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
P06378 UniProt NPD GO	RK2_MARPO	Chloroplast 50S ribosomal protein L2	0.65	-	nuc	0	Plastid; chloroplast				277
P11534 UniProt NPD GO	RK2_WHEAT	Chloroplast 50S ribosomal protein L2	0.65	+	nuc	0	Plastid; chloroplast				273
P12197 UniProt NPD GO	RK32_ORYSA	Chloroplast 50S ribosomal protein L32	0.65	-	nuc	0	Plastid; chloroplast				62
Q6CND0 UniProt NPD GO	EAF3_KLULA	Chromatin modification-related protein EAF3	0.65	-	nuc	0	Nucleus (By similarity)				358
Q8IWY9 UniProt NPD GO	CDAN1_HUMAN	Codanin-1	0.65	-	end	0			607465		1226
Q8R344 UniProt NPD GO	CCD12_MOUSE	Coiled-coil domain-containing protein 12	0.65	+	nuc	0					166
Q95J40 UniProt NPD GO	CCDC7_MACFA	Coiled-coil domain-containing protein 7	0.65	-	nuc	0					477
Q5RCA7 UniProt NPD GO	CCD91_PONPY	Coiled-coil domain-containing protein 91 (GGA-binding partner)	0.65	-	nuc	0	Membrane; peripheral membrane protein (By similarity). Golgi apparatus; trans-Golgi network; trans-G ...				405
Q7Z6B0 UniProt NPD GO	CCD91_HUMAN	Coiled-coil domain-containing protein 91 (GGA-binding partner) (p56 accessory protein)	0.65	-	nuc	0	Membrane; peripheral membrane protein. Golgi apparatus; trans-Golgi network; trans-Golgi network mem ...			1OM9	441
Q9CRB9 UniProt NPD GO	CHCH3_MOUSE	Coiled-coil-helix-coiled-coil-helix domain-containing protein 3	0.65	-	nuc	0		mitochondrial inner membrane [IDA] mitochondrion [IDA]			227
Q13617 UniProt NPD GO	CUL2_HUMAN	Cullin-2 (CUL-2)	0.65	-	cyt	0			603135		745
Q5RCF3 UniProt NPD GO	CUL2_PONPY	Cullin-2 (CUL-2)	0.65	-	cyt	0					745
Q9D5V5 UniProt NPD GO	CUL5_MOUSE	Cullin-5 (CUL-5)	0.65	-	nuc	0					780
Q5RB36 UniProt NPD GO	CUL5_PONPY	Cullin-5 (CUL-5)	0.65	-	nuc	0					780
Q93034 UniProt NPD GO	CUL5_HUMAN	Cullin-5 (CUL-5) (Vasopressin-activated calcium-mobilizing receptor) (VACM-1)	0.65	-	nuc	0			601741		780
O65718 UniProt NPD GO	CNGC2_ARATH	Cyclic nucleotide-gated ion channel 2 (AtCNGC2) (Cyclic nucleotide-and calmodulin-regulated ion chan ...	0.65	-	end	7	Cell membrane; multi-pass membrane protein (Potential)				726
P34158 UniProt NPD GO	CFTR_RAT	Cystic fibrosis transmembrane conductance regulator (CFTR) (cAMP-dependent chloride channel) (ATP-bi ...	0.65	-	mit	2	Membrane; multi-pass membrane protein	apical plasma membrane [IDA] cytoplasmic vesicle membrane [IDA]			524
Q09128 UniProt NPD GO	CP24A_RAT	Cytochrome P450 24A1, mitochondrial precursor (EC 1.14.-.-) (P450-CC24) (Vitamin D(3) 24-hydroxylase ...	0.65	-	nuc	0	Mitochondrion				514
P24464 UniProt NPD GO	CP4AC_RAT	Cytochrome P450 4A12 (EC 1.14.14.1) (CYPIVA12) (CYPIVA8) (P450-KP1) (P450-PP1)	0.65	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	microsome [TAS]			508
Q9HCS2 UniProt NPD GO	CP4FC_HUMAN	Cytochrome P450 4F12 (EC 1.14.14.1) (CYPIVF12)	0.65	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				524
Q9VS79 UniProt NPD GO	CP4D8_DROME	Cytochrome P450 4d8 (EC 1.14.-.-) (CYPIVD8)	0.65	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				463
Q9SB89 UniProt NPD GO	RH27_ARATH	DEAD-box ATP-dependent RNA helicase 27 (EC 3.6.1.-)	0.65	+	nuc	0					633
Q9LRE6 UniProt NPD GO	DPOD1_ORYSA	DNA polymerase delta catalytic subunit (EC 2.7.7.7)	0.65	+	cyt	0	Nucleus				1105
O48901 UniProt NPD GO	DPOD1_SOYBN	DNA polymerase delta catalytic subunit (EC 2.7.7.7)	0.65	+	cyt	0	Nucleus				1088
Q642A5 UniProt NPD GO	DPOE3_RAT	DNA polymerase epsilon subunit 3 (EC 2.7.7.7) (DNA polymerase II subunit 3) (DNA polymerase epsilon ...	0.65	-	nuc	0	Nucleus (Potential)				145
Q9JKP7 UniProt NPD GO	DPOE3_MOUSE	DNA polymerase epsilon subunit 3 (EC 2.7.7.7) (DNA polymerase II subunit 3) (DNA polymerase epsilon ...	0.65	-	nuc	0	Nucleus (Potential)				145
Q9JJN0 UniProt NPD GO	POLH_MOUSE	DNA polymerase eta (EC 2.7.7.7) (RAD30 homolog A) (Xeroderma pigmentosum variant type protein homolo ...	0.65	-	nuc	0	Nucleus (By similarity). Accumulates at replication forks after DNA damage (By similarity)	nucleus [TAS]			694
Q5XG87 UniProt NPD GO	POLS_HUMAN	DNA polymerase sigma (EC 2.7.7.7) (Topoisomerase-related function protein 4-1) (TRF4-1) (LAK-1) (DNA ...	0.65	-	nuc	0	Nucleus (Probable)	nucleus [IDA]	605198		542
