Result : Q824W6
| Protein Information |
| Information Type | Description |
|---|---|
| Protein name | UPF0109 protein CCA_00022 |
| NCBI Accession ID | AE015925.1 |
| Organism | Chlamydophila caviae (strain ATCC VR-813 / DSM 19441 / GPIC) (Chlamydia caviae) |
| Left | 31875 |
| Right | 32111 |
| Strand | - |
| Nucleotide Sequence | ATGAAAGACTTTTTAGCTTATATTATCAAAAACCTTGTAGACCGCCCTGAGGAAGTACATATCAAAGAAGTTCAAGGCACCCACACGATTATCTATGAATTAACAGTTGCGAAGCCCGATATCGGCAAAATCATCGGAAAAGAGGGTCGCACAATCAAAGCTATCCGCACTCTACTTGTCTCTGTAGCCAGCAGAAACAACGTAAAAGTCAGCTTAGAAATTATGGAAGACAAGTAG |
| Sequence | MKDFLAYIIKNLVDRPEEVHIKEVQGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLVSVASRNNVKVSLEIMEDK |
| Source of smORF | Swiss-Prot |
| Function | The ORF matches to the profile of cl00098. Profile Description: K homology (KH) RNA-binding domain, type I. Rrp40, also called exosome component 3 (EXOSC3), or ribosomal RNA-processing protein 40, is a non-catalytic component of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Mutations of EXOSC3 gene are associated with neurological diseases. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif. |
| Pubmed ID | 12682364 |
| Domain | CDD:412160 |
| Functional Category | RNA-binding |
| Uniprot ID | Q824W6 |
| ORF Length (Amino Acid) | 78 |
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| Conservation Analysis |
No. of Species: 52
| Sr.No. | Left Position | Right Position | Strand | NCBI Accession id | Species Name |
|---|---|---|---|---|---|
| 1 | 31875 | 32111 | - | NC_003361.3 | Chlamydia caviae GPIC |
| 2 | 31991 | 32227 | - | NC_017287.1 | Chlamydia psittaci 6BC |
| 3 | 1133981 | 1134217 | + | NC_007899.1 | Chlamydia felis Fe/C-56 |
| 4 | 463439 | 463675 | - | NZ_CP015840.1 | Chlamydia gallinacea 08-1274/3 |
| 5 | 31481 | 31717 | - | NC_022439.1 | Chlamydia pecorum PV3056/3 |
| 6 | 804310 | 804546 | + | NC_005043.1 | Chlamydia pneumoniae TW-183 |
| 7 | 34594 | 34830 | + | NC_002620.2 | Chlamydia muridarum str. Nigg |
| 8 | 754647 | 754883 | + | NC_000117.1 | Chlamydia trachomatis D/UW-3/CX |
| 9 | 802882 | 803118 | + | NZ_LS398098.1 | Chlamydia suis |
| 10 | 1629423 | 1629698 | - | NC_014225.1 | Waddlia chondrophila WSU 86-1044 |
| 11 | 3129805 | 3130035 | + | NZ_AP021876.1 | Desulfosarcina ovata subsp. sediminis |
| 12 | 1562005 | 1562235 | - | NZ_AP021876.1 | Desulfosarcina ovata subsp. sediminis |
| 13 | 785690 | 785941 | + | NC_015702.1 | Parachlamydia acanthamoebae UV-7 |
| 14 | 490486 | 490716 | - | NZ_AP021874.1 | Desulfosarcina alkanivorans |
| 15 | 5681072 | 5681302 | + | NZ_AP021874.1 | Desulfosarcina alkanivorans |
| 16 | 6559151 | 6559381 | - | NZ_AP021875.1 | Desulfosarcina widdelii |
| 17 | 2574031 | 2574261 | + | NZ_CP061800.1 | Desulfonema magnum |
| 18 | 2619695 | 2619889 | + | NZ_LT907975.1 | Pseudodesulfovibrio profundus |
| 19 | 436424 | 436654 | + | NC_018025.1 | Desulfomonile tiedjei DSM 6799 |
| 20 | 1794629 | 1794823 | + | NZ_CP046400.1 | Pseudodesulfovibrio cashew |
| 21 | 2014962 | 2015216 | + | NC_015713.1 | Simkania negevensis Z |
| 22 | 81499 | 81717 | - | NZ_CP008796.1 | Thermodesulfobacterium commune DSM 2178 |
| 23 | 815553 | 815747 | + | NZ_AP014945.1 | Caldimicrobium thiodismutans |
| 24 | 2411058 | 2411291 | - | NC_013943.1 | Denitrovibrio acetiphilus DSM 12809 |
| 25 | 705886 | 706080 | + | NC_015682.1 | Thermodesulfobacterium geofontis OPF15 |
