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
O60613 UniProt NPD GO	SEP15_HUMAN	15 kDa selenoprotein precursor	0.07	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen. The association with UGCGL1/UGTR is essential fo ...	endoplasmic reticulum lumen [IDA]	606254		162
Q923V8 UniProt NPD GO	SEP15_RAT	15 kDa selenoprotein precursor	0.07	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen. The association with UGCGL1/UGTR is essential fo ...	endoplasmic reticulum lumen [ISS]			162
P27777 UniProt NPD GO	HSP11_ORYSA	16.9 kDa class I heat shock protein 1	0.07	-	cyt	0	Cytoplasm				150
Q943E6 UniProt NPD GO	HSP12_ORYSA	16.9 kDa class I heat shock protein 2	0.07	-	cyt	0	Cytoplasm				150
Q943E7 UniProt NPD GO	HSP13_ORYSA	16.9 kDa class I heat shock protein 3	0.07	-	cyt	0	Cytoplasm				149
P30693 UniProt NPD GO	HSP11_HELAN	17.6 kDa class I heat shock protein	0.07	-	cyt	0	Cytoplasm				153
P29830 UniProt NPD GO	HSP21_ARATH	17.6 kDa class II heat shock protein	0.07	-	cyt	0	Cytoplasm				155
P30221 UniProt NPD GO	HSP11_LYCES	17.8 kDa class I heat shock protein	0.07	-	mit	0	Cytoplasm				154
P11928 UniProt NPD GO	OAS1A_MOUSE	2'-5'-oligoadenylate synthetase 1A (EC 2.7.7.-) ((2-5')oligo(A) synthetase 1A) (2-5A synthetase 1A) ...	0.07	-	nuc	0					367
P38787 UniProt NPD GO	PANE_YEAST	2-dehydropantoate 2-reductase (EC 1.1.1.169) (Ketopantoate reductase) (KPA reductase) (KPR)	0.07	-	exc	1 *		cytoplasm [IDA] soluble fraction [IDA]			379
Q9UJ83 UniProt NPD GO	HPCL_HUMAN	2-hydroxyphytanoyl-CoA lyase (EC 4.1.-.-) (2-HPCL)	0.07	-	end	0	Peroxisome	peroxisome [IDA]	604300		578
O59736 UniProt NPD GO	LEU1_SCHPO	2-isopropylmalate synthase (EC 2.3.3.13) (Alpha-isopropylmalate synthase) (Alpha-IPM synthetase)	0.07	-	cyt	0					584
Q96P68 UniProt NPD GO	OXGR1_HUMAN	2-oxoglutarate receptor 1 (Alpha-ketoglutarate receptor 1) (G-protein coupled receptor 80) (G-protei ...	0.07	-	end	6 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]	606922		337
P30236 UniProt NPD GO	HSP41_SOYBN	22.0 kDa class IV heat shock protein precursor	0.07	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Probable). In the endomembrane, probably in the ...				192
Q8VDM4 UniProt NPD GO	PSD2_MOUSE	26S proteasome non-ATPase regulatory subunit 2 (26S proteasome regulatory subunit RPN1) (26S proteas ...	0.07	-	end	0					908
P26516 UniProt NPD GO	PSD7_MOUSE	26S proteasome non-ATPase regulatory subunit 7 (26S proteasome regulatory subunit rpn8) (26S proteas ...	0.07	-	end	0					321
P43588 UniProt NPD GO	RPN11_YEAST	26S proteasome regulatory subunit RPN11 (Protein MPR1)	0.07	-	cyt	0		nucleus [IDA] proteasome regulatory particle, lid subcomp... [IDA]			306
Q9CQE3 UniProt NPD GO	RT17_MOUSE	28S ribosomal protein S17, mitochondrial precursor (S17mt) (MRP-S17)	0.07	-	mit	0	Mitochondrion (By similarity)	mitochondrion [IDA]			120
Q60555 UniProt NPD GO	3BHS1_MESAU	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type I (3Beta-HSD I) [Includes: 3-beta-hyd ...	0.07	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...				372
Q62878 UniProt NPD GO	3BHS4_RAT	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase type IV (3Beta-HSD IV) [Includes: 3-beta-h ...	0.07	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...				372
Q59XQ1 UniProt NPD GO	HAL22_CANAL	3'(2'),5'-bisphosphate nucleotidase 2 (EC 3.1.3.7) (3'(2'),5-bisphosphonucleoside 3'(2')-phosphohydr ...	0.07	-	nuc	0					358
