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
P56504 UniProt NPD GO	BAP11_SCHCO	Mating-type pheromone BAP1(1) precursor	0.08	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				50
Q10738 UniProt NPD GO	MMP7_MOUSE	Matrilysin precursor (EC 3.4.24.23) (Pump-1 protease) (Uterine metalloproteinase) (Matrix metallopro ...	0.08	-	exc	0					264
Q58T41 UniProt NPD GO	M11H1_BOMMX	Maximins 11/H1 precursor [Contains: Maximin-11; Maximin-H1 (Maximin-6)]	0.08	-	end	0	Secreted protein				144
Q58T51 UniProt NPD GO	M1111_BOMMX	Maximins 11/H11 precursor [Contains: Maximin-11; Maximin-H11]	0.08	-	end	0	Secreted protein				144
Q58T56 UniProt NPD GO	M8H7_BOMMX	Maximins 8/H7 precursor [Contains: Maximin-8; Maximin-H7]	0.08	-	exc	0	Secreted protein				144
Q58T93 UniProt NPD GO	MYH16_BOMMX	Maximins y/H16 precursor [Contains: Maximin-y; Maximin-H16]	0.08	-	end	0	Secreted protein				142
P91641 UniProt NPD GO	MED20_DROME	Mediator complex subunit 20 (Protein trf-proximal) (Protein transcription mediator-related)	0.08	-	mit	0	Nucleus (Potential)	Srb-mediator complex [ISS]			252
P12797 UniProt NPD GO	BRK_MEGFL	Megascoliakinin ([Thr6]-bradykinin-Lys-Ala) [Contains: Bradykinin-like peptide ([Thr6]-bradykinin)]	0.08	-		0	Secreted protein. Venom reservoirs	extracellular space [IDA]			11
Q61845 UniProt NPD GO	MEIG1_MOUSE	Meiosis expressed protein 1	0.08	+	cyt	0		nucleus [IDA]			88
P41149 UniProt NPD GO	MC5R_MOUSE	Melanocortin receptor 5 (MC5-R)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				325
Q9TT23 UniProt NPD GO	MC5R_PANTR	Melanocortin receptor 5 (MC5-R)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				325
P35345 UniProt NPD GO	MC5R_RAT	Melanocortin receptor 5 (MC5-R)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				325
P33032 UniProt NPD GO	MC5R_HUMAN	Melanocortin receptor 5 (MC5-R) (MC-2)	0.08	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600042		325
Q864G6 UniProt NPD GO	MSHR_ALOSE	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.08	-	end	7 *	Membrane; multi-pass membrane protein				317
P56443 UniProt NPD GO	MSHR_CAPCA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.08	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864K1 UniProt NPD GO	MSHR_CERNE	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.08	-	end	4 *	Membrane; multi-pass membrane protein				317
P56446 UniProt NPD GO	MSHR_DAMDA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.08	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864K9 UniProt NPD GO	MSHR_GORGO	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.08	-	end	6 *	Membrane; multi-pass membrane protein				316
Q865E5 UniProt NPD GO	MSHR_HERYA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.08	-	end	7 *	Membrane; multi-pass membrane protein				317
Q865E8 UniProt NPD GO	MSHR_PANON	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.08	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864H3 UniProt NPD GO	MSHR_SAGGE	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.08	-	end	7 *	Membrane; multi-pass membrane protein				316
P43362 UniProt NPD GO	MAGA9_HUMAN	Melanoma-associated antigen 9 (MAGE-9 antigen)	0.08	-	mit	0			300342		315
P08582 UniProt NPD GO	TRFM_HUMAN	Melanotransferrin precursor (Melanoma-associated antigen p97) (CD228 antigen)	0.08	-	end	0	Isoform 1: Cell membrane; lipid-anchor; GPI-anchor	integral to plasma membrane [TAS]	155750		738
Q11000 UniProt NPD GO	AMPM_HELVI	Membrane alanyl aminopeptidase precursor (EC 3.4.11.-) (Aminopeptidase N-like protein) (CryIA(C) rec ...	0.08	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				1009
Q8TEZ7 UniProt NPD GO	MPRB_HUMAN	Membrane progestin receptor beta (mPR beta) (Progestin and adipoQ receptor family member VIII) (Lyso ...	0.08	-	end	6	Cell membrane; multi-pass membrane protein. Colocalizes with a lysosomal protein cathepsin D		607780		354
