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
P51048 UniProt NPD GO	MTR1A_XENLA	Melatonin receptor type 1A X2.0 (MEL-1A-R) (Fragment)	0.01	-	end	3 *	Membrane; multi-pass membrane protein				153
P49288 UniProt NPD GO	MTR1C_CHICK	Melatonin receptor type 1C (MEL-1C-R) (CKB)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				346
Q7ZVH1 UniProt NPD GO	MPRG_BRARE	Membrane progestin receptor gamma (mPR gamma) (Progestin and adipoQ receptor family member V)	0.01	-	end	8	Membrane; multi-pass membrane protein (By similarity)				345
Q9BY19 UniProt NPD GO	M4A8B_HUMAN	Membrane-spanning 4-domains subfamily A member 8B (Four-span transmembrane protein 4)	0.01	-	end	4	Membrane; multi-pass membrane protein		606549		250
P81511 UniProt NPD GO	MCPI_HIRME	Metallocarboxypeptidase inhibitor precursor (Leech carboxypeptidase inhibitor) (LCI)	0.01	-	exc	0				2ABZ	81
O77717 UniProt NPD GO	TIMP2_HORSE	Metalloproteinase inhibitor 2 (TIMP-2) (Tissue inhibitor of metalloproteinases 2) (Fragment)	0.01	-	cyt	0	Secreted protein				91
P39876 UniProt NPD GO	TIMP3_MOUSE	Metalloproteinase inhibitor 3 precursor (TIMP-3) (Tissue inhibitor of metalloproteinases 3)	0.01	-	mit	0	Secreted protein; extracellular space; extracellular matrix	basement membrane [IDA]			211
P55953 UniProt NPD GO	MT_STENE	Metallothionein (MT)	0.01	-	nuc	0					64
P04734 UniProt NPD GO	MTA_STRPU	Metallothionein-A (MTA)	0.01	-	nuc	0				1QJL	64
Q27287 UniProt NPD GO	MTB_STRPU	Metallothionein-B (MTB)	0.01	-	nuc	0					65
P43396 UniProt NPD GO	MT1_COFAR	Metallothionein-like protein 1 (MT-1)	0.01	-	nuc	0					80
Q39269 UniProt NPD GO	MT2_BRARP	Metallothionein-like protein BIF98	0.01	-	nuc	0					80
Q96353 UniProt NPD GO	MT2_BRANA	Metallothionein-like protein type 2 LSC210 (Fragment)	0.01	-	nuc	0					28
P93134 UniProt NPD GO	MT2_FRAAN	Metallothionein-like protein type 2 MET1	0.01	-	nuc	0					80
Q9UHZ2 UniProt NPD GO	MALAT_HUMAN	Metastasis-associated lung adenocarcinoma transcript 1	0.01	-	cyt	0			607924		57
Q9SLN5 UniProt NPD GO	AMP1A_ARATH	Methionine aminopeptidase 1A (EC 3.4.11.18) (MetAP 1A) (MAP 1A) (Peptidase M 1A)	0.01	-	cyt	0	Cytoplasm				398
P05375 UniProt NPD GO	PEM2_YEAST	Methylene-fatty-acyl-phospholipid synthase (EC 2.1.1.16) (Unsaturated phospholipid methyltransferase ...	0.01	-	end	0		mitochondrion [IDA]			206
Q2KIZ3 UniProt NPD GO	MCEE_BOVIN	Methylmalonyl-CoA epimerase, mitochondrial precursor (EC 5.1.99.1) (DL-methylmalonyl-CoA racemase)	0.01	-	mit	0	Mitochondrion (Probable)				175
P54106 UniProt NPD GO	ICLN_XENLA	Methylosome subunit pICln (Chloride conductance regulatory protein ICln) (I(Cln))	0.01	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				241
Q06489 UniProt NPD GO	MTNA_YEAST	Methylthioribose-1-phosphate isomerase (EC 5.3.1.23) (MTR-1-P isomerase) (S-methyl-5-thioribose-1-ph ...	0.01	-	cyt	0		cytoplasm [IDA] nucleus [IDA]		1W2W	411
Q74Z81 UniProt NPD GO	SPC1_ASHGO	Microsomal signal peptidase subunit 1 (EC 3.4.-.-)	0.01	-	end	2 *	Membrane; multi-pass membrane protein (By similarity)				91
P81037 UniProt NPD GO	MILT_ONCKE	Miltpain (EC 3.4.22.-) (Fragment)	0.01	-		0					15
P49278 UniProt NPD GO	ALL2_DERPT	Mite group 2 allergen Der p 2 precursor (Der p II) (DPX)	0.01	-	end	0	Secreted protein			1KTJ	146
Q9CRB8 UniProt NPD GO	MTP18_MOUSE	Mitochondrial 18 kDa protein (MTP18)	0.01	-	cyt	0	Mitochondrion (By similarity)				166
Q9BQT8 UniProt NPD GO	ODC_HUMAN	Mitochondrial 2-oxodicarboxylate carrier (Solute carrier family 25 member 21)	0.01	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein		607571		299
Q5RFB7 UniProt NPD GO	ODC_PONPY	Mitochondrial 2-oxodicarboxylate carrier (Solute carrier family 25 member 21)	0.01	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				299
P82923 UniProt NPD GO	RT02_BOVIN	Mitochondrial 28S ribosomal protein S2 (S2mt) (MRP-S2) (Fragment)	0.01	-		0	Mitochondrion				10
P82924 UniProt NPD GO	RT30_BOVIN	Mitochondrial 28S ribosomal protein S30 (S30mt) (MRP-S30) (Fragments)	0.01	-	nuc	0	Mitochondrion				40
