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
Q8BG40 UniProt NPD GO	KTNB1_MOUSE	Katanin p80 WD40-containing subunit B1 (Katanin p80 subunit B1) (p80 katanin)	0.41	-	nuc	0	Cytoplasm (By similarity). Predominantly. Centrosome (By similarity). Spindle (By similarity). Also ...	axon [IDA] centrosome [IDA]			658
Q8BFQ9 UniProt NPD GO	KLDC5_MOUSE	Kelch domain-containing protein 5	0.41	-	cyt	0					493
Q9P2G3 UniProt NPD GO	KLH14_HUMAN	Kelch-like protein 14	0.41	-	mit	0					628
Q61897 UniProt NPD GO	K1H3_MOUSE	Keratin, type I cuticular Ha3 (Hair keratin, type I Ha3) (Fragment)	0.41	-	nuc	0					323
Q14533 UniProt NPD GO	KRHB1_HUMAN	Keratin, type II cuticular Hb1 (Hair keratin, type II Hb1) (ghHKb1) (ghHb1) (MLN 137)	0.41	-	nuc	0			602153		505
O43790 UniProt NPD GO	KRHB6_HUMAN	Keratin, type II cuticular Hb6 (Hair keratin, type II Hb6) (ghHb6)	0.41	-	nuc	0		intermediate filament [NAS]	601928		486
Q922U2 UniProt NPD GO	K2C5_MOUSE	Keratin, type II cytoskeletal 5 (Cytokeratin-5) (CK-5) (Keratin-5) (K5)	0.41	-	cyt	0					580
Q6P6Q2 UniProt NPD GO	K2C5_RAT	Keratin, type II cytoskeletal 5 (Cytokeratin-5) (CK-5) (Keratin-5) (K5)	0.41	-	cyt	0					576
P08729 UniProt NPD GO	K2C7_HUMAN	Keratin, type II cytoskeletal 7 (Cytokeratin-7) (CK-7) (Keratin-7) (K7) (Sarcolectin)	0.41	-	mit	0		intermediate filament [NAS]	148059		468
P02537 UniProt NPD GO	K1C0_XENLA	Keratin-3, type I cytoskeletal 51 kDa (51 kDa cytokeratin)	0.41	-	cyt	0					486
Q3SY46 UniProt NPD GO	KR133_HUMAN	Keratin-associated protein 13-3	0.41	-	nuc	0					172
Q9BYQ7 UniProt NPD GO	KR410_HUMAN	Keratin-associated protein 4-10 (Keratin-associated protein 4.10) (Ultrahigh sulfur keratin-associat ...	0.41	-	nuc	0					127
Q9Z2Y9 UniProt NPD GO	KLOT_RAT	Klotho precursor (EC 3.2.1.31) [Contains: Klotho peptide]	0.41	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Its shedding leads to a soluble ...	membrane [TAS]			1014
P05229 UniProt NPD GO	KNOB_PLAFD	Knob-associated histidine-rich protein (KAHRP) (Fragment)	0.41	+	nuc	0	Host: Cell membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of the membrane ...				277
Q9R097 UniProt NPD GO	SPIT1_MOUSE	Kunitz-type protease inhibitor 1 precursor (Hepatocyte growth factor activator inhibitor type 1) (HA ...	0.41	-	end	1	Secreted protein (By similarity)				507
Q9JJ69 UniProt NPD GO	KCIP2_MOUSE	Kv channel-interacting protein 2 (KChIP2) (A-type potassium channel modulatory protein 2) (Potassium ...	0.41	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity)				270
Q9JM59 UniProt NPD GO	KCIP2_RAT	Kv channel-interacting protein 2 (KChIP2) (A-type potassium channel modulatory protein 2) (Potassium ...	0.41	-	nuc	0	Cell membrane; peripheral membrane protein				270
Q96G23 UniProt NPD GO	LASS2_HUMAN	LAG1 longevity assurance homolog 2 (Tumor metastasis-suppressor gene 1 protein) (SP260)	0.41	-	end	5 *	Nucleus; nuclear membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum; endoplasm ...		606920		380
Q9SK08 UniProt NPD GO	LBD11_ARATH	LOB domain-containing protein 11	0.41	-	nuc	0					229
Q17093 UniProt NPD GO	LWA_ANESU	LWamide neuropeptides precursor [Contains: LWamide I; LWamide II; Metamorphosin A (MMA); IWamide] (F ...	0.41	-	nuc	0	Secreted protein				126
P38096 UniProt NPD GO	LAMB_EMENI	Lactam utilization protein lamB	0.41	-	cyt	0					262
Q05190 UniProt NPD GO	LE19A_HORVU	Late embryogenesis abundant protein B19.1A (B19.1)	0.41	-	nuc	0					93
P54684 UniProt NPD GO	LEB1_BOMMO	Lebocin-1/2 precursor	0.41	-	mit	0	Secreted protein				179
O15946 UniProt NPD GO	LEB4_BOMMO	Lebocin-4 precursor (Leb 4)	0.41	-	mit	0	Secreted protein				179
Q4WS57 UniProt NPD GO	LCMT1_ASPFU	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-) (Protein phosphatase methyltransferase 1)	0.41	-	mit	0					398
Q9ULH4 UniProt NPD GO	LRFN2_HUMAN	Leucine-rich repeat and fibronectin type-III domain-containing protein 2 precursor	0.41	-	end	1	Membrane; single-pass type I membrane protein (Potential)				789
Q9BE71 UniProt NPD GO	LRFN2_MACFA	Leucine-rich repeat and fibronectin type-III domain-containing protein 2 precursor	0.41	-	end	1	Membrane; single-pass type I membrane protein (Potential)				789
