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
Q28611 UniProt NPD GO	UD16_RABIT	UDP-glucuronosyltransferase 1-6 precursor (EC 2.4.1.17) (UDPGT) (UGT1*6) (UGT1-06) (UGT1.6) (UGT1A6) ...	0.03	-	end	1	Microsome				531
P36510 UniProt NPD GO	UDA1_RAT	UDP-glucuronosyltransferase 2A1 precursor (EC 2.4.1.17) (UDPGT) (UGT-OLF)	0.03	-	end	1 *					527
Q9TSL6 UniProt NPD GO	UDB23_MACFA	UDP-glucuronosyltransferase 2B23 precursor (EC 2.4.1.17) (UDPGT)	0.03	-	cyt	1 *	Microsome				529
P36511 UniProt NPD GO	UDB4_RAT	UDP-glucuronosyltransferase 2B4 precursor (EC 2.4.1.17) (UDPGT) (UDP-glucuronosyltransferase 2B12)	0.03	-	end	1	Microsome				530
Q94AA1 UniProt NPD GO	UN93L_ARATH	UNC93-like protein	0.03	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				464
P53212 UniProt NPD GO	YG1D_YEAST	UPF0082 protein YGR021W	0.03	-	nuc	0		mitochondrion [IDA]			290
Q7ZWI4 UniProt NPD GO	CN129_BRARE	UPF0279 protein C14orf129 homolog	0.03	-	cyt	0					133
Q9BSY9 UniProt NPD GO	CG146_HUMAN	UPF0326 protein CGI-146	0.03	-	cyt	0					194
Q5R456 UniProt NPD GO	CG146_PONPY	UPF0326 protein CGI-146 homolog	0.03	-	cyt	0					194
P38340 UniProt NPD GO	YB9H_YEAST	UPF0351 protein YBR261C	0.03	-	cyt	0	Cytoplasm	cytoplasm [IDA]			232
Q12125 UniProt NPD GO	YO164_YEAST	UPF0363 protein YOR164C	0.03	-	cyt	0	Cytoplasm	cytoplasm [IDA]			312
P00130 UniProt NPD GO	UCR10_BOVIN	Ubiquinol-cytochrome c reductase complex 7.2 kDa protein (EC 1.10.2.2) (Cytochrome c1 nonheme 7 kDa ...	0.03	-	mit	1 *	Mitochondrion; mitochondrial inner membrane			3BCC	63
Q9UDW1 UniProt NPD GO	UCR10_HUMAN	Ubiquinol-cytochrome c reductase complex 7.2 kDa protein (EC 1.10.2.2) (Cytochrome c1 nonheme 7 kDa ...	0.03	-	mit	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)				62
P48504 UniProt NPD GO	UCRH_SOLTU	Ubiquinol-cytochrome c reductase complex 7.8 kDa protein (EC 1.10.2.2) (Mitochondrial hinge protein) ...	0.03	-	cyt	0	Mitochondrion; mitochondrial inner membrane				68
P46270 UniProt NPD GO	UCR10_SOLTU	Ubiquinol-cytochrome c reductase complex 8.0 kDa protein (EC 1.10.2.2)	0.03	-	cyt	0	Mitochondrion; mitochondrial inner membrane; intermembrane side (By similarity)				72
P37299 UniProt NPD GO	UCR10_YEAST	Ubiquinol-cytochrome c reductase complex 8.5 kDa protein (Complex III subunit 10) (Cytochrome b-c1 c ...	0.03	-	mit	1 *	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA] respiratory chain complex III (sensu Eukary... [IDA]			76
P50523 UniProt NPD GO	UCRQ_SCHPO	Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C (EC 1.10.2.2) (Ubiquinol-cy ...	0.03	-	cyt	1	Mitochondrion; mitochondrial inner membrane				92
P81247 UniProt NPD GO	UCRQ_EQUAR	Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C (EC 1.10.2.2) (Ubiquinol-cy ...	0.03	-		0	Mitochondrion; mitochondrial inner membrane (By similarity)				20
Q69BJ8 UniProt NPD GO	UCRI_LAGLA	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.03	-	cyt	0	Mitochondrion; mitochondrial inner membrane (By similarity)				274
Q69BK3 UniProt NPD GO	UCRI_PONPY	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.03	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				274
P20788 UniProt NPD GO	UCRI_RAT	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.03	-	mit	0	Mitochondrion; mitochondrial inner membrane	ubiquinol-cytochrome-c reductase complex [TAS]			274
P07257 UniProt NPD GO	UQCR2_YEAST	Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor (Complex III subuni ...	0.03	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA] respiratory chain complex III (sensu Eukary... [IDA]		1P84	368
P23004 UniProt NPD GO	UQCR2_BOVIN	Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor (EC 1.10.2.2) (Comp ...	0.03	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side			2A06	453
