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
Q9HB21 UniProt NPD GO	PKHA1_HUMAN	Pleckstrin homology domain-containing family A member 1 (Tandem PH domain-containing protein 1) (TAP ...	0.66	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein. Nucleus. Locates to the plasma membrane after ...		607772	1EAZ	404
P51805 UniProt NPD GO	PLXA3_HUMAN	Plexin-A3 precursor (Plexin-4) (Semaphorin receptor SEX)	0.66	-	end	0	Membrane; single-pass type I membrane protein (Potential)	membrane [TAS]	300022		1871
Q5KKY3 UniProt NPD GO	PFS2_CRYNE	Polyadenylation factor subunit 2	0.66	+	nuc	0	Nucleus (By similarity)				712
Q61423 UniProt NPD GO	KCNA4_MOUSE	Potassium voltage-gated channel subfamily A member 4 (Voltage-gated potassium channel subunit Kv1.4) ...	0.66	+	end	3	Membrane; multi-pass membrane protein				654
Q9QWS8 UniProt NPD GO	KCNH8_RAT	Potassium voltage-gated channel subfamily H member 8 (Voltage-gated potassium channel subunit Kv12.1 ...	0.66	-	end	6	Membrane; multi-pass membrane protein				1102
O43526 UniProt NPD GO	KCNQ2_HUMAN	Potassium voltage-gated channel subfamily KQT member 2 (Voltage-gated potassium channel subunit Kv7. ...	0.66	-	nuc	5	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	606437		872
O43525 UniProt NPD GO	KCNQ3_HUMAN	Potassium voltage-gated channel subfamily KQT member 3 (Voltage-gated potassium channel subunit Kv7. ...	0.66	-	end	5	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	602232		872
Q8K3F6 UniProt NPD GO	KCNQ3_MOUSE	Potassium voltage-gated channel subfamily KQT member 3 (Voltage-gated potassium channel subunit Kv7. ...	0.66	-	end	5	Membrane; multi-pass membrane protein (By similarity)				873
O88944 UniProt NPD GO	KCNQ3_RAT	Potassium voltage-gated channel subfamily KQT member 3 (Voltage-gated potassium channel subunit Kv7. ...	0.66	-	end	5	Membrane; multi-pass membrane protein				873
Q9JKB0 UniProt NPD GO	HCN1_RAT	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1	0.66	-	nuc	2	Membrane; multi-pass membrane protein				910
O88704 UniProt NPD GO	HCN1_MOUSE	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1 (Brain cyclic nucleot ...	0.66	-	nuc	2	Membrane; multi-pass membrane protein	axon [IDA]			910
P26023 UniProt NPD GO	PIG1_DROME	Pre-intermoult gene 1 protein precursor (Gland-specific protein)	0.66	+	exc	0					187
Q8BM39 UniProt NPD GO	PRP18_MOUSE	Pre-mRNA-splicing factor 18 (PRP18 homolog)	0.66	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Colocalizes with spliceosomal snRNPs (By simi ...				342
P52868 UniProt NPD GO	CWC23_YEAST	Pre-mRNA-splicing factor CWC23 (Complexed with CEF1 protein 23)	0.66	-	nuc	0	Cytoplasm. Nucleus	spliceosome complex [IPI]			283
P28004 UniProt NPD GO	PRP45_YEAST	Pre-mRNA-splicing factor PRP45 (Pre-mRNA-processing protein 45)	0.66	-	mit	0	Nucleus	nucleus [IDA]			379
P38241 UniProt NPD GO	SLT11_YEAST	Pre-mRNA-splicing factor SLT11 (Synthetic lethality with U2 protein 11) (Extracellular matrix protei ...	0.66	-	nuc	0	Nucleus	nucleus [IDA]			364
Q6CPI4 UniProt NPD GO	SYF2_KLULA	Pre-mRNA-splicing factor SYF2	0.66	-	nuc	0	Nucleus (By similarity)				221
Q4WDD0 UniProt NPD GO	CWC21_ASPFU	Pre-mRNA-splicing factor cwc21	0.66	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				217
Q4ICM9 UniProt NPD GO	PAM17_GIBZE	Presequence translocated-associated motor subunit PAM17, mitochondrial precursor	0.66	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				235
Q5BGF9 UniProt NPD GO	PAM17_EMENI	Presequence translocated-associated motor subunit pam17, mitochondrial precursor	0.66	-	nuc	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				243
Q9CAF6 UniProt NPD GO	GYRA_ARATH	Probable DNA gyrase subunit A, chloroplast/mitochondrial precursor (EC 5.99.1.3)	0.66	-	mit	0	Plastid; chloroplast. Mitochondrion				950
Q86SP6 UniProt NPD GO	GP149_HUMAN	Probable G-protein coupled receptor 149 (G-protein coupled receptor PGR10)	0.66	-	end	7 *	Membrane; multi-pass membrane protein				731
