<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Document definition -->
<!DOCTYPE gomo[
	<!ELEMENT gomo (program, motif*)>
	<!ATTLIST gomo xmlns:xsi CDATA #IMPLIED
			 version CDATA #REQUIRED
			 release CDATA #REQUIRED
			>
		<!ELEMENT program (gomapfile, seqscorefile*)>
		<!ATTLIST program
				 name CDATA #REQUIRED
				 cmd CDATA #REQUIRED
				 gene_url CDATA #IMPLIED
				 outdir CDATA #REQUIRED
				 clobber CDATA #REQUIRED
				 text_only CDATA #REQUIRED
				 use_e_values CDATA #REQUIRED
				 score_e_thresh CDATA #REQUIRED
				 min_gene_count CDATA #REQUIRED
				 motifs CDATA #IMPLIED
				 shuffle_scores CDATA #REQUIRED
				 q_threshold CDATA #REQUIRED
				>
			<!ELEMENT gomapfile EMPTY>
			<!ATTLIST gomapfile path CDATA #REQUIRED >
			<!ELEMENT seqscorefile EMPTY>
			<!ATTLIST seqscorefile path CDATA #REQUIRED >
		<!ELEMENT motif (goterm*)>
		<!ATTLIST motif
				 id CDATA #REQUIRED
				 genecount CDATA #REQUIRED
				 logo CDATA #IMPLIED
				>
			<!ELEMENT goterm (gene*)>
			<!ATTLIST goterm
					 id CDATA #REQUIRED
					 score CDATA #REQUIRED
					 pvalue CDATA #REQUIRED
					 qvalue CDATA #REQUIRED
					 annotated CDATA #REQUIRED
					 group CDATA #REQUIRED
					 nabove CDATA #REQUIRED
					 nbelow CDATA #REQUIRED
					 implied (u|y|n) #REQUIRED
					 name CDATA #REQUIRED
					>
				<!ELEMENT gene EMPTY>
				<!ATTLIST gene
						 id CDATA #REQUIRED
						 rank CDATA #REQUIRED
						>
]>
<gomo xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="5.5.3" release="Fri Jun 9 08:12:01 2023 -0700">
	<program name="gomo"
			 seed="3814754854"
			 cmd="gomo --oc gomo_example_output_files --dag go.dag --motifs dpinteract_subset.meme bacteria_escherichia_coli_k12_1000_199.na.csv ama.xml"
			 gene_url="http://regulondb.ccg.unam.mx/search?term=!!GENEID!!&amp;amp;type=gene&amp;amp;organism=ECK12"
			 outdir="gomo_example_output_files" clobber="true" text_only="false"
			 use_e_values="true" score_e_thresh="0"
			 min_gene_count="1"
			 shuffle_scores="1000" q_threshold="0.05"
			>
		<gomapfile path="bacteria_escherichia_coli_k12_1000_199.na.csv" />
		<seqscorefile path="ama.xml" />
	</program>
	<motif id="crp" genecount="2518" logo="logo1.png">
		<goterm id="GO:0044248" score="1.341e-06" pvalue="5.615e-07" qvalue="4.550e-04" annotated="52" group="b" nabove="5" nbelow="852" implied="y"
				name="cellular catabolic process">
			<gene id="deoC" rank="25" />
			<gene id="fucP" rank="51" />
			<gene id="fucA" rank="52" />
			<gene id="uxaC" rank="64" />
			<gene id="exuT" rank="65" />
			<gene id="tdcA" rank="71" />
			<gene id="rhaB" rank="83" />
			<gene id="araB" rank="144" />
			<gene id="fruB" rank="147" />
			<gene id="fruB" rank="148" />
		</goterm>
		<goterm id="GO:0009056" score="8.869e-07" pvalue="5.615e-07" qvalue="4.550e-04" annotated="59" group="b" nabove="2" nbelow="1073" implied="y"
				name="catabolic process">
			<gene id="deoC" rank="25" />
			<gene id="iraP" rank="37" />
			<gene id="fucP" rank="51" />
			<gene id="fucA" rank="52" />
			<gene id="uxaC" rank="64" />
			<gene id="exuT" rank="65" />
			<gene id="tdcA" rank="71" />
			<gene id="rhaB" rank="83" />
			<gene id="araB" rank="144" />
