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
O14301 UniProt NPD GO	YE85_SCHPO	Hypothetical WD repeat protein C9G1.05 in chromosome I	0.09	-	cyt	0					595
P93293 UniProt NPD GO	M300_ARATH	Hypothetical mitochondrial protein AtMg00300 (ORF145a) (ORF1451)	0.09	-	nuc	0	Mitochondrion (Potential)				145
P92520 UniProt NPD GO	M820_ARATH	Hypothetical mitochondrial protein AtMg00820 (ORF170)	0.09	-	nuc	0	Mitochondrion (Potential)				170
P92536 UniProt NPD GO	M1020_ARATH	Hypothetical mitochondrial protein AtMg01020 (ORF153b)	0.09	-	end	3 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (Potential)				153
O13917 UniProt NPD GO	YDWD_SCHPO	Hypothetical protein C23C11.13c in chromosome I	0.09	-	cyt	0					206
Q09243 UniProt NPD GO	YP92_CAEEL	Hypothetical protein C28H8.2 precursor	0.09	-	cyt	0					162
Q09278 UniProt NPD GO	YQI5_CAEEL	Hypothetical protein C45G9.5	0.09	-	cyt	0					316
P34365 UniProt NPD GO	YLHA_CAEEL	Hypothetical protein C48B4.11	0.09	-	end	6 *					307
Q10215 UniProt NPD GO	YAY7_SCHPO	Hypothetical protein C4H3.07c in chromosome I	0.09	-	mit	0					171
Q10220 UniProt NPD GO	YAYD_SCHPO	Hypothetical protein C4H3.13 in chromosome I	0.09	-	cyt	0					88
Q9P6M5 UniProt NPD GO	YKS1_SCHPO	Hypothetical protein C652.01 in chromosome I	0.09	-	mit	1 *					108
Q9HDZ1 UniProt NPD GO	YELI_SCHPO	Hypothetical protein C6F6.18c precursor	0.09	-	mit	0					121
Q9VMC8 UniProt NPD GO	PHF5_DROME	Hypothetical protein CG9548	0.09	-	nuc	0					111
P34395 UniProt NPD GO	YLU1_CAEEL	Hypothetical protein F10E9.1	0.09	-	end	4 *					197
P34398 UniProt NPD GO	YLU4_CAEEL	Hypothetical protein F10E9.4	0.09	-	cyt	0					262
O45363 UniProt NPD GO	YSWJ_CAEEL	Hypothetical protein F14H3.2 in chromosome V	0.09	-	end	3 *					434
Q20728 UniProt NPD GO	YXHK_CAEEL	Hypothetical protein F53F4.3 in chromosome V	0.09	-	cyt	0				1TOV	229
P34521 UniProt NPD GO	YM45_CAEEL	Hypothetical protein K11H3.5 precursor	0.09	-	exc	1 *					107
Q09344 UniProt NPD GO	YRP2_CAEEL	Hypothetical protein R10H1.2	0.09	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				294
P82639 UniProt NPD GO	SCR20_ARATH	Hypothetical protein SCRL20 precursor	0.09	-	nuc	1 *					96
O04373 UniProt NPD GO	ILL4_ARATH	IAA-amino acid hydrolase ILR1-like 4 precursor (EC 3.5.1.-)	0.09	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				440
P01862 UniProt NPD GO	IGHG2_CAVPO	Ig gamma-2 chain C region	0.09	-	nuc	0					329
P03981 UniProt NPD GO	HV02_CAICR	Ig heavy chain V region E1 precursor	0.09	-	exc	0					117
P01819 UniProt NPD GO	HV43_MOUSE	Ig heavy chain V region MOPC 141 precursor	0.09	-	exc	0					144
P04438 UniProt NPD GO	HV2H_HUMAN	Ig heavy chain V-II region SESS precursor	0.09	-	nuc	0		extracellular region [NAS]			147
P01836 UniProt NPD GO	KACA_RAT	Ig kappa chain C region, A allele	0.09	-	nuc	0					106
P01690 UniProt NPD GO	KV09_RABIT	Ig kappa chain V region 3381 (Fragment)	0.09	-	nuc	0					92
P03976 UniProt NPD GO	KV2E_MOUSE	Ig kappa chain V-II region 17S29.1	0.09	-	nuc	0					113
P01842 UniProt NPD GO	LAC_HUMAN	Ig lambda chain C regions	0.09	-	nuc	0			147220	7FAB	105
