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
Q8N5W8 UniProt NPD GO	FA24B_HUMAN	Protein FAM24B precursor	0.00	-	vac	1 *					94
Q96BQ1 UniProt NPD GO	FAM3D_HUMAN	Protein FAM3D precursor	0.00	-	mit	1 *	Secreted protein (Potential)	extracellular region [NAS]	608619		224
Q71RH2 UniProt NPD GO	FA57B_HUMAN	Protein FAM57B	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				274
O74631 UniProt NPD GO	FD123_TRAVE	Protein FDD123 (CvHSP30/1)	0.00	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				283
P32907 UniProt NPD GO	FUN34_YEAST	Protein FUN34	0.00	-	end	5	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			282
P27349 UniProt NPD GO	GOS9_ORYSA	Protein GOS9	0.00	-	cyt	0					139
P47119 UniProt NPD GO	HAM1_YEAST	Protein HAM1	0.00	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			197
P46973 UniProt NPD GO	HIT1_YEAST	Protein HIT1	0.00	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			164
P40037 UniProt NPD GO	HMF1_YEAST	Protein HMF1 (High dosage growth inhibitor)	0.00	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] cytosol [IDA] nucleus [IDA]		1JD1	129
Q14656 UniProt NPD GO	ITBA1_HUMAN	Protein ITBA1 (CXorf12 protein) (DXS9878E)	0.00	-	end	6 *			300059		261
P52778 UniProt NPD GO	L18A_LUPLU	Protein LlR18A (LlPR10.1A)	0.00	-	cyt	0				1ICX	156
P52779 UniProt NPD GO	L18B_LUPLU	Protein LlR18B (EC 3.1.27.-) (LlPR10.1B)	0.00	-	cyt	0				1IFV	156
Q969L2 UniProt NPD GO	MAL2_HUMAN	Protein MAL2	0.00	-	end	4 *	Cell membrane; multi-pass membrane protein. Associated with lipid rafts. Cell membrane; apical cell ...		609684		176
Q8BI08 UniProt NPD GO	MAL2_MOUSE	Protein MAL2	0.00	-	end	4 *	Cell membrane; multi-pass membrane protein (By similarity). Associated with lipid rafts. Cell membra ...				175
Q5RAI2 UniProt NPD GO	MAL2_PONPY	Protein MAL2	0.00	-	end	4 *	Cell membrane; multi-pass membrane protein (By similarity). Associated with lipid rafts. Cell membra ...				176
P06106 UniProt NPD GO	MET17_YEAST	Protein MET17 [Includes: O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) (OAH sulfhydrylase) (Homocys ...	0.00	-	cyt	0	Cytoplasm	cytoplasm [IDA]			443
Q9WUQ7 UniProt NPD GO	MYLE_MOUSE	Protein MYLE (Dexamethasone-induced protein)	0.00	-	mit	1 *					95
Q76LT9 UniProt NPD GO	NEF1_CHICK	Protein NEF1	0.00	-	end	2 *					79
Q2KJ11 UniProt NPD GO	NKG7_BOVIN	Protein NKG7 (Natural killer cell protein 7)	0.00	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				165
P83363 UniProt NPD GO	PL1_LUPLU	Protein PR-L1 (Fragment)	0.00	-		0					20
P83364 UniProt NPD GO	PL2_LUPLU	Protein PR-L2 (Fragment)	0.00	-		0					20
P83366 UniProt NPD GO	PL4_LUPLU	Protein PR-L4 (Fragment)	0.00	-		0					20
P83368 UniProt NPD GO	PL6_LUPLU	Protein PR-L6 (Fragment)	0.00	-		0					20
Q02722 UniProt NPD GO	Q300_MOUSE	Protein Q300	0.00	-	end	2 *	Membrane; single-pass membrane protein (Potential)				77
P40113 UniProt NPD GO	RTM1_YEAST	Protein RTM1	0.00	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				309
Q9Y068 UniProt NPD GO	RIC1_PHYIN	Protein Ric1	0.00	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				57
P02639 UniProt NPD GO	S10A1_BOVIN	Protein S100-A1 (S100 calcium-binding protein A1) (S-100 protein alpha subunit) (S-100 protein alpha ...	0.00	-	cyt	0					93
P23297 UniProt NPD GO	S10A1_HUMAN	Protein S100-A1 (S100 calcium-binding protein A1) (S-100 protein alpha subunit) (S-100 protein alpha ...	0.00	-	cyt	0	Cytoplasm	protein complex [NAS] sarcoplasmic reticulum [IDA]	176940		93
P56565 UniProt NPD GO	S10A1_MOUSE	Protein S100-A1 (S100 calcium-binding protein A1) (S-100 protein alpha subunit) (S-100 protein alpha ...	0.00	-	cyt	0	Cytoplasm (By similarity)	sarcoplasmic reticulum [IDA]			93
