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
P36221 UniProt NPD GO	TBB1_NOTCO	Tubulin beta-1 chain (Beta-1 tubulin)	0.13	-	cyt	0					446
P30156 UniProt NPD GO	TBB5_ECTVR	Tubulin beta-5 chain (Beta-5 tubulin)	0.13	-	cyt	0					447
Q6VAF7 UniProt NPD GO	TBB5_GOSHI	Tubulin beta-5 chain (Beta-5 tubulin)	0.13	-	cyt	0					445
P46265 UniProt NPD GO	TBB5_ORYSA	Tubulin beta-5 chain (Beta-5 tubulin)	0.13	-	cyt	0					447
P09653 UniProt NPD GO	TBB5_CHICK	Tubulin beta-5 chain (Beta-tubulin class-V)	0.13	-	cyt	0					446
Q41784 UniProt NPD GO	TBB7_MAIZE	Tubulin beta-7 chain (Beta-7 tubulin)	0.13	-	cyt	0					445
Q75A43 UniProt NPD GO	TBG_ASHGO	Tubulin gamma chain (Gamma tubulin)	0.13	-	cyt	0					470
Q8HZD9 UniProt NPD GO	TNFA_PANTR	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.13	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				232
Q6KB54 UniProt NPD GO	SIA10_PANTR	Type 2 lactosamine alpha-2,3-sialyltransferase (EC 2.4.99.-) (CMP-NeuAc:beta-galactoside alpha-2,3-s ...	0.13	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				331
P49894 UniProt NPD GO	IOD1_CANFA	Type I iodothyronine deiodinase (EC 1.97.1.10) (Type-I 5'deiodinase) (DIOI) (Type 1 DI) (5DI)	0.13	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				244
Q95N00 UniProt NPD GO	IOD1_SUNMU	Type I iodothyronine deiodinase (EC 1.97.1.10) (Type-I 5'deiodinase) (DIOI) (Type 1 DI) (5DI)	0.13	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				257
Q9IAX2 UniProt NPD GO	IOD2_CHICK	Type II iodothyronine deiodinase (EC 1.97.1.10) (Type-II 5'deiodinase) (DIOII) (Type 2 DI) (5DII)	0.13	-	nuc	0		integral to membrane [NAS]			279
O93830 UniProt NPD GO	BET2_CANAL	Type-2 proteins geranylgeranyltransferase subunit beta (EC 2.5.1.60) (Type II proteins geranylgerany ...	0.13	-	cyt	0					341
P18461 UniProt NPD GO	CEK3_CHICK	Tyrosine kinase receptor CEK3 precursor (EC 2.7.10.1)	0.13	-	end	1	Membrane; single-pass type I membrane protein				823
P00528 UniProt NPD GO	SRC64_DROME	Tyrosine-protein kinase Src64B (EC 2.7.10.2) (Dsrc64)	0.13	-	cyt	0		ring canal (sensu Insecta) [TAS]			552
P27447 UniProt NPD GO	YES_XIPHE	Tyrosine-protein kinase Yes (EC 2.7.10.2) (p61-Yes)	0.13	-	cyt	0					543
P28203 UniProt NPD GO	PTP11_STYPL	Tyrosine-protein phosphatase 11 (EC 3.1.3.48) (Fragment)	0.13	-	cyt	0					114
P28212 UniProt NPD GO	PTP20_STYPL	Tyrosine-protein phosphatase 20 (EC 3.1.3.48) (Fragment)	0.13	-	cyt	0					116
P28215 UniProt NPD GO	PTP23_STYPL	Tyrosine-protein phosphatase 23 (EC 3.1.3.48) (Fragment)	0.13	-	cyt	0					115
P28198 UniProt NPD GO	PTP6_STYPL	Tyrosine-protein phosphatase 6 (EC 3.1.3.48) (Fragment)	0.13	-	nuc	0					109
Q9Y4X1 UniProt NPD GO	UDA1_HUMAN	UDP-glucuronosyltransferase 2A1 precursor (EC 2.4.1.17)	0.13	-	cyt	1 *			604716		527
P36514 UniProt NPD GO	UDC1_RABIT	UDP-glucuronosyltransferase 2C1 (EC 2.4.1.17) (UDPGT) (Fragment)	0.13	-	cyt	1	Microsome				502
Q5RAK7 UniProt NPD GO	UGTAP_PONPY	UGA suppressor tRNA-associated protein	0.13	-	nuc	0	Cytoplasm (By similarity)				501
Q8BZT9 UniProt NPD GO	U124_MOUSE	UPF0124 protein	0.13	-	nuc	0					430
O74432 UniProt NPD GO	YC4C_SCHPO	UPF0363 protein C1672.12c	0.13	-	nuc	0					303
Q99807 UniProt NPD GO	COQ7_HUMAN	Ubiquinone biosynthesis protein COQ7 homolog (Coenzyme Q biosynthesis protein 7 homolog) (Timing pro ...	0.13	-	mit	0		mitochondrion [TAS]	601683		217
P15174 UniProt NPD GO	UBIQ_TRYBB	Ubiquitin	0.13	-	cyt	0	Cytoplasm. Nucleus				76
Q8VE47 UniProt NPD GO	UE1D1_MOUSE	Ubiquitin-activating enzyme E1 domain-containing protein 1 (UFM1-activating enzyme)	0.13	-	nuc	1					403
