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
P80190 UniProt NPD GO	LYSCK_SHEEP	Lysozyme C, kidney isozyme (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.14	-	cyt	0					130
P00705 UniProt NPD GO	LYSC1_ANAPL	Lysozyme C-1 precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.14	-	exc	0					147
Q90VZ3 UniProt NPD GO	LYG_PAROL	Lysozyme g (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase)	0.14	-	cyt	0					195
Q7LZR3 UniProt NPD GO	LYG_CASCA	Lysozyme g (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase) (Goose-type lysozyme)	0.14	-	cyt	0	Secreted protein				185
P27042 UniProt NPD GO	LYG_CHICK	Lysozyme g precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase) (Goose-type lysozyme)	0.14	-	mit	1 *	Secreted protein				211
Q01900 UniProt NPD GO	MFS14_MAIZE	MFS14 protein precursor	0.14	-	exc	1 *					126
Q5T089 UniProt NPD GO	MORN1_HUMAN	MORN repeat-containing protein 1	0.14	-	cyt	0					497
Q27151 UniProt NPD GO	MNCP_OXYTR	Macronuclear solute carrier homolog CR-MSC	0.14	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				371
O94360 UniProt NPD GO	MOB1_SCHPO	Maintenance of ploidy protein mob1	0.14	-	nuc	0	Spindle pole body. Spindle pole body throughout mitosis, relocates to the medial ring during interph ...	medial ring [IDA]			210
Q01940 UniProt NPD GO	MALF1_MALFU	Major allergen Mal f 1 precursor (Pit o 1)	0.14	-	exc	0	Cell wall				350
P53021 UniProt NPD GO	MSP1_GLORO	Major sperm protein 1	0.14	-	cyt	0					125
P53023 UniProt NPD GO	MSP3_GLORO	Major sperm protein 3	0.14	-	cyt	0					125
P21360 UniProt NPD GO	MASY_PICAN	Malate synthase, glyoxysomal (EC 2.3.3.9)	0.14	-	nuc	0	Glyoxysome				555
Q64327 UniProt NPD GO	MEA1_MOUSE	Male-enhanced antigen 1 (Mea-1)	0.14	-	cyt	0		cytoplasm [IDA]			174
O77422 UniProt NPD GO	HBPM_RHIAP	Male-specific histamine-binding salivary protein precursor (MS-HBP)	0.14	-	exc	0	Secreted protein				200
P28375 UniProt NPD GO	MAMB_DENJA	Mambin (Glycoprotein IIb-IIIa antagonist) (Platelet aggregation inhibitor) (Dendroaspin)	0.14	-	nuc	0	Secreted protein			1DRS	59
Q58T87 UniProt NPD GO	M1H12_BOMMX	Maximins 1/H12 precursor [Contains: Maximin-1; Maximin-H12]	0.14	-	exc	0	Secreted protein				144
P83417 UniProt NPD GO	MRN1_MEGVI	Megourin-1	0.14	-	nuc	0	Secreted protein				63
Q39009 UniProt NPD GO	DMC1_ARATH	Meiotic recombination protein DMC1 homolog	0.14	-	cyt	0	Nucleus (Potential)				344
Q29154 UniProt NPD GO	MSHR_VULVU	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.14	-	end	7 *	Membrane; multi-pass membrane protein				317
P69101 UniProt NPD GO	NEUY_RANRI	Melanostatin (Melanotropin release-inhibiting factor) (Neuropeptide Y) (NPY)	0.14	-	nuc	0	Secreted protein				36
P69102 UniProt NPD GO	NEUY_RANTE	Melanostatin (Melanotropin release-inhibiting factor) (Neuropeptide Y) (NPY)	0.14	-	nuc	0	Secreted protein				36
P51049 UniProt NPD GO	MR1B1_BRARE	Melatonin receptor type 1B Z2.6 (MEL-1B-R) (Fragment)	0.14	-	end	3 *	Membrane; multi-pass membrane protein				153
Q4ZIN3 UniProt NPD GO	MBRL_HUMAN	Membralin	0.14	-	end	6	Membrane; multi-pass membrane protein (Potential)				620
Q16853 UniProt NPD GO	AOC3_HUMAN	Membrane copper amine oxidase (EC 1.4.3.6) (Semicarbazide-sensitive amine oxidase) (SSAO) (Vascular ...	0.14	-	vac	1 *	Membrane; single-pass type II membrane protein	cell surface [IDA] integral to membrane [IDA] plasma membrane [IDA]	603735	1US1	762
Q01441 UniProt NPD GO	GTR2_LEIDO	Membrane transporter D2	0.14	-	end	10 *	Membrane; multi-pass membrane protein				558
Q9P0N8 UniProt NPD GO	MARH2_HUMAN	Membrane-associated RING finger protein 2 (Membrane-associated RING-CH protein II) (MARCH-II) (RING ...	0.14	+	end	2	Membrane; multi-pass membrane protein (Potential)				246
Q99N08 UniProt NPD GO	M4A6C_MOUSE	Membrane-spanning 4-domains subfamily A member 6C	0.14	-	end	4 *	Membrane; multi-pass membrane protein				217
