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
P25669 UniProt NPD GO	NXL2_NAJNA	Long neurotoxin 2 (Toxin B)	0.26	-	nuc	0	Secreted protein				71
Q06738 UniProt NPD GO	LTI78_ARATH	Low-temperature-induced 78 kDa protein (Desiccation-responsive protein 29A)	0.26	-	nuc	0					710
Q6UWN5 UniProt NPD GO	LYPD5_HUMAN	Ly6/PLAUR domain-containing protein 5 precursor	0.26	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				251
P17897 UniProt NPD GO	LYSCP_MOUSE	Lysozyme C type P precursor (EC 3.2.1.17) (1,4-beta-N-acetylmuramidase C)	0.26	-	nuc	0					148
Q9Y2B0 UniProt NPD GO	MSAP_HUMAN	MIR-interacting saposin-like protein precursor (Transmembrane protein 4) (Putative secreted protein ...	0.26	-	end	0		integral to plasma membrane [TAS]	605861		182
Q13434 UniProt NPD GO	MKRN4_HUMAN	Makorin-4 (Zinc finger protein 127-Xp) (ZNF127-Xp) (RING finger protein 64)	0.26	-	nuc	0					485
Q9DBG5 UniProt NPD GO	M6PBP_MOUSE	Mannose-6-phosphate receptor-binding protein 1 (Cargo selection protein TIP47)	0.26	-	nuc	0	Cytoplasm (By similarity). Endosome (By similarity). Membrane associated on endosomes. Detected in t ...			1SZI	437
P39098 UniProt NPD GO	MA1A2_MOUSE	Mannosyl-oligosaccharide 1,2-alpha-mannosidase IB (EC 3.2.1.113) (Processing alpha-1,2-mannosidase I ...	0.26	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	Golgi membrane [IDA]			641
O13596 UniProt NPD GO	MTA1_SORFI	Mating type protein mtA-1	0.26	-	cyt	0	Nucleus (Potential)				301
Q9XT90 UniProt NPD GO	MMP14_PIG	Matrix metalloproteinase-14 precursor (EC 3.4.24.80) (MMP-14) (Membrane-type matrix metalloproteinas ...	0.26	-	end	1	Membrane; single-pass type I membrane protein (Potential)				580
Q95220 UniProt NPD GO	MMP14_RABIT	Matrix metalloproteinase-14 precursor (EC 3.4.24.80) (MMP-14) (Membrane-type matrix metalloproteinas ...	0.26	-	end	1	Membrane; single-pass type I membrane protein (Potential)				582
P50281 UniProt NPD GO	MMP14_HUMAN	Matrix metalloproteinase-14 precursor (EC 3.4.24.80) (MMP-14) (Membrane-type matrix metalloproteinas ...	0.26	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	600754	1BUV	582
Q9JHI0 UniProt NPD GO	MMP19_MOUSE	Matrix metalloproteinase-19 precursor (EC 3.4.24.-) (MMP-19) (Matrix metalloproteinase RASI)	0.26	-	mit	0	Cell membrane; lipid-anchor; GPI-anchor (Probable)				527
Q9NPJ1 UniProt NPD GO	MKKS_HUMAN	McKusick-Kaufman/Bardet-Biedl syndromes putative chaperonin (Bardet-Biedl syndrome 6 protein)	0.26	-	nuc	0			604896		570
Q61880 UniProt NPD GO	DMC1_MOUSE	Meiotic recombination protein DMC1/LIM15 homolog	0.26	-	cyt	0	Nucleus (Potential)				340
P51811 UniProt NPD GO	XK_HUMAN	Membrane transport protein XK (Kx antigen) (Kell complex 37 kDa component) (XK-related protein 1)	0.26	-	end	9 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [TAS]	314850		444
Q49LS5 UniProt NPD GO	XK_PANTR	Membrane transport protein XK (XK-related protein 1)	0.26	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				444
Q8BRX9 UniProt NPD GO	MARH3_MOUSE	Membrane-associated RING finger protein 3 (Membrane-associated RING-CH protein III) (MARCH-III)	0.26	-	mit	2	Membrane; multi-pass membrane protein (Potential)				218
O88559 UniProt NPD GO	MEN1_MOUSE	Menin	0.26	-	mit	0	Nucleus (By similarity). Concentrated in nuclear body-like structures. Relocates to the nuclear matr ...	nucleus [TAS]			611
P02806 UniProt NPD GO	MT2_SCYSE	Metallothionein-2 (MT-2) (Metallothionein-II) (MT-II)	0.26	-	nuc	0					57
O21251 UniProt NPD GO	RM14_RECAM	Mitochondrial 60S ribosomal protein L14	0.26	-	cyt	0	Mitochondrion				122
P46763 UniProt NPD GO	RM02_ACACA	Mitochondrial 60S ribosomal protein L2	0.26	-	mit	0	Mitochondrion				253
P49388 UniProt NPD GO	RM05_BRANA	Mitochondrial 60S ribosomal protein L5	0.26	-	cyt	0	Mitochondrion				185
Q5K8Z5 UniProt NPD GO	TIM54_CRYNE	Mitochondrial import inner membrane translocase subunit TIM54	0.26	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				458
Q59MI8 UniProt NPD GO	TIM8_CANAL	Mitochondrial import inner membrane translocase subunit TIM8	0.26	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				88
Q6BN23 UniProt NPD GO	TIM8_DEBHA	Mitochondrial import inner membrane translocase subunit TIM8	0.26	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				90
