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
P34777 UniProt NPD GO	YCX3_ASTLO	Hypothetical 20.0 kDa protein in rps12-trnP intergenic region (ORF160)	0.71	-	nuc	0	Plastid				160
Q04461 UniProt NPD GO	YM01_YEAST	Hypothetical 52.4 kDa protein in ILV2-ADE17 intergenic region	0.71	-	nuc	0		nucleus [IDA]			462
P36112 UniProt NPD GO	YKZ6_YEAST	Hypothetical 61.1 kDa protein in YPT52-DBP7 intergenic region	0.71	-	mit	1 *		mitochondrion [IDA]			540
P40360 UniProt NPD GO	YJH1_YEAST	Hypothetical 65.6 kDa protein in SMC3-MRPL8 intergenic region	0.71	-	nuc	0		mitochondrial matrix [IDA]			574
P51234 UniProt NPD GO	YCXB_PORPU	Hypothetical 73.8 kDa protein in cemA-psbI intergenic region (ORF621)	0.71	-	nuc	0	Plastid; chloroplast				621
Q10222 UniProt NPD GO	YL31_SCHPO	Hypothetical protein C1071.01c in chromosome I	0.71	-	end	0					670
Q9USN6 UniProt NPD GO	YJY3_SCHPO	Hypothetical protein C132.03 in chromosome III	0.71	+	nuc	0					176
Q10492 UniProt NPD GO	YDG2_SCHPO	Hypothetical protein C26F1.02 in chromosome I	0.71	-	nuc	0					197
O14013 UniProt NPD GO	YDPA_SCHPO	Hypothetical protein C29A4.10 in chromosome I	0.71	-	nuc	0		nucleolus [IDA] RNA polymerase I upstream activating factor... [TAS]			556
Q09857 UniProt NPD GO	YAF3_SCHPO	Hypothetical protein C29E6.03c in chromosome I	0.71	-	nuc	0					1044
P46581 UniProt NPD GO	YLB7_CAEEL	Hypothetical protein C34E10.7 in chromosome III	0.71	-	nuc	0	Nucleus (Potential)	nucleus [IDA]			192
Q10310 UniProt NPD GO	YD57_SCHPO	Hypothetical protein C6C3.07 in chromosome I	0.71	-	nuc	0					515
P34606 UniProt NPD GO	YO66_CAEEL	Hypothetical protein ZK1098.6	0.71	-	nuc	0					278
P25407 UniProt NPD GO	YCA1_PLAFA	Hypothetical protein in calmodulin 5'region (Fragment)	0.71	+	nuc	0					252
P17950 UniProt NPD GO	IER2_MOUSE	Immediate early response gene 2 protein (T-lymphocyte-activated protein) (Cycloheximide-induced gene ...	0.71	+	nuc	0		cytoplasm [IDA]			221
P07995 UniProt NPD GO	INHBA_BOVIN	Inhibin beta A chain precursor (Activin beta-A chain)	0.71	+	nuc	0	Secreted protein				425
P78990 UniProt NPD GO	COX18_KLULA	Inner membrane protein COX18, mitochondrial precursor (Cytochrome c oxidase assembly protein 18)	0.71	-	nuc	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				313
P39952 UniProt NPD GO	OXA1_YEAST	Inner membrane protein OXA1, mitochondrial precursor (Oxidase assembly protein 1) (Cytochrome oxidas ...	0.71	-	mit	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			402
Q8WN95 UniProt NPD GO	ITPR3_BOVIN	Inositol 1,4,5-trisphosphate receptor type 3 (Type 3 inositol 1,4,5-trisphosphate receptor) (Type 3 ...	0.71	+	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Secretory vesicl ...				2664
Q9H0H0 UniProt NPD GO	INT2_HUMAN	Integrator complex subunit 2 (Int2)	0.71	-	cyt	0	Nucleus; nuclear membrane; single-pass membrane protein (Potential)	integrator complex [IDA]			1204
Q9TTB0 UniProt NPD GO	IFNG_PANTR	Interferon gamma (IFN-gamma) (Immune interferon) (Fragment)	0.71	-	nuc	0	Secreted protein (By similarity)				143
P33237 UniProt NPD GO	MX1_SHEEP	Interferon-induced GTP-binding protein Mx1	0.71	-	cyt	0	Cytoplasm (By similarity)				654
P32456 UniProt NPD GO	GBP2_HUMAN	Interferon-induced guanylate-binding protein 2 (GTP-binding protein 2) (Guanine nucleotide-binding p ...	0.71	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		600412		591
O00458 UniProt NPD GO	IFRD1_HUMAN	Interferon-related developmental regulator 1 (Nerve growth factor-inducible protein PC4)	0.71	-	nuc	0			603502		451
Q21065 UniProt NPD GO	IFA3_CAEEL	Intermediate filament protein ifa-3 (Intermediate filament protein A3) (IF-A3) (Cel IF A3)	0.71	-	nuc	0	Cytoplasm				581
P52192 UniProt NPD GO	IRK1_CAEEL	Inward rectifier potassium channel irk-1	0.71	-	mit	3	Membrane; multi-pass membrane protein (Potential)				505
Q9ER75 UniProt NPD GO	IRX6_MOUSE	Iroquois-class homeodomain protein IRX-6 (Iroquois homeobox protein 6) (Homeodomain protein IRXB3)	0.71	-	nuc	0	Nucleus (By similarity)				438
