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
Q14956 UniProt NPD GO	GPNMB_HUMAN	Transmembrane glycoprotein NMB precursor (Transmembrane glycoprotein HGFIN)	0.15	-	cyt	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [TAS]	604368		572
Q2KIB3 UniProt NPD GO	TM101_BOVIN	Transmembrane protein 101	0.15	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				257
Q8BK08 UniProt NPD GO	TMM11_MOUSE	Transmembrane protein 11 (Protein PM1)	0.15	-	mit	0	Membrane; multi-pass membrane protein (Potential)				190
Q5M7A3 UniProt NPD GO	TMM22_RAT	Transmembrane protein 22	0.15	-	end	10	Membrane; multi-pass membrane protein (Potential)				412
Q3SZ48 UniProt NPD GO	TM55A_BOVIN	Transmembrane protein 55A (EC 3.1.3.-) (Type II phosphatidylinositol 4,5-bisphosphate 4-phosphatase) ...	0.15	-	mit	2	Endosome; late endosome; late endosomal membrane; multi-pass membrane protein (By similarity). Lysos ...				257
Q9P0T7 UniProt NPD GO	TMEM9_HUMAN	Transmembrane protein 9 precursor (Dermal papilla-derived protein 4)	0.15	-	end	1	Endosome; late endosome; late endosomal membrane; single-pass type I membrane protein. Lysosome; lys ...	late endosome [IEP] lysosome [IEP]			183
P03936 UniProt NPD GO	YAC9_MAIZE	Transposable element activator hypothetical 23 kDa protein (AC 23 kDa protein)	0.15	-	mit	0					210
Q60587 UniProt NPD GO	ECHB_RAT	Trifunctional enzyme subunit beta, mitochondrial precursor (TP-beta) [Includes: 3-ketoacyl-CoA thiol ...	0.15	-	mit	0	Mitochondrion; mitochondrial matrix				475
Q9NP99 UniProt NPD GO	TREM1_HUMAN	Triggering receptor expressed on myeloid cells 1 precursor (TREM-1) (Triggering receptor expressed o ...	0.15	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein (Potential). Isoform 2: Secreted prote ...		605085	1SMO	234
Q86UV6 UniProt NPD GO	TRI74_HUMAN	Tripartite motif-containing protein 74 (Tripartite motif-containing protein 50C)	0.15	-	cyt	0					250
P11968 UniProt NPD GO	ITR2_BRYDI	Trypsin inhibitor 2 (Trypsin inhibitor II) (BDTI-II)	0.15	-	nuc	0	Secreted protein				29
P84712 UniProt NPD GO	TRIN1_HYPSU	Trypsin inhibitor HSTI (Fragment)	0.15	-		0		extracellular space [IDA]			18
Q9FT36 UniProt NPD GO	TBA_DAUCA	Tubulin alpha chain	0.15	-	cyt	0					451
P02554 UniProt NPD GO	TBB_PIG	Tubulin beta chain	0.15	-	cyt	0				1TVK	445
P12457 UniProt NPD GO	TBB_EUGGR	Tubulin beta chain (Beta tubulin)	0.15	-	cyt	0					442
P93176 UniProt NPD GO	TBB_HORVU	Tubulin beta chain (Beta tubulin)	0.15	-	cyt	0					447
P34108 UniProt NPD GO	TBB_NAEGR	Tubulin beta chain (Beta tubulin)	0.15	-	cyt	0	Cytoplasm				451
Q92268 UniProt NPD GO	TBB_PLESA	Tubulin beta chain (Beta tubulin)	0.15	-	cyt	0					446
Q91240 UniProt NPD GO	TBB_PSEAM	Tubulin beta chain (Beta tubulin)	0.15	-	cyt	0					445
P53376 UniProt NPD GO	TBB_RHYSE	Tubulin beta chain (Beta tubulin)	0.15	-	cyt	0					447
Q24560 UniProt NPD GO	TBB1_DROME	Tubulin beta-1 chain (Beta-1 tubulin)	0.15	-	cyt	0		tubulin [ISS]			447
Q9ZPP0 UniProt NPD GO	TBB1_ELEIN	Tubulin beta-1 chain (Beta-1 tubulin)	0.15	-	cyt	0					445
P12459 UniProt NPD GO	TBB1_SOYBN	Tubulin beta-1 chain (Beta-1 tubulin)	0.15	-	cyt	0					445
P40905 UniProt NPD GO	TBB2_ERYPI	Tubulin beta-2 chain (Beta-2 tubulin)	0.15	-	cyt	0					447
P32925 UniProt NPD GO	TBB2_GEOCN	Tubulin beta-2 chain (Beta-2 tubulin)	0.15	-	cyt	0					453
P18026 UniProt NPD GO	TBB2_MAIZE	Tubulin beta-2 chain (Beta-2 tubulin)	0.15	-	cyt	0					444