			<gene id="fruB" rank="147" />
		</goterm>
		<goterm id="GO:0008643" score="1.075e-04" pvalue="7.299e-06" qvalue="3.943e-03" annotated="7" group="b" nabove="4" nbelow="93" implied="n"
				name="carbohydrate transport">
			<gene id="fucP" rank="51" />
			<gene id="malK" rank="138" />
			<gene id="malE" rank="139" />
			<gene id="ulaA" rank="174" />
			<gene id="xylF" rank="179" />
			<gene id="idnD" rank="198" />
			<gene id="yjjL" rank="824" />
		</goterm>
		<goterm id="GO:0051119" score="2.285e-04" pvalue="1.965e-05" qvalue="6.673e-03" annotated="5" group="m" nabove="6" nbelow="113" implied="n"
				name="sugar transmembrane transporter activity">
			<gene id="fucP" rank="51" />
			<gene id="glpT" rank="99" />
			<gene id="malK" rank="138" />
			<gene id="malE" rank="139" />
			<gene id="xylF" rank="179" />
		</goterm>
		<goterm id="GO:0044275" score="2.652e-04" pvalue="2.471e-05" qvalue="6.673e-03" annotated="20" group="b" nabove="9" nbelow="124" implied="n"
				name="cellular carbohydrate catabolic process">
			<gene id="fucP" rank="51" />
			<gene id="fucA" rank="52" />
			<gene id="rhaB" rank="83" />
			<gene id="araB" rank="144" />
			<gene id="fruB" rank="147" />
			<gene id="fruB" rank="148" />
			<gene id="nagB" rank="153" />
			<gene id="xylA" rank="178" />
			<gene id="idnD" rank="198" />
			<gene id="nanA" rank="201" />
		</goterm>
		<goterm id="GO:0015144" score="2.665e-04" pvalue="2.471e-05" qvalue="6.673e-03" annotated="7" group="m" nabove="5" nbelow="157" implied="y"
				name="carbohydrate transmembrane transporter activity">
			<gene id="fucP" rank="51" />
			<gene id="glpT" rank="99" />
			<gene id="malK" rank="138" />
			<gene id="malE" rank="139" />
			<gene id="ulaA" rank="174" />
			<gene id="xylF" rank="179" />
			<gene id="ycaI" rank="1391" />
		</goterm>
		<goterm id="GO:0016861" score="3.954e-04" pvalue="4.436e-05" qvalue="1.027e-02" annotated="13" group="m" nabove="4" nbelow="25" implied="n"
				name="intramolecular oxidoreductase activity, interconverting aldoses and ketoses">
			<gene id="fucP" rank="51" />
			<gene id="uxaC" rank="64" />
			<gene id="rhaB" rank="83" />
			<gene id="srlA" rank="111" />
			<gene id="araB" rank="144" />
			<gene id="nagB" rank="153" />
			<gene id="xylA" rank="178" />
			<gene id="hisL" rank="641" />
			<gene id="yihU" rank="858" />
			<gene id="rpiB" rank="897" />
		</goterm>
		<goterm id="GO:0016860" score="4.737e-04" pvalue="5.559e-05" qvalue="1.126e-02" annotated="14" group="m" nabove="3" nbelow="70" implied="y"
				name="intramolecular oxidoreductase activity">
			<gene id="fucP" rank="51" />
			<gene id="uxaC" rank="64" />
			<gene id="rhaB" rank="83" />
			<gene id="srlA" rank="111" />
			<gene id="araB" rank="144" />
			<gene id="nagB" rank="153" />
			<gene id="xylA" rank="178" />
			<gene id="hisL" rank="641" />
			<gene id="yihU" rank="858" />
			<gene id="rpiB" rank="897" />
		</goterm>
		<goterm id="GO:0016052" score="5.421e-04" pvalue="6.513e-05" qvalue="1.147e-02" annotated="24" group="b" nabove="5" nbelow="182" implied="y"
				name="carbohydrate catabolic process">
			<gene id="fucP" rank="51" />
			<gene id="fucA" rank="52" />
			<gene id="rhaB" rank="83" />