P82925 UniProt NPD GO	RT31_BOVIN	Mitochondrial 28S ribosomal protein S31 (S31mt) (MRP-S31) (Fragments)	0.01	-	cyt	0	Mitochondrion				98
P36515 UniProt NPD GO	YLM1_YEAST	Mitochondrial 60S ribosomal protein L1 (YmL1) (Fragment)	0.01	-		0	Mitochondrion				4
O21037 UniProt NPD GO	RM06_DICDI	Mitochondrial 60S ribosomal protein L6	0.01	-	nuc	0	Mitochondrion				170
Q04013 UniProt NPD GO	YHM2_YEAST	Mitochondrial DNA replication protein YHM2	0.01	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial nucleoid [IDA]			314
P12242 UniProt NPD GO	UCP1_MOUSE	Mitochondrial brown fat uncoupling protein 1 (UCP 1) (Thermogenin)	0.01	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial envelope [IDA] mitochondrion [IDA]			306
P04633 UniProt NPD GO	UCP1_RAT	Mitochondrial brown fat uncoupling protein 1 (UCP 1) (Thermogenin)	0.01	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [TAS]			306
Q12289 UniProt NPD GO	CRC1_YEAST	Mitochondrial carnitine carrier	0.01	-	nuc	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			327
O43772 UniProt NPD GO	MCAT_HUMAN	Mitochondrial carnitine/acylcarnitine carrier protein (Carnitine/acylcarnitine translocase) (CAC) (S ...	0.01	-	end	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein		212138		301
Q8HXY2 UniProt NPD GO	MCAT_MACFA	Mitochondrial carnitine/acylcarnitine carrier protein (Carnitine/acylcarnitine translocase) (CAC) (S ...	0.01	-	end	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				301
P97521 UniProt NPD GO	MCAT_RAT	Mitochondrial carnitine/acylcarnitine carrier protein (Carnitine/acylcarnitine translocase) (CAC) (S ...	0.01	-	cyt	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [TAS]			301
Q9Z2Z6 UniProt NPD GO	MCAT_MOUSE	Mitochondrial carnitine/acylcarnitine carrier protein (Carnitine/acylcarnitine translocase) (CAC) (m ...	0.01	-	mit	3 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [IDA]			301
Q791T5 UniProt NPD GO	MTCH1_MOUSE	Mitochondrial carrier homolog 1 (Mitochondrial carrier-like protein 1)	0.01	-	end	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				389
Q9NZJ7 UniProt NPD GO	MTCH1_HUMAN	Mitochondrial carrier homolog 1 (Presenilin-associated protein)	0.01	-	end	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	intracellular [ISS] mitochondrion [ISS]			389
O60200 UniProt NPD GO	MDM35_YEAST	Mitochondrial distribution and morphology protein 35	0.01	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			86
Q8BMG8 UniProt NPD GO	MFTC_MOUSE	Mitochondrial folate transporter/carrier (Solute carrier family 25 member 32)	0.01	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				316
Q6C6U1 UniProt NPD GO	TIM10_YARLI	Mitochondrial import inner membrane translocase subunit TIM10	0.01	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				140
Q9CQV7 UniProt NPD GO	TIM14_MOUSE	Mitochondrial import inner membrane translocase subunit TIM14 (DnaJ homolog subfamily C member 19)	0.01	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				115
Q6FT37 UniProt NPD GO	TIM22_CANGA	Mitochondrial import inner membrane translocase subunit TIM22	0.01	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				193
Q5KKL8 UniProt NPD GO	TIM22_CRYNE	Mitochondrial import inner membrane translocase subunit TIM22	0.01	-	mit	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				187
Q9ZW33 UniProt NPD GO	TIM10_ARATH	Mitochondrial import inner membrane translocase subunit Tim10	0.01	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				83
Q8IN78 UniProt NPD GO	TIM22_DROME	Mitochondrial import inner membrane translocase subunit Tim22	0.01	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane protein insert... [ISS]			195
Q9CQ85 UniProt NPD GO	TIM22_MOUSE	Mitochondrial import inner membrane translocase subunit Tim22	0.01	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				194

You are viewing entries 89551 to 89600 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.