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The visual representation of the position weight matrix otherwise known as the motif logo.

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The number of term predictions.

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If specificity data is avaliable then this displays the top 5 specific predictions, otherwise it just displays the top 5 predictions.

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A measure of the relative position in the GO hierarchy showing how specific a term is. A value of 100% implies that the GO term is the most specific form whereas a value of 0% implies that the GO term is one of the three roots of the Gene Ontology with only terms below it. A tilda (~) infront of the percentage implies that the value shown has been rounded and is not exact.

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The Gene Ontology hierarchy and Gene Ontology name of the term. The hierarchy is specified by the abbreviations BP for biological process, CC for cellular component and MF for molecular function.

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Gene name and rank of (up to) top 10 genes annotated with the GO term for the primary species.

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# GOMo

## Gene Ontology for Motifs

For further information on how to interpret these results please access http://meme-suite.org/doc/gomo-output-format.html.
To get a copy of the MEME software please access http://meme-suite.org.

If you use GOMo in your research, please cite the following paper:
Fabian A. Buske, Mikael Bodén, Denis C. Bauer and Timothy L. Bailey, "Assigning roles to DNA regulatory motifs using comparative genomics", Bioinformatics, 26(7), 860-866, 2010. [full text]

Investigated Motifs | Program information | Results in TSV Format | Results in XML Format

## Investigated Motifs

#### Overview

Motif | Logo | Predictions | Top 5 specific predictions
--- | --- | --- | ---
crp |  | 13 | BP carbohydrate transport MF sugar transmembrane transporter activity BP cellular carbohydrate catabolic process MF intramolecular oxidoreductase activity, interconverting aldoses and ketoses BP cellular macromolecule catabolic process
nagC |  | 9 | BP biofilm formation BP peptidoglycan biosynthetic process BP peptidoglycan-based cell wall organization MF hydrolase activity, hydrolyzing O-glycosyl compounds
narP |  | 14 | BP anaerobic respiration MF molybdenum ion binding BP cytochrome complex assembly BP chemical homeostasis BP cellular homeostasis

## Motif crp

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GO terms are shown in grey if a more specific GO term was also significantly associated with this motif. The most specific GO terms are shown in black.
BP stands for biological process, CC stands for cellular component and MF stands for molecular function.

GO term | score | p-value | q-value | Specificity | GO name | Gene ID / Rank (2518 genes in total)
--- | --- | --- | --- | --- | --- | ---
GO:0044248 | 1.341e-06 | 5.615e-07 | 4.550e-04 | ~1% | BP | cellular catabolic process | deoC (25), fucP (51), fucA (52), uxaC (64), exuT (65), tdcA (71), rhaB (83), araB (144), fruB (147), fruB (148), ...42 more...
GO:0009056 | 8.869e-07 | 5.615e-07 | 4.550e-04 | ~0% | BP | catabolic process | deoC (25), iraP (37), fucP (51), fucA (52), uxaC (64), exuT (65), tdcA (71), rhaB (83), araB (144), fruB (147), ...49 more...
GO:0008643 | 1.075e-04 | 3.369e-06 | 1.820e-03 | ~4% | BP | carbohydrate transport | fucP (51), malK (138), malE (139), ulaA (174), xylF (179), idnD (198), yjjL (824)
GO:0051119 | 2.285e-04 | 1.516e-05 | 6.067e-03 | ~5% | MF | sugar transmembrane transporter activity | fucP (51), glpT (99), malK (138), malE (139), xylF (179)
GO:0044275 | 2.652e-04 | 2.246e-05 | 6.067e-03 | ~7% | BP | cellular carbohydrate catabolic process | fucP (51), fucA (52), rhaB (83), araB (144), fruB (147), fruB (148), nagB (153), xylA (178), idnD (198), nanA (201), ...10 more...
GO:0015144 | 2.665e-04 | 2.246e-05 | 6.067e-03 | ~3% | MF | carbohydrate transmembrane transporter activity | fucP (51), glpT (99), malK (138), malE (139), ulaA (174), xylF (179), ycaI (1391)
GO:0016861 | 3.954e-04 | 3.706e-05 | 8.580e-03 | ~14% | MF | intramolecular oxidoreductase activity, interconverting aldoses and ketoses | fucP (51), uxaC (64), rhaB (83), srlA (111), araB (144), nagB (153), xylA (178), hisL (641), yihU (858), rpiB (897), ...3 more...
GO:0016860 | 4.737e-04 | 4.660e-05 | 9.442e-03 | ~4% | MF | intramolecular oxidoreductase activity | fucP (51), uxaC (64), rhaB (83), srlA (111), araB (144), nagB (153), xylA (178), hisL (641), yihU (858), rpiB (897), ...4 more...
GO:0016052 | 5.421e-04 | 5.671e-05 | 1.021e-02 | ~3% | BP | carbohydrate catabolic process | fucP (51), fucA (52), rhaB (83), araB (144), fruB (147), fruB (148), nagB (153), ybjQ (158), xylA (178), idnD (198), ...14 more...
GO:0009057 | 5.850e-04 | 6.345e-05 | 1.028e-02 | ~2% | BP | macromolecule catabolic process | iraP (37), fucP (51), fucA (52), rhaB (83), araB (144), fruB (147), fruB (148), nagB (153), ybjQ (158), xylA (178), ...20 more...
GO:0016853 | 7.322e-04 | 8.198e-05 | 1.208e-02 | ~1% | MF | isomerase activity | fucP (51), uxaC (64), yqcC (77), rhaB (83), srlA (111), araB (144), nagB (153), xylA (178), nanA (201), nanC (239), ...27 more...
GO:0044265 | 8.893e-04 | 1.072e-04 | 1.448e-02 | ~6% | BP | cellular macromolecule catabolic process | fucP (51), fucA (52), rhaB (83), araB (144), fruB (147), fruB (148), nagB (153), xylA (178), idnD (198), nanA (201), ...13 more...
GO:0019321 | 1.272e-03 | 1.859e-04 | 2.317e-02 | ~16% | BP | pentose metabolic process | fucP (51), fucA (52), rhaB (83), araB (144), xylA (178), rbsD (364), aldA (1071), yiaK (1938)