Q5RC36 UniProt NPD GO	S10A1_PONPY	Protein S100-A1 (S100 calcium-binding protein A1) (S-100 protein alpha subunit) (S-100 protein alpha ...	0.00	-	cyt	0	Cytoplasm (By similarity)				93
P35467 UniProt NPD GO	S10A1_RAT	Protein S100-A1 (S100 calcium-binding protein A1) (S-100 protein alpha subunit) (S-100 protein alpha ...	0.00	-	nuc	0	Cytoplasm			1ZFS	93
P62504 UniProt NPD GO	S10AA_MACMU	Protein S100-A10 (S100 calcium-binding protein A10) (Calpactin-1 light chain) (Calpactin I light cha ...	0.00	-	cyt	1					96
Q6SQH4 UniProt NPD GO	S10AA_RABIT	Protein S100-A10 (S100 calcium-binding protein A10) (Calpactin-1 light chain) (Calpactin I light cha ...	0.00	-	cyt	1					96
P60902 UniProt NPD GO	S10AA_BOVIN	Protein S100-A10 (S100 calcium-binding protein A10) (Calpactin-1 light chain) (Calpactin I light cha ...	0.00	-	cyt	1					96
P60903 UniProt NPD GO	S10AA_HUMAN	Protein S100-A10 (S100 calcium-binding protein A10) (Calpactin-1 light chain) (Calpactin I light cha ...	0.00	-	cyt	1			114085	1BT6	96
P04163 UniProt NPD GO	S10AA_PIG	Protein S100-A10 (S100 calcium-binding protein A10) (Calpactin-1 light chain) (Calpactin I light cha ...	0.00	-	cyt	1					95
P80511 UniProt NPD GO	S10AC_HUMAN	Protein S100-A12 (S100 calcium-binding protein A12) (Calgranulin-C) (CAGC) (CGRP) (Neutrophil S100 p ...	0.00	-	cyt	0		cytosol [TAS] insoluble fraction [TAS]	603112	1ODB	91
P02638 UniProt NPD GO	S100B_BOVIN	Protein S100-B (S100 calcium-binding protein B) (S-100 protein beta subunit) (S-100 protein beta cha ...	0.00	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] extracellular region [ISS]		1PSB	91
P04271 UniProt NPD GO	S100B_HUMAN	Protein S100-B (S100 calcium-binding protein B) (S-100 protein beta subunit) (S-100 protein beta cha ...	0.00	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [ISS] extracellular region [ISS]	176990	1UWO	91
P50114 UniProt NPD GO	S100B_MOUSE	Protein S100-B (S100 calcium-binding protein B) (S-100 protein beta subunit) (S-100 protein beta cha ...	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cell soma [IDA] cytoplasm [NAS] extracellular region [NAS] nucleus [IDA]			91
Q6YNR6 UniProt NPD GO	S100B_RABIT	Protein S100-B (S100 calcium-binding protein B) (S-100 protein beta subunit) (S-100 protein beta cha ...	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				91
P04631 UniProt NPD GO	S100B_RAT	Protein S100-B (S100 calcium-binding protein B) (S-100 protein subunit beta) (S-100 protein beta cha ...	0.00	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] extracellular region [ISS]		1XYD	91
P25815 UniProt NPD GO	S100P_HUMAN	Protein S100-P (S100 calcium-binding protein P)	0.00	-	cyt	0		cytoplasm [TAS] nucleus [IDA]	600614	1OZO	95
P32564 UniProt NPD GO	SCM4_YEAST	Protein SCM4	0.00	-	mit	4 *		mitochondrial outer membrane [IDA] mitochondrion [IDA]			187
P56508 UniProt NPD GO	SNA2_YEAST	Protein SNA2	0.00	-	vac	2 *	Membrane; multi-pass membrane protein (Potential). Localized to punctate structures and lipid partic ...	cytoplasm [IDA]			79
Q58DA4 UniProt NPD GO	TX261_BOVIN	Protein TEX261	0.00	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				193
Q9NK57 UniProt NPD GO	A36A_DROME	Protein anon-35F/36A	0.00	-	mit	0					292
P81246 UniProt NPD GO	PDIA3_PAPHA	Protein disulfide-isomerase A3 (EC 5.3.4.1) (58 kDa microsomal protein) (ER58) (Fragments)	0.00	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum lumen				39
Q12730 UniProt NPD GO	PDI_ASPNG	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI)	0.00	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				515
Q00248 UniProt NPD GO	PDI_ASPOR	Protein disulfide-isomerase precursor (EC 5.3.4.1) (PDI)	0.00	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				515

You are viewing entries 97301 to 97350 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.