| blob | 9990c8f74c8167e168c583e669ddad82b9c38a64 |
1 ID SC10H5 standard; DNA; PRO; 4870 BP.
2 XX
3 AC AL031232;
4 XX
5 DE Streptomyces coelicolor cosmid 10H5.
6 XX
7 KW integral membrane protein.
8 XX
9 OS Streptomyces coelicolor
10 OC Eubacteria; Firmicutes; Actinomycetes; Streptomycetes;
11 OC Streptomycetaceae; Streptomyces.
12 XX
13 RN [1]
14 RP 1-4870
15 RA Oliver K., Harris D.;
16 RT ;
17 RL Unpublished.
18 XX
19 RN [2]
20 RP 1-4870
21 RA Parkhill J., Barrell B.G., Rajandream M.A.;
22 RT ;
23 RL Submitted (10-AUG-1998) to the EMBL/GenBank/DDBJ databases.
24 RL Streptomyces coelicolor sequencing project,
25 RL Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA
26 RL E-mail: barrell@sanger.ac.uk
27 RL Cosmids supplied by Prof. David A. Hopwood, [3]
28 RL John Innes Centre, Norwich Research Park, Colney,
29 RL Norwich, Norfolk NR4 7UH, UK.
30 XX
31 RN [3]
32 RP 1-4870
33 RA Redenbach M., Kieser H.M., Denapaite D., Eichner A.,
34 RA Cullum J., Kinashi H., Hopwood D.A.;
35 RT "A set of ordered cosmids and a detailed genetic and physical
36 RT map for the 8 Mb Streptomyces coelicolor A3(2) chromosome.";
37 RL Mol. Microbiol. 21(1):77-96(1996).
38 XX
39 CC Notes:
40 CC
41 CC Streptomyces coelicolor sequencing at The Sanger Centre is funded
42 CC by the BBSRC.
43 CC
44 CC Details of S. coelicolor sequencing at the Sanger Centre
45 CC are available on the World Wide Web.
46 CC (URL; http://www.sanger.ac.uk/Projects/S_coelicolor/)
47 CC
48 CC CDS are numbered using the following system eg SC7B7.01c.
49 CC SC (S. coelicolor), 7B7 (cosmid name), .01 (first CDS),
50 CC c (complementary strand).
51 CC
52 CC The more significant matches with motifs in the PROSITE
53 CC database are also included but some of these may be fortuitous.
54 CC
55 CC The length in codons is given for each CDS.
56 CC
57 CC Usually the highest scoring match found by fasta -o is given for
58 CC CDS which show significant similarity to other CDS in the database.
59 CC The position of possible ribosome binding site sequences are
60 CC given where these have been used to deduce the initiation codon.
61 CC
62 CC Gene prediction is based on positional base preference in codons
63 CC using a specially developed Hidden Markov Model (Krogh et al.,
64 CC Nucleic Acids Research, 22(22):4768-4778(1994)) and the FramePlot
65 CC program of Bibb et al., Gene 30:157-66(1984) as implemented at
66 CC http://www.nih.go.jp/~jun/cgi-bin/frameplot.pl. CAUTION: We may
67 CC not have predicted the correct initiation codon. Where possible
68 CC we choose an initiation codon (atg, gtg, ttg or (att)) which is
69 CC preceded by an upstream ribosome binding site sequence (optimally
70 CC 5-13bp before the initiation codon). If this cannot be identified
71 CC we choose the most upstream initiation codon.
72 CC
73 CC IMPORTANT: This sequence MAY NOT be the entire insert of
74 CC the sequenced clone. It may be shorter because we only
75 CC sequence overlapping sections once, or longer, because we
76 CC arrange for a small overlap between neighbouring submissions.
77 CC
