplast				237
P01601 UniProt NPD GO	KV1I_HUMAN	Ig kappa chain V-I region HK101 precursor (Fragment)	0.38	-	exc	0		extracellular region [NAS]			117
Q8TAG5 UniProt NPD GO	IGX1_HUMAN	Immunoglobulin-like domain protein MGC33530 precursor	0.38	-	nuc	0	Secreted protein (Potential)				243
P52293 UniProt NPD GO	IMA2_MOUSE	Importin alpha-2 subunit (Karyopherin alpha-2 subunit) (SRP1-alpha) (RAG cohort protein 1) (Pendulin ...	0.38	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)			2C1M	529
O00629 UniProt NPD GO	IMA4_HUMAN	Importin alpha-4 subunit (Karyopherin alpha-4 subunit) (Qip1 protein)	0.38	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)		602970		521
P40015 UniProt NPD GO	ISC1_YEAST	Inositol phosphosphingolipids phospholipase C (EC 3.1.4.-) (IPS phospholipase C) (IPS-PLC) (Neutral ...	0.38	-	end	2	Membrane; multi-pass membrane protein	endoplasmic reticulum [IDA] mitochondrion [IDA]			477
Q01101 UniProt NPD GO	INSM1_HUMAN	Insulinoma-associated protein 1 (Zinc finger protein IA-1)	0.38	-	nuc	0	Nucleus (Potential)		600010		510
Q03600 UniProt NPD GO	INA1_CAEEL	Integrin alpha ina-1 precursor	0.38	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				1139
Q61738 UniProt NPD GO	ITA7_MOUSE	Integrin alpha-7 precursor [Contains: Integrin alpha-7 heavy chain; Integrin alpha-7 light chain]	0.38	+	end	2 *	Membrane; single-pass type I membrane protein				1179
P09055 UniProt NPD GO	ITB1_MOUSE	Integrin beta-1 precursor (Fibronectin receptor subunit beta) (Integrin VLA-4 subunit beta) (CD29 an ...	0.38	-	end	1	Membrane; single-pass type I membrane protein	plasma membrane [IDA] synaptosome [IDA]			798
Q5RCA9 UniProt NPD GO	ITB1_PONPY	Integrin beta-1 precursor (Fibronectin receptor subunit beta) (Integrin VLA-4 subunit beta) (CD29 an ...	0.38	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				798
O70309 UniProt NPD GO	ITB5_MOUSE	Integrin beta-5 precursor	0.38	-	exc	1	Membrane; single-pass type I membrane protein				798
P26010 UniProt NPD GO	ITB7_HUMAN	Integrin beta-7 precursor	0.38	-	exc	1	Membrane; single-pass type I membrane protein	integrin complex [TAS]	147559	2BRQ	798
Q61703 UniProt NPD GO	ITIH2_MOUSE	Inter-alpha-trypsin inhibitor heavy chain H2 precursor (ITI heavy chain H2) (Inter-alpha-inhibitor h ...	0.38	-	exc	0					946
P07350 UniProt NPD GO	IFNA6_MOUSE	Interferon alpha-6 precursor	0.38	-	end	0	Secreted protein				189
P17660 UniProt NPD GO	IFNA8_MOUSE	Interferon alpha-8 precursor	0.38	-	end	0	Secreted protein				189
P51527 UniProt NPD GO	IFNA_MELGA	Interferon precursor (TkIFN)	0.38	-	exc	1 *	Secreted protein				192
P23611 UniProt NPD GO	IRF8_MOUSE	Interferon regulatory factor 8 (IRF-8) (Interferon consensus sequence-binding protein) (ICSBP)	0.38	-	mit	0	Nucleus				424
P15696 UniProt NPD GO	IFNT1_BOVIN	Interferon tau-1 precursor (IFN-tau1) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolysin ...	0.38	-	vac	0	Secreted protein. Secreted into the uterine lumen				195
Q01638 UniProt NPD GO	ILRL1_HUMAN	Interleukin-1 receptor-like 1 precursor (ST2 protein)	0.38	-	mit	1	Cell membrane; single-pass type I membrane protein. Isoform B: Secreted protein. Isoform C: Cell mem ...		601203		556
Q9JIP3 UniProt NPD GO	I17RB_MOUSE	Interleukin-17 receptor B precursor (IL-17 receptor B) (IL-17RB) (Interleukin-17B receptor) (IL-17B ...	0.38	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein	cell surface [IDA] cytoplasm [IDA]			499
Q9Z2B1 UniProt NPD GO	I18RA_MOUSE	Interleukin-18 receptor accessory protein precursor (IL-18 receptor accessory protein) (IL-18RAcP) ( ...	0.38	-	end	1	Membrane; single-pass type I membrane protein (Potential)				614
Q8CGK5 UniProt NPD GO	I28RA_MOUSE	Interleukin-28 receptor alpha chain precursor (IL-28R-alpha) (IL-28RA) (Cytokine receptor family 2 m ...	0.38	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				535
P16382 UniProt NPD GO	IL4RA_MOUSE	Interleukin-4 receptor alpha chain precursor (IL-4R-alpha) (CD124 antigen) [Contains: Soluble interl ...	0.38	-	exc	0	Cell membrane; single-pass type I membrane protein. Isoform 2: Secreted protein				810
Q865X6 UniProt NPD GO	IL6_LAMGL	Interleukin-6 precursor (IL-6)	0.38	-	exc	0	Secreted protein				211
P26895 UniProt NPD GO	IL7_BOVIN	Interleukin-7 precursor (IL-7)	0.38	-	exc	0	Secreted protein	extracellular region [ISS]			176
O15554 UniProt NPD GO	KCNN4_HUMAN	Intermediate conductance calcium-activated potassium channel protein 4 (SK4) (KCa4) (IK1) (IKCa1) (P ...	0.38	+	end	5 *	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	602754		427
P14591 UniProt NPD GO	INVO_PANPA	Involucrin	0.38	-	nuc	0	Cytoplasm. Constituent of the scaffolding of the cornified envelope	cornified envelope [ISS] cytoplasm [ISS]			560
Q26491 UniProt NPD GO	ITP_SCHGR	Ion transport peptide precursor (ITP)	0.38	-	nuc	1 *	Secreted protein				130
Q6BRY4 UniProt NPD GO	ACEA_DEBHA	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.38	-	cyt	0	Peroxisome (By similarity)				550
Q90334 UniProt NPD GO	ITR_CATCO	Isotocin receptor (ITR)	0.38	-	end	7 *	Membrane; multi-pass membrane protein				390
Q9Y664 UniProt NPD GO	KPTN_HUMAN	Kaptin (Actin-associated protein 2E4)	0.38	+	cyt	0	Cytoplasm. Cytoplasm; perinuclear region. Perinuclear at the tips of stereocilium in the inner ear. ...	actin cytoskeleton [TAS] microtubule organizing center [TAS] nucleus [TAS]			436

You are viewing entries 33501 to 33550 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.