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
Q8TGT9 UniProt NPD GO	YG146_YEAST	Uncharacterized protein YGR146C-A	0.03	-	mit	1 *	Membrane; single-pass membrane protein (Potential)				53
P38834 UniProt NPD GO	YHT0_YEAST	Uncharacterized protein YHR130C	0.03	-	vac	2 *					111
Q3E743 UniProt NPD GO	YJ112_YEAST	Uncharacterized protein YJR112W-A	0.03	-	mit	1	Membrane; single-pass membrane protein (Potential)				109
Q3E775 UniProt NPD GO	YJ151_YEAST	Uncharacterized protein YJR151W-A	0.03	-		0					16
Q3E771 UniProt NPD GO	YL285_YEAST	Uncharacterized protein YLR285C-A	0.03	-	mit	0					56
Q04299 UniProt NPD GO	YMX7_YEAST	Uncharacterized protein YML087W	0.03	-	cyt	0				1TY8	284
Q8TGS7 UniProt NPD GO	YM182_YEAST	Uncharacterized protein YMR182W-A	0.03	-	mit	1 *	Membrane; single-pass membrane protein (Potential)				28
Q8TGS6 UniProt NPD GO	YM242_YEAST	Uncharacterized protein YMR242W-A	0.03	-	cyt	0					29
Q3E824 UniProt NPD GO	YO020_YEAST	Uncharacterized protein YOR020W-A	0.03	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				90
Q8TGR9 UniProt NPD GO	YP152_YEAST	Uncharacterized protein YPL152W-A	0.03	-	nuc	0					32
Q05899 UniProt NPD GO	YL297_YEAST	Uncharacterized vacuolar protein YLR297W	0.03	-	nuc	1	Vacuole; vacuolar membrane; single-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			129
P80501 UniProt NPD GO	MMPX_SOLTU	Unidentified mitochondrial matrix protein (Fragment)	0.03	-		0	Mitochondrion; mitochondrial matrix				16
P30095 UniProt NPD GO	UPA9_HUMAN	Unknown protein from 2D-PAGE of plasma (Spot 35) (Fragment)	0.03	-		0					10
P82322 UniProt NPD GO	UT103_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 103) (Fragment)	0.03	-		0	Plastid; chloroplast; chloroplast thylakoid	chloroplast [NAS] thylakoid [NAS]			14
P82337 UniProt NPD GO	UT019_PEA	Unknown protein from 2D-PAGE of thylakoid (Spot 19) (Fragments)	0.03	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid				33
Q28614 UniProt NPD GO	UT2_RABIT	Urea transporter, kidney (Vasopressin-regulated urea transporter)	0.03	-	end	8	Membrane; multi-pass membrane protein				397
P40752 UniProt NPD GO	TKU2_UREUN	Urechistachykinin-2 (Urechistachykinin II)	0.03	-		0	Secreted protein				10
P78609 UniProt NPD GO	URIC_PICJA	Uricase (EC 1.7.3.3) (Urate oxidase)	0.03	-	cyt	0	Peroxisome				303
O04420 UniProt NPD GO	URIC_ARATH	Uricase (EC 1.7.3.3) (Urate oxidase) (Nodulin 35 homolog)	0.03	-	pox	0	Peroxisome (Potential)				309
O95848 UniProt NPD GO	NUD14_HUMAN	Uridine diphosphate glucose pyrophosphatase (EC 3.6.1.45) (UDPG pyrophosphatase) (UGPPase) (Nucleosi ...	0.03	-	cyt	0	Cytoplasm		609219		222
Q16831 UniProt NPD GO	UPP1_HUMAN	Uridine phosphorylase 1 (EC 2.4.2.3) (UrdPase 1) (UPase 1)	0.03	-	cyt	0			191730		310
P52624 UniProt NPD GO	UPP1_MOUSE	Uridine phosphorylase 1 (EC 2.4.2.3) (UrdPase 1) (UPase 1)	0.03	-	nuc	0					311
P81827 UniProt NPD GO	UP1_RAT	Urinary protein 1 precursor (RUP-1) (Liver regeneration-related protein LRRG05)	0.03	-	exc	0	Secreted protein				101
O75631 UniProt NPD GO	UPK3A_HUMAN	Uroplakin-3A precursor (Uroplakin III) (UPIII)	0.03	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				287
O18601 UniProt NPD GO	DCUP_DROVI	Uroporphyrinogen decarboxylase (EC 4.1.1.37) (URO-D) (UPD)	0.03	-	vac	0	Cytoplasm				386
Q9TS45 UniProt NPD GO	UTER_MACFU	Uteroglobin (Secretoglobin family 1A member 1) (Clara cell phospholipid-binding protein) (CCPBP) (Cl ...	0.03	-	nuc	0	Secreted protein				70
P06913 UniProt NPD GO	UTER_LEPCA	Uteroglobin precursor (Secretoglobin family 1A member 1) (Blastokinin)	0.03	-	exc	1 *	Secreted protein				91
