1. gene 260302..261231
/locus_tag="SPO0241"
/db_xref="GeneID:3194549"
CDS 260302..261231
/db_xref="GeneID:3194549"
gene 261910..263364
/gene="rrsA"
/locus_tag="SPO_Sp16SA"
/db_xref="GeneID:3196347"
rRNA 261910..263364
/gene="rrsA"
/locus_tag="SPO_Sp16SA"
/product="16S ribosomal RNA"
/db_xref="GeneID:3196347"
gene 263580..263656
/locus_tag="SPO_tRNA-Ile-1"
/db_xref="GeneID:3196399"
tRNA 263580..263656
/locus_tag="SPO_tRNA-Ile-1"
/product="tRNA-Ile"
/db_xref="GeneID:3196399"
gene 263730..263805
/locus_tag="SPO_tRNA-Ala-1"
/db_xref="GeneID:3195549"
tRNA 263730..263805
/locus_tag="SPO_tRNA-Ala-1"
/product="tRNA-Ala"
/db_xref="GeneID:3195549"
gene 264255..267149
/gene="rrlA"
/locus_tag="SPO_Sp23SA"
/db_xref="GeneID:3194652"
rRNA 264255..267149
/gene="rrlA"
/locus_tag="SPO_Sp23SA"
/product="23S ribosomal RNA"
/db_xref="GeneID:3194652"
gene 267353..267470
/gene="rrfD"
/locus_tag="SPO_Sp5SD"
/db_xref="GeneID:3196376"
rRNA 267353..267470
/gene="rrfD"
/locus_tag="SPO_Sp5SD"
/product="5S ribosomal RNA"
/db_xref="GeneID:3196376"
gene complement(267660..269588)
/gene="dxs"
/locus_tag="SPO0247"
/db_xref="GeneID:3196253"

2. Ruegeria pomeroyi DSS-3 chromosome, complete genome
NCBI Reference Sequence: NC_003911.11
FASTA Graphics
LOCUS NC_003911 7359 bp DNA linear BCT 21-JAN-2012
DEFINITION Ruegeria pomeroyi DSS-3 chromosome, complete genome.
ACCESSION NC_003911 REGION: 260302..267660
VERSION NC_003911.11 GI:56694928
DBLINK Project: 57863
KEYWORDS .
SOURCE Ruegeria pomeroyi DSS-3
gene 1..930
gene 1609..3063
/gene="rrsA"
/locus_tag="SPO_Sp16SA"
/db_xref="GeneID:3196347"
rRNA 1609..3063
/gene="rrsA"
/locus_tag="SPO_Sp16SA"
/product="16S ribosomal RNA"
/db_xref="GeneID:3196347"
gene 3279..3355
/locus_tag="SPO_tRNA-Ile-1"
/db_xref="GeneID:3196399"
tRNA 3279..3355
/locus_tag="SPO_tRNA-Ile-1"
/product="tRNA-Ile"
/db_xref="GeneID:3196399"
gene 3429..3504
/locus_tag="SPO_tRNA-Ala-1"
/db_xref="GeneID:3195549"
tRNA 3429..3504
/locus_tag="SPO_tRNA-Ala-1"
/product="tRNA-Ala"
/db_xref="GeneID:3195549"
gene 3954..6848
/gene="rrlA"
/locus_tag="SPO_Sp23SA"
/db_xref="GeneID:3194652"
rRNA 3954..6848
/gene="rrlA"
/locus_tag="SPO_Sp23SA"
/product="23S ribosomal RNA"
/db_xref="GeneID:3194652"
gene 7052..7169
/gene="rrfD"
/locus_tag="SPO_Sp5SD"
/db_xref="GeneID:3196376"

3. rRNA 7052..7169
/gene="rrfD"
/locus_tag="SPO_Sp5SD"
/product="5S ribosomal RNA"
/db_xref="GeneID:3196376"
gene complement(7359..>7359)
/gene="dxs"
/locus_tag="SPO0247"
/db_xref="GeneID:3196253"
