AlignACE 3.0 10/20/99
AlignACE2 -i EC_profile066_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943442839
 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	sohB	219	putative protease
#5	dapF	300	diaminopimelate epimerase
#6	murB	300	UDP-N-acetylenolpyruvoylglucosamine reductase
#7	serB	105	3-phosphoserine phosphatase
#8	sms	48	probable ATP-dependent protease

Motif 1
CCTCTTATTTTAGTCTGAGTCAGTGTC        	0	75	1
CTCAACGACGTTGTCTGTCGCGCTGCCAGTGTACT	4	18	1
GCATTTCAATCAGCCTGGGGCGATAACACCGCAAA	4	88	1
  CTTTTACGTCTTCTCCTGCGATGATAGAAAGCA	5	8	1
TTACTCTCTTCAGCCTGACGGGCTGCGGTCTGAAA	5	107	1
TCTACCGGTTTGGTCGGCGGCGGTGCGTTTTTATC	5	166	0
CGATCGTTTTTATCCGGCACCGTGGATTGCGTTTG	5	205	0
GGATGGACCATCGCCAGTGGCGCGATCGTTTTTAT	5	227	0
TAGGACAAATCCGCCGGGAGCGGATTTGAACGTTG	6	87	1
TGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGAC	6	120	1
AGCAGAAGGCCATCCTGACGGATGGCCTTTTTGCG	6	185	1
    AGCTGCTTTCCTGATGCAAAAACGAGGCTAG	6	279	0
AGACTTAATGTTGCCAGAAGCAATGGATACAAGGT	7	31	1
GGATACAAGGTAGCCTCATGCGTTATTTTCCCTGC	7	55	1
TCCTGTAAAATCGTTCGAAGCAGGGAAAATAACGC	7	74	0
TAATGCTGTGCCGCCCGCAGGATGGCGGGCGAGCA	8	11	0
          * *** *  *** **
MAP Score: 25.263

Motif 2
GGCGGGCGTCCTGCCCGCCACCCTCCGGGCC	6	131	0
TAATGCTGTGCCGCCCGCAGGATGGCGGGCG	8	15	0
GCAGGGAGAGCGCCCCGGCACTAGACTACCC	0	43	1
TTACTCTCTTCAGCCTGACGGGCTGCGGTCT	5	107	1
TGCGAAGCAACGGCCCGGAGGGTGGCGGGCA	6	120	1
CAGATAAAAACGCACCGCCGCCGACCAAACC	5	164	1
AGCAGAAGGCCATCCTGACGGATGGCCTTTT	6	185	1
GTTCAAATCCGCTCCCGGCGGATTTGTCCTA	6	87	0
AGTACACTGGCAGCGCGACAGACAACGTCGT	4	22	0
GCATTTCAATCAGCCTGGGGCGATAACACCG	4	88	1
CGGCACTAGACTACCCGCCTCTTATTTTAGT	0	58	1
          TTCCGCGGCGCTGGTTTAAAA	1	0	1
GCGGACCTTTCAGACCGCAGCCCGTCAGGCT	5	118	0
ATCTACAAGCCATCCCCCCACAGATACGGTA	6	246	1
CCGGGGCGCTCTCCCTGCAACCTTTACCCCC	0	30	0
GGATAAAAACGATCGCGCCACTGGCGATGGT	5	225	1
GTCCGCTCTATTTCCCGCCTGCAGATAAAAA	5	143	1
AATAACATCTCTGCGAGACGGCTTAACATGC	4	150	1
AAACGCAATCCACGGTGCCGGATAAAAACGA	5	206	1
GCTTAATTTGATGCCTGGCAGTTTATGGCGG	6	157	0
      TTGCTCGCCCGCCATCCTGCGGGCG	8	4	1
          * *********
MAP Score: 20.4101

