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
P53872 UniProt NPD GO	YNT0_YEAST	Hypothetical 22.0 kDa protein in CHS1-SRP1 intergenic region	0.11	-	exc	0		cell wall (sensu Fungi) [IDA]			204
O19904 UniProt NPD GO	YCF23_CYACA	Hypothetical 27.4 kDa protein ycf23	0.11	-	nuc	0	Plastid; chloroplast				249
P36121 UniProt NPD GO	YK05_YEAST	Hypothetical 32.1 kDa protein in DBP7-GCN3 intergenic region	0.11	-	cyt	0		DNA-directed RNA polymerase III complex [TAS]			282
Q39635 UniProt NPD GO	Y38K_CORSE	Hypothetical 38.1 kDa protein	0.11	-	cyt	0					338
P34246 UniProt NPD GO	YKJ8_YEAST	Hypothetical 39.8 kDa protein in APE1/LAP4-CWP1 intergenic region	0.11	-	cyt	0					357
Q04806 UniProt NPD GO	YM85_YEAST	Hypothetical 42.4 kDa protein in FAA4-HOR7 intergenic region	0.11	-	cyt	0					366
Q04835 UniProt NPD GO	YM87_YEAST	Hypothetical 46.7 kDa protein in HOR7-COX7 intergenic region	0.11	-	end	10	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA]			414
P22377 UniProt NPD GO	YPA4_ASCIM	Hypothetical 6.8 kDa protein (ORF4A/ORF4B)	0.11	-	mit	0					59
P48446 UniProt NPD GO	YCF18_AGLNE	Hypothetical 7.0 kDa protein ycf18	0.11	-	nuc	0	Plastid; chloroplast				57
P51229 UniProt NPD GO	YCF34_PORPU	Hypothetical 8.9 kDa protein ycf34 (ORF76)	0.11	-	nuc	0	Plastid; chloroplast				76
P08889 UniProt NPD GO	YCX1_VICFA	Hypothetical 9.9 kDa protein	0.11	-	mit	1 *	Plastid; chloroplast				82
P52057 UniProt NPD GO	YU68_CAEEL	Hypothetical UPF0001 protein F09E5.8 in chromosome II	0.11	-	cyt	0					244
Q10081 UniProt NPD GO	YAO2_SCHPO	Hypothetical UPF0039 protein C11D3.02c in chromosome I	0.11	-	cyt	0					150
Q03051 UniProt NPD GO	YD543_YEAST	Hypothetical UPF0320 protein YDR543C	0.11	-	nuc	0					99
P0C0B1 UniProt NPD GO	Y1401_ARATH	Hypothetical protein At1g24010	0.11	-	cyt	0					141
Q09791 UniProt NPD GO	YA9F_SCHPO	Hypothetical protein C13G6.15c in chromosome I	0.11	-	nuc	0					163
O60083 UniProt NPD GO	YQK9_SCHPO	Hypothetical protein C1494.09c in chromosome III	0.11	-	cyt	0					157
Q10317 UniProt NPD GO	YD65_SCHPO	Hypothetical protein C17G8.05 in chromosome I	0.11	-	cyt	0					180
O94752 UniProt NPD GO	YBSB_SCHPO	Hypothetical protein C18E5.11c in chromosome II	0.11	-	nuc	0					454
O13909 UniProt NPD GO	YDW1_SCHPO	Hypothetical protein C23C11.01 in chromosome I	0.11	-	end	10	Membrane; multi-pass membrane protein (Potential)				441
Q9P6S2 UniProt NPD GO	YNL5_SCHPO	Hypothetical protein C27.05 in chromosome II	0.11	-	cyt	2 *	Membrane; multi-pass membrane protein (Potential)				108
O14020 UniProt NPD GO	YDPH_SCHPO	Hypothetical protein C29A4.17c in chromosome I	0.11	-	mit	0					147
O14038 UniProt NPD GO	YEY5_SCHPO	Hypothetical protein C2C4.05 in chromosome I	0.11	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				134
P34363 UniProt NPD GO	YLH9_CAEEL	Hypothetical protein C48B4.9	0.11	-	end	4 *					182
Q09284 UniProt NPD GO	YQJ3_CAEEL	Hypothetical protein C52A11.3	0.11	-	cyt	0					164
O94428 UniProt NPD GO	YHK9_SCHPO	Hypothetical protein C660.09 in chromosome II	0.11	-	nuc	0					115
