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
P49895 UniProt NPD GO	IOD1_HUMAN	Type I iodothyronine deiodinase (EC 1.97.1.10) (Type-I 5'deiodinase) (DIOI) (Type 1 DI) (5DI)	0.18	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)		147892		249
Q00655 UniProt NPD GO	KSYK_PIG	Tyrosine-protein kinase SYK (EC 2.7.10.2) (Spleen tyrosine kinase) [Contains: 72 kDa tyrosine-protei ...	0.18	-	cyt	0	40 kDa tyrosine-protein kinase SYK: Cytoplasm. 72 kDa tyrosine-protein kinase SYK: Membrane. The 40 ...				628
P28219 UniProt NPD GO	PTP27_STYPL	Tyrosine-protein phosphatase 27 (EC 3.1.3.48) (Fragment)	0.18	-	mit	0					114
P32587 UniProt NPD GO	PYP3_SCHPO	Tyrosine-protein phosphatase 3 (EC 3.1.3.48) (Protein-tyrosine phosphatase 3) (PTPase 3)	0.18	-	cyt	0	Cytoplasm				303
Q8VIK1 UniProt NPD GO	CP033_MOUSE	U11/U12 snRNP 25 kDa protein	0.18	-	cyt	0	Nucleus (By similarity)	minor (U12-dependent) spliceosome complex [ISS]		1V2Y	123
P42000 UniProt NPD GO	UTP18_CAEEL	U3 small nucleolar RNA-associated protein 18 homolog	0.18	-	nuc	0	Nucleus; nucleolus (By similarity)				429
Q3ZBK6 UniProt NPD GO	LSM4_BOVIN	U6 snRNA-associated Sm-like protein LSm4	0.18	-	cyt	0	Nucleus (Potential)				139
Q9Y4Z0 UniProt NPD GO	LSM4_HUMAN	U6 snRNA-associated Sm-like protein LSm4 (Glycine-rich protein) (GRP)	0.18	-	cyt	0	Nucleus (Potential)	snRNP U6 [TAS]	607284		139
P62313 UniProt NPD GO	LSM6_MOUSE	U6 snRNA-associated Sm-like protein LSm6	0.18	-	cyt	0	Nucleus (Potential)				80
P62312 UniProt NPD GO	LSM6_HUMAN	U6 snRNA-associated Sm-like protein LSm6 (Sm protein F)	0.18	-	cyt	0	Nucleus (Potential)	small nuclear ribonucleoprotein complex [TAS]	607286		80
Q16222 UniProt NPD GO	UAP1_HUMAN	UDP-N-acetylhexosamine pyrophosphorylase (Antigen X) (AGX) (Sperm-associated antigen 2) [Includes: U ...	0.18	-	cyt	0	Cytoplasm. In spermatozoa, localized to the principal piece of the tail, the neck region of the head ...		602862	1JVG	522
P12378 UniProt NPD GO	UGDH_BOVIN	UDP-glucose 6-dehydrogenase (EC 1.1.1.22) (UDP-Glc dehydrogenase) (UDP-GlcDH) (UDPGDH)	0.18	-	cyt	0					494
O60701 UniProt NPD GO	UGDH_HUMAN	UDP-glucose 6-dehydrogenase (EC 1.1.1.22) (UDP-Glc dehydrogenase) (UDP-GlcDH) (UDPGDH)	0.18	-	cyt	0			603370		494
O70475 UniProt NPD GO	UGDH_MOUSE	UDP-glucose 6-dehydrogenase (EC 1.1.1.22) (UDP-Glc dehydrogenase) (UDP-GlcDH) (UDPGDH)	0.18	-	cyt	0					493
Q9H1C4 UniProt NPD GO	UN93B_HUMAN	UNC93 homolog B1 (UNC-93B protein) (hUNC93B1)	0.18	-	end	12	Membrane; multi-pass membrane protein (Potential)		608204		597
O73881 UniProt NPD GO	CI016_FUGRU	UPF0184 protein C9orf16 homolog (EST00098)	0.18	-	nuc	0					108
Q9VTC4 UniProt NPD GO	U195A_DROME	UPF0195 protein CG7949	0.18	-	nuc	0					156
O14068 UniProt NPD GO	YFF7_SCHPO	UPF0357 protein C1687.07 precursor	0.18	-	mit	1 *					124
P31800 UniProt NPD GO	UQCR1_BOVIN	Ubiquinol-cytochrome-c reductase complex core protein I, mitochondrial precursor (EC 1.10.2.2)	0.18	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side			2A06	480
P42739 UniProt NPD GO	UBIQ_ACECL	Ubiquitin	0.18	-	cyt	0	Cytoplasm. Nucleus				76
P59263 UniProt NPD GO	UBIQ_ARATH	Ubiquitin	0.18	-	cyt	0	Cytoplasm. Nucleus				76
