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
Q6IRN2 UniProt NPD GO	QKIB_XENLA	Quaking protein B	0.33	+	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity)			2BL5	342
Q9Y243 UniProt NPD GO	AKT3_HUMAN	RAC-gamma serine/threonine-protein kinase (EC 2.7.11.1) (RAC-PK-gamma) (Protein kinase Akt-3) (Prote ...	0.33	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Membrane-associated after cell stimulation leading ...				479
P34147 UniProt NPD GO	RACA_DICDI	RAS-related protein racA	0.33	-	cyt	0					598
P36113 UniProt NPD GO	YKZ7_YEAST	RING finger protein YKR017C	0.33	-	nuc	0					551
O82353 UniProt NPD GO	ATL2M_ARATH	RING-H2 finger protein ATL2M	0.33	-	nuc	1 *					214
P01894 UniProt NPD GO	HA1A_RABIT	RLA class I histocompatibility antigen, alpha chain 11/11 precursor	0.33	-	end	1	Membrane; single-pass type I membrane protein				361
P47821 UniProt NPD GO	SSN8_YEAST	RNA polymerase II holoenzyme cyclin-like subunit	0.33	-	nuc	0	Nucleus (Potential)	transcription factor complex [TAS]			323
Q99ND9 UniProt NPD GO	RWDD1_RAT	RWD domain-containing protein 1 (Small androgen receptor-interacting protein)	0.33	-	cyt	0					243
Q9UIY3 UniProt NPD GO	RWDD2_HUMAN	RWD domain-containing protein 2	0.33	-	cyt	0				2DAW	292
Q38942 UniProt NPD GO	RAE1L_ARATH	Rae1-like protein At1g80670	0.33	-	nuc	0					349
Q01730 UniProt NPD GO	RSU1_MOUSE	Ras suppressor protein 1 (Rsu-1) (RSP-1)	0.33	-	nuc	0					276
P41925 UniProt NPD GO	RYL2_YARLI	Ras-like GTP-binding protein RYL2	0.33	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				209
P15064 UniProt NPD GO	RASG_DICDI	Ras-like protein rasG	0.33	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				189
Q96A58 UniProt NPD GO	RERG_HUMAN	Ras-related and estrogen-regulated growth inhibitor	0.33	-	cyt	0	Cytoplasm	cytosol [IEP] nucleus [IDA]		2ATV	199
O14807 UniProt NPD GO	RASM_HUMAN	Ras-related protein M-Ras (Ras-related protein R-Ras3)	0.33	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)	plasma membrane [TAS]	608435		208
Q6PHN9 UniProt NPD GO	RAB35_MOUSE	Ras-related protein Rab-35	0.33	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				201
Q5U316 UniProt NPD GO	RAB35_RAT	Ras-related protein Rab-35	0.33	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				201
Q15286 UniProt NPD GO	RAB35_HUMAN	Ras-related protein Rab-35 (Rab-1C) (GTP-binding protein RAY)	0.33	-	mit	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		604199		201
P0C0E4 UniProt NPD GO	RB40L_HUMAN	Ras-related protein Rab-40A-like	0.33	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				278
P47735 UniProt NPD GO	RLK5_ARATH	Receptor-like protein kinase 5 precursor (EC 2.7.11.1)	0.33	-	exc	1					999
P25343 UniProt NPD GO	RV161_YEAST	Reduced viability upon starvation protein 161	0.33	-	cyt	0		actin cortical patch [TAS] lipid raft [IDA] mating projection [IDA]			265
O08899 UniProt NPD GO	RGS4_MOUSE	Regulator of G-protein signaling 4 (RGS4)	0.33	-	nuc	0		cytoplasm [TAS]			205
P53330 UniProt NPD GO	RT102_YEAST	Regulator of Ty1 transposition protein 102	0.33	-	nuc	0	Nucleus	nucleus [IDA] RSC complex [IPI] SWI/SNF complex [IPI]			157
P53016 UniProt NPD GO	RFC4_CAEEL	Replication factor C subunit 4 (Replication factor C 37 kDa subunit) (RF-C 37 kDa subunit) (RFC37) ( ...	0.33	-	cyt	0	Nucleus (Probable)	DNA replication factor C complex [NAS]			334
O08603 UniProt NPD GO	RAE1B_MOUSE	Retinoic acid early inducible protein 1 beta precursor (RAE-1beta)	0.33	-	nuc	1	Cell membrane; lipid-anchor; GPI-anchor	anchored to plasma membrane [IDA]		1JSK	253
Q03271 UniProt NPD GO	PO13_NASVI	Retrovirus-related Pol polyprotein from type-1 retrotransposable element R1 3 (Retrovirus-related Po ...	0.33	-	cyt	0					383
