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
P54869 UniProt NPD GO	HMCS2_MOUSE	Hydroxymethylglutaryl-CoA synthase, mitochondrial precursor (EC 2.3.3.10) (HMG-CoA synthase) (3-hydr ...	0.64	-	mit	0	Mitochondrion	mitochondrial inner membrane [IDA] mitochondrion [IDA]			508
P38428 UniProt NPD GO	YM8E_YEAST	Hypothetical 22.8 kDa protein in TPS3-IPP2 intergenic region (ORF1)	0.64	-	nuc	0		integral to endoplasmic reticulum membrane [IDA] mitochondrion [IDA]			203
Q10958 UniProt NPD GO	YT31_CAEEL	Hypothetical protein B0353.1	0.64	+	nuc	0					182
Q10154 UniProt NPD GO	YAT9_SCHPO	Hypothetical protein C1D4.09c in chromosome I	0.64	-	nuc	0					240
O94643 UniProt NPD GO	YBV1_SCHPO	Hypothetical protein C21.01 in chromosome II	0.64	-	nuc	0		Mis6-Sim4 complex [TAS]			441
Q10165 UniProt NPD GO	YAUA_SCHPO	Hypothetical protein C26A3.10 in chromosome I	0.64	-	nuc	0					923
Q09267 UniProt NPD GO	YQD7_CAEEL	Hypothetical protein C32D5.7	0.64	-	nuc	4					435
Q10186 UniProt NPD GO	YAWC_SCHPO	Hypothetical protein C3F10.12c in chromosome I	0.64	+	nuc	0	Nucleus (Potential)				201
P34379 UniProt NPD GO	YLM5_CAEEL	Hypothetical protein D2007.5	0.64	-	nuc	0					443
Q8ST94 UniProt NPD GO	Y110_ENCCU	Hypothetical protein ECU01_0100/ECU01_1510/ECU08_0030	0.64	+	cyt	0					619
P41882 UniProt NPD GO	YPT4_CAEEL	Hypothetical protein F37A4.4 in chromosome III	0.64	-	end	1					1163
P34542 UniProt NPD GO	YNC9_CAEEL	Hypothetical protein R05D3.9 precursor	0.64	-	nuc	0					646
Q09608 UniProt NPD GO	YRN8_CAEEL	Hypothetical protein R07B1.8	0.64	-	exc	0					425
Q09346 UniProt NPD GO	YRR5_CAEEL	Hypothetical protein R144.5	0.64	-	nuc	1					511
Q23495 UniProt NPD GO	HEAT1_CAEEL	Hypothetical protein ZK430.1 in chromosome II	0.64	-	cyt	0	Nucleus; nucleolus (By similarity)				1650
P34651 UniProt NPD GO	YOT5_CAEEL	Hypothetical protein ZK632.5	0.64	-	cyt	0					824
Q3T116 UniProt NPD GO	ICT1_BOVIN	Immature colon carcinoma transcript 1 protein precursor	0.64	-	mit	0					206
P54987 UniProt NPD GO	IRG1_MOUSE	Immune-responsive protein 1 (Fragment)	0.64	-	cyt	0					646
Q9SLX0 UniProt NPD GO	IMA1B_ORYSA	Importin alpha-1b subunit	0.64	-	nuc	0	Cytoplasm; perinuclear region				534
Q42191 UniProt NPD GO	OXA1_ARATH	Inner membrane protein OXA1, mitochondrial precursor (Oxidase assembly 1 protein) (AtOXA1)	0.64	-	end	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrion [IDA]			429
Q9FY06 UniProt NPD GO	PPF1_PEA	Inner membrane protein PPF-1, chloroplast precursor (Post-floral-specific protein 1)	0.64	-	end	4	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Potential)				442
Q9CXV0 UniProt NPD GO	ISL2_MOUSE	Insulin gene enhancer protein ISL-2 (Islet-2)	0.64	+	nuc	0	Nucleus (By similarity)				359
P53406 UniProt NPD GO	ISL2_BRARE	Insulin gene enhancer protein isl-2 (Islet-2)	0.64	+	nuc	0	Nucleus				359
P06213 UniProt NPD GO	INSR_HUMAN	Insulin receptor precursor (EC 2.7.10.1) (IR) (CD220 antigen) [Contains: Insulin receptor subunit al ...	0.64	+	end	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	125853	2B4S	1382
O44386 UniProt NPD GO	ITA3_DROME	Integrin alpha-PS3 precursor (Position-specific antigen 3 alpha chain) (Protein scab) (Protein volad ...	0.64	-	end	1 *	Membrane; single-pass type I membrane protein	integrin complex [NAS]			1115
P16144 UniProt NPD GO	ITB4_HUMAN	Integrin beta-4 precursor (GP150) (CD104 antigen)	0.64	-	exc	0	Membrane; single-pass type I membrane protein	integrin complex [TAS]	147557	1QG3	1822
Q8R4E0 UniProt NPD GO	IRF2_SIGHI	Interferon regulatory factor 2 (IRF-2)	0.64	-	nuc	0	Nucleus				349
