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
Q23369 UniProt NPD GO	YHDI_CAEEL	Hypothetical protein ZC518.1 in chromosome IV	0.22	-	mit	2 *					499
P34620 UniProt NPD GO	YO84_CAEEL	Hypothetical protein ZK1236.4	0.22	-	cyt	0					364
Q9TC94 UniProt NPD GO	YMF16_NEPOL	Hypothetical tatC-like protein ymf16	0.22	-	end	6 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				247
P69499 UniProt NPD GO	CXI_CONST	I-superfamily conotoxin precursor	0.22	-	mit	1 *	Secreted protein (By similarity)				68
Q7SDZ1 UniProt NPD GO	ISN1_NEUCR	IMP-specific 5'-nucleotidase 1 (EC 3.1.3.-)	0.22	-	end	0					431
P01619 UniProt NPD GO	KV3A_HUMAN	Ig kappa chain V-III region B6	0.22	-	nuc	0					108
Q91612 UniProt NPD GO	IHH_XENLA	Indian hedgehog protein precursor (IHH) (Banded hedgehog protein) (X-BHH) [Contains: Indian hedgehog ...	0.22	+	mit	0	The C-terminal peptide diffuses from the cell, while the N-terminal peptide remains associated with ...				409
P42390 UniProt NPD GO	TRPA_MAIZE	Indole-3-glycerol phosphate lyase, chloroplast precursor (EC 4.1.2.-) (Indole synthase) (Tryptophan ...	0.22	-	mit	0	Plastid; chloroplast (Probable)			1TJR	347
P33085 UniProt NPD GO	SHAKB_DROME	Innexin shaking-B (Protein passover)	0.22	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	gap junction [IEP] integral to membrane [NAS]			372
Q9QXN5 UniProt NPD GO	MIOX_MOUSE	Inositol oxygenase (EC 1.13.99.1) (Myo-inositol oxygenase) (Aldehyde reductase-like 6) (Renal-specif ...	0.22	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [IDA] inclusion body [ISS]			285
P01330 UniProt NPD GO	INS_MYOCO	Insulin [Contains: Insulin B chain; Insulin A chain]	0.22	-	mit	0	Secreted protein				51
P70389 UniProt NPD GO	ALS_MOUSE	Insulin-like growth factor-binding protein complex acid labile chain precursor (ALS)	0.22	-	exc	0	Secreted protein; extracellular space				603
P53708 UniProt NPD GO	ITA8_HUMAN	Integrin alpha-8 precursor [Contains: Integrin alpha-8 heavy chain; Integrin alpha-8 light chain]	0.22	-	end	1	Membrane; single-pass type I membrane protein	integrin complex [TAS]	604063		1063
Q9QYE7 UniProt NPD GO	ITAD_RAT	Integrin alpha-D precursor (CD11d antigen)	0.22	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				1161
P20593 UniProt NPD GO	MX_PERFL	Interferon-induced GTP-binding protein Mx (Fragment)	0.22	-	cyt	0					301
Q8R459 UniProt NPD GO	IL1FA_MOUSE	Interleukin-1 family member 10 (IL-1F10)	0.22	-	nuc	0	Secreted protein (By similarity)				152
P51496 UniProt NPD GO	IL10_MACMU	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.22	-	exc	0	Secreted protein	extracellular region [ISS]			178
P51497 UniProt NPD GO	IL10_MACNE	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.22	-	exc	0	Secreted protein	extracellular region [ISS]			178
Q5Q0V6 UniProt NPD GO	IL10_PAPHA	Interleukin-10 precursor (IL-10) (Cytokine synthesis inhibitory factor) (CSIF)	0.22	-	exc	0	Secreted protein				178
P17108 UniProt NPD GO	IL2_RAT	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.22	-	vac	0	Secreted protein				155
Q9BDX4 UniProt NPD GO	IL3_CANFA	Interleukin-3 precursor (IL-3) (Multipotential colony-stimulating factor) (Hematopoietic growth fact ...	0.22	-	exc	0	Secreted protein	extracellular space [ISS]			143
Q9Y366 UniProt NPD GO	IFT52_HUMAN	Intraflagellar transport 52 homolog (Protein NGD5 homolog)	0.22	-	cyt	0					437
P12966 UniProt NPD GO	IAPP_CAVPO	Islet amyloid polypeptide precursor (Amylin)	0.22	-	mit	0	Secreted protein				92
Q6T267 UniProt NPD GO	ACEA_ASPFU	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.22	-	cyt	0	Peroxisome (By similarity)				538
Q96TP5 UniProt NPD GO	ACEA_COCIM	Isocitrate lyase (EC 4.1.3.1) (Isocitrase) (Isocitratase) (ICL)	0.22	-	cyt	0	Peroxisome (By similarity)				538
Q4R646 UniProt NPD GO	SYIM_MACFA	Isoleucyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS) (F ...	0.22	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				993