Q9V333 UniProt NPD GO	JHD3A_DROME	Probable JmjC domain-containing histone demethylation protein 3A (EC 1.14.11.-)	0.66	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			495
Q5KER0 UniProt NPD GO	TAH18_CRYNE	Probable NADPH reductase TAH18 (EC 1.-.-.-)	0.66	-	mit	0					617
P59583 UniProt NPD GO	WRK32_ARATH	Probable WRKY transcription factor 32 (WRKY DNA-binding protein 32)	0.66	-	nuc	0	Nucleus (Probable)				466
Q9CAR4 UniProt NPD GO	WRK36_ARATH	Probable WRKY transcription factor 36 (WRKY DNA-binding protein 36)	0.66	-	nuc	0	Nucleus (Potential)				387
Q93WV7 UniProt NPD GO	WRK67_ARATH	Probable WRKY transcription factor 67 (WRKY DNA-binding protein 67)	0.66	-	nuc	0	Nucleus (Probable)				254
Q9VYQ5 UniProt NPD GO	CP318_DROME	Probable cytochrome P450 318a1 (EC 1.14.-.-) (CYPCCCXVIIIA1)	0.66	+	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				536
P34548 UniProt NPD GO	SQV3_CAEEL	Probable galactosyltransferase sqv-3 (EC 2.4.1.-) (Squashed vulva protein 3)	0.66	+	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				289
Q6C3V4 UniProt NPD GO	NUF2_YARLI	Probable kinetochore protein NUF2	0.66	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				452
Q2UEA0 UniProt NPD GO	NUF2_ASPOR	Probable kinetochore protein nuf2	0.66	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				463
P32660 UniProt NPD GO	ATC5_YEAST	Probable phospholipid-transporting ATPase DNF1 (EC 3.6.3.1)	0.66	-	end	9	Membrane; multi-pass membrane protein	mitochondrion [IDA] plasma membrane [IDA]			1571
Q12675 UniProt NPD GO	ATC4_YEAST	Probable phospholipid-transporting ATPase DNF2 (EC 3.6.3.1)	0.66	-	end	9	Membrane; multi-pass membrane protein	plasma membrane [IDA]			1612
Q7ZTZ2 UniProt NPD GO	RLP24_BRARE	Probable ribosome biogenesis protein RLP24	0.66	+	nuc	0	Nucleus; nucleolus (By similarity)				161
Q10441 UniProt NPD GO	TILS_SCHPO	Probable tRNA(Ile)-lysidine synthase (EC 6.3.4.-) (tRNA(Ile)-lysidine synthetase) (tRNA(Ile)-2-lysyl ...	0.66	-	nuc	0	Cytoplasm (Probable)				456
P79522 UniProt NPD GO	PRR3_HUMAN	Proline-rich protein 3 (MHC class I region proline-rich protein CAT56)	0.66	-	nuc	0					188
Q92824 UniProt NPD GO	PCSK5_HUMAN	Proprotein convertase subtilisin/kexin type 5 precursor (EC 3.4.21.-) (Proprotein convertase PC5) (S ...	0.66	-	nuc	0	Secreted protein (By similarity)	extracellular space [TAS]	600488		913
P01347 UniProt NPD GO	REL1_RAT	Prorelaxin 1 precursor [Contains: Relaxin B chain; Relaxin A chain]	0.66	-	exc	0	Secreted protein				186
P38822 UniProt NPD GO	BZZ1_YEAST	Protein BZZ1	0.66	-	nuc	0		actin cortical patch [IDA] cytoplasm [IDA]			633
O74522 UniProt NPD GO	YQKA_SCHPO	Protein C1494.10 in chromosome III	0.66	-	nuc	0	Cytoplasm. Nucleus				964
Q8K190 UniProt NPD GO	CF064_MOUSE	Protein C6orf64 homolog	0.66	-	nuc	1					188
Q8N350 UniProt NPD GO	DOS_HUMAN	Protein Dos	0.66	-	nuc	1 *					725
Q9D9J2 UniProt NPD GO	EAN57_MOUSE	Protein EAN57	0.66	-	nuc	0					266
Q9GLZ5 UniProt NPD GO	FA40A_MACFA	Protein FAM40A	0.66	-	end	0					837
Q5R7S4 UniProt NPD GO	FA40A_PONPY	Protein FAM40A	0.66	-	end	0					837
Q08023 UniProt NPD GO	FMP25_YEAST	Protein FMP25, mitochondrial precursor (Found in mitochondrial proteome protein 25)	0.66	-	nuc	1	Mitochondrion. Mitochondrial membrane; single-pass membrane protein (Potential)	mitochondrion [IDA]			583
Q02508 UniProt NPD GO	HGV2_HALRO	Protein HGV2	0.66	-	nuc	0	Nucleus				510
P47135 UniProt NPD GO	JSN1_YEAST	Protein JSN1 (Protein PUF1)	0.66	-	nuc	0					1091
P32336 UniProt NPD GO	NUD1_YEAST	Protein NUD1	0.66	-	nuc	0	Localizes to the meiotic outer plaque of the SPB, at the end of the meiotic spindles	spindle pole body [IDA]			851
P32896 UniProt NPD GO	PDC2_YEAST	Protein PDC2	0.66	-	nuc	0		nucleus [IC]			925

You are viewing entries 15951 to 16000 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.