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
P53375 UniProt NPD GO	TBB_PENDI	Tubulin beta chain (Beta tubulin)	0.16	-	cyt	0					447
Q7KQL5 UniProt NPD GO	TBB_PLAF7	Tubulin beta chain (Beta tubulin)	0.16	-	cyt	0					445
P14140 UniProt NPD GO	TBB_PLAFA	Tubulin beta chain (Beta tubulin)	0.16	-	cyt	0					445
P14643 UniProt NPD GO	TBB_PLAFK	Tubulin beta chain (Beta tubulin)	0.16	-	cyt	0				1LX0	445
P22852 UniProt NPD GO	TBB_POLAG	Tubulin beta chain (Beta tubulin)	0.16	-	cyt	0					443
P10876 UniProt NPD GO	TBB_TETPY	Tubulin beta chain (Beta tubulin)	0.16	-	cyt	0					443
P41352 UniProt NPD GO	TBB_TETTH	Tubulin beta chain (Beta tubulin)	0.16	-	cyt	0					443
P18699 UniProt NPD GO	TBB_LYMST	Tubulin beta chain (Beta tubulin) (Fragment)	0.16	-	cyt	0					111
Q9H4B7 UniProt NPD GO	TBB1_HUMAN	Tubulin beta-1 chain	0.16	-	cyt	0					451
P33188 UniProt NPD GO	TBB1_PARTE	Tubulin beta-1 chain (Beta-1 tubulin)	0.16	-	cyt	0					442
P31864 UniProt NPD GO	TBB1_TRIVI	Tubulin beta-1 chain (Beta-1 tubulin)	0.16	-	cyt	0					446
P61858 UniProt NPD GO	TBB2_DROHY	Tubulin beta-2 chain (Beta-2 tubulin)	0.16	-	cyt	0					446
P61857 UniProt NPD GO	TBB2_DROME	Tubulin beta-2 chain (Beta-2 tubulin)	0.16	-	cyt	0					446
P10874 UniProt NPD GO	TBB2_EMENI	Tubulin beta-2 chain (Beta-2 tubulin)	0.16	-	cyt	0					449
Q8H7U1 UniProt NPD GO	TBB2_ORYSA	Tubulin beta-2 chain (Beta-2 tubulin)	0.16	-	cyt	0					447
P31863 UniProt NPD GO	TBB2_TRIVI	Tubulin beta-2 chain (Beta-2 tubulin)	0.16	-	cyt	0					446
Q2T9S0 UniProt NPD GO	TBB3_BOVIN	Tubulin beta-3 chain	0.16	-	cyt	0					450
Q6VAF8 UniProt NPD GO	TBB3_GOSHI	Tubulin beta-3 chain (Beta-3 tubulin)	0.16	-	cyt	0					430
Q60HC2 UniProt NPD GO	TBB3_MACFA	Tubulin beta-3 chain (Tubulin beta-4)	0.16	-	cyt	0					450
Q13509 UniProt NPD GO	TBB3_HUMAN	Tubulin beta-3 chain (Tubulin beta-III) (Tubulin beta-4)	0.16	-	cyt	0			602661		450
P24636 UniProt NPD GO	TBB4_ARATH	Tubulin beta-4 chain (Beta-4 tubulin)	0.16	-	cyt	0					444
Q9ZRA9 UniProt NPD GO	TBB4_WHEAT	Tubulin beta-4 chain (Beta-4 tubulin)	0.16	-	cyt	0					445
Q43697 UniProt NPD GO	TBB5_MAIZE	Tubulin beta-5 chain (Beta-5 tubulin)	0.16	-	cyt	0					445
P37832 UniProt NPD GO	TBB7_ORYSA	Tubulin beta-7 chain (Beta-7 tubulin) (pTUB22)	0.16	-	cyt	0					444
Q9UJT0 UniProt NPD GO	TBE_HUMAN	Tubulin epsilon chain (Epsilon tubulin)	0.16	-	cyt	0	Centrosome. Associated with pericentriolar material	pericentriolar material [TAS]	607345		475
Q99426 UniProt NPD GO	TBCB_HUMAN	Tubulin-specific chaperone B (Tubulin folding cofactor B) (Cytoskeleton-associated protein 1) (Cytos ...	0.16	-	cyt	0		microtubule cytoskeleton [TAS]	601303		244
P29553 UniProt NPD GO	TNFA_HORSE	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.16	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				234
Q9CR75 UniProt NPD GO	TNR12_MOUSE	Tumor necrosis factor receptor superfamily member 12A precursor (Fibroblast growth factor-inducible ...	0.16	-	end	1 *	Membrane; single-pass type I membrane protein	cell surface [IDA] plasma membrane [IDA] ruffle [IDA]			129
P08138 UniProt NPD GO	TNR16_HUMAN	Tumor necrosis factor receptor superfamily member 16 precursor (Low-affinity nerve growth factor rec ...	0.16	-	nuc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	162010		427