78 CC Cosmid 10H5 lies to the right of 3A7 on the AseI-B genomic restriction
79 CC fragment.
80 XX
81 FH Key Location/Qualifiers
82 FH
83 FT source 1..4870
84 FT /organism="Streptomyces coelicolor"
85 FT /strain="A3(2)"
86 FT /clone="cosmid 10H5"
87 FT CDS complement(<1..327)
88 FT /note="SC10H5.01c, unknown, partial CDS, len >109 aa;
89 FT possible integral membrane protein"
90 FT /gene="SC10H5.01c"
91 FT /product="hypothetical protein SC10H5.01c"
92 FT CDS complement(350..805)
93 FT /note="SC10H5.02c, probable integral membrane protein, len:
94 FT 151 aa; similar to S. coelicolor hypothetical protein
95 FT TR:O54194 (EMBL:AL021411) SC7H1.35 (155 aa), fasta scores;
96 FT opt: 431 z-score: 749.8 E(): 0, 53.5% identity in 114 aa
97 FT overlap."
98 FT /product="putative integral membrane protein"
99 FT /gene="SC10H5.02c"
100 FT RBS complement(812..815)
101 FT /note="possible RBS upstream of SC10H5.02c"
102 FT CDS complement(837..1301)
103 FT /note="SC10H5.03c, probable integral membrane protein, len:
104 FT 154 aa"
105 FT /product="putative integral membrane protein"
106 FT /gene="SC10H5.03c"
107 FT RBS complement(1308..1312)
108 FT /note="possible RBS upstream of SC10H5.03c"
109 FT CDS complement(1427..1735)
110 FT /note="SC10H5.04c, unknown, len: 103 aa; possible membrane"
111 FT /gene="SC10H5.04c"
112 FT /product="hypothetical protein SC10H5.04c"
113 FT RBS complement(1738..1741)
114 FT /note="possible RBS upstream of SC10H5.05c"
115 FT misc_feature 1800^1801
116 FT /note="Zero-length feature added to test Bioperl parsing"
117 FT CDS 1933..2022
118 FT /note="SC10H5.05, questionable ORF, len: 29 aa"
119 FT /gene="SC10H5.05"
120 FT /product="hypothetical protein SC10H5.05"
121 FT CDS 2019..2642
122 FT /note="SC10H5.06, probable membrane protein, len: 207 aa;
123 FT similar to S. coelicolor TR:O54192 SC7H1.33c (191 aa),
124 FT fasta scores; opt: 312 z-score: 355.2 E(): 1.6e-12, 36.8%
125 FT identity in 182 aa overlap"
126 FT /product="putative membrane protein"
127 FT /gene="SC10H5.06"
128 FT RBS 2627..2631
129 FT /note="possible RBS upstream of SC10H5.07"
130 FT CDS 2639..4048
131 FT /note="SC10H5.07, unknown, len: 469 aa"
132 FT /gene="SC10H5.07"
133 FT /product="hypothetical protein SC10H5.07"
134 FT CDS complement(4100..4297)
135 FT /note="SC10H5.08c, unknown, len: 65 aa"
136 FT /gene="SC10H5.08c"
137 FT /product="hypothetical protein SC10H5.08c"
138 FT RBS complement(4314..4319)
139 FT /note="possible RBS upstream of SC10H5.08c"
140 FT CDS complement(4439..>4870)
141 FT /note="SC10H5.09c, probable integral membrane protein,
142 FT partial CDS len: >143 aa; some similarity in C-terminus to
143 FT S. coelicolor hypothetical protein TR:O54106
144 FT (EMBL:AL021529) SC10A5.15 (114 aa), fasta scores; opt: 145
145 FT z-score: 233.8 E(): 9.2e-06, 33.3% identity in 81 aa
146 FT overlap. Overlaps and extends SC3A7.01c"
147 FT /product="putative integral membrane protein"
148 FT /gene="SC10H5.09c"
149 FT misc_feature 4769..4870
150 FT /note="overlap with cosmid 3A7 from 1 to 102"
151 XX
