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
P01646 UniProt NPD GO	KV5M_MOUSE	Ig kappa chain V-V region HP 123E6	0.35	-	nuc	0					108
O00505 UniProt NPD GO	IMA3_HUMAN	Importin alpha-3 subunit (Karyopherin alpha-3 subunit) (SRP1-gamma)	0.35	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	nuclear pore [TAS]	601892		521
P52296 UniProt NPD GO	IMB1_RAT	Importin beta-1 subunit (Karyopherin beta-1 subunit) (Nuclear factor P97)	0.35	-	cyt	0	Cytoplasm. Nucleus; nuclear envelope				875
O18388 UniProt NPD GO	IMB_DROME	Importin subunit beta (Karyopherin beta-4 subunit) (Protein ketel)	0.35	-	cyt	0	Cytoplasm	cytoplasm [IDA] nuclear envelope [IDA]			884
Q24008 UniProt NPD GO	INAD_DROME	Inactivation-no-after-potential D protein	0.35	-	cyt	0	Cell membrane; peripheral membrane protein	inaD signaling complex [IPI]		1IHJ	674
P05111 UniProt NPD GO	INHA_HUMAN	Inhibin alpha chain precursor	0.35	-	exc	0	Secreted protein	extracellular region [TAS]	147380		366
Q6C8H7 UniProt NPD GO	MRS2_YARLI	Inner membrane magnesium transporter MRS2, mitochondrial precursor (RNA-splicing protein MRS2)	0.35	-	nuc	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				455
Q29000 UniProt NPD GO	IGF1R_PIG	Insulin-like growth factor 1 receptor (EC 2.7.10.1) (Insulin-like growth factor I receptor) (IGF-I r ...	0.35	-	nuc	1	Membrane; single-pass type I membrane protein				304
Q9WUG6 UniProt NPD GO	INSL5_MOUSE	Insulin-like peptide INSL5 precursor (Insulin-like peptide 5) (Relaxin/insulin-like protein) (Relaxi ...	0.35	-	exc	0	Secreted protein (Probable)				135
P34446 UniProt NPD GO	PAT2_CAEEL	Integrin alpha pat-2 precursor	0.35	-	end	1 *	Membrane; single-pass type I membrane protein (By similarity)				1226
P61622 UniProt NPD GO	ITA11_MOUSE	Integrin alpha-11 precursor	0.35	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				1188
P49134 UniProt NPD GO	ITB1_RAT	Integrin beta-1 precursor (Fibronectin receptor subunit beta) (Integrin VLA-4 subunit beta) (CD29 an ...	0.35	-	end	1	Membrane; single-pass type I membrane protein				799
P38565 UniProt NPD GO	MUCB1_XENLA	Integumentary mucin B.1 (FIM-B.1) (Fragment)	0.35	-	nuc	0	Secreted protein				398
P35849 UniProt NPD GO	IFNA_FELCA	Interferon alpha precursor (IFN-alpha)	0.35	-	exc	0	Secreted protein				194
P05003 UniProt NPD GO	IFNA1_HORSE	Interferon alpha-1 precursor	0.35	-	exc	0	Secreted protein				184
P05015 UniProt NPD GO	IFN16_HUMAN	Interferon alpha-16 precursor (Interferon alpha-WA)	0.35	-	mit	0	Secreted protein		147580		189
P70499 UniProt NPD GO	IFNB_RAT	Interferon beta precursor (IFN-beta)	0.35	-	exc	0	Secreted protein				184
P97431 UniProt NPD GO	IRF6_MOUSE	Interferon regulatory factor 6 (IRF-6)	0.35	-	nuc	0	Nucleus (Potential)				467
P70434 UniProt NPD GO	IRF7_MOUSE	Interferon regulatory factor 7 (IRF-7)	0.35	-	mit	0	Nucleus. Cytoplasm. The phosphorylated and active form accumulates selectively in the nucleus (By si ...				457
P56832 UniProt NPD GO	IFNT3_SHEEP	Interferon tau-3 (IFN-tau3) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolysin) (Trophob ...	0.35	-	cyt	0	Secreted protein. Secreted into the uterine lumen				172
Q08072 UniProt NPD GO	IFNT8_SHEEP	Interferon tau-8 precursor (IFN-tau8) (Trophoblast protein 1) (TP-1) (Trophoblastin) (Antiluteolysin ...	0.35	-	vac	1 *	Secreted protein. Secreted into the uterine lumen				195
P10749 UniProt NPD GO	IL1B_MOUSE	Interleukin-1 beta precursor (IL-1 beta)	0.35	-	cyt	0	Secreted protein. The lack of a specific hydrophobic segment in the precursor sequence suggests that ...			8I1B	269
P26890 UniProt NPD GO	IL1RA_RABIT	Interleukin-1 receptor antagonist protein precursor (IL-1ra) (IRAP) (IL1 inhibitor) (IL-1RN)	0.35	-	exc	0	Secreted protein (By similarity)				177
P13504 UniProt NPD GO	IL1R1_MOUSE	Interleukin-1 receptor type I precursor (IL-1R-1) (p80) (CD121a antigen)	0.35	-	end	1	Membrane; single-pass type I membrane protein			1OU3	576
P46649 UniProt NPD GO	IL2_CERTO	Interleukin-2 precursor (IL-2) (T-cell growth factor) (TCGF)	0.35	-	mit	0	Secreted protein	extracellular space [ISS]			154