P69308 UniProt NPD GO	UBIQ_ASPOF	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69309 UniProt NPD GO	UBIQ_AVEFA	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69310 UniProt NPD GO	UBIQ_AVESA	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69311 UniProt NPD GO	UBIQ_BRARA	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P14624 UniProt NPD GO	UBIQ_CHLRE	Ubiquitin	0.18	-	cyt	0	Cytoplasm. Nucleus				76
P69312 UniProt NPD GO	UBIQ_DAUCA	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P0C072 UniProt NPD GO	UBIQ_DESAN	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69313 UniProt NPD GO	UBIQ_HELAN	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69314 UniProt NPD GO	UBIQ_HORVU	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69315 UniProt NPD GO	UBIQ_LINUS	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69316 UniProt NPD GO	UBIQ_LUPAL	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69317 UniProt NPD GO	UBIQ_LUPPO	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69318 UniProt NPD GO	UBIQ_LYCES	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69319 UniProt NPD GO	UBIQ_MAIZE	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69320 UniProt NPD GO	UBIQ_NICSY	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69321 UniProt NPD GO	UBIQ_ORYSA	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69322 UniProt NPD GO	UBIQ_PEA	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69323 UniProt NPD GO	UBIQ_PETCR	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69324 UniProt NPD GO	UBIQ_SOLTU	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69325 UniProt NPD GO	UBIQ_SOYBN	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
P69326 UniProt NPD GO	UBIQ_WHEAT	Ubiquitin	0.18	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				76
Q92890 UniProt NPD GO	UFD1_HUMAN	Ubiquitin fusion degradation protein 1 homolog (UB fusion protein 1)	0.18	-	mit	0			601754		343
Q1RMX2 UniProt NPD GO	UB2D2_BOVIN	Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) (Ubiquitin-protein ligase D2) (Ubiquitin carrier pr ...	0.18	-	nuc	0					147
P62837 UniProt NPD GO	UB2D2_HUMAN	Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) (Ubiquitin-protein ligase D2) (Ubiquitin carrier pr ...	0.18	-	nuc	0			602962	2ESQ	147
P62838 UniProt NPD GO	UB2D2_MOUSE	Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) (Ubiquitin-protein ligase D2) (Ubiquitin carrier pr ...	0.18	-	nuc	0					147
P62839 UniProt NPD GO	UB2D2_RAT	Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) (Ubiquitin-protein ligase D2) (Ubiquitin carrier pr ...	0.18	-	nuc	0					147
P62840 UniProt NPD GO	UB2D2_XENLA	Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) (Ubiquitin-protein ligase D2) (Ubiquitin carrier pr ...	0.18	-	nuc	0					147
P42750 UniProt NPD GO	UBC6_ARATH	Ubiquitin-conjugating enzyme E2-21 kDa 3 (EC 6.3.2.19) (Ubiquitin-protein ligase 6) (Ubiquitin carri ...	0.18	-	cyt	0					183
P0C033 UniProt NPD GO	UBL1_ORYSA	Ubiquitin-like protein 1	0.18	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable)				76

You are viewing entries 53801 to 53850 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.