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
Q2VL79 UniProt NPD GO	MSX1_DAUMA	Homeobox protein MSX-1 (Msh homeobox 1-like protein)	0.41	+	nuc	0	Nucleus (By similarity)				297
Q2VL78 UniProt NPD GO	MSX1_LEMCA	Homeobox protein MSX-1 (Msh homeobox 1-like protein)	0.41	+	nuc	0	Nucleus (By similarity)				297
Q2VL83 UniProt NPD GO	MSX1_LEORO	Homeobox protein MSX-1 (Msh homeobox 1-like protein)	0.41	+	nuc	0	Nucleus (By similarity)				297
Q2VL76 UniProt NPD GO	MSX1_PROVC	Homeobox protein MSX-1 (Msh homeobox 1-like protein)	0.41	+	nuc	0	Nucleus (By similarity)				297
Q24703 UniProt NPD GO	UBX_DROVI	Homeotic protein ultrabithorax (Fragment)	0.41	+	nuc	0	Nucleus				87
Q9MTN3 UniProt NPD GO	YCX5_OENHO	Hypothetical 12.8 kDa protein in ycf9-trnS intergenic region (ORF111)	0.41	-	nuc	0	Plastid; chloroplast				111
P53105 UniProt NPD GO	YGS7_YEAST	Hypothetical 13.7 kDa protein in MPT5-SAE2 intergenic region	0.41	-	nuc	2					115
P36061 UniProt NPD GO	YKO7_YEAST	Hypothetical 22.7 kDa protein in SDH1-CIM5/YTA3 intergenic region	0.41	-	mit	0					205
P15610 UniProt NPD GO	YM09_PARTE	Hypothetical 22.9 kDa protein (ORF9)	0.41	-	cyt	0					204
P53274 UniProt NPD GO	YG36_YEAST	Hypothetical 25.8 kDa protein in ASN2-PHB1 intergenic region	0.41	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			230
O18211 UniProt NPD GO	MO25M_CAEEL	Hypothetical MO25-like protein Y53C12A.4 in chromosome II	0.41	-	nuc	0					338
P54008 UniProt NPD GO	YXX1_ACHAM	Hypothetical UPF0202 protein (Fragment)	0.41	-	nuc	0	Nucleus (By similarity)				373
O14186 UniProt NPD GO	YDSB_SCHPO	Hypothetical WD repeat protein C4F8.11 in chromosome I	0.41	-	mit	0					846
P93294 UniProt NPD GO	M320_ARATH	Hypothetical mitochondrial protein AtMg00320 (ORF127)	0.41	-	nuc	0	Mitochondrion (Potential)				127
P92553 UniProt NPD GO	M1230_ARATH	Hypothetical mitochondrial protein AtMg01230 (ORF145b)	0.41	-	nuc	1	Mitochondrion (Potential)				145
Q11109 UniProt NPD GO	YX02_CAEEL	Hypothetical protein C03B1.2	0.41	-	nuc	0					280
Q10410 UniProt NPD GO	YD85_SCHPO	Hypothetical protein C1F3.05 in chromosome I	0.41	-	nuc	0					510
O94644 UniProt NPD GO	YBV2_SCHPO	Hypothetical protein C21.02 in chromosome II	0.41	-	cyt	0					511
O14138 UniProt NPD GO	YFC3_SCHPO	Hypothetical protein C25A8.03c in chromosome I	0.41	-	mit	0					467
O14358 UniProt NPD GO	YB4C_SCHPO	Hypothetical protein C30D10.12c in chromosome II	0.41	-	nuc	0					93
P46583 UniProt NPD GO	YLB9_CAEEL	Hypothetical protein C34E10.9	0.41	-	nuc	0					122
Q10138 UniProt NPD GO	YAS2_SCHPO	Hypothetical protein C3H8.02 in chromosome I	0.41	-	cyt	0					444
Q10140 UniProt NPD GO	YAS4_SCHPO	Hypothetical protein C3H8.04 in chromosome I	0.41	-	nuc	0					338
Q8SW74 UniProt NPD GO	Y313_ENCCU	Hypothetical protein ECU03_0130	0.41	-	end	6 *					266
Q10008 UniProt NPD GO	YSV2_CAEEL	Hypothetical protein T19C3.2	0.41	-	mit	1 *					269
P34584 UniProt NPD GO	YN25_CAEEL	Hypothetical protein T26G10.5	0.41	-	mit	1 *					125
Q23469 UniProt NPD GO	YPTJ_CAEEL	Hypothetical protein ZK381.2	0.41	-	mit	1 *					503
P34657 UniProt NPD GO	YOTB_CAEEL	Hypothetical protein ZK632.12	0.41	+	cyt	0					266
P30629 UniProt NPD GO	YOU2_CAEEL	Hypothetical protein ZK637.2	0.41	-	nuc	0					143
Q9P7X4 UniProt NPD GO	YH6B_SCHPO	Hypothetical serine-rich protein P23A10.11c precursor	0.41	-	exc	0	Secreted protein (Potential)				507
P06311 UniProt NPD GO	KV3K_HUMAN	Ig kappa chain V-III region IARC/BL41 precursor	0.41	-	nuc	0		extracellular region [NAS]			128
