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
P26187 UniProt NPD GO	MGMT_MOUSE	Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) (6-O-methylguanine-DNA methyltransf ...	0.02	-	cyt	0	Nucleus (Probable)				210
P24528 UniProt NPD GO	MGMT_RAT	Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) (6-O-methylguanine-DNA methyltransf ...	0.02	-	cyt	0	Nucleus (Probable)				208
Q02252 UniProt NPD GO	MMSA_HUMAN	Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (EC 1.2.1.27) (MMSDH) ...	0.02	-	mit	1	Mitochondrion	mitochondrion [NAS]	603178		535
Q02253 UniProt NPD GO	MMSA_RAT	Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial precursor (EC 1.2.1.27) (MMSDH) ...	0.02	-	mit	1	Mitochondrion	mitochondrion [ISS]			535
P10620 UniProt NPD GO	MGST1_HUMAN	Microsomal glutathione S-transferase 1 (EC 2.5.1.18) (Microsomal GST-1) (Microsomal GST-I)	0.02	-	mit	1 *	Microsome (By similarity). Mitochondrion; mitochondrial outer membrane; peripheral membrane protein ...		138330		155
P39675 UniProt NPD GO	DERP3_DERPT	Mite allergen Der p 3 precursor (EC 3.4.21.-) (Der p III)	0.02	-	exc	0	Secreted protein				261
P49277 UniProt NPD GO	DERP6_DERPT	Mite allergen Der p 6 (EC 3.4.21.-) (Der p VI) (DP5) (Fragment)	0.02	-		0	Secreted protein				20
Q6PCS6 UniProt NPD GO	MTP18_BRARE	Mitochondrial 18 kDa protein (MTP18)	0.02	-	cyt	0	Mitochondrion (By similarity)				165
Q8BZ09 UniProt NPD GO	ODC_MOUSE	Mitochondrial 2-oxodicarboxylate carrier (Solute carrier family 25 member 21)	0.02	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				298
Q99JD3 UniProt NPD GO	ODC_RAT	Mitochondrial 2-oxodicarboxylate carrier (Solute carrier family 25 member 21)	0.02	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				298
Q03028 UniProt NPD GO	ODC1_YEAST	Mitochondrial 2-oxodicarboxylate carrier 1	0.02	-	cyt	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA] mitochondrion [IDA]			310
Q99297 UniProt NPD GO	ODC2_YEAST	Mitochondrial 2-oxodicarboxylate carrier 2	0.02	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			307
Q32PC3 UniProt NPD GO	RM27_BOVIN	Mitochondrial 39S ribosomal protein L27 (L27mt) (MRP-L27)	0.02	-	vac	0	Mitochondrion (By similarity)				148
Q9P0M9 UniProt NPD GO	RM27_HUMAN	Mitochondrial 39S ribosomal protein L27 (L27mt) (MRP-L27)	0.02	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [NAS]			148
Q99N92 UniProt NPD GO	RM27_MOUSE	Mitochondrial 39S ribosomal protein L27 (L27mt) (MRP-L27)	0.02	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IDA] mitochondrion [IDA]			148
Q3ZBX6 UniProt NPD GO	RM03_BOVIN	Mitochondrial 39S ribosomal protein L3 (L3mt) (MRP-L3)	0.02	-	mit	0	Mitochondrion (By similarity)				348
P09001 UniProt NPD GO	RM03_HUMAN	Mitochondrial 39S ribosomal protein L3 (L3mt) (MRP-L3)	0.02	-	mit	0	Mitochondrion		607118		348
O21275 UniProt NPD GO	RM27_RECAM	Mitochondrial 60S ribosomal protein L27	0.02	-	nuc	0	Mitochondrion				81
P36530 UniProt NPD GO	YX35_YEAST	Mitochondrial 60S ribosomal protein YmL35 (Fragment)	0.02	-		0	Mitochondrion				17
Q9ER18 UniProt NPD GO	UCP1_PHOSU	Mitochondrial brown fat uncoupling protein 1 (UCP 1) (Thermogenin)	0.02	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				307
Q9N285 UniProt NPD GO	MTCH2_BOVIN	Mitochondrial carrier homolog 2	0.02	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)				303
Q9BZJ4 UniProt NPD GO	CG69_HUMAN	Mitochondrial carrier protein CGI-69	0.02	-	cyt	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				359
Q9H2D1 UniProt NPD GO	MFTC_HUMAN	Mitochondrial folate transporter/carrier (Solute carrier family 25 member 32)	0.02	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [NAS]			315
Q95J75 UniProt NPD GO	MFTC_MACFA	Mitochondrial folate transporter/carrier (Solute carrier family 25 member 32)	0.02	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				315
Q6CRJ6 UniProt NPD GO	TIM22_KLULA	Mitochondrial import inner membrane translocase subunit TIM22	0.02	-	cyt	2 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				196
