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
O94384 UniProt NPD GO	YGS6_SCHPO	Hypothetical protein C29A10.06c in chromosome II	0.39	-	mit	0					295
Q10181 UniProt NPD GO	YAW6_SCHPO	Hypothetical protein C3F10.06c in chromosome I	0.39	-	cyt	0					453
Q9USH8 UniProt NPD GO	YJQ2_SCHPO	Hypothetical protein C825.02 precursor	0.39	-	exc	0	Secreted protein (Potential)				506
Q8STI0 UniProt NPD GO	Y5G5_ENCCU	Hypothetical protein ECU05_1650/ECU11_0080	0.39	-	cyt	0					116
P34404 UniProt NPD GO	YLW1_CAEEL	Hypothetical protein F22B7.1	0.39	-	exc	0					348
Q10123 UniProt NPD GO	YSM3_CAEEL	Hypothetical protein F52C9.3	0.39	-	cyt	0					439
Q21045 UniProt NPD GO	YB70_CAEEL	Hypothetical protein F59F5.2	0.39	-	nuc	0					179
Q09415 UniProt NPD GO	YRM4_CAEEL	Hypothetical protein R06F6.4 in chromosome II	0.39	-	nuc	0	Nucleus (Potential)				429
P34549 UniProt NPD GO	YNJ5_CAEEL	Hypothetical protein R10E11.5	0.39	-	nuc	0					444
Q22634 UniProt NPD GO	YW60_CAEEL	Hypothetical protein T21C12.3	0.39	-	exc	0					145
P59868 UniProt NPD GO	IPTXA_PANIM	Imperatoxin-A (IpTxa) (Imperatoxin activator)	0.39	-	nuc	0	Secreted protein			1IE6	33
P36228 UniProt NPD GO	INF56_UROAP	Infection structure-specific protein 56	0.39	-	exc	0					128
Q9R0T8 UniProt NPD GO	IKKE_MOUSE	Inhibitor of nuclear factor kappa-B kinase epsilon subunit (EC 2.7.11.1) (I kappa-B kinase epsilon) ...	0.39	-	cyt	0	Cytoplasm (Probable)				717
Q7SY78 UniProt NPD GO	ITPK1_XENLA	Inositol-tetrakisphosphate 1-kinase (EC 2.7.1.134) (Inositol-triphosphate 5/6-kinase) (EC 2.7.1.-) ( ...	0.39	-	cyt	0					396
P52945 UniProt NPD GO	IPF1_HUMAN	Insulin promoter factor 1 (IPF-1) (Pancreas/duodenum homeobox 1) (PDX-1) (Islet/duodenum homeobox-1) ...	0.39	+	nuc	0	Nucleus		606392		283
O73798 UniProt NPD GO	IGF1R_XENLA	Insulin-like growth factor 1 receptor precursor (EC 2.7.10.1) (xIGF-1R) (xIGFR) [Contains: Insulin-l ...	0.39	-	end	2 *	Cell membrane; single-pass type I membrane protein. Expressed at the oocyte surface	integral to plasma membrane [IC]			1358
Q9PTH3 UniProt NPD GO	IBP2_BRARE	Insulin-like growth factor-binding protein 2 precursor (IGFBP-2) (IBP-2) (IGF-binding protein 2)	0.39	-	exc	0	Secreted protein				276
Q9Y5Q6 UniProt NPD GO	INSL5_HUMAN	Insulin-like peptide INSL5 precursor (Insulin-like peptide 5) [Contains: Insulin-like peptide INSL5 ...	0.39	-	exc	0	Secreted protein (Probable)		606413		135
Q63ZV0 UniProt NPD GO	INSM1_MOUSE	Insulinoma-associated protein 1 (Zinc finger protein IA-1)	0.39	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			521
P13597 UniProt NPD GO	ICAM1_MOUSE	Intercellular adhesion molecule 1 precursor (ICAM-1) (MALA-2)	0.39	-	end	1	Membrane; single-pass type I membrane protein				537
Q29429 UniProt NPD GO	IFNT6_SHEEP	Interferon tau-6 precursor (IFN-tau6) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolysin ...	0.39	-	vac	1 *	Secreted protein. Secreted into the uterine lumen				195
Q08071 UniProt NPD GO	IFNT7_SHEEP	Interferon tau-7 precursor (IFN-tau7) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolysin ...	0.39	-	vac	1 *	Secreted protein. Secreted into the uterine lumen				195
O14862 UniProt NPD GO	AIM2_HUMAN	Interferon-inducible protein AIM2 (Absent in melanoma 2)	0.39	-	mit	0			604578		343
Q9WVG1 UniProt NPD GO	IL1B_CAVPO	Interleukin-1 beta precursor (IL-1 beta)	0.39	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				266
Q02955 UniProt NPD GO	IL1R1_RAT	Interleukin-1 receptor type I precursor (IL-1R-1) (p80) (CD121a antigen)	0.39	-	end	1	Membrane; single-pass type I membrane protein				576
Q38IC8 UniProt NPD GO	IL2RA_PANTR	Interleukin-2 receptor alpha chain precursor (IL-2 receptor alpha subunit) (IL-2-RA) (IL2-RA) (CD25 ...	0.39	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				265
P04823 UniProt NPD GO	IL3_RAT	Interleukin-3 precursor (IL-3) (Multipotential colony-stimulating factor) (Hematopoietic growth fact ...	0.39	-	nuc	0	Secreted protein	extracellular space [ISS]			166
