Result : O31738
| Protein Information |
| Information Type | Description |
|---|---|
| Protein name | UPF0109 protein YlqC |
| NCBI Accession ID | AL009126.3 |
| Organism | Bacillus subtilis (strain 168) |
| Left | 1673892 |
| Right | 1674137 |
| Strand | + |
| Nucleotide Sequence | ATGACTGATCAACACTTGGAAGATTTGATTGTCCACATTGTGACGCCGCTTGTTGATCATCCAGATGACATTCGCGTCATAAGAGAAGAAACCGATCAAAAGATTGCGCTGCGCTTATCTGTCCATAAGTCAGATACCGGTAAAGTTATCGGAAAGCAAGGCCGGACTGCAAAAGCGATTCGAACAGCTGTATTTGCAGCTGGCGTACAGTCTTCTAAGAAAGTTCAATTTGAAATATTTGACTAA |
| Sequence | MTDQHLEDLIVHIVTPLVDHPDDIRVIREETDQKIALRLSVHKSDTGKVIGKQGRTAKAIRTAVFAAGVQSSKKVQFEIFD |
| 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 | 9384377 |
| Domain | CDD:412160 |
| Functional Category | RNA-binding |
| Uniprot ID | O31738 |
| ORF Length (Amino Acid) | 81 |
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| Conservation Analysis |
No. of Species: 117
| Sr.No. | Left Position | Right Position | Strand | NCBI Accession id | Species Name |
|---|---|---|---|---|---|
| 1 | 1673892 | 1674137 | + | NC_000964.3 | Bacillus subtilis subsp. subtilis str. 168 |
| 2 | 1641692 | 1641937 | + | NZ_CP034943.1 | Bacillus subtilis subsp. spizizenii ATCC 6633 = JCM 2499 |
| 3 | 1646763 | 1647008 | + | NZ_CP013984.1 | Bacillus inaquosorum |
| 4 | 1678012 | 1678257 | + | NZ_CP051464.1 | Bacillus mojavensis |
| 5 | 311989 | 312234 | - | NZ_CP029364.1 | Bacillus halotolerans |
| 6 | 1581574 | 1581819 | + | NZ_CP048852.1 | Bacillus tequilensis |
| 7 | 1852254 | 1852499 | + | NZ_CP033052.1 | Bacillus vallismortis |
| 8 | 2332026 | 2332271 | - | NZ_CP011937.1 | Bacillus velezensis |
| 9 | 1628875 | 1629120 | + | NZ_CP053376.1 | Bacillus amyloliquefaciens |
| 10 | 1801225 | 1801470 | + | NZ_LT603683.1 | Bacillus glycinifermentans |
| 11 | 1779254 | 1779499 | + | NC_006270.3 | Bacillus licheniformis DSM 13 = ATCC 14580 |
| 12 | 1801864 | 1802109 | + | NZ_CP023665.1 | Bacillus paralicheniformis |
| 13 | 123783 | 124028 | - | NZ_CP017786.1 | Bacillus xiamenensis |
| 14 | 1575439 | 1575684 | + | NZ_CP011150.1 | Bacillus altitudinis |
| 15 | 3743501 | 3743746 | - | NZ_CP043404.1 | Bacillus safensis |
| 16 | 2371706 | 2371951 | - | NZ_CP016020.1 | Bacillus weihaiensis |
| 17 | 1825360 | 1825566 | - | NC_013891.1 | Listeria seeligeri serovar 1/2b str. SLCC3954 |
| 18 | 1841207 | 1841413 | - | NZ_LT906444.1 | Listeria welshimeri |
| 19 | 1921797 | 1922003 | - | NZ_CP009577.1 | Listeria ivanovii subsp. ivanovii |
| 20 | 1867180 | 1867386 | - | NC_003210.1 | Listeria monocytogenes EGD-e |
| 21 | 1050671 | 1050877 | + | NZ_LR134483.1 | Listeria grayi |
| 22 | 3401680 | 3401907 | + | NZ_CP063356.1 | Anaerobacillus isosaccharinicus |