Motif 3
TGCGAAGCAACGGCCCGGAGGGTGGCGGGCAG	6	120	1
TAATGCTGTGCCGCCCGCAGGATGGCGGGCGA	8	14	0
CGTTTTAAACCAGCGCCGCGGAA         	1	1	0
TTACTCTCTTCAGCCTGACGGGCTGCGGTCTG	5	107	1
TAGGACAAATCCGCCGGGAGCGGATTTGAACG	6	87	1
GCCCGGAGGGTGGCGGGCAGGACGCCCGCCAT	6	132	1
GCGTTTTTATCTGCAGGCGGGAAATAGAGCGG	5	145	0
AATAACATCTCTGCGAGACGGCTTAACATGCC	4	150	1
CCGGTTTGGTCGGCGGCGGTGCGTTTTTATCT	5	165	0
CGTTTTTATCCGGCACCGTGGATTGCGTTTGC	5	204	0
AGTACACTGGCAGCGCGACAGACAACGTCGTT	4	21	0
GCATTTCAATCAGCCTGGGGCGATAACACCGC	4	88	1
GTTTCTGTACCCGCGTGATTGGAGTAA     	5	283	1
GTTGCAGGGAGAGCGCCCCGGCACTAGACTAC	0	40	1
GCCCGCAGGATGGCGGGCGAGCAA        	8	2	0
ATAAAAACGATCGCGCCACTGGCGATGGTCCA	5	227	1
ACCGTATCTGTGGGGGGATGGCTTGTAGATAT	6	244	0
AAAGGCCATCCGTCAGGATGGCCTTCTGCTTA	6	183	0
GGATACAAGGTAGCCTCATGCGTTATTTTCCC	7	55	1
AGACTTAATGTTGCCAGAAGCAATGGATACAA	7	31	1
          * ****** ***
MAP Score: 16.6939

Motif 4
TCTAGTGCCGGGGCGCTCTCCCTGCAACCTTTA	0	35	0
AACGTTTTAAACCAGCGCCGCGGAA        	1	2	0
AAAGTACACTGGCAGCGCGACAGACAACGTCGT	4	22	0
GATGAACTTTACAGGCAATCCATAATGAAAAAC	5	49	1
GGACCTTTCAGACCGCAGCCCGTCAGGCTGAAG	5	114	0
CTGCAGATAAAAACGCACCGCCGCCGACCAAAC	5	161	1
GTAGAGACGCAAACGCAATCCACGGTGCCGGAT	5	196	1
GGATAAAAACGATCGCGCCACTGGCGATGGTCC	5	225	1
GTTTGTCGGTGAACGCTCTCCTGAGTAGGACAA	6	62	1
CGGGCGTCCTGCCCGCCACCCTCCGGGCCGTTG	6	127	0
GTGGCGGGCAGGACGCCCGCCATAAACTGCCAG	6	141	1
AAATTAAGCAGAAGGCCATCCTGACGGATGGCC	6	179	1
AGAAACGCAAAAAGGCCATCCGTCAGGATGGCC	6	192	0
CGTCATATCTACAAGCCATCCCCCCACAGATAC	6	240	1
        TTGCTCGCCCGCCATCCTGCGGGCG	8	2	1
CCGCCATCCTGCGGGCGGCACAGCATTAACGAG	8	18	1
          ** *** **** *
MAP Score: 15.5309

Motif 5
GGGTAAAGGTTGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCT	0	32	1
GAAACAGAAGGGCATTTCAATCAGCCTGGGGCGATAACACCGCAAA	4	77	1
ATCTCTGCGAGACGGCTTAACATGCCTGTTGTAAACTGTGAGCCAA	4	156	1
CATCGCTTTCTGCTTTCTATCATCGCAGGAGAAGACGTAAAAG   	5	7	0
CTGAAAGGTCCGCTCTATTTCCCGCCTGCAGATAAAAACGCACCGC	5	136	1
AAAAACGCACCGCCGCCGACCAAACCGGTAGAGACGCAAACGCAAT	5	169	1
GAGACGCAAACGCAATCCACGGTGCCGGATAAAAACGATCGCGCCA	5	199	1
TCGCGCCACTGGCGATGGTCCATCCCAGGTGAATTACTAAAAGTCA	5	237	1
ATTTGAACGTTGCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACG	6	110	1
GATGGCCTTCTGCTTAATTTGATGCCTGGCAGTTTATGGCGGGCGT	6	153	0
TTTGTAGAAACGCAAAAAGGCCATCCGTCAGGATGGCCTTCTGCTT	6	184	0
CTTTTTGCGTTTCTACAAACTCTTCCTGTCGTCATATCTACAAGCC	6	211	1
         TTGCTCGCCCGCCATCCTGCGGGCGGCACAGCATTAA	8	1	1
          ***       **  ** *  *    *
MAP Score: 14.5312