CDS complement(7359..>7359)
ORIGIN
1 ttgaatttca agctgagaca gttggaggcc tttcgcgcgg tggcgcagac aggctcgatc
61 acacgtgcag cgcagcaatt gggaatctcg caaccagccg ccagccgcct gcttgccgat
121 ttctcggctt cggtcgagtt tccactgttc gtacgcgagg ggggcagcat gagcccgacc
181 cccgaatcgc gctatatgct ggccgagatc aaccgggtgt tcgaggggct cgcccatctg
241 gaagagctgc gtcacaatct caaggaccgc accgccgggc atctgcgcat cgcctgtctg
301 cccggttttg ccaccagcca tctgcccagg gttctgaccg cgttcctgaa ggacaggccc
361 ggcgtgaccg tcacgcttga acccgacagg cccgagcgca tcctggaatg gatcgtcggc
421 cagcaatatg actgtgccat taccgacggc ttcgccggcc atccggcaac cgaaagtacc
481 gatatcgcga tccgcaccgt ctgcatcctg cctccggggc atccgttgtc agatcgaccc
541 gaaatcacgc cgcacgatct gcgcggcgag aagatcatcc attcccgccg cgacagcccg
601 ttctttcgcc gcctggcgca ggcctttacc gatagcgaag tggagttgtc ctcgtggatc
661 gaggtgcgcc agttcaccac cgcctgcacc atcgtggccg aggggcaggg ggcggcggtg
721 ctgtcggcgc tggatgcgga gcagtatcgc gaccgcggcc tggtgatccg gccctttgtg
781 ccccggatcg cccatcgcct gtcactgctg cgacccgtta ccggcagcct gtcgcctctg
841 gtgctggatt tcctggaggc gttcacggcc agtctggctc cgttcatcga ccatgaggaa
901 cgtcgggcga acccggttgg cgcacgctag ctgcgccagc ggccgcagag cgtttgcgtt
961 gtttggaaaa tttgcggttg aagtgctggc tctttggtgc agggcacccg ggaggtggct
1021 aaagttttca caatttcaat gcattgaggg gagatttcag ttttttctat tttttgtatt
1081 tttgtgcttg cgactctttt tggttgggcc tagaaccccc ttcaccggcg gcgctgaggt
1141 gctgctgacg ggccggagag acggtcggac acgctggaga gacggcggca ttcgagggat
1201 gagcgaggcg ggcgcgctga gggattggcg catcggtctt gtttttggct ctggggcgca
1261 gcgctgtttg acattgctgg atactgaaga gatatgtggg cggtttggtt cgtttcgacg
1321 gattgaaagt ctgtatatcg cactcttagg ttcgatgcct gcgctttagt agcgtaggcg
1381 gtagcgccga tgatggagtg tcagcttcac tgtttgagcg tgcaacgttt cttttggaac
1441 gatgtacatc agacagatga ctcttgatgt ttgccctggc ctagccgggt tgggggagcg
1501 acgttgtttg ggatggttta tctgtcctca agtagcggag cggtaggaca tcaaggatgt
1561 gcagaggttc gactgtcatg gaaatgctgg taacggcatt ttaacttgag agtttgatcc
1621 tggctcagaa cgaacgctgg cggcaggcct aacacatgca agtcgagcgc gcccttcggg
1681 gtgagcggcg gacgggttag taacgcgtgg gaacgtaccc tttggtaggg aatagccact
1741 ggaaacggtg agtaataccc tatgagccct tcgggggaaa gatttatcgc caaaggatcg
1801 gcccgcgtta gattaggtag ttggtggggt aatggcctac caagcctacg atctatagct
1861 ggttttagag gatgatcagc aacactggga ctgagacacg gcccagactc ctacgggagg
1921 cagcagtggg gaatcttgga caatgggggc aaccctgatc cagccatgcc gcgtgagtga
1981 agaaggcctt agggtcgtaa agctctttcg cctgtgaaga taatgacggt agcaggtaaa
2041 gaaaccccgg ctaactccgt gccagcagcc gcggtaatac ggagggggtt agcgttgttc