Q875L2 UniProt NPD GO	TBB2_TRIVE	Tubulin beta-2 chain (Beta-2 tubulin)	0.15	-	cyt	0					446
Q9ERD7 UniProt NPD GO	TBB3_MOUSE	Tubulin beta-3 chain	0.15	-	cyt	0		microtubule cytoskeleton [IDA] mitochondrion [IDA]			450
Q4QRB4 UniProt NPD GO	TBB3_RAT	Tubulin beta-3 chain	0.15	-	cyt	0					450
Q9ZPN7 UniProt NPD GO	TBB4_ELEIN	Tubulin beta-4 chain (Beta-4 tubulin)	0.15	-	cyt	0					446
Q41782 UniProt NPD GO	TBB4_MAIZE	Tubulin beta-4 chain (Beta-4 tubulin)	0.15	-	cyt	0					447
P09207 UniProt NPD GO	TBB6_CHICK	Tubulin beta-6 chain (Beta-tubulin class-VI)	0.15	-	cyt	0					446
P29517 UniProt NPD GO	TBB9_ARATH	Tubulin beta-9 chain (Beta-9 tubulin)	0.15	-	cyt	0					444
Q6VAF4 UniProt NPD GO	TBB9_GOSHI	Tubulin beta-9 chain (Beta-9 tubulin)	0.15	-	cyt	0					445
O94811 UniProt NPD GO	P25A_HUMAN	Tubulin polymerization-promoting protein (TPPP) (25 kDa brain-specific protein) (p25-alpha) (p24) (p ...	0.15	-	nuc	0			608773		219
Q9GZM7 UniProt NPD GO	TINAL_HUMAN	Tubulointerstitial nephritis antigen-like precursor (Tubulointerstitial nephritis antigen-related pr ...	0.15	-	end	0	Secreted protein	extracellular region [NAS]			467
P25942 UniProt NPD GO	TNR5_HUMAN	Tumor necrosis factor receptor superfamily member 5 precursor (CD40L receptor) (B-cell surface antig ...	0.15	-	exc	1	Isoform I: Cell membrane; single-pass type I membrane protein. Isoform II: Secreted protein	integral to plasma membrane [TAS] plasma membrane [TAS]	109535	1LB6	277
Q9P896 UniProt NPD GO	TCSA_EMENI	Two-component system protein A (EC 2.7.13.3)	0.15	-	cyt	0	Cytoplasm (Potential)	cytoplasm [NAS]			719
P18460 UniProt NPD GO	CEK2_CHICK	Tyrosine kinase receptor CEK2 precursor (EC 2.7.10.1)	0.15	-	end	2 *	Membrane; single-pass type I membrane protein				806
Q7ZX51 UniProt NPD GO	SYYC_XENLA	Tyrosyl-tRNA synthetase, cytoplasmic (EC 6.1.1.1) (Tyrosyl--tRNA ligase) (TyrRS)	0.15	-	cyt	0	Cytoplasm (By similarity)				528
P62310 UniProt NPD GO	LSM3_HUMAN	U6 snRNA-associated Sm-like protein LSm3	0.15	-	nuc	0	Nucleus (Potential)	nucleus [TAS]	607283		101
P62311 UniProt NPD GO	LSM3_MOUSE	U6 snRNA-associated Sm-like protein LSm3	0.15	-	nuc	0	Nucleus (Potential)				101
Q5B5W2 UniProt NPD GO	HUT1_EMENI	UDP-galactose transporter homolog 1	0.15	-	mit	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				424
Q19905 UniProt NPD GO	UGDH_CAEEL	UDP-glucose 6-dehydrogenase (EC 1.1.1.22) (UDP-Glc dehydrogenase) (UDP-GlcDH) (UDPGDH) (Squashed vul ...	0.15	-	cyt	0					481
O48917 UniProt NPD GO	SQD1_ARATH	UDP-sulfoquinovose synthase, chloroplast precursor (EC 3.13.1.1) (Sulfite:UDP-glucose sulfotransfera ...	0.15	-	mit	0	Plastid; chloroplast			1QRR	477
Q803A7 UniProt NPD GO	UGTAP_BRARE	UGA suppressor tRNA-associated protein homolog (Soluble liver antigen/Liver pancreas antigen-like)	0.15	-	nuc	0	Cytoplasm (By similarity)				490
Q8J1F7 UniProt NPD GO	ECM15_ASHGO	UPF0045 protein ECM15	0.15	-	cyt	0					105
O62252 UniProt NPD GO	U195_CAEEL	UPF0195 protein F45G2.10	0.15	-	cyt	0					160
P40388 UniProt NPD GO	UVI15_SCHPO	UV-induced protein uvi15	0.15	-	nuc	0					87
P07919 UniProt NPD GO	UCRH_HUMAN	Ubiquinol-cytochrome c reductase complex 11 kDa protein, mitochondrial precursor (EC 1.10.2.2) (Mito ...	0.15	-	nuc	0	Mitochondrion; mitochondrial inner membrane	mitochondrial electron transport chain [TAS]			91

You are viewing entries 57751 to 57800 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.