O35736 UniProt NPD GO	IL6_MARMO	Interleukin-6 precursor (IL-6)	0.35	-	exc	0	Secreted protein				207
P40190 UniProt NPD GO	IL6RB_RAT	Interleukin-6 receptor beta chain precursor (IL-6R-beta) (Interleukin 6 signal transducer) (Membrane ...	0.35	-	nuc	1	Membrane; single-pass type I membrane protein				918
Q6TA49 UniProt NPD GO	IYD1_PIG	Iodotyrosine dehalogenase 1 precursor (EC 1.-.-.-) (IYD-1)	0.35	-	mit	1 *	Membrane; single-pass membrane protein (By similarity)				289
Q26492 UniProt NPD GO	ITPL_SCHGR	Ion transport peptide-like precursor	0.35	-	mit	1 *	Secreted protein				134
P38310 UniProt NPD GO	FTH1_YEAST	Iron transporter FTH1	0.35	-	end	7 *	Vacuole; vacuolar membrane; multi-pass membrane protein	vacuolar membrane (sensu Fungi) [IDA]			465
Q5ZKA2 UniProt NPD GO	SYIM_CHICK	Isoleucyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS)	0.35	-	nuc	0	Mitochondrion; mitochondrial matrix (By similarity)				1000
Q9NSE4 UniProt NPD GO	SYIM_HUMAN	Isoleucyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.5) (Isoleucine--tRNA ligase) (IleRS)	0.35	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				1012
Q9Y4A0 UniProt NPD GO	JERKL_HUMAN	Jerky protein homolog-like (HHMJG)	0.35	-	cyt	0		nucleus [TAS]	603211		442
P40034 UniProt NPD GO	JHD1_YEAST	JmjC domain-containing histone demethylation protein 1 (EC 1.14.11.-) (ScJHDM1)	0.35	+	nuc	0	Nucleus (By similarity)				492
Q09848 UniProt NPD GO	YAE8_SCHPO	KH domain-containing protein C23D3.08	0.35	-	nuc	0					382
Q60749 UniProt NPD GO	SAM68_MOUSE	KH domain-containing, RNA-binding, signal transduction-associated protein 1 (p21 Ras GTPase-activati ...	0.35	-	nuc	0	Nucleus. Membrane	membrane [ISS] nucleus [ISS]			443
Q6TDP4 UniProt NPD GO	KLH17_HUMAN	Kelch-like protein 17 (Actinfilin)	0.35	-	cyt	0	Postsynaptic density (By similarity)				642
P08131 UniProt NPD GO	KRB2D_SHEEP	Keratin, high-sulfur matrix protein, B2D	0.35	-	mit	0					181
Q6IFV1 UniProt NPD GO	K1C14_RAT	Keratin, type I cytoskeletal 14 (Cytokeratin-14) (CK-14) (Keratin-14) (K14) (Type I keratin Ka14)	0.35	-	nuc	0		keratin filament [IDA]			485
P48667 UniProt NPD GO	K2C6D_HUMAN	Keratin, type II cytoskeletal 6D (Cytokeratin-6D) (CK 6D) (K6d keratin) (Fragment)	0.35	-	nuc	0					384
Q8IUG1 UniProt NPD GO	KRA13_HUMAN	Keratin-associated protein 1-3 (Keratin-associated protein 1.8) (Keratin-associated protein 1.9)	0.35	-	nuc	0			608820		177
P60014 UniProt NPD GO	KR10A_HUMAN	Keratin-associated protein 10-10 (Keratin-associated protein 10.10) (High sulfur keratin-associated ...	0.35	-	nuc	0					251
Q8IUC0 UniProt NPD GO	KR131_HUMAN	Keratin-associated protein 13-1 (High sulfur keratin-associated protein 13.1)	0.35	-	nuc	0			608718		172
Q9BYQ1 UniProt NPD GO	KRA95_HUMAN	Keratin-associated protein 9-5 (Keratin-associated protein 9.5) (Ultrahigh sulfur keratin-associated ...	0.35	-	mit	0					111
P46870 UniProt NPD GO	KLP1_CHLRE	Kinesin-like protein KLP1	0.35	-	mit	0	Flagellum; flagellar axoneme. Bound to the central pair microtubule C2 or to projections that are at ...				776
P83055 UniProt NPD GO	KNL2_BOMMX	Kininogen-2 precursor (BMK-2) [Contains: Maximakinin; Bradykinin; Maximakinin-associated peptide]	0.35	-	exc	0	Secreted protein				114
Q90Y90 UniProt NPD GO	KREM1_XENLA	Kremen protein 1 precursor (Kringle-containing protein marking the eye and the nose) (Dickkopf recep ...	0.35	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				452
P83036 UniProt NPD GO	ILLA_LEUGL	Kunitz-type trypsin inhibitor LlTI, alpha chain	0.35	-	nuc	0	Secreted protein			1LT2	137
Q924Z4 UniProt NPD GO	LASS2_MOUSE	LAG1 longevity assurance homolog 2 (Translocating chain-associating membrane protein homolog 3) (TRA ...	0.35	-	end	6 *	Nucleus; nuclear membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum; endoplasm ...				380
Q3U9G9 UniProt NPD GO	LBR_MOUSE	Lamin-B receptor (Integral nuclear envelope inner membrane protein)	0.35	+	end	7	Nucleus; nuclear inner membrane; multi-pass membrane protein (By similarity)	nuclear inner membrane [TAS] nuclear lamina [TAS]			626

You are viewing entries 35951 to 36000 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.