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
O42368 UniProt NPD GO	HXB3A_BRARE	Homeobox protein Hox-B3a (Hox-B3)	0.54	+	nuc	0	Nucleus				417
P24340 UniProt NPD GO	HXD9_CHICK	Homeobox protein Hox-D9 (Chox-4.4) (Fragment)	0.54	+	nuc	0	Nucleus				60
Q26603 UniProt NPD GO	SMOX4_SCHMA	Homeobox protein SMOX-4 (Fragment)	0.54	-	nuc	0	Nucleus (Probable)				98
Q4V793 UniProt NPD GO	HIPK4_RAT	Homeodomain-interacting protein kinase 4 (EC 2.7.11.1)	0.54	-	cyt	0	Cytoplasm (Probable)				616
P38839 UniProt NPD GO	YHT6_YEAST	Hypothetical 17.0 kDa protein in YCK1-ARO9 intergenic region	0.54	-	nuc	0		cytoplasm [IDA]			148
P92524 UniProt NPD GO	M880_ARATH	Hypothetical mitochondrial protein AtMg00880 (ORF187)	0.54	-	nuc	0	Mitochondrion (Potential)				187
P42171 UniProt NPD GO	YKL4_CAEEL	Hypothetical protein C03C10.4	0.54	-	nuc	0					244
P42173 UniProt NPD GO	YKL6_CAEEL	Hypothetical protein C03C10.6	0.54	-	nuc	0					870
Q10204 UniProt NPD GO	YBX4_SCHPO	Hypothetical protein C17D1.04 in chromosome II	0.54	-	nuc	0					250
Q18078 UniProt NPD GO	YXT2_CAEEL	Hypothetical protein C18B2.2	0.54	-	nuc	1 *					356
O60147 UniProt NPD GO	YNSH_SCHPO	Hypothetical protein C18H10.17c in chromosome II	0.54	-	nuc	0					175
O14116 UniProt NPD GO	YKX1_SCHPO	Hypothetical protein C328.01c in chromosome I	0.54	-	vac	0					1234
O13647 UniProt NPD GO	YGWB_SCHPO	Hypothetical protein C8D2.11 in chromosome II	0.54	-	nuc	0					122
P34504 UniProt NPD GO	YMV2_CAEEL	Hypothetical protein K04H4.2 precursor	0.54	-	exc	0					967
Q21955 UniProt NPD GO	YNL5_CAEEL	Hypothetical protein R12B2.5	0.54	-	nuc	0					780
Q03609 UniProt NPD GO	YN83_CAEEL	Hypothetical protein ZC84.3	0.54	-	nuc	0					826
Q94402 UniProt NPD GO	YHHN_CAEEL	Hypothetical protein ZK265.6	0.54	+	nuc	0					189
Q09664 UniProt NPD GO	YS55_CAEEL	Hypothetical protein ZK673.5	0.54	-	nuc	0					146
P01881 UniProt NPD GO	IGHD_MOUSE	Ig delta chain C region secreted form	0.54	-	nuc	0	Secreted protein				257
O95163 UniProt NPD GO	IKAP_HUMAN	IkappaB kinase complex-associated protein (IKK complex-associated protein) (p150)	0.54	-	cyt	0	Cytoplasm		603722		1332
P91276 UniProt NPD GO	IMA2_CAEEL	Importin alpha-2 subunit (Karyopherin alpha-2 subunit)	0.54	-	cyt	0	Cytoplasm	cytoplasm [IEP] nuclear pore [ISS]			531
O15111 UniProt NPD GO	IKKA_HUMAN	Inhibitor of nuclear factor kappa-B kinase alpha subunit (EC 2.7.11.10) (I kappa-B kinase alpha) (Ik ...	0.54	-	nuc	0	Cytoplasm	cytoplasm [TAS]	600664		745
P70118 UniProt NPD GO	IPF1_MESAU	Insulin promoter factor 1 (IPF-1) (Homeodomain protein PDX1)	0.54	+	nuc	0	Nucleus (By similarity)				283
Q02816 UniProt NPD GO	IGF2_ONCMY	Insulin-like growth factor II precursor (IGF-II) (Erythrotropin)	0.54	-	nuc	1 *	Secreted protein				214
P20959 UniProt NPD GO	IBP3_BOVIN	Insulin-like growth factor-binding protein 3 precursor (IGFBP-3) (IBP-3) (IGF-binding protein 3)	0.54	-	nuc	0	Secreted protein	extracellular region [ISS]			291
P15473 UniProt NPD GO	IBP3_RAT	Insulin-like growth factor-binding protein 3 precursor (IGFBP-3) (IBP-3) (IGF-binding protein 3)	0.54	-	nuc	0	Secreted protein	extracellular region [ISS]			292
Q9WV41 UniProt NPD GO	INSL6_RAT	Insulin-like peptide INSL6 precursor (Insulin-like peptide 6) [Contains: Insulin-like peptide INSL6 ...	0.54	-	exc	0	Secreted protein (By similarity)				188
Q96CB8 UniProt NPD GO	PHF22_HUMAN	Integrator complex subunit 12 (PHD finger protein 22)	0.54	-	nuc	0		integrator complex [IDA]			462
