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
Q6EIH3 UniProt NPD GO	MATK_TILAM	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				502
Q9GHM0 UniProt NPD GO	MATK_UMBCA	Maturase K (Intron maturase)	0.59	-	cyt	0	Plastid; chloroplast				507
Q6PSB9 UniProt NPD GO	MATK_VIGMU	Maturase K (Intron maturase)	0.59	-	nuc	0	Plastid; chloroplast				504
Q8WHJ9 UniProt NPD GO	MATK_WOLAR	Maturase K (Intron maturase)	0.59	-	nuc	0	Plastid; chloroplast				508
O74909 UniProt NPD GO	MEU23_SCHPO	Meiotic expression up-regulated protein 23	0.59	+	nuc	0					254
Q9Y800 UniProt NPD GO	MEU33_SCHPO	Meiotic expression up-regulated protein 33	0.59	-	nuc	2	Membrane; multi-pass membrane protein (Potential)				335
O94423 UniProt NPD GO	MFR1_SCHPO	Meiotic fizzy-related protein 1	0.59	-	nuc	0	Nucleus				421
P13388 UniProt NPD GO	XMRK_XIPMA	Melanoma receptor tyrosine-protein kinase precursor (EC 2.7.10.1)	0.59	+	exc	1	Membrane; single-pass type I membrane protein				1167
Q5RFC2 UniProt NPD GO	MAGD2_PONPY	Melanoma-associated antigen D2 (MAGE-D2 antigen)	0.59	-	nuc	0					606
Q9ERE7 UniProt NPD GO	MESD2_MOUSE	Mesoderm development candidate 2	0.59	-	exc	0					224
P35192 UniProt NPD GO	MAC1_YEAST	Metal-binding activator 1	0.59	-	mit	0	Nucleus	nucleus [IDA]			417
P55157 UniProt NPD GO	MTP_HUMAN	Microsomal triglyceride transfer protein large subunit precursor	0.59	-	exc	0	Endoplasmic reticulum		200100		894
P27546 UniProt NPD GO	MAP4_MOUSE	Microtubule-associated protein 4 (MAP 4)	0.59	-	nuc	0					1125
O70583 UniProt NPD GO	TRI18_MOUSE	Midline-1 (EC 6.3.2.-) (Tripartite motif-containing protein 18) (Midin)	0.59	-	nuc	0	Cytoplasm (By similarity). Microtubule-associated (By similarity)	microtubule cytoskeleton [IDA]			680
Q9VUJ0 UniProt NPD GO	RM39_DROME	Mitochondrial 39S ribosomal protein L39 (MRP-L39) (MRP-L5)	0.59	-	mit	0	Mitochondrion (By similarity)	mitochondrial large ribosomal subunit [NAS]			333
P35999 UniProt NPD GO	PMIP_YEAST	Mitochondrial intermediate peptidase, mitochondrial precursor (EC 3.4.24.59) (MIP)	0.59	-	nuc	0	Mitochondrion; mitochondrial matrix	mitochondrion [IGI]			772
O94826 UniProt NPD GO	TOM70_HUMAN	Mitochondrial precursor proteins import receptor (Translocase of outer membrane TOM70)	0.59	-	exc	2 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)		606081		608
Q9MF82 UniProt NPD GO	RT07_BETVU	Mitochondrial ribosomal protein S7	0.59	-	cyt	0	Mitochondrion				148
Q61532 UniProt NPD GO	MK06_MOUSE	Mitogen-activated protein kinase 6 (EC 2.7.11.24) (Extracellular signal-regulated kinase 3) (ERK-3)	0.59	-	nuc	0		cytoplasm [IDA]			720
P27704 UniProt NPD GO	MK06_RAT	Mitogen-activated protein kinase 6 (EC 2.7.11.24) (Extracellular signal-regulated kinase 3) (ERK-3) ...	0.59	-	nuc	0					720
O15198 UniProt NPD GO	SMAD9_HUMAN	Mothers against decapentaplegic homolog 9 (SMAD 9) (Mothers against DPP homolog 9) (Smad9) (Madh6)	0.59	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...	intracellular [TAS]	603295		467
P04370 UniProt NPD GO	MBP_MOUSE	Myelin basic protein (MBP) (Myelin A1 protein)	0.59	-	nuc	0	Isoform 4, isoform 5, isoform 6, isoform 7, isoform 8, isoform 9, isoform 10, isoform 11, isoform 12 ...				250
P04462 UniProt NPD GO	MYH8_RAT	Myosin-8 (Myosin heavy chain, skeletal muscle, perinatal) (MyHC-perinatal) (Fragment)	0.59	-	nuc	0	Thick filaments of the myofibrils				257
Q9UBF9 UniProt NPD GO	MYOTI_HUMAN	Myotilin (Titin immunoglobulin domain protein) (Myofibrillar titin-like Ig domains protein) (57 kDa ...	0.59	-	nuc	0	Sarcomeric; also localized to the sarcolemma. Colocalizes with MYOZ1 at the Z-lines in skeletal musc ...	actin cytoskeleton [TAS]	609200		498
P53397 UniProt NPD GO	OGG1_YEAST	N-glycosylase/DNA lyase [Includes: 8-oxoguanine DNA glycosylase (EC 3.2.2.-); DNA-(apurinic or apyri ...	0.59	-	nuc	0	Nucleus	mitochondrion [IDA]			376
P20389 UniProt NPD GO	MYC2_MARMO	N-myc 2 proto-oncogene protein	0.59	+	nuc	0	Nucleus (Potential)				454
Q86W26 UniProt NPD GO	NAL10_HUMAN	NACHT, LRR and PYD-containing protein 10 (Nucleotide-binding oligomerization domain protein 8)	0.59	-	cyt	0			609662		655
