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
Q09675 UniProt NPD GO	YA02_SCHPO	Hypothetical protein C5H10.02c in chromosome I	0.03	-	cyt	0					240
Q9UT14 UniProt NPD GO	YF1H_SCHPO	Hypothetical protein C9E9.17c precursor	0.03	-	mit	1 *					72
P41953 UniProt NPD GO	YLK5_CAEEL	Hypothetical protein D1044.5	0.03	-	nuc	0					68
Q8STJ2 UniProt NPD GO	Y5G0_ENCCU	Hypothetical protein ECU05_1600/ECU11_0130	0.03	-	end	5					298
P34415 UniProt NPD GO	YLZ2_CAEEL	Hypothetical protein F42H10.2	0.03	-	cyt	0					115
P98080 UniProt NPD GO	YMT1_CAEEL	Hypothetical protein F56D2.1 in chromosome III	0.03	-	mit	0					471
Q09954 UniProt NPD GO	YSR6_CAEEL	Hypothetical protein F59B10.6	0.03	-	nuc	1 *					105
P34494 UniProt NPD GO	YMQ3_CAEEL	Hypothetical protein K02D10.3	0.03	-	nuc	0					105
Q09418 UniProt NPD GO	YRMB_CAEEL	Hypothetical protein R06F6.11 precursor	0.03	-	vac	0					99
P82644 UniProt NPD GO	SCR25_ARATH	Hypothetical protein SCRL25 precursor	0.03	-	exc	0					87
Q10049 UniProt NPD GO	YRU3_CAEEL	Hypothetical protein T09B9.3 precursor	0.03	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				340
P34596 UniProt NPD GO	YOD4_CAEEL	Hypothetical protein ZC262.4	0.03	-	cyt	0					149
P34614 UniProt NPD GO	YOG5_CAEEL	Hypothetical protein ZK112.5	0.03	-	cyt	0					159
P34615 UniProt NPD GO	YOG6_CAEEL	Hypothetical protein ZK112.6	0.03	-	mit	0					149
P34667 UniProt NPD GO	YO11_CAEEL	Hypothetical protein ZK686.1	0.03	-	nuc	0					44
O74512 UniProt NPD GO	WTF14_SCHPO	Hypothetical protein wtf14	0.03	-	end	4	Membrane; multi-pass membrane protein (Potential)				222
Q9P3V0 UniProt NPD GO	WTF4_SCHPO	Hypothetical protein wtf4	0.03	-	end	8	Membrane; multi-pass membrane protein (Potential)				363
Q7Z9I5 UniProt NPD GO	WTF7_SCHPO	Hypothetical protein wtf7	0.03	-	end	3	Membrane; multi-pass membrane protein (Potential)				220
Q9XPS5 UniProt NPD GO	YCF70_WHEAT	Hypothetical protein ycf70 (ORF42)	0.03	-	mit	1 *	Plastid; chloroplast				42
Q6B8S9 UniProt NPD GO	YCF43_GRATL	Hypothetical tatC-like protein ycf43	0.03	-	end	6 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				238
P25594 UniProt NPD GO	YCG9_YEAST	Hypothetical transport protein YCL069W	0.03	-	end	11 *	Membrane; multi-pass membrane protein (Probable)	vacuolar membrane (sensu Fungi) [IDA]			458
Q21882 UniProt NPD GO	TTHY1_CAEEL	Hypothetical transthyretin-like protein R09H10.3 in chromosome IV	0.03	-	vac	0					135
P27605 UniProt NPD GO	HPRT_RAT	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) (HGPRT) (HGPRTase)	0.03	-	cyt	0	Cytoplasm				218
P09383 UniProt NPD GO	HPRT_SCHMA	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) (HGPRT) (HGPRTase)	0.03	-	end	1 *	Cytoplasm				284
Q64531 UniProt NPD GO	HPRT_MUSSP	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) (HGPRT) (HGPRTase) (HPRT A) (Fragment)	0.03	-	cyt	0	Cytoplasm				213