Q8R502 UniProt NPD GO	LRC8C_MOUSE	Leucine-rich repeat-containing protein 8C (Protein AD158)	0.41	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				803
Q8N6C8 UniProt NPD GO	LIRA3_HUMAN	Leukocyte immunoglobulin-like receptor subfamily A member 3 precursor (Leukocyte immunoglobulin-like ...	0.41	-	nuc	0	Secreted protein (Probable)	plasma membrane [TAS]	604818		439
Q7YKW4 UniProt NPD GO	CHLN_CHLPR	Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) (LI-POR subunit N) (DPOR sub ...	0.41	+	cyt	0	Plastid; chloroplast				435
P56303 UniProt NPD GO	CHLN_CHLVU	Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) (LI-POR subunit N) (DPOR sub ...	0.41	+	cyt	0	Plastid; chloroplast				435
P35950 UniProt NPD GO	LDLR_CRIGR	Low-density lipoprotein receptor precursor (LDL receptor)	0.41	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS] plasma membrane [ISS]			854
O00754 UniProt NPD GO	MA2B1_HUMAN	Lysosomal alpha-mannosidase precursor (EC 3.2.1.24) (Mannosidase, alpha B) (Lysosomal acid alpha-man ...	0.41	-	cyt	0	Lysosome		609458		1010
Q5RFQ6 UniProt NPD GO	LOXL2_PONPY	Lysyl oxidase homolog 2 precursor (EC 1.4.3.-) (Lysyl oxidase-like protein 2)	0.41	-	exc	0	Secreted protein; extracellular space (Potential)				774
Q62190 UniProt NPD GO	RON_MOUSE	Macrophage-stimulating protein receptor precursor (EC 2.7.10.1) (MSP receptor) (p185-Ron) (Stem cell ...	0.41	-	end	1	Membrane; single-pass type I membrane protein	plasma membrane [IDA] stress fiber [IDA]			1378
Q6P3L0 UniProt NPD GO	MVP_BRARE	Major vault protein (MVP)	0.41	-	cyt	0	Cytoplasm (By similarity)				863
Q9DGM7 UniProt NPD GO	MVP_ICTPU	Major vault protein (MVP) (Fragment)	0.41	-	cyt	0	Cytoplasm (By similarity)				871
P34118 UniProt NPD GO	MVPA_DICDI	Major vault protein alpha (MVP-alpha)	0.41	-	cyt	0	Cytoplasm				843
P51512 UniProt NPD GO	MMP16_HUMAN	Matrix metalloproteinase-16 precursor (EC 3.4.24.-) (MMP-16) (Membrane-type matrix metalloproteinase ...	0.41	-	end	1	Isoform Long: Cell membrane; single-pass type I membrane protein (Potential). Isoform Short: Secrete ...	integral to plasma membrane [TAS] plasma membrane [TAS]	602262	1RM8	607
Q58T40 UniProt NPD GO	M3H16_BOMMX	Maximins 3/H16 precursor [Contains: Maximin-3; Maximin-H16]	0.41	-	end	0	Secreted protein				144
Q58T69 UniProt NPD GO	M3H91_BOMMX	Maximins 3/H9 type 1 precursor [Contains: Maximin-3; Maximin-H9]	0.41	-	end	0	Secreted protein				145
Q58T80 UniProt NPD GO	M3H92_BOMMX	Maximins 3/H9 type 2 precursor [Contains: Maximin-3; Maximin-H9]	0.41	-	end	0	Secreted protein				144
Q9NPJ6 UniProt NPD GO	MED4_HUMAN	Mediator complex subunit 4 (Mediator of RNA polymerase II transcription subunit 4) (Vitamin D3 recep ...	0.41	-	nuc	0	Nucleus	mediator complex [IEP] nucleus [IDA]	605718		270
Q02721 UniProt NPD GO	RE102_YEAST	Meiotic recombination protein REC102	0.41	-	mit	0		condensed nuclear chromosome [IDA] nucleus [IPI]			200
Q92378 UniProt NPD GO	RE104_SACPA	Meiotic recombination protein REC104	0.41	-	nuc	0					183
P31424 UniProt NPD GO	MGR5_RAT	Metabotropic glutamate receptor 5 precursor (mGluR5)	0.41	-	end	6	Membrane; multi-pass membrane protein	membrane fraction [IDA] postsynaptic membrane [TAS]		1DDV	1203
O77480 UniProt NPD GO	FMT_BOVIN	Methionyl-tRNA formyltransferase, mitochondrial precursor (EC 2.1.2.9) (MtFMT) (Fragment)	0.41	-	mit	0	Mitochondrion				372
Q9WU20 UniProt NPD GO	MTHR_MOUSE	Methylenetetrahydrofolate reductase (EC 1.5.1.20)	0.41	-	nuc	0					654
P55158 UniProt NPD GO	MTP_MESAU	Microsomal triglyceride transfer protein large subunit precursor	0.41	-	exc	0	Endoplasmic reticulum				895
Q5YCW0 UniProt NPD GO	TAU_GORGO	Microtubule-associated protein tau	0.41	-	nuc	0	Cytoplasm; cytosol (By similarity). Cell membrane (By similarity). Mostly found in the axons of neur ...	axon [ISS] cytosol [ISS] growth cone [ISS] microtubule associated complex [ISS] plasma membrane [ISS] tubulin [ISS]			775

You are viewing entries 31201 to 31250 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.)

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