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
Q42533 UniProt NPD GO	BCCP_ARATH	Biotin carboxyl carrier protein of acetyl-CoA carboxylase, chloroplast precursor (BCCP)	0.36	-	mit	0	Plastid; chloroplast				280
P16343 UniProt NPD GO	IBB4_LONCA	Bowman-Birk type proteinase inhibitor DE-4 (DE4)	0.36	-	nuc	0					80
P83965 UniProt NPD GO	ANFB_ACITR	Brain natriuretic peptide precursor (B-type natriuretic peptide)	0.36	-	mit	0	Secreted protein				150
Q805E8 UniProt NPD GO	ANFB_OREMO	Brain natriuretic peptide precursor (B-type natriuretic peptide)	0.36	-	nuc	0	Secreted protein				138
Q61140 UniProt NPD GO	BCAR1_MOUSE	Breast cancer anti-estrogen resistance protein 1 (CRK-associated substrate) (p130cas)	0.36	-	nuc	0	Cell membrane; cell-matrix junction; focal adhesion (By similarity). Cytoplasm (By similarity). Unph ...	cytoplasm [ISS] focal adhesion [ISS] lamellipodium [IDA] membrane fraction [ISS] ruffle [ISS]			874
P39011 UniProt NPD GO	BEM4_YEAST	Bud emergence protein 4	0.36	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			633
Q8BNX1 UniProt NPD GO	CLC4G_MOUSE	C-type lectin domain family 4 member G	0.36	-	nuc	1 *	Membrane; single-pass type II membrane protein (Potential)				294
Q800I7 UniProt NPD GO	ANFC4_ORYLA	C-type natriuretic peptide 4 precursor	0.36	-	nuc	0	Secreted protein				121
P05990 UniProt NPD GO	PYR1_DROME	CAD protein (Protein rudimentary) [Includes: Glutamine-dependent carbamoyl-phosphate synthase (EC 6. ...	0.36	-	nuc	0	Cytoplasm				2224
O46634 UniProt NPD GO	CD166_CANFA	CD166 antigen (Activated leukocyte-cell adhesion molecule) (ALCAM) (SB-10 antigen) (Fragment)	0.36	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				521
Q5REX6 UniProt NPD GO	CK5P3_PONPY	CDK5 regulatory subunit-associated protein 3	0.36	-	cyt	0					506
Q96JB5 UniProt NPD GO	CK5P3_HUMAN	CDK5 regulatory subunit-associated protein 3 (CDK5 activator-binding protein C53) (HSF-27 protein)	0.36	-	cyt	0			608202		506
P53681 UniProt NPD GO	CRK_DAUCA	CDPK-related protein kinase (EC 2.7.11.1) (PK421)	0.36	-	cyt	0					602
Q9XH42 UniProt NPD GO	CET4_TOBAC	CEN-like protein 4	0.36	-	cyt	0	Cytoplasm (By similarity)				175
Q9HFR0 UniProt NPD GO	CSN2_SCHPO	COP9 signalosome complex subunit 2 (CSN complex subunit 2) (SGN2)	0.36	-	nuc	0	Cytoplasm. Nucleus				437
Q6BMQ3 UniProt NPD GO	CSN5_DEBHA	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	0.36	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				469
P19022 UniProt NPD GO	CADH2_HUMAN	Cadherin-2 precursor (Neural-cadherin) (N-cadherin) (CDw325 antigen)	0.36	-	end	1	Membrane; single-pass type I membrane protein		114020		906
Q9MYV1 UniProt NPD GO	CALCA_CANFA	Calcitonin gene-related peptide 1 precursor (Calcitonin gene-related peptide I) (CGRP-I) (Alpha-type ...	0.36	-	exc	0	Secreted protein				128
P01258 UniProt NPD GO	CALC_HUMAN	Calcitonin precursor [Contains: Calcitonin; Katacalcin (Calcitonin carboxyl-terminal peptide) (CCP) ...	0.36	-	exc	0	Secreted protein	endoplasmic reticulum [TAS] extracellular space [TAS] soluble fraction [TAS]	114130		141
Q7M3V5 UniProt NPD GO	CSK_CALVO	Callisulfakinin precursor [Contains: Callisulfakinin-1 (Callisulfakinin I); Callisulfakinin-2 (Calli ...	0.36	-	nuc	1 *	Secreted protein				140
P29402 UniProt NPD GO	CALX1_ARATH	Calnexin homolog 1 precursor	0.36	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				530
Q11002 UniProt NPD GO	CANA_DROME	Calpain A (EC 3.4.22.-) (Calcium-activated neutral proteinase A) (CANP A) [Contains: Calpain A catal ...	0.36	-	cyt	0	Cytoplasm	actin cytoskeleton [IDA] cell soma [IDA] intracellular [IDA]			828
Q9R1S8 UniProt NPD GO	CAN7_MOUSE	Calpain-7 (EC 3.4.22.-) (PalB homolog) (PalBH)	0.36	-	nuc	0	Nucleus (By similarity)				813
Q9EQC0 UniProt NPD GO	CHST1_MOUSE	Carbohydrate sulfotransferase 1 (EC 2.8.2.21) (Keratan sulfate Gal-6 sulfotransferase) (KSST) (KSGal ...	0.36	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				411
Q5RJQ0 UniProt NPD GO	CHST1_RAT	Carbohydrate sulfotransferase 1 (EC 2.8.2.21) (Keratan sulfate Gal-6 sulfotransferase) (KSST) (KSGal ...	0.36	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				411
