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
Q642B9 UniProt NPD GO	ZNF18_RAT	Zinc finger protein 18 (Zinc finger protein 535)	0.53	-	nuc	0	Nucleus (Potential)				556
P17024 UniProt NPD GO	ZNF20_HUMAN	Zinc finger protein 20 (Zinc finger protein KOX13)	0.53	-	nuc	0	Nucleus (Potential)		194557		532
Q9UL59 UniProt NPD GO	ZN214_HUMAN	Zinc finger protein 214 (BWSCR2-associated zinc-finger protein 1) (BAZ 1)	0.53	-	nuc	0	Nucleus (Probable)	nucleus [NAS]	605015		606
Q99592 UniProt NPD GO	ZN238_HUMAN	Zinc finger protein 238 (Transcriptional repressor RP58) (58 kDa repressor protein) (Zinc finger pro ...	0.53	-	nuc	0	Nucleus. Associates with condensed chromatin	nuclear chromosome [TAS] nucleus [TAS]	608433		522
Q9WUK6 UniProt NPD GO	ZN238_MOUSE	Zinc finger protein 238 (Zfp-238) (Transcriptional repressor RP58) (58 kDa repressor protein)	0.53	-	nuc	0	Nucleus. Associates with condensed chromatin				522
O14978 UniProt NPD GO	ZN263_HUMAN	Zinc finger protein 263 (Zinc finger protein FPM315)	0.53	-	nuc	0	Nucleus (By similarity)		604191		683
P17036 UniProt NPD GO	ZNF38_HUMAN	Zinc finger protein 38 (Zinc finger protein KOX25) (Zinc finger protein HF.12) (Zinc finger protein ...	0.53	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	601261		446
Q32KV8 UniProt NPD GO	ZN414_BOVIN	Zinc finger protein 414	0.53	-	nuc	0	Nucleus (Probable)				391
Q8TAQ5 UniProt NPD GO	ZN420_HUMAN	Zinc finger protein 420	0.53	-	nuc	0	Nucleus (Potential)				688
Q02386 UniProt NPD GO	ZNF45_HUMAN	Zinc finger protein 45 (BRC1744)	0.53	-	nuc	0	Nucleus		601781		682
Q96H40 UniProt NPD GO	ZN486_HUMAN	Zinc finger protein 486	0.53	-	nuc	0	Nucleus (Potential)				216
Q86UE3 UniProt NPD GO	ZN546_HUMAN	Zinc finger protein 546	0.53	-	nuc	0	Nucleus (Probable)				836
Q8N972 UniProt NPD GO	ZN709_HUMAN	Zinc finger protein 709	0.53	-	nuc	0	Nucleus (Probable)				641
Q9Z1D7 UniProt NPD GO	ZNF96_MOUSE	Zinc finger protein 96 (Zfp-96)	0.53	-	nuc	0	Nucleus (Potential)				501
Q07120 UniProt NPD GO	GFI1_RAT	Zinc finger protein Gfi-1 (Growth factor independence 1)	0.53	-	nuc	0	Nucleus				423
Q80ZJ6 UniProt NPD GO	ZYGBL_MOUSE	Zyg-11 protein homolog (Zyg-11 homolog B-like)	0.53	-	cyt	0					779
Q86SH2 UniProt NPD GO	ZAR1_HUMAN	Zygote arrest 1 (Oocyte-specific maternal effect factor)	0.53	-	nuc	0	Cytoplasm (By similarity)		607520		424
Q6P1V8 UniProt NPD GO	MCM6Z_XENTR	Zygotic DNA replication licensing factor mcm6 (Zygotic minichromosome maintenance protein 6) (zMCM6) ...	0.53	-	cyt	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	MCM complex [ISS]			823
P10644 UniProt NPD GO	KAP0_HUMAN	cAMP-dependent protein kinase type I-alpha regulatory subunit (Tissue-specific extinguisher 1) (TSE1 ...	0.53	-	mit	0			255960		381
Q6CU63 UniProt NPD GO	PALA_KLULA	pH-response regulator protein palA/RIM20	0.53	-	nuc	0					652
Q4WXA1 UniProt NPD GO	TRM10_ASPFU	tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.31) (tRNA methyltransferase 10)	0.53	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				396
P07884 UniProt NPD GO	MOD5_YEAST	tRNA isopentenyltransferase (EC 2.5.1.8) (Isopentenyl-diphosphate: tRNA isopentenyltransferase) (IPP ...	0.53	-	nuc	0	Mitochondrion. Cytoplasm. Nucleus	cytosol [IDA] mitochondrion [IDA] nucleolus [IDA] nucleus [IDA]			428
Q1HAQ0 UniProt NPD GO	PCAT1_RAT	1-acylglycerophosphocholine O-acyltransferase 1 (EC 2.3.1.23) (Lung-type acyl-coa:lysophosphatidylch ...	0.52	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...				534
