AlignACE 3.0 10/20/99
AlignACE2 -i EC_sum_all075_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943441821
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	queA	92	synthesis of queuine in tRNA; probably S-adenosylmethionine:tRNA ribosyltransferase-isomerase
#1	tgt	55	tRNA-guanine transglycosylase
#2	yajC	22	orf, hypothetical protein
#3	secD	27	protein secretion; membrane protein, part of the channel
#4	apt	152	adenine phosphoribosyltransferase
#5	relA	47	(p)ppGpp synthetase I (GTP pyrophosphokinase); regulation of RNA synthesis; stringent factor
#6	ygcA	56	putative enzyme
#7	dsbC	24	protein disulfide isomerase II
#8	xerD	111	site-specific recombinase
#9	gmk	251	guanylate kinase
#10	rpoZ	54	RNA polymerase, omega subunit
#11	yihV	161	putative kinase
#12	yihX	77	putative phosphatase

Motif 1
TATATTCTATCCAAAAGGGGGTAAAGGTTG	0	14	1
TAAAATTTTTCCCTAAGGGAATTGCC    	3	11	1
GCCGAAATCGGCAAATCGCAA         	5	1	0
CAGGTCTGGTCCCTAAAGGAGAGGACG   	5	30	1
CTTAATTGTCCCATAACGGAACTCC     	6	5	0
TACACTAGCCGCAAAAGCCACAGCAGAATC	8	24	0
GCACAATAAGGCATAATGGATCAAATGAGT	8	74	1
AAATGAGTGACCATAAGGGGCGCAA     	8	96	1
CGTGATGAAAGCAAAGCCGAGTGGCAAAAA	9	41	1
AAGCCGAGTGGCAAAAACGGAGTCTGCGAG	9	54	1
TGAATGACAGGCAAATGCGGAAGCAGCTAC	9	114	1
AAGCAGCTACGCAAAACGCAACAACTTTGC	9	134	1
TTGCCACATAGCCAAACCCATCCTTTCCCG	12	41	1
          **********
MAP Score: 11.5998

Motif 2
AGAAAAACAGTCCAACGTTTTAAACCAGCGC	1	17	0
GCCAGTACATTCTGGCGTTTTCGAGCACAGG	4	44	1
GTTAAACAACTGTTACTTTTGATACGTTTAA	4	90	1
GTGGTACTCACGGCGCGTTTTAAACGTATCA	4	109	0
TCGATTCTGCTGTGGCTTTTGCGGCTAGTGT	8	22	1
TGCGCAAAGTTGTTGCGTTTTGCGTAGCTGC	9	136	0
TAGCCCTTGCTCACACTTTTTGCGCAAAGTT	9	156	0
TCTTCACCTGTGGAGCTTTTTAAGT      	10	39	1
AATACAGTTATGTCACTTTTTGTCATTTATG	11	22	1
AAGTGACGGCTGTCAATTTTTTGACGATAAA	11	90	0
AATTGACAGCCGTCACTTTTTAAACAATTGG	11	103	1
          *** *******
MAP Score: 11.3885

Motif 3
CAAAAGTAACAGTTGTTTAACCTTTGACCGCCTGCGC	4	74	0
AACAACTGTTACTTTTGATACGTTTAAAACGCGCCGT	4	94	1
   GGAGTTCCGTTATGGGACAATTAAGGTCACACTG	6	7	1
TCCTGAATACAGTTATGTCACTTTTTGTCATTTATGA	11	17	1
ACTTTTTGTCATTTATGACATGCTTTGCTTGTCTGTT	11	36	1
GACGGCTGTCAATTTTTTGACGATAAATTACAAATAC	11	80	0
GACAGCCGTCACTTTTTAAACAATTGGTGAAATTAAA	11	107	1
          ATTTTTGTGACCGTTAACCTGGCTTCA	12	0	1
          * ** **  **  ** *
MAP Score: 7.24095

Motif 4
         GACACTGACTCAGACTAAAATAAGAGGCGGGTAG	0	68	0
ACGCCAGAATGTACTGGCTGTACGCAATAATTGCAACTGCGAT	4	19	0
GCGTTTTCGAGCACAGGCGCAGGCGGTCAAAGGTTAAACAACT	4	58	1
TTTAAAACGCGCCGTGAGTACCACCGTAACAAGCAGGCATACA	4	116	1
TGCCGATTTCGGCAGGTCTGGTCCCTAAAGGAGAGGACG    	5	18	1
CGTGATGAAAGCAAAGCCGAGTGGCAAAAACGGAGTCTGCGAG	9	41	1
AACGGAGTCTGCGAGGACGCTTCCTGAAAATCGTCTTTATTGC	9	69	1
CGTCTTTATTGCAGTGAATGACAGGCAAATGCGGAAGCAGCTA	9	100	1
TACGCAAAACGCAACAACTTTGCGCAAAAAGTGTGAGCAAGGG	9	141	1
AAAAGTGTGAGCAAGGGCTACGTCACATGGCCGCGCCGTGTAT	9	167	1
TGAAGAAATGACTGGGCATGATACTGAAATCAGGT        	10	2	0
          **   * **    *  ***   *
MAP Score: 6.76057

