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
Q10003 UniProt NPD GO	YRS7_CAEEL	Hypothetical protein T05H10.7	0.42	-	mit	0					796
P34654 UniProt NPD GO	YOT9_CAEEL	Hypothetical protein ZK632.9	0.42	-	nuc	0					62
Q5A8X9 UniProt NPD GO	ISN1_CANAL	IMP-specific 5'-nucleotidase 1 (EC 3.1.3.-)	0.42	-	nuc	0					460
P01649 UniProt NPD GO	KV5P_MOUSE	Ig kappa chain V-V regions (Anti-arsonate antibodies)	0.42	-	nuc	0					108
Q02783 UniProt NPD GO	LPE10_YEAST	Inner membrane magnesium transporter LPE10, mitochondrial precursor	0.42	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			413
Q08561 UniProt NPD GO	IES4_YEAST	Ino eighty subunit 4	0.42	-	nuc	0	Nucleus	nucleus [IDA]			116
Q9W2Q7 UniProt NPD GO	IPPK_DROME	Inositol-pentakisphosphate 2-kinase (EC 2.7.1.-) (Inositol-1,3,4,5,6-pentakisphosphate 2-kinase) (In ...	0.42	-	nuc	0					621
Q16270 UniProt NPD GO	IBP7_HUMAN	Insulin-like growth factor-binding protein 7 precursor (IGFBP-7) (IBP-7) (IGF-binding protein 7) (MA ...	0.42	-	exc	0	Secreted protein		602867		282
P98153 UniProt NPD GO	IDD_HUMAN	Integral membrane protein DGCR2/IDD precursor	0.42	-	end	1	Membrane; single-pass type I membrane protein		600594		550
P01573 UniProt NPD GO	IFNA2_MOUSE	Interferon alpha-2 precursor	0.42	-	mit	1 *	Secreted protein				190
Q4JF28 UniProt NPD GO	IRF3_BOVIN	Interferon regulatory factor 3 (IRF-3)	0.42	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Shuttles between cytoplasmic and nuclear compart ...				417
Q90871 UniProt NPD GO	IRF8_CHICK	Interferon regulatory factor 8 (IRF-8) (Interferon consensus sequence-binding protein) (ICSBP)	0.42	-	nuc	0	Nucleus				425
P43431 UniProt NPD GO	IL12A_MOUSE	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.42	-	mit	0	Secreted protein				215
Q91ZK6 UniProt NPD GO	IL12A_SIGHI	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.42	-	mit	0	Secreted protein (By similarity)				215
Q8IU57 UniProt NPD GO	I28RA_HUMAN	Interleukin-28 receptor alpha chain precursor (IL-28R-alpha) (IL-28RA) (Cytokine receptor family 2 m ...	0.42	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)	integral to membrane [NAS] interleukin-28 receptor complex [IDA]	607404		520
P08700 UniProt NPD GO	IL3_HUMAN	Interleukin-3 precursor (IL-3) (Multipotential colony-stimulating factor) (Hematopoietic growth fact ...	0.42	-	exc	0	Secreted protein	extracellular space [ISS]	147740	1JLI	152
O18796 UniProt NPD GO	IL6RA_PIG	Interleukin-6 receptor alpha chain precursor (IL-6R-alpha) (IL-6R 1) (CD126 antigen)	0.42	-	exc	1	Membrane; single-pass type I membrane protein				467
P45456 UniProt NPD GO	ACEA1_SOYBN	Isocitrate lyase 1 (EC 4.1.3.1) (Isocitrase 1) (Isocitratase 1) (ICL 1) (Fragment)	0.42	-	cyt	0	Glyoxysome				558
Q8BU30 UniProt NPD GO	SYIC_MOUSE	Isoleucyl-tRNA synthetase, cytoplasmic (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS) (IRS)	0.42	-	cyt	0	Cytoplasm				1262
Q9HDC5 UniProt NPD GO	JPH1_HUMAN	Junctophilin-1 (Junctophilin type 1) (JP-1)	0.42	-	nuc	1	Cell membrane; peripheral membrane protein (By similarity). Endoplasmic reticulum; endoplasmic retic ...	junctional membrane complex [NAS]	605266		661
P34569 UniProt NPD GO	KEL10_CAEEL	Kelch repeat-containing protein kel-10	0.42	-	cyt	0					566
Q9Z2K1 UniProt NPD GO	K1C16_MOUSE	Keratin, type I cytoskeletal 16 (Cytokeratin-16) (CK-16) (Keratin-16) (K16)	0.42	-	nuc	0		intermediate filament [IDA]			468
Q04695 UniProt NPD GO	K1C17_HUMAN	Keratin, type I cytoskeletal 17 (Cytokeratin-17) (CK-17) (Keratin-17) (K17) (39.1)	0.42	-	nuc	0		intermediate filament [TAS]	184500		431
P02534 UniProt NPD GO	K1M1_SHEEP	Keratin, type I microfibrillar 48 kDa, component 8C-1 (Low-sulfur keratin)	0.42	-	nuc	0					412
Q99M73 UniProt NPD GO	KRHB4_MOUSE	Keratin, type II cuticular Hb4 (Hair keratin, type II Hb4) (65 kDa type II keratin)	0.42	-	mit	0					603
P13647 UniProt NPD GO	K2C5_HUMAN	Keratin, type II cytoskeletal 5 (Cytokeratin-5) (CK-5) (Keratin-5) (K5) (58 kDa cytokeratin)	0.42	-	cyt	0		intermediate filament [TAS]	609352		590