Q80V53 UniProt NPD GO	CHSTE_MOUSE	Carbohydrate sulfotransferase D4ST1 (EC 2.8.2.-) (Dermatan 4-sulfotransferase 1) (D4ST-1)	0.36	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)	integral to membrane [ISS]			376
Q02723 UniProt NPD GO	RKIN1_SECCE	Carbon catabolite derepressing protein kinase (EC 2.7.11.1)	0.36	-	nuc	0					502
Q8CI85 UniProt NPD GO	CAH12_MOUSE	Carbonic anhydrase 12 precursor (EC 4.2.1.1) (Carbonic anhydrase XII) (Carbonate dehydratase XII) (C ...	0.36	+	end	1	Membrane; single-pass type I membrane protein (By similarity)				354
O43570 UniProt NPD GO	CAH12_HUMAN	Carbonic anhydrase 12 precursor (EC 4.2.1.1) (Carbonic anhydrase XII) (Carbonate dehydratase XII) (C ...	0.36	-	nuc	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS]	603263	1JD0	354
Q95203 UniProt NPD GO	CAH11_SHEEP	Carbonic anhydrase-related protein 2 precursor (CARP 2) (CA-RP II) (CA-XI)	0.36	-	exc	0	Secreted protein (Potential)				328
Q8HY46 UniProt NPD GO	CPT1B_PIG	Carnitine O-palmitoyltransferase I, muscle isoform (EC 2.3.1.21) (CPT I) (CPTI-M) (Carnitine palmito ...	0.36	-	nuc	1	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				772
P97864 UniProt NPD GO	CASP7_MOUSE	Caspase-7 precursor (EC 3.4.22.-) (CASP-7) (LICE2 cysteine protease) (Apoptotic protease Mch-3) [Con ...	0.36	-	nuc	0	Cytoplasm				303
O14613 UniProt NPD GO	BORG1_HUMAN	Cdc42 effector protein 2 (Binder of Rho GTPases 1)	0.36	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein	cytoplasm [IDA] membrane [IDA]	606132		210
Q5F362 UniProt NPD GO	CC50A_CHICK	Cell cycle control protein 50A (Transmembrane protein 30A)	0.36	-	mit	2	Membrane; multi-pass membrane protein (Potential)				372
P25694 UniProt NPD GO	CDC48_YEAST	Cell division control protein 48	0.36	+	nuc	0	Microsome. Bound loosely to components of the microsomal fraction	cytosol [IDA] endoplasmic reticulum membrane [IDA] microsome [IDA] nucleus [IDA]			835
Q9NWW5 UniProt NPD GO	CLN6_HUMAN	Ceroid-lipofuscinosis neuronal protein 6 (Protein CLN6)	0.36	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein		606725		311
Q85FW4 UniProt NPD GO	DNAK_CYAME	Chaperone protein dnaK (Heat shock protein 70) (Heat shock 70 kDa protein) (HSP70)	0.36	-	cyt	0	Plastid; chloroplast				607
P30600 UniProt NPD GO	CHS1_EXODE	Chitin synthase 1 (EC 2.4.1.16) (Chitin-UDP acetyl-glucosaminyl transferase 1) (Class-II chitin synt ...	0.36	-	end	7	Cell membrane; multi-pass membrane protein				988
P35523 UniProt NPD GO	CLCN1_HUMAN	Chloride channel protein, skeletal muscle (Chloride channel protein 1) (ClC-1)	0.36	-	end	11	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	255700		988
P59758 UniProt NPD GO	RR13_CYAME	Chloroplast 30S ribosomal protein S13	0.36	-	nuc	0	Plastid; chloroplast				123
Q9TLQ7 UniProt NPD GO	RR14_CYACA	Chloroplast 30S ribosomal protein S14	0.36	-	nuc	0	Plastid; chloroplast				100
Q6ENB2 UniProt NPD GO	RR15_ORYNI	Chloroplast 30S ribosomal protein S15	0.36	-	nuc	0	Plastid; chloroplast				90
P12150 UniProt NPD GO	RR15_ORYSA	Chloroplast 30S ribosomal protein S15	0.36	-	nuc	0	Plastid; chloroplast				90
Q6B8V9 UniProt NPD GO	RR3_GRATL	Chloroplast 30S ribosomal protein S3	0.36	-	mit	0	Plastid; chloroplast				217
Q85WZ0 UniProt NPD GO	RR3_PINKO	Chloroplast 30S ribosomal protein S3	0.36	-	mit	0	Plastid; chloroplast				217
Q95H49 UniProt NPD GO	RR3_WHEAT	Chloroplast 30S ribosomal protein S3	0.36	-	nuc	0	Plastid; chloroplast				239
Q9TLY7 UniProt NPD GO	RR4A_CYACA	Chloroplast 30S ribosomal protein S4	0.36	-	nuc	0	Plastid; chloroplast				202
Q9SMG1 UniProt NPD GO	RR4_FUNHY	Chloroplast 30S ribosomal protein S4	0.36	-	mit	0	Plastid; chloroplast				201
P49495 UniProt NPD GO	RR7_ODOSI	Chloroplast 30S ribosomal protein S7	0.36	-	mit	0	Plastid; chloroplast				158
Q5SD18 UniProt NPD GO	RK16_HUPLU	Chloroplast 50S ribosomal protein L16	0.36	-	mit	0	Plastid; chloroplast				142

You are viewing entries 34801 to 34850 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.