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
Q810Y4 UniProt NPD GO	CONA1_RAT	Collagen alpha-1(XXIII) chain	0.16	-	nuc	0	Membrane; single-pass type II membrane protein				532
Q14055 UniProt NPD GO	CO9A2_HUMAN	Collagen alpha-2(IX) chain precursor	0.16	-	exc	0		collagen type IX [TAS]	603932		689
P20023 UniProt NPD GO	CR2_HUMAN	Complement receptor type 2 precursor (Cr2) (Complement C3d receptor) (Epstein-Barr virus receptor) ( ...	0.16	-	exc	1 *	Membrane; single-pass type I membrane protein	integral to membrane [NAS] plasma membrane [NAS]	120650	1W2S	1033
P83390 UniProt NPD GO	CX_CONAA	Conotoxin	0.16	-	mit	0	Secreted protein				27
P12960 UniProt NPD GO	CNTN1_MOUSE	Contactin-1 precursor (Neural cell surface protein F3)	0.16	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				1020
Q63198 UniProt NPD GO	CNTN1_RAT	Contactin-1 precursor (Neural cell surface protein F3)	0.16	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				1021
P70705 UniProt NPD GO	ATP7A_RAT	Copper-transporting ATPase 1 (EC 3.6.3.4) (Copper pump 1) (Menkes disease-associated protein homolog ...	0.16	-	end	8	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; multi-pass membrane protein (By ...				1492
Q10996 UniProt NPD GO	LCRP_PETMA	Corticostatin-related peptide LCRP	0.16	-		0	Secreted protein				19
P00566 UniProt NPD GO	KCRM_TORMA	Creatine kinase M-type (EC 2.7.3.2) (Creatine kinase M chain) (M-CK) (NU-2 protein)	0.16	-	cyt	0	Cytoplasm				381
P80363 UniProt NPD GO	CCB23_ORCLI	Crustacean calcium-binding protein 23 (CCBP-23 protein)	0.16	-	cyt	0					202
P60177 UniProt NPD GO	TXC2_HOLCU	Curtatoxin-2 (CT-II)	0.16	-	nuc	0	Secreted protein				38
P12114 UniProt NPD GO	SQT1_CAEEL	Cuticle collagen sqt-1 (Protein squat-1) (Protein roller-5)	0.16	-	nuc	1 *					324
P83353 UniProt NPD GO	CU13_LIMPO	Cuticle protein 13 (LpCP13)	0.16	-	nuc	0					110
P32964 UniProt NPD GO	CYHY_GLOSO	Cyanide hydratase (EC 4.2.1.66) (Formamide hydrolyase)	0.16	-	cyt	0					368
Q62398 UniProt NPD GO	CNGA2_MOUSE	Cyclic nucleotide-gated olfactory channel (Cyclic nucleotide-gated cation channel 2) (CNG channel 2) ...	0.16	-	vac	3	Membrane; multi-pass membrane protein				664
Q5SCB5 UniProt NPD GO	CCND_OSTTA	Cyclin-D	0.16	-	mit	0					374
Q58CN7 UniProt NPD GO	CDKA2_BOVIN	Cyclin-dependent kinase 2-associated protein 2 (CDK2-associated protein 2) (DOC-1-related protein) ( ...	0.16	-	nuc	0					127
O75956 UniProt NPD GO	CDKA2_HUMAN	Cyclin-dependent kinase 2-associated protein 2 (CDK2-associated protein 2) (DOC-1-related protein) ( ...	0.16	-	nuc	0					126
P53780 UniProt NPD GO	METC_ARATH	Cystathionine beta-lyase, chloroplast precursor (EC 4.4.1.8) (CBL) (Beta-cystathionase) (Cysteine ly ...	0.16	-	mit	0	Plastid; chloroplast			1IBJ	464
P55217 UniProt NPD GO	METB_ARATH	Cystathionine gamma-synthase, chloroplast precursor (EC 2.5.1.48) (CGS) (O-succinylhomoserine (thiol ...	0.16	-	nuc	0	Plastid; chloroplast				563
P01035 UniProt NPD GO	CYTC_BOVIN	Cystatin C precursor (Colostrum thiol proteinase inhibitor)	0.16	-	exc	1 *					148
Q6GPU1 UniProt NPD GO	ATG4A_XENLA	Cysteine protease ATG4A (EC 3.4.22.-) (Autophagy-related protein 4 homolog A)	0.16	-	cyt	0	Cytoplasm (Probable)				397
Q10716 UniProt NPD GO	CYSP1_MAIZE	Cysteine proteinase 1 precursor (EC 3.4.22.-)	0.16	-	exc	0					371
P16563 UniProt NPD GO	CRIS2_MOUSE	Cysteine-rich secretory protein 2 precursor (CRISP-2) (Testis-specific protein TPX-1)	0.16	-	exc	0	Secreted protein (Probable)			2A05	243
Q8UW25 UniProt NPD GO	CRVP1_LAPHA	Cysteine-rich venom protein 1 precursor (CRVP)	0.16	-	exc	0	Secreted protein				238
Q8UW11 UniProt NPD GO	CRVP2_LAPHA	Cysteine-rich venom protein 2 precursor (CRVP)	0.16	-	exc	0	Secreted protein				238
P32320 UniProt NPD GO	CDD_HUMAN	Cytidine deaminase (EC 3.5.4.5) (Cytidine aminohydrolase)	0.16	+	nuc	0		cytosol [TAS] extracellular region [TAS]	123920	1MQ0	146