P60410 UniProt NPD GO	KR108_HUMAN	Keratin-associated protein 10-8 (Keratin-associated protein 10.8) (High sulfur keratin-associated pr ...	0.42	-	nuc	0					259
Q9BYQ9 UniProt NPD GO	KRA48_HUMAN	Keratin-associated protein 4-8 (Keratin-associated protein 4.8) (Ultrahigh sulfur keratin-associated ...	0.42	-	mit	0					114
Q9BYQ3 UniProt NPD GO	KRA93_HUMAN	Keratin-associated protein 9-3 (Keratin-associated protein 9.3) (Ultrahigh sulfur keratin-associated ...	0.42	-	mit	0					159
Q99706 UniProt NPD GO	KI2L4_HUMAN	Killer cell immunoglobulin-like receptor 2DL4 precursor (MHC class I NK cell receptor KIR103AS) (Kil ...	0.42	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	604945		377
Q3ZBF8 UniProt NPD GO	LASS2_BOVIN	LAG1 longevity assurance homolog 2	0.42	-	end	5 *	Nucleus; nuclear membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum; endoplasm ...				380
Q9QXD8 UniProt NPD GO	LIMD1_MOUSE	LIM domains-containing protein 1	0.42	-	nuc	0					668
O97581 UniProt NPD GO	LHX3_PIG	LIM/homeobox protein Lhx3 (Homeobox protein LIM-3) (Homeobox protein P-LIM) (LIM homeobox protein 3) ...	0.42	+	nuc	0	Nucleus (Probable)	nucleus [IDA]			383
Q9HAP6 UniProt NPD GO	LIN7B_HUMAN	LIN-7 homolog B (LIN-7B) (hLin7B) (Mammalian LIN-seven protein 2) (MALS-2) (Vertebrate LIN 7 homolog ...	0.42	-	cyt	0	Cell membrane; peripheral membrane protein. Cell membrane; cell-cell junction; peripheral membrane p ...				207
Q5TA79 UniProt NPD GO	LCE2A_HUMAN	Late cornified envelope protein 2A (Late envelope protein 9)	0.42	-	mit	0					106
Q4WVD1 UniProt NPD GO	LCMT2_ASPFU	Leucine carboxyl methyltransferase 2 (EC 2.1.1.-)	0.42	-	cyt	0					1047
Q2U6D4 UniProt NPD GO	LCMT2_ASPOR	Leucine carboxyl methyltransferase 2 (EC 2.1.1.-)	0.42	+	cyt	0					1032
Q80TG9 UniProt NPD GO	LRFN2_MOUSE	Leucine-rich repeat and fibronectin type-III domain-containing protein 2 precursor	0.42	-	end	1	Membrane; single-pass type I membrane protein (Potential)				788
Q3ZBI5 UniProt NPD GO	LRC33_BOVIN	Leucine-rich repeat-containing protein 33 precursor	0.42	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				692
Q5M8G4 UniProt NPD GO	LRC40_XENTR	Leucine-rich repeat-containing protein 40	0.42	-	nuc	0					605
Q9CQ33 UniProt NPD GO	LZTR1_MOUSE	Leucine-zipper-like transcriptional regulator 1 (LZTR-1)	0.42	-	cyt	0					837
O70535 UniProt NPD GO	LIFR_RAT	Leukemia inhibitory factor receptor precursor (LIF receptor) (LIF-R) (CD118 antigen)	0.42	-	nuc	1	Isoform 1: Cell membrane; single-pass type I membrane protein (By similarity). Isoform 2: Secreted p ...				1093
P48099 UniProt NPD GO	CHLB_CYAPA	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.42	-	cyt	0	Plastid; cyanelle				440
Q06005 UniProt NPD GO	LIPB_YEAST	Lipoate-protein ligase, mitochondrial precursor (EC 6.-.-.-) (Lipoate biosynthesis protein) (Lipoyl ...	0.42	-	mit	0	Mitochondrion (Potential)	mitochondrion [IDA]			328
Q99KC8 UniProt NPD GO	LHR2A_MOUSE	Loss of heterozygosity 11 chromosomal region 2 gene A protein homolog	0.42	-	cyt	0					793
P08508 UniProt NPD GO	FCGR3_MOUSE	Low affinity immunoglobulin gamma Fc region receptor III precursor (IgG Fc receptor III) (Fc-gamma R ...	0.42	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				261
P30730 UniProt NPD GO	LSHR_MOUSE	Lutropin-choriogonadotropic hormone receptor precursor (LH/CG-R) (LSH-R) (Luteinizing hormone recept ...	0.42	-	end	7	Membrane; multi-pass membrane protein				700
Q5R8C0 UniProt NPD GO	PPA6_PONPY	Lysophosphatidic acid phosphatase type 6 precursor (EC 3.1.3.2) (Acid phosphatase 6, lysophosphatidi ...	0.42	-	nuc	0	Secreted protein (By similarity)				428
Q9EQ31 UniProt NPD GO	EDG7_MOUSE	Lysophosphatidic acid receptor Edg-7 (LPA receptor 3) (LPA-3)	0.42	-	end	7 *	Membrane; multi-pass membrane protein				354
Q03674 UniProt NPD GO	PLB2_YEAST	Lysophospholipase 2 precursor (EC 3.1.1.5) (Phospholipase B 2)	0.42	-	exc	0	Secreted protein (Potential)	cell wall (sensu Fungi) [IDA] extracellular region [IDA]			706

You are viewing entries 30451 to 30500 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.)

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