Q9BYX4 UniProt NPD GO	IFIH1_HUMAN	Interferon-induced helicase C domain-containing protein 1 (EC 3.6.1.-) (Interferon-induced with heli ...	0.64	-	cyt	0	Cytoplasm. Nucleus (Potential). May be found in the nucleus, during apoptosis		606951		1025
P20695 UniProt NPD GO	IFRD1_RAT	Interferon-related developmental regulator 1 (Nerve growth factor-inducible protein PC4) (IRPR)	0.64	-	nuc	0	Cytoplasm. Cell membrane. Nucleus. Presents a NGF-dependent pattern of intracellular localization. W ...				449
P01582 UniProt NPD GO	IL1A_MOUSE	Interleukin-1 alpha precursor (IL-1 alpha)	0.64	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				270
P18430 UniProt NPD GO	IL1A_PIG	Interleukin-1 alpha precursor (IL-1 alpha)	0.64	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				270
P16598 UniProt NPD GO	IL1A_RAT	Interleukin-1 alpha precursor (IL-1 alpha)	0.64	-	nuc	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...	extracellular region [IDA]			270
Q62406 UniProt NPD GO	IRAK1_MOUSE	Interleukin-1 receptor-associated kinase 1 (EC 2.7.11.1) (IRAK-1) (IRAK) (Pelle-like protein kinase) ...	0.64	-	nuc	0					710
P38978 UniProt NPD GO	KS1_HYDAT	KS1 protein precursor (Head-specific protein 1) (Kopf-spezifisches protein 1)	0.64	+	nuc	0					217
P38853 UniProt NPD GO	KEL1_YEAST	Kelch repeat-containing protein 1	0.64	-	nuc	0		bud neck [IDA] bud tip [IDA] cytoplasm [IDA] mating projection tip [IDA]			1164
Q05090 UniProt NPD GO	KLC_STRPU	Kinesin light chain (KLC)	0.64	-	nuc	0					686
Q96FN5 UniProt NPD GO	KIF12_HUMAN	Kinesin-like protein KIF12	0.64	-	nuc	0					646
P33895 UniProt NPD GO	NUF2_YEAST	Kinetochore protein NUF2	0.64	-	nuc	0	Nucleus. Associated with kinetochores	condensed nuclear chromosome kinetochore [IDA] Ndc80 complex [IDA] spindle microtubule [IDA]			451
Q99612 UniProt NPD GO	KLF6_HUMAN	Krueppel-like factor 6 (Core promoter element-binding protein) (B-cell-derived protein 1) (Proto-onc ...	0.64	-	nuc	0	Nucleus	nucleus [TAS]	602053		283
O75840 UniProt NPD GO	KLF7_HUMAN	Krueppel-like factor 7 (Ubiquitous krueppel-like factor)	0.64	-	nuc	0	Nucleus (Probable)		604865		302
O42565 UniProt NPD GO	LIMK1_XENLA	LIM domain kinase 1 (EC 2.7.11.1) (LIMK-1) (xLIMK1)	0.64	-	nuc	0	Cytoplasm (By similarity)				615
Q5T754 UniProt NPD GO	LCE1F_HUMAN	Late cornified envelope protein 1F (Late envelope protein 6)	0.64	-	mit	0					118
Q66HD6 UniProt NPD GO	LRC18_RAT	Leucine-rich repeat-containing protein 18	0.64	-	nuc	0	Cytoplasm				256
Q9CQ07 UniProt NPD GO	LRC18_MOUSE	Leucine-rich repeat-containing protein 18 (Testis-specific LRR protein)	0.64	-	nuc	0	Cytoplasm				262
Q8CIM1 UniProt NPD GO	LRC45_MOUSE	Leucine-rich repeat-containing protein 45	0.64	-	nuc	0					670
Q96FV0 UniProt NPD GO	LRC46_HUMAN	Leucine-rich repeat-containing protein 46	0.64	-	nuc	0					321
P70193 UniProt NPD GO	LRIG1_MOUSE	Leucine-rich repeats and immunoglobulin-like domains protein 1 precursor (LIG-1)	0.64	-	exc	1	Membrane; single-pass type I membrane protein (By similarity)				1091
O75023 UniProt NPD GO	LIRB5_HUMAN	Leukocyte immunoglobulin-like receptor subfamily B member 5 precursor (Leukocyte immunoglobulin-like ...	0.64	-	end	1	Membrane; single-pass type I membrane protein		604814		590
Q91XL2 UniProt NPD GO	LNX2_MOUSE	Ligand of Numb-protein X 2 (Numb-binding protein 2)	0.64	-	nuc	0					687
P50538 UniProt NPD GO	MAD_MOUSE	MAD protein (MAX dimerizer) (MAX dimerization protein 1)	0.64	-	nuc	0	Nucleus				227

You are viewing entries 16901 to 16950 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.