P00493 UniProt NPD GO	HPRT_MOUSE	Hypoxanthine-guanine phosphoribosyltransferase (EC 2.4.2.8) (HGPRT) (HGPRTase) (HPRT B)	0.03	-	nuc	0	Cytoplasm				217
Q7Z092 UniProt NPD GO	CXI14_CONRA	I-superfamily conotoxin R11.14 (r11b)	0.03	-	nuc	0	Secreted protein				46
Q7Z094 UniProt NPD GO	CXI6_CONRA	I-superfamily conotoxin R11.6 (r11a)	0.03	-	nuc	0	Secreted protein				46
Q7Z095 UniProt NPD GO	CXI7_CONRA	I-superfamily conotoxin R11.7	0.03	-	nuc	0	Secreted protein				46
Q7M4K5 UniProt NPD GO	CXIE_CONRA	I-superfamily conotoxin r11e	0.03	-	nuc	0	Secreted protein				37
P69497 UniProt NPD GO	CXI3_CONIM	I-superfamily conotoxin-3 precursor	0.03	-	mit	1 *	Secreted protein (By similarity)				64
P19606 UniProt NPD GO	ANP3_MACAM	Ice-structuring protein lambda OP-3 precursor (ISP lambda OP-3) (Antifreeze protein lambda OP-3)	0.03	-	end	0					91
P01741 UniProt NPD GO	HV00_MOUSE	Ig heavy chain V region (Anti-arsonate antibody)	0.03	-	cyt	0					114
P01758 UniProt NPD GO	HV14_MOUSE	Ig heavy chain V region 108A precursor	0.03	-	exc	0					117
P01754 UniProt NPD GO	HV10_MOUSE	Ig heavy chain V region 145 precursor	0.03	-	cyt	0					117
P01747 UniProt NPD GO	HV03_MOUSE	Ig heavy chain V region 36-65	0.03	-	cyt	0				1JFQ	120
P18530 UniProt NPD GO	HV59_MOUSE	Ig heavy chain V region 7-39 precursor	0.03	-	exc	0					117
P01810 UniProt NPD GO	HV40_MOUSE	Ig heavy chain V region J539	0.03	-	cyt	0				2FBJ	119
P01783 UniProt NPD GO	HV16_MOUSE	Ig heavy chain V region MOPC 21 precursor (Fragment)	0.03	-	exc	0				1IGC	136
P06328 UniProt NPD GO	HV49_MOUSE	Ig heavy chain V region VH558 B4 precursor	0.03	-	nuc	0					117
P01807 UniProt NPD GO	HV37_MOUSE	Ig heavy chain V region X44	0.03	-	cyt	0					119
P80421 UniProt NPD GO	HV1H_HUMAN	Ig heavy chain V-I region DOT	0.03	-	cyt	0		extracellular region [NAS]			120
P01743 UniProt NPD GO	HV1B_HUMAN	Ig heavy chain V-I region HG3 precursor	0.03	-	exc	0		extracellular region [NAS]			117
P01816 UniProt NPD GO	HV2C_HUMAN	Ig heavy chain V-II region DAW	0.03	-	mit	0		extracellular region [NAS]			119
P01804 UniProt NPD GO	HV35_MOUSE	Ig heavy chain V-III region HPC76 (Fragment)	0.03	-	cyt	0					111
P01772 UniProt NPD GO	HV3K_HUMAN	Ig heavy chain V-III region KOL	0.03	-	cyt	0		extracellular region [NAS]		2IG2	126
P01770 UniProt NPD GO	HV3I_HUMAN	Ig heavy chain V-III region NIE	0.03	-	cyt	0		extracellular region [NAS]			119
P01764 UniProt NPD GO	HV3C_HUMAN	Ig heavy chain V-III region VH26 precursor	0.03	-	mit	0		extracellular region [NAS]		1HOU	117
P01776 UniProt NPD GO	HV3O_HUMAN	Ig heavy chain V-III region WAS	0.03	-	cyt	0		extracellular region [NAS]			117
P01778 UniProt NPD GO	HV3Q_HUMAN	Ig heavy chain V-III region ZAP	0.03	-	cyt	0		extracellular region [NAS]			116

You are viewing entries 80301 to 80350 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.