P04210 UniProt NPD GO	LV1_CHICK	Ig lambda chain V-1 region precursor	0.09	-	exc	0					113
P06316 UniProt NPD GO	LV1G_HUMAN	Ig lambda chain V-I region BL2 precursor	0.09	-	exc	0		extracellular region [NAS]			130
P01702 UniProt NPD GO	LV1D_HUMAN	Ig lambda chain V-I region NIG-64	0.09	-	nuc	0		extracellular region [NAS]			111
P01844 UniProt NPD GO	LAC2_MOUSE	Ig lambda-2 chain C region	0.09	-	nuc	0					104
P23735 UniProt NPD GO	MUCM_ICTPU	Ig mu chain C region membrane-bound form	0.09	-	cyt	1					481
P48262 UniProt NPD GO	HIS5_CYAPA	Imidazole glycerol phosphate synthase subunit hisH (EC 2.4.2.-) (IGP synthase glutamine amidotransfe ...	0.09	-	nuc	0	Plastid; cyanelle				215
Q92447 UniProt NPD GO	HIS7_PICPA	Imidazoleglycerol-phosphate dehydratase (EC 4.2.1.19) (IGPD)	0.09	-	cyt	0					224
P20765 UniProt NPD GO	IGLL1_MUSSP	Immunoglobulin lambda-like polypeptide 1 (Ig lambda-5) (CD179b antigen) (Fragment)	0.09	-	nuc	0	Secreted protein (Potential)				105
Q8R366 UniProt NPD GO	IGSF8_MOUSE	Immunoglobulin superfamily member 8 precursor (CD81 partner 3) (Glu-Trp-Ile EWI motif-containing pro ...	0.09	-	exc	1	Membrane; single-pass membrane protein (Potential)	integral to membrane [ISS]			611
P14902 UniProt NPD GO	I23O_HUMAN	Indoleamine 2,3-dioxygenase (EC 1.13.11.42) (IDO) (Indoleamine-pyrrole 2,3-dioxygenase)	0.09	-	nuc	0			147435	2D0U	403
P27716 UniProt NPD GO	INX1_DROME	Innexin inx1 (Innexin-1) (Protein ogre) (Protein optic ganglion reduced)	0.09	-	nuc	4 *	Membrane; multi-pass membrane protein (Potential)	gap junction [IEP] integral to membrane [NAS]			362
P50098 UniProt NPD GO	IMDH_TRYBB	Inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) (IMP dehydrogenase) (IMPDH) (IMPD)	0.09	-	pox	0					512
P49442 UniProt NPD GO	INPP_MOUSE	Inositol polyphosphate 1-phosphatase (EC 3.1.3.57) (IPPase) (IPP)	0.09	-	cyt	0					396
P68724 UniProt NPD GO	SIX1D_LEIQH	Insect neurotoxin 1d precursor (Lqh IT1-d) (LqhIT1-d)	0.09	-	nuc	0	Secreted protein				88
P55904 UniProt NPD GO	SIX5_BUTOC	Insect toxin 5 (BotIT5)	0.09	-	cyt	0	Secreted protein				61
P19856 UniProt NPD GO	SIX1_LEIQU	Insect toxins 1 and 1' (Insect toxin LqqIT1/LqqIT1')	0.09	-	nuc	0	Secreted protein				70
O73727 UniProt NPD GO	INS_BRARE	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.09	-	end	0	Secreted protein				108
Q98TA8 UniProt NPD GO	INS_PANBU	Insulin precursor [Contains: Insulin B chain; Insulin A chain]	0.09	-	exc	0	Secreted protein				110
Q80ZA0 UniProt NPD GO	ITL1B_MOUSE	Intelectin-1b precursor (Intelectin-2)	0.09	-	vac	0	Cell membrane; lipid-anchor; GPI-anchor. Secreted protein (By similarity)				313
Q60625 UniProt NPD GO	ICAM5_MOUSE	Intercellular adhesion molecule 5 precursor (ICAM-5) (Telencephalin)	0.09	-	mit	2 *	Membrane; single-pass type I membrane protein	plasma membrane [IDA]			917
Q6NZ06 UniProt NPD GO	ILF2_BRARE	Interleukin enhancer-binding factor 2 homolog	0.09	-	mit	0	Nucleus (By similarity)	nucleolus [ISS] nucleus [ISS]			387

You are viewing entries 66351 to 66400 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.