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
P26861 UniProt NPD GO	RM06_MARPO	Mitochondrial 60S ribosomal protein L6	0.04	-	mit	0	Mitochondrion				101
Q623S8 UniProt NPD GO	MIRO_CAEBR	Mitochondrial Rho GTPase (EC 3.6.5.-) (Miro)	0.04	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				625
Q94263 UniProt NPD GO	MIRO_CAEEL	Mitochondrial Rho GTPase (EC 3.6.5.-) (Miro)	0.04	-	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				625
P87108 UniProt NPD GO	TIM10_YEAST	Mitochondrial import inner membrane translocase subunit TIM10 (Mitochondrial intermembrane protein M ...	0.04	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side	mitochondrial intermembrane space protein t... [IDA]			93
Q6BXP3 UniProt NPD GO	TIM16_DEBHA	Mitochondrial import inner membrane translocase subunit TIM16 (Presequence translocated-associated m ...	0.04	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein (By similarity)				128
Q6BT35 UniProt NPD GO	TIM22_DEBHA	Mitochondrial import inner membrane translocase subunit TIM22	0.04	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				182
Q12328 UniProt NPD GO	TIM22_YEAST	Mitochondrial import inner membrane translocase subunit TIM22	0.04	-	mit	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein. Import into inner membrane ...	mitochondrial inner membrane protein insert... [IDA]			207
Q9Z0V7 UniProt NPD GO	TI17B_MOUSE	Mitochondrial import inner membrane translocase subunit Tim17-B	0.04	-	mit	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			172
Q5U4U5 UniProt NPD GO	TIM22_XENLA	Mitochondrial import inner membrane translocase subunit Tim22	0.04	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				184
Q9Y584 UniProt NPD GO	TIM22_HUMAN	Mitochondrial import inner membrane translocase subunit Tim22 (Testis-expressed sequence 4)	0.04	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)		607251		194
O35093 UniProt NPD GO	TIM23_RAT	Mitochondrial import inner membrane translocase subunit Tim23	0.04	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity). Mitochondr ...	mitochondrial inner membrane presequence tr... [IPI]			209
P82872 UniProt NPD GO	TO201_ARATH	Mitochondrial import receptor subunit TOM20-1 (Translocase of outer membrane 20 kDa subunit 1)	0.04	-	cyt	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein				188
P33448 UniProt NPD GO	TOM6_YEAST	Mitochondrial import receptor subunit TOM6 (Mitochondrial import-site protein ISP6) (Translocase of ...	0.04	-	cyt	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein	mitochondrial outer membrane translocase co... [IMP]			61
Q9WVD5 UniProt NPD GO	ORNT1_MOUSE	Mitochondrial ornithine transporter 1 (Solute carrier family 25 member 15)	0.04	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			301
P25491 UniProt NPD GO	MAS5_YEAST	Mitochondrial protein import protein MAS5 (Yeast dnaJ protein 1)	0.04	-	cyt	0	Cytoplasm. Cytoplasm; perinuclear region. Concentrated in a perinuclear ring as well as in the cytop ...	cytosol [IDA]		1NLT	409
Q9W725 UniProt NPD GO	UCP2_CYPCA	Mitochondrial uncoupling protein 2 (UCP 2)	0.04	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				310
Q9N2I9 UniProt NPD GO	UCP3_CANFA	Mitochondrial uncoupling protein 3 (UCP 3)	0.04	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				311
P53778 UniProt NPD GO	MK12_HUMAN	Mitogen-activated protein kinase 12 (EC 2.7.11.24) (Extracellular signal-regulated kinase 6) (ERK-6) ...	0.04	-	cyt	0	Cytoplasm. Mitochondrion. Mitochondrial when associated with SH3BP5	cytoplasm [IEP]	602399	1CM8	367
Q9Z224 UniProt NPD GO	MOS2S_MOUSE	Molybdenum cofactor synthesis protein 2 small subunit (Molybdopterin synthase small subunit) (MOCS2A ...	0.04	-	cyt	0					88