Q63722 UniProt NPD GO	JAG1_RAT	Jagged-1 precursor (Jagged1) (CD339 antigen)	0.71	+	nuc	1	Membrane; single-pass type I membrane protein	extracellular region [ISS] integral to plasma membrane [ISS]			1219
Q6PCM1 UniProt NPD GO	JHD2A_MOUSE	JmjC domain-containing histone demethylation protein 2A (EC 1.14.11.-) (Jumonji domain-containing pr ...	0.71	+	nuc	0	Nucleus (By similarity)				1323
Q8VCD7 UniProt NPD GO	JHD3C_MOUSE	JmjC domain-containing histone demethylation protein 3C (EC 1.14.11.-) (Jumonji domain-containing pr ...	0.71	+	nuc	0	Nucleus (By similarity)				1054
Q3U2K5 UniProt NPD GO	JHD3D_MOUSE	JmjC domain-containing histone demethylation protein 3D (EC 1.14.11.-) (Jumonji domain-containing pr ...	0.71	-	nuc	0	Nucleus (By similarity)				510
O14362 UniProt NPD GO	YB4H_SCHPO	KNR4/SMI1 homolog	0.71	-	nuc	0					504
O61577 UniProt NPD GO	KTNA1_STRPU	Katanin p60 ATPase-containing subunit (EC 3.6.4.3) (Katanin p60 subunit) (p60 katanin)	0.71	-	nuc	0	Cytoplasm. Predominantly. Centrosome. Also localized to the interphase centrosome. Spindle. Enhanced ...				516
P23276 UniProt NPD GO	KELL_HUMAN	Kell blood group glycoprotein (EC 3.4.24.-) (CD238 antigen)	0.71	-	mit	1 *	Cell membrane; single-pass type II membrane protein. Spans the erythrocyte membrane, and is attached ...	integral to plasma membrane [TAS]	110900		732
P39690 UniProt NPD GO	KHS1_YEAST	Killer toxin KHS precursor (Killer of heat sensitive)	0.71	-	end	2 *	Cell membrane; multi-pass membrane protein				708
P32744 UniProt NPD GO	CLS2_CAEEL	Kinetochore protein CLASP-2	0.71	-	nuc	0	Kinetochore. Spindle. Localized to kinetochores during metaphase, and to the spindle region				1020
Q9HA82 UniProt NPD GO	LASS4_HUMAN	LAG1 longevity assurance homolog 4	0.71	-	end	5 *	Nucleus; nuclear membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum; endoplasm ...				394
Q04650 UniProt NPD GO	LMX1A_MESAU	LIM homeobox transcription factor 1 alpha (LIM/homeobox protein LMX1A) (LMX-1) (LIM-homeobox protein ...	0.71	-	nuc	0	Nucleus				382
P37137 UniProt NPD GO	LHX5_XENLA	LIM/homeobox protein Lhx5 (Homeobox protein LIM-5) (xLIM-5) (xLIM-2A)	0.71	+	nuc	0	Nucleus (Probable)				402
Q62733 UniProt NPD GO	LAP2_RAT	Lamina-associated polypeptide 2 isoform beta (Thymopoietin isoform beta) (TP beta)	0.71	+	nuc	1	Nucleus; nuclear inner membrane; single-pass type II membrane protein. Tightly associated with the n ...				451
P24043 UniProt NPD GO	LAMA2_HUMAN	Laminin alpha-2 chain precursor (Laminin M chain) (Merosin heavy chain)	0.71	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. Major component	basement membrane [TAS]	607855		3110
P15800 UniProt NPD GO	LAMB2_RAT	Laminin beta-2 chain precursor (S-laminin) (Laminin chain B3)	0.71	-	nuc	0	Secreted protein; extracellular space				1801
Q61292 UniProt NPD GO	LAMB2_MOUSE	Laminin beta-2 chain precursor (S-laminin) (S-LAM)	0.71	-	nuc	0	Secreted protein; extracellular space	basement membrane [IDA]			1799
Q5A931 UniProt NPD GO	LCMT2_CANAL	Leucine carboxyl methyltransferase 2 (EC 2.1.1.-)	0.71	+	nuc	0					689
Q9CXD9 UniProt NPD GO	LRC17_MOUSE	Leucine-rich repeat-containing protein 17 precursor	0.71	-	exc	0					443
Q96CN5 UniProt NPD GO	LRC45_HUMAN	Leucine-rich repeat-containing protein 45	0.71	-	nuc	0					670
Q9D2H9 UniProt NPD GO	LRC50_MOUSE	Leucine-rich repeat-containing protein 50	0.71	-	nuc	0					634
P62046 UniProt NPD GO	LRCH1_MOUSE	Leucine-rich repeats and calponin homology domain-containing protein 1 (Calponin homology domain-con ...	0.71	-	nuc	0					709
Q95M25 UniProt NPD GO	LEAP2_MACMU	Liver-expressed antimicrobial peptide 2 precursor (LEAP-2)	0.71	-	exc	0	Secreted protein				77
P20693 UniProt NPD GO	FCER2_MOUSE	Low affinity immunoglobulin epsilon Fc receptor (Lymphocyte IGE receptor) (Fc-epsilon-RII) (CD23 ant ...	0.71	-	nuc	1 *	Membrane; single-pass type II membrane protein	external side of plasma membrane [IDA]		1HLJ	331

You are viewing entries 13301 to 13350 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.