Q05921 UniProt NPD GO	RN5A_MOUSE	2-5A-dependent ribonuclease (EC 3.1.26.-) (2-5A-dependent RNase) (Ribonuclease L) (RNase L) (Ribonuc ...	0.52	-	cyt	0	Cytoplasm. Mitochondrion				735
Q2KI42 UniProt NPD GO	PSD11_BOVIN	26S proteasome non-ATPase regulatory subunit 11	0.52	-	cyt	0					421
O00231 UniProt NPD GO	PSD11_HUMAN	26S proteasome non-ATPase regulatory subunit 11 (26S proteasome regulatory subunit S9) (26S proteaso ...	0.52	-	cyt	0		proteasome complex (sensu Eukaryota) [TAS]	604449		421
Q8BG32 UniProt NPD GO	PSD11_MOUSE	26S proteasome non-ATPase regulatory subunit 11 (26S proteasome regulatory subunit S9) (26S proteaso ...	0.52	-	cyt	0					421
Q9Y676 UniProt NPD GO	RT18B_HUMAN	28S ribosomal protein S18b, mitochondrial precursor (MRP-S18-b) (Mrps18b) (MRP-S18-2)	0.52	-	mit	0	Mitochondrion	mitochondrial small ribosomal subunit [NAS]			258
P17092 UniProt NPD GO	RR17_PEA	30S ribosomal protein S17, chloroplast precursor (CS17) (Fragment)	0.52	-	nuc	0	Plastid; chloroplast (Probable)				134
O13784 UniProt NPD GO	RS24A_SCHPO	40S ribosomal protein S24-A	0.52	+	mit	0					133
Q2KHT7 UniProt NPD GO	RS27_BOVIN	40S ribosomal protein S27	0.52	+	nuc	0					83
Q6ZWU9 UniProt NPD GO	RS27_MOUSE	40S ribosomal protein S27	0.52	+	nuc	0					83
Q71TY3 UniProt NPD GO	RS27_RAT	40S ribosomal protein S27	0.52	+	nuc	0					83
P42677 UniProt NPD GO	RS27_HUMAN	40S ribosomal protein S27 (Metallopan-stimulin 1) (MPS-1)	0.52	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	603702		83
Q757I0 UniProt NPD GO	RT09_ASHGO	40S ribosomal protein S9, mitochondrial precursor	0.52	-	mit	0	Mitochondrion (Potential)				279
Q13131 UniProt NPD GO	AAPK1_HUMAN	5'-AMP-activated protein kinase catalytic subunit alpha-1 (EC 2.7.11.1) (AMPK alpha-1 chain)	0.52	-	nuc	0		intracellular [IC]	602739		550
Q4R5P3 UniProt NPD GO	RL10A_MACFA	60S ribosomal protein L10a	0.52	+	nuc	0					216
P41128 UniProt NPD GO	RL131_BRANA	60S ribosomal protein L13-1 (Cold-induced protein C24A)	0.52	-	mit	0					206
Q9VNE9 UniProt NPD GO	RL13A_DROME	60S ribosomal protein L13A	0.52	+	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [ISS]			205
Q3SZ90 UniProt NPD GO	RL13A_BOVIN	60S ribosomal protein L13a	0.52	+	cyt	0					202
Q4R8Z2 UniProt NPD GO	RL13A_MACFA	60S ribosomal protein L13a	0.52	+	cyt	0					202
P19253 UniProt NPD GO	RL13A_MOUSE	60S ribosomal protein L13a (Transplantation antigen P198) (Tum-P198 antigen)	0.52	+	cyt	0					202
Q7T2N5 UniProt NPD GO	RL15_PELFU	60S ribosomal protein L15	0.52	-	nuc	0					203
P46990 UniProt NPD GO	RL17B_YEAST	60S ribosomal protein L17-B (YL17-B)	0.52	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			183
P39023 UniProt NPD GO	RL3_HUMAN	60S ribosomal protein L3 (HIV-1 TAR RNA-binding protein B) (TARBP-B)	0.52	-	mit	0	Cytoplasm	cytosolic large ribosomal subunit (sensu Eu... [TAS] nucleolus [TAS]	604163		402
P34662 UniProt NPD GO	RL35_CAEEL	60S ribosomal protein L35	0.52	-	nuc	0					123
Q9M5L0 UniProt NPD GO	RL35_EUPES	60S ribosomal protein L35	0.52	-	nuc	0					123
O74904 UniProt NPD GO	RL35_SCHPO	60S ribosomal protein L35	0.52	-	nuc	0					122
P49212 UniProt NPD GO	RL37_LYCES	60S ribosomal protein L37 (Fragment)	0.52	-	mit	0					64
Q9C2B9 UniProt NPD GO	RL38_NEUCR	60S ribosomal protein L38	0.52	-	nuc	0					80

You are viewing entries 23501 to 23550 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.