| 23 | 139769 | 140002 | + | NZ_CP009709.1 | Weizmannia coagulans DSM 1 = ATCC 7050 |
| 24 | 1949671 | 1949904 | - | NZ_CP016539.2 | Planococcus plakortidis |
| 25 | 1581258 | 1581488 | + | NZ_CP011102.1 | Listeria weihenstephanensis |
| 26 | 2420828 | 2421055 | - | NZ_CP020772.1 | Halobacillus mangrovi |
| 27 | 1764377 | 1764607 | + | NC_022524.1 | Bacillus infantis NRRL B-14911 |
| 28 | 2567324 | 2567521 | - | NZ_CP018866.1 | Sutcliffiella cohnii |
| 29 | 3027810 | 3028043 | + | NZ_CP015108.1 | Sporosarcina ureae |
| 30 | 1545942 | 1546175 | + | NZ_CP009416.1 | Jeotgalibacillus malaysiensis |
| 31 | 1767896 | 1768129 | - | NZ_CP013659.2 | Planococcus rifietoensis |
| 32 | 2670994 | 2671227 | - | NZ_LS483476.1 | Lederbergia lentus |
| 33 | 149477 | 149680 | - | NZ_CP022983.1 | Cytobacillus kochii |
| 34 | 371099 | 371326 | + | NZ_CP013862.1 | Lentibacillus amyloliquefaciens |
| 35 | 4965418 | 4965624 | - | NZ_CP041305.1 | Cytobacillus ciccensis |
| 36 | 6385927 | 6386157 | - | NC_017672.3 | Paenibacillus mucilaginosus K02 |
| 37 | 1972222 | 1972455 | - | NZ_CP016538.2 | Planococcus maritimus |
| 38 | 1995465 | 1995698 | - | NZ_CP059540.1 | Planococcus maritimus |
| 39 | 2586006 | 2586233 | - | NZ_CP024109.1 | Bacillus cytotoxicus |
| 40 | 2722852 | 2723079 | - | NC_014829.1 | Evansella cellulosilytica DSM 2522 |
| 41 | 3277036 | 3277269 | - | NZ_CP014616.1 | Sporosarcina psychrophila |
| 42 | 3906900 | 3907127 | - | NZ_CP018622.1 | Virgibacillus dokdonensis |
| 43 | 2012402 | 2012629 | + | NC_017668.1 | Halobacillus halophilus DSM 2266 |
| 44 | 3397664 | 3397894 | - | NZ_CP017703.1 | Aeribacillus pallidus |
| 45 | 2110753 | 2110986 | - | NZ_CP016540.2 | Planococcus versutus |
| 46 | 3018702 | 3018935 | + | NZ_CP013661.2 | Planococcus kocurii |
| 47 | 2244878 | 2245111 | - | NZ_CP019401.1 | Planococcus faecalis |
| 48 | 1262454 | 1262684 | - | NZ_CP068053.1 | Peribacillus psychrosaccharolyticus |
| 49 | 1467429 | 1467662 | + | NZ_CP031223.1 | Psychrobacillus glaciei |
| 50 | 959655 | 959885 | - | NZ_CP017704.1 | Peribacillus simplex NBRC 15720 = DSM 1321 |
| 51 | 2066987 | 2067217 | + | NZ_CP042593.1 | Bacillus dafuensis |
| 52 | 4233004 | 4233234 | + | NZ_CP030926.1 | Peribacillus butanolivorans |
| 53 | 3658136 | 3658363 | - | NC_007530.2 | Bacillus anthracis str. 'Ames Ancestor' |
| 54 | 1691980 | 1692207 | + | NZ_CP029797.1 | Paraliobacillus zengyii |
| 55 | 1794882 | 1795109 | + | NZ_CP024848.1 | Oceanobacillus zhaokaii |
| 56 | 1501579 | 1501806 | + | NZ_CP040336.1 | Bacillus luti |
| 57 | 2092796 | 2093023 | - | NZ_CP017962.1 | Virgibacillus halodenitrificans |
| 58 | 1987748 | 1987975 | - | NZ_CP012502.1 | Bacillus beveridgei |
| 59 | 3727681 | 3727908 | - | NZ_CP064875.1 | Bacillus toyonensis |
