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
Q3SZ47 UniProt NPD GO	RM33_BOVIN	Mitochondrial 39S ribosomal protein L33 (L33mt) (MRP-L33)	0.19	-	mit	0	Mitochondrion (By similarity)				65
Q4R5K7 UniProt NPD GO	RM49_MACFA	Mitochondrial 39S ribosomal protein L49 (L49mt) (MRP-L49)	0.19	-	mit	0	Mitochondrion				166
P28778 UniProt NPD GO	RT17_YEAST	Mitochondrial 40S ribosomal protein MRP17 (Mitochondrial ribosomal protein 17) (YmS16)	0.19	-	nuc	0	Mitochondrion	mitochondrial small ribosomal subunit [IDA]			131
Q4PB75 UniProt NPD GO	GEM1_USTMA	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (GTPase EF-hand protein of mitochondria 1)	0.19	-	nuc	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				752
Q5ZM73 UniProt NPD GO	MIRO1_CHICK	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (MIRO-1) (Ras homolog gene family member T1)	0.19	-	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				619
P38323 UniProt NPD GO	MCX1_YEAST	Mitochondrial clpX-like chaperone MCX1	0.19	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			520
Q75DV9 UniProt NPD GO	MG101_ASHGO	Mitochondrial genome maintenance protein MGM101, mitochondrial precursor	0.19	-	mit	0	Mitochondrion. Associated with the mitochondrial nucleoid structure (By similarity)				254
Q759D2 UniProt NPD GO	TIM14_ASHGO	Mitochondrial import inner membrane translocase subunit TIM14 (Presequence translocated-associated m ...	0.19	-	nuc	1	Mitochondrion; mitochondrial inner membrane; single-pass membrane protein (By similarity)				158
P42949 UniProt NPD GO	TIM16_YEAST	Mitochondrial import inner membrane translocase subunit TIM16 (Presequence translocated-associated m ...	0.19	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein	mitochondrion [IDA] presequence translocase-associated import m... [IDA]			149
Q6FRT3 UniProt NPD GO	TIM9_CANGA	Mitochondrial import inner membrane translocase subunit TIM9	0.19	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				87
Q61TH2 UniProt NPD GO	TIM9_CAEBR	Mitochondrial import inner membrane translocase subunit Tim9	0.19	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				78
Q9Y8C0 UniProt NPD GO	TIM8_NEUCR	Mitochondrial import inner membrane translocase subunit tim-8	0.19	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side				92
P62512 UniProt NPD GO	MIM1_ASHGO	Mitochondrial import protein 1	0.19	-	cyt	0	Mitochondrion; mitochondrial outer membrane (By similarity)				155
Q6PBC3 UniProt NPD GO	MIA40_XENTR	Mitochondrial intermembrane space import and assembly protein 40 (Coiled-coil-helix-coiled-coil-heli ...	0.19	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				139
P26874 UniProt NPD GO	RT19_MARPO	Mitochondrial ribosomal protein S19	0.19	-	mit	0	Mitochondrion				93
P50893 UniProt NPD GO	RT19_PLASU	Mitochondrial ribosomal protein S19	0.19	-	mit	0	Mitochondrion				83
P26696 UniProt NPD GO	MK01_XENLA	Mitogen-activated protein kinase 1 (EC 2.7.11.24) (Myelin xP42 protein kinase) (Myelin basic protein ...	0.19	-	cyt	0					361
Q9FJV0 UniProt NPD GO	M2K6_ARATH	Mitogen-activated protein kinase kinase 6 (EC 2.7.12.2) (MAP kinase kinase 6) (AtMKK6) (Protein Arab ...	0.19	-	cyt	0					356
Q8MXI4 UniProt NPD GO	PMK2_CAEEL	Mitogen-activated protein kinase pmk-2 (EC 2.7.11.24) (p38 MAP kinase 2) (Stress-activated protein k ...	0.19	-	cyt	0	Cytoplasm	cytoplasm [IEP]			419
Q13257 UniProt NPD GO	MD2L1_HUMAN	Mitotic spindle assembly checkpoint protein MAD2A (MAD2-like 1) (HsMAD2)	0.19	-	cyt	0	Nucleus	kinetochore [TAS]	601467	1S2H	205
O14417 UniProt NPD GO	MAD2_SCHPO	Mitotic spindle checkpoint component mad2	0.19	-	mit	0	Nucleus (Probable)	condensed nuclear chromosome kinetochore [TAS]			203
P31241 UniProt NPD GO	MPI5_LYMST	Molluscan insulin-related peptide 5 precursor (MIP V) [Contains: Molluscan insulin-related peptide 5 ...	0.19	-	exc	1 *	Secretory granules				138
O95907 UniProt NPD GO	MOT3_HUMAN	Monocarboxylate transporter 3 (MCT 3)	0.19	-	end	12 *	Cell membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]			504
P57788 UniProt NPD GO	MOT4_CHICK	Monocarboxylate transporter 4 (MCT 4)	0.19	-	end	12 *	Cell membrane; multi-pass membrane protein (By similarity)				473