Q9GYV5 UniProt NPD GO	NEMO_DROME	NF-kappa-B essential modulator (Inhibitor of nuclear factor kappa B kinase subunit gamma) (DmIKKgamm ...	0.59	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [IDA] nucleus [IDA]			387
Q5TM19 UniProt NPD GO	IKBL_MACMU	NF-kappa-B inhibitor-like protein 1 (Inhibitor of kappa B-like) (I-kappa-B-like) (IkappaBL) (Nuclear ...	0.59	+	nuc	0					381
Q15599 UniProt NPD GO	NHRF2_HUMAN	Na(+)/H(+) exchange regulatory cofactor NHE-RF2 (NHERF-2) (Tyrosine kinase activator protein 1) (TKA ...	0.59	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein. Nucleus. Nuclear, in a punctate pattern	nucleus [TAS] plasma membrane [TAS]	606553		337
Q7T1K6 UniProt NPD GO	CRVP1_NAJAT	Natrin-1 precursor (Cysteine-rich venom protein 1) (NA-CRVP1) (Protein G2a)	0.59	+	nuc	0	Secreted protein			1XX5	239
Q26261 UniProt NPD GO	UNC5_CAEEL	Netrin receptor unc-5 precursor (Uncoordinated protein 5)	0.59	-	nuc	1	Membrane; single-pass type I membrane protein (Probable)				919
O14594 UniProt NPD GO	CSPG3_HUMAN	Neurocan core protein precursor (Chondroitin sulfate proteoglycan 3)	0.59	+	nuc	0			600826		1321
P97685 UniProt NPD GO	NFASC_RAT	Neurofascin precursor	0.59	-	exc	2 *	Cell membrane; single-pass type I membrane protein. Isoform 1 colocalizes with ankyrin G at the node ...				1240
Q9H2A3 UniProt NPD GO	NGN2_HUMAN	Neurogenin 2	0.59	-	nuc	0	Nucleus (Potential)		606624		272
Q90703 UniProt NPD GO	NOS2_CHICK	Nitric oxide synthase, inducible (EC 1.14.13.39) (NOS type II) (Inducible NO synthase) (Inducible NO ...	0.59	-	mit	0					1136
Q13470 UniProt NPD GO	TNK1_HUMAN	Non-receptor tyrosine-protein kinase TNK1 (EC 2.7.10.2) (CD38 negative kinase 1)	0.59	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein	cytoplasm [IDA] membrane [IDA]	608076		666
Q6CVH3 UniProt NPD GO	NHP6_KLULA	Nonhistone chromosomal protein 6	0.59	-	nuc	0	Nucleus (By similarity)				93
P87057 UniProt NPD GO	NHP6_SCHPO	Nonhistone chromosomal protein 6	0.59	-	nuc	0	Nucleus (By similarity)				108
Q9H4D5 UniProt NPD GO	NXF3_HUMAN	Nuclear RNA export factor 3 (TAP-like protein 3) (TAPL-3)	0.59	-	nuc	0	Nucleus. Cytoplasm. Shuttles between the nucleus and the cytoplasm	cytoplasm [IDA] nuclear RNA export factor complex [IDA] nucleus [IDA]	300316		531
Q24142 UniProt NPD GO	HR78_DROME	Nuclear hormone receptor HR78 (dHR78) (Nuclear receptor XR78E/F)	0.59	-	nuc	0	Nucleus	nucleus [IDA]			601
Q9N4Q7 UniProt NPD GO	NHR13_CAEEL	Nuclear hormone receptor family member nhr-13	0.59	-	nuc	0	Nucleus (By similarity)				414
O01931 UniProt NPD GO	NH154_CAEEL	Nuclear hormone receptor family member nhr-154	0.59	-	nuc	0	Nucleus (Potential)				412
Q9XUK7 UniProt NPD GO	NHR85_CAEEL	Nuclear hormone receptor family member nhr-85	0.59	-	nuc	0	Nucleus (Potential)				514
P34343 UniProt NPD GO	NU133_CAEEL	Nuclear pore complex protein 15 (Nucleoporin npp-15)	0.59	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex	integral to membrane [NAS]			1127
O75694 UniProt NPD GO	NU155_HUMAN	Nuclear pore complex protein Nup155 (Nucleoporin Nup155) (155 kDa nucleoporin)	0.59	-	end	0	Nucleus; nuclear envelope; nuclear pore complex; peripheral membrane protein; cytoplasmic side (By s ...		606694		1391
Q9W1X4 UniProt NPD GO	NU214_DROME	Nuclear pore complex protein Nup214 (Nucleoporin Nup214) (214 kDa nucleoporin) (DNup214)	0.59	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex	nuclear pore [IMP]			1711
P49793 UniProt NPD GO	NUP98_RAT	Nuclear pore complex protein Nup98 (Nucleoporin Nup98) (98 kDa nucleoporin)	0.59	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex				937
Q6CM00 UniProt NPD GO	NOG1_KLULA	Nucleolar GTP-binding protein 1	0.59	-	cyt	0	Nucleus; nucleolus (By similarity)				643
Q9VIF0 UniProt NPD GO	NOC2L_DROME	Nucleolar complex protein 2 homolog (Protein NOC2 homolog)	0.59	+	nuc	0	Nucleus (By similarity)				766

You are viewing entries 19701 to 19750 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.