P15211 UniProt NPD GO	NEU2_CATCO	Isoticin-neurophysin IT 2 precursor [Contains: Isotocin (IT); Neurophysin IT 2]	0.22	-	exc	0					148
Q15040 UniProt NPD GO	JOS1_HUMAN	Josephin-1 (Josephin domain-containing 1)	0.22	-	mit	0					202
Q5R739 UniProt NPD GO	JOS1_PONPY	Josephin-1 (Josephin domain-containing protein 1)	0.22	-	mit	0					202
P41228 UniProt NPD GO	JAD1C_CRIGR	Jumonji/ARID domain-containing protein 1C (SmcX protein) (Xe169 protein) (Fragment)	0.22	-	mit	0					180
P50425 UniProt NPD GO	CASK_SAITA	Kappa-casein precursor	0.22	-	exc	0	Secreted protein				202
Q96I82 UniProt NPD GO	KAZD1_HUMAN	Kazal-type serine protease inhibitor domain-containing protein 1 precursor	0.22	-	nuc	0	Secreted protein (Probable)		609208		304
Q3LI70 UniProt NPD GO	KR196_HUMAN	Keratin-associated protein 19-6	0.22	-	cyt	1 *					84
Q14943 UniProt NPD GO	KI3S1_HUMAN	Killer cell immunoglobulin-like receptor 3DS1 precursor (MHC class I NK cell receptor) (Natural kill ...	0.22	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	604946		387
Q9JJ57 UniProt NPD GO	KCIP1_MOUSE	Kv channel-interacting protein 1 (KChIP1) (A-type potassium channel modulatory protein 1) (Potassium ...	0.22	-	cyt	0	Cell membrane; peripheral membrane protein				227
Q8R426 UniProt NPD GO	KCIP1_RAT	Kv channel-interacting protein 1 (KChIP1) (A-type potassium channel modulatory protein 1) (Potassium ...	0.22	-	cyt	0	Cell membrane; peripheral membrane protein (By similarity)			1S6C	227
Q9NZI2 UniProt NPD GO	KCIP1_HUMAN	Kv channel-interacting protein 1 (KChIP1) (A-type potassium channel modulatory protein 1) (Potassium ...	0.22	-	cyt	0	Cell membrane; peripheral membrane protein (By similarity)		604660	1S1E	227
Q2KI69 UniProt NPD GO	KCIP4_BOVIN	Kv channel-interacting protein 4 (KChIP4)	0.22	-	mit	0	Cell membrane; peripheral membrane protein (By similarity)				250
Q8HYN7 UniProt NPD GO	KCIP4_MACFA	Kv channel-interacting protein 4 (KChIP4) (A-type potassium channel modulatory protein 4) (Potassium ...	0.22	-	mit	0	Cell membrane; peripheral membrane protein (By similarity)				250
Q99MG9 UniProt NPD GO	KCIP4_RAT	Kv channel-interacting protein 4 (KChIP4) (A-type potassium channel modulatory protein 4) (Potassium ...	0.22	-	mit	0	Cell membrane; peripheral membrane protein				250
Q6PIL6 UniProt NPD GO	KCIP4_HUMAN	Kv channel-interacting protein 4 (KChIP4) (A-type potassium channel modulatory protein 4) (Potassium ...	0.22	-	mit	0	Cell membrane; peripheral membrane protein (By similarity)		608182		250
Q6PHZ8 UniProt NPD GO	KCIP4_MOUSE	Kv channel-interacting protein 4 (KChIP4) (A-type potassium channel modulatory protein 4) (Potassium ...	0.22	-	mit	0	Cell membrane; peripheral membrane protein				250
Q9CQF6 UniProt NPD GO	ADPPT_MOUSE	L-aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase (EC 2.7.8.-) (4'-phosphopa ...	0.22	-	mit	0	Cytoplasm (By similarity)				309
Q9FFL3 UniProt NPD GO	LBD35_ARATH	LOB domain-containing protein 35	0.22	-	nuc	0					206
P14632 UniProt NPD GO	TRFL_PIG	Lactotransferrin precursor (EC 3.4.21.-) (Lactoferrin)	0.22	-	exc	0	Secreted protein				704
O89112 UniProt NPD GO	LANC1_MOUSE	LanC-like protein 1 (40 kDa erythrocyte membrane protein) (p40)	0.22	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				399
Q80TR1 UniProt NPD GO	LPHN1_MOUSE	Latrophilin-1 (Calcium-independent alpha-latrotoxin receptor 1) (Lectomedin-2) (Fragment)	0.22	-	end	7	Membrane; multi-pass membrane protein				1406
O88917 UniProt NPD GO	LPHN1_RAT	Latrophilin-1 precursor (Calcium-independent alpha-latrotoxin receptor 1) (CIRL-1)	0.22	-	end	8 *	Membrane; multi-pass membrane protein				1515
P11219 UniProt NPD GO	AGI_ORYSA	Lectin precursor (Agglutinin) [Contains: Lectin 10 kDa peptide; Lectin 8 kDa peptide]	0.22	-	exc	0					227
P49046 UniProt NPD GO	LEGU_CANEN	Legumain precursor (EC 3.4.22.34) (Asparaginyl endopeptidase)	0.22	-	exc	0					475

You are viewing entries 48551 to 48600 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.