2101 ggaattactg ggcgtaaagc gcgcgtaggc ggaccagaaa gttgggggtg aaatcccggg

4. 2161 gctcaacccc ggaactgcct ccaaaactcc tggtcttgag ttcgagagag gtgagtggaa
2221 ttccgagtgt agaggtgaaa ttcgtagata ttcggaggaa caccagtggc gaaggcggct
2281 cactggctcg atactgacgc tgaggtgcga aagtgtgggg agcaaacagg attagatacc
2341 ctggtagtcc acaccgtaaa cgatgaatgc cagtcgtcgg gtagcatgct gctcggtgac
2401 acacctaacg gattaagcat tccgcctggg gagtacggcc gcaaggttaa aactcaaagg
2461 aattgacggg ggcccgcaca agcggtggag catgtggttt aattcgaagc aacgcgcaga
2521 accttaccaa cccttgacat cctcggaccg tcccagagat gggtctttca cttcggtgac
2581 cgagtgacag gtgctgcatg gctgtcgtca gctcgtgtcg tgagatgttc ggttaagtcc
2641 ggcaacgagc gcaacccaca cccttagttg ccagcattca gttgggcact ctaggggaac
2701 tgcccgtgat aagcgggagg aaggtgtgga tgacgtcaag tcctcatggc ccttacgggt
2761 tgggctacac acgtgctaca atggcagtga caatgggtta atcccaaaaa actgtctcag
2821 ttcggattgg ggtctgcaac tcgaccccat gaagtcggaa tcgctagtaa tcgcgtaaca
2881 gcatgacgcg gtgaatacgt tcccgggcct tgtacacacc gcccgtcaca ccatgggagt
2941 tgggtctacc cgaagacggt gcgccaacct ttcgaggagg cagctggcca cggtaggctc
3001 agcgactggg gtgaagtcgt aacaaggtag ccgtagggga acctgcggct ggatcacctc
3061 ctttctaagg atgtatctag ttagatttgt tcgcaaatct cgtgatacac ttagcagaag
3121 atcaacaaac aaagttgatc aaactccgga ccggaccgtc ctcatatctc ttcaggaaca
3181 tatcaggccc atgacaatct ggggtctggc cctccgtcgt cgcttgcaag caaacgacgt
3241 aatcgggcaa cgtcgatttg ccctggggca aatcaactgg gtcggtagct caggtggtta
3301 gagcgcacgc ctgataagcg tgaggtcgga ggttcaagtc ctcctcgacc caccaagcct
3361 tttgcggagc aaagggcgtt gtcgcggcag ttgcttttgg tcacaaaagc aatgagagcg
3421 acctttatgg ggccttagct cagctgggag agcgcctgat ttgcattcag gaggtcagga
3481 gttcgatcct cctaggctcc accatatcct cgatttgacc gccaagcact gtgtcagtgt
3541 ttggccgtcc aatcggactg tgcttctacg gaagcgttga catcgtttag agagaaatca
3601 atcaactctg tttgatcgca ccgcgtgagg tgtcgatctc agcgggttct gctttcgccc
3661 caagttgccg caaggcggtg gggcatttgc cctcaagtag ccgcaaggcg gtagggcagg
3721 tgaagagagc ggaaggcgcg ggttgggtct agccggctcg atctgttgta tccctgttga
3781 aacgaacaga agttgtccaa gtcaagtaca ctaacccggt gcggtccgcg aggatacgca
3841 ccactaagtt cagccctgac gggctgagcg ggaaaagtga cttttggttc agaagaaggc
3901 ctggtcgaac cagcccgggc cgtgagagtt cagtctctct ttttctggat cgaatcaagc
3961 gcgagaaggg cgtttggtgg atgccttggc agcaagaggc gatgaaggac gtgatactct
4021 gcgataagtc atggggagcc gagaataggc tttgatccat gaatctccga atggggcaac
4081 ccacctgaca ttctgttatt gttagccttc gggttatcaa taacggggtg aaacaggtac
4141 ttaagacctg aatacatagg gttttaagag caaacccggg gaactgaaac atctaagtac