Q8SW76 UniProt NPD GO	Y311_ENCCU	Hypothetical protein ECU03_0110	0.11	-	end	7 *					267
Q8STZ0 UniProt NPD GO	YBL1_ENCCU	Hypothetical protein ECU11_2110	0.11	-	end	6 *					221
Q19297 UniProt NPD GO	YZ73_CAEEL	Hypothetical protein F10D7.3 in chromosome X	0.11	-	exc	0					146
P50438 UniProt NPD GO	YSH7_CAEEL	Hypothetical protein F12A10.7 precursor	0.11	-	vac	0					113
P52881 UniProt NPD GO	YAF2_CAEEL	Hypothetical protein F46C5.2	0.11	-	nuc	1					182
Q02333 UniProt NPD GO	YOL6_CAEEL	Hypothetical protein ZK370.6	0.11	-	exc	0					164
Q7Z090 UniProt NPD GO	CXI3_CONRA	I-superfamily conotoxin R11.3	0.11	-	nuc	0	Secreted protein				40
P80422 UniProt NPD GO	LV2L_HUMAN	Ig gamma lambda chain V-II region DOT	0.11	-	nuc	0		extracellular region [NAS]			111
P01857 UniProt NPD GO	IGHG1_HUMAN	Ig gamma-1 chain C region	0.11	-	nuc	0		membrane fraction [NAS]	147100	2RCS	330
P01863 UniProt NPD GO	GCAA_MOUSE	Ig gamma-2A chain C region, A allele	0.11	-	nuc	0		immunoglobulin complex, circulating [IDA] multivesicular body [IDA]		1MNU	330
P01824 UniProt NPD GO	HV2F_HUMAN	Ig heavy chain V-II region WAH	0.11	-	cyt	0		extracellular region [NAS]		1ZVO	129
P01697 UniProt NPD GO	KV16_RABIT	Ig kappa chain V region AH80-5	0.11	-	nuc	0					114
P01679 UniProt NPD GO	KV6E_MOUSE	Ig kappa chain V-VI region J539	0.11	-	nuc	0				2FBJ	107
P01675 UniProt NPD GO	KV6A_MOUSE	Ig kappa chain V-VI region XRPC 44	0.11	-	nuc	0					107
P01847 UniProt NPD GO	LAC_RABIT	Ig lambda chain C region	0.11	-	nuc	0					105
P04208 UniProt NPD GO	LV1F_HUMAN	Ig lambda chain V-I region WAH	0.11	-	nuc	0		extracellular region [NAS]		1ZVO	109
P01713 UniProt NPD GO	LV2J_HUMAN	Ig lambda chain V-II region NIG-58	0.11	-	nuc	0		extracellular region [NAS]			110
P04209 UniProt NPD GO	LV2K_HUMAN	Ig lambda chain V-II region NIG-84	0.11	-	nuc	0		extracellular region [NAS]			112
Q61559 UniProt NPD GO	FCGRN_MOUSE	IgG receptor FcRn large subunit p51 precursor (FcRN) (Neonatal Fc receptor) (IgG Fc fragment recepto ...	0.11	-	end	1	Membrane; single-pass type I membrane protein				365
P13599 UniProt NPD GO	FCGRN_RAT	IgG receptor FcRn large subunit p51 precursor (FcRn) (Neonatal Fc receptor) (IgG Fc fragment recepto ...	0.11	-	end	1	Membrane; single-pass type I membrane protein			3FRU	366
P83743 UniProt NPD GO	IGW2_HETFR	IgW chain C region, secreted form 2 (Fragment)	0.11	-	nuc	0	Secreted protein				133
Q02986 UniProt NPD GO	HIS7_SACKL	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.11	+	cyt	0					232
Q9Y6W8 UniProt NPD GO	ICOS_HUMAN	Inducible T-cell co-stimulator precursor (Activation-inducible lymphocyte immunomediatory molecule) ...	0.11	-	nuc	1	Isoform 1: Cell membrane; single-pass type I membrane protein (Potential). Isoform 2: Secreted prote ...	integral to membrane [NAS]	607594		199
Q29545 UniProt NPD GO	ICA_PIG	Inhibitor of carbonic anhydrase precursor	0.11	-	exc	0	Secreted protein				704

You are viewing entries 62851 to 62900 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.