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
Q9SN58 UniProt NPD GO	GALE2_ARATH	Probable UDP-glucose 4-epimerase At4g10960 (EC 5.1.3.2) (Galactowaldenase) (UDP-galactose 4-epimeras ...	0.00	-	mit	0					350
Q9T0A7 UniProt NPD GO	GALE3_ARATH	Probable UDP-glucose 4-epimerase At4g23920 (EC 5.1.3.2) (Galactowaldenase) (UDP-galactose 4-epimeras ...	0.00	-	cyt	0					350
Q9M9P3 UniProt NPD GO	UGPA2_ARATH	Probable UTP--glucose-1-phosphate uridylyltransferase 2 (EC 2.7.7.9) (UDP-glucose pyrophosphorylase ...	0.00	-	cyt	0	Cytoplasm (By similarity)			1Z90	469
Q9FIK7 UniProt NPD GO	THIC2_ARATH	Probable acetyl-CoA acetyltransferase, cytosolic 2 (EC 2.3.1.9) (Cytosolic acetoacetyl-CoA thiolase ...	0.00	-	cyt	0	Cytoplasm (Potential)				415
Q8W036 UniProt NPD GO	NIP42_ARATH	Probable aquaporin NIP4.2 (NOD26-like intrinsic protein 4.2) (Nodulin-26-like major intrinsic protei ...	0.00	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				283
Q9M1K3 UniProt NPD GO	SIP21_ARATH	Probable aquaporin SIP2.1 (Small basic intrinsic protein 2.1)	0.00	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				237
P42067 UniProt NPD GO	TIP1_MEDSA	Probable aquaporin TIP-type (Membrane channel protein 1) (MsMCP1)	0.00	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				249
Q9FY14 UniProt NPD GO	TIP1_MEDTR	Probable aquaporin TIP-type (MtAQP1)	0.00	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				250
P24422 UniProt NPD GO	TIP2_TOBAC	Probable aquaporin TIP-type RB7-18C (Tonoplast intrinsic protein, root-specific RB7-18C) (TobRB7) (R ...	0.00	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				250
P21653 UniProt NPD GO	TIP1_TOBAC	Probable aquaporin TIP-type RB7-5A (Tonoplast intrinsic protein, root-specific RB7-5A) (TobRB7) (RT- ...	0.00	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				250
P50156 UniProt NPD GO	TIP11_ORYSA	Probable aquaporin TIP1.1 (Tonoplast intrinsic protein 1.1) (OsTIP1.1) (rTIP1)	0.00	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				250
Q7XA61 UniProt NPD GO	TIP21_ORYSA	Probable aquaporin TIP2.1 (Tonoplast intrinsic protein 2.1) (OsTIP2.1)	0.00	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				248
Q41975 UniProt NPD GO	TIP22_ARATH	Probable aquaporin TIP2.2 (Tonoplast intrinsic protein 2.2)	0.00	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast				250
Q5Z6F0 UniProt NPD GO	TIP22_ORYSA	Probable aquaporin TIP2.2 (Tonoplast intrinsic protein 2.2) (OsTIP2.2)	0.00	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				248
Q9FGL2 UniProt NPD GO	TIP23_ARATH	Probable aquaporin TIP2.3 (Tonoplast intrinsic protein 2.3)	0.00	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				250
Q7XKI5 UniProt NPD GO	TIP32_ORYSA	Probable aquaporin TIP3.2 (Tonoplast intrinsic protein 3.2) (OsTIP3.2)	0.00	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				265
O82316 UniProt NPD GO	TIP41_ARATH	Probable aquaporin TIP4.1 (Tonoplast intrinsic protein 4.1) (Epsilon-tonoplast intrinsic protein) (E ...	0.00	-	end	7 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				249
Q9LWR0 UniProt NPD GO	TIP42_ORYSA	Probable aquaporin TIP4.2 (Tonoplast intrinsic protein 4.2) (OsTIP4.2)	0.00	-	end	6 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Tonoplast				251
O97069 UniProt NPD GO	ASSY_DROME	Probable argininosuccinate synthase (EC 6.3.4.5) (Citrulline--aspartate ligase)	0.00	-	cyt	0					419
P78780 UniProt NPD GO	DHAS_SCHPO	Probable aspartate-semialdehyde dehydrogenase (EC 1.2.1.11) (ASA dehydrogenase) (ASA DH)	0.00	-	mit	0					357
Q5JLM1 UniProt NPD GO	PIN6_ORYSA	Probable auxin efflux carrier component 6 (OsPIN6)	0.00	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				363
Q8SRK8 UniProt NPD GO	KAPC_ENCCU	Probable cAMP-dependent protein kinase catalytic subunit (EC 2.7.11.11)	0.00	-	cyt	0					322
Q9C5D7 UniProt NPD GO	CAMT3_ARATH	Probable caffeoyl-CoA O-methyltransferase At4g26220 (EC 2.1.1.104) (Trans-caffeoyl-CoA 3-O-methyltra ...	0.00	-	cyt	0					232