			<gene id="araB" rank="144" />
			<gene id="fruB" rank="147" />
			<gene id="fruB" rank="148" />
			<gene id="nagB" rank="153" />
			<gene id="ybjQ" rank="158" />
			<gene id="xylA" rank="178" />
			<gene id="idnD" rank="198" />
		</goterm>
		<goterm id="GO:0009057" score="5.850e-04" pvalue="7.075e-05" qvalue="1.147e-02" annotated="30" group="b" nabove="4" nbelow="215" implied="y"
				name="macromolecule catabolic process">
			<gene id="iraP" rank="37" />
			<gene id="fucP" rank="51" />
			<gene id="fucA" rank="52" />
			<gene id="rhaB" rank="83" />
			<gene id="araB" rank="144" />
			<gene id="fruB" rank="147" />
			<gene id="fruB" rank="148" />
			<gene id="nagB" rank="153" />
			<gene id="ybjQ" rank="158" />
			<gene id="xylA" rank="178" />
		</goterm>
		<goterm id="GO:0016853" score="7.322e-04" pvalue="9.770e-05" qvalue="1.439e-02" annotated="37" group="m" nabove="2" nbelow="232" implied="y"
				name="isomerase activity">
			<gene id="fucP" rank="51" />
			<gene id="uxaC" rank="64" />
			<gene id="yqcC" rank="77" />
			<gene id="rhaB" rank="83" />
			<gene id="srlA" rank="111" />
			<gene id="araB" rank="144" />
			<gene id="nagB" rank="153" />
			<gene id="xylA" rank="178" />
			<gene id="nanA" rank="201" />
			<gene id="nanC" rank="239" />
		</goterm>
		<goterm id="GO:0044265" score="8.893e-04" pvalue="1.286e-04" qvalue="1.737e-02" annotated="23" group="b" nabove="9" nbelow="133" implied="n"
				name="cellular macromolecule catabolic process">
			<gene id="fucP" rank="51" />
			<gene id="fucA" rank="52" />
			<gene id="rhaB" rank="83" />
			<gene id="araB" rank="144" />
			<gene id="fruB" rank="147" />
			<gene id="fruB" rank="148" />
			<gene id="nagB" rank="153" />
			<gene id="xylA" rank="178" />
			<gene id="idnD" rank="198" />
			<gene id="nanA" rank="201" />
		</goterm>
		<goterm id="GO:0019321" score="1.272e-03" pvalue="2.004e-04" qvalue="2.499e-02" annotated="8" group="b" nabove="10" nbelow="53" implied="n"
				name="pentose metabolic process">
			<gene id="fucP" rank="51" />
			<gene id="fucA" rank="52" />
			<gene id="rhaB" rank="83" />
			<gene id="araB" rank="144" />
			<gene id="xylA" rank="178" />
			<gene id="rbsD" rank="364" />
			<gene id="aldA" rank="1071" />
			<gene id="yiaK" rank="1938" />
		</goterm>
	</motif>
	<motif id="nagC" genecount="2518" logo="logo2.png">
		<goterm id="GO:0051704" score="1.801e-04" pvalue="1.797e-05" qvalue="2.620e-02" annotated="13" group="b" nabove="1" nbelow="1141" implied="y"
				name="multi-organism process">
			<gene id="srlA" rank="79" />
			<gene id="solA" rank="181" />
			<gene id="yjbE" rank="305" />
			<gene id="bhsA" rank="376" />
			<gene id="ymgC" rank="387" />
			<gene id="dcuB" rank="442" />
			<gene id="yihR" rank="478" />
			<gene id="hlyE" rank="536" />
			<gene id="ttdA" rank="588" />
			<gene id="zwf" rank="720" />
		</goterm>
		<goterm id="GO:0042710" score="4.020e-04" pvalue="5.278e-05" qvalue="2.748e-02" annotated="11" group="b" nabove="2" nbelow="11" implied="n"
				name="biofilm formation">
			<gene id="srlA" rank="79" />
			<gene id="solA" rank="181" />
			<gene id="yjbE" rank="305" />
			<gene id="bhsA" rank="376" />
