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
Q31652 UniProt NPD GO	CYB_ANSCE	Cytochrome b (Fragment)	0.08	-	mit	1 *					74
Q4G380 UniProt NPD GO	PSBE_EMIHU	Cytochrome b559 alpha subunit (PSII reaction center subunit V)	0.08	-	cyt	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				84
P10897 UniProt NPD GO	CY561_BOVIN	Cytochrome b561 (Cytochrome b-561)	0.08	-	end	6 *	Secretory vesicle; secretory vesicle membrane; multi-pass membrane protein. Secretory vesicles conta ...				252
Q95204 UniProt NPD GO	CY561_SHEEP	Cytochrome b561 (Cytochrome b-561)	0.08	-	end	6 *	Secretory vesicle; secretory vesicle membrane; multi-pass membrane protein (By similarity). Secretor ...				252
Q641Y1 UniProt NPD GO	C56D2_RAT	Cytochrome b561 domain-containing protein 2	0.08	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				222
Q9WUE3 UniProt NPD GO	C56D2_MOUSE	Cytochrome b561 domain-containing protein 2 (Putative tumor suppressor protein 101F6)	0.08	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				222
P00059 UniProt NPD GO	CYC_ABUTH	Cytochrome c	0.08	-	nuc	0	Mitochondrion; mitochondrial matrix				111
P00063 UniProt NPD GO	CYC_ACENE	Cytochrome c	0.08	-	nuc	0	Mitochondrion; mitochondrial matrix				112
P00020 UniProt NPD GO	CYC_ANAPL	Cytochrome c	0.08	-	cyt	0	Mitochondrion; mitochondrial matrix	cytosol [ISS] mitochondrial intermembrane space [ISS]			104
P00030 UniProt NPD GO	CYC_EISFO	Cytochrome c	0.08	-	cyt	0	Mitochondrion; mitochondrial matrix				108
P00058 UniProt NPD GO	CYC_GOSBA	Cytochrome c	0.08	-	nuc	0	Mitochondrion; mitochondrial matrix				111
P00042 UniProt NPD GO	CYC_HANAN	Cytochrome c	0.08	-	mit	0	Mitochondrion; mitochondrial matrix				109
P00048 UniProt NPD GO	CYC_NEUCR	Cytochrome c	0.08	-	cyt	0	Mitochondrion; mitochondrial matrix				107
O93863 UniProt NPD GO	CYC_PACTA	Cytochrome c	0.08	-	mit	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				109
P00062 UniProt NPD GO	CYC_SAMNI	Cytochrome c	0.08	-	nuc	0	Mitochondrion; mitochondrial matrix				111
Q41346 UniProt NPD GO	CYC_STELP	Cytochrome c	0.08	-	cyt	0	Mitochondrion; mitochondrial matrix				108
P21665 UniProt NPD GO	CYC_VARVA	Cytochrome c	0.08	-	cyt	0	Mitochondrion; mitochondrial matrix				104
Q640U4 UniProt NPD GO	CYC_XENTR	Cytochrome c	0.08	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				104
P56770 UniProt NPD GO	CCSA_ARATH	Cytochrome c biogenesis protein ccsA	0.08	-	end	7 *	Plastid; chloroplast				328
P00045 UniProt NPD GO	CYC7_YEAST	Cytochrome c iso-2	0.08	-	nuc	0	Mitochondrion; mitochondrial intermembrane space	mitochondrial intermembrane space [IDA]		1YTC	113
Q863F9 UniProt NPD GO	COX81_TARSY	Cytochrome c oxidase polypeptide VIII-heart, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxid ...	0.08	-	mit	0	Mitochondrion; mitochondrial inner membrane				70
Q5RC38 UniProt NPD GO	CX6A2_PONPY	Cytochrome c oxidase polypeptide VIa-heart, mitochondrial precursor (EC 1.9.3.1) (COXVIAH)	0.08	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				97
Q7YRK0 UniProt NPD GO	COX6C_CALDO	Cytochrome c oxidase polypeptide VIc precursor (EC 1.9.3.1)	0.08	-	mit	1 *	Mitochondrion; mitochondrial inner membrane				75
Q7YRJ8 UniProt NPD GO	COX6C_NYCCO	Cytochrome c oxidase polypeptide VIc precursor (EC 1.9.3.1)	0.08	-	mit	1 *	Mitochondrion; mitochondrial inner membrane				75
Q8VY40 UniProt NPD GO	CX5C1_HELAN	Cytochrome c oxidase polypeptide Vc-1 (EC 1.9.3.1) (Cytochrome c oxidase subunit 5c-1)	0.08	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				63
Q8VY39 UniProt NPD GO	CX5C2_HELAN	Cytochrome c oxidase polypeptide Vc-2 (EC 1.9.3.1) (Cytochrome c oxidase subunit 5c-2)	0.08	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				64
P18943 UniProt NPD GO	COX1_CHICK	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.08	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				515