152 SQ Sequence 4870 BP; 769 A; 1717 C; 1693 G; 691 T; 0
153 SQ other;
154 gatcagtaga cccagcgaca gcagggcggg gcccagcagg ccggccgtgg cgtagagcgc 60
155 gaggacggcg accggcgtgg ccaccgacag gatggctgcg gcgacgcgga cgacaccgga 120
156 gtgtgccagg gcccaccaca cgccgatggc cgcgagcgcg agtcccgcgc tgccgaacag 180
157 ggcccacagc acactgcgca gaccggcggc cacgagtggc gccaggacgg tgcccagcag 240
158 gagcagcagg gtgacgtggg cgcgcgctgc actgtggccg ccccgtccgc ccgacgcgcg 300
159 cggctcgtca tctcgcggtc ccaccaccgg tcggccccat tactcgtcct caaccctgtg 360
160 gcgactgacg ttccccggac aggtcgtacc gattgccgcc acgccccacc acgcacaggg 420
161 cccagacgac gaagcctgac atggtgatca tgacgacgga ccacaccggg tagtacggca 480
162 gcgagaggaa gttggcgatg atcaccagcc cggcgatggc gaccccggtg acacgtgccc 540
163 acatcgccgt tttgagcagc ccggcgctga cgaccatggc gagcgcgccg agcgcgagat 600
164 ggatccaccc ccacccggtg agatcgaact ggaaaacgta gttgggcgtg gtgacgaaga 660
165 cgtcgtcctc ggcgatggcc atgatgcccc ggaagaggct gagcagcccg gcgaggaaga 720
166 gcatcaccgc cgcgaaggcg gtaaggcccg tcgcccattc ctgcctcgcg gtgtgtgccg 780
167 ggtggtgggt atgtgacgtg gtcatctcgg acctcgtttc gtggaatgcg gatgcttcag 840
168 cgagcggagg cgccggtgcc cgccgcgccc gtgtgccctg ccgggccgtg accggacagg 900
169 accaattcct tcgccttgcg gaactcctcg tccgtgatgg caccccggtc tcggatctcg 960
170 gagagccggg ccagctcgtc gacgctgctg gacccgccgc ccacggtctt cctgatgtag 1020
171 gcgtcgaact cctcctgctg agcccgtgcc cgcgttgtct cccggctgcc catgttcttg 1080
172 ccgcgagcga tcacgtagac gaaaacgccc aggaagggca ggaggatgca gaacaccaac 1140
173 cagccggcct tcgcccagcc actcagtccg tcgtcccgga agatgtcggt gacgacgcgg 1200
174 aagagcagga cgaaccacat gatccacagg aagatcatca gcatcgtcca gaaggcaccc 1260
175 agcagtgggt agtcgtacgc caggtaggtc tgtgcactca tgtccgtcct ccgtcctccg 1320
176 gggcgcggcc cggcggccct cgttccgtac tgacatcagg gtggtcacgg gtcccaccgg 1380
177 tcggcatcac ccggcacggg tgagtggggc gccgaggccg tcgtggtcag gcccgggaca 1440
178 ccggtgtgac cctggtggaa ggacgcgtcc cgtggggcac gcaccgccgg ccgagggcga 1500
179 ccaccgcctc ggtcagtccg agcaggccca gccacaggcc gagaagtcgg gtcagggcac 1560
180 gggccgactc ggcgggcagc gcgaggacga cgattccggc gacgtcgacg gccagcgggt 1620
181 tgcgcaggcc cagcactccg gccggggcgc ccggcaccag cgtggcgagg gccgatgcca 1680
182 tgagccaggt ccaggaaccc ccaagcctgg cgaggacgtg cgccggatcg ctcaatgctc 1740
183 cggtgaccgc cccgcccgac ccgtctccct tgtcggcagg ttccgccgca tcacgcggaa 1800
184 cggagatggc tcccctgtgg atcgggcggc cgctgcgggg ccgcccggtt ggtcggtcgg 1860
185 tgagcgccgg actccccctt cagctcttcc agggtcgggg tcgacaccga ggtcctggat 1920
186 cacccgtcag gggtgatccg ggcatgccgt cgtggcggtg aggtgggata cgggaacgat 1980
187 cggcccacgg gggaccggac gagacgaaga gacgtgagat gagcgatacg aactcgggcg 2040
188 gcgggcgcca ggccgcttcc ggaccggccc cacgtggccg actccctttc cgccggcgcg 2100
189 tggccctggt cgctgtcgca cgtcccctga tcgtcacggt cggtctcgtc accgcctact 2160
190 acctgcttcc cctggacgag agactcagcg ccggcaccct ggtgtcgctg gtgtgcggac 2220
191 tgctcgcagt ccttctggtg ttctgctggg aggtgcgggc catcacgcgc tccccgcatc 2280
192 cgcgtctgag agcgatcgag ggcctggccg ccacgctggt gctgttcctg gtcctcttcg 2340
193 ccggctccta ctacctgctg ggtcgctccg cgcccggctc cttcagcgag ccgctgaaca 2400
194 ggacggacgc gctgtacttc actctgacca cgttcgccac cgtcggcttc ggggacatca 2460