4201 ccggaggaaa ggaaatcaat tgatactccc ctagtagtgg cgagcgaacg gggatcagcc
4261 gagccttgag aatgagaaga acatgttggg aagcatggcc atagcgggtg atagccccgt
4321 attcgaagtt cgatgggacg tattaagtag ggcgggacac gtgaaatcct gtctgaagat
4381 cggaggacca ccttcgaagg ctaagtactc cttgctgacc gatagcgaac cagtaccgtg
4441 agggaaaggt gaaaagcacc ccgacgaggg gagtgaaaca gtacctgaaa ccggacgcct
4501 acaagcagtc ggagggacct cgagtcctga cggcgtacct tttgtataat gggtcatcga
4561 cttggtctca cgagcaagct taagccgtta ggtgtaggcg cagcgaaagc gagtcttaat
4621 agggcgtcga gttcgtggga tcagacccga aaccgagtga tctaggcatg gccaggttga
4681 aggcaaggta acacttgctg gaggaccgaa cccacatccg ttgaaaagga tcgggatgag
4741 ctgtgcctag gggtgaaagg ccaatcaaac tcggagatag ctggttctcc gcgaaatcta
4801 tttaggtaga gcgtcatccg aataccccgg ggggtagagc actggatggg taatggggcc
4861 ccacaggctt actgatccta accaaactcc gaatacccgg gagtactaga tggcagacac
4921 actgcgggtg ctaacgcccg tagtggagag ggaaacaacc ctgacctcca gctaaggccc
4981 ccaattcatg gctaagtggg aaagcaggtg ggatgtccaa aacaaccagg aggttggctt
5041 agaagcagcc atcctttaaa gatagcgtaa cagctcactg gtctaatcaa gacgtcctgc

5. 5101 ggcgaagatg taacggggct caagccatga gccgaagctg aggatgccgt aaggcatggt
5161 agcggagcgt agtgtgacat agtctcatgt ctctttagct catttgatct cgaccaatcg
5221 ctgagtgggt gcaggcaact gccctcaagt agcgaagcgg tagggcatca aaaatgagcg
5281 tcggagacgc gaggctttcg atgaagccgg ggcgtgagcc atccggtgga gagatcacta
5341 gcgagaatga tgacatgagt agcgacaaag agtgtgagag acactctcgc cgaaagtcca
5401 agggttcctg cttaaagcta atctgagcag ggtaagccgg cccctaagcc gaggccgaaa
5461 ggcgtaggcg atgggaacta ggttaatatt cctaggccag gaggatgtga cggatcacgg
5521 atgtagttca gccttatcgg attggctggg ctgctgagtg gtccctggaa atagccctcc
5581 atcagaccgt accctaaacc gacacaggtg gactggtaga gaataccaag gcgcttgaga
5641 gaacgatgtt gaaggaactc ggcaaaatac ctccgtaagt tcgcgagaag gaggcccggg
5701 ttcaaggcaa cttggatccg ggggcacaaa ccagggggtg gcgactgttt attaaaaaca
5761 cagggctctg cgaagtcgca agacgacgta tagggtctga cgcctgcccg gtgcctgaag
5821 gttaaaagga ggggtgcaag ctccgaattg aagcccaggt aaacggcggc cgtaactata
5881 acggtcctaa ggtagcgaaa ttccttgtcg ggtaagttcc gacctgcacg aatggcgtaa
5941 cgacttcccc gctgtctcca acatcgactc agcgaaattg aattgcctgt caagatgcag
6001 gcttcccgcg gttagacgga aagaccccgt gcacctttac tacagcttcg cactggcatc
6061 aggattgtga tgtgcaggat aggtggtagg ctttgaagca ggaacgccag ttcccgtgga
6121 gccaaccttg agataccacc cttcgcactc ttgatgtcta accgcggtcc gttatccgga
6181 tccgggaccc tgcgtggcgg gtagtttgac tggggcggtc gcctcctaaa gcgtaacgga
6241 ggcgcgcgaa ggttggctca gagcggtcgg aaatcgctcg ttgagtgcaa tggcagaagc