Q35536 UniProt NPD GO	COX1_PETMA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.08	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				517
P92692 UniProt NPD GO	COX1_PONPA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.08	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				514
O21399 UniProt NPD GO	COX1_STRCA	Cytochrome c oxidase subunit 1 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide I)	0.08	-	end	12 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				516
P29870 UniProt NPD GO	COX2_ACHDO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.08	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P50267 UniProt NPD GO	COX2_APIFL	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.08	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				225
O47669 UniProt NPD GO	COX2_CANAU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.08	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P67780 UniProt NPD GO	COX2_CANFA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.08	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P67781 UniProt NPD GO	COX2_CANLA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.08	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P67782 UniProt NPD GO	COX2_CANLU	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.08	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O47668 UniProt NPD GO	COX2_CUOAL	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.08	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P14573 UniProt NPD GO	COX2_LOCMI	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.08	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P92662 UniProt NPD GO	COX2_MACRO	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.08	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P98042 UniProt NPD GO	COX2_PROTA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.08	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P50691 UniProt NPD GO	COX2_SCICA	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.08	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
O47679 UniProt NPD GO	COX2_SPEVE	Cytochrome c oxidase subunit 2 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide II)	0.08	-	end	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				227
P34843 UniProt NPD GO	COX3_APILI	Cytochrome c oxidase subunit 3 (EC 1.9.3.1) (Cytochrome c oxidase polypeptide III)	0.08	-	end	7 *					259
O46577 UniProt NPD GO	COX41_PANTR	Cytochrome c oxidase subunit 4 isoform 1 (EC 1.9.3.1) (Cytochrome c oxidase subunit IV isoform 1) (C ...	0.08	-	nuc	1	Mitochondrion; mitochondrial inner membrane				144
P13073 UniProt NPD GO	COX41_HUMAN	Cytochrome c oxidase subunit 4 isoform 1, mitochondrial precursor (EC 1.9.3.1) (Cytochrome c oxidase ...	0.08	-	nuc	1	Mitochondrion; mitochondrial inner membrane		123864		169
P00015 UniProt NPD GO	CYC2_MOUSE	Cytochrome c, testis-specific	0.08	-	nuc	0	Mitochondrion; mitochondrial matrix				104
Q9HC73 UniProt NPD GO	CRLF2_HUMAN	Cytokine receptor-like factor 2 precursor (Cytokine receptor-like 2) (CRL2) (IL-XR) (Thymic stromal ...	0.08	-	end	2 *	Isoform 1: Cell membrane; single-pass type I membrane protein (Probable). Isoform 2, isoform 3: Secr ...		400023		371
P42072 UniProt NPD GO	CTLA4_RABIT	Cytotoxic T-lymphocyte protein 4 precursor (Cytotoxic T-lymphocyte-associated antigen 4) (CTLA-4) (C ...	0.08	-	end	1 *	Membrane; single-pass type I membrane protein				223
P14541 UniProt NPD GO	CXH_NAJKA	Cytotoxin homolog (CLBP)	0.08	-	nuc	0	Secreted protein				62
P42289 UniProt NPD GO	DRD1_XENLA	D(1A) dopamine receptor	0.08	-	end	7 *	Membrane; multi-pass membrane protein				451

You are viewing entries 67851 to 67900 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.