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
Q91766 UniProt NPD GO	HNF4A_XENLA	Hepatocyte nuclear factor 4-alpha (HNF-4-alpha)	0.66	-	nuc	0	Nucleus				455
P49698 UniProt NPD GO	HNF4A_MOUSE	Hepatocyte nuclear factor 4-alpha (HNF-4-alpha) (Transcription factor HNF-4) (Transcription factor 1 ...	0.66	-	nuc	0	Nucleus	nucleus [IDA]			465
Q4U3Y2 UniProt NPD GO	HXK1_ASPFU	Hexokinase-1 (EC 2.7.1.1) (Hexokinase I)	0.66	+	cyt	0					549
P52926 UniProt NPD GO	HMGA2_HUMAN	High mobility group protein HMGI-C (High mobility group AT-hook protein 2)	0.66	+	nuc	0	Nucleus		600698		109
P27326 UniProt NPD GO	H2B_URECA	Histone H2B	0.66	+	nuc	0	Nucleus				122
P40285 UniProt NPD GO	H3_LEIIN	Histone H3	0.66	-	nuc	0	Nucleus (By similarity)				129
Q750F5 UniProt NPD GO	HAT1_ASHGO	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.66	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				391
P46692 UniProt NPD GO	HMD1_CHICK	Homeobox protein CHOX-CAD	0.66	+	nuc	0	Nucleus				248
Q99160 UniProt NPD GO	HOY1_YARLI	Homeobox protein HOY1	0.66	-	nuc	0	Nucleus (Potential)				509
Q08821 UniProt NPD GO	HXA1_XENLA	Homeobox protein Hox-A1 (Hox.lab2) (Fragment)	0.66	+	nuc	0	Nucleus				240
O42365 UniProt NPD GO	HXA2B_BRARE	Homeobox protein Hox-A2b (Hox-A2)	0.66	+	nuc	0	Nucleus				363
Q7T3J5 UniProt NPD GO	HXA3_CHICK	Homeobox protein Hox-A3	0.66	+	nuc	0	Nucleus (By similarity)				413
Q9YGT6 UniProt NPD GO	HXA5A_BRARE	Homeobox protein Hox-A5a	0.66	+	nuc	0	Nucleus (By similarity)				265
Q5YLH5 UniProt NPD GO	HXA6_CHICK	Homeobox protein Hox-A6	0.66	+	nuc	0	Nucleus (By similarity)				231
P09092 UniProt NPD GO	HXA6_MOUSE	Homeobox protein Hox-A6 (Hox-1.2) (M5-4)	0.66	+	nuc	0	Nucleus				232
P31267 UniProt NPD GO	HXA6_HUMAN	Homeobox protein Hox-A6 (Hox-1B)	0.66	+	nuc	0	Nucleus		142951		233
P14653 UniProt NPD GO	HXB1_HUMAN	Homeobox protein Hox-B1 (Hox-2I)	0.66	+	nuc	0	Nucleus	nucleus [NAS]	142968	1B72	301
P31276 UniProt NPD GO	HXC13_HUMAN	Homeobox protein Hox-C13 (Hox-3G)	0.66	+	nuc	0	Nucleus	nucleus [NAS]	142976		330
P14858 UniProt NPD GO	HXC6_NOTVI	Homeobox protein Hox-C6 (NvHox-1) (FH-2)	0.66	+	nuc	0	Nucleus				234
O93353 UniProt NPD GO	HXD3_CHICK	Homeobox protein Hox-D3	0.66	+	nuc	0	Nucleus				413
P28361 UniProt NPD GO	MSX1_CHICK	Homeobox protein MSX-1 (Msh homeobox 1-like protein) (CHOX-7)	0.66	+	nuc	0	Nucleus				249
O14770 UniProt NPD GO	MEIS2_HUMAN	Homeobox protein Meis2 (Meis1-related protein 1)	0.66	-	nuc	0	Nucleus (Probable)		601740		477
Q9UIU6 UniProt NPD GO	SIX4_HUMAN	Homeobox protein SIX4 (Sine oculis homeobox homolog 4)	0.66	-	nuc	0	Nucleus (By similarity)		606342		760
Q61321 UniProt NPD GO	SIX4_MOUSE	Homeobox protein SIX4 (Sine oculis homeobox homolog 4) (Skeletal muscle-specific ARE-binding protein ...	0.66	-	nuc	0	Cytoplasm. Nucleus	nucleus [IC]			775
P46602 UniProt NPD GO	HAT3_ARATH	Homeobox-leucine zipper protein HAT3 (HD-ZIP protein 3)	0.66	+	nuc	0	Nucleus (Potential)				315
Q9JKY5 UniProt NPD GO	HIP1R_MOUSE	Huntingtin-interacting protein 1-related protein (Hip1-related)	0.66	-	nuc	0	Cytoplasm; perinuclear region. Intracytoplasmic membrane. Membrane-associated protein, mainly locali ...	coated pit [IDA] cytoskeleton [IDA]			1068