Q9LEL5 UniProt NPD GO	4OMT_COPJA	3'-hydroxy-N-methyl-(S)-coclaurine 4'-O-methyltransferase (EC 2.1.1.116) (S-adenosyl-L-methionine:3' ...	0.07	-	cyt	0					350
P23965 UniProt NPD GO	D3D2_RAT	3,2-trans-enoyl-CoA isomerase, mitochondrial precursor (EC 5.3.3.8) (Dodecenoyl-CoA isomerase) (Delt ...	0.07	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [IDA]		1XX4	289
Q99258 UniProt NPD GO	RIB3_YEAST	3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP synthase)	0.07	-	cyt	0		cytosol [IDA] mitochondrial intermembrane space [IDA]			208
O24594 UniProt NPD GO	HMDH_MAIZE	3-hydroxy-3-methylglutaryl-coenzyme A reductase (EC 1.1.1.34) (HMG-CoA reductase)	0.07	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				579
P33291 UniProt NPD GO	THIKB_CANTR	3-ketoacyl-CoA thiolase B, peroxisomal precursor (EC 2.3.1.16) (Beta-ketothiolase B) (Acetyl-CoA acy ...	0.07	-	nuc	0	Peroxisome				408
Q6B945 UniProt NPD GO	FABH_GRATL	3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.41) (3-oxoacyl-[acyl-carrier-protein] synthase ...	0.07	-	mit	0	Plastid; chloroplast				330
P52815 UniProt NPD GO	RM12_HUMAN	39S ribosomal protein L12, mitochondrial precursor (L12mt) (MRP-L12) (5c5-2)	0.07	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]	602375		198
Q6CDR5 UniProt NPD GO	HPPD_YARLI	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase)	0.07	-	cyt	0					394
P42733 UniProt NPD GO	RS11C_ARATH	40S ribosomal protein S11-3	0.07	-	cyt	0	Cytoplasm				159
P19800 UniProt NPD GO	RS14_TRYBB	40S ribosomal protein S14	0.07	-	cyt	0					144
Q6BSI7 UniProt NPD GO	RS16_DEBHA	40S ribosomal protein S16	0.07	-	cyt	0					142
P49688 UniProt NPD GO	RS2_ARATH	40S ribosomal protein S2	0.07	-	cyt	0					285
Q4GXP3 UniProt NPD GO	RS21_AGRLI	40S ribosomal protein S21	0.07	-	nuc	0					83
Q75BL6 UniProt NPD GO	RS21_ASHGO	40S ribosomal protein S21	0.07	-	nuc	0					87
P0C0V8 UniProt NPD GO	RS21A_YEAST	40S ribosomal protein S21-A (S26) (YS25)	0.07	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			87
O14469 UniProt NPD GO	RS22_SCHPO	40S ribosomal protein S22	0.07	-	cyt	0					130
Q6FLA8 UniProt NPD GO	RS23_CANGA	40S ribosomal protein S23	0.07	-	mit	0					145
Q86FP7 UniProt NPD GO	RS23_DERVA	40S ribosomal protein S23	0.07	-	nuc	0					143
Q6YIA3 UniProt NPD GO	RS23_SACBA	40S ribosomal protein S23	0.07	-	mit	0					145
Q6YIA2 UniProt NPD GO	RS23_SACCA	40S ribosomal protein S23	0.07	-	mit	0					145
P32827 UniProt NPD GO	RS23_YEAST	40S ribosomal protein S23 (S28) (YS14) (RP37)	0.07	-	mit	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]		1K5X	145
P34789 UniProt NPD GO	RS28_ARATH	40S ribosomal protein S28	0.07	-	cyt	0	Cytoplasm				64
P46302 UniProt NPD GO	RS28_MAIZE	40S ribosomal protein S28	0.07	-	cyt	0	Cytoplasm				65
P48154 UniProt NPD GO	RS3A_CAEEL	40S ribosomal protein S3a	0.07	-	nuc	0					256
P47836 UniProt NPD GO	RS4_CHICK	40S ribosomal protein S4	0.07	-	mit	0					262
P05753 UniProt NPD GO	RS4_YEAST	40S ribosomal protein S4 (S7) (YS6) (RP5)	0.07	-	mit	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			260
O62738 UniProt NPD GO	RS4X_MONDO	40S ribosomal protein S4, X isoform	0.07	-	mit	0		ribosome [ISS]			262
Q8H173 UniProt NPD GO	RSSAB_ARATH	40S ribosomal protein SA-2 (p40 protein homolog)	0.07	-	nuc	0	Cytoplasm				280
P19324 UniProt NPD GO	HSP47_MOUSE	47 kDa heat shock protein precursor (Collagen-binding protein 1) (Serine protease inhibitor J6)	0.07	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				417

You are viewing entries 69301 to 69350 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.