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
P34950 UniProt NPD GO	ITR5_LUFCY	Trypsin inhibitor 5 precursor (Trypsin inhibitor II) (TGT-II)	0.05	-	nuc	0	Secreted protein				63
P19799 UniProt NPD GO	TRY1_XENLA	Trypsin precursor (EC 3.4.21.4)	0.05	-	vac	0	Secreted protein; extracellular space				243
P35049 UniProt NPD GO	TRYP_FUSOX	Trypsin precursor (EC 3.4.21.4)	0.05	-	exc	0	Secreted protein			1XVO	248
P51382 UniProt NPD GO	TRPA_PORPU	Tryptophan synthase alpha chain (EC 4.2.1.20)	0.05	-	nuc	0	Plastid; chloroplast				273
P14671 UniProt NPD GO	TRPB1_ARATH	Tryptophan synthase beta chain 1, chloroplast precursor (EC 4.2.1.20)	0.05	-	mit	0	Plastid; chloroplast (Probable)				470
Q12109 UniProt NPD GO	SYWC_YEAST	Tryptophanyl-tRNA synthetase, cytoplasmic (EC 6.1.1.2) (Tryptophan--tRNA ligase) (TrpRS)	0.05	-	cyt	0	Cytoplasm	cytoplasm [TAS]			432
P84822 UniProt NPD GO	TY4_ASCTR	Tryptophyllin-4	0.05	-		0	Secreted protein	extracellular region [IDA]			9
Q752Y2 UniProt NPD GO	TBA_ASHGO	Tubulin alpha chain	0.05	-	cyt	0					448
P24635 UniProt NPD GO	TBA_OCTVU	Tubulin alpha chain (Fragment)	0.05	-	cyt	0					240
P06606 UniProt NPD GO	TBA4_DROME	Tubulin alpha-4 chain	0.05	-	cyt	0					462
Q96TU8 UniProt NPD GO	TBB_UROFA	Tubulin beta chain (Beta tubulin)	0.05	-	cyt	0					447
Q8JFG3 UniProt NPD GO	TNFA_SPAAU	Tumor necrosis factor (TNF-alpha)	0.05	-	mit	1 *	Membrane; single-pass type II membrane protein				253
Q9Z2P3 UniProt NPD GO	TNFL4_RAT	Tumor necrosis factor ligand superfamily member 4 (OX40 ligand) (OX40L) (CD252 antigen)	0.05	-	cyt	1 *	Membrane; single-pass type II membrane protein				199
Q06599 UniProt NPD GO	TNFA_BOVIN	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.05	-	nuc	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233
O77764 UniProt NPD GO	TNFA_MACEU	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.05	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				233
P25104 UniProt NPD GO	AGTR1_BOVIN	Type-1 angiotensin II receptor (AT1)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				359
O77590 UniProt NPD GO	AGTR1_SHEEP	Type-1 angiotensin II receptor (AT1)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				359
P29754 UniProt NPD GO	AGTRA_MOUSE	Type-1A angiotensin II receptor (AT1) (AT1A)	0.05	-	end	7 *	Membrane; multi-pass membrane protein	cytoplasm [IDA] endosome [IDA] plasma membrane [IDA]			359
P25095 UniProt NPD GO	AGTRA_RAT	Type-1A angiotensin II receptor (AT1) (AT1A)	0.05	-	end	7 *	Membrane; multi-pass membrane protein	cytoplasmic vesicle [IDA] Golgi apparatus [IDA] integral to membrane [TAS] plasma membrane [IDA]			359
P29755 UniProt NPD GO	AGTRB_MOUSE	Type-1B angiotensin II receptor (AT1B) (AT3)	0.05	-	end	7 *	Membrane; multi-pass membrane protein				359
P17735 UniProt NPD GO	ATTY_HUMAN	Tyrosine aminotransferase (EC 2.6.1.5) (L-tyrosine:2-oxoglutarate aminotransferase) (TAT)	0.05	-	cyt	0			276600		454
Q64434 UniProt NPD GO	PTK6_MOUSE	Tyrosine-protein kinase 6 (EC 2.7.10.2) (SRC-related intestinal kinase)	0.05	-	cyt	0	Cytoplasm. Nucleus. Also found to be membrane-associated. Colocalizes with KHDRBS1, within the nucle ...	nucleus [IDA]			451
P54769 UniProt NPD GO	TYDC2_PAPSO	Tyrosine/DOPA decarboxylase 2 [Includes: DOPA decarboxylase (EC 4.1.1.28) (DDC); Tyrosine decarboxyl ...	0.05	-	cyt	0					531
P54770 UniProt NPD GO	TYDC3_PAPSO	Tyrosine/DOPA decarboxylase 3 [Includes: DOPA decarboxylase (EC 4.1.1.28) (DDC); Tyrosine decarboxyl ...	0.05	-	cyt	0					533
Q6CF02 UniProt NPD GO	ALG14_YARLI	UDP-N-acetylglucosamine transferase subunit ALG14 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.05	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				216
P42864 UniProt NPD GO	GPT_LEIAM	UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase (EC 2.7.8.15) (GPT ...	0.05	-	end	9 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				466