195 ccgcacgctc cgagaccggg cggatcctca cgatggcgca gatgacggga gggctactgc 2520
196 tcgtcggagt cgccgcccgg gtgctggcga gcgcagtgca ggcggggctg caccgacagg 2580
197 gccggggacc ggcggcatcg ccacgctccg gtgctgcgga ggagccggag gccggaccat 2640
198 gaccgtaccc ggtggcttca ccgcctccct gccgccggcc gagcgagccg cgtacggcag 2700
199 gaaggcccgt aaaagggcct cacgttcgtg ccacggctgg tacgagccgg ggcagcggcg 2760
200 gcctgacccc gtcgacctgc tggagcgcca gtccggcgag cgtgtcccgg cactcgtgcc 2820
201 catccgctac ggtcgcatgc tggagtcgcc gttccgcttc taccgcggtg cggcagcgat 2880
202 catggcggcg gacctggcac ccctgcccag cagcggactc caggtgcaat tgtgcgggga 2940
203 cgcgcacccg ttgaacttcc ggctcctggc ctcaccggag cgccggctgg tcttcgacat 3000
204 caacgacttc gacgagacgc tgcccggccc cttcgagtgg gacgtcaaac ggctggcggc 3060
205 cggattcgtg atcgcggccc ggtcgaacgg cttctcgtcc aaggaacaga accgcaccgt 3120
206 tcgggcctgt gtgcgggcct accgggagcg catgagggag ttcgccgtca tgccgaccct 3180
207 ggacatctgg tacgcccagg acgacgccga ccacgtacgg caactgctgg ctacggaggc 3240
208 cagaggagaa gctgagcagc ggctcaggga cgcggctgcg aaggcccgca cacgcaccca 3300
209 catgagggcg ttcgcgaagc tcacccgcgt cacggccgag ggccggcgca tcacccccga 3360
210 cccgccgctg atcaccccac tcggcgatct gctcaccgac ccggccgaag ccggccggga 3420
211 ggaggaactg cggtccgtcg tgaacggcta cgcacggtcc ctgccgcccg agcgccggca 3480
212 cctgctgcgt cactaccggc ttgtggacat ggcgcgcaag gtggtcggcg tcggcagtgt 3540
213 cggcacccgc tgctgggtac tgcttctgct cggcagggac gacgacgatc ctctgctgct 3600
214 ccaggccaag gaagcctcgg aatcggtgct ggcggcccac acgggcggcg aacgctacga 3660
215 ccatcagggc cgcagggtcg tggccggcca gcgtctgatc cagaccaccg gtgacatctt 3720
216 tctcggctgg gcgcgcgtca ccggcttcga cggaaaggcc cgggacttct acgtgcgtca 3780
217 actgtgggac tggaagggcg tcgcgcggcc ggaaaccatg gggcccgacc tgctctccct 3840
218 cttcgcccgg ctgtgcggtg cctgcctggc gagggcccac gcccgttccg gtgaccccgt 3900
219 cgcgctcgcc gcgtacctgg gcggcagcga ccgcttcgac ggcgcgctca ccgagttcgc 3960
220 ccagtcctac gccgatcaga atgaacgcga ccacgaagct ctgctggcgg cctgccgctc 4020
221 cggcagggtc acggccgccc gtttgtgagg ccgacccggg aacggccggc gggctggcac 4080
222 acaccgccgc cggtcggcgt cattccggaa gctgccgcat ctccaggacg cgcaggccca 4140
223 gcgactggca gcgggtgagc aacccgtaca gatgggcctc gtcgatcacc gtgccgaaca 4200
224 gcacggtctg gccggacatg acgacgtgct ccagctccgg gaacgcgttg gccagcgtcc 4260
225 gtgacaggtg tccctcgacg cggatctcgt agcgcacgag cggtcctttc accgtaggag 4320
226 ctcgggacac cgcccggggc tccgggtcgg acggtgctct tggtgacgag cctgcgcctc 4380
227 gtcgccctcc ggtgccctca cccagcacag gtgactccaa ccgcagtgtc agtgcctttc 4440
228 agtgcgtcac tgtgatcttg acgacgacga tcaccaggcc gagcagtacg ttgaccgtcg 4500
229 cggtgacggc caccagtcgt cgcgaggcgc ccgcgcggtg cgccgcggcg acggaccagc 4560
230 ccacctgacc ggcgacggcg acggacagcg ccagccacag ggtgcccggg acgtccagcc 4620
231 ccagtacggg gctgacggcg atggccgcgg ccggaggcac ggcggccttg acgatcggcc 4680
232 actcctcgcg gcacacacgc agaatcaccc gccggtccgg agtgtgccgc gcgagacgcg 4740
233 ctccgaacag ttcggcgtgg acgtgagcga tccagaacac caagctggtg agcaacagca 4800
234 gaagaaccag ttcggcgcgg gggaacgagc ccagggtgcc ggcgccgatc acgacggagg 4860
235 ctgcgagcat 4870
236 //