## Motif nagC

Previous Next Top

GO terms are shown in grey if a more specific GO term was also significantly associated with this motif. The most specific GO terms are shown in black.
BP stands for biological process, CC stands for cellular component and MF stands for molecular function.

GO term | score | p-value | q-value | Specificity | GO name | Gene ID / Rank (2518 genes in total)
--- | --- | --- | --- | --- | --- | ---
GO:0051704 | 1.801e-04 | 2.077e-05 | 3.268e-02 | ~0% | BP | multi-organism process | srlA (79), solA (181), yjbE (305), bhsA (376), ymgC (387), dcuB (442), yihR (478), hlyE (536), ttdA (588), zwf (720), ...3 more...
GO:0042710 | 4.020e-04 | 4.997e-05 | 3.432e-02 | ~15% | BP | biofilm formation | srlA (79), solA (181), yjbE (305), bhsA (376), ymgC (387), dcuB (442), yihR (478), ttdA (588), ymgA (821), yjiP (889), ...1 more...
GO:0009252 | 8.308e-04 | 1.527e-04 | 3.432e-02 | ~89% | BP | peptidoglycan biosynthetic process | mltB (78), mltA (98), mipA (128), mraZ (166), zwf (720)
GO:0007047 | 8.308e-04 | 1.527e-04 | 3.432e-02 | ~37% | BP | cellular cell wall organization | mltB (78), mltA (98), mipA (128), mraZ (166), zwf (720)
GO:0031504 | 8.308e-04 | 1.527e-04 | 3.432e-02 | 100% | BP | peptidoglycan-based cell wall organization | mltB (78), mltA (98), mipA (128), mraZ (166), zwf (720)
GO:0009273 | 8.308e-04 | 1.527e-04 | 3.432e-02 | ~29% | BP | peptidoglycan-based cell wall biogenesis | mltB (78), mltA (98), mipA (128), mraZ (166), zwf (720)
GO:0042546 | 8.308e-04 | 1.527e-04 | 3.432e-02 | ~8% | BP | cell wall biogenesis | mltB (78), mltA (98), mipA (128), mraZ (166), zwf (720)
GO:0016798 | 1.101e-03 | 2.038e-04 | 3.562e-02 | ~1% | MF | hydrolase activity, acting on glycosyl bonds | chiA (11), uidA (95), mltA (98), essD (386)
GO:0004553 | 1.101e-03 | 2.038e-04 | 3.562e-02 | ~2% | MF | hydrolase activity, hydrolyzing O-glycosyl compounds | chiA (11), uidA (95), mltA (98), essD (386)

## Motif narP

Previous Top

GO terms are shown in grey if a more specific GO term was also significantly associated with this motif. The most specific GO terms are shown in black.
BP stands for biological process, CC stands for cellular component and MF stands for molecular function.