6301 cagcctgact gcaagactga caagtcgagc agagacgaaa gtcggccata gtgatccggt
6361 ggtcccgagt ggaagggcca tcgctcaacg gataaaaggt acgccgggga taacaggctg
6421 atactgccca agagtccata tcgacggcag tgtttggcac ctcgatgtcg gctcatctca
6481 tcctggggct ggagcaggtc ccaagggtac ggctgttcgc cgtttaaaga ggtacgtgag
6541 ctgggtttag aacgtcgtga gacagttcgg tccctatctg ccgtgggtgt aggatacttg
6601 agaggagttg cccctagtac gagaggaccg gggtgaacga tccactggtg gacctgttgt
6661 tgcgccagca gcagtgcagg gtagctatga tcggacagga taaccgctga aggcatctaa
6721 gcgggaagcc cccctcaaaa caaggtatcc ctgagggccg tggaagacca ccacgtcaat
6781 aggccggaga tgtaagcgca gcaatgcgtt cagttgaccg gtactaatcg cccgataggc
6841 ttgatccgat ccagtaacag aaagactgat caaatggcct caagtagcgc tccgcgcgcc
6901 aggccaaatc aagaaccaaa agcaccaact cgacttggac aacacccgat tgatactccc
6961 gcccggacaa tacgggtggc aacgcgcttt cctccggaaa acgctgcctg ccaccctcac
7021 tgtccgcaag gcggacagtg agtatttatt cggtttggtg gtcatagcga gcgcaataca
7081 cccggtccct tcccgaaccc ggaagttaag tgcctccgcg ccaatggtac tcgggctcaa
7141 gccccgggag agtaggtcac cgccaaacct aataaatact caatcctctc tacaacgatc
7201 aaaaactact caaaaaaaca aacagccaga aacgcataca tgtcgcgttg tcttctgcat
7261 tcgtgcgtgc cgcaggcgcg catcggtacc tgcgtcaggt aacagttgac ccaatgtcgt
7321 aagcgtcagg tttcaccggc cgcttactaa tgtctgggt

6. TRANSCRIPCION
Promoter predictions for 1 prokaryotic sequence with score cutoff 0.80 (transcription start shown in
larger font):
Promoter predictions for seq0 :
Start End Score Promoter Sequence
991 1036 0.93 TCTTTGGTGCAGGGCACCCGGGAGGTGGCTAAAGTTTTCACAATTTCAAT
1022 1067 0.99 AAGTTTTCACAATTTCAATGCATTGAGGGGAGATTTCAGTTTTTTCTATT
1039 1084 0.91 ATGCATTGAGGGGAGATTTCAGTTTTTTCTATTTTTTGTATTTTTGTGCT
1048 1093 0.80 GGGGAGATTTCAGTTTTTTCTATTTTTTGTATTTTTGTGCTTGCGACTCT
1082 1127 0.90 TTGTGCTTGCGACTCTTTTTGGTTGGGCCTAGAACCCCCTTCACCGGCGG
1573 1618 0.96 CTGTCATGGAAATGCTGGTAACGGCATTTTAACTTGAGAGTTTGATCCTG
1780 1825 0.90 AGATTTATCGCCAAAGGATCGGCCCGCGTTAGATTAGGTAGTTGGTGGGG
1818 1863 0.88 TAGTTGGTGGGGTAATGGCCTACCAAGCCTACGATCTATAGCTGGTTTTA
2208 2253 0.98 GAGGTGAGTGGAATTCCGAGTGTAGAGGTGAAATTCGTAGATATTCGGAG
3582 3627 0.85 ATCGTTTAGAGAGAAATCAATCAACTCTGTTTGATCGCACCGCGTGAGGT
4158 4203 0.91 AGGGTTTTAAGAGCAAACCCGGGGAACTGAAACATCTAAGTACCCGGAGG
5053 5098 0.89 CCTTTAAAGATAGCGTAACAGCTCACTGGTCTAATCAAGACGTCCTGCGG
5647 5692 0.88 TGTTGAAGGAACTCGGCAAAATACCTCCGTAAGTTCGCGAGAAGGAGGCC
6364 6409 0.98 CCCGAGTGGAAGGGCCATCGCTCAACGGATAAAAGGTACGCCGGGGATAA
6447 6492 0.85 GCAGTGTTTGGCACCTCGATGTCGGCTCATCTCATCCTGGGGCTGGAGCA
