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
P36522 UniProt NPD GO	RM12_YEAST	Mitochondrial 60S ribosomal protein L12 (YmL12) (Fragment)	0.00	-		0	Mitochondrion				15
P25874 UniProt NPD GO	UCP1_HUMAN	Mitochondrial brown fat uncoupling protein 1 (UCP 1) (Thermogenin)	0.00	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [NAS]	113730		307
P04575 UniProt NPD GO	UCP1_MESAU	Mitochondrial brown fat uncoupling protein 1 (UCP 1) (Thermogenin)	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				306
P14271 UniProt NPD GO	UCP1_RABIT	Mitochondrial brown fat uncoupling protein 1 (UCP 1) (Thermogenin)	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				306
P10861 UniProt NPD GO	UCP1_BOVIN	Mitochondrial brown fat uncoupling protein 1 (UCP 1) (Thermogenin) (Fragment)	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				288
Q93XM7 UniProt NPD GO	MCAT_ARATH	Mitochondrial carnitine/acylcarnitine carrier-like protein (Protein A BOUT DE SOUFFLE) (Carnitine/ac ...	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				300
Q3T0I5 UniProt NPD GO	FIS1_BOVIN	Mitochondrial fission 1 protein (Fis1 homolog)	0.00	-	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass membrane protein (By similarity)				152
Q9CQ92 UniProt NPD GO	FIS1_MOUSE	Mitochondrial fission 1 protein (Fis1 homolog) (Tetratricopeptide repeat protein 11) (TPR repeat pro ...	0.00	-	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass membrane protein. Peroxisome; peroxisomal m ...	integral to mitochondrial outer membrane [ISS] integral to peroxisomal membrane [ISS] mitochondrion [IDA]		1IYG	152
Q9Y3D6 UniProt NPD GO	FIS1_HUMAN	Mitochondrial fission 1 protein (Fis1 homolog) (hFis1) (Tetratricopeptide repeat protein 11) (TPR re ...	0.00	-	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass membrane protein. Peroxisome; peroxisomal m ...	integral to mitochondrial outer membrane [IDA] integral to peroxisomal membrane [IDA]	609003	1PC2	152
P84817 UniProt NPD GO	FIS1_RAT	Mitochondrial fission 1 protein (Fis1 homolog) (rFis1) (Tetratricopeptide repeat protein 11) (TPR re ...	0.00	-	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass membrane protein. Peroxisome; peroxisomal m ...	integral to mitochondrial outer membrane [ISS] integral to peroxisomal membrane [ISS]			152
Q55U43 UniProt NPD GO	TIM10_CRYNE	Mitochondrial import inner membrane translocase subunit TIM10	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				102
Q617M0 UniProt NPD GO	TIM14_CAEBR	Mitochondrial import inner membrane translocase subunit TIM14 (DnaJ homolog subfamily C member 21)	0.00	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				111
P91454 UniProt NPD GO	TIM14_CAEEL	Mitochondrial import inner membrane translocase subunit TIM14 (DnaJ homolog subfamily C member 21)	0.00	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				112
Q59ZW9 UniProt NPD GO	TIM16_CANAL	Mitochondrial import inner membrane translocase subunit TIM16 (Presequence translocated-associated m ...	0.00	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				121
Q6BZY4 UniProt NPD GO	TIM22_YARLI	Mitochondrial import inner membrane translocase subunit TIM22	0.00	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				189
Q9C1E8 UniProt NPD GO	TIM22_NEUCR	Mitochondrial import inner membrane translocase subunit tim-22	0.00	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				194
Q08176 UniProt NPD GO	MIM1_YEAST	Mitochondrial import protein 1 (Mitochondrial 13 kDa outer membrane protein)	0.00	-	nuc	0	Mitochondrion; mitochondrial outer membrane	integral to mitochondrial outer membrane [IDA] mitochondrial outer membrane [IDA]			113
Q9SD80 UniProt NPD GO	TOM5_ARATH	Mitochondrial import receptor subunit TOM5 homolog (Translocase of outer membrane 5 kDa subunit homo ...	0.00	-	cyt	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein				53
O82067 UniProt NPD GO	TOM7A_SOLTU	Mitochondrial import receptor subunit TOM7-1 (Translocase of outer membrane 7 kDa subunit 1)	0.00	-	nuc	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein				71
P81794 UniProt NPD GO	TOM7B_SOLTU	Mitochondrial import receptor subunit TOM7-2 (Translocase of outer membrane 7 kDa subunit 2) (Fragme ...	0.00	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein				26
P28627 UniProt NPD GO	IMP1_YEAST	Mitochondrial inner membrane protease subunit 1 (EC 3.4.99.-)	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane peptidase complex [IDA]			189