| 26 | 2009451 | 2009681 | + | NC_016627.1 | Acetivibrio clariflavus DSM 19732 |
| 27 | 2220810 | 2221040 | - | NZ_CP048436.1 | Flavonifractor plautii |
| 28 | 2700349 | 2700576 | - | NZ_CP019870.1 | Clostridioides difficile |
| 29 | 187728 | 187967 | - | NZ_CP023671.1 | Clostridium septicum |
| 30 | 3001069 | 3001299 | + | NC_016803.1 | Pseudodesulfovibrio mercurii |
| 31 | 2204548 | 2204775 | - | NC_008261.1 | Clostridium perfringens ATCC 13124 |
| 32 | 1457378 | 1457608 | - | NC_016630.1 | Filifactor alocis ATCC 35896 |
| 33 | 1905388 | 1905615 | + | NC_015687.1 | Clostridium acetobutylicum DSM 1731 |
| 34 | 705170 | 705403 | - | NC_020127.1 | Lawsonia intracellularis N343 |
| 35 | 1536313 | 1536540 | - | NC_014654.1 | Halanaerobium hydrogeniformans |
| 36 | 3252275 | 3252505 | - | NC_007517.1 | Geobacter metallireducens GS-15 |
| 37 | 1574236 | 1574466 | + | NC_009922.1 | Alkaliphilus oremlandii OhILAs |
| 38 | 1572936 | 1573163 | - | NZ_CP034118.1 | Staphylospora marina |
| 39 | 1144835 | 1145065 | - | NC_008609.1 | Pelobacter propionicus DSM 2379 |
| 40 | 3094413 | 3094646 | - | NZ_CP014176.1 | Clostridium argentinense |
| 41 | 2905550 | 2905777 | - | NZ_CP015756.1 | Clostridium estertheticum subsp. estertheticum |
| 42 | 3861517 | 3861747 | - | NZ_AP023213.1 | Citrifermentans bremense |
| 43 | 3942967 | 3943197 | - | NC_011146.1 | Citrifermentans bemidjiense Bem |
| 44 | 3276048 | 3276275 | + | NC_011831.1 | Chloroflexus aggregans DSM 9485 |
| 45 | 2918434 | 2918664 | - | NZ_CP009788.1 | Geobacter pickeringii |
| 46 | 1439602 | 1439832 | + | NC_015318.1 | Hippea maritima DSM 10411 |
| 47 | 2618095 | 2618325 | + | NC_010814.1 | Geobacter lovleyi SZ |
| 48 | 1640078 | 1640308 | + | NC_011979.1 | Geobacter daltonii FRC-32 |
| 49 | 4401893 | 4402123 | - | NC_009483.1 | Geobacter uraniireducens Rf4 |
| 50 | 2586006 | 2586233 | - | NZ_CP024109.1 | Bacillus cytotoxicus |
| 51 | 1501579 | 1501806 | + | NZ_CP040336.1 | Bacillus luti |
| 52 | 3862731 | 3862958 | - | NC_011725.1 | Bacillus cereus B4264 |
| 53 | 3727681 | 3727908 | - | NZ_CP064875.1 | Bacillus toyonensis |
| 54 | 1431836 | 1432072 | + | NZ_CP015438.1 | Anoxybacillus amylolyticus |
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| Neighborhood Conservation Analysis |
* Arrows marked in Genome Diagram shows ORFs; Multiple PFAMs can be mapped to a single ORF.
* 'Small ORF' represents the entry/query analyzed.
* Image generated using 'gggenes'(R-Package).
Neighborhood Representative Chosen(Species): NZ_CP061800.1
| Sr.No. | Domain | Co-occurrence Frequency | No. of species in which domain occurs with smORF | Median distance b/w smORF and domain bearing ORFs | Orientation relative to smORF | PFAM Information |
|---|---|---|---|---|---|---|
| 1 | PF00448.24 | 0.67 | 35 | 399 | same-strand | SRP54-type protein, GTPase domain |
| 2 | PF02978.21 | 0.67 | 35 | 383 | same-strand | Signal peptide binding domain |
| 3 | PF02881.21 | 0.67 | 35 | 399 | same-strand | SRP54-type protein, helical bundle domain |
| 4 | PF00886.21 | 0.71 | 37 | 52 | same-strand | Ribosomal protein S16 |
| 5 | PF01782.20 | 0.69 | 36 | 65.5 | same-strand | RimM N-terminal domain |
| 6 | PF05239.18 | 0.69 | 36 | 65.5 | same-strand | PRC-barrel domain |
| 7 | PF01746.23 | 0.67 | 35 | 590 | same-strand | tRNA (Guanine-1)-methyltransferase |
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