Q91V93 UniProt NPD GO	RHBT2_MOUSE	Rho-related BTB domain-containing protein 2 (Deleted in breast cancer 2 gene protein homolog)	0.33	-	mit	0					728
Q63651 UniProt NPD GO	RK_RAT	Rhodopsin kinase precursor (EC 2.7.11.14) (RK) (G protein-coupled receptor kinase 1)	0.33	+	cyt	0	Membrane; lipid-anchor				564
P84844 UniProt NPD GO	RNAS1_CHEMY	Ribonuclease (EC 3.1.27.5)	0.33	-	nuc	0	Secreted protein				119
P04061 UniProt NPD GO	RNAS1_CHESE	Ribonuclease (EC 3.1.27.5)	0.33	-	nuc	0	Secreted protein				119
O00584 UniProt NPD GO	RNT2_HUMAN	Ribonuclease T2 precursor (EC 3.1.27.-) (Ribonuclease 6)	0.33	-	nuc	0	Secreted protein (Potential)	extracellular region [TAS]			256
P67928 UniProt NPD GO	RNAS1_CAMDR	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.33	-	nuc	0	Secreted protein				124
P80287 UniProt NPD GO	RNAS1_IGUIG	Ribonuclease pancreatic (EC 3.1.27.5) (RNase 1) (RNase A)	0.33	-	nuc	0	Secreted protein				119
Q8SPN5 UniProt NPD GO	RNAS1_MACMU	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A)	0.33	-	nuc	1 *	Secreted protein (By similarity)				152
P07998 UniProt NPD GO	RNAS1_HUMAN	Ribonuclease pancreatic precursor (EC 3.1.27.5) (RNase 1) (RNase A) (RNase UpI-1) (RIB-1) (HP-RNase) ...	0.33	-	exc	1 *	Secreted protein		180440	1Z7X	156
Q7YRH1 UniProt NPD GO	RNAS9_CERAE	Ribonuclease-like protein 9 precursor	0.33	-	exc	0	Secreted protein (Probable)				204
Q7LG56 UniProt NPD GO	RIR2B_HUMAN	Ribonucleoside-diphosphate reductase M2 subunit B (EC 1.17.4.1) (TP53-inducible ribonucleotide reduc ...	0.33	-	cyt	1	Cytoplasm. Translocates from cytoplasm to nucleus in response to DNA damage		604712		351
Q6P5R6 UniProt NPD GO	RL22L_HUMAN	Ribosomal protein L22-like 1	0.33	-	nuc	0					122
P38771 UniProt NPD GO	RRF1_YEAST	Ribosomal recycling factor, mitochondrial precursor	0.33	-	mit	0	Mitochondrion	mitochondrion [IDA]			230
Q5RKI9 UniProt NPD GO	RRFM_RAT	Ribosome recycling factor, mitochondrial precursor	0.33	-	nuc	0	Mitochondrion (By similarity)				262
P13821 UniProt NPD GO	SANT_PLAFW	S-antigen protein precursor	0.33	-	nuc	0	Parasitophorous vacuole				640
P58875 UniProt NPD GO	S14L2_BOVIN	SEC14-like protein 2 (Alpha-tocopherol-associated protein) (TAP) (bTAP)	0.33	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in absence of alpha-tocopherol, and ...	cytoplasm [ISS] nucleus [ISS]			403
P97443 UniProt NPD GO	SMYD1_MOUSE	SET and MYND domain-containing protein 1 (Zinc-finger protein BOP) (m-BOP) (CD8b-opposite)	0.33	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			485
Q6ZV89 UniProt NPD GO	SH2D5_HUMAN	SH2 domain-containing protein 5	0.33	-	nuc	0					339
Q96A28 UniProt NPD GO	SLAF9_HUMAN	SLAM family member 9 precursor (CD2 family member 10) (CD2F-10) (CD84 homolog 1) (CD84-H1)	0.33	-	exc	1	Membrane; single-pass type I membrane protein		608589		289
Q9Z266 UniProt NPD GO	S25BP_MOUSE	SNARE-associated protein Snapin (Synaptosomal-associated protein 25-binding protein) (SNAP-associate ...	0.33	-	nuc	0	Cytoplasm (Ref.4). Membrane; peripheral membrane protein (Ref.4). Cytoplasmic vesicle; cytoplasmic v ...	cytosol [IDA]			136
P60192 UniProt NPD GO	S25BP_RAT	SNARE-associated protein Snapin (Synaptosomal-associated protein 25-binding protein) (SNAP-associate ...	0.33	-	nuc	0	Or: Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity). Or: Cytoplasmi ...				136
Q6FXC1 UniProt NPD GO	HSV2_CANGA	SVP1-like protein 2	0.33	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein (By similarity). Cytoplasmic vesicle; cytopl ...				445
Q94FT4 UniProt NPD GO	SALAT_PAPSO	Salutaridinol 7-O-acetyltransferase (EC 2.3.1.150) (salAT)	0.33	-	cyt	0					474
Q9BG78 UniProt NPD GO	SOST_CERAE	Sclerostin precursor	0.33	-	exc	0	Secreted protein (Potential)				213

You are viewing entries 37951 to 38000 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.