P22309 UniProt NPD GO	UD11_HUMAN	UDP-glucuronosyltransferase 1-1 precursor (EC 2.4.1.17) (UDP-glucuronosyltransferase 1A1) (UDPGT) (U ...	0.05	-	end	2 *	Microsome		606785		533
Q9HAW8 UniProt NPD GO	UD110_HUMAN	UDP-glucuronosyltransferase 1-10 precursor (EC 2.4.1.17) (UDPGT) (UGT1*10) (UGT1-10) (UGT1.10) (UGT- ...	0.05	-	end	1	Microsome		606435		530
Q64637 UniProt NPD GO	UD13_RAT	UDP-glucuronosyltransferase 1-3 precursor (EC 2.4.1.17) (UDPGT) (UGT1*3) (UGT1-03) (UGT1.3) (UGT1A3) ...	0.05	-	end	1	Microsome				531
P35504 UniProt NPD GO	UD15_HUMAN	UDP-glucuronosyltransferase 1-5 precursor (EC 2.4.1.17) (UDP-glucuronosyltransferase 1A5) (UDPGT) (U ...	0.05	-	end	1	Microsome	microsome [NAS]	606430		534
Q9HAW7 UniProt NPD GO	UD17_HUMAN	UDP-glucuronosyltransferase 1-7 precursor (EC 2.4.1.17) (UDP-glucuronosyltransferase 1A7) (UDPGT) (U ...	0.05	-	end	1 *	Microsome		606432		530
Q64633 UniProt NPD GO	UD17_RAT	UDP-glucuronosyltransferase 1-7 precursor (EC 2.4.1.17) (UDPGT) (UGT1*7) (UGT1-07) (UGT1.7) (UGT1A7) ...	0.05	-	cyt	1	Microsome				531
Q64634 UniProt NPD GO	UD18_RAT	UDP-glucuronosyltransferase 1-8 precursor (EC 2.4.1.17) (UDPGT) (UGT1*8) (UGT1-08) (UGT1.8) (UGT1A8) ...	0.05	-	end	1	Microsome				530
O97951 UniProt NPD GO	UDB18_MACFA	UDP-glucuronosyltransferase 2B18 precursor (EC 2.4.1.17) (UDPGT)	0.05	-	cyt	1 *	Microsome (By similarity)				529
Q9BY64 UniProt NPD GO	UDB28_HUMAN	UDP-glucuronosyltransferase 2B28 precursor (EC 2.4.1.17) (UDPGT)	0.05	-	end	1 *	Microsome	endoplasmic reticulum [IDA]	606497		529
P16662 UniProt NPD GO	UDB7_HUMAN	UDP-glucuronosyltransferase 2B7 precursor (EC 2.4.1.17) (UDPGT) (3,4-catechol estrogen specific) (UD ...	0.05	-	end	1	Microsome	membrane fraction [TAS]	600068		529
O02663 UniProt NPD GO	UDB9_MACFA	UDP-glucuronosyltransferase 2B9 precursor (EC 2.4.1.17) (UDPGT)	0.05	-	cyt	1 *	Microsome				529
Q7ZW46 UniProt NPD GO	S35B4_BRARE	UDP-xylose and UDP-N-acetylglucosamine transporter (Solute carrier family 35 member B4)	0.05	-	end	10 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				331
Q9W429 UniProt NPD GO	S35B4_DROME	UDP-xylose and UDP-N-acetylglucosamine transporter-like	0.05	-	end	10 *	Membrane; multi-pass membrane protein (By similarity)	Golgi apparatus [ISS]			352
Q03161 UniProt NPD GO	YMY9_YEAST	UPF0010 protein YMR099C	0.05	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			297
Q10166 UniProt NPD GO	YAUB_SCHPO	UPF0012 protein C26A3.11 (EC 3.5.-.-)	0.05	-	mit	0					322
Q24093 UniProt NPD GO	A23D_DROME	UPF0017 protein CG3488	0.05	-	end	1 *					398
Q7RTV5 UniProt NPD GO	CI021_HUMAN	UPF0308 protein C9orf21	0.05	-	cyt	0					226
Q9D1A0 UniProt NPD GO	CI021_MOUSE	UPF0308 protein C9orf21 homolog	0.05	-	mit	0					226
Q04371 UniProt NPD GO	YMR7_YEAST	UPF0364 protein YMR027W	0.05	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			470
Q9XY35 UniProt NPD GO	UCR10_DROME	Ubiquinol-cytochrome c reductase complex 6.3 kDa protein (EC 1.10.2.2) (Complex III subunit X) (Prot ...	0.05	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				55
P48505 UniProt NPD GO	UCR11_SOLTU	Ubiquinol-cytochrome c reductase complex 6.7 kDa protein (EC 1.10.2.2) (CR6)	0.05	-	mit	0	Mitochondrion; mitochondrial inner membrane				61
Q8R1I1 UniProt NPD GO	UCR10_MOUSE	Ubiquinol-cytochrome c reductase complex 7.2 kDa protein (EC 1.10.2.2) (Cytochrome c1 nonheme 7 kDa ...	0.05	-	mit	1 *	Mitochondrion; mitochondrial inner membrane (By similarity)	mitochondrion [IDA]			64
Q5ZLL5 UniProt NPD GO	COQ5_CHICK	Ubiquinone biosynthesis methyltransferase COQ5, mitochondrial precursor (EC 2.1.1.-)	0.05	-	mit	0	Mitochondrion (By similarity)				311
P52492 UniProt NPD GO	UBC11_YEAST	Ubiquitin-conjugating enzyme E2-18 kDa (EC 6.3.2.19) (Ubiquitin-protein ligase) (Ubiquitin carrier p ...	0.05	-	nuc	0		cytoplasm [IC]			156

You are viewing entries 75851 to 75900 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.