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
O19990 UniProt NPD GO	RR4_BELCH	Chloroplast 30S ribosomal protein S4 (Fragment)	0.49	-	mit	0	Plastid; chloroplast				182
P69642 UniProt NPD GO	RR4_FESGI	Chloroplast 30S ribosomal protein S4 (Fragment)	0.49	-	mit	0	Plastid; chloroplast				196
P69646 UniProt NPD GO	RR4_LOLPR	Chloroplast 30S ribosomal protein S4 (Fragment)	0.49	-	mit	0	Plastid; chloroplast				196
Q6EMA4 UniProt NPD GO	RR7_CANWI	Chloroplast 30S ribosomal protein S7	0.49	-	nuc	0	Plastid; chloroplast				155
Q9GFL8 UniProt NPD GO	RR7_DIOBU	Chloroplast 30S ribosomal protein S7	0.49	-	nuc	0	Plastid; chloroplast				155
Q6EVZ0 UniProt NPD GO	RR7_NYMAL	Chloroplast 30S ribosomal protein S7	0.49	-	nuc	0	Plastid; chloroplast				155
Q9MSP1 UniProt NPD GO	RR7_NYMOD	Chloroplast 30S ribosomal protein S7	0.49	-	nuc	0	Plastid; chloroplast				155
Q2VEE3 UniProt NPD GO	RK16_SOLTU	Chloroplast 50S ribosomal protein L16	0.49	-	mit	0	Plastid; chloroplast				134
Q85FI1 UniProt NPD GO	RK2_ADICA	Chloroplast 50S ribosomal protein L2	0.49	-	nuc	0	Plastid; chloroplast				273
Q2MI61 UniProt NPD GO	RK22_LYCES	Chloroplast 50S ribosomal protein L22	0.49	-	nuc	0	Plastid; chloroplast				155
O62952 UniProt NPD GO	RK22_PICAB	Chloroplast 50S ribosomal protein L22	0.49	-	nuc	0	Plastid; chloroplast	chloroplast ribosome [NAS]			142
Q2MIE8 UniProt NPD GO	RK22_SOLBU	Chloroplast 50S ribosomal protein L22	0.49	-	nuc	0	Plastid; chloroplast				155
Q68RV8 UniProt NPD GO	RK32_PANGI	Chloroplast 50S ribosomal protein L32	0.49	-	mit	0	Plastid; chloroplast				54
O78440 UniProt NPD GO	RK34_GUITH	Chloroplast 50S ribosomal protein L34	0.49	-	mit	0	Plastid; chloroplast				46
Q4P827 UniProt NPD GO	EAF3_USTMA	Chromatin modification-related protein EAF3	0.49	-	nuc	0	Nucleus (By similarity)				303
P30376 UniProt NPD GO	1A02_GORGO	Class I histocompatibility antigen, GOGO-A0201 alpha chain precursor	0.49	-	end	1 *	Membrane; single-pass type I membrane protein				365
Q9USP6 UniProt NPD GO	CLC1_SCHPO	Clathrin light chain (CLC)	0.49	-	nuc	0	Cytoplasmic face of coated pits and vesicles (By similarity)				229
Q8IWL3 UniProt NPD GO	HSC20_HUMAN	Co-chaperone protein HscB, mitochondrial precursor (Hsc20)	0.49	-	nuc	0	Mitochondrion (Potential)		608142		235
Q9JIF7 UniProt NPD GO	COPB_MOUSE	Coatomer subunit beta (Beta-coat protein) (Beta-COP)	0.49	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein; cytoplasmic ...	Golgi apparatus [IDA]			953
Q8N4L8 UniProt NPD GO	CCD24_HUMAN	Coiled-coil domain-containing protein 24	0.49	-	nuc	0					307
Q5R7J0 UniProt NPD GO	CCD56_PONPY	Coiled-coil domain-containing protein 56	0.49	-	nuc	1	Membrane; single-pass membrane protein (Potential)				106
Q9JI03 UniProt NPD GO	CO5A1_RAT	Collagen alpha-1(V) chain precursor	0.49	-	exc	1 *		collagen type V [TAS]			1840
Q91VF6 UniProt NPD GO	EMID2_MOUSE	Collagen alpha-1(XXVI) chain precursor (EMI domain-containing protein 2) (Protein Emu2) (Emilin and ...	0.49	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix	endoplasmic reticulum [IDA] extracellular matrix (sensu Metazoa) [IDA] Golgi apparatus [IDA]			440
P00751 UniProt NPD GO	CFAB_HUMAN	Complement factor B precursor (EC 3.4.21.47) (C3/C5 convertase) (Properdin factor B) (Glycine-rich b ...	0.49	-	mit	0	Secreted protein		138470	1RTK	764
Q864W0 UniProt NPD GO	CFAB_PANTR	Complement factor B precursor (EC 3.4.21.47) (C3/C5 convertase) [Contains: Complement factor B Ba fr ...	0.49	-	cyt	0	Secreted protein				764
Q28085 UniProt NPD GO	CFAH_BOVIN	Complement factor H precursor (H factor 1)	0.49	-	exc	0	Secreted protein				1236