Q8WNV2 UniProt NPD GO	PHF22_MACFA	Integrator complex subunit 12 (PHD finger protein 22)	0.54	-	nuc	0					462
Q5RCV7 UniProt NPD GO	PHF22_PONPY	Integrator complex subunit 12 (PHD finger protein 22)	0.54	-	nuc	0					462
Q60677 UniProt NPD GO	ITAE_MOUSE	Integrin alpha-E precursor (Integrin alpha M290) (CD103 antigen) [Contains: Integrin alpha-E light c ...	0.54	-	cyt	1	Membrane; single-pass type I membrane protein				1167
Q64282 UniProt NPD GO	IFIT1_MOUSE	Interferon-induced protein with tetratricopeptide repeats 1 (IFIT-1) (Interferon-induced 56 kDa prot ...	0.54	-	cyt	0					463
P09913 UniProt NPD GO	IFIT2_HUMAN	Interferon-induced protein with tetratricopeptide repeats 2 (IFIT-2) (Interferon-induced 54 kDa prot ...	0.54	-	nuc	0			147040		472
P51617 UniProt NPD GO	IRAK1_HUMAN	Interleukin-1 receptor-associated kinase 1 (EC 2.7.11.1) (IRAK-1)	0.54	-	nuc	0		interleukin-1 receptor complex [NAS]	300283		712
O02743 UniProt NPD GO	IL12A_FELCA	Interleukin-12 alpha chain precursor (IL-12A) (Cytotoxic lymphocyte maturation factor 35 kDa subunit ...	0.54	-	exc	0	Secreted protein				222
Q7T2L7 UniProt NPD GO	I17RD_CHICK	Interleukin-17 receptor D precursor (IL-17 receptor D) (IL-17RD) (Interleukin-17D receptor) (IL-17D ...	0.54	-	end	0	Membrane; single-pass type I membrane protein				741
Q6L7I9 UniProt NPD GO	IL21_CANFA	Interleukin-21 precursor (IL-21)	0.54	-	nuc	0	Secreted protein (By similarity)				146
Q21067 UniProt NPD GO	IFC2_CAEEL	Intermediate filament protein ifc-2 (Intermediate filament protein C2) (IF-C2) (Cel IF C2)	0.54	-	cyt	0	Cytoplasm				622
Q9JKQ4 UniProt NPD GO	IRX5_MOUSE	Iroquois-class homeodomain protein IRX-5 (Iroquois homeobox protein 5) (Homeodomain protein IRXB2)	0.54	-	nuc	0	Nucleus (By similarity)				484
P04264 UniProt NPD GO	K2C1_HUMAN	Keratin, type II cytoskeletal 1 (Cytokeratin-1) (CK-1) (Keratin-1) (K1) (67 kDa cytokeratin) (Hair a ...	0.54	+	nuc	0		cytoskeleton [TAS] intermediate filament [TAS] membrane [IDA]	607654		643
Q5K2N3 UniProt NPD GO	K2C8_PROAT	Keratin, type II cytoskeletal 8 (Cytokeratin-8) (CK-8) (Keratin-8) (K8)	0.54	-	mit	0					496
P05786 UniProt NPD GO	K2C8_BOVIN	Keratin, type II cytoskeletal 8 (Cytokeratin-8) (CK-8) (Keratin-8) (K8) (Cytokeratin-A)	0.54	-	mit	0					477
P04265 UniProt NPD GO	K2C2_XENLA	Keratin, type II cytoskeletal I (Clone PUF164) (Fragment)	0.54	-	cyt	2					419
Q4W7G7 UniProt NPD GO	KR134_CEBAP	Keratin-associated protein 13-4	0.54	-	nuc	0					156
Q4W7G9 UniProt NPD GO	KR134_MACFA	Keratin-associated protein 13-4	0.54	-	nuc	0					156
Q4W7G8 UniProt NPD GO	KR134_MACFU	Keratin-associated protein 13-4	0.54	-	nuc	0					156
Q6P597 UniProt NPD GO	KLC3_HUMAN	Kinesin light chain 3 (kinesin light chain 2) (KLC2-like)	0.54	-	nuc	0	Elongating spermatid tail midpiece, localized in outer dense fibers (ODFs) and associates with mitoc ...		601334		504
Q5E9R6 UniProt NPD GO	LASS4_BOVIN	LAG1 longevity assurance homolog 4	0.54	-	end	5 *	Nucleus; nuclear membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum; endoplasm ...				393
P15131 UniProt NPD GO	LIRP_LOCMI	LIRP precursor (Locusta insulin-related peptide) [Contains: LIRP B chain; 5 kDa peptide (C chain); L ...	0.54	-	exc	0	Secreted protein				145
Q16998 UniProt NPD GO	LWA_ACTEQ	LWamide neuropeptides precursor [Contains: LWamide I; LWamide II; LWamide III; LWamide IV; LWamide V ...	0.54	-	nuc	0	Secreted protein				164

You are viewing entries 22551 to 22600 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.