O19074 UniProt NPD GO	CMAH_PIG	Cytidine monophosphate-N-acetylneuraminic acid hydroxylase (EC 1.14.18.2) (CMP-N-acetylneuraminate m ...	0.16	-	cyt	0	Cytoplasm (By similarity)				435
P33273 UniProt NPD GO	CP2CO_RAT	Cytochrome P450 2C24 (EC 1.14.14.1) (CYPIIC24) (P450-PROS2) (Fragment)	0.16	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein				434
Q64464 UniProt NPD GO	CP3AD_MOUSE	Cytochrome P450 3A13 (EC 1.14.14.1) (CYPIIIA13)	0.16	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	membrane fraction [ISS]			503
P05184 UniProt NPD GO	CP3A3_HUMAN	Cytochrome P450 3A3 (EC 1.14.14.1) (CYPIIIA3) (HLp)	0.16	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein	cell surface [IEP] membrane fraction [ISS] microsome [TAS]			503
P08684 UniProt NPD GO	CP3A4_HUMAN	Cytochrome P450 3A4 (EC 1.14.13.67) (Quinine 3-monooxygenase) (CYPIIIA4) (Nifedipine oxidase) (Tauro ...	0.16	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein	membrane fraction [ISS]	124010	1W0G	502
Q9Y757 UniProt NPD GO	CP52L_DEBHA	Cytochrome P450 52A12 (EC 1.14.14.-) (Alkane hydroxylase 1) (Alkane-inducible p450alk 1) (DH-ALK2)	0.16	-	cyt	1 *					519
P43083 UniProt NPD GO	CP52V_CANAP	Cytochrome P450 52E1 (EC 1.14.14.-) (CYPLIIE1)	0.16	-	end	2 *					519
O49342 UniProt NPD GO	C71AD_ARATH	Cytochrome P450 71A13 (EC 1.14.-.-)	0.16	-	nuc	0					497
Q9STL0 UniProt NPD GO	C71AN_ARATH	Cytochrome P450 71A23 (EC 1.14.-.-)	0.16	-	end	1 *					483
Q9LVD2 UniProt NPD GO	C71BA_ARATH	Cytochrome P450 71B10 (EC 1.14.-.-)	0.16	-	mit	2 *					502
Q9LTL2 UniProt NPD GO	C71BP_ARATH	Cytochrome P450 71B25 (EC 1.14.-.-)	0.16	-	mit	0					501
O65785 UniProt NPD GO	C71B3_ARATH	Cytochrome P450 71B3 (EC 1.14.-.-)	0.16	-	end	1 *					501
Q9UNU6 UniProt NPD GO	CP8B1_HUMAN	Cytochrome P450 8B1 (EC 1.14.13.95) (CYPVIIIB1) (7-alpha-hydroxycholest-4-en-3-one 12-alpha-hydroxyl ...	0.16	-	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein		602172		501
Q5AL10 UniProt NPD GO	COX19_CANAL	Cytochrome c oxidase assembly protein COX19	0.16	-	nuc	0	Cytoplasm (By similarity). Mitochondrion; mitochondrial intermembrane space (By similarity)				133
Q9N234 UniProt NPD GO	CX7A1_PRECR	Cytochrome c oxidase polypeptide VIIa-heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.16	-	mit	1	Mitochondrion; mitochondrial inner membrane (By similarity)				79
P24310 UniProt NPD GO	CX7A1_HUMAN	Cytochrome c oxidase polypeptide VIIa-heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.16	-	mit	1	Mitochondrion; mitochondrial inner membrane	mitochondrion [TAS]	123995		79
Q9CPQ1 UniProt NPD GO	COX6C_MOUSE	Cytochrome c oxidase polypeptide VIc (EC 1.9.3.1)	0.16	-	mit	1 *	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA] mitochondrion [IDA]			75
P80971 UniProt NPD GO	COX42_THUOB	Cytochrome c oxidase subunit 4 isoform 2, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxidase ...	0.16	-	nuc	1	Mitochondrion; mitochondrial inner membrane				176
Q7YRK6 UniProt NPD GO	CX6B1_TARSY	Cytochrome c oxidase subunit VIb isoform 1 (EC 1.9.3.1) (COX VIb-1)	0.16	-	nuc	0					85
Q5KIK5 UniProt NPD GO	CCPR_CRYNE	Cytochrome c peroxidase, mitochondrial precursor (EC 1.11.1.5) (CCP)	0.16	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				377
P0C0V3 UniProt NPD GO	CCPR_EMENI	Cytochrome c peroxidase, mitochondrial precursor (EC 1.11.1.5) (CCP)	0.16	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				361
P20114 UniProt NPD GO	CY1_EUGGR	Cytochrome c1, heme protein	0.16	-	cyt	0	Mitochondrion; mitochondrial intermembrane space				243
Q8R4S8 UniProt NPD GO	CRLF2_RAT	Cytokine receptor-like factor 2 precursor (Thymic stromal lymphopoietin protein receptor) (TSLPR)	0.16	-	end	1	Membrane; single-pass type I membrane protein (Probable)				360

You are viewing entries 55501 to 55550 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.