Q6V915 UniProt NPD GO	IOD1_FELCA	Type I iodothyronine deiodinase (EC 1.97.1.10) (Type-I 5'deiodinase) (DIOI) (Type 1 DI) (5DI)	0.16	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				244
Q13882 UniProt NPD GO	PTK6_HUMAN	Tyrosine-protein kinase 6 (EC 2.7.10.2) (Breast tumor kinase) (Tyrosine-protein kinase BRK)	0.16	-	mit	0	Cytoplasm. Nucleus. Colocalizes with KHDRBS1, KHDRBS2 or KHDRBS3, within the nucleus. In secretory e ...		602004	1RJA	451
P51451 UniProt NPD GO	BLK_HUMAN	Tyrosine-protein kinase BLK (EC 2.7.10.2) (B lymphocyte kinase) (p55-BLK)	0.16	-	nuc	0			191305		504
P50545 UniProt NPD GO	HCK_RAT	Tyrosine-protein kinase HCK (EC 2.7.10.2) (p56-HCK) (Hemopoietic cell kinase)	0.16	-	nuc	0	Membrane; lipid-anchor				502
Q6DIJ1 UniProt NPD GO	SYYC_XENTR	Tyrosyl-tRNA synthetase, cytoplasmic (EC 6.1.1.1) (Tyrosyl--tRNA ligase) (TyrRS)	0.16	-	cyt	0	Cytoplasm (By similarity)				528
P36421 UniProt NPD GO	SYYC_YEAST	Tyrosyl-tRNA synthetase, cytoplasmic (EC 6.1.1.1) (Tyrosyl--tRNA ligase) (TyrRS)	0.16	-	cyt	0	Cytoplasm. Nucleus. Predominantly cytoplasmic, only a small fraction (about 1.5%) found in the nucle ...	cytoplasm [IDA] nucleus [IDA]			393
Q5E9Z8 UniProt NPD GO	LSM1_BOVIN	U6 snRNA-associated Sm-like protein LSm1	0.16	-	cyt	0	Nucleus (Potential)				133
O15116 UniProt NPD GO	LSM1_HUMAN	U6 snRNA-associated Sm-like protein LSm1 (Small nuclear ribonuclear CaSm) (Cancer-associated Sm-like ...	0.16	-	cyt	0	Nucleus (Potential)	nucleus [TAS]	607281		133
Q9QXA5 UniProt NPD GO	LSM4_MOUSE	U6 snRNA-associated Sm-like protein LSm4	0.16	-	nuc	0	Nucleus (Potential)				137
Q4WJM7 UniProt NPD GO	HUT1_ASPFU	UDP-galactose transporter homolog 1	0.16	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				415
Q4P9R2 UniProt NPD GO	HUT1_USTMA	UDP-galactose transporter homolog 1	0.16	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				384
P58557 UniProt NPD GO	CU057_HUMAN	UPF0054 protein C21orf57	0.16	-	mit	0					167
Q9ZUU2 UniProt NPD GO	U308_ARATH	UPF0308 protein At2g37240, chloroplast precursor	0.16	-	mit	0	Plastid; chloroplast (Potential)				248
P78761 UniProt NPD GO	UQCR2_SCHPO	Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor (EC 1.10.2.2)	0.16	-	mit	0	Mitochondrion; mitochondrial inner membrane				426
P08618 UniProt NPD GO	UBIQ_DICDI	Ubiquitin	0.16	-	cyt	0	Cytoplasm. Nucleus				76
Q05550 UniProt NPD GO	UBIQ_LEIMA	Ubiquitin	0.16	-	cyt	0	Cytoplasm. Nucleus				76
P22515 UniProt NPD GO	UBA1_YEAST	Ubiquitin-activating enzyme E1 1	0.16	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			1024
O13685 UniProt NPD GO	UBC13_SCHPO	Ubiquitin-conjugating enzyme E2 13 (EC 6.3.2.19) (Ubiquitin-protein ligase 13) (Ubiquitin carrier pr ...	0.16	-	nuc	0					148
P52490 UniProt NPD GO	UBC13_YEAST	Ubiquitin-conjugating enzyme E2 13 (EC 6.3.2.19) (Ubiquitin-protein ligase 13) (Ubiquitin carrier pr ...	0.16	-	nuc	0		cytoplasm [IDA] nucleus [IDA] ubiquitin conjugating enzyme complex [IPI]		1JBB	153
P56616 UniProt NPD GO	UBE2C_XENLA	Ubiquitin-conjugating enzyme E2 C (EC 6.3.2.19) (Ubiquitin-protein ligase C) (Ubiquitin carrier prot ...	0.16	-	nuc	0					179
P35134 UniProt NPD GO	UBC11_ARATH	Ubiquitin-conjugating enzyme E2-17 kDa 11 (EC 6.3.2.19) (Ubiquitin-protein ligase 11) (Ubiquitin car ...	0.16	-	nuc	0					148

You are viewing entries 56401 to 56450 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.