Q39054 UniProt NPD GO	CNX1_ARATH	Molybdopterin biosynthesis protein CNX1 (Molybdenum cofactor biosynthesis enzyme CNX1)	0.04	-	cyt	0				1UUY	670
Q8VXX5 UniProt NPD GO	SKS1_ARATH	Monocopper oxidase-like protein SKS1 precursor	0.04	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor	anchored to membrane [TAS]			589
Q9V492 UniProt NPD GO	MPV17_DROME	Mpv17-like protein	0.04	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [ISS]			168
P11061 UniProt NPD GO	TXMG5_AGEAP	Mu-agatoxin-5	0.04	-	nuc	0	Secreted protein				37
Q28488 UniProt NPD GO	CRYM_MACFL	Mu-crystallin	0.04	-	nuc	0	Cytoplasm				314
Q13155 UniProt NPD GO	MCA2_HUMAN	Multisynthetase complex auxiliary component p38 (Protein JTV-1)	0.04	-	cyt	0			600859		320
P81030 UniProt NPD GO	TXM1_DENAN	Muscarinic toxin 1 (MT1) (MTx1)	0.04	-	nuc	0	Secreted protein				66
Q9PSN1 UniProt NPD GO	TXM4_DENAN	Muscarinic toxin 4 (MT4)	0.04	-	nuc	0	Secreted protein				66
P80494 UniProt NPD GO	TXMA_DENPO	Muscarinic toxin alpha (MT-alpha)	0.04	-	nuc	0	Secreted protein				66
P25189 UniProt NPD GO	MYP0_HUMAN	Myelin P0 protein precursor (Myelin protein zero) (Myelin peripheral protein) (MPP)	0.04	-	end	1 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [NAS]	607791		248
P24526 UniProt NPD GO	MYP2_MOUSE	Myelin P2 protein	0.04	-	cyt	0					131
Q16653 UniProt NPD GO	MOG_HUMAN	Myelin-oligodendrocyte glycoprotein precursor	0.04	-	end	3 *	Isoform 1, isoform 5: Cell membrane; multi-pass membrane protein (Potential). Isoform 2, isoform 3, ...	plasma membrane [NAS]	159465	1Q70	247
Q7LZM5 UniProt NPD GO	MYG_AETPY	Myoglobin	0.04	-	cyt	0					153
P02199 UniProt NPD GO	MYG_APTFO	Myoglobin	0.04	-	cyt	0					152
Q7LZM4 UniProt NPD GO	MYG_CERMN	Myoglobin	0.04	-	cyt	0					153
P02156 UniProt NPD GO	MYG_ERIEU	Myoglobin	0.04	-	cyt	0					153
P04250 UniProt NPD GO	MYG_LAGMA	Myoglobin	0.04	-	cyt	0					153
P02183 UniProt NPD GO	MYG_MESCA	Myoglobin	0.04	-	cyt	0					153
P02164 UniProt NPD GO	MYG_ORYAF	Myoglobin	0.04	-	cyt	0					153
Q7LZM3 UniProt NPD GO	MYG_PHAFI	Myoglobin	0.04	-	cyt	0					153
P02182 UniProt NPD GO	MYG_ZIPCA	Myoglobin	0.04	-	cyt	0					153
P05977 UniProt NPD GO	MLE1_MOUSE	Myosin light chain 1, skeletal muscle isoform (MLC1F) (A1 catalytic) (Alkali myosin light chain 1)	0.04	-	cyt	0					187
P02600 UniProt NPD GO	MLE1_RAT	Myosin light chain 1, skeletal muscle isoform (MLC1F) (A1 catalytic) (Alkali myosin light chain 1)	0.04	-	cyt	0					188
P25323 UniProt NPD GO	MYLK_DICDI	Myosin light chain kinase (EC 2.7.11.18) (MLCK)	0.04	-	cyt	0					295
P08053 UniProt NPD GO	MLR_PHYPO	Myosin regulatory light chain (Calcium-binding light chain)	0.04	-	cyt	0				2BL0	147
P02613 UniProt NPD GO	MLR_PATSP	Myosin regulatory light chain (EDTA light chain)	0.04	-	cyt	0					153
P05944 UniProt NPD GO	MLRC_PATYE	Myosin regulatory light chain, striated adductor muscle	0.04	-	nuc	0					156
Q64191 UniProt NPD GO	ASPG_MOUSE	N(4)-(beta-N-acetylglucosaminyl)-L-asparaginase precursor (EC 3.5.1.26) (Glycosylasparaginase) (Aspa ...	0.04	-	end	0	Lysosome				346
Q01128 UniProt NPD GO	TRPF_LIPST	N-(5'-phosphoribosyl)anthranilate isomerase (EC 5.3.1.24) (PRAI)	0.04	-	cyt	0					232
P81799 UniProt NPD GO	NAGK_RAT	N-acetylglucosamine kinase (EC 2.7.1.59) (GlcNAc kinase) (Fragments)	0.04	-	cyt	0					83
P14769 UniProt NPD GO	GGTA1_BOVIN	N-acetyllactosaminide alpha-1,3-galactosyltransferase (EC 2.4.1.87) (Galactosyltransferase) (UDP-gal ...	0.04	-	cyt	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...			1VZX	368

You are viewing entries 77551 to 77600 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.