Q863Z5 UniProt NPD GO	IL4RA_PIG	Interleukin-4 receptor alpha chain precursor (IL-4R-alpha) (CD124 antigen)	0.39	-	nuc	0	Membrane; single-pass type I membrane protein (By similarity)				830
P04401 UniProt NPD GO	IL5_MOUSE	Interleukin-5 precursor (IL-5) (T-cell replacing factor) (TRF) (B-cell growth factor II) (BCGF-II) ( ...	0.39	-	exc	0	Secreted protein				133
Q9QYW1 UniProt NPD GO	KCNN4_RAT	Intermediate conductance calcium-activated potassium channel protein 4 (SK4) (KCa4) (IK1)	0.39	+	end	5 *	Membrane; multi-pass membrane protein				425
P14923 UniProt NPD GO	PLAK_HUMAN	Junction plakoglobin (Desmoplakin-3) (Desmoplakin III)	0.39	-	nuc	0	Cytoplasm. Cytoplasmic in a soluble and membrane-associated form	cytoplasm [TAS] cytoskeleton [TAS] membrane fraction [TAS] soluble fraction [TAS]	601214		743
Q91V33 UniProt NPD GO	SAM68_RAT	KH domain-containing, RNA-binding, signal transduction-associated protein 1 (p21 Ras GTPase-activati ...	0.39	-	nuc	0	Nucleus (By similarity). Membrane (By similarity)	cytoplasm [IDA] membrane [ISS] nucleus [ISS]			443
Q75AQ9 UniProt NPD GO	SMI1_ASHGO	KNR4/SMI1 homolog	0.39	-	nuc	0					657
Q5ZIU8 UniProt NPD GO	KTNB1_CHICK	Katanin p80 WD40-containing subunit B1 (Katanin p80 subunit B1) (p80 katanin)	0.39	-	nuc	0	Cytoplasm (By similarity). Predominantly. Centrosome (By similarity). Spindle (By similarity). Also ...				657
Q7ZUV2 UniProt NPD GO	KTNB1_BRARE	Katanin p80 WD40-containing subunit B1 homolog	0.39	-	nuc	0	Cytoplasm (By similarity). Predominantly. Centrosome (By similarity). Spindle (By similarity). Also ...				694
Q9Y2M5 UniProt NPD GO	KLH20_HUMAN	Kelch-like protein 20 (Kelch-like ECT2-interacting protein) (Kelch-like protein X)	0.39	-	mit	0		actin cytoskeleton [TAS] cell surface [IEP]			604
Q61414 UniProt NPD GO	K1C15_MOUSE	Keratin, type I cytoskeletal 15 (Cytokeratin-15) (CK-15) (Keratin-15) (K15)	0.39	-	cyt	0					452
P08779 UniProt NPD GO	K1C16_HUMAN	Keratin, type I cytoskeletal 16 (Cytokeratin-16) (CK-16) (Keratin-16) (K16)	0.39	-	nuc	0		intermediate filament [NAS]	600962		472
P25690 UniProt NPD GO	K1M2_SHEEP	Keratin, type I microfibrillar, 47.6 kDa (Low-sulfur keratin)	0.39	-	nuc	0					403
P02539 UniProt NPD GO	K2M1_SHEEP	Keratin, type II microfibrillar (Low-sulfur keratin) (Fragment)	0.39	-	nuc	0					109
Q9BYS1 UniProt NPD GO	KRA15_HUMAN	Keratin-associated protein 1-5 (Keratin-associated protein 1.5) (High sulfur keratin-associated prot ...	0.39	-	nuc	0			608822		174
P60409 UniProt NPD GO	KR107_HUMAN	Keratin-associated protein 10-7 (Keratin-associated protein 10.7) (High sulfur keratin-associated pr ...	0.39	-	exc	0					370
P60411 UniProt NPD GO	KR109_HUMAN	Keratin-associated protein 10-9 (Keratin-associated protein 10.9) (High sulfur keratin-associated pr ...	0.39	-	nuc	0					292
Q9BYR9 UniProt NPD GO	KRA24_HUMAN	Keratin-associated protein 2-4 (Keratin-associated protein 2.4) (High sulfur keratin-associated prot ...	0.39	-	nuc	0					128
Q6PEX3 UniProt NPD GO	KR261_HUMAN	Keratin-associated protein 26-1	0.39	-	nuc	0					210
Q9BYQ0 UniProt NPD GO	KRA98_HUMAN	Keratin-associated protein 9-8 (Keratin-associated protein 9.8) (Ultrahigh sulfur keratin-associated ...	0.39	-	mit	0					159
Q9US60 UniProt NPD GO	KLP3_SCHPO	Kinesin-like protein 3 (Kinesin-related protein 1)	0.39	-	nuc	0	Cytoplasm				554
P40014 UniProt NPD GO	SPC25_YEAST	Kinetochore protein SPC25	0.39	-	cyt	0	Nucleus. Associated with kinetochores	condensed nuclear chromosome kinetochore [IDA] Ndc80 complex [IDA]		2FV4	221
Q12143 UniProt NPD GO	NSL1_YEAST	Kinetochore-associated protein NSL1	0.39	-	nuc	0	Nucleus. Associated with the kinetochore	kinetochore [IDA] MIND complex [IDA] spindle pole [IDA]			216
O35082 UniProt NPD GO	KLOT_MOUSE	Klotho precursor (EC 3.2.1.31) [Contains: Klotho peptide]	0.39	-	mit	2 *	Isoform 1: Cell membrane; single-pass type I membrane protein. Its shedding leads to a soluble pepti ...				1014

You are viewing entries 32701 to 32750 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.