GO term | score | p-value | q-value | Specificity | GO name | Gene ID / Rank (2518 genes in total)
--- | --- | --- | --- | --- | --- | ---
GO:0009061 | 3.737e-04 | 3.930e-05 | 3.594e-02 | ~54% | BP | anaerobic respiration | fdnG (3), nirB (9), narG (21), frdA (25), dmsA (32), torC (228), lldP (715), narZ (798), zwf (2156), ...1 more...
GO:0045333 | 5.182e-04 | 6.457e-05 | 3.594e-02 | 15% | BP | cellular respiration | fdnG (3), nirB (9), narG (21), frdA (25), dmsA (32), torC (228), sdhC (672), lldP (715), narZ (798), cyoA (984), ...5 more...
GO:0030151 | 6.633e-04 | 9.096e-05 | 3.594e-02 | 100% | MF | molybdenum ion binding | fdnG (3), narG (21), dmsA (32), torC (228), narZ (798)
GO:0015980 | 9.717e-04 | 1.381e-04 | 3.594e-02 | ~6% | BP | energy derivation by oxidation of organic compounds | fdnG (3), nirB (9), narG (21), frdA (25), dmsA (32), torC (228), sdhC (672), lldP (715), narZ (798), cyoA (984), ...6 more...
GO:0006091 | 9.717e-04 | 1.381e-04 | 3.594e-02 | ~4% | BP | generation of precursor metabolites and energy | fdnG (3), nirB (9), narG (21), frdA (25), dmsA (32), torC (228), sdhC (672), lldP (715), narZ (798), cyoA (984), ...6 more...
GO:0017004 | 1.063e-03 | 1.544e-04 | 3.594e-02 | ~46% | BP | cytochrome complex assembly | napF (1), fdnG (3), narG (21), cydA (609), sdhC (672)
GO:0043623 | 1.063e-03 | 1.544e-04 | 3.594e-02 | ~9% | BP | cellular protein complex assembly | napF (1), fdnG (3), narG (21), cydA (609), sdhC (672)
GO:0042592 | 1.382e-03 | 2.072e-04 | 3.594e-02 | ~1% | BP | homeostatic process | aqpZ (28), nhaB (30), adiC (60), gadB (80), mscS (155), gadA (255), adiA (370), nhaA (532), kefA (565), mscL (821), ...3 more...
GO:0048878 | 1.382e-03 | 2.072e-04 | 3.594e-02 | ~2% | BP | chemical homeostasis | aqpZ (28), nhaB (30), adiC (60), gadB (80), mscS (155), gadA (255), adiA (370), nhaA (532), kefA (565), mscL (821), ...3 more...
GO:0019725 | 1.382e-03 | 2.072e-04 | 3.594e-02 | ~4% | BP | cellular homeostasis | aqpZ (28), nhaB (30), adiC (60), gadB (80), mscS (155), gadA (255), adiA (370), nhaA (532), kefA (565), mscL (821), ...3 more...
GO:0009055 | 1.539e-03 | 2.465e-04 | 3.887e-02 | ~13% | MF | electron carrier activity | fdnG (3), narG (21), frdA (25), dmsA (32), torC (228), cydA (609), sdhC (672), narZ (798), cyoA (984), ndh (1013), ...4 more...
GO:0065007 | 1.695e-03 | 2.819e-04 | 4.075e-02 | ~0% | BP | biological regulation | napF (1), aqpZ (28), nhaB (30), adiC (60), gadB (80), acnA (106), lptA (147), mscS (155), sohA (224), alaS (236), ...36 more...
GO:0065008 | 1.839e-03 | 3.099e-04 | 4.136e-02 | ~0% | BP | regulation of biological quality | aqpZ (28), nhaB (30), adiC (60), gadB (80), mscS (155), sohA (224), gadA (255), adiA (370), nhaA (532), kefA (565), ...5 more...
GO:0043169 | 2.049e-03 | 3.638e-04 | 4.508e-02 | ~9% | MF | cation binding | fdnG (3), nirB (9), narG (21), dmsA (32), uxaC (172), torC (228), alaS (236), nagB (246), yfdR (378), fucA (510), ...16 more...

GOMo version:
5.1.0 (Release date: Wed Oct 09 15:58:02 2019 -0700)
Reference:
Mikael Bodén and Timothy L. Bailey, "Associating transcription factor binding site motifs with target Go terms and target genes", Nucleic Acids Research, 36, 4108-4117, 2008. [full text]
Fabian A. Buske, Mikael Bodén, Denis C. Bauer and Timothy L. Bailey, "Assigning roles to DNA regulatory motifs using comparative genomics", Bioinformatics, 26, 860-866, 2010. [full text]
Input Data:
go-term-sequence mapping: bacteria_escherichia_coli_k12_1000_199.na.csv
scored sequence file: ama.xml
Command line summary:
This information can also be useful in the event you wish to report a problem with the GOMo software.
Command:
gomo --oc gomo_example_output_files --dag go.dag --motifs dpinteract_subset.meme bacteria_escherichia_coli_k12_1000_199.na.csv ama.xml
Seed: 3943978896
Significance Threshold: 0.05