			<gene id="ymgC" rank="387" />
			<gene id="dcuB" rank="442" />
			<gene id="yihR" rank="478" />
			<gene id="ttdA" rank="588" />
			<gene id="ymgA" rank="821" />
			<gene id="yjiP" rank="889" />
		</goterm>
		<goterm id="GO:0009252" score="8.308e-04" pvalue="1.319e-04" qvalue="2.748e-02" annotated="5" group="b" nabove="31" nbelow="4" implied="n"
				name="peptidoglycan biosynthetic process">
			<gene id="mltB" rank="78" />
			<gene id="mltA" rank="98" />
			<gene id="mipA" rank="128" />
			<gene id="mraZ" rank="166" />
			<gene id="zwf" rank="720" />
		</goterm>
		<goterm id="GO:0007047" score="8.308e-04" pvalue="1.319e-04" qvalue="2.748e-02" annotated="5" group="b" nabove="7" nbelow="12" implied="y"
				name="cellular cell wall organization">
			<gene id="mltB" rank="78" />
			<gene id="mltA" rank="98" />
			<gene id="mipA" rank="128" />
			<gene id="mraZ" rank="166" />
			<gene id="zwf" rank="720" />
		</goterm>
		<goterm id="GO:0031504" score="8.308e-04" pvalue="1.319e-04" qvalue="2.748e-02" annotated="5" group="b" nabove="8" nbelow="0" implied="n"
				name="peptidoglycan-based cell wall organization">
			<gene id="mltB" rank="78" />
			<gene id="mltA" rank="98" />
			<gene id="mipA" rank="128" />
			<gene id="mraZ" rank="166" />
			<gene id="zwf" rank="720" />
		</goterm>
		<goterm id="GO:0009273" score="8.308e-04" pvalue="1.319e-04" qvalue="2.748e-02" annotated="5" group="b" nabove="6" nbelow="15" implied="y"
				name="peptidoglycan-based cell wall biogenesis">
			<gene id="mltB" rank="78" />
			<gene id="mltA" rank="98" />
			<gene id="mipA" rank="128" />
			<gene id="mraZ" rank="166" />
			<gene id="zwf" rank="720" />
		</goterm>
		<goterm id="GO:0042546" score="8.308e-04" pvalue="1.319e-04" qvalue="2.748e-02" annotated="5" group="b" nabove="5" nbelow="59" implied="y"
				name="cell wall biogenesis">
			<gene id="mltB" rank="78" />
			<gene id="mltA" rank="98" />
			<gene id="mipA" rank="128" />
			<gene id="mraZ" rank="166" />
			<gene id="zwf" rank="720" />
		</goterm>
		<goterm id="GO:0016798" score="1.101e-03" pvalue="1.752e-04" qvalue="2.838e-02" annotated="5" group="m" nabove="3" nbelow="215" implied="y"
				name="hydrolase activity, acting on glycosyl bonds">
			<gene id="chiA" rank="11" />
			<gene id="uidA" rank="95" />
			<gene id="mltA" rank="98" />
			<gene id="essD" rank="386" />
		</goterm>
		<goterm id="GO:0004553" score="1.101e-03" pvalue="1.752e-04" qvalue="2.838e-02" annotated="5" group="m" nabove="4" nbelow="163" implied="n"
				name="hydrolase activity, hydrolyzing O-glycosyl compounds">
			<gene id="chiA" rank="11" />
			<gene id="uidA" rank="95" />
			<gene id="mltA" rank="98" />
			<gene id="essD" rank="386" />
		</goterm>
	</motif>
	<motif id="narP" genecount="2518" logo="logo3.png">
		<goterm id="GO:0009061" score="3.737e-04" pvalue="3.650e-05" qvalue="3.850e-02" annotated="11" group="b" nabove="7" nbelow="6" implied="n"
				name="anaerobic respiration">
			<gene id="fdnG" rank="3" />
			<gene id="nirB" rank="9" />
			<gene id="narG" rank="21" />
			<gene id="frdA" rank="25" />
			<gene id="dmsA" rank="32" />
			<gene id="torC" rank="228" />
			<gene id="lldP" rank="715" />
