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
Q27591 UniProt NPD GO	ITBN_DROME	Integrin beta-nu precursor	0.44	-	nuc	1	Membrane; single-pass type I membrane protein	integrin complex [TAS]			799
Q29052 UniProt NPD GO	ITIH1_PIG	Inter-alpha-trypsin inhibitor heavy chain H1 precursor (ITI heavy chain H1) (Inter-alpha-inhibitor h ...	0.44	-	mit	0					902
O46633 UniProt NPD GO	IFNT_CEREL	Interferon tau precursor (IFN-tau) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolysin) ( ...	0.44	-	exc	0	Secreted protein. Secreted into the uterine lumen				195
P09914 UniProt NPD GO	IFIT1_HUMAN	Interferon-induced protein with tetratricopeptide repeats 1 (IFIT-1) (Interferon-induced 56 kDa prot ...	0.44	-	cyt	0		cytoplasm [NAS]	147690		478
Q9TU27 UniProt NPD GO	IL12A_SHEEP	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.44	-	mit	0	Secreted protein				221
Q8K4C2 UniProt NPD GO	I17RC_MOUSE	Interleukin-17 receptor C precursor (IL-17 receptor C) (IL-17RC) (Interleukin-17 receptor-like prote ...	0.44	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				674
P14784 UniProt NPD GO	IL2RB_HUMAN	Interleukin-2 receptor beta chain precursor (IL-2 receptor) (P70-75) (p75) (High affinity IL-2 recep ...	0.44	-	end	2 *	Membrane; single-pass type I membrane protein	external side of plasma membrane [ISS] integral to plasma membrane [TAS] plasma membrane [TAS]	146710	2ERJ	551
P08887 UniProt NPD GO	IL6RA_HUMAN	Interleukin-6 receptor alpha chain precursor (IL-6R-alpha) (IL-6R 1) (Membrane glycoprotein 80) (gp8 ...	0.44	-	exc	1	Isoform 1: Cell membrane; basolateral cell membrane; single-pass type I membrane protein. Isoform 2: ...	extracellular region [IDA] interleukin-6 receptor complex [TAS]	147880	1P9M	468
P87059 UniProt NPD GO	MIA40_SCHPO	Intermembrane space import and assembly protein 40, mitochondrial precursor (Mitochondrial import in ...	0.44	-	mit	0	Mitochondrion; mitochondrial inner membrane; single-pass type II membrane protein; intermembrane sid ...				313
P18175 UniProt NPD GO	INVO_PIG	Involucrin	0.44	-	nuc	0	Cytoplasm. Constituent of the scaffolding of the cornified envelope				347
P78414 UniProt NPD GO	IRX1_HUMAN	Iroquois-class homeodomain protein IRX-1 (Iroquois homeobox protein 1) (Homeodomain protein IRXA1)	0.44	-	nuc	0	Nucleus (Probable)		606197		480
Q8K0T4 UniProt NPD GO	KATL1_MOUSE	Katanin p60 ATPase-containing subunit A-like 1 (EC 3.6.4.3) (Katanin p60 subunit A-like 1) (p60 kata ...	0.44	-	nuc	0					488
Q5XHZ6 UniProt NPD GO	KLHL7_RAT	Kelch-like protein 7	0.44	+	nuc	0					586
P02443 UniProt NPD GO	KRA3A_SHEEP	Keratin, high-sulfur matrix protein, IIIA3A	0.44	-	nuc	0					130
O76015 UniProt NPD GO	K1H8_HUMAN	Keratin, type I cuticular Ha8 (Hair keratin, type I Ha8)	0.44	-	exc	0			604542		456
Q99456 UniProt NPD GO	K1C12_HUMAN	Keratin, type I cytoskeletal 12 (Cytokeratin-12) (CK-12) (Keratin-12) (K12)	0.44	-	nuc	0			601687		494
Q9QWL7 UniProt NPD GO	K1C17_MOUSE	Keratin, type I cytoskeletal 17 (Cytokeratin-17) (CK-17) (Keratin-17) (K17)	0.44	-	mit	0					432
P05783 UniProt NPD GO	K1C18_HUMAN	Keratin, type I cytoskeletal 18 (Cytokeratin-18) (CK-18) (Keratin-18) (K18)	0.44	-	mit	0		intermediate filament [TAS]	215600		429
P05784 UniProt NPD GO	K1C18_MOUSE	Keratin, type I cytoskeletal 18 (Cytokeratin-18) (CK-18) (Keratin-18) (K18) (Cytokeratin endo B) (Ke ...	0.44	-	mit	0		mitochondrion [IDA]			422
P60331 UniProt NPD GO	KR101_HUMAN	Keratin-associated protein 10-1 (Keratin-associated protein 10.1) (High sulfur keratin-associated pr ...	0.44	-	nuc	0					282
P60413 UniProt NPD GO	KR10C_HUMAN	Keratin-associated protein 10-12 (Keratin-associated protein 10.12) (High sulfur keratin-associated ...	0.44	-	nuc	0					245
Q7T3L1 UniProt NPD GO	KNL1A_BOMMX	Kininogen-1a precursor [Contains: Maximakinin (Bombinakinin M); Bradykinin; Bombinakinin-GAP (Bombin ...	0.44	-	exc	0	Secreted protein	extracellular region [IDA]			294
Q90WZ1 UniProt NPD GO	KNL1B_BOMMX	Kininogen-1b precursor [Contains: Maximakinin (Bombinakinin M); Bradykinin]	0.44	-	exc	0	Secreted protein	extracellular region [IDA]			208
Q9UGP4 UniProt NPD GO	LIMD1_HUMAN	LIM domains-containing protein 1	0.44	-	nuc	0			604543		676