Motif 5
GCAATAATTGCAACTGCGATTGTTGTGCT      	4	4	0
CGTTTTCGAGCACAGGCGCAGGCGGTCAAAGGTTA	4	59	1
TTAAACGTATCAAAAGTAACAGTTGTTTAACCTTT	4	86	0
TGATACGTTTAAAACGCGCCGTGAGTACCACCGTA	4	109	1
ACACTAGCCGCAAAAGCCACAGCAGAATCGAGAAG	8	18	0
AGCCGAGTGGCAAAAACGGAGTCTGCGAGGACGCT	9	55	1
GAATGACAGGCAAATGCGGAAGCAGCTACGCAAAA	9	115	1
AACTTTGCGCAAAAAGTGTGAGCAAGGGCTACGTC	9	156	1
AGGGCTACGTCACATGGCCGCGCCGTGTATAATAA	9	180	1
CCAATTGTTTAAAAAGTGACGGCTGTCAATTTTTT	11	99	0
          **** ***   ** *
MAP Score: 4.85916

Motif 6
TTCCGCGGCGCTGGTTTAAAACGTTGGACTGTTTTTCTGAC	1	10	1
TCAAAAGTAACAGTTGTTTAACCTTTGACCGCCTGCGCCTG	4	71	0
        TTGCGATTTGCCGATTTCGGCAGGTCTGGTCCC	5	2	1
CTTCTCGATTCTGCTGTGGCTTTTGCGGCTAGTGTATCAGA	8	18	1
        CTCCGCTGTAGATAGTCAGGCAGATATACAACG	9	2	1
CTCGCAGACTCCGTTTTTGCCACTCGGCTTTGCTTTCATCA	9	43	0
TCACATGGCCGCGCCGTGTATAATAAGCTCGTATGTAGGCT	9	189	1
TAAAAAGTGACGGCTGTCAATTTTTTGACGATAAATTACAA	11	84	0
          * * ***  *   *  * * *
MAP Score: 4.71388

Motif 7
GTTTTTGCCACTCGGCTTTGCTTTCATCAC	9	42	0
  GAGTATCTTTCGTATGTGATTAGCGAAA	9	233	0
TTTGACCGCCTGCGCCTGTGCTCGAAAACG	4	59	0
CAGTCATTTCTTCACCTGTGGAGCTTTTTA	10	31	1
AGCTTCTCGATTCTGCTGTGGCTTTTGCGG	8	16	1
GTATAATAAGCTCGTATGTAGGCTTTATTT	9	206	1
TCTGTTTTTGATCGTATTTGTAATTTATCG	11	67	1
CGTAGCTGCTTCCGCATTTGCCTGTCATTC	9	115	0
CTTCCTGAAAATCGTCTTTATTGCAGTGAA	9	88	1
      CGTCCTCTCCTTTAGGGACCAGAC	5	33	0
          CTCCGCTGTAGATAGTCAGG	9	0	1
          **********
MAP Score: 1.58788

Motif 8
CTATCCAAAAGGGGGTAAAGGTTGCAGGGAGAGCGCCCCGG	0	20	1
AATAAGAGGCGGGTAGTCTAGTGCCGGGGCGCTCTCCCTGC	0	43	0
AGTACATTCTGGCGTTTTCGAGCACAGGCGCAGGCGGTCAA	4	47	1
TGCCGATTTCGGCAGGTCTGGTCCCTAAAGGAGAGGACG  	5	18	1
ATTCTGCTGTGGCTTTTGCGGCTAGTGTATCAGAATCGCTT	8	25	1
AAAGCCGAGTGGCAAAAACGGAGTCTGCGAGGACGCTTCCT	9	53	1
GTGAATGACAGGCAAATGCGGAAGCAGCTACGCAAAACGCA	9	113	1
          ***   * ***   * *   *
MAP Score: 1.08309

Motif 9
AATAAGAGGCGGGTAGTCTAGTGCCGGGGCGCTCTCCCTGCA	0	42	0
   TTCCGCGGCGCTGGTTTAAAACGTTGGACTGTTTTTCTG	1	7	1
GTACATTCTGGCGTTTTCGAGCACAGGCGCAGGCGGTCAAAG	4	48	1
      TTGCGATTTGCCGATTTCGGCAGGTCTGGTCCCTAA	5	4	1
TCTCGATTCTGCTGTGGCTTTTGCGGCTAGTGTATCAGAATC	8	20	1
AACGGAGTCTGCGAGGACGCTTCCTGAAAATCGTCTTTATTG	9	69	1
TGAATGACAGGCAAATGCGGAAGCAGCTACGCAAAACGCAAC	9	114	1
AAAAGTGTGAGCAAGGGCTACGTCACATGGCCGCGCCGTGTA	9	167	1
CACAGGTGAAGAAATGACTGGGCATGATACTGAAATCAGGT 	10	9	0
          **   * **    * *  ** *
MAP Score: 0.0731727