CRISPR info
CRISPRs from JGI:
ID: Halomicrobium mukohataei DSM 12286, unfinished sequence: NZ_ABTY01000001
Start Potision: 1000310
End Position: 1002443
CRISPR length: 2133
ID: Halomicrobium mukohataei DSM 12286, unfinished sequence: NZ_ABTY01000002
Start Position: 201627
End Position: 204293
CRISPR length: 2666
Found on CRISPRFInder:
Two confirmed CRISPRs:
CRISPR id : tmp_1_Crispr_12
START crispr position : 2723382
END crispr position : 2725579
Crispr length : 2197
DR consensus : GTTTCAGACGGACCCTTGTGGGATTGAAGC DR length : 30
Number of spacers : 33
CRISPR id : tmp_2_Crispr_1
START crispr position : 31920
END crispr position : 34849
Crispr length : 2929
DR consensus : GCTTCAATCCCACAAGGGTCCGTCTGAAAC DR length : 30
Number of spacers : 44
These are likely the same CRISPRs that were found by JGI. It's difficult to say with absolute certainty since the start and end coordinates were labeled using the draft sequence but JGI now uses the finished sequence for whole-genome searches.
11 Questionable CRISPRs:
CRISPR id : tmp_1_PossibleCrispr_1
START crispr position : 451036
END crispr position : 451146
Crispr length : 110
DR consensus : CCTCGACCGTGTCGGCCGCGCCGCC DR length : 25
Number of spacers : 1
CRISPR id : tmp_1_PossibleCrispr_2
START crispr position : 451266
END crispr position : 451422
Crispr length : 156
DR consensus : CCTCGACCGTGTCGGCCGCGCCGCC DR length : 25
Number of spacers : 2
CRISPR id : tmp_1_PossibleCrispr_3
START crispr position : 723910
END crispr position : 724040
Crispr length : 130
DR consensus : CCGCCCGAACACGCCGGTCCCGACCACGAGAACGAGAC DR length : 38
Number of spacers : 1
RISPR id : tmp_1_PossibleCrispr_4
START crispr position : 775514
END crispr position : 775595
Crispr length : 81
DR consensus : TGATTCGCCCAGCGAGCGCGTTCGTG DR length : 26
Number of spacers : 1
CRISPR id : tmp_1_PossibleCrispr_5
START crispr position : 1587713
END crispr position : 1587871
Crispr length : 158
DR consensus : TCGAAGGGGCTGTCGCTGTCGGTG DR length : 24
Number of spacers : 2
CRISPR id : tmp_1_PossibleCrispr_6
START crispr position : 1635784
END crispr position : 1635940
Crispr length : 156
DR consensus : CCTCGACCGTGTCGGCCGCGCCGCC DR length : 25
Number of spacers : 2
CRISPR id : tmp_1_PossibleCrispr_7
START crispr position : 1733154
END crispr position : 1733268
Crispr length : 114
DR consensus : GTTCGCCGGACCGTGTGGGTGTCG DR length : 24
Number of spacers : 2
CRISPR id : tmp_1_PossibleCrispr_8
START crispr position : 2087618
END crispr position : 2087725
Crispr length : 107
DR consensus : AGCGCCGGGCGACGACGGGCCAGC DR length : 24
Number of spacers : 1
CRISPR id : tmp_1_PossibleCrispr_9
START crispr position : 2127953
END crispr position : 2128039
Crispr length : 86
DR consensus : CGCTCGCTTCGAGGGCCGACACTCGCT DR length : 27
Number of spacers : 1
CRISPR id : tmp_1_PossibleCrispr_10
START crispr position : 2206888
END crispr position : 2206968
Crispr length : 80
DR consensus : CAGTCCAGTGAGGCGTCTCGTCGTCG DR length : 26
Number of spacers : 1
CRISPR id : tmp_1_PossibleCrispr_11
START crispr position : 2293949
END crispr position : 2294199
Crispr length : 250
DR consensus : CGTTCGCAGCAAAACGGGCCGGAAGGGATTTGAACC DR length : 36
Number of spacers : 2
BLASTing CRISPRs
I Blasted the two confirmed direct repeat (DR) sequences found by CRISPR Finder in order to see if these repeats are found in any other archaea.
DR sequences: 1. GTTTCAGACGGACCCTTGTGGGATTGAAGC 2. GCTTCAATCCCACAAGGGTCCGTCTGAAAC
For both DRs 1 and 2 had top hits with the three archaeal species with which we commonly compare H. mukohataei:
- Haloarcula marismortui
- Halorhabdus utahensis
- Natronomonas pharaonis
