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
Q10360 UniProt NPD GO	YDB8_SCHPO	Hypothetical protein C22E12.08 in chromosome I	0.00	-	cyt	0		nucleolus [IDA] RNA polymerase I upstream activating factor... [TAS]			97
Q10365 UniProt NPD GO	YDBF_SCHPO	Hypothetical protein C22E12.15 in chromosome I	0.00	-	cyt	0					59
Q10167 UniProt NPD GO	YAUE_SCHPO	Hypothetical protein C26A3.14c in chromosome I	0.00	-	mit	0					73
Q10227 UniProt NPD GO	YD03_SCHPO	Hypothetical protein C2E12.03c in chromosome I	0.00	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				283
Q09814 UniProt NPD GO	YABF_SCHPO	Hypothetical protein C2G11.15c in chromosome I	0.00	-	cyt	0					239
Q18319 UniProt NPD GO	YTO2_CAEEL	Hypothetical protein C30B5.2 in chromosome II	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				132
Q09506 UniProt NPD GO	YQI7_CAEEL	Hypothetical protein C45G9.7	0.00	-	cyt	0					124
P34360 UniProt NPD GO	YLH6_CAEEL	Hypothetical protein C48B4.6	0.00	-	end	4 *					176
Q09677 UniProt NPD GO	YA05_SCHPO	Hypothetical protein C5H10.05c in chromosome I	0.00	-	cyt	0					196
O46204 UniProt NPD GO	YACP_DROME	Hypothetical protein CG15841 in chromosome 2	0.00	-	cyt	0					43
Q18973 UniProt NPD GO	YYS7_CAEEL	Hypothetical protein D2024.7	0.00	-	mit	0					225
Q8SVF7 UniProt NPD GO	Y605_ENCCU	Hypothetical protein ECU06_0050	0.00	-	cyt	0					158
Q09311 UniProt NPD GO	YQS3_CAEEL	Hypothetical protein F21H12.3	0.00	-	cyt	0					62
P34407 UniProt NPD GO	YLW4_CAEEL	Hypothetical protein F22B7.4	0.00	-	exc	1 *					63
P34436 UniProt NPD GO	YL56_CAEEL	Hypothetical protein F44E2.6 in chromosome III	0.00	-	cyt	0					152
Q9VQ62 UniProt NPD GO	NPC2_DROME	Hypothetical protein NPC2 precursor (Niemann Pick type C2 protein homolog)	0.00	-	cyt	0	Secreted protein (Potential)				148
P45898 UniProt NPD GO	YNL6_CAEEL	Hypothetical protein R12B2.6	0.00	-	cyt	0					106
P51072 UniProt NPD GO	RJ21_FRAAN	Hypothetical protein RJ21 (Fragment)	0.00	-	cyt	0					27
P82620 UniProt NPD GO	SCRL1_ARATH	Hypothetical protein SCRL1 precursor	0.00	-	nuc	0					92
P82633 UniProt NPD GO	SCR14_ARATH	Hypothetical protein SCRL14 precursor	0.00	-	exc	0					86
P82645 UniProt NPD GO	SCR26_ARATH	Hypothetical protein SCRL26 precursor	0.00	-	exc	0					87
Q09361 UniProt NPD GO	YS13_CAEEL	Hypothetical protein ZK1307.3	0.00	-	nuc	0					115
P34625 UniProt NPD GO	YOJ2_CAEEL	Hypothetical protein ZK353.2	0.00	-	nuc	2 *					99
O94409 UniProt NPD GO	WTF23_SCHPO	Hypothetical protein wtf23	0.00	-	end	7	Membrane; multi-pass membrane protein (Potential)				368
P51264 UniProt NPD GO	YCF43_PORPU	Hypothetical tatC-like protein ycf43	0.00	-	end	6 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				254