Q9HDW8 UniProt NPD GO	GLRX4_SCHPO	Monothiol glutaredoxin-4	0.19	-	mit	0		mitochondrion [IDA]			146
Q8VEL0 UniProt NPD GO	MSPD1_MOUSE	Motile sperm domain-containing protein 1	0.19	-	end	2	Membrane; multi-pass membrane protein (Potential)				213
Q5RJS6 UniProt NPD GO	MSPD1_RAT	Motile sperm domain-containing protein 1	0.19	-	end	2	Membrane; multi-pass membrane protein (Potential)				213
P05482 UniProt NPD GO	CXM3C_CONGE	Mu-conotoxin GIIIC	0.19	-	nuc	0	Secreted protein				22
Q86DU6 UniProt NPD GO	CXM3A_CONST	Mu-conotoxin SIIIA precursor	0.19	-	exc	0	Secreted protein (By similarity)				73
Q02505 UniProt NPD GO	MUC3A_HUMAN	Mucin-3A (Intestinal mucin-3A) (Fragments)	0.19	-	nuc	0	Secreted protein	extracellular region [NAS]	158371		213
Q61826 UniProt NPD GO	MADCA_MOUSE	Mucosal addressin cell adhesion molecule 1 precursor (MAdCAM-1) (mMAdCAM-1)	0.19	-	end	1	Membrane; single-pass type I membrane protein				405
Q8LPK2 UniProt NPD GO	MDR2_ARATH	Multidrug resistance protein 2 (P-glycoprotein 2)	0.19	-	end	12 *	Membrane; multi-pass membrane protein (Potential)				1233
P33527 UniProt NPD GO	MRP1_HUMAN	Multidrug resistance-associated protein 1 (ATP-binding cassette sub-family C member 1) (Leukotriene ...	0.19	-	end	16 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	158343	2CBZ	1531
O35379 UniProt NPD GO	MRP1_MOUSE	Multidrug resistance-associated protein 1 (ATP-binding cassette sub-family C member 1) (Leukotriene ...	0.19	-	end	16 *	Membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [IDA]			1528
Q6FJN0 UniProt NPD GO	MBF1_CANGA	Multiprotein-bridging factor 1	0.19	-	nuc	0					151
P31230 UniProt NPD GO	MCA1_MOUSE	Multisynthetase complex auxiliary component p43 [Contains: Endothelial monocyte-activating polypepti ...	0.19	-	nuc	0					310
P80495 UniProt NPD GO	TXMB_DENPO	Muscarinic toxin beta (MT-beta)	0.19	-	nuc	0	Secreted protein				65
P37301 UniProt NPD GO	MYP0_CHICK	Myelin P0 protein precursor (Myelin protein zero) (Myelin peripheral protein) (MPP)	0.19	-	end	2 *	Membrane; single-pass type I membrane protein				249
P02689 UniProt NPD GO	MYP2_HUMAN	Myelin P2 protein	0.19	-	cyt	0			170715		131
Q3TEW6 UniProt NPD GO	MPZL1_MOUSE	Myelin protein zero-like protein 1 precursor (Protein zero-related)	0.19	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				270
P24158 UniProt NPD GO	PRTN3_HUMAN	Myeloblastin precursor (EC 3.4.21.76) (Leukocyte proteinase 3) (PR-3) (PR3) (AGP7) (Wegener autoanti ...	0.19	-	end	0			177020	1FUJ	256
Q9UJ70 UniProt NPD GO	NAGK_HUMAN	N-acetylglucosamine kinase (EC 2.7.1.59) (GlcNAc kinase)	0.19	-	cyt	0			606828		343
O43505 UniProt NPD GO	B3GN6_HUMAN	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase (EC 2.4.1.149) (Poly-N-acetyllactosam ...	0.19	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	integral to Golgi membrane [NAS]	605517		415
Q5R4S2 UniProt NPD GO	B3GN6_PONPY	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase (EC 2.4.1.149) (Poly-N-acetyllactosam ...	0.19	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				415
P30337 UniProt NPD GO	CHIN_RAT	N-chimaerin (NC) (N-chimerin) (Alpha chimerin) (A-chimaerin) (Rho-GTPase-activating protein 2)	0.19	-	nuc	0					334
Q05885 UniProt NPD GO	ARD1H_LEIDO	N-terminal acetyltransferase complex ARD1 subunit homolog (EC 2.3.1.-)	0.19	-	cyt	0					186
Q84K00 UniProt NPD GO	NAC78_ARATH	NAC domain-containing protein 78 (ANAC078)	0.19	-	nuc	1	Nucleus (Potential)				567
P06263 UniProt NPD GO	NU4C_MARPO	NAD(P)H-quinone oxidoreductase chain 4, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain 4) (N ...	0.19	-	end	14 *	Plastid; chloroplast				499
Q9MTH6 UniProt NPD GO	NUCC_OENHO	NAD(P)H-quinone oxidoreductase chain H, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain H) (N ...	0.19	-	cyt	0	Plastid; chloroplast				393
Q02370 UniProt NPD GO	NDUA2_BOVIN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.19	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side				98

You are viewing entries 52101 to 52150 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.