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
P82647 UniProt NPD GO	SCR28_ARATH	Hypothetical protein SCRL28 precursor	0.07	-	nuc	1 *					63
Q22544 UniProt NPD GO	YAE7_CAEEL	Hypothetical protein T18D3.7 in chromosome X	0.07	-	nuc	0					102
P34593 UniProt NPD GO	YOD1_CAEEL	Hypothetical protein ZC262.1	0.07	-	nuc	0					131
Q09364 UniProt NPD GO	YS22_CAEEL	Hypothetical protein ZK1320.2	0.07	-	exc	0					208
Q09371 UniProt NPD GO	YS42_CAEEL	Hypothetical protein ZK177.2	0.07	-	nuc	0					296
P34628 UniProt NPD GO	YOJ5_CAEEL	Hypothetical protein ZK353.5	0.07	-	mit	0					114
P34639 UniProt NPD GO	YOQ1_CAEEL	Hypothetical protein ZK512.1	0.07	-	end	1					332
Q09662 UniProt NPD GO	YS51_CAEEL	Hypothetical protein ZK673.1 precursor	0.07	-	exc	0					154
P48329 UniProt NPD GO	YCX8_CYAPA	Hypothetical protein in petA-psaM intergenic region (ORF180)	0.07	-	cyt	0	Plastid; cyanelle				180
Q8VYX0 UniProt NPD GO	ILL6_ARATH	IAA-amino acid hydrolase ILR1-like 6 precursor (EC 3.5.1.-) (Protein gr1)	0.07	-	end	1 *					464
P01878 UniProt NPD GO	IGHA_MOUSE	Ig alpha chain C region	0.07	-	exc	0					344
P03982 UniProt NPD GO	HV03_CAICR	Ig heavy chain V region G4 precursor	0.07	-	vac	0					117
P01821 UniProt NPD GO	HV45_MOUSE	Ig heavy chain V region MC101 precursor	0.07	-	exc	0					116
P06326 UniProt NPD GO	HV1F_HUMAN	Ig heavy chain V-I region Mot	0.07	-	cyt	0		extracellular region [NAS]			125
P01815 UniProt NPD GO	HV2B_HUMAN	Ig heavy chain V-II region COR	0.07	-	mit	0		extracellular region [NAS]			120
P01825 UniProt NPD GO	HV2G_HUMAN	Ig heavy chain V-II region NEWM	0.07	-	mit	0		extracellular region [NAS]		7FAB	117
P01632 UniProt NPD GO	KV1A_MOUSE	Ig kappa chain V-I region S107A	0.07	-	nuc	0					114
P01703 UniProt NPD GO	LV1E_HUMAN	Ig lambda chain V-I region NEWM	0.07	-	mit	0		extracellular region [NAS]		7FAB	103
P01708 UniProt NPD GO	LV2E_HUMAN	Ig lambda chain V-II region BUR	0.07	-	nuc	0		extracellular region [NAS]			109
P20767 UniProt NPD GO	LAC2_RAT	Ig lambda-2 chain C region	0.07	-	nuc	0					104
P82701 UniProt NPD GO	IM18_DROME	Immune-induced peptide 18 precursor (DIM-18)	0.07	-	exc	1 *	Secreted protein	extracellular region [IDA]			71
Q969P0 UniProt NPD GO	IGSF8_HUMAN	Immunoglobulin superfamily member 8 precursor (CD81 partner 3) (Glu-Trp-Ile EWI motif-containing pro ...	0.07	-	end	1	Membrane; single-pass membrane protein (Potential)	integral to membrane [IDA]	606644		613
O97972 UniProt NPD GO	INMT_RABIT	Indolethylamine N-methyltransferase (EC 2.1.1.49) (Aromatic alkylamine N-methyltransferase) (Indolam ...	0.07	-	cyt	0	Cytoplasm				263
Q7YRZ9 UniProt NPD GO	MCL1_FELCA	Induced myeloid leukemia cell differentiation protein Mcl-1 homolog	0.07	-	cyt	1	Membrane; single-pass membrane protein (By similarity). Cytoplasm (By similarity). Mitochondrion (By ...				350
Q5REY9 UniProt NPD GO	MIOX_PONPY	Inositol oxygenase (EC 1.13.99.1) (Myo-inositol oxygenase)	0.07	-	cyt	0	Cytoplasm (By similarity)				285
Q6C6Q7 UniProt NPD GO	IPK1_YARLI	Inositol-pentakisphosphate 2-kinase (EC 2.7.1.-) (Inositol-1,3,4,5,6-pentakisphosphate 2-kinase) (In ...	0.07	-	cyt	0	Nucleus (By similarity)				292
Q17230 UniProt NPD GO	SIX4_MESMA	Insect toxin 4 precursor (BmK IT4) (Fragment)	0.07	-	cyt	0	Secreted protein				64
P60269 UniProt NPD GO	SCX4_BUTEU	Insectotoxin-I4 (BeI4)	0.07	-	nuc	0	Secreted protein				35
P67972 UniProt NPD GO	INS_AOTTR	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.07	-	cyt	0	Secreted protein				108