			<gene id="narZ" rank="798" />
			<gene id="zwf" rank="2156" />
		</goterm>
		<goterm id="GO:0045333" score="5.182e-04" pvalue="5.334e-05" qvalue="3.850e-02" annotated="15" group="b" nabove="6" nbelow="34" implied="y"
				name="cellular respiration">
			<gene id="fdnG" rank="3" />
			<gene id="nirB" rank="9" />
			<gene id="narG" rank="21" />
			<gene id="frdA" rank="25" />
			<gene id="dmsA" rank="32" />
			<gene id="torC" rank="228" />
			<gene id="sdhC" rank="672" />
			<gene id="lldP" rank="715" />
			<gene id="narZ" rank="798" />
			<gene id="cyoA" rank="984" />
		</goterm>
		<goterm id="GO:0030151" score="6.633e-04" pvalue="7.524e-05" qvalue="3.850e-02" annotated="5" group="m" nabove="6" nbelow="0" implied="n"
				name="molybdenum ion binding">
			<gene id="fdnG" rank="3" />
			<gene id="narG" rank="21" />
			<gene id="dmsA" rank="32" />
			<gene id="torC" rank="228" />
			<gene id="narZ" rank="798" />
		</goterm>
		<goterm id="GO:0015980" score="9.717e-04" pvalue="1.404e-04" qvalue="3.850e-02" annotated="16" group="b" nabove="5" nbelow="75" implied="y"
				name="energy derivation by oxidation of organic compounds">
			<gene id="fdnG" rank="3" />
			<gene id="nirB" rank="9" />
			<gene id="narG" rank="21" />
			<gene id="frdA" rank="25" />
			<gene id="dmsA" rank="32" />
			<gene id="torC" rank="228" />
			<gene id="sdhC" rank="672" />
			<gene id="lldP" rank="715" />
			<gene id="narZ" rank="798" />
			<gene id="cyoA" rank="984" />
		</goterm>
		<goterm id="GO:0006091" score="9.717e-04" pvalue="1.404e-04" qvalue="3.850e-02" annotated="16" group="b" nabove="4" nbelow="102" implied="y"
				name="generation of precursor metabolites and energy">
			<gene id="fdnG" rank="3" />
			<gene id="nirB" rank="9" />
			<gene id="narG" rank="21" />
			<gene id="frdA" rank="25" />
			<gene id="dmsA" rank="32" />
			<gene id="torC" rank="228" />
			<gene id="sdhC" rank="672" />
			<gene id="lldP" rank="715" />
			<gene id="narZ" rank="798" />
			<gene id="cyoA" rank="984" />
		</goterm>
		<goterm id="GO:0017004" score="1.063e-03" pvalue="1.567e-04" qvalue="3.850e-02" annotated="5" group="b" nabove="12" nbelow="14" implied="n"
				name="cytochrome complex assembly">
			<gene id="napF" rank="1" />
			<gene id="fdnG" rank="3" />
			<gene id="narG" rank="21" />
			<gene id="cydA" rank="609" />
			<gene id="sdhC" rank="672" />
		</goterm>
		<goterm id="GO:0043623" score="1.063e-03" pvalue="1.567e-04" qvalue="3.850e-02" annotated="5" group="b" nabove="11" nbelow="105" implied="y"
				name="cellular protein complex assembly">
			<gene id="napF" rank="1" />
			<gene id="fdnG" rank="3" />
			<gene id="narG" rank="21" />
			<gene id="cydA" rank="609" />
			<gene id="sdhC" rank="672" />
		</goterm>
		<goterm id="GO:0042592" score="1.382e-03" pvalue="2.212e-04" qvalue="3.850e-02" annotated="13" group="b" nabove="3" nbelow="275" implied="y"
				name="homeostatic process">
			<gene id="aqpZ" rank="28" />
			<gene id="nhaB" rank="30" />
			<gene id="adiC" rank="60" />
			<gene id="gadB" rank="80" />
			<gene id="mscS" rank="155" />
			<gene id="gadA" rank="255" />
			<gene id="adiA" rank="370" />
			<gene id="nhaA" rank="532" />