Q34940 UniProt NPD GO	RT12_LEITA	Mitochondrial ribosomal protein S12	0.00	-	end	2 *	Mitochondrion				85
P99502 UniProt NPD GO	GRP75_CANFA	Mitochondrial stress-70 protein (75 kDa glucose-regulated protein) (GRP 75) (Fragment)	0.00	-		0	Mitochondrion				14
Q6GLJ0 UniProt NPD GO	MFN2A_XENLA	Mitoferrin-2A (Mitochondrial iron transporter 2-A) (Solute carrier family 25 member 28-A)	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				186
Q68F18 UniProt NPD GO	MFN2B_XENLA	Mitoferrin-2B (Mitochondrial iron transporter 2-B) (Solute carrier family 25 member 28-B)	0.00	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				186
Q5ZIP2 UniProt NPD GO	MK1I1_CHICK	Mitogen-activated protein kinase kinase 1-interacting protein 1	0.00	-	cyt	0	Endosome; late endosome; late endosomal membrane; peripheral membrane protein; cytoplasmic side (By ...				124
Q5R3Z6 UniProt NPD GO	MK1I1_PONPY	Mitogen-activated protein kinase kinase 1-interacting protein 1	0.00	-	cyt	0	Endosome; late endosome; late endosomal membrane; peripheral membrane protein; cytoplasmic side (By ...				124
Q5U204 UniProt NPD GO	MK1I1_RAT	Mitogen-activated protein kinase kinase 1-interacting protein 1	0.00	-	cyt	0	Endosome; late endosome; late endosomal membrane; peripheral membrane protein; cytoplasmic side (By ...				124
Q9UHA4 UniProt NPD GO	MK1I1_HUMAN	Mitogen-activated protein kinase kinase 1-interacting protein 1 (MEK-binding partner 1) (Mp1)	0.00	-	cyt	0	Endosome; late endosome; late endosomal membrane; peripheral membrane protein; cytoplasmic side (By ...		603296	1SKO	124
O88653 UniProt NPD GO	MK1I1_MOUSE	Mitogen-activated protein kinase kinase 1-interacting protein 1 (MEK-binding partner 1) (Mp1)	0.00	-	cyt	0				1VEU	124
P16350 UniProt NPD GO	LECA_VICSA	Mitogenic lectin alpha chain	0.00	-	cyt	0					52
P55848 UniProt NPD GO	MIH_PROCL	Molt-inhibiting hormone (MIH)	0.00	-	cyt	0	Secreted protein				75
P83636 UniProt NPD GO	MIH_ORCLI	Molt-inhibiting hormone precursor (MIH)	0.00	-	mit	0	Secreted protein				106
P61870 UniProt NPD GO	MDLA_PENCA	Mono- and diacylglycerol lipase precursor (EC 3.1.1.-) (MDGL)	0.00	-	end	0				1TIA	305
P61869 UniProt NPD GO	MDLA_PENCY	Mono- and diacylglycerol lipase precursor (EC 3.1.1.-) (MDGL)	0.00	-	end	0					305
O35439 UniProt NPD GO	MOT1_MERUN	Monocarboxylate transporter 1 (MCT 1) (Fragment)	0.00	-	cyt	2 *	Cell membrane; multi-pass membrane protein (By similarity)				76
O35440 UniProt NPD GO	MOT2_MERUN	Monocarboxylate transporter 2 (MCT 2) (Fragment)	0.00	-	gol	2 *	Cell membrane; multi-pass membrane protein (By similarity)				71
Q9S926 UniProt NPD GO	MDAR2_SOYBN	Monodehydroascorbate reductase II (EC 1.6.5.4) (MDARII) (MRII) (Ascorbate free radical reductase II) ...	0.00	-		0					10
P83966 UniProt NPD GO	MDARF_CUCSA	Monodehydroascorbate reductase, fruit isozyme (EC 1.6.5.4) (MDAR fruit) (Ascorbate free radical redu ...	0.00	-	cyt	0					166
Q99685 UniProt NPD GO	MGLL_HUMAN	Monoglyceride lipase (EC 3.1.1.23) (MGL) (HU-K5) (Lysophospholipase homolog) (Lysophospholipase-like ...	0.00	-	cyt	0			609699		303
P15506 UniProt NPD GO	NPMA_BOVIN	Morphine-modulating neuropeptide A	0.00	-		0	Secreted protein				18
P69207 UniProt NPD GO	MORN_ANTEL	Morphogenetic neuropeptide (Head activator) (HA)	0.00	-		0					11
P69206 UniProt NPD GO	MORN_BOVIN	Morphogenetic neuropeptide (Head activator) (HA)	0.00	-		0					11
P69208 UniProt NPD GO	MORN_HUMAN	Morphogenetic neuropeptide (Head activator) (HA)	0.00	-		0					11
P69251 UniProt NPD GO	MORN_HYDAT	Morphogenetic neuropeptide (Head activator) (HA)	0.00	-		0					11
P69209 UniProt NPD GO	MORN_RAT	Morphogenetic neuropeptide (Head activator) (HA)	0.00	-		0					11
P46057 UniProt NPD GO	MLE_TRICU	Muconate cycloisomerase 1 (EC 5.5.1.1) (Muconate cycloisomerase I) (Cis,cis-muconate lactonizing enz ...	0.00	-	cyt	0					373
P81797 UniProt NPD GO	MULC_ECHML	Multactivase catalytic subunit (EC 3.4.24.-) (Fragment)	0.00	-	cyt	0					27
P21145 UniProt NPD GO	MAL_HUMAN	Myelin and lymphocyte protein (T-lymphocyte maturation-associated protein)	0.00	-	end	4 *	Membrane; multi-pass membrane protein	apical plasma membrane [TAS] endoplasmic reticulum [IDA] endosome [TAS] insoluble fraction [TAS] integral to plasma membrane [TAS] lipid raft [IDA] membrane fraction [TAS]	188860		153
O09198 UniProt NPD GO	MAL_MOUSE	Myelin and lymphocyte protein (T-lymphocyte maturation-associated protein)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				153

You are viewing entries 95651 to 95700 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.