| 60 | 1007898 | 1008125 | + | NZ_CP047361.1 | Macrococcus canis |
| 61 | 2097037 | 2097270 | - | NZ_CP016543.2 | Planococcus donghaensis |
| 62 | 2385279 | 2385512 | - | NZ_CP016534.2 | Planococcus antarcticus DSM 14505 |
| 63 | 3786034 | 3786264 | - | NZ_CP009288.1 | Paenibacillus durus |
| 64 | 1554947 | 1555174 | + | NZ_CP041666.1 | Radiobacillus deserti |
| 65 | 2573569 | 2573802 | - | NZ_CP065425.1 | Heyndrickxia vini |
| 66 | 3266968 | 3267195 | - | NZ_CP022315.1 | Virgibacillus phasianinus |
| 67 | 1788890 | 1789123 | - | NZ_CP038012.1 | Sporosarcina pasteurii |
| 68 | 2540181 | 2540414 | - | NZ_CP017560.1 | Sporosarcina ureilytica |
| 69 | 3988490 | 3988720 | - | NZ_CP024035.1 | Priestia aryabhattai |
| 70 | 2200337 | 2200570 | - | NZ_CP016537.2 | Planococcus halocryophilus |
| 71 | 2172209 | 2172439 | + | NZ_CP053989.1 | Niallia circulans |
| 72 | 2763319 | 2763555 | - | NZ_CP018058.1 | Geobacillus thermocatenulatus |
| 73 | 3268282 | 3268512 | - | NZ_CP004078.1 | Paenibacillus sabinae T27 |
| 74 | 1241009 | 1241239 | + | NZ_CP013652.1 | Paenibacillus naphthalenovorans |
| 75 | 3491352 | 3491582 | - | NZ_CP020028.1 | Paenibacillus kribbensis |
| 76 | 1051071 | 1051304 | + | NZ_CP006837.1 | Lysinibacillus varians |
| 77 | 3619236 | 3619469 | - | NZ_CP019980.1 | Lysinibacillus sphaericus |
| 78 | 3743739 | 3743972 | - | NZ_CP010820.1 | Lysinibacillus fusiformis |
| 79 | 4067838 | 4068068 | - | NZ_CP034346.1 | Paenibacillus lutimineralis |
| 80 | 799524 | 799754 | + | NZ_CP035492.1 | Paenibacillus protaetiae |
| 81 | 712718 | 712945 | - | NZ_CP065729.1 | Macrococcus caseolyticus |
| 82 | 3448847 | 3449077 | - | NZ_CP009286.1 | Paenibacillus stellifer |
| 83 | 3503724 | 3503954 | + | NZ_CP034235.1 | Paenibacillus psychroresistens |
| 84 | 1103766 | 1103993 | + | NZ_CP054482.1 | Macrococcus bohemicus |
| 85 | 1047283 | 1047510 | + | NC_014377.1 | Thermosediminibacter oceani DSM 16646 |
| 86 | 3586201 | 3586431 | + | NZ_CP011388.1 | Paenibacillus swuensis |
| 87 | 4576847 | 4577068 | + | NZ_CP011058.1 | Paenibacillus beijingensis |
| 88 | 1670247 | 1670480 | + | NZ_CP023704.1 | Caldibacillus thermoamylovorans |
| 89 | 2165262 | 2165471 | - | NZ_CP048103.1 | Kroppenstedtia eburnea |
| 90 | 4236312 | 4236542 | - | NZ_CP009287.1 | Paenibacillus graminis |
| 91 | 6168811 | 6169041 | - | NZ_CP048429.1 | Paenibacillus jilunlii |
| 92 | 6308674 | 6308904 | - | NZ_CP068595.1 | Paenibacillus sonchi |
| 93 | 4767369 | 4767599 | - | NZ_LN831776.1 | Paenibacillus riograndensis SBR5 |
| 94 | 4956675 | 4956905 | - | NZ_CP009285.1 | Paenibacillus borealis |
| 95 | 2603824 | 2604054 | + | NZ_CP013023.1 | Paenibacillus bovis |
| 96 | 2411058 | 2411291 | - | NC_013943.1 | Denitrovibrio acetiphilus DSM 12809 |