Q06142 UniProt NPD GO	IMB1_YEAST	Importin beta-1 subunit (Karyopherin beta-1 subunit) (Importin 95)	0.41	-	cyt	0	Cytoplasm (By similarity). Nucleus; nuclear envelope (By similarity)	cytoplasm [IDA] nuclear pore [IDA]		2BPT	861
Q14164 UniProt NPD GO	IKKE_HUMAN	Inhibitor of nuclear factor kappa-B kinase epsilon subunit (EC 2.7.11.1) (I kappa-B kinase epsilon) ...	0.41	-	cyt	0	Cytoplasm (Probable)	cytoplasm [NAS]	605048		716
Q5CZK5 UniProt NPD GO	INSL5_PANTR	Insulin-like peptide INSL5 precursor (Insulin-like peptide 5) [Contains: Insulin-like peptide INSL5 ...	0.41	-	exc	0	Secreted protein (Probable)				135
Q63264 UniProt NPD GO	IL1B_RAT	Interleukin-1 beta precursor (IL-1 beta)	0.41	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...	extracellular region [IMP]			268
P01584 UniProt NPD GO	IL1B_HUMAN	Interleukin-1 beta precursor (IL-1 beta) (Catabolin)	0.41	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...	extracellular region [NAS] extracellular space [TAS]	147720	9ILB	269
P14628 UniProt NPD GO	IL1B_RABIT	Interleukin-1 beta precursor (IL-1 beta) (Lymphocyte proliferation potentiating factor)	0.41	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...				268
P46661 UniProt NPD GO	IL12A_CERTO	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.41	-	mit	0	Secreted protein				219
Q9R103 UniProt NPD GO	IL12A_RAT	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.41	-	mit	0	Secreted protein (By similarity)				215
Q60943 UniProt NPD GO	I17RA_MOUSE	Interleukin-17 receptor A precursor (IL-17 receptor)	0.41	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				864
Q8CJ70 UniProt NPD GO	IL19_MOUSE	Interleukin-19 precursor (IL-19)	0.41	-	nuc	1 *	Secreted protein				176
Q38J84 UniProt NPD GO	IL2RB_PANTR	Interleukin-2 receptor beta chain precursor (IL-2 receptor) (P70-75) (High affinity IL-2 receptor su ...	0.41	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				551
P24708 UniProt NPD GO	INVO_AOTTR	Involucrin	0.41	-	nuc	0	Cytoplasm. Constituent of the scaffolding of the cornified envelope	cornified envelope [ISS] cytoplasm [ISS]			544
P07476 UniProt NPD GO	INVO_HUMAN	Involucrin	0.41	-	nuc	0	Cytoplasm. Constituent of the scaffolding of the cornified envelope	cornified envelope [IDA] cytoplasm [IDA]	147360	1EU0	585
P24711 UniProt NPD GO	INVO_TARBA	Involucrin	0.41	-	nuc	0	Cytoplasm. Constituent of the scaffolding of the cornified envelope				387
Q08957 UniProt NPD GO	AFT2_YEAST	Iron-regulated transcriptional activator AFT2 (Activator of iron transcription protein 2)	0.41	-	nuc	0	Nucleus (Probable)	mitochondrion [IDA] nucleus [IMP]			416
Q8WNW3 UniProt NPD GO	PLAK_PIG	Junction plakoglobin	0.41	-	nuc	0	Cytoplasm (By similarity). Cytoplasmic in a soluble and membrane-associated form (By similarity)				745
Q6P0K8 UniProt NPD GO	PLAK_RAT	Junction plakoglobin	0.41	-	nuc	0	Cytoplasm (By similarity). Cytoplasmic in a soluble and membrane-associated form (By similarity)				745
Q02257 UniProt NPD GO	PLAK_MOUSE	Junction plakoglobin (Desmoplakin-3) (Desmoplakin III)	0.41	-	nuc	0	Cytoplasm. Cytoplasmic in a soluble and membrane-associated form	cell-cell adherens junction [IDA] cytosol [IDA] desmosome [IDA]			745
Q7Z4H8 UniProt NPD GO	KDEL2_HUMAN	KDEL motif-containing protein 2 precursor	0.41	-	mit	0	Endoplasmic reticulum; Endoplasmic reticulum lumen (Potential)				507

You are viewing entries 31151 to 31200 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.