P07835 UniProt NPD GO	ANPX_PSEAM	Ice-structuring protein 2A7 precursor (ISP 2A7) (Antifreeze protein IIA7) (AFP)	0.00	-	end	0					91
P35751 UniProt NPD GO	ANP1_RHIDE	Ice-structuring protein RD1 (ISP RD1) (Antifreeze peptide RD1)	0.00	-	cyt	0				1UCS	64
P12102 UniProt NPD GO	ANP2_RHIDE	Ice-structuring protein RD2 (ISP RD2) (Antifreeze peptide RD2)	0.00	-	cyt	0					64
P04368 UniProt NPD GO	ANP8_MYOSC	Ice-structuring protein SS-8 (ISP SS-8) (Antifreeze peptide SS-8)	0.00	-	mit	0					45
P23699 UniProt NPD GO	ANPY_PSEAM	Ice-structuring protein precursor (ISP) (Antifreeze protein) (AFP)	0.00	-	end	0					91
P09031 UniProt NPD GO	ANP_LIMFE	Ice-structuring protein precursor (ISP) (Antifreeze protein) (AFP)	0.00	-	end	0					97
Q91061 UniProt NPD GO	S10I_ICTPU	Ictacalcin	0.00	-	cyt	0					92
P01759 UniProt NPD GO	HV15_MOUSE	Ig heavy chain V region BCL1 precursor	0.00	-	vac	0					136
P01784 UniProt NPD GO	HV01_CANFA	Ig heavy chain V region GOM	0.00	-	cyt	0					114
P01788 UniProt NPD GO	HV19_MOUSE	Ig heavy chain V region H8	0.00	-	cyt	0					123
P01793 UniProt NPD GO	HV24_MOUSE	Ig heavy chain V region HPCG13	0.00	-	cyt	0					123
P01794 UniProt NPD GO	HV25_MOUSE	Ig heavy chain V region HPCG14	0.00	-	cyt	0					123
P01792 UniProt NPD GO	HV23_MOUSE	Ig heavy chain V region HPCG8	0.00	-	cyt	0					123
P01791 UniProt NPD GO	HV22_MOUSE	Ig heavy chain V region HPCM6	0.00	-	cyt	0					123
P01789 UniProt NPD GO	HV20_MOUSE	Ig heavy chain V region M603	0.00	-	cyt	0				2MCP	122
P01811 UniProt NPD GO	HV41_MOUSE	Ig heavy chain V region UPC10	0.00	-	cyt	0					117
P01787 UniProt NPD GO	HV18_MOUSE	Ig heavy chain V regions TEPC 15/S107/HPCM1/HPCM2/HPCM3	0.00	-	cyt	0					123
P01829 UniProt NPD GO	HV2C_RABIT	Ig heavy chain V-A2 region P-MU-3 precursor	0.00	-	exc	0					136
P01761 UniProt NPD GO	HV1E_HUMAN	Ig heavy chain V-I region SIE	0.00	-	cyt	0		extracellular region [NAS]			124
P01773 UniProt NPD GO	HV3L_HUMAN	Ig heavy chain V-III region BUR	0.00	-	cyt	0		extracellular region [NAS]			119
P01768 UniProt NPD GO	HV3G_HUMAN	Ig heavy chain V-III region CAM	0.00	-	cyt	0		extracellular region [NAS]			122
P01692 UniProt NPD GO	KV11_RABIT	Ig kappa-B5 chain V region 2699 (Fragments)	0.00	-	cyt	0					94
P20769 UniProt NPD GO	MUCM_HUMAN	Ig mu chain C region membrane-bound segment	0.00	-	nuc	1 *		membrane [NAS]			41
P83981 UniProt NPD GO	IGW1_GINCI	IgW transmembrane form Tm1T3/Tm6T3/Tm3C4 (Fragment)	0.00	-	nuc	1 *	Membrane; multi-pass membrane protein (Potential)				53
P83978 UniProt NPD GO	IGW4_HETFR	IgW transmembrane form Tm2T7/Tm7T7/Tm3T3 (Fragment)	0.00	-	nuc	1 *	Membrane; multi-pass membrane protein (Potential)				49

You are viewing entries 95251 to 95300 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.