Replicon Annotation Table
Stenotrophomonas_maltophilia_K279a - IS_012560
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IS Name
ISStma2
HELP
- Name of the reference IS - Must respect the
ISfinder nomenclature standarts
.
ORF Name
Smlt0808
- Predicted ORF Name. Automatic generated in protein annotation steps.
Previous Annotation
- Previous orf annotation (for comparison purpose)
IS Structure
ND
C
P
SIR
-
[ C ]
complete,
[ P ]
partials,
[ SIR ]
solo IRs
[ ND ]
Not determined.
Complete and broken IS ?
ND
Y
N
- Occurrence of
complete
and
disrupted IS
(Y for yes, N for no and ND not determined [solo IRs]
Number of ORFs
0
1
2
3
4
5
6
7
8
9
+9
- Number of Open Reading frames in the detected IS(s).
False Positive Prediction?
NO
YES
- Set YES for false positive IS transposase prediction.
IS ORF(s) List
- ID of each ORF composed by this ISs (Partial ISs with no ORFs please put `not_found`)
% of DNA Similarity
- % of DNA Similarity against the reference IS sequence.
% of Similarity AAs
(ISfinder First hit)
- % of Protein Similarity against the first hit in ISfinder Database.
% of AAs Similarity
(Replicon First hit)
- % of Protein Similarity against the first hit in this replicon.
Identified IS Family
IS3 ssgr IS150
- IS family detected by the automatic annotation.
ORF Left End
- ORF Left postion in the replicon.
ORF Right End
- ORF Right postion in the replicon.
ORF Size
(bp)
- ORF size in base pairs (included stop codon).
ORF Size
(aa)
- ORF size in aminoacids.
Strand
ND
+
-
- ORF Orientation.
Type
ND
T
P
A
-
[ T ]
for transposase,
[ P ]
for passenger genes,
[ A ]
for accessory gene or
[ ND ]
for not determined.
IS Left End
- IS Left coordinate in the replicon.
IS Right End
- IS Right coordinate in the replicon.
IS Length
(bp)
- IS Length in base pairs (included Inverted Repeats, and excluding the Direct Repeats).
DR Size
(bp)
ND
0
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
- Direct Repeats Size in base pairs. [Some IS(s) doesn't have DRs]
IR Size
(bp)
- Inverted Repeats Size in base pairs. [example 22/30, 22 matches in 30 nucleotides]
IS Coordinates Present
(for partials)
Only for Partials
- Coordinates of the partials IS. [example 100366 (218) - 101333 (1185)] )
Length of Partial
(bp)
Only for Partials
- Partials IS size in base pairs.
General Comments
- General Comments: Feel free to put all observations regarding the annotation.
The automatic annotation process could generate automatic comments between brackets
ORF protein sequence
AAQGSRLSACGDRLPKKTRCLDPGRAGGARRKAQAIQGLRQVHTLSLLLEAAELSRSTFYYQNHVLAHPDQDEAALCERIRAIYDQSQGRYGYRTVTLELANQGHRTNHKRVQRLMGEMGLKSRVRVKRYRSFKGAANVVVGNDLNRQFHAERPNQKWVTDVTEFKVQGMKLYLSPIMDLYNGEIVAYQIKRQPVFDLVGQMLEEAIMKLSPDERPMIHSDQGWQYQHENYRHMLEKHSLKQSMSRRGNCLDNAAMESFFGTLKSEFFYLNSFDSIESLEAGLVEYIQYYNQERIKLKLKGLSPVEYRERAQSAA*
- Fasta protein sequence of this open reading frame.
[Not present in solo IRs and in some cases of partial ISs].
IS fasta sequence
TGAAGTGACCCCCGGGAGTTGGACGTCAGATCCAACCCCGAGGGATACATGAACAGATATGACGCACGTTTCAAACTGCAGGTCGCCAAGGAGGCCTGCAAGACCTCCACATCGGTCAAAGCCATTGCCCGTCGCCACGGCCTTGAGTTCTCCACGGTCAGGCGCTGGGTGGCGACCTATCGGCTGCATGGTTGGCGCGGATTTCAACGCCAGGCCCAGTTCTATGACCTCCCGTTCAAGCTGGCTGTCCTGGAAAAAATGAGCCAGGACGGCATGTCCGGGCGGGAGGCCACCACCTACTTCCAGATTGGTGATGCCGGCGCGGTGGGGCGATGGCGGCGCCTGTATGCTCAAGGCGGTGCCCAAGCGTTGGCACCGCCTCCGCCGCTGCCCCGAAAGCCGATGAAAAAGACCCGTTCGTCCAAGCCGCCTGAGGAAATGAGCCGCGATGAGCTGCTCAAGGAAGTCGCCTATCTGCGTGCGGAGACCGACTACCTAAAAAAACTCGATGCCTTGATCCGGGAAGAGCAGGCGGCGCAAGACGCAAAGCGCAAGCCATCCAAGGATTGAGGCAGGTTCATACGCTGTCGCTTCTGCTCGAAGCGGCGGAGCTGTCACGCAGTACGTTCTATTACCAGAACCATGTCCTGGCCCATCCGGATCAGGACGAGGCAGCCCTGTGCGAGCGCATCCGTGCAATCTACGATCAAAGCCAAGGGCGCTATGGCTATCGCACGGTGACGCTGGAATTGGCCAATCAGGGTCATCGGACCAATCACAAGCGGGTACAGCGCCTGATGGGGGAGATGGGCCTGAAATCACGGGTACGGGTGAAGCGCTACCGGTCCTTCAAGGGGGCCGCCAATGTTGTGGTTGGCAATGACCTCAATCGCCAATTCCACGCCGAGCGCCCCAACCAGAAGTGGGTGACCGACGTGACCGAGTTCAAGGTACAAGGCATGAAGCTGTACCTGTCGCCGATCATGGACCTCTACAACGGCGAAATCGTGGCTTATCAGATCAAGCGCCAGCCCGTGTTCGATCTGGTAGGTCAGATGCTGGAGGAGGCCATCATGAAGCTTTCGCCGGATGAACGCCCCATGATCCACTCCGACCAGGGCTGGCAGTACCAGCATGAAAACTACCGGCACATGCTGGAAAAACATTCGTTGAAACAAAGCATGTCCCGGCGTGGCAACTGCCTGGACAATGCGGCGATGGAGAGCTTCTTCGGGACGCTGAAGTCGGAGTTCTTCTACCTGAACAGCTTTGACAGCATCGAGAGTCTGGAGGCTGGCCTGGTGGAATACATCCAGTACTACAACCAGGAGCGCATCAAACTGAAACTGAAAGGTCTGAGCCCGGTAGAGTACCGGGAGCGGGCCCAATCGGCCGCCTGACCCCGTCCAAGTCTCGGGGGTCACTTCA
- IS Fasta sequence (with IRs and without DRs)
IS Left End
- Left end of the element. [For IR identification - Some ISs do not have IRs ]
IS Right End
- Right
inverted
end of the element [For IR identification - Some ISs don not have IRs ].
Insertion Site
GTGGGGTGGCGGGGTGGGTCCGGTGGCGGGGGACGCCGTAAACCCGT (CCC) TGGGGGCTTGGCCGCGGCATCCATGCCGCGGACACCCCCGCCACCGG
- Insertion site with the presence or absence of DRs [Only show in
complete ISs
].
(Please respect the example: ATCGATCG ( ATCG ) ATCGATCG ).