Q6P073 UniProt NPD GO	UB2J2_MOUSE	Ubiquitin-conjugating enzyme E2 J2 (EC 6.3.2.19) (Non-canonical ubiquitin-conjugating enzyme 2) (NCU ...	0.13	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type IV membrane protein	endoplasmic reticulum [IDA]			259
Q06107 UniProt NPD GO	YP114_YEAST	Uncharacterized TLC domain-containing protein YPR114W	0.13	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			315
Q5ZLR7 UniProt NPD GO	CN109_CHICK	Uncharacterized protein C14orf109 homolog	0.13	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				131
Q8N128 UniProt NPD GO	CN024_HUMAN	Uncharacterized protein C14orf24	0.13	-	cyt	0					213
Q8N511 UniProt NPD GO	CQ032_HUMAN	Uncharacterized protein C17orf32	0.13	-	end	2	Membrane; multi-pass membrane protein (Potential)				208
Q8N1N2 UniProt NPD GO	CR026_HUMAN	Uncharacterized protein C18orf26	0.13	-	nuc	1					210
Q12025 UniProt NPD GO	YD056_YEAST	Uncharacterized protein YDR056C precursor	0.13	-	exc	0	Endoplasmic reticulum	endoplasmic reticulum [IDA] membrane fraction [IDA]			205
P43594 UniProt NPD GO	YFI1_YEAST	Uncharacterized protein YFR011C	0.13	-	nuc	0		cytoplasm [IDA] mitochondrion [IDA]			170
P43604 UniProt NPD GO	YFJ6_YEAST	Uncharacterized protein YFR026C	0.13	-	nuc	1 *					169
Q3E802 UniProt NPD GO	YG006_YEAST	Uncharacterized protein YGL006W-A	0.13	-	mit	0					36
P38842 UniProt NPD GO	YHU0_YEAST	Uncharacterized protein YHR140W	0.13	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				239
P40576 UniProt NPD GO	YIU4_YEAST	Uncharacterized protein YIR024C	0.13	-	mit	1 *		mitochondrion [IDA]			216
Q8TGJ7 UniProt NPD GO	YL066_YEAST	Uncharacterized protein YLL066W-B	0.13	-	nuc	0					56
P53906 UniProt NPD GO	YNO6_YEAST	Uncharacterized protein YNL146W	0.13	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			100
Q08974 UniProt NPD GO	YP257_YEAST	Uncharacterized protein YPL257W	0.13	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				193
P31754 UniProt NPD GO	PYR5_BOVIN	Uridine 5'-monophosphate synthase (UMP synthase) [Includes: Orotate phosphoribosyltransferase (EC 2. ...	0.13	-	cyt	0					480
P13439 UniProt NPD GO	PYR5_MOUSE	Uridine 5'-monophosphate synthase (UMP synthase) [Includes: Orotate phosphoribosyltransferase (EC 2. ...	0.13	-	cyt	0					481
P27590 UniProt NPD GO	UROM_RAT	Uromodulin precursor (Tamm-Horsfall urinary glycoprotein) (THP)	0.13	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor. Secreted protein. Secreted after cleavage in the urine	cytoplasmic membrane-bound vesicle [TAS]			644
Q9D132 UniProt NPD GO	UPK1A_MOUSE	Uroplakin-1a (Uroplakin Ia) (UPIa) (UPKa)	0.13	-	end	4 *	Membrane; multi-pass membrane protein	endoplasmic reticulum [ISS] integral to membrane [TAS] plasma membrane [ISS]			257
Q08537 UniProt NPD GO	UPK2_BOVIN	Uroplakin-2 precursor (UP 2) (Uroplakin II) (UPII)	0.13	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential). Heterodimer formation with Uroplakin Ia i ...	endoplasmic reticulum [IDA] integral to membrane [IDA] plasma membrane [IDA]			185
P38574 UniProt NPD GO	UPK3A_BOVIN	Uroplakin-3A precursor (Uroplakin III) (UPIII)	0.13	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein. Heterodi ...	endoplasmic reticulum [IDA] integral to membrane [IDA] plasma membrane [IDA]			287
O19889 UniProt NPD GO	SUMT_CYACA	Uroporphyrin-III C-methyltransferase (EC 2.1.1.107) (Urogen III methylase) (SUMT) (Uroporphyrinogen ...	0.13	-	cyt	0	Plastid; chloroplast				251

You are viewing entries 60601 to 60650 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.