Motif 6
GTAAAGGTTGCAGGGAGAGCGCCCCGGCACTA	0	34	1
        TTCCGCGGCGCTGGTTTAAAACGT	1	2	1
ACGACGTTGTCTGTCGCGCTGCCAGTGTACTT	4	22	1
GCATTTCAATCAGCCTGGGGCGATAACACCGC	4	88	1
AATAACATCTCTGCGAGACGGCTTAACATGCC	4	150	1
TTACTCTCTTCAGCCTGACGGGCTGCGGTCTG	5	107	1
TGACGGGCTGCGGTCTGAAAGGTCCGCTCTAT	5	122	1
CCGGTTTGGTCGGCGGCGGTGCGTTTTTATCT	5	165	0
TCGTTTTTATCCGGCACCGTGGATTGCGTTTG	5	205	0
ATAAAAACGATCGCGCCACTGGCGATGGTCCA	5	227	1
GTTTCTGTACCCGCGTGATTGGAGTAA     	5	283	1
TAGGACAAATCCGCCGGGAGCGGATTTGAACG	6	87	1
TGCGAAGCAACGGCCCGGAGGGTGGCGGGCAG	6	120	1
CGGAGGGTGGCGGGCAGGACGCCCGCCATAAA	6	135	1
AAAAGGCCATCCGTCAGGATGGCCTTCTGCTT	6	184	0
TACCGTATCTGTGGGGGGATGGCTTGTAGATA	6	245	0
TGCTGTGCCGCCCGCAGGATGGCGGGCGAGCA	8	11	0
          ***** ** ***
MAP Score: 14.0197

Motif 7
TGCAGGGAGAGCGCCCCGGCACTAGACTACCCGCCTCTTATTTT	0	42	1
TGATTGAAATGCCCTTCTGTTTCAGGCATAAAGCCCCAAAGTCA	4	56	0
GGGCATTTCAATCAGCCTGGGGCGATAACACCGCAAAATGGATA	4	86	1
ATGTTAAGCCGTCTCGCAGAGATGTTATTGCAGCGAAAGTATGA	4	135	0
TTCAGCCTGACGGGCTGCGGTCTGAAAGGTCCGCTCTATTTCCC	5	115	1
CTCTATTTCCCGCCTGCAGATAAAAACGCACCGCCGCCGACCAA	5	148	1
AACGCACCGCCGCCGACCAAACCGGTAGAGACGCAAACGCAATC	5	172	1
AACGCAATCCACGGTGCCGGATAAAAACGATCGCGCCACTGGCG	5	207	1
TCGGTGAACGCTCTCCTGAGTAGGACAAATCCGCCGGGAGCGGA	6	67	1
ACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCC	6	91	1
GAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAA	6	123	1
ACAAGCCATCCCCCCACAGATACGGTAAACTAGCCTCGTTTTTG	6	250	1
GCCCGCCATCCTGCGGGCGGCACAGCATTAACGAGGTACACC  	8	16	1
          * *   * *    ** *    ***
MAP Score: 8.33992

Motif 8
GAGGCGGGTAGTCTAGTGCCGGGGCGCTCTCCCTGCAACCTTTACC	0	33	0
        GACACTGACTCAGACTAAAATAAGAGGCGGGTAGTCTA	0	64	0
        TTCCGCGGCGCTGGTTTAAAACGTTGGACTGTTTTTCT	1	2	1
ACTCCTCAACGACGTTGTCTGTCGCGCTGCCAGTGTACTTTATGAC	4	14	1
AAGGGCATTTCAATCAGCCTGGGGCGATAACACCGCAAAATGGATA	4	84	1
TACTTTGTCATACTTTCGCTGCAATAACATCTCTGCGAGACGGCTT	4	128	1
   CTTTTACGTCTTCTCCTGCGATGATAGAAAGCAGAAAGCGATG	5	7	1
TCTTCAGCCTGACGGGCTGCGGTCTGAAAGGTCCGCTCTATTTCCC	5	113	1
CGCTCTATTTCCCGCCTGCAGATAAAAACGCACCGCCGCCGACCAA	5	146	1
CACCGCCGCCGACCAAACCGGTAGAGACGCAAACGCAATCCACGGT	5	176	1
CAAACGCAATCCACGGTGCCGGATAAAAACGATCGCGCCACTGGCG	5	205	1
CGGCGGATTTGTCCTACTCAGGAGAGCGTTCACCGACAAACAACAG	6	57	0
GGACAAATCCGCCGGGAGCGGATTTGAACGTTGCGAAGCAACGGCC	6	89	1
GCGAAGCAACGGCCCGGAGGGTGGCGGGCAGGACGCCCGCCATAAA	6	121	1
        AGCTGCTTTCCTGATGCAAAAACGAGGCTAGTTTACCG	6	272	0
GAAAATTTGAGACTTAATGTTGCCAGAAGCAATGGATACAAGGTAG	7	22	1
TTAATGCTGTGCCGCCCGCAGGATGGCGGGCGAGCAA         	8	1	0
          * **    * *    **      ***
MAP Score: 6.33902