			<gene id="kefA" rank="565" />
			<gene id="mscL" rank="821" />
		</goterm>
		<goterm id="GO:0048878" score="1.382e-03" pvalue="2.212e-04" qvalue="3.850e-02" annotated="13" group="b" nabove="4" nbelow="188" implied="n"
				name="chemical homeostasis">
			<gene id="aqpZ" rank="28" />
			<gene id="nhaB" rank="30" />
			<gene id="adiC" rank="60" />
			<gene id="gadB" rank="80" />
			<gene id="mscS" rank="155" />
			<gene id="gadA" rank="255" />
			<gene id="adiA" rank="370" />
			<gene id="nhaA" rank="532" />
			<gene id="kefA" rank="565" />
			<gene id="mscL" rank="821" />
		</goterm>
		<goterm id="GO:0019725" score="1.382e-03" pvalue="2.212e-04" qvalue="3.850e-02" annotated="13" group="b" nabove="5" nbelow="131" implied="n"
				name="cellular homeostasis">
			<gene id="aqpZ" rank="28" />
			<gene id="nhaB" rank="30" />
			<gene id="adiC" rank="60" />
			<gene id="gadB" rank="80" />
			<gene id="mscS" rank="155" />
			<gene id="gadA" rank="255" />
			<gene id="adiA" rank="370" />
			<gene id="nhaA" rank="532" />
			<gene id="kefA" rank="565" />
			<gene id="mscL" rank="821" />
		</goterm>
		<goterm id="GO:0009055" score="1.539e-03" pvalue="2.560e-04" qvalue="4.051e-02" annotated="14" group="m" nabove="1" nbelow="7" implied="n"
				name="electron carrier activity">
			<gene id="fdnG" rank="3" />
			<gene id="narG" rank="21" />
			<gene id="frdA" rank="25" />
			<gene id="dmsA" rank="32" />
			<gene id="torC" rank="228" />
			<gene id="cydA" rank="609" />
			<gene id="sdhC" rank="672" />
			<gene id="narZ" rank="798" />
			<gene id="cyoA" rank="984" />
			<gene id="ndh" rank="1013" />
		</goterm>
		<goterm id="GO:0065007" score="1.695e-03" pvalue="2.835e-04" qvalue="4.112e-02" annotated="46" group="b" nabove="1" nbelow="6719" implied="y"
				name="biological regulation">
			<gene id="napF" rank="1" />
			<gene id="aqpZ" rank="28" />
			<gene id="nhaB" rank="30" />
			<gene id="adiC" rank="60" />
			<gene id="gadB" rank="80" />
			<gene id="acnA" rank="106" />
			<gene id="lptA" rank="147" />
			<gene id="mscS" rank="155" />
			<gene id="sohA" rank="224" />
			<gene id="alaS" rank="236" />
		</goterm>
		<goterm id="GO:0065008" score="1.839e-03" pvalue="3.111e-04" qvalue="4.164e-02" annotated="15" group="b" nabove="2" nbelow="1381" implied="y"
				name="regulation of biological quality">
			<gene id="aqpZ" rank="28" />
			<gene id="nhaB" rank="30" />
			<gene id="adiC" rank="60" />
			<gene id="gadB" rank="80" />
			<gene id="mscS" rank="155" />
			<gene id="sohA" rank="224" />
			<gene id="gadA" rank="255" />
			<gene id="adiA" rank="370" />
			<gene id="nhaA" rank="532" />
			<gene id="kefA" rank="565" />
		</goterm>
		<goterm id="GO:0043169" score="2.049e-03" pvalue="3.672e-04" qvalue="4.564e-02" annotated="26" group="m" nabove="3" nbelow="29" implied="y"
				name="cation binding">
			<gene id="fdnG" rank="3" />
			<gene id="nirB" rank="9" />
			<gene id="narG" rank="21" />
			<gene id="dmsA" rank="32" />
			<gene id="uxaC" rank="172" />
			<gene id="torC" rank="228" />
			<gene id="alaS" rank="236" />
			<gene id="nagB" rank="246" />
			<gene id="yfdR" rank="378" />
			<gene id="fucA" rank="510" />
		</goterm>
	</motif>
</gomo>