P13827 UniProt NPD GO	MSP1_PLAFD	Merozoite surface protein 1 precursor (Merozoite surface antigens) (PMMSA) (Glycoprotein 185) (GP185 ...	0.14	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				233
P08472 UniProt NPD GO	M130_STRPU	Mesenchyme-specific cell surface glycoprotein precursor (MSP130)	0.14	+	end	1	Cell membrane; lipid-anchor; GPI-anchor (Probable)				779
P08162 UniProt NPD GO	NEUM_BUFJA	Mesotocin-neurophysin MT precursor [Contains: Mesotocin (MT); Neurophysin MT]	0.14	-	nuc	0	Secreted protein				125
P30120 UniProt NPD GO	TIMP1_RAT	Metalloproteinase inhibitor 1 precursor (TIMP-1)	0.14	-	exc	0	Secreted protein				217
Q9W6B4 UniProt NPD GO	TIMP3_SCYTO	Metalloproteinase inhibitor 3 precursor (TIMP-3) (Tissue inhibitor of metalloproteinases 3)	0.14	-	vac	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				214
Q05890 UniProt NPD GO	MT_XENLA	Metallothionein (MT)	0.14	-	nuc	0					62
Q9XST5 UniProt NPD GO	MT2_CANFA	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II)	0.14	-	nuc	0					61
P02798 UniProt NPD GO	MT2_MOUSE	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II)	0.14	-	nuc	0					61
Q6XMH6 UniProt NPD GO	AMPM2_ENCHE	Methionine aminopeptidase 2 (EC 3.4.11.18) (MetAP 2) (Peptidase M 2) (MetAP2) (MAP-2)	0.14	-	cyt	0					358
O14880 UniProt NPD GO	MGST3_HUMAN	Microsomal glutathione S-transferase 3 (EC 2.5.1.18) (Microsomal GST-3) (Microsomal GST-III)	0.14	-	mit	4 *	Microsome; microsomal membrane; multi-pass membrane protein (Potential)	membrane fraction [TAS] microsome [TAS]	604564		152
P46765 UniProt NPD GO	RM06_ACACA	Mitochondrial 60S ribosomal protein L6	0.14	-	cyt	0	Mitochondrion				181
Q6FT88 UniProt NPD GO	TIM16_CANGA	Mitochondrial import inner membrane translocase subunit TIM16 (Presequence translocated-associated m ...	0.14	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				146
Q5M995 UniProt NPD GO	TI16B_XENLA	Mitochondrial import inner membrane translocase subunit TIM16-B	0.14	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				122
Q9Y0V6 UniProt NPD GO	TIM10_CAEEL	Mitochondrial import inner membrane translocase subunit Tim10	0.14	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				86
Q9Y5L4 UniProt NPD GO	TIM13_HUMAN	Mitochondrial import inner membrane translocase subunit Tim13	0.14	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side	mitochondrial inner membrane presequence tr... [TAS]	607383		95
P62075 UniProt NPD GO	TIM13_MOUSE	Mitochondrial import inner membrane translocase subunit Tim13	0.14	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				95
Q9XGY5 UniProt NPD GO	TIM13_ORYSA	Mitochondrial import inner membrane translocase subunit Tim13	0.14	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side				84
P62076 UniProt NPD GO	TIM13_RAT	Mitochondrial import inner membrane translocase subunit Tim13	0.14	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				95
Q9Y5J9 UniProt NPD GO	TIM8B_HUMAN	Mitochondrial import inner membrane translocase subunit Tim8 B (Deafness dystonia protein 2) (DDP-li ...	0.14	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...	mitochondrial inner membrane presequence tr... [TAS]	606659		83
Q4R3C7 UniProt NPD GO	TOM22_MACFA	Mitochondrial import receptor subunit TOM22 homolog (Translocase of outer membrane 22 kDa subunit ho ...	0.14	-	cyt	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				141
Q9NS69 UniProt NPD GO	TOM22_HUMAN	Mitochondrial import receptor subunit TOM22 homolog (Translocase of outer membrane 22 kDa subunit ho ...	0.14	-	cyt	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)	integral to membrane [TAS] mitochondrial outer membrane translocase co... [TAS]	607046		141
P40035 UniProt NPD GO	PIC2_YEAST	Mitochondrial phosphate carrier protein 2 (Phosphate transport protein 2) (PTP 2) (mPic 2) (Pi carri ...	0.14	-	mit	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrion [IDA]			300

You are viewing entries 58601 to 58650 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.