| 97 | 2287595 | 2287792 | - | NZ_AP017378.1 | Desulfovibrio ferrophilus |
| 98 | 2045273 | 2045506 | - | NZ_CP038015.1 | Paenisporosarcina antarctica |
| 99 | 1706611 | 1706841 | - | NC_014614.1 | Acetoanaerobium sticklandii |
| 100 | 3301306 | 3301536 | + | NZ_CP034437.1 | Paenibacillus albus |
| 101 | 3238966 | 3239196 | - | NZ_AP023367.1 | Anaerocolumna cellulosilytica |
| 102 | 3753963 | 3754193 | + | NZ_CP048000.1 | Anaerocolumna sedimenticola |
| 103 | 3988630 | 3988860 | - | NZ_CP034248.1 | Paenibacillus lentus |
| 104 | 1208494 | 1208724 | + | NZ_LN879430.1 | Herbinix luporum |
| 105 | 2301159 | 2301389 | + | NZ_CP059066.1 | Koleobacter methoxysyntrophicus |
| 106 | 4177444 | 4177674 | - | NZ_CP009428.1 | Paenibacillus odorifer |
| 107 | 1954446 | 1954673 | - | NZ_CP048104.1 | Kroppenstedtia pulmonis |
| 108 | 1069199 | 1069429 | + | NZ_CP045293.1 | Paenibacillus guangzhouensis |
| 109 | 3194332 | 3194568 | - | NZ_CP036250.1 | Egicoccus halophilus |
| 110 | 1251506 | 1251733 | + | NC_015519.1 | Tepidanaerobacter acetatoxydans Re1 |
| 111 | 821371 | 821598 | - | NZ_CP029256.1 | Christensenella minuta |
| 112 | 2526420 | 2526650 | - | NC_015275.1 | Cellulosilyticum lentocellum DSM 5427 |
| 113 | 1218405 | 1218617 | + | NZ_CP039710.1 | Thermoactinomyces vulgaris |
| 114 | 937944 | 938174 | - | NZ_CP035485.1 | Salicibibacter halophilus |
| 115 | 2209774 | 2210004 | - | NC_019897.1 | Thermobacillus composti KWC4 |
| 116 | 1431836 | 1432072 | + | NZ_CP015438.1 | Anoxybacillus amylolyticus |
| 117 | 187728 | 187967 | - | NZ_CP023671.1 | Clostridium septicum |
| 118 | 2290073 | 2290300 | + | NC_014393.1 | Clostridium cellulovorans 743B |
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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_LT603683.1
| 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 | 1.0 | 117 | 630.0 | same-strand | SRP54-type protein, GTPase domain |
| 2 | PF02881.21 | 1.0 | 117 | 630.0 | same-strand | SRP54-type protein, helical bundle domain |
| 3 | PF04297.16 | 0.92 | 108 | 1752 | same-strand | Putative helix-turn-helix protein, YlxM / p13 like |
| 4 | PF02978.21 | 1.0 | 117 | 383.0 | same-strand | Signal peptide binding domain |
| 5 | PF00886.21 | 1.0 | 117 | 15.5 | same-strand | Ribosomal protein S16 |
| 6 | PF01782.20 | 0.99 | 116 | 226.5 | same-strand | RimM N-terminal domain |
| 7 | PF05239.18 | 0.99 | 116 | 230 | same-strand | PRC-barrel domain |
| 8 | PF01746.23 | 0.95 | 111 | 890.5 | same-strand | tRNA (Guanine-1)-methyltransferase |
| 9 | PF01245.22 | 0.83 | 97 | 1852.0 | same-strand | Ribosomal protein L19 |
| 10 | PF06470.15 | 0.61 | 71 | 3223.0 | same-strand | SMC proteins Flexible Hinge Domain |
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