Q5BIN4 UniProt NPD GO	TIM22_BOVIN	Mitochondrial import inner membrane translocase subunit Tim22	0.02	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				194
Q9NAQ9 UniProt NPD GO	TIM22_CAEEL	Mitochondrial import inner membrane translocase subunit tim-22	0.02	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				213
Q9Y8A8 UniProt NPD GO	TIM10_EMENI	Mitochondrial import inner membrane translocase subunit tim10	0.02	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; intermembrane side (By sim ...				93
Q2UAP8 UniProt NPD GO	TIM22_ASPOR	Mitochondrial import inner membrane translocase subunit tim22	0.02	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				184
Q9C1W7 UniProt NPD GO	MIM1_SCHPO	Mitochondrial import protein 1	0.02	-	cyt	1 *	Mitochondrion; mitochondrial outer membrane (By similarity)				71
P53507 UniProt NPD GO	TOM7_YEAST	Mitochondrial import receptor subunit TOM7 (Translocase of outer membrane 7 kDa subunit)	0.02	-	cyt	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein	mitochondrial outer membrane translocase co... [IMP]			59
Q3ECI7 UniProt NPD GO	TOM7B_ARATH	Mitochondrial import receptor subunit TOM7-2 (Translocase of outer membrane 7 kDa subunit 2)	0.02	-	nuc	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				77
O13813 UniProt NPD GO	TOM22_SCHPO	Mitochondrial import receptor subunit tom22 (Mitochondrial 22 kDa outer membrane protein) (Transloca ...	0.02	-	cyt	0	Mitochondrion; mitochondrial outer membrane; single-pass type II membrane protein (By similarity)				144
Q9BXI2 UniProt NPD GO	ORNT2_HUMAN	Mitochondrial ornithine transporter 2 (Solute carrier family 25 member 2)	0.02	-	nuc	1	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein		608157		301
P32332 UniProt NPD GO	OAC1_YEAST	Mitochondrial oxaloacetate transport protein (Mitochondrial carrier protein PMT)	0.02	-	end	1 *	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (Potential)	mitochondrial inner membrane [IDA]			324
Q00302 UniProt NPD GO	MPPB_BLAEM	Mitochondrial-processing peptidase subunit beta, mitochondrial precursor (EC 3.4.24.64) (Beta-MPP) ( ...	0.02	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				465
Q23125 UniProt NPD GO	MFRN_CAEEL	Mitoferrin	0.02	-	cyt	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				312
Q63454 UniProt NPD GO	MK04_RAT	Mitogen-activated protein kinase 4 (EC 2.7.11.24) (Extracellular signal-regulated kinase 4) (ERK-4) ...	0.02	-	cyt	0					274
Q9BRX9 UniProt NPD GO	MORG1_HUMAN	Mitogen-activated protein kinase organizer 1 (MAPK organizer 1)	0.02	-	nuc	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Partially (By similarity)				315
Q9XFH3 UniProt NPD GO	MAD2_MAIZE	Mitotic spindle checkpoint protein MAD2	0.02	-	mit	0	Nucleus (Probable)				208
P55847 UniProt NPD GO	MIH_PENJP	Molt-inhibiting hormone precursor (MIH) (PeJ-SGP-IV)	0.02	-	mit	1 *	Secreted protein			1J0T	105
O35678 UniProt NPD GO	MGLL_MOUSE	Monoglyceride lipase (EC 3.1.1.23) (MGL)	0.02	-	nuc	0					303
P82810 UniProt NPD GO	MORA_RABIT	Morphine 6-dehydrogenase (EC 1.1.1.218) (Fragments)	0.02	-	cyt	0	Cytoplasm				125
Q70IA6 UniProt NPD GO	MOB2_HUMAN	Mps one binder kinase activator-like 2 (Mob2 homolog) (HCCA2)	0.02	-	cyt	0	Nucleus. Cytoplasm; perinuclear region				237
Q14894 UniProt NPD GO	CRYM_HUMAN	Mu-crystallin homolog (NADP-regulated thyroid-hormone-binding protein)	0.02	-	cyt	0	Cytoplasm		123740		314
Q91507 UniProt NPD GO	VSP1_TRIMU	Mucrofibrase-1 precursor (EC 3.4.21.-)	0.02	-	exc	0	Secreted protein				257
Q91509 UniProt NPD GO	VSP3_TRIMU	Mucrofibrase-3 precursor (EC 3.4.21.-)	0.02	-	exc	0	Secreted protein				257
P81798 UniProt NPD GO	MULR_ECHML	Multactivase regulatory subunit (Fragment)	0.02	-	cyt	0					29
P18328 UniProt NPD GO	TXM2_DENAN	Muscarinic toxin 2 precursor (MT2) (MTx2)	0.02	-	mit	1 *	Secreted protein			1FF4	86
Q61885 UniProt NPD GO	MOG_MOUSE	Myelin-oligodendrocyte glycoprotein precursor	0.02	-	end	3 *	Membrane; multi-pass membrane protein			1PY9	246

You are viewing entries 84351 to 84400 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.