P01284 UniProt NPD GO	VIP_PIG	VIP peptides precursor [Contains: Intestinal peptide PHI-27 (Peptide histidine isoleucinamide 27); V ...	0.03	-	cyt	0	Secreted protein				72
P32649 UniProt NPD GO	VIP_RABIT	VIP peptides precursor [Contains: Intestinal peptide PHI-27 (Peptide histidine isoleucinamide 27); V ...	0.03	-	cyt	0	Secreted protein				72
P48602 UniProt NPD GO	VATA1_DROME	Vacuolar ATP synthase catalytic subunit A isoform 1 (EC 3.6.3.14) (V-ATPase subunit A 1) (Vacuolar p ...	0.03	-	nuc	0		hydrogen-transporting ATPase V1 domain [ISS]			614
Q04236 UniProt NPD GO	VATA1_EQUAR	Vacuolar ATP synthase catalytic subunit A, isoform 1 (EC 3.6.3.14) (Fragment)	0.03	-	cyt	0					30
O44091 UniProt NPD GO	VATF1_DROPS	Vacuolar ATP synthase subunit F (EC 3.6.3.14) (V-ATPase F subunit) (Vacuolar proton pump F subunit) ...	0.03	-	cyt	0					124
Q9W4P5 UniProt NPD GO	VA0D1_DROME	Vacuolar ATP synthase subunit d 1 (EC 3.6.3.14) (V-ATPase d subunit 1) (Vacuolar proton pump subunit ...	0.03	-	cyt	0					350
Q56ZQ3 UniProt NPD GO	VSR4_ARATH	Vacuolar sorting receptor 4 precursor (AtVSR4) (Epidermal growth factor receptor-like protein 2b) (A ...	0.03	-	end	1					628
P40046 UniProt NPD GO	VTC1_YEAST	Vacuolar transporter chaperone 1 (Phosphate metabolism protein 4) (Negative regulator of CDC42 prote ...	0.03	-	end	3 *	Vacuole; vacuolar membrane; multi-pass membrane protein	intrinsic to vacuolar membrane [IDA]			128
P81701 UniProt NPD GO	PRXV_ASCNO	Vanadium haloperoxidase (EC 1.11.1.-) (V-BPO)	0.03	-	cyt	0				1QI9	557
P58452 UniProt NPD GO	VARG_VIOAR	Varv peptide G	0.03	-	nuc	0					30
P84771 UniProt NPD GO	VIP_AMICA	Vasoactive intestinal peptide (VIP) (Vasoactive intestinal polypeptide)	0.03	-	nuc	0	Secreted protein				28
P84772 UniProt NPD GO	VIP_ONCMY	Vasoactive intestinal peptide (VIP) (Vasoactive intestinal polypeptide)	0.03	-	nuc	0	Secreted protein				28
P48044 UniProt NPD GO	V2R_BOVIN	Vasopressin V2 receptor (Renal-type arginine vasopressin receptor) (Antidiuretic hormone receptor) ( ...	0.03	-	end	7 *	Membrane; multi-pass membrane protein				370
P35759 UniProt NPD GO	VA5_POLEX	Venom allergen 5 (Antigen 5) (Ag5) (Allergen Pol e 5) (Pol e V)	0.03	-	nuc	0	Secreted protein. Venom reservoirs				205
Q7Z156 UniProt NPD GO	VA5_POLSR	Venom allergen 5 (Antigen 5) (Ag5) (Allergen Pol s 5) (Pol s V)	0.03	-	cyt	0	Secreted protein. Venom reservoirs				207
P35787 UniProt NPD GO	VA5_VESVI	Venom allergen 5 (Antigen 5) (Ag5) (Allergen Ves vi 5) (Ves vi V)	0.03	-	nuc	0	Secreted protein. Venom reservoirs				206
P10737 UniProt NPD GO	VA53_DOLMA	Venom allergen 5.02 precursor (Antigen 5 form 3) (Ag5-3) (Allergen Dol m 5.02) (Dol m V-B) (Fragment ...	0.03	-	nuc	0	Secreted protein. Venom reservoirs				215
P61898 UniProt NPD GO	NGFV_NAJAT	Venom nerve growth factor (v-NGF)	0.03	-	cyt	0	Secreted protein				116
P61899 UniProt NPD GO	NGFV_NAJKA	Venom nerve growth factor (v-NGF)	0.03	-	cyt	0	Secreted protein				116
P84015 UniProt NPD GO	TXC5_PHONI	Venom protein PN10C5	0.03	-	nuc	0	Secreted protein				33
Q9DF67 UniProt NPD GO	VSP2_TRIJE	Venom serine proteinase 2 precursor (EC 3.4.21.-) (SP2)	0.03	-	end	0	Secreted protein				258
O42886 UniProt NPD GO	YBN2_SCHPO	Very hypothetical protein C8E4.02c in chromosome II	0.03	-	mit	0					129
P39561 UniProt NPD GO	YAN1_YEAST	Very hypothetical protein YAR061W/YHR212W-A	0.03	-	nuc	0					67

You are viewing entries 82001 to 82050 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.