Q9Y193 UniProt NPD GO	TIM13_BRUMA	Mitochondrial import inner membrane translocase subunit Tim13	0.26	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				98
Q9WVA1 UniProt NPD GO	TIM8A_RAT	Mitochondrial import inner membrane translocase subunit Tim8 A (Deafness dystonia protein 1 homolog) ...	0.26	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...	cytoplasm [IDA] mitochondrial inner membrane [TAS] mitochondrial outer membrane [IDA]			97
O60220 UniProt NPD GO	TIM8A_HUMAN	Mitochondrial import inner membrane translocase subunit Tim8 A (Deafness dystonia protein 1) (X-link ...	0.26	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side		311150		97
Q9W762 UniProt NPD GO	TIM9_BRARE	Mitochondrial import inner membrane translocase subunit Tim9	0.26	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				84
Q9N408 UniProt NPD GO	TIM8_CAEEL	Mitochondrial import inner membrane translocase subunit tim-8	0.26	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				83
P23955 UniProt NPD GO	MPPA_NEUCR	Mitochondrial-processing peptidase alpha subunit, mitochondrial precursor (EC 3.4.24.64) (Alpha-MPP) ...	0.26	-	mit	0	Mitochondrion; mitochondrial matrix				577
Q9LMM5 UniProt NPD GO	MPK11_ARATH	Mitogen-activated protein kinase 11 (EC 2.7.11.24) (MAP kinase 11) (AtMPK11)	0.26	-	cyt	0					369
Q9WTU6 UniProt NPD GO	MK09_MOUSE	Mitogen-activated protein kinase 9 (EC 2.7.11.24) (Stress-activated protein kinase JNK2) (c-Jun N-te ...	0.26	-	nuc	0		nucleus [IC]			423
P45984 UniProt NPD GO	MK09_HUMAN	Mitogen-activated protein kinase 9 (EC 2.7.11.24) (Stress-activated protein kinase JNK2) (c-Jun N-te ...	0.26	-	nuc	0			602896		424
P32485 UniProt NPD GO	HOG1_YEAST	Mitogen-activated protein kinase HOG1 (EC 2.7.11.24) (MAP kinase HOG1) (Osmosensing protein HOG1)	0.26	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			435
Q94A06 UniProt NPD GO	M2K1_ARATH	Mitogen-activated protein kinase kinase 1 (EC 2.7.12.2) (MAP kinase kinase 1) (NMAPKK) (AtMEK1)	0.26	-	nuc	0					354
P01524 UniProt NPD GO	CXM3B_CONGE	Mu-conotoxin GIIIB (Myotoxin II) (Geographutoxin II) (GTx-II)	0.26	-	nuc	0	Secreted protein			1GIB	22
O70540 UniProt NPD GO	MADCA_RAT	Mucosal addressin cell adhesion molecule 1 precursor (MAdCAM-1) (rMAdCAM-1)	0.26	-	nuc	1	Membrane; single-pass type I membrane protein				394
Q9SGY1 UniProt NPD GO	MDR10_ARATH	Multidrug resistance protein 10 (P-glycoprotein 10)	0.26	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				1316
Q08201 UniProt NPD GO	MDR2_RAT	Multidrug resistance protein 2 (EC 3.6.3.44) (P-glycoprotein 2) (P-glycoprotein 3)	0.26	-	end	10	Membrane; multi-pass membrane protein				1278
P21447 UniProt NPD GO	MDR3_MOUSE	Multidrug resistance protein 3 (EC 3.6.3.44) (P-glycoprotein 3) (MDR1A)	0.26	-	end	11 *	Membrane; multi-pass membrane protein	intercellular canaliculus [IDA]			1276
Q9LK64 UniProt NPD GO	MRP3_ARATH	Multidrug resistance-associated protein 3 (EC 3.6.3.44) (Glutathione S-conjugate-transporting ATPase ...	0.26	-	end	14 *	Membrane; multi-pass membrane protein (Potential)				1514
Q6CIP4 UniProt NPD GO	MBF1_KLULA	Multiprotein-bridging factor 1	0.26	-	nuc	0					150
O94700 UniProt NPD GO	MBF1_SCHPO	Multiprotein-bridging factor 1	0.26	-	nuc	0					148
P29269 UniProt NPD GO	MLRN_PIG	Myosin regulatory light chain 2, smooth muscle isoform (Myosin RLC) (LC20) (Myosin regulatory light ...	0.26	-	mit	0					171
Q9CQ19 UniProt NPD GO	MLRN_MOUSE	Myosin regulatory light chain 2, smooth muscle isoform (Myosin RLC) (Myosin regulatory light chain 9 ...	0.26	-	mit	0					171
Q5RBA4 UniProt NPD GO	MLRN_PONPY	Myosin regulatory light chain 2, smooth muscle isoform (Myosin RLC) (Myosin regulatory light chain 9 ...	0.26	-	mit	0					171
P24844 UniProt NPD GO	MLRN_HUMAN	Myosin regulatory light chain 2, smooth muscle isoform (Myosin RLC) (Myosin regulatory light chain 9 ...	0.26	-	mit	0		muscle myosin [TAS]	609905		171
P02612 UniProt NPD GO	MLRM_CHICK	Myosin regulatory light chain 2, smooth muscle major isoform (G1) (DTNB) (MLC-2) (Isoform L20-A)	0.26	-	mit	0					171

You are viewing entries 44351 to 44400 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.