P22791 UniProt NPD GO	HMCS2_RAT	Hydroxymethylglutaryl-CoA synthase, mitochondrial precursor (EC 2.3.3.10) (HMG-CoA synthase) (3-hydr ...	0.66	-	mit	0	Mitochondrion	mitochondrion [TAS]			508
P47115 UniProt NPD GO	YJ26_YEAST	Hypothetical 27.4 kDa protein in HIT1-CDC8 intergenic region	0.66	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			236
Q8TA81 UniProt NPD GO	YSYF_CAEEL	Hypothetical F-box protein ZK328.6	0.66	+	nuc	0					394
Q11108 UniProt NPD GO	YX01_CAEEL	Hypothetical protein C03B1.1	0.66	-	mit	0					297
O42910 UniProt NPD GO	YBI3_SCHPO	Hypothetical protein C16A3.03c in chromosome II	0.66	-	mit	0					658
Q10109 UniProt NPD GO	YAQA_SCHPO	Hypothetical protein C18G6.10 in chromosome I	0.66	-	nuc	2	Membrane; multi-pass membrane protein (Potential)				688
Q10408 UniProt NPD GO	YD83_SCHPO	Hypothetical protein C1F3.03 in chromosome I	0.66	-	nuc	0	Membrane; multi-pass membrane protein (Potential)				1004
Q09263 UniProt NPD GO	YQD3_CAEEL	Hypothetical protein C32D5.3	0.66	-	end	0	Membrane; multi-pass membrane protein (Potential)				859
Q18674 UniProt NPD GO	YXX7_CAEEL	Hypothetical protein C47E12.7	0.66	-	cyt	0	Nucleus (Potential)				397
Q09830 UniProt NPD GO	YAD4_SCHPO	Hypothetical protein C4G8.04 in chromosome I	0.66	-	nuc	0					772
P83474 UniProt NPD GO	Y818_DROME	Hypothetical protein CG31818 in chromosome 2	0.66	+	nuc	0					202
Q8ST70 UniProt NPD GO	Y503_ENCCU	Hypothetical protein ECU05_0030/ECU10_1870	0.66	-	nuc	6					489
Q9GQ60 UniProt NPD GO	YNPI_CAEEL	Hypothetical protein R08C7.12	0.66	-	nuc	0					278
P34601 UniProt NPD GO	YO62_CAEEL	Hypothetical protein ZK1098.2	0.66	-	cyt	0					626
Q09368 UniProt NPD GO	YS31_CAEEL	Hypothetical protein ZK1321.1	0.66	-	nuc	0					158
O35094 UniProt NPD GO	TIM44_RAT	Import inner membrane translocase subunit TIM44, mitochondrial precursor	0.66	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane presequence tr... [IPI]			453
Q7TMY7 UniProt NPD GO	IPO8_MOUSE	Importin-8 (Imp8) (Ran-binding protein 8) (RanBP8)	0.66	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				1010
Q04998 UniProt NPD GO	INHBA_MOUSE	Inhibin beta A chain precursor (Activin beta-A chain)	0.66	+	nuc	0	Secreted protein				424
P18331 UniProt NPD GO	INHBA_RAT	Inhibin beta A chain precursor (Activin beta-A chain)	0.66	+	nuc	0	Secreted protein (By similarity)				424
Q9USK0 UniProt NPD GO	IPK1_SCHPO	Inositol-pentakisphosphate 2-kinase (EC 2.7.1.-) (Inositol-1,3,4,5,6-pentakisphosphate 2-kinase) (In ...	0.66	+	nuc	0	Nucleus (By similarity)				640
P15208 UniProt NPD GO	INSR_MOUSE	Insulin receptor precursor (EC 2.7.10.1) (IR) [Contains: Insulin receptor subunit alpha; Insulin rec ...	0.66	+	end	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [ISS] plasma membrane [IDA]		1LK2	1372
P22334 UniProt NPD GO	ILP_BRACL	Insulin-like peptide precursor [Contains: Insulin-like peptide B chain; Insulin-like peptide A chain ...	0.66	-	exc	0	Secreted protein				305
Q05049 UniProt NPD GO	MUC1_XENLA	Integumentary mucin C.1 (FIM-C.1) (Fragment)	0.66	-	nuc	0	Secreted protein				662
P78504 UniProt NPD GO	JAG1_HUMAN	Jagged-1 precursor (Jagged1) (hJ1) (CD339 antigen)	0.66	+	nuc	1	Membrane; single-pass type I membrane protein	extracellular region [NAS] integral to plasma membrane [NAS] membrane [TAS]	601920		1218

You are viewing entries 15801 to 15850 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.