P10169 UniProt NPD GO	CON8_NEUCR	Conidiation-specific protein 8	0.49	-	nuc	0					176
Q9UHC6 UniProt NPD GO	CNTP2_HUMAN	Contactin-associated protein-like 2 precursor (Cell recognition molecule Caspr2)	0.49	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [NAS]	610042		1331
P19402 UniProt NPD GO	COLI_CAVPO	Corticotropin-lipotropin precursor (Pro-opiomelanocortin) (POMC) [Contains: NPP; Melanotropin gamma ...	0.49	-	exc	0					256
P17009 UniProt NPD GO	RR10_CYAPA	Cyanelle 30S ribosomal protein S10	0.49	-	nuc	0	Plastid; cyanelle				105
P23407 UniProt NPD GO	RK18_CYAPA	Cyanelle 50S ribosomal protein L18	0.49	-	nuc	0	Plastid; cyanelle				121
P42751 UniProt NPD GO	CCND1_ARATH	Cyclin delta-1	0.49	-	mit	0					339
O88874 UniProt NPD GO	CCNK_MOUSE	Cyclin-K	0.49	-	nuc	0					554
O88833 UniProt NPD GO	CP4AA_MOUSE	Cytochrome P450 4A10 (EC 1.14.15.3) (CYPIVA10) (Lauric acid omega-hydroxylase) (P450-LA-omega 1) (P4 ...	0.49	+	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [IDA]			509
P33274 UniProt NPD GO	CP4F1_RAT	Cytochrome P450 4F1 (EC 1.14.14.1) (CYPIVF1) (P450-A3)	0.49	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				524
Q5RCN6 UniProt NPD GO	CP4V2_PONPY	Cytochrome P450 4V2 (EC 1.14.-.-)	0.49	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (Potential)				525
P18125 UniProt NPD GO	CP7A1_RAT	Cytochrome P450 7A1 (EC 1.14.13.17) (Cholesterol 7-alpha-monooxygenase) (CYPVII) (Cholesterol 7-alph ...	0.49	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [TAS]			503
O21280 UniProt NPD GO	CCMA_RECAM	Cytochrome c biogenesis ATP-binding export protein ccmA (EC 3.6.3.41)	0.49	-	nuc	0	Mitochondrion; mitochondrial membrane; peripheral membrane protein (By similarity)				222
Q8GY84 UniProt NPD GO	RH10_ARATH	DEAD-box ATP-dependent RNA helicase 10 (EC 3.6.1.-)	0.49	+	nuc	0					456
O94263 UniProt NPD GO	DPB2_SCHPO	DNA polymerase epsilon subunit B (EC 2.7.7.7) (DNA polymerase II subunit B)	0.49	-	nuc	0	Nucleus (By similarity)				594
O74761 UniProt NPD GO	PRI2_SCHPO	DNA primase large subunit (EC 2.7.7.-)	0.49	-	nuc	0		alpha DNA polymerase:primase complex [TAS]			459
O14215 UniProt NPD GO	PRI1_SCHPO	DNA primase small subunit (EC 2.7.7.-)	0.49	-	nuc	0		alpha DNA polymerase:primase complex [TAS]			454
P29774 UniProt NPD GO	ETS3_DROME	DNA-binding protein D-ETS-3	0.49	-	nuc	0	Nucleus				490
P92969 UniProt NPD GO	RPOT1_ARATH	DNA-directed RNA polymerase 1, mitochondrial precursor (EC 2.7.7.6)	0.49	-	cyt	0	Mitochondrion				976
P30876 UniProt NPD GO	RPB2_HUMAN	DNA-directed RNA polymerase II 140 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 2) (RPB2) ...	0.49	-	cyt	0	Nucleus	DNA-directed RNA polymerase II, core complex [TAS]	180661		1174
Q8CFI7 UniProt NPD GO	RPB2_MOUSE	DNA-directed RNA polymerase II 140 kDa polypeptide (EC 2.7.7.6) (RNA polymerase II subunit 2) (RPB2) ...	0.49	-	cyt	0	Nucleus				1174
Q10578 UniProt NPD GO	RPB2_CAEEL	DNA-directed RNA polymerase II second largest subunit (EC 2.7.7.6) (RNA polymerase I subunit 2)	0.49	-	cyt	0	Nucleus				1193
Q5QA74 UniProt NPD GO	RPOA_ACOGR	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.49	-	nuc	0	Plastid; chloroplast				337
P92429 UniProt NPD GO	RPOA_AEGTA	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.49	-	cyt	0	Plastid; chloroplast				339
Q85X01 UniProt NPD GO	RPOA_PINKO	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.49	-	cyt	0	Plastid; chloroplast				335

You are viewing entries 25501 to 25550 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.