Q04432 UniProt NPD GO	HSP31_YEAST	Probable chaperone HSP31	0.00	-	cyt	0		soluble fraction [IDA]		1RW7	237
P81083 UniProt NPD GO	HSP11_PINPS	Probable class I heat shock protein (Water stress-responsive protein 3) (Fragment)	0.00	-		0	Cytoplasm (By similarity)				15
Q9SUT0 UniProt NPD GO	CPR3_ARATH	Probable cysteine proteinase At4g11310 precursor (EC 3.4.22.-)	0.00	-	exc	1 *					364
O80995 UniProt NPD GO	AFP2_ARATH	Probable cysteine-rich antifungal protein At2g26010 precursor (AFP)	0.00	-	exc	1 *	Secreted protein (By similarity)				80
O80994 UniProt NPD GO	AFP3_ARATH	Probable cysteine-rich antifungal protein At2g26020 precursor (AFP)	0.00	-	cyt	1 *	Secreted protein (By similarity)				80
O94391 UniProt NPD GO	CYB51_SCHPO	Probable cytochrome b5 1	0.00	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				124
O48845 UniProt NPD GO	CYB52_ARATH	Probable cytochrome b5 isoform 2	0.00	-	cyt	1	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein; cytoplasmic side ...				134
O74766 UniProt NPD GO	PUT2_SCHPO	Probable delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12) (P5C dehydrogenase)	0.00	-	cyt	0					548
Q9P6Q5 UniProt NPD GO	DUT_SCHPO	Probable deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) (dUTPase) (dUTP pyrophosphat ...	0.00	-	cyt	0					140
Q9BVK2 UniProt NPD GO	ALG8_HUMAN	Probable dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase (EC 2.4.1.-) (Dolichyl ...	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	integral to membrane [NAS]	608104		526
Q21557 UniProt NPD GO	DYL2_CAEEL	Probable dynein light chain 2, cytoplasmic	0.00	-	cyt	0	Cytoplasm (By similarity)				90
P78790 UniProt NPD GO	ETFA_SCHPO	Probable electron transfer flavoprotein subunit alpha, mitochondrial precursor (Alpha-ETF)	0.00	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				341
O80594 UniProt NPD GO	ERG28_ARATH	Probable ergosterol biosynthetic protein 28	0.00	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				110
Q61K76 UniProt NPD GO	IF3C_CAEBR	Probable eukaryotic translation initiation factor 3 subunit 12 (eIF-3 p25) (eIF3k)	0.00	-	cyt	0					240
Q9XUP3 UniProt NPD GO	IF3C_CAEEL	Probable eukaryotic translation initiation factor 3 subunit 12 (eIF-3 p25) (eIF3k)	0.00	-	cyt	0					240
Q03134 UniProt NPD GO	FDH_EMENI	Probable formate dehydrogenase (EC 1.2.1.2) (NAD-dependent formate dehydrogenase) (FDH)	0.00	-	nuc	0					377
Q09610 UniProt NPD GO	LEC8_CAEEL	Probable galaptin lec-8	0.00	-	cyt	0					180
Q9GTW8 UniProt NPD GO	GLK2_TRIVA	Probable glucokinase 2 (EC 2.7.1.2) (Glucose kinase 2) (Hexokinase 2)	0.00	-	cyt	0					377
P81107 UniProt NPD GO	GLNA2_PINPS	Probable glutamine synthetase leaf isozyme (EC 6.3.1.2) (Glutamate--ammonia ligase) (S2205/S2287) (N ...	0.00	-		0	Plastid; chloroplast (By similarity)				15
P32110 UniProt NPD GO	GSTX6_SOYBN	Probable glutathione S-transferase (EC 2.5.1.18) (Heat shock protein 26A) (G2-4)	0.00	-	mit	0					225
P32111 UniProt NPD GO	GSTX1_SOLTU	Probable glutathione S-transferase (EC 2.5.1.18) (Pathogenesis-related protein 1)	0.00	-	nuc	0					217
P91254 UniProt NPD GO	GST8_CAEEL	Probable glutathione S-transferase 8 (EC 2.5.1.18) (GST class-sigma)	0.00	-	cyt	0					206
O22850 UniProt NPD GO	GPX3_ARATH	Probable glutathione peroxidase 3, mitochondrial precursor (EC 1.11.1.9)	0.00	-	mit	1 *	Mitochondrion (Potential)				206
Q8LBU2 UniProt NPD GO	GPX8_ARATH	Probable glutathione peroxidase 8 (EC 1.11.1.9)	0.00	-	cyt	0					167
O02621 UniProt NPD GO	GPX1_CAEEL	Probable glutathione peroxidase F26E4.12 (EC 1.11.1.9)	0.00	-	cyt	0	Cytoplasm (Potential)				163
P90916 UniProt NPD GO	LIN53_CAEEL	Probable histone-binding protein lin-53 (Abnormal cell lineage protein 53)	0.00	-	cyt	0	Nucleus				417
O43056 UniProt NPD GO	KHSE_SCHPO	Probable homoserine kinase (EC 2.7.1.39) (HSK) (HK)	0.00	-	cyt	0					338

You are viewing entries 97151 to 97200 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.