P01317 UniProt NPD GO	INS_BOVIN	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.07	-	vac	0	Secreted protein			2INS	105
P01335 UniProt NPD GO	INS_CYPCA	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.07	-	end	0	Secreted protein				108
Q6X7V3 UniProt NPD GO	INSL3_CANFA	Insulin-like 3 precursor (Leydig insulin-like peptide) (Ley-I-L) (Relaxin-like factor) [Contains: In ...	0.07	-	end	1 *	Secreted protein				132
O42204 UniProt NPD GO	ITM2B_CHICK	Integral membrane protein 2B (Transmembrane protein E3-16)	0.07	-	nuc	1 *	Membrane; single-pass type II membrane protein (Potential)				262
Q28730 UniProt NPD GO	ICAM5_RABIT	Intercellular adhesion molecule 5 precursor (ICAM-5) (Telencephalin)	0.07	-	end	1	Membrane; single-pass type I membrane protein				912
Q28292 UniProt NPD GO	IL1B_CANFA	Interleukin-1 beta precursor (IL-1 beta) (Fragment)	0.07	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				127
Q9D6Z6 UniProt NPD GO	IL1F8_MOUSE	Interleukin-1 family member 8 (IL-1F8)	0.07	-	cyt	0	Secreted protein (Potential)				183
Q95LF0 UniProt NPD GO	I13R2_CANFA	Interleukin-13 receptor alpha-2 chain precursor (CD213a2 antigen)	0.07	-	end	1	Membrane; single-pass type I membrane protein				386
Q8QFQ8 UniProt NPD GO	IL18_CHICK	Interleukin-18 precursor (IL-18)	0.07	-	cyt	0	Secreted protein (By similarity)				196
O19073 UniProt NPD GO	IL18_PIG	Interleukin-18 precursor (IL-18) (Interferon-gamma-inducing factor) (IFN-gamma-inducing factor) (Int ...	0.07	-	nuc	0	Secreted protein	extracellular region [ISS]			192
P51747 UniProt NPD GO	IL2_CEREL	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.07	-	exc	0	Secreted protein				162
P51740 UniProt NPD GO	PPBJ_RAT	Intestinal alkaline phosphatase 2 precursor (EC 3.1.3.1) (IAP-II)	0.07	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				551
P03880 UniProt NPD GO	ANI1_EMENI	Intron-encoded DNA endonuclease I-AniI precursor (mRNA maturase bI1) (COB intron protein) [Contains: ...	0.07	-	end	5 *	Mitochondrion			1P8K	488
P28999 UniProt NPD GO	INU1_KLUMA	Inulinase precursor (EC 3.2.1.7) (2,1-beta-D-fructanfructanohydrolase) (Inulase)	0.07	-	exc	0	Secreted protein				555
Q811J3 UniProt NPD GO	IREB2_MOUSE	Iron-responsive element-binding protein 2 (IRE-BP 2) (Iron regulatory protein 2) (IRP2)	0.07	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [IDA]			963
Q62751 UniProt NPD GO	IREB2_RAT	Iron-responsive element-binding protein 2 (IRE-BP 2) (Iron regulatory protein 2) (IRP2)	0.07	-	cyt	0	Cytoplasm				963
P48735 UniProt NPD GO	IDHP_HUMAN	Isocitrate dehydrogenase [NADP], mitochondrial precursor (EC 1.1.1.42) (Oxalosuccinate decarboxylase ...	0.07	-	mit	0	Mitochondrion		147650		452
O13302 UniProt NPD GO	IDH1_AJECA	Isocitrate dehydrogenase [NAD] subunit 1, mitochondrial precursor (EC 1.1.1.41) (Isocitric dehydroge ...	0.07	-	mit	0	Mitochondrion (By similarity)				388
O35586 UniProt NPD GO	IDI1_MESAU	Isopentenyl-diphosphate delta-isomerase 1 (EC 5.3.3.2) (IPP isomerase 1) (Isopentenyl pyrophosphate ...	0.07	-	cyt	0	Peroxisome				227
O48965 UniProt NPD GO	IDI2_CAMAC	Isopentenyl-diphosphate delta-isomerase II (EC 5.3.3.2) (IPP isomerase II) (Isopentenyl pyrophosphat ...	0.07	-	mit	0					309
Q9FS87 UniProt NPD GO	IVD2_SOLTU	Isovaleryl-CoA dehydrogenase 2, mitochondrial precursor (EC 1.3.99.10) (IVD 2) (Fragment)	0.07	-	cyt	0	Mitochondrion				401

You are viewing entries 70251 to 70300 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.