Q14416 UniProt NPD GO	MGR2_HUMAN	Metabotropic glutamate receptor 2 precursor (mGluR2)	0.08	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	604099		872
Q9LXS1 UniProt NPD GO	MTPA2_ARATH	Metal tolerance protein A2 (AtMTPa2) (AtMTP3)	0.08	-	end	6	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				378
Q6DBM8 UniProt NPD GO	MTPB_ARATH	Metal tolerance protein B (AtMTPb) (AtMTP4)	0.08	-	end	5	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				375
Q9CZJ0 UniProt NPD GO	MPPD2_MOUSE	Metallophosphoesterase domain-containing protein 2	0.08	-	cyt	0					294
P25785 UniProt NPD GO	TIMP2_MOUSE	Metalloproteinase inhibitor 2 precursor (TIMP-2) (Tissue inhibitor of metalloproteinases 2)	0.08	-	exc	0	Secreted protein	basement membrane [IDA] cell surface [IDA]			220
P30121 UniProt NPD GO	TIMP2_RAT	Metalloproteinase inhibitor 2 precursor (TIMP-2) (Tissue inhibitor of metalloproteinases 2)	0.08	-	exc	0	Secreted protein				220
P16035 UniProt NPD GO	TIMP2_HUMAN	Metalloproteinase inhibitor 2 precursor (TIMP-2) (Tissue inhibitor of metalloproteinases 2) (CSC-21K ...	0.08	-	exc	0	Secreted protein		188825	2TMP	220
Q60453 UniProt NPD GO	TIMP2_CRILO	Metalloproteinase inhibitor 2 precursor (TIMP-2) (Tissue inhibitor of metalloproteinases 2) (Fragmen ...	0.08	-	nuc	0	Secreted protein				196
P80258 UniProt NPD GO	MT23B_MYTED	Metallothionein 20-III isoform B (MT-20-IIIB)	0.08	-	nuc	0					71
Q8T6B3 UniProt NPD GO	MT1_TETTH	Metallothionein-1 (MT-1)	0.08	-	nuc	0					107
P02804 UniProt NPD GO	MT1_CRIGR	Metallothionein-1 (MT-1) (Metallothionein-I) (MT-I)	0.08	-	nuc	0					61
P02802 UniProt NPD GO	MT1_MOUSE	Metallothionein-1 (MT-1) (Metallothionein-I) (MT-I)	0.08	-	nuc	0		cytosol [IDA] lysosome [IDA]		1DFT	61
P80394 UniProt NPD GO	MT1_TETPI	Metallothionein-1 precursor (MT-1) [Contains: Metallothionein-2 (MT-2)]	0.08	-	nuc	0					107
P13640 UniProt NPD GO	MT1G_HUMAN	Metallothionein-1G (MT-1G) (Metallothionein-IG) (MT-IG) (Metallothionein-1K) (MT-1K)	0.08	-	nuc	0			156353		62
Q5NVS0 UniProt NPD GO	MT2_PONPY	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II)	0.08	-	nuc	0					61
P02795 UniProt NPD GO	MT2_HUMAN	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II) (Metallothionein-2A)	0.08	-	nuc	0			156360	2MHU	61
P55944 UniProt NPD GO	MT3_PIG	Metallothionein-3 (MT-3) (Metallothionein-III) (MT-III) (Growth inhibitory factor) (GIF)	0.08	-	nuc	0		synaptic vesicle [ISS]			68
Q38803 UniProt NPD GO	MT1B_ARATH	Metallothionein-like protein 1B (MT-1B)	0.08	-	nuc	0					45
Q9HCC0 UniProt NPD GO	MCCC2_HUMAN	Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial precursor (EC 6.4.1.4) (3-Methylcrotonyl-C ...	0.08	-	nuc	0	Mitochondrion; mitochondrial matrix	mitochondrion [NAS]	609014		563
Q9R008 UniProt NPD GO	KIME_MOUSE	Mevalonate kinase (EC 2.7.1.36) (MK)	0.08	-	mit	0	Cytoplasm. Peroxisome				395
Q9D3X9 UniProt NPD GO	MFA3L_MOUSE	Microfibrillar-associated protein 3-like precursor	0.08	-	end	1	Membrane; single-pass type I membrane protein (Potential)				409
Q15691 UniProt NPD GO	MARE1_HUMAN	Microtubule-associated protein RP/EB family member 1 (APC-binding protein EB1) (End-binding protein ...	0.08	-	cyt	0	Cytoplasm. Associated with the microtubule network at the growing distal tip of microtubules. Also e ...	cortical microtubule cytoskeleton [IDA]	603108	1YIG	267
Q5R7Z5 UniProt NPD GO	MARE1_PONPY	Microtubule-associated protein RP/EB family member 1 (APC-binding protein EB1) (End-binding protein ...	0.08	-	cyt	0	Cytoplasm (By similarity). Associated with the microtubule network at the growing distal tip of micr ...				267
P82664 UniProt NPD GO	RT10_HUMAN	Mitochondrial 28S ribosomal protein S10 (S10mt) (MRP-S10)	0.08	-	mit	0	Mitochondrion	mitochondrial ribosome [IDA]			201
Q5RFM3 UniProt NPD GO	RT10_PONPY	Mitochondrial 28S ribosomal protein S10 (S10mt) (MRP-S10)	0.08	-	mit	0	Mitochondrion (By similarity)				201

You are viewing entries 68401 to 68450 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.