O43325 UniProt NPD GO	YG01_HUMAN	LYR family protein A-211C6.1	0.44	-	nuc	0					122
P22064 UniProt NPD GO	LTB1S_HUMAN	Latent-transforming growth factor beta-binding protein, isoform 1S precursor (LTBP-1) (Transforming ...	0.44	-	nuc	0	Secreted protein		150390	1KSQ	1394
P05693 UniProt NPD GO	LEGK_PEA	Legumin K [Contains: Legumin K alpha chain (Legumin K acidic chain); Legumin K beta chain (Legumin K ...	0.44	-	nuc	0					350
P16079 UniProt NPD GO	LEGB6_VICFA	Legumin type B [Contains: Legumin type B alpha chain (Legumin type B acidic chain); Legumin type B b ...	0.44	-	nuc	0					329
P16080 UniProt NPD GO	LEGB7_VICFA	Legumin type B [Contains: Legumin type B alpha chain (Legumin type B acidic chain); Legumin type B b ...	0.44	-	nuc	0					335
Q8MKF0 UniProt NPD GO	L2GL1_BOVIN	Lethal(2) giant larvae protein homolog 1 (LLGL) (Bgl-1) (Giant larvae-1)	0.44	-	nuc	0	Cytoplasm. Localized to the lateral membrane during the polarization and formation cell-cell contact ...				1036
Q6C997 UniProt NPD GO	LCMT1_YARLI	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-) (Protein phosphatase methyltransferase 1)	0.44	-	cyt	0					324
Q5XIA3 UniProt NPD GO	LCMT2_RAT	Leucine carboxyl methyltransferase 2 (EC 2.1.1.-)	0.44	-	mit	0					686
Q9JMH2 UniProt NPD GO	LRC21_RAT	Leucine-rich repeat-containing protein 21 precursor (Photoreceptor-associated LRR superfamily protei ...	0.44	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein	integral to endoplasmic reticulum membrane [IDA]			617
Q9D5E4 UniProt NPD GO	LRC48_MOUSE	Leucine-rich repeat-containing protein 48	0.44	-	cyt	0					523
Q5DU41 UniProt NPD GO	LRC8B_MOUSE	Leucine-rich repeat-containing protein 8B	0.44	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				791
Q498T9 UniProt NPD GO	LRC8C_RAT	Leucine-rich repeat-containing protein 8C	0.44	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				803
Q7TQH7 UniProt NPD GO	LRP10_MOUSE	Low-density lipoprotein receptor-related protein 10 precursor	0.44	-	exc	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [IDA]			713
Q86VZ4 UniProt NPD GO	LRP11_HUMAN	Low-density lipoprotein receptor-related protein 11 precursor	0.44	-	nuc	1	Membrane; single-pass type I membrane protein (Potential)				500
P38656 UniProt NPD GO	LA_RAT	Lupus La protein homolog (La ribonucleoprotein) (La autoantigen homolog)	0.44	-	nuc	0	Nucleus (Probable)				415
Q8TG07 UniProt NPD GO	PLB1_CANGA	Lysophospholipase 1 precursor (EC 3.1.1.5) (Phospholipase B 1)	0.44	-	mit	0	Secreted protein (Probable)				659
Q60HE9 UniProt NPD GO	MA2B1_MACFA	Lysosomal alpha-mannosidase precursor (EC 3.2.1.24) (Mannosidase, alpha B) (Lysosomal acid alpha-man ...	0.44	-	nuc	0	Lysosome (By similarity)				1012
Q944S9 UniProt NPD GO	MAD16_ORYSA	MADS-box transcription factor 16 (OsMADS16) (Protein SUPERWOMAN1) (Protein APETALA3-like)	0.44	-	cyt	0	Nucleus (Probable)				224
Q8S151 UniProt NPD GO	MAD32_ORYSA	MADS-box transcription factor 32 (OsMADS32)	0.44	-	nuc	0	Nucleus (Probable)				196
O22752 UniProt NPD GO	MLO7_ARATH	MLO-like protein 7 (AtMlo7)	0.44	+	end	8 *	Membrane; multi-pass membrane protein (By similarity)				542
Q4R4M1 UniProt NPD GO	MRS2L_MACFA	Magnesium transporter MRS2L, mitochondrial precursor (MRS2-like protein)	0.44	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				408
Q8K2Y9 UniProt NPD GO	CCM2_MOUSE	Malcavernin (Cerebral cavernous malformations protein 2 homolog) (Osmosensing scaffold for MEKK3)	0.44	-	nuc	0	Cytoplasm. Treatment with sorbitol caused relocalization to ruffle-like structures				453
O93958 UniProt NPD GO	MATA2_YARLI	Mating-type protein A2 (MATA2 transcription factor)	0.44	-	nuc	0	Nucleus (By similarity)				291
O13402 UniProt NPD GO	MAT1_COCCA	Mating-type protein MAT-1	0.44	-	nuc	0	Nucleus (Potential)				379
Q9WTR0 UniProt NPD GO	MMP16_MOUSE	Matrix metalloproteinase-16 precursor (EC 3.4.24.-) (MMP-16) (Membrane-type matrix metalloproteinase ...	0.44	-	end	1	Cell membrane; single-pass type I membrane protein (Potential). Localized at the cell surface of mel ...				607
O98840 UniProt NPD GO	MATK_HYDQU	Maturase K (Intron maturase) (Fragment)	0.44	-	cyt	0	Plastid; chloroplast				354

You are viewing entries 29051 to 29100 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.