P22695 UniProt NPD GO	UQCR2_HUMAN	Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor (EC 1.10.2.2) (Comp ...	0.03	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side	mitochondrial inner membrane [TAS]	191329		453
Q63619 UniProt NPD GO	COQ7_RAT	Ubiquinone biosynthesis protein COQ7 homolog (Coenzyme Q biosynthesis protein 7 homolog) (Timing pro ...	0.03	-	nuc	0					179
Q3SZ52 UniProt NPD GO	UB2V1_BOVIN	Ubiquitin-conjugating enzyme E2 variant 1 (UEV-1)	0.03	-	mit	0	Nucleus (By similarity)				147
P21734 UniProt NPD GO	UBC1_YEAST	Ubiquitin-conjugating enzyme E2-24 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.03	-	nuc	0		proteasome complex (sensu Eukaryota) [IPI]		1TTE	215
P49427 UniProt NPD GO	UB2R1_HUMAN	Ubiquitin-conjugating enzyme E2-32 kDa complementing (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiqu ...	0.03	-	cyt	0		nucleus [NAS]	116948		236
Q641F1 UniProt NPD GO	UBCP1_XENLA	Ubiquitin-like domain-containing CTD phosphatase 1 (EC 3.1.3.16)	0.03	-	cyt	0	Nucleus (By similarity)				318
Q28EX9 UniProt NPD GO	UBCP1_XENTR	Ubiquitin-like domain-containing CTD phosphatase 1 (EC 3.1.3.16)	0.03	-	cyt	0	Nucleus (By similarity)				318
O95164 UniProt NPD GO	UBL3_HUMAN	Ubiquitin-like protein 3 (HCG-1 protein)	0.03	-	nuc	0			604711	2GOW	117
Q9Z2M6 UniProt NPD GO	UBL3_MOUSE	Ubiquitin-like protein 3 (HCG-1 protein)	0.03	-	nuc	0				1WGH	117
Q9V998 UniProt NPD GO	UBL5_DROME	Ubiquitin-like protein 5	0.03	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [ISS]			73
Q9CR09 UniProt NPD GO	UFC1_MOUSE	Ufm1-conjugating enzyme 1 (Ubiquitin-fold modifier-conjugating enzyme 1)	0.03	-	cyt	0					167
P34280 UniProt NPD GO	YKK3_CAEEL	Uncharacterized GTP-binding protein C02F5.3	0.03	-	cyt	0					366
P38893 UniProt NPD GO	YH10_YEAST	Uncharacterized isomerase YHR210C (EC 5.-.-.-)	0.03	-	cyt	0					341
Q9H3H3 UniProt NPD GO	CK068_HUMAN	Uncharacterized protein C11orf68 (Basophilic leukemia expressed protein Bles03) (Protein p5326)	0.03	-	cyt	0				1ZTP	251
Q9NQR7 UniProt NPD GO	CN162_HUMAN	Uncharacterized protein C14orf162 (Myelin proteolipid protein-like protein)	0.03	-	mit	0					88
Q5R5V2 UniProt NPD GO	CT103_PONPY	Uncharacterized protein C20orf103 homolog precursor	0.03	-	mit	0					223
Q5ZLH4 UniProt NPD GO	CT030_CHICK	Uncharacterized protein C20orf30 homolog	0.03	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				120
Q8CIB6 UniProt NPD GO	CT030_MOUSE	Uncharacterized protein C20orf30 homolog	0.03	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				120
Q5R8X3 UniProt NPD GO	CT030_PONPY	Uncharacterized protein C20orf30 homolog	0.03	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				120
Q5BJP5 UniProt NPD GO	CT030_RAT	Uncharacterized protein C20orf30 homolog	0.03	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				120
P34370 UniProt NPD GO	YLJ7_CAEEL	Uncharacterized protein C50C3.7 (EC 3.1.3.-)	0.03	-	cyt	0					398
P38256 UniProt NPD GO	YBU6_YEAST	Uncharacterized protein YBR096W	0.03	-	mit	0		endoplasmic reticulum [IDA]			230
P38325 UniProt NPD GO	YB80_YEAST	Uncharacterized protein YBR230C	0.03	-	nuc	0	Membrane; multi-pass membrane protein (Potential)	integral to mitochondrial outer membrane [IDA] mitochondrion [IDA]			134
P38957 UniProt NPD GO	YD078_YEAST	Uncharacterized protein YDR078C	0.03	-	cyt	0					223
Q12359 UniProt NPD GO	YD384_YEAST	Uncharacterized protein YDR384C	0.03	-	end	6	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA] plasma membrane [IDA]			275
P32613 UniProt NPD GO	YEF8_YEAST	Uncharacterized protein YEL048C	0.03	-	cyt	0					152
P43558 UniProt NPD GO	YFE4_YEAST	Uncharacterized protein YFL044C	0.03	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			301

You are viewing entries 81951 to 82000 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.