Q7KQM1 UniProt NPD GO	PRI1_PLAF7	DNA primase small subunit (EC 2.7.7.-) (DNA primase 53 kDa subunit)	0.65	-	cyt	0					452
Q25998 UniProt NPD GO	PRI1_PLAFK	DNA primase small subunit (EC 2.7.7.-) (DNA primase 53 kDa subunit)	0.65	-	cyt	0					452
P53091 UniProt NPD GO	MCM6_YEAST	DNA replication licensing factor MCM6 (Minichromosome maintenance protein 6)	0.65	+	nuc	0	Nucleus (Potential)	cytoplasm [IDA] MCM complex [IDA] nucleus [IDA] pre-replicative complex [IDA]			1017
Q91876 UniProt NPD GO	MCM7A_XENLA	DNA replication licensing factor mcm7-A (Minichromosome maintenance protein 7-A) (xMCM7-A) (CDC47 ho ...	0.65	-	cyt	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	chromatin [IDA] MCM complex [IDA]			720
P16989 UniProt NPD GO	DBPA_HUMAN	DNA-binding protein A (Cold shock domain-containing protein A) (Single-strand DNA-binding protein NF ...	0.65	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [TAS]	603437		372
Q01981 UniProt NPD GO	CREA_EMENI	DNA-binding protein creA (Carbon catabolite repressor)	0.65	-	nuc	0	Nucleus				416
Q3BAP8 UniProt NPD GO	RPOB_PHAAO	DNA-directed RNA polymerase beta chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit be ...	0.65	-	cyt	0	Plastid; chloroplast				1091
Q56P12 UniProt NPD GO	RPOC1_LACSA	DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase beta' sub ...	0.65	-	cyt	0	Plastid; chloroplast				689
O13993 UniProt NPD GO	RPOM_SCHPO	DNA-directed RNA polymerase, mitochondrial precursor (EC 2.7.7.6)	0.65	-	cyt	0	Mitochondrion				1120
Q8VDR9 UniProt NPD GO	DOCK6_MOUSE	Dedicator of cytokinesis protein 6 (Fragment)	0.65	-	cyt	0					849
Q9CWH0 UniProt NPD GO	DPPA2_MOUSE	Developmental pluripotency-associated protein 2 (Pluripotent embryonic stem cell-related protein 1)	0.65	-	nuc	0	Nucleus				301
Q9UBT3 UniProt NPD GO	DKK4_HUMAN	Dickkopf-related protein 4 precursor (Dkk-4) (Dickkopf-4) (hDkk-4) [Contains: Dickkopf-related prote ...	0.65	-	exc	0	Secreted protein		605417		224
Q8N7S2 UniProt NPD GO	DNJ5G_HUMAN	DnaJ homolog subfamily C member 5G (Gamma cysteine string protein) (Gamma-CSP)	0.65	-	nuc	0	Membrane; lipid-anchor (By similarity)				189
Q8LFV3 UniProt NPD GO	DOF33_ARATH	Dof zinc finger protein DOF3.3 (AtDOF3.3) (H-protein promoter-binding factor 2a)	0.65	-	nuc	0	Nucleus (Probable)				448
Q8LAP8 UniProt NPD GO	DOF46_ARATH	Dof zinc finger protein DOF4.6 (AtDOF4.6)	0.65	-	nuc	0	Nucleus (Probable)				342
P32829 UniProt NPD GO	MRE11_YEAST	Double-strand break repair protein MRE11	0.65	-	nuc	0	Nucleus	mitochondrion [IDA] Mre11 complex [IPI] nucleus [IDA]			692
Q9MZF4 UniProt NPD GO	DUOX1_CANFA	Dual oxidase 1 precursor (EC 1.6.3.1) (EC 1.11.1.-) (NADPH thyroid oxidase 1) (Thyroid oxidase 1)	0.65	-	end	6	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Localizes to the a ...	apical plasma membrane [NAS]			1551
Q9Y6W6 UniProt NPD GO	DUS10_HUMAN	Dual specificity protein phosphatase 10 (EC 3.1.3.48) (EC 3.1.3.16) (Mitogen-activated protein kinas ...	0.65	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [TAS] nucleus [TAS]	608867		482
Q8K1M6 UniProt NPD GO	DNM1L_MOUSE	Dynamin-1-like protein (EC 3.6.5.5) (Dynamin-related protein 1) (Dynamin family member proline-rich ...	0.65	-	nuc	0	Cytoplasm; cytosol (By similarity). Mainly. Intracellular membrane; peripheral membrane protein (By ...				742
Q96PU5 UniProt NPD GO	NED4L_HUMAN	E3 ubiquitin-protein ligase NEDD4-like protein (EC 6.3.2.-) (Nedd4-2) (NEDD4.2)	0.65	-	nuc	0	Cytoplasm	intracellular [IC]	606384		975
Q811X5 UniProt NPD GO	EAF2_RAT	ELL-associated factor 2 (Testosterone-regulated apoptosis inducer and tumor suppressor protein)	0.65	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Colocalizes with ELL to nuclear speckles (By ...				262
Q08230 UniProt NPD GO	EMI5_YEAST	Early meiotic induction protein 5, mitochondrial precursor	0.65	-	nuc	0	Mitochondrion	mitochondrion [IDA]			162

You are viewing entries 16251 to 16300 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.