6519 6564 0.88 GCCGTTTAAAGAGGTACGTGAGCTGGGTTTAGAACGTCGTGAGACAGTTC
6807 6852 0.87 CGTTCAGTTGACCGGTACTAATCGCCCGATAGGCTTGATCCGATCCAGTA
TERMINADORES
TTGAATTTCAAGCTGAGACAGTTGGAGGCCTTTCGCGCGGTGGCGCAGACAGGCTCGATCACACGTGCAG
1504 Rnamotif + TGTCATGGAAATGCTGGTAACGGCATTTTAACTTGAG -6.20
3658 Rnamotif + AGCGGAAGGCGCGGGTTGGGTCTAGCCGGCTCGaTCTGTTGTATCC -11.00
6936 Rnamotif + GCCTGCCACCCTCACTGTCCGCAAGGCGGACAGTGAgTATTTATTCGGT -12.40
Total number of predicted transcription terminators: 3

7. TRADUCCIÓN
ARN de transferencia
Results
Sequence tRNA Bounds tRNA Anti Intron Bounds Cove
Name tRNA # Begin End Type Codon Begin End Score
-------- ------ ---- ------ ---- ----- ----- ---- ------
Your-seq 1 3279 3355 Ile GAT 0 0 94.31
Your-seq 2 3429 3504 Ala TGC 0 0 89.52
Run Statistics:
Started: Wed May 9 09:23:47 PDT 2012
------------------------------------------------------------
Search Mode: Bacterial
Searching with: tRNAscan + EufindtRNA -> Cove
Covariance model: TRNA2-bact.cm
tRNAscan parameters: Strict
EufindtRNA parameters: Relaxed (Int Cutoff= -36)
------------------------------------------------------------
First-pass (tRNAscan/EufindtRNA) Stats:
---------------
Sequences read: 1
Seqs w/at least 1 hit: 1
Bases read: 7359 (x2 for both strands)
Bases in tRNAs: 254
tRNAs predicted: 3
Av. tRNA length: 84
Script CPU time: 0.00 s
Scan CPU time: 0.00 s
Scan speed: 14718.0 Kbp/sec
First pass search(es) ended: Wed May 9 09:23:47 PDT 2012
Cove Stats:
-----------
Candidate tRNAs read: 3
Cove-confirmed tRNAs: 2
Bases scanned by covels: 296
% seq scanned by covels: 2.0 %
Script CPU time: 0.00 s
Cove CPU time: 0.37 s
Scan speed: 800.0 bp/sec
Cove analysis of tRNAs ended: Wed May 9 09:23:47 PDT 2012
Summary
--------
Overall scan speed: 39778.4 bp/sec
tRNAs decoding Standard 20 AA: 2
Selenocysteine tRNAs (TCA): 0
Possible suppressor tRNAs (CTA,TTA): 0

8. tRNAs with undetermined/unknown isotypes: 0
Predicted pseudogenes: 0
-------
Total tRNAs: 2
tRNAs with introns: 0
|
Isotype / Anticodon Counts:
Ala : 1 AGC: GGC: CGC: TGC: 1
Gly : 0 ACC: GCC: CCC: TCC:
Pro : 0 AGG: GGG: CGG: TGG:
Thr : 0 AGT: GGT: CGT: TGT:
Val : 0 AAC: GAC: CAC: TAC:
Ser : 0 AGA: GGA: CGA: TGA: ACT: GCT:
Arg : 0 ACG: GCG: CCG: TCG: CCT: TCT:
Leu : 0 AAG: GAG: CAG: TAG: CAA: TAA:
Phe : 0 AAA: GAA:
Asn : 0 ATT: GTT:
Lys : 0 CTT: TTT:
Asp : 0 ATC: GTC:
Glu : 0 CTC: TTC:
His : 0 ATG: GTG:
Gln : 0 CTG: TTG:
Ile : 1 AAT: GAT: 1 TAT:
Met : 0 CAT:
Tyr : 0 ATA: GTA:
Supres: 0 CTA: TTA:
Cys : 0 ACA: GCA:
Trp : 0 CCA:
SelCys: 0 TCA: