PaperBLAST

PaperBLAST Hits for sp|Q9HXY9|RNH2_PSEAE Ribonuclease HII OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=rnhB PE=3 SV=1 (201 a.a., MQLGLDFNLV...)

Show query sequence

>sp|Q9HXY9|RNH2_PSEAE Ribonuclease HII OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=rnhB PE=3 SV=1
MQLGLDFNLVEDLVAGVDEVGRGPLCGPVVTAAVILDPSRPILGLNDSKKLSEARREALF
EEIREKALAWCIARAEVEEIDRLNILHATMLAMQRAVEGLSVIPRLALIDGNRCPKLAVP
CAPVVKGDSQVPAIAAASILAKVSRDREMVELDRVYPGYGMAGHKGYPTAVHLEALSRLG
PTPIHRRSFAPVRELLDVSVQ

Running BLASTp...

Found 81 similar proteins in the literature:

PA3642 ribonuclease HII from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage

• Differential transcription profiling of the phage LUZ19 infection process in different growth media
  Brandão, RNA biology 2021 (secret)

PP1605 ribonuclease HII from Pseudomonas putida KT2440
87% identity, 93% coverage

• UEG Week 2023 Poster Presentations
  , United European gastroenterology journal 2023

S0176 RNAse HII from Shigella flexneri 2a str. 2457T
71% identity, 94% coverage

• Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri
  Venkatesan, Infection and immunity 2001
  • “...TTG 39.9 111 M. tuberculosis S0120 S0121 S0122 S0141 S0176 S0177 S0179 S0193 S0194 S0205 S0208 S0209 S0210 S0211 S0212 S0213 S0214 S0225 S0235 88198 88260 88540...”

RnhB / b0183 RNase HII (EC 3.1.26.4) from Escherichia coli K-12 substr. MG1655 (see 20 papers)
rnhB / P10442 RNase HII (EC 3.1.26.4) from Escherichia coli (strain K12) (see 19 papers)
RNH2_ECOLI / P10442 Ribonuclease HII; RNase HII; EC 3.1.26.4 from Escherichia coli (strain K12) (see paper)
P10442 ribonuclease H (EC 3.1.26.4) from Escherichia coli (see paper)
NP_414725 RNase HII from Escherichia coli str. K-12 substr. MG1655
71% identity, 94% coverage

• function: Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
  catalytic activity: Endonucleolytic cleavage to 5'-phosphomonoester.
  cofactor: Mn(2+) Mg(2+) (Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding.)
• RNase HII Saves rnhA Mutant Escherichia coli from R-Loop-Associated Chromosomal Fragmentation.
  Kouzminova, Journal of molecular biology 2017
  • GeneRIF: The authors propose that RNase H-deficient mutants convert some R-loops into R-tracts, which progress into R-gaps and then to double-strand breaks-explaining why R-tracts do not accumulate in RNase H-deficient cells, while double-strand breaks do.
• The pH-dependence of the Escherichia coli RNase HII-catalysed reaction suggests that an active site carboxylate group participates directly in catalysis.
  Bastock, Journal of molecular biology 2007 (PubMed)
  • GeneRIF: The data suggest a requirement for ionisation of an active site carboxylic acid for metal ion binding or correct positioning of metal ion(s) in the enzyme-substrate complex and a role for a second active site carboxylate in general base catalysis.
• Isolation and characterization of a second RNase H (RNase HII) of Escherichia coli K-12 encoded by the rnhB gene.
  Itaya, Proceedings of the National Academy of Sciences of the United States of America 1990
  • GeneRIF: N-terminus verified by Edman degradation on complete protein
• Gene cloning and characterization of recombinant RNase HII from a hyperthermophilic archaeon
  Haruki, Journal of bacteriology 1998
  • “...Z66524, product T13H5.2); Eco, E. coli (Swiss-Prot code no. P10442); and Bsu, B. subtilis (EMBL accession no. 299112). VOL. 180, 1998 RNase HII FROM A...”

7uwhC / P10442 Cryoem structure of e. Coli transcription-coupled ribonucleotide excision repair (tc-rer) complex bound to ribonucleotide substrate (see paper)
70% identity, 94% coverage

• Ligand: dna (7uwhC)

HD1026 ribonuclease HII from Haemophilus ducreyi 35000HP
65% identity, 92% coverage

• A <i>Haemophilus ducreyi</i> strain lacking the <i>yfeABCD</i> iron transport system is virulent in human volunteers
  Fortney, Infection and immunity 2024 (secret)

APL_0129 ribonuclease HII from Actinobacillus pleuropneumoniae L20
67% identity, 92% coverage

• Comparative profiling of the transcriptional response to iron restriction in six serotypes of Actinobacillus pleuropneumoniae with different virulence potential
  Klitgaard, BMC genomics 2010
  • “...yfeB Iron (chelated) transporter, ATP-binding protein P 0.76 APL_0149 nfuA Fe/S biogenesis protein O 0.62 APL_0129 rnhB RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids (DNA synthesis pathway) L 0.50 APL_0128 + yfeC Putative iron transport system membrane protein P 0.45...”

HI1059 ribonuclease HII (rnhB) from Haemophilus influenzae Rd KW20
P43808 Ribonuclease HII from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
66% identity, 92% coverage

• High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness of Haemophilus influenzae
  Bayliss, Nucleic acids research 2006
  • “...genome sequences (strains Rd, R2866 and R2864; Supplementary Figure 1). The sequences started within gene HI1059 ( rnhB ) which was conserved with 11 polymorphic sites in 123 nt (9%; region i in Figure 1 ). The intergenic region between this gene and mod also exhibited...”
• Cloning of the cDNA encoding the large subunit of human RNase HI, a homologue of the prokaryotic RNase HII
  Frank, Proceedings of the National Academy of Sciences of the United States of America 1998
  • “...11, EMBL D32253), H. influenzae (lanes 12, Swiss-Prot P43808), E. coli (lanes 13, GenBank U70214), and V. cholerae (lanes 14, Swiss-Prot P52021). Numbering of...”

ABUW_2751 ribonuclease HII from Acinetobacter baumannii
62% identity, 92% coverage

• Copy Number of an Integron-Encoded Antibiotic Resistance Locus Regulates a Virulence and Opacity Switch in Acinetobacter baumannii AB5075
  Anderson, mBio 2020
  • “...Inconsistent switching phenotype No change ABUW_1369 rnz Increased switching ND ABUW_2146 NA Increased switching ND ABUW_2751 rnhB Increased switching ND ABUW_2826 rnt Increased switching ND ABUW_3316 NA Increased switching ND ABUW_3367 NA Increased switching ND ABUW_3478 rne Too mucoid to see switching No change ABUW_3518 pnp...”

P52021 Ribonuclease HII from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
62% identity, 90% coverage

• Cloning of the cDNA encoding the large subunit of human RNase HI, a homologue of the prokaryotic RNase HII
  Frank, Proceedings of the National Academy of Sciences of the United States of America 1998
  • “...GenBank U70214), and V. cholerae (lanes 14, Swiss-Prot P52021). Numbering of amino acids above the alignment corresponds to the consecutive sequence of human...”

swp_3507 Ribonuclease H from Shewanella piezotolerans WP3
62% identity, 90% coverage

• Condition-Specific Molecular Network Analysis Revealed That Flagellar Proteins Are Involved in Electron Transfer Processes of Shewanella piezotolerans WP3
  Ding, Genetics research 2021
  • “...swp_4806, swp_2182, swp_4116, swp_2918, swp_2183, swp_3403, swp_0613 8 8 0.64 2.70 E 03 Lipopolysaccharide biosynthesis swp_3507, swp_3506, swp_0834, swp_3511, swp_3509, swp_3508, swp_3516, swp_3515 9 5 0.70 2.79 E 03 swp_3204, swp_3981, swp_0083, swp_3979, swp_1828 10 4 0.67 1.01 E 02 swp_2103, swp_3188, swp_3190, swp_3192 11 5...”

lpg1373 ribonuclease HII from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
63% identity, 92% coverage

• The LetA/S two-component system regulates transcriptomic changes that are essential for the culturability of Legionella pneumophila in water
  Mendis, Scientific reports 2018
  • “...1.41 2.15 Lpg1423 TPR domain protein (heat shock protein) N-acetylglucosaminyl transferase 1.93 1.58 DNA/RNA Degradation Lpg1373 ribonuclease HII rnhB 1.37 1.11 Lpg1383 ribonuclease HI rnhA 1.00 1.73 Lpg1869 ribonuclease III (dsRNA-specific ribonuclease) (RNAse III, dsRNA) rnc 2.04 2.24 Lpg0609 alanyl tRNA synthetase alaS 1.16 2.57 Lpg2004...”
• bdhA-patD operon as a virulence determinant, revealed by a novel large-scale approach for identification of Legionella pneumophila mutants defective for amoeba infection
  Aurass, Applied and environmental microbiology 2009
  • “...lpg0685 lpg1019 lpg1110 lpg1121 lpg1146 lpg1188 lpg1349 lpg1373 lpg1376 lpg1426 lpg1441 lpg1466 lpg1469 lpg1507 lpg1596 lpg1610 lpg1615 lpg1634 lpg1638 lpg1653...”

SO_1643 ribonuclease HII from Shewanella oneidensis MR-1
63% identity, 89% coverage

• An extracytoplasmic function sigma factor-dependent periplasmic glutathione peroxidase is involved in oxidative stress response of Shewanella oneidensis
  Dai, BMC microbiology 2015
  • “...zinc metalloprotease bamA (SO_1637)- skp (SO_1638)- lpxD (SO_1639)- fabZ (SO_1640)- lpxA (SO_1641)- lpxB (SO_1642)- rnhB (SO_1643) SO_1880 GAACTT TCTGAGCAATGTCATG GTCTGT bamC OMP assembly complex subunit C SO_3309 GAACTC AAAGGCGACTTCTTT GTTCGT bamB OMP assembly complex subunit B SO_3580 GAACCG TACCCGCGTTTTGGG GTCCAA bamD OMP assembly complex subunit D...”

Q25C12 ribonuclease H (EC 3.1.26.4) from Shewanella sp. (see paper)
62% identity, 87% coverage

LHK_00722 Rnh2 from Laribacter hongkongensis HLHK9
65% identity, 94% coverage

• Environmental adaptability and stress tolerance of Laribacter hongkongensis: a genome-wide analysis
  Lau, Cell & bioscience 2011
  • “...strands LHK_00880 L. nitroferrum 77.3 2.00E-59 rnhB Ribonuclease HII Endonuclease degrades RNA of RNA-DNA hybrids LHK_00722 L. nitroferrum 71.88 1.00E-68 polA DNA polymerase I DNA polymerase exhibits 3' to 5' and 5' to 3' exonuclease activity LHK_02983 C. violaceum 68.03 0 ligA DNA ligase Catalyzes phosphodiester...”

CCNA_00383 ribonuclease HII from Caulobacter crescentus NA1000
62% identity, 85% coverage

• The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions
  Nandana, Cell reports 2023 (secret)

CV_2210 ribonuclease HII from Chromobacterium violaceum ATCC 12472
65% identity, 91% coverage

• Guava leaf extract inhibits quorum-sensing and Chromobacterium violaceum induced lysis of human hepatoma cells: whole transcriptome analysis reveals differential gene expression
  Ghosh, PloS one 2014
  • “...biosynthesis 41.56 4.12 3.33 0.01 CV_2209 lpxB lipid-A-disaccharide synthase, Lipopolysaccharide biosynthesis 29.44 3.69 3 0 CV_2210 rnhB ribonuclease HII 29.44 3.69 3 0 CV_2212 hypothetical protein 561.06 41.05 3.77 0 CV_4338 ftsZ cell division protein 61.92 7.3 3.08 9.58E-005 CV_4340 ftsQ cell division transmembrane protein 41.07...”

NGO1789 RnhB from Neisseria gonorrhoeae FA 1090
58% identity, 92% coverage

• Transcriptional initiation of a small RNA, not R-loop stability, dictates the frequency of pilin antigenic variation in Neisseria gonorrhoeae
  Prister, Molecular microbiology 2019
  • “...the FA1090 locus NGO1162 and an RNase HII ortholog ( rnhB ) at the locus NGO1789. An insertional mutant of rnhB showed no defects in growth, no other obvious phenotypes, and had parental levels of pilin Av when measured by the surrogate PDCMC assay ( Supplemental...”
  • “...is not a perfectly quantitative assay. Gc also encodes the RNase HII family enzyme rnhB (NGO1789). A rnhB mutant and complement had similar growth phenotypes and no effect on pilin Av as measured by PDCMC. While RNase HII family enzymes can act on R-loops, they are...”
• Fur-mediated activation of gene transcription in the human pathogen Neisseria gonorrhoeae
  Yu, Journal of bacteriology 2012
  • “...iron-upregulated genes we examined, NGO0376, NGO0432, NGO1290, NGO1789, and NGO1957 showed increased transcription in the fur mutant strain (Fur-repressed...”
  • “...NGO1290 NGO1317 NGO1430 NGO1685 NGO1751-NGO1747 NGO1788 NGO1789 NGO1842-NGO1841 NGO1850 NGO1851 NGO1859 NGO1865-NGO1864 NGO1913 NGO1937 NGO1957 NGO1960 NGO2011...”

E2P69_RS10975 ribonuclease HII from Xanthomonas perforans
56% identity, 76% coverage

• Transcriptome profiling of type VI secretion system core gene tssM mutant of Xanthomonas perforans highlights regulators controlling diverse functions ranging from virulence to metabolism
  Ramamoorthy, Microbiology spectrum 2024
  • “...environment. In the transcriptome analysis, we identified the mRNA level of two genes (E2P69_RS00065 and E2P69_RS10975) coding for ribonuclease P protein component, and ribonuclease HII was significantly upregulated in the mutant strain at 8 and 16 hours, while two genes (E2P69_RS10175 and E2P69_RS09245) coding for ribonuclease...”

FTN_1293 ribonuclease HII from Francisella tularensis subsp. novicida U112
48% identity, 92% coverage

• Exploitation of host cell biology and evasion of immunity by francisella tularensis
  Asare, Frontiers in microbiology 2010
  • “...system, subunit S FTN_1176 uvrB Excinuclease ABC, subunit B FTN_1197 recR RecFOR complex, RecR component FTN_1293 rnhB Ribonuclease HII FTN_1357 recB ATP-dependent exoDNase_subunit FTN_1487 Restriction endonuclease TRANSCRIPTION/TRANSLATION FTL_1542 migR Macrophage intracellular growth regulator FTL_1606 sspA Stringent starvation protein A/regulator of transcription FTL_1914 ripA Required for intracellular...”
• Molecular bases of proliferation of Francisella tularensis in arthropod vectors
  Asare, Environmental microbiology 2010
  • “...component 2 4 # tnfn1_pw060510p02q106 FTN_1197 recR RecFOR complex, RecR component 3 3 # tnfn1_pw060328p06q158 FTN_1293 rnhB ribonuclease HII 2 5 tnfn1_pw060323p07q175 FTN_1487 restriction endonuclease 3 6 Cell Division tnfn1_pw060328p03q149 FTN_0162 ftsQ cell division protein FtsQ 2 2 # tnfn1_pw060328p01q167 FTN_0330 minD septum formation inhibitor-activating ATPase...”
  • “...2 50% 6.5E-01 tnfn1_pw060323p03q167 FTN_1197 recR RecFOR complex, RecR component 4 2 44% 6.7E-04 tnfn1_pw060328p06q158 FTN_1293 rnhB ribonuclease HII 5 3 40% 1.4E+00 tnfn1_pw060328p05q121 FTN_1487 restriction endonuclease 1 1 40% 9.0E+00 tnfn1_pw060510p04q193 FTN_0680 uvrC excinuclease ABC, subunit C 3 6 20% 1.0E-01 tnfn1_pw060510p01q153 FTN_1154 type I...”
• Molecular complexity orchestrates modulation of phagosome biogenesis and escape to the cytosol of macrophages by Francisella tularensis
  Asare, Environmental microbiology 2010
  • “...component 2 4 # tnfn1_pw060510p02q106 FTN_1197 recR RecFOR complex, RecR component 3 3 # tnfn1_pw060328p06q158 FTN_1293 rnhB ribonuclease HII 2 5 tnfn1_pw060323p07q175 FTN_1487 restriction endonuclease 3 6 Cell Division tnfn1_pw060328p03q149 FTN_0162 ftsQ cell division protein FtsQ 2 2 # tnfn1_pw060328p01q167 FTN_0330 minD septum formation inhibitor-activating ATPase...”

SAR11_0108 Ribonuclease HII (RNase HII) from Candidatus Pelagibacter ubique HTCC1062
46% identity, 92% coverage

• Identification of candidate structured RNAs in the marine organism 'Candidatus Pelagibacter ubique'
  Meyer, BMC genomics 2009
  • “...25 SAR11_0046 autotransporter (-) SAR11_0047 transcription regulator (+) 120095120215 121 28.93 211 bablM element (+) SAR11_0108 rnhB (+) SAR11_0109 babIM (+) 762114762332 219 28.31 55 SAR11_0784 hyp. protein (+) SAR11_0785 hyp. protein (+) 834435834636 202 28.22 42 SAR11_0864 hyp. protein (+) SAR11_0865 transporter (+) 11642391164384 146...”

WP_109143090 ribonuclease HII from Bradyrhizobium sp. SUTN9-2
56% identity, 69% coverage

• Differential responses of Bradyrhizobium sp. SUTN9-2 to plant extracts and implications for endophytic interactions within different host plants
  Greetatorn, Scientific reports 2025
  • “...and was also upregulated upon exposure to chili and tomato extracts ( RNase HII ; WP_109143090; 16.91 and 11.08 FC, respectively). DNA methyltransferase ( ccrM ; WP_109143112.1) is used for methylation of DNA replication 25 and showed upregulation in all three plant extracts. The upregulation of...”

SMSK321_0568 ribonuclease HII from Streptococcus mitis SK321
49% identity, 71% coverage

• Capsular Polysaccharide Expression in Commensal Streptococcus Species: Genetic and Antigenic Similarities to Streptococcus pneumoniae
  Skov, mBio 2016
  • “...and a hypothetical protein (SMSK321_0548) upstream and a conserved hypothetical protein (SMSK321_0567) and RNase HII (SMSK321_0568) downstream of the cps locus. An analysis extended to all other strains revealed a similar cps- like locus at the same genome site in SK137 (SK137_1072 to SK137_1090) in addition...”

LSA0993 Ribonuclease HII (RNase HII) from Lactobacillus sakei subsp. sakei 23K
51% identity, 73% coverage

• Global transcriptome response in Lactobacillus sakei during growth on ribose
  McLeod, BMC microbiology 2011
  • “...reductase, NrdH-redoxin 1.1 LSA0950 pyrR Bifunctional protein: uracil phosphoribosyltransferase and pyrimidine operon transcriptional regulator -0.6 LSA0993 rnhB Ribonuclease HII (RNase HII) 0.6 LSA1018 cmk Cytidylate kinase 0.6 LSA1097 lsa1097 Putative ADP-ribose phosphorylase, NUDIX family 0.5 LSA1352 lsa1352 Putative phosphomethylpyrimidine kinase -0.8 LSA1651 lsa1651 Putative purine phosphoribosyltransferase,...”

SPD_1020 ribonuclease HII from Streptococcus pneumoniae D39
49% identity, 71% coverage

• A Novel Iron Transporter SPD_1590 in Streptococcus pneumoniae Contributing to Bacterial Virulence Properties
  Miao, Frontiers in microbiology 2018
  • “...holB 0.80 0.010 SPD_1105 Ribonuclease 3 (EC 3.1.26.3) (Ribonuclease III) (RNase III) rnc 0.76 0.018 SPD_1020 Ribonuclease HII (RNase HII) (EC 3.1.26.4) rnhB 0.82 0.016 Other SPD_0335 Cell wall surface anchor family protein SPD_0335 0.56 0.000 SPD_0126 Pneumococcal surface protein A pspA 0.57 0.000 SPD_1201 Phosphotransferase...”

BSU16060 ribonuclease HII from Bacillus subtilis subsp. subtilis str. 168
50% identity, 72% coverage

• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...BSU00550 BSU27480 No No No No No rnhB recA BSU16060 BSU16940 No No Other/unknown ppaC ylaN yitI yitW yqhY ykwC ylbN ypfD yugI BSU40550 BSU14840 BSU11000...”

SSU05_0996 ribonuclease HII from Streptococcus suis 05ZYH33
46% identity, 72% coverage

• The roles of RelA/(p)ppGpp in glucose-starvation induced adaptive response in the zoonotic Streptococcus suis
  Zhang, Scientific reports 2016
  • “...encoding DNA helicase, ssb (SSU05_1833) encoding single-stranded DNA binding protein, dnaG (SSU05_1429) encoding primase, rnhB (SSU05_0996) encoding ribonuclease HII and four subunits of DNA polymerase III (SSU05_0662, SSU05_1540, SSU05_1627 and SSU05_1954). In contrast, only two subunits of DNA polymerase III (SSU05_1540, SSU05_1954) and ssb , which...”
• GidA, a tRNA Modification Enzyme, Contributes to the Growth, and Virulence of Streptococcus suis Serotype 2
  Gao, Frontiers in cellular and infection microbiology 2016
  • “...DNA repair ATPase 0.8321 14 35.99 RmuC SSU05_1991 DNA recombination protein 0.7751 8 19.90 RnhB SSU05_0996 Ribonuclease HII 0.8074 8 35.41 RnmV SSU05_2010 DNA primase 0.7144 6 26.53 RNase H SSU05_0226 Ribonuclease HIII 0.7297 4 14.86 StkP SSU05_0428 Serine/threonine protein kinase 0.8129 5 32.53 Tag SSU05_0061...”

A7J09_06320 ribonuclease HII from Streptococcus suis
46% identity, 72% coverage

• Comparative virulence and antimicrobial resistance distribution of Streptococcus suis isolates obtained from the United States
  Nicholson, Frontiers in microbiology 2022
  • “...40432, 40437, 40450, 40456, 40464, ISU2514 c4221_g154_s4221 137,371 IS Element, Prophage, IME ermB (A7J09_06245), tetO (A7J09_06320) ISU2812 c4912_g121_s4912 17,439 Unclassified Genomic Island tetO (HCB98_00820) 40525, ISU2614 c5870_g53_s5870 2,659 Islet ermB (HCB73_07125) 30413, 38728, 40426, 40431, 40436, 40451, 40452, 40456, 40459, 40463, 40467, 40470, 40472, 40473, 40524,...”

SPy1162 putative ribonuclease HII from Streptococcus pyogenes M1 GAS
48% identity, 69% coverage

• Novel conserved group A streptococcal proteins identified by the antigenome technology as vaccine candidates for a non-M protein-based vaccine
  Fritzer, Infection and immunity 2010
  • “...Spy1054 Putative collagen-like protein (SclC) 1,295 9 Spy1063 Spy1162 Putative periplasmic-iron-binding protein Putative RNase HII 4 8 1 2 A:71, B:13, C:233,...”

lp_1853 ribonuclease HII from Lactobacillus plantarum WCFS1
52% identity, 71% coverage

• Transcriptional Reprogramming at Genome-Scale of Lactobacillus plantarum WCFS1 in Response to Olive Oil Challenge
  Esteban-Torres, Frontiers in microbiology 2017
  • “...five RNA modification enzymes. Two out of these genes code for RNase H activity [ lp_1853 (ribonuclease HII), lp_2953 (ribonuclease H)], while other for exodeoxyribonuclease V ( lp_2168 ). The remaining two genes encode for enzymes dedicated to tRNA modification ( lp_1579 ( miaA )) and...”

Q9X017 ribonuclease H (EC 3.1.26.4) from Thermotoga maritima (see 2 papers)
55% identity, 77% coverage

SAOUHSC_01215 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
YP_499752 ribonuclease HII from Staphylococcus aureus subsp. aureus NCTC 8325
46% identity, 72% coverage

• RNA Degradation in Staphylococcus aureus: Diversity of Ribonucleases and Their Impact
  Bonnin, International journal of genomics 2015
  • “...None SA1266 SAOUHSC_01443 N RNase HII rnhB Endonuclease, degradation of RNA/DNA duplexes 0.47 0.44 SA1087 SAOUHSC_01215 N RNase HIII rnhC Endonuclease, degradation of RNA/DNA duplexes 0.46 None SA0987 SAOUHSC_01095 N NanoRNase A nrnA Oligoribonuclease, 3,5-bisphosphate nucleotidase 0.49 None SA1526 SAOUHSC_01812 N a Function: demonstrated experimentally; function...”
• Structural insights into a novel functional dimer of Staphylococcus aureus RNase HII.
  Hang, Biochemical and biophysical research communications 2018 (PubMed)
  • GeneRIF: Staphylococcus aureus RNase HII dimer undergoes a large conformational change upon substrate binding, but remains a dimer to catalyze the reaction.

SA1087 RNase HII from Staphylococcus aureus subsp. aureus N315
46% identity, 72% coverage

• RNA Degradation in Staphylococcus aureus: Diversity of Ribonucleases and Their Impact
  Bonnin, International journal of genomics 2015
  • “...0.33 None SA1266 SAOUHSC_01443 N RNase HII rnhB Endonuclease, degradation of RNA/DNA duplexes 0.47 0.44 SA1087 SAOUHSC_01215 N RNase HIII rnhC Endonuclease, degradation of RNA/DNA duplexes 0.46 None SA0987 SAOUHSC_01095 N NanoRNase A nrnA Oligoribonuclease, 3,5-bisphosphate nucleotidase 0.49 None SA1526 SAOUHSC_01812 N a Function: demonstrated experimentally;...”
• CvfA protein and polynucleotide phosphorylase act in an opposing manner to regulate Staphylococcus aureus virulence
  Numata, The Journal of biological chemistry 2014
  • “...RNases, including RNase III (SA1076), SA0489, RNase HII (SA1087), SA1335, SA0450, PNPase (SA1117), RNase R (SA0735), and YhaM (SA1660), and examined their...”
  • “...mutant was not successful. Disruption of SA0450 or SA1087 in the cvfAdeleted mutant had no effect on hemolysin production. cvfAdeleted mutants with disruption...”

3o3fA / Q9X017 T. Maritima rnase h2 d107n in complex with nucleic acid substrate and magnesium ions (see paper)
54% identity, 83% coverage

• Ligands: dna; magnesium ion (3o3fA)

A0QV44 ribonuclease H (EC 3.1.26.4) from Mycolicibacterium smegmatis (see paper)
MSMEG_2442 ribonuclease HII from Mycobacterium smegmatis str. MC2 155
51% identity, 68% coverage

• Genome-Wide Transcriptional Response of Mycobacterium smegmatis MC²155 to G-Quadruplex Ligands BRACO-19 and TMPyP4
  Shitikov, Frontiers in microbiology 2022
  • “...polymerase IV 1.20 1.97E-07 0.18 0.259968 MSMEG_6443 dinB3 DNA polymerase IV 1.52 1.96E-07 0.33 0.104471 MSMEG_2442 Rv2902c rnhB Ribonuclease HII 1.098 6.33E-08 0.45 0.001482 MSMEG_6896 Rv0054 ssbA Single-stranded DNA-binding protein 1.43 3.92E-09 0.39 0.003882 MSMEG_4701 Rv2478c ssbB Hypothetical protein 0.93 0.00116 1.24 8.09E-05 MSMEG_1327 Rv0630c recB...”
• MS_RHII-RSD, a dual-function RNase HII-(p)ppGpp synthetase from Mycobacterium smegmatis
  Murdeshwar, Journal of bacteriology 2012
  • “...RNase HI (MSMEG_5562) (14, 32) and RNase HII (MSMEG_2442) of M. smegmatis under UV damage conditions. The RHII domain of MS_RHII-RSD would then function...”

Rv2902c ribonuclease HII from Mycobacterium tuberculosis H37Rv
52% identity, 70% coverage

• The C-Terminal Acid Phosphatase Module of the RNase HI Enzyme RnhC Controls Rifampin Sensitivity and Light-Dependent Colony Pigmentation of Mycobacterium smegmatis
  Dupuy, Journal of bacteriology 2023 (secret)
• Genome-Wide Transcriptional Response of Mycobacterium smegmatis MC²155 to G-Quadruplex Ligands BRACO-19 and TMPyP4
  Shitikov, Frontiers in microbiology 2022
  • “...IV 1.20 1.97E-07 0.18 0.259968 MSMEG_6443 dinB3 DNA polymerase IV 1.52 1.96E-07 0.33 0.104471 MSMEG_2442 Rv2902c rnhB Ribonuclease HII 1.098 6.33E-08 0.45 0.001482 MSMEG_6896 Rv0054 ssbA Single-stranded DNA-binding protein 1.43 3.92E-09 0.39 0.003882 MSMEG_4701 Rv2478c ssbB Hypothetical protein 0.93 0.00116 1.24 8.09E-05 MSMEG_1327 Rv0630c recB Exodeoxyribonuclease...”
• Small RNAs Asserting Big Roles in Mycobacteria
  Coskun, Non-coding RNA 2021
  • “...abscessus Involved in mRNA degradation. Hydrolyses single-stranded polyribonucleotides processively in the 3 to 5 direction. rv2902c RnhB M. marinum, M. leprae, M.bovis, Mtb, M. abscessus Probable ribonuclease HII protein RnhB. rv2907c RimM M. marinum, M. leprae, M. bovis, Mtb, M. smegmatis, M. abscessus Essential for efficient...”
• Division of labor among Mycobacterium smegmatis RNase H enzymes: RNase H1 activity of RnhA or RnhC is essential for growth whereas RnhB and RnhA guard against killing by hydrogen peroxide in stationary phase
  Gupta, Nucleic acids research 2017
  • “...(referred to henceforth as RnhD). Neither M. smegmatis RnhB (272-aa) nor its M. tuberculosis counterpart Rv2902c (264-aa), both of which are single-domain proteins homologous to Escherichia coli RNase H2, has been characterized biochemically. Deletion of the M. smegmatis rnhB gene has no impact on bacterial growth...”
• DNA Replication in Mycobacterium tuberculosis
  Ditse, Microbiology spectrum 2017
  • “...DNA ligase Nonessential; role in Ku-dependent nonhomologous end-joining (NHEJ) DSB repair pathway 195 RnhB rnhB Rv2902c MSMEG_2442 ML1611 RNase HII RNase Nonessential 196 LigD ligD Rv0938 MSMEG_5570 Absent DNA ligase, DSB repair ATP-dependent DNA ligase Nonessential; plays a central role in the mutagenic NHEJ pathway of...”
• Functional Characterization of PknI-Rv2159c Interaction in Redox Homeostasis of Mycobacterium tuberculosis
  Venkatesan, Frontiers in microbiology 2016
  • “...gi 15607162 4.65/56.88 More in AsRv2159c GROUP 5: INFORMATION PATHWAY 6 Ribonuclease HII protein, RnhB Rv2902c 64 3 gi 686045826 10.47/27.64 Absent in AsRv2159c In comparison to Rv, over-expression of Rv2159c (S-Rv2159c) leads to high abundance of two metabolic pathway proteins such as, Rv1240 (Malate dehydrogenase...”
  • “...Rv2460c (ATP-dependent CLP protease protelytic subunit 2 ClpP2), Rv3506 (Fatty acid CoA synthetase FaD17) and Rv2902c (Ribonuclease HII protein RnhB). The three stress regulated proteins, Rv2031c (Heat shock protein HspX), Rv2623 (Universal stress protein family protein TB31.7), Rv1636 (Iron-regulated universal stress protein TB15.3) and a cell...”
• Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection
  Anand, Scientific reports 2014
  • “...Rv1530; Rv1650; Rv1663; Rv1843c; Rv1872c; Rv1905c; Rv2165c; Rv2231c; Rv2439c; Rv2524c; Rv2610c; Rv2613c; Rv2623; Rv2678c; Rv2897c; Rv2902c; Rv2941; Rv3255c; Rv3405c; Rv3582c; Rv3585; Rv3635; Rv3737; Rv3825c; Rv3871; Rv3882c; Rv3886c; Rv3887c; Indicated in combination with capecitabine for the treatment of patients with advanced or metastatic breast cancer whose tumors...”
• Structural and functional characterization of an RNase HI domain from the bifunctional protein Rv2228c from Mycobacterium tuberculosis
  Watkins, Journal of bacteriology 2010
  • “...classical rnhA gene, although one rnhB gene, encoding Rv2902c, is present. BLAST searches do, however, identify the N-terminal domain of the open reading frame...”
• More

TTHA0198 ribonuclease HII from Thermus thermophilus HB8
51% identity, 90% coverage

• The role of ribonucleases in regulating global mRNA levels in the model organism Thermus thermophilus HB8
  Ohyama, BMC genomics 2014
  • “...(49%) (46%) RNase HI TTHA1556 YP_144822.1 DNA/RNA hybrid Endo [ 18 ] (50%) RNase HII TTHA0198 YP_143464.1 DNA/RNA hybrid Endo [ 18 ] (38%) (40%) RNase P* TTHA0445 YP_143711.1 tRNA precursor Endo [ 19 ] (22%) (18%) Argonaute TTHB068 YP_145307.1 Phage RNA Endo [ 20 ]...”
  • “...identified 15 putative RNases genes (Table 1 ). BLAST searches showed that TTHA1140, TTHA1817, TTHA1139, TTHA0198, TTHA1556 and TTHA0445 shared a high level of sequence similarity with RNase J, RNase Y, PNPase, RNase HII (type II RNase H), RNase HI (type I RNase H) and RNase...”
• Junction ribonuclease: a ribonuclease HII orthologue from Thermus thermophilus HB8 prefers the RNA-DNA junction to the RNA/DNA heteroduplex
  Ohtani, The Biochemical journal 2008 (PubMed)
  • “...with RNase (ribonuclease) HII enzymes, the ORF TTHA0198 could not suppress the temperature-sensitive growth defect of an RNase-H-deficient Escherichia coli...”
  • “...RNA strand of an RNA/DNA heteroduplex, suggesting that the TTHA0198 exhibited no RNase H activity both in vivo and in vitro. When oligomeric RNA-DNA/DNAs were...”

AMK58_19355 ribonuclease HII from Azospirillum brasilense
55% identity, 83% coverage

• Transcriptome analysis of Azospirillum brasilense vegetative and cyst states reveals large-scale alterations in metabolic and replicative gene expression
  Malinich, Microbial genomics 2018
  • “...cells ( Fig. 3 ). Specifically, genes involved in DNA replication initiation and elongation (AMK58_19645, AMK58_19355, AMK58_17670, AMK58_12150, AMK58_06095 and AMK58_21855) were generally repressed, while many genes involved in DNA repair were elevated. This indicates that cysts prioritize the maintenance of DNA integrity over DNA replication,...”

alr4332 ribonuclease HII from Nostoc sp. PCC 7120
48% identity, 84% coverage

• "Life is short, and art is long": RNA degradation in cyanobacteria and model bacteria
  Zhang, mLife 2022
  • “.../ slr0080 alr0142 RNase HII Cleaving the RNA strand in RNADNA hybrids rnhB rnhB slr1130 alr4332 RNase HIII Cleaving the RNA strand in RNADNA hybrids / rnhC / / YbeY Cleaving ssRNAs, mainly participating in 16S rRNA maturation ybeY ybeY slr0053 all0271 RNase P Cleaving tRNA...”

Rru_A3209 Ribonuclease H from Rhodospirillum rubrum ATCC 11170
54% identity, 84% coverage

• Toxicogenomic response of Rhodospirillum rubrum S1H to the micropollutant triclosan
  Pycke, Applied and environmental microbiology 2010
  • “...and Rru_A3710), (deoxy)ribonucleases (Rru_A1700, Rru_A1769, Rru_A2767, Rru_A3209, and Rru_A3696), and helicases (Rru_A1915 and Rru_A2718). One gene of the...”

Q8Y7K4 ribonuclease H (EC 3.1.26.4) from Listeria monocytogenes EGD-e (see paper)
lmo1273 similar to ribonuclease H rnh from Listeria monocytogenes EGD-e
NP_464798 ribonuclease HII from Listeria monocytogenes EGD-e
50% identity, 69% coverage

• lmo1273, a novel gene involved in Listeria monocytogenes virulence
  Bigot, Microbiology (Reading, England) 2009 (PubMed)
  • “...lmo1273, a novel gene involved in Listeria monocytogenes virulence Armelle Bigot,1,2 Catherine Raynaud,1,2 Iharilalao Dubail,1,2 Marion Dupuis,1,2 Hamid Hossain,3 Torsten Hain,3 Trinad Chakraborty3 and Alain...”
  • “...two distal genes of the locus (lmo1272 and lmo1273), encoding proteins sharing significant similarities with the YlqF and RnhB proteins, respectively, of...”
• lmo1273, a novel gene involved in Listeria monocytogenes virulence.
  Bigot, Microbiology (Reading, England) 2009 (PubMed)
  • GeneRIF: lmo1273 controls the expression of multiple genes and is involved in the in vivo survival of L. monocytogenes.

DVU0834 ribonuclease HII from Desulfovibrio vulgaris Hildenborough
49% identity, 82% coverage

• Prediction and Characterization of Missing Proteomic Data in Desulfovibrio vulgaris
  Li, Comparative and functional genomics 2011
  • “...Transcriptional regulator, Fur family DVU0721 4.20 1085.90 x 7.19 513.28 x Sensory box histidine kinase DVU0834 5.73 2795.50 x 12.17 13860.00 x Ribonuclease HII (rnhB) DVU1075 13.63 30772.00 x 15.45 27576.00 x Ribonuclease P protein component (rnpA) Transport and binding proteins DVU0593 2.58 992.23 x 3.28...”

LLKF_1359 ribonuclease HII from Lactococcus lactis subsp. lactis KF147
48% identity, 72% coverage

• Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
  Dijkstra, PloS one 2016
  • “...negative 5.8 LLKF_1331 ymjE family 2 glycosyltransferase positive 2.3 LLKF_0093 ABC transporter permease negative 8.2 LLKF_1359 rnhB ribonuclease HII positive 0.9 LLKF_0165 ybhD GNAT family acetyltransferase positive 0.5 LLKF_1075 pp146 phage protein positive 2.7 LLKF_0310 hypothetical protein negative 0.6 LLKF_0981 hrcA Heat-inducible transcription repressor HrcA negative...”

Q9CG17 Ribonuclease HII from Lactococcus lactis subsp. lactis (strain IL1403)
48% identity, 72% coverage

• Nisin-based therapy: a realistic and eco-friendly biocontrol strategy to contrast Xylella fastidiosa subsp. pauca infections in planta
  Sabri, Frontiers in microbiology 2024
  • “...subunit beta 858.5 2+ 10.2 VDTIQETLRIQADGR Q9CFX8 Toxic anion resistance protein 1017.4 2+ 11.4 ELYSQEIELIAGIDEVGR Q9CG17 Ribonuclease HII m / z , mass-to-charge ratio; RT, retention time. 3.3 Determination of MLC of nisin During this investigation, the antimicrobial efficacy of nisin against Xf was systematically assessed...”
• Protein signatures as potential surrogate biomarkers for stratification and prediction of treatment response in chronic myeloid leukemia patients.
  Alaiya, International journal of oncology 2016
  • “...Ras-like protein F54C8.5 P34295 2 0.02474 1.4695 TKI-Y CMR-N Regulator of G protein signaling rgs-1 Q9CG17 a 1 0.00003 1.7092 CMR-Y TKI-N Ribonuclease HII (EC 3.1.26.4) (RNase HII) P 56566 b 2 0.00478 3.4601 TKI-N CMR-N S100 calcium-binding protein A3 (S-100E protein) P12346 b 2 0.00000...”

CP0654 ribonuclease HII from Chlamydophila pneumoniae AR39
Q9Z962 Ribonuclease HII from Chlamydia pneumoniae
46% identity, 86% coverage

• Biochemical characterization and functional complementation of ribonuclease HII and ribonuclease HIII from Chlamydophila pneumoniae AR39
  Liang, Microbiology (Reading, England) 2007 (PubMed)
  • “...Chlamydophila pneumoniae AR39 contains two different ORFs (CP0654 and CP0782) encoding ribonuclease H (RNase H) homologues, Cpn-RNase HII and Cpn-RNase HIII....”
  • “...al., 2000). Two prospective RNase HII and HIII genes, CP0654 and CP0782, have been isolated from C. pneumoniae AR39 and expressed in E. coli previously (Pei et...”
• Prediction of Chlamydia pneumoniae protein localization in host mitochondria and cytoplasm and possible involvements in lung cancer etiology: a computational approach
  Alshamsan, Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society 2017
  • “...ribonucleases such as ribonuclease III (Q9Z9C7), ribonuclease Z (Q9Z9F6), ribonuclease G (Q9Z6U9), and ribonuclease HII (Q9Z962) were analysed to localize in cytoplasm of host cell. Ribonuclease III (Q9Z9C7) is involved in processing mRNA, rRNA, and tRNA, whereas ribonuclease Z (Q9Z9F6) is involved in 3-tRNA processing activity....”

TRQ7_RS00060 ribonuclease HII from Thermotoga sp. RQ7
50% identity, 75% coverage

• Adapted laboratory evolution of Thermotoga sp. strain RQ7 under carbon starvation
  Gautam, BMC research notes 2022
  • “...CT Missense: L280F 1618115 TRQ7_RS08290 Sensor domain-containing diguanylate cyclase Transversion: TA Missense: V390E Others 12579 TRQ7_RS00060 Ribonuclease HII Transition: GA Missense: A237T 26360 TRQ7_RS00155 Galactose-1-phosphate uridylyltransferase Transition: CT Missense: P274L 721511 TRQ7_RS03655 UDP-N-acetylmuramoyl-tripeptideD-alanyl-D- alanine ligase Transition: GA Missense: D148N 731443 TRQ7_RS03700 NADH-quinone oxidoreductase subunit NuoE Transition:...”

Dgeo_1623 Ribonuclease H from Deinococcus geothermalis DSM 11300
49% identity, 82% coverage

• Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria
  Sghaier, BMC genomics 2008
  • “...Dgeo_0824 Krad_2554 Rxyl_0449 Exonuclease SbcD, putative 2.36 DR_1922 Dgeo_0823 Krad_2553 Rxyl_0448 Exonuclease SbcC 1.82 DR_1949 Dgeo_1623 Krad_1405 Rxyl_1394 Ribonuclease HII n.a. -1.642 DR_2074 Dgeo_1660 Krad_3154 Rxyl_1309 Putative 3-methyladenine DNA glycosylase 3.25 DR_2275 Dgeo_1890 Krad_2942 Rxyl_2021 Excinuclease ABC, subunit B* n.a. -1.767 DR_2285 Dgeo_0019 Krad_0599 Rxyl_2229 A/G-specific...”

DR1949, DR_1949 ribonuclease HII from Deinococcus radiodurans R1
48% identity, 86% coverage

• A Mur regulator protein in the extremophilic bacterium Deinococcus radiodurans
  Ul, PloS one 2014
  • “...consequently results in the inhibition of cell growth. Five ribonucleases ( dr0020 , dr0859 , dr1949 , dr2374 and drb0107 ) were induced at least two-fold in the Mt-0865 mutant (Table S1 in File S1 ). Ribonucleases in prokaryotic toxin-antitoxin systems are proposed to function as...”
• Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria
  Sghaier, BMC genomics 2008
  • “...DR_1921 Dgeo_0824 Krad_2554 Rxyl_0449 Exonuclease SbcD, putative 2.36 DR_1922 Dgeo_0823 Krad_2553 Rxyl_0448 Exonuclease SbcC 1.82 DR_1949 Dgeo_1623 Krad_1405 Rxyl_1394 Ribonuclease HII n.a. -1.642 DR_2074 Dgeo_1660 Krad_3154 Rxyl_1309 Putative 3-methyladenine DNA glycosylase 3.25 DR_2275 Dgeo_1890 Krad_2942 Rxyl_2021 Excinuclease ABC, subunit B* n.a. -1.767 DR_2285 Dgeo_0019 Krad_0599 Rxyl_2229...”

BB0046 ribonuclease H (rnhB) from Borrelia burgdorferi B31
41% identity, 88% coverage

• Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi
  Petroni, Nature communications 2023
  • “...orthologs of RNase Y ( bb0504 ), RNase III ( bb0750 ), RNase HII ( bb0046 ), RNase P ( bb0441 ), RNase Z (tRNA 3 endonuclease; bb0755 ), RNase M5 (5S maturation nuclease; bb0626 ), YbeY ( bb0060 ) and exoribonuclease orthologs of Oligoribonuclease (...”
• Gene Regulation and Transcriptomics
  Samuels, Current issues in molecular biology 2021
  • “...(BB0441), RNase Z (BB0755), YbeY (BB0060), RNase Y (BB0504), RNase M5 (BB0626), and RNase HII (BB0046) and the exoribonuclease PNPase (BB0805) ( Fraser et al., 1997 ; Archambault et al., 2013 ; Anacker et al., 2018 ; Drecktrah et al., 2020 ). Lyme disease spirochetes lack...”
• Transcript decay mediated by RNase III in Borrelia burgdorferi
  Snow, Biochemical and biophysical research communications 2020
  • “...Y (BB0504), RNase III (BB0750), RNase Z (BB0755), RNase M5 (BB0626), PNPase (BB0805), RNase HII (BB0046), RNase P (BB0441), YbeY (BB0060) and Oligoribonuclease (BB0619) [ 13 ]. Of these, only two loci, bb0626 and bb0046 , were disrupted by signature-tagged transposons in the construction of a...”

slr1130 ribonuclease HII from Synechocystis sp. PCC 6803
45% identity, 88% coverage

• "Life is short, and art is long": RNA degradation in cyanobacteria and model bacteria
  Zhang, mLife 2022
  • “...rnhA / slr0080 alr0142 RNase HII Cleaving the RNA strand in RNADNA hybrids rnhB rnhB slr1130 alr4332 RNase HIII Cleaving the RNA strand in RNADNA hybrids / rnhC / / YbeY Cleaving ssRNAs, mainly participating in 16S rRNA maturation ybeY ybeY slr0053 all0271 RNase P Cleaving...”
• Transcriptome-wide in vivo mapping of cleavage sites for the compact cyanobacterial ribonuclease E reveals insights into its function and substrate recognition
  Hoffmann, Nucleic acids research 2021
  • “...by rne , is essential ( 2022 ) and forms an operon with rnhB ( slr1130 ) encoding RNase HII ( 46 ), which is a widely conserved arrangement in cyanobacteria ( Supplementary Figure S2 ). Analyses in E. coli , Salmonella , Rhodobacter sphaeroides (...”
• Impact of RNase E and RNase J on Global mRNA Metabolism in the Cyanobacterium Synechocystis PCC6803
  Cavaiuolo, Frontiers in microbiology 2020
  • “...mutants, with the exception of an increase of the RNA-DNA hybrid specific RNase HII ( slr1130 ) in the rne mutant. However, since rne is co-transcribed with slr1130 the increase in coverage observed over slr1130 might simply be due to read-through transcription from the upstream spc...”

Krad_1405 ribonuclease HII from Kineococcus radiotolerans SRS30216 = ATCC BAA-149
43% identity, 68% coverage

• Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria
  Sghaier, BMC genomics 2008
  • “...Krad_2554 Rxyl_0449 Exonuclease SbcD, putative 2.36 DR_1922 Dgeo_0823 Krad_2553 Rxyl_0448 Exonuclease SbcC 1.82 DR_1949 Dgeo_1623 Krad_1405 Rxyl_1394 Ribonuclease HII n.a. -1.642 DR_2074 Dgeo_1660 Krad_3154 Rxyl_1309 Putative 3-methyladenine DNA glycosylase 3.25 DR_2275 Dgeo_1890 Krad_2942 Rxyl_2021 Excinuclease ABC, subunit B* n.a. -1.767 DR_2285 Dgeo_0019 Krad_0599 Rxyl_2229 A/G-specific adenine...”

SCO5812 ribonuclease HII from Streptomyces coelicolor A3(2)
44% identity, 76% coverage

• Manipulating and understanding antibiotic production in Streptomyces coelicolor A3(2) with decoy oligonucleotides
  McArthur, Proceedings of the National Academy of Sciences of the United States of America 2008
  • “...identified regulatory elements occurred upstream of gene SCO5812, deletion of which reduced actinorhodin production, confirming that experimental analysis of...”
  • “...BLAST searches with all five decoy sequences identified one such gene. SCO5812 contained strong matches to A24.1 (a run of 10 of 14 bp) and A24.3 (a run of 11...”

LA_2386 ribonuclease H II from Leptospira interrogans serovar lai str. 56601
38% identity, 78% coverage

• Biocomputational Identification of sRNAs in Leptospira interrogans Serovar Lai
  Tan, Indian journal of microbiology 2023
  • “...iron stress, serum stress, 37 and 39 C Antisense LA_2386 N/A Mid-log, stationery, serum stress, 37 and 39 C Intergenic tRNA Mid-log, stationery, iron stress,...”

Francci3_3588 Ribonuclease H from Frankia sp. CcI3
46% identity, 75% coverage

• Transcriptomes of Frankia sp. strain CcI3 in growth transitions
  Bickhart, BMC microbiology 2011
  • “...hypothetical protein Francci3_0159 1184 sigma 54 modulation protein Francci3_0764 3004 cold-shock DNA-binding Francci3_4469 1458 ribonucleaseHII Francci3_3588 1161 cold-shock DNA-binding Francci3_4469 2949 putative DNA-binding Francci3_1949 1392 GDP-mannose 4,6-dehydratase Francci3_1307 1134 Alcohol dehydrogenase Francci3_2945 2916 LuxR family regulator Francci3_0765 1361 hypothetical protein Francci3_4023 1122 putative Lsr2-like protein Francci3_3498...”

Cj0010c ribonuclease HII from Campylobacter jejuni subsp. jejuni NCTC 11168
35% identity, 92% coverage

• RNase III-mediated processing of a trans-acting bacterial sRNA and its cis-encoded antagonist
  Svensson, eLife 2021
  • “...(Cj0631c); pnp PNPase (Cj1253); rbn RNase BN (Cj1212c); rnhA RNase HI (Cj1636c); rnhB RNase HII (Cj0010c); rppH RNA 5' pyrophosphohydrolase (Cj0581); ybeY endoribonuclease YbeY (Cj0121). ( B ) RNase III affects PtmG expression via CJnc190 processing. Related to main Figure 3B . PtmG-3FLAG protein and transcript...”

HP1323 ribonuclease HII (rnhB) from Helicobacter pylori 26695
32% identity, 89% coverage

• The Role of a Dipeptide Transporter in the Virulence of Human Pathogen, Helicobacter pylori
  Xu, Frontiers in microbiology 2021
  • “...Predicted gene 1.4378 HP1286 Predicted gene 1.6787 HP1288 Predicted gene 2.66 HP1289 Predicted gene 1.3261 HP1323 rnhB 2.4111 HP1324 Predicted gene 1.2158 HP1325 fumC 1.2411 HP1326 Predicted gene 1.9589 HP1327 Predicted gene 2.4519 HP1333 Predicted gene 1.1022 HP1334 Predicted gene 1.3602 HP1338 nikR 1.3032 HP1372 MreC...”
• Comparative genomic analysis of East Asian and non-Asian Helicobacter pylori strains identifies rapidly evolving genes
  Duncan, PloS one 2013
  • “...replication, recombination, and repair HP0661 ribonuclease H (RnhA) DNA metabolism DNA replication, recombination, and repair HP1323 ribonuclease HII (RnhB) DNA metabolism Restriction/modification HP0463 type I restriction enzyme M protein/HsdM DNA metabolism Restriction/modification HP0850 type I restriction enzyme M protein (HsdM) DNA metabolism Restriction/modification HP1354 type IIG...”
  • “...0.101 0.229 ribonuclease H (rnhA) HP0661 79.16 0.020 0.020 0.149 0.076 0.206 ribonuclease HII (rnhB) HP1323 87.90 0.035 0.042 0.165 0.173 0.222 type I restriction enzyme M protein (hsdM) HP0463 89.23 0.025 0.037 0.091 0.147 0.250 type I restriction enzyme M protein (hsdM) HP0850 87.75 0.026...”
• Metabolism and genetics of Helicobacter pylori: the genome era
  Marais, Microbiology and molecular biology reviews : MMBR 1999
  • “...to uvrD, coding for DNA helicase II; HP0661 and HP1323 to rnhA and rnhB, whose products are RNase H and RNase HII, respectively; HP0116, HP0440, and ORF02428...”

HMPREF0421_21216 ribonuclease HII from Gardnerella vaginalis ATCC 14019
32% identity, 81% coverage

• Transcriptomic and Proteomic Analysis of Gardnerella vaginalis Responding to Acidic pH and Hydrogen Peroxide Stress
  Zhang, Microorganisms 2023
  • “...Transferring glycosyl groups HMPREF0421_21002 2.90 4.39 10 79 1.09 10 77 Cell division protein FtsK HMPREF0421_21216 2.45 1.91 10 119 9.13 10 118 Ribonuclease HII HMPREF0421_20331 2.40 4.83 10 258 7.35 10 57 Serine/threonine protein kinase HMPREF0421_20297 2.33 8.19 10 91 2.49 10 89 Shikimate kinase...”

BL_RS05100 ribonuclease HII from Bifidobacterium longum
33% identity, 64% coverage

• Comparative Genomics Analyses Reveal the Differences between B. longum subsp. infantis and B. longum subsp. longum in Carbohydrate Utilisation, CRISPR-Cas Systems and Bacteriocin Operons
  Li, Microorganisms 2021
  • “...cluster consisted of six genes ( Table 3 ), among which the genes of BL_RS05095, BL_RS05100 and BL_RS05105 were found in all the strains. Genes araA , araB and araD were present in all B. longum subsp. longum (except CECT7347), but most B. longum subsp. infantis...”
  • “...4-epimerase BL_RS05090 araD WP_007051390.1 FGGY-family carbohydrate kinase BL_RS05095 - WP_008782880.1 LacI family DNA-binding transcriptional regulator BL_RS05100 - WP_011068401.1 ribonuclease HII BL_RS05105 lepB WP_010081174.1 signal peptidase I microorganisms-09-01713-t004_Table 4 Table 4 Class and sources of predicted bacteriocins in B. longum . Bacteriocin B. longum subsp. longum B....”

M164_0197 ribonuclease HII from Sulfolobus islandicus M.16.4
35% identity, 84% coverage

• The essential genome of the crenarchaeal model Sulfolobus islandicus
  Zhang, Nature communications 2018
  • “...i.e., lig ( M164_1953 ), priL ( M164_1568 ), priX ( M164_1652 ), rnhII ( M164_0197 ), and tfs2 ( M164_1524 ), were called essential via EI but not log 2 FC, while thrS1 ( M164_0290 ) was called essential based on log 2 FC but...”

Q8U036 ribonuclease H (EC 3.1.26.4) from Pyrococcus furiosus (see paper)
WP_011012922 ribonuclease HII from Pyrococcus furiosus DSM 3638
PF1781 RNaseH II from Pyrococcus furiosus DSM 3638
34% identity, 81% coverage

• Characterization of RNase HII substrate recognition using RNase HII-argonaute chimaeric enzymes from Pyrococcus furiosus.
  Kitamura, The Biochemical journal 2010 (PubMed)
  • GeneRIF: By using Pf-RNase HII-Pf-Ago(argonaute) chimaeric mutants, studies show that residues Asp110, Arg113 and Phe114 are responsible for the dsRNA digestion activity of Pf-RNase HII.
• Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)
  Hura, Nature methods 2009
  • “...generates ATP, CoASH and acetate and was purified from Pfu biomass as a heteromeric complex (PF1781 and PF1540) with an 2 2 stoichiometry 28 . How the trimeric solution structure of PF1787 acts in this ACS reaction can now be experimentally investigated. The JCSG protein set...”

H0H31_RS04250 ribonuclease HII from Micrococcus luteus
38% identity, 71% coverage

• Adaptive laboratory evolution of Micrococcus luteus and identification of genes associated with radioresistance through genome-wide association study
  Tang, Scientific reports 2025
  • “...selected for functional validation. Inactivating 6 of these genes, including H0H31_RS03855 (SMC family ATPase, SbcC), H0H31_RS04250 (ribonuclease HII), H0H31_RS04570 (endonuclease VIII), H0H31_RS07595 (bifunctional 3'-5' exonuclease/DNA polymerase I), H0H31_RS00170 (serine/threonine phosphatase PPP), and H0H31_RS05860 (CBS-domain-containing protein), significantly increased sensitivity to gamma radiation, underscoring their importance in radioresistance....”

Q8WR57 ribonuclease H (EC 3.1.26.4) from Leishmania donovani (see paper)
38% identity, 21% coverage

Q8WSZ0 ribonuclease H (EC 3.1.26.4) from Leishmania major (see paper)
38% identity, 21% coverage

TERMP_00671, TERMP_RS03345 ribonuclease HII from Thermococcus barophilus MP
33% identity, 81% coverage

• Processing of matched and mismatched rNMPs in DNA by archaeal ribonucleotide excision repair
  Reveil, iScience 2023
  • “...517 (TERMP_RS02570) UBO Culture collection UBOCC-M-3300 Tba polB (TERMP_RS08040) UBO Culture collection UBOCC-M-3302 Tba rnhB (TERMP_RS03345) UBO Culture collection UBOCC-M-3303 Tba polB ::Pab polB (PAB_RS09320) This paper UBOCC-M-3435 Tba rnhB ::Pab rnhB (PAB_RS02765) This paper UBOCC-M-3436 Oligonucleotides Oligonucleotides used for invitro study, see TableS3 Eurogentec Primers...”
• Development of an Effective 6-Methylpurine Counterselection Marker for Genetic Manipulation in Thermococcus barophilus
  Birien, Genes 2018
  • “...barophilus TERMP_00517 , T. barophilus TERMP_00517, TERMP_01623 ( polB ) and T. barophilus TERMP_00517 , TERMP_00671 ( rnhB ). The strains were cultivated at 85 C and 0.1 MPa in TRM medium containing different concentration of 6-MP: T. barophilus TERMP_00517 , rnhB ( ), T. barophilus...”
  • “...study UBOCC-M-3302 TB TERMP_00517 , TERMP_01623 T. barophilus MP This study UBOCC-M-3303 TB TERMP_00517 , TERMP_00671 T. barophilus MP This study genes-09-00077-t002_Table 2 Table 2 List of primers used in this study. Primers Used for Amplification of Flanking Regions of Targeted Gene Sequence (5-3) Tm (C)...”

PAB0352 ribonuclease HII from Pyrococcus abyssi GE5
Q9V1A9 Ribonuclease HII from Pyrococcus abyssi (strain GE5 / Orsay)
PAB_RS02765 ribonuclease HII from Pyrococcus abyssi GE5
33% identity, 81% coverage

• Structure-specific nuclease activities of Pyrococcus abyssi RNase HII
  Le, Journal of bacteriology 2010
  • “...of PabRNase HII. The gene encoding PabRNase HII (PAB0352) was cloned into the pQE-80L expression vector (Qiagen). PabRNase HII was overexpressed in Escherichia...”
• An extended network of genomic maintenance in the archaeon Pyrococcus abyssi highlights unexpected associations between eucaryotic homologs
  Pluchon, PloS one 2013
  • “...24 ] Fen1 ( Q9V0P9 ) Replication/Repair HIS/N-ter FL [ 24 ] Ribonuclease HII ( Q9V1A9 ) Replication/Repair HIS/N-ter FL [ 74 ] DNA2 homolog ( Q9V2G5 ) Helicase/nuclease of unknown function HIS/N-ter C-ter domain 1070K-1308 [ 18 ] Replication Protein A ( Q9V1Z1, Q9V1Y9, Q9V1Z0...”
• Processing of matched and mismatched rNMPs in DNA by archaeal ribonucleotide excision repair
  Reveil, iScience 2023
  • “...data Tba polB ::Pab polB (PAB_RS09320) strain UBO Culture collection UBOCC-M-3435 Tba rnhB ::Pab rnhB (PAB_RS02765) strain UBO Culture collection UBOCC-M-3436 Tba polB ::Pab polB Sequencing data This paper NCBI SRA: SRR21319269 Bioproject:PRJNA875043 Biosample: SAMN30594391 https://www.ncbi.nlm.nih.gov/bioproject/PRJNA875043 Tba rnhB ::Pab rnhB Sequencing data This paper NCBI SRA:...”
  • “...Culture collection UBOCC-M-3303 Tba polB ::Pab polB (PAB_RS09320) This paper UBOCC-M-3435 Tba rnhB ::Pab rnhB (PAB_RS02765) This paper UBOCC-M-3436 Oligonucleotides Oligonucleotides used for invitro study, see TableS3 Eurogentec Primers used for genetic construction, see TableS4 Eurogentec Primers used for qPCR, see TableS5 Eurogentec Recombinant DNA Plasmid:...”

WP_010978497 ribonuclease HII from Sulfurisphaera tokodaii
ST0519 208aa long hypothetical ribonuclease HII from Sulfolobus tokodaii str. 7
33% identity, 88% coverage

• Characterization of a new RNase HII and its essential amino acid residues in the archaeon Sulfolobus tokodaii reveals a regulatory C-terminus.
  Zhan, Biochemistry. Biokhimiia 2010 (PubMed)
  • GeneRIF: C-terminal alpha-helix is involved in the Mn2+-dependent substrate cleavage activity through stabilization of a flexible loop structure.
• Characterization of a new RNase HII and its essential amino acid residues in the archaeon Sulfolobus tokodaii reveals a regulatory C-terminus
  Zhan, Biochemistry. Biokhimiia 2010 (PubMed)
  • “...unknown. In the present study, we have characterized the ST0519 RNase HII from S. tokodaii as a new form. The enzyme utilized hybrid RNA/DNA as a substrate...”
  • “...in the S. tokodaii RNase HII. One mutant, ST0519 (residues 1195), retained only partial activity, while ST0519 (residues 1196) completely lost its activity....”

WP_019177553 ribonuclease HII from Methanomassiliicoccus luminyensis B10
35% identity, 86% coverage

• Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine
  Borrel, BMC genomics 2014
  • “...large subunit AGI85559 AGN26596 WP_019176873 RFC small subunit AGI85778 AGN26166 WP_019177244 RNaseH II AGI86158 AGN25790 WP_019177553 TopoVI subunit A AGI85998 AGN26743 WP_019177592 X TopoVI subunit B AGI85997 AGN26742 WP_019177591 X Topo IB X X X X X X SSB X X X X RPA2 AGI84916 AGN25568...”

O59351 ribonuclease H (EC 3.1.26.4) from Pyrococcus horikoshii OT3 (see paper)
30% identity, 83% coverage

O74035 ribonuclease H (EC 3.1.26.4) from Thermococcus kodakarensis (see 2 papers)
WP_011249756 ribonuclease HII from Thermococcus kodakarensis
TK0805 ribonuclease HII from Thermococcus kodakaraensis KOD1
35% identity, 68% coverage

• Osmolyte effect on the stability and folding of a hyperthermophilic protein.
  Mukaiyama, Proteins 2008 (PubMed)
  • GeneRIF: the conformational stability of Tk-RNase HII in the presence of 0.5M TMAO was higher than that in the absence of TMAO at all examined temperatures.
• Hydrophobic effect on the stability and folding of a hyperthermophilic protein.
  Dong, Journal of molecular biology 2008 (PubMed)
  • GeneRIF: These results indicate that the buried hydrophobic residues strongly contribute to the kinetic robustness of Tk-RNase HII.
• Effect of the disease-causing mutations identified in human ribonuclease (RNase) H2 on the activities and stabilities of yeast RNase H2 and archaeal RNase HII.
  Rohman, The FEBS journal 2008
  • GeneRIF: Gly42 is conserved as Gly10 in Thermococcus kodakareansis RNase HII. 4 mutant proteins, Tk-G10S, Tk-G10A, Tk-G10L, and Tk-G10P, were constructed. All mutant proteins were less stable than the wild-type protein by 2.9-7.6 degrees C in T(m).
• Capillary Electrophoresis-Based Functional Genomics Screening to Discover Novel Archaeal DNA Modifying Enzymes
  Zatopek, Applied and environmental microbiology 2022
  • “...H4 lysate contains RNase H2 activity and its sequence (starting at position 702,722) overlaps with TK0805, the gene encoding RNaseH2 (703,189 to 703,875) ( Fig. 4A and C ). We then screened for the T. kodakarensis DNA ligase (TK2140), an important enzyme in DNA replication and...”
• The GAN Exonuclease or the Flap Endonuclease Fen1 and RNase HII Are Necessary for Viability of Thermococcus kodakarensis
  Burkhart, Journal of bacteriology 2017
  • “...for T. kodakarensis (25-29) to generate strains with TK0805 (RNase HII), TK1252 (GAN), or TK1281 (Fen1) deleted. The results confirm that neither GAN, Fen1,...”
  • “...readily generated strains with TK1281 (Fen1), TK1252 (GAN), or TK0805 (RNase HII) deleted (see Table S1 in the supplemental material), and these strains grew at...”
• Genome Replication in Thermococcus kodakarensis Independent of Cdc6 and an Origin of Replication
  Gehring, Frontiers in microbiology 2017
  • “...1996 ; Maduike et al., 2014 ). The T. kodakarensis strains investigated here all express TK0805, the gene that encodes RNase HII (Heider et al., 2017 ) and thus R-loop accumulation is unlikely to be responsible for origin-independent genome replication in T. kodakarensis . Employing RDR...”

DDB_G0277705 hypothetical protein from Dictyostelium discoideum AX4
32% identity, 28% coverage

• The amoebal MAP kinase response to Legionella pneumophila is regulated by DupA
  Li, Cell host & microbe 2009
  • “...0.86 between_DDB_G0272334_and_DDB_G0272336 Ribonuclease, putative 0.49 0.45 0.81 Enhanced Expression DDB_G0275469 Endonuclease V 5.97 12.77 1.34 DDB_G0277705 Ribonuclease HII 2.89 5.03 1.16 DDB_G0269630 IliI, IliK; TatD related Dnases 3.56.3 12.013.7 1.251.96 DDB_G0289921 XRN 5-3exonuclease N-terminus 2.69 5.19 1.09 DDB_G0284255 Zinc finger, C2H2 type, nucleic acid binding 4.37...”

Q9YET5 ribonuclease H (EC 3.1.26.4) from Aeropyrum pernix (see paper)
33% identity, 81% coverage

RNH2_ARCFU / O29634 Ribonuclease HII; RNase HII; EC 3.1.26.4 from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16) (see paper)
33% identity, 76% coverage

• function: Endonuclease that specifically degrades the RNA of RNA-DNA hybrids.
  catalytic activity: Endonucleolytic cleavage to 5'-phosphomonoester.
  cofactor: Mn(2+) Mg(2+) (Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding.)

AT2G25100 ribonuclease HII family protein from Arabidopsis thaliana
NP_565584 Polynucleotidyl transferase, ribonuclease H-like superfamily protein from Arabidopsis thaliana
30% identity, 46% coverage

• Bridging Plant and Human Radiation Response and DNA Repair through an In Silico Approach
  Nikitaki, Cancers 2017
  • “...GINS4 SLD5 GTF2H4 AT4G17020 ALKBH3 ALKBH2 NSMCE2 MMS21 UNG ATUNG DCLRE1A SNM1 XRCC1 XRCC1 RNASEH2A AT2G25100 APTX BHLH140 XRCC5 KU80 XRCC2 XRCC2 TOP3A TOP3A ALKBH1 AT1G11780 NSMCE1 emb1379 XRCC4 XRCC4 RECQL RECQL5 WRN BLM RECQL4A MED34 RAD23A RAD23B RAD23A RAD23B RAD23C RAD23D RPA1 RPA1A RPA1B RPA1C...”
  • “...BLM RECQL4A PARP2 PARP1 PARP2 NTHL1 NTH2 NTH1 RAD23B RAD23A RAD23A RAD23B RAD23C RAD23D RNASEH2A AT2G25100 RAD51 DMC1 RAD51 XRCC6 KU70 UNG ATUNG ERCC2 UVH6 MLH1 MLH1 FIGNL1 AT3G27120 XRCC5 KU80 FEN1 FEN1 GTF2H2 GTF2H2C ATGTF2H2 PCNA PCNA PCNA2 RAD54L RAD54B CHR25 XRCC1 XRCC1 MRE11A MRE11...”
• Crosstalk between Photoreceptor and Sugar Signaling Modulates Floral Signal Transduction
  Matsoukas, Frontiers in physiology 2017
  • “...microRNA156a miR156a Ath-MIR156a; gene family: MIPF0000008; Accession: MI0000178 Next upstream gene: At2g25090; next downstream gene: At2g25100 Arabidopsis miR156 is an ambient temperature-responsive miRNA. It plays an important role in regulating floral signal transduction. Telfer et al., 1997 ; Telfer and Poethig, 1998 ; Aukerman and Sakai,...”
• Erratum
  , Genes & development 2002
• MicroRNAs in plants
  Reinhart, Genes & development 2002
  • “...10 Distance to nearest gene 5 82 2 3.2 kb downstream of At2g25100 (s) 5 80 4 0.36 kb upstream of At4g30970 (a) MIR156c 5 83 4 3.2 kb downstream of At4g31875 (s)...”
  • “...4 5 3 5 3 2 3 4 3.2 kb downstream of At2g25100 (s) 0.36 kb upstream of At4g30970 (a) 3.2 kb downstream of At4g31875 (s) 2.6 kb upstream of At5g10940 (s) 1.6 kb...”
• Arabidopsis thaliana RNase H2 deficiency counteracts the needs for the WEE1 checkpoint kinase but triggers genome instability.
  Kalhorzadeh, The Plant cell 2014
  • GeneRIF: mutant alleles of the genes encoding subunits of the ribonuclease H2 (RNase H2) complex, known for its role in removing ribonucleotides from DNA-RNA duplexes, were identified as suppressor mutants of WEE1 knockout plants.

MMP1374 Ribonuclease HII from Methanococcus maripaludis S2
27% identity, 77% coverage

• Evolution of the archaeal and mammalian information processing systems: towards an archaeal model for human disease
  Lyu, Cellular and molecular life sciences : CMLS 2017
  • “...RNASEH1 78 97 2E-50 26 3E-12 26 4CHT_A AAV38476.1 MMP1374 rnhB - RNASEH2A 90 2E-30 33 CAG33122.1 Endonuclease MMP1313 fen1 - FEN1 95 8E-55 35 NP_004102.1 Ligase...”
• Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis
  Hendrickson, Journal of bacteriology 2004
  • “...using flap endonuclease (Fen1/Rad2 and Mmp1313) and RNase HII (Mmp1374) (58, 89). M. maripaludis is unique among Archaea in that it also encodes a homolog of...”

HVO_1978 ribonuclease H II from Haloferax volcanii DS2
34% identity, 72% coverage

• Haloferax volcanii-a model archaeon for studying DNA replication and repair
  Pérez-Arnaiz, Open biology 2020
  • “...HVO_0732; RNase H-A, HVO_2438; RNase H-C, HVO_A0463) and a single type 2 protein (RNase H-B HVO_1978). RNase H-D (HVO_A0277) does not fit clearly into either group and its function remains unknown. Type 2 RNase H-B is non-essential in H. volcanii . It encodes a C-terminal PIP...”
• The complete genome sequence of Haloferax volcanii DS2, a model archaeon
  Hartman, PloS one 2010
  • “...14413931443312 0187 type II, B subunit (gyrase) rnhA HVO_2438 Chromosome 654302654895 0328 type I rnhB HVO_1978 Chromosome 18242401824887 0164 type II rnhC HVO_A0463 pHV4 469311469961 0328 type I rnhD HVO_A0277 pHV4 284563285140 0328 type I - pseudogene ginS HVO_2698 Chromosome 25451692546164 1711 dna2 HVO_2767 Chromosome 26072742609928...”

NP_956520 ribonuclease H2 subunit A from Danio rerio
29% identity, 61% coverage

• Second generation lethality in RNAseH2a knockout zebrafish.
  Thomas, Nucleic acids research 2024
  • GeneRIF: Second generation lethality in RNAseH2a knockout zebrafish.

EHI_134360 ribonuclease H2 subunit A, putative from Entamoeba histolytica HM-1:IMSS
28% identity, 38% coverage

• Exploring the Interactome of the Queuine Salvage Protein DUF2419 in <i>Entamoeba histolytica</i>
  Ye, Cells 2024
  • “...pseudouridine synthase and archaeosine transglycosylase domain RNA-binding motif containing protein (EHI_016460), EhDUF2419 and an endonuclease (EHI_134360) and so on ( Table S3 ). Notably, the pseudouridine synthase and archaeosine transglycosylase domain RNA-binding motif-containing protein (EHI_016460) is one of the proteins identified in the EhDUF2419 interactome (...”

RNH2A_MOUSE / Q9CWY8 Ribonuclease H2 subunit A; RNase H2 subunit A; Ribonuclease HI large subunit; RNase HI large subunit; Ribonuclease HI subunit A; EC 3.1.26.4 from Mus musculus (Mouse) (see paper)
Q9CWY8 ribonuclease H (EC 3.1.26.4) from Mus musculus (see paper)
NP_081463 ribonuclease H2 subunit A isoform 1 from Mus musculus
30% identity, 58% coverage

• function: Catalytic subunit of RNase HII, an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. Participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication. Mediates the excision of single ribonucleotides from DNA:RNA duplexes.
  catalytic activity: Endonucleolytic cleavage to 5'-phosphomonoester.
  cofactor: Mn(2+) Mg(2+) (Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding.)
  subunit: The RNase H2 complex is a heterotrimer composed of the catalytic subunit RNASEH2A and the non-catalytic subunits RNASEH2B and RNASEH2C.
• RNaseH2A downregulation drives inflammatory gene expression via genomic DNA fragmentation in senescent and cancer cells.
  Sugawara, Communications biology 2022
  • GeneRIF: RNaseH2A downregulation drives inflammatory gene expression via genomic DNA fragmentation in senescent and cancer cells.
• Two RNase H2 Mutants with Differential rNMP Processing Activity Reveal a Threshold of Ribonucleotide Tolerance for Embryonic Development.
  Uehara, Cell reports 2018
  • GeneRIF: An RNase H2 mutant lacking ribonucleotide excision repair activity but supporting R-loop removal revealed that ribonucleotides in DNA initiate p53-dependent DNA damage response and early embryonic arrest in mouse.
• RNase H2 catalytic core Aicardi-Goutières syndrome-related mutant invokes cGAS-STING innate immune-sensing pathway in mice.
  Pokatayev, The Journal of experimental medicine 2016
  • GeneRIF: the G37S mutation of RNaseH2 led to increased expression of interferon-stimulated genes dependent on the cGAS-STING signaling pathway.
• Aicardi-Goutières syndrome: clues from the RNase H2 knock-out mouse.
  Rabe, Journal of molecular medicine (Berlin, Germany) 2013 (PubMed)
  • GeneRIF: Recent evidence gathered from ribonuclease H2 knock-out mice provides insight into the molecular mechanisms underlying Aicardi-Goutieres syndrome development and a potential role of DNA damage as a trigger of autoimmunity is discussed. [review]
• Functional consequences of the RNase H2A subunit mutations that cause Aicardi-Goutieres syndrome.
  Coffin, The Journal of biological chemistry 2011
  • GeneRIF: analysis of the RNase H2A subunit mutations that cause Aicardi-Goutieres syndrome
• The structure of the mammalian RNase H2 complex provides insight into RNA.NA hybrid processing to prevent immune dysfunction.
  Shaban, The Journal of biological chemistry 2010
  • GeneRIF: Data show that the interwoven architecture of RNase H2B and RNase H2C that interface with RNase H2A in a complex ideally suited for nucleic acid binding and hydrolysis coupled to protein-protein interaction motifs.

E8T217 ribonuclease H (EC 3.1.26.4) from Thermovibrio ammonificans (see paper)
28% identity, 64% coverage

RNH2A_BOVIN / Q2TBT5 Ribonuclease H2 subunit A; RNase H2 subunit A; Ribonuclease HI large subunit; RNase HI large subunit; Ribonuclease HI subunit A; EC 3.1.26.4 from Bos taurus (Bovine) (see paper)
29% identity, 59% coverage

• function: Catalytic subunit of RNase HII, an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. Participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication. Mediates the excision of single ribonucleotides from DNA:RNA duplexes.
  catalytic activity: Endonucleolytic cleavage to 5'-phosphomonoester.
  cofactor: Mn(2+) Mg(2+) (Manganese or magnesium. Binds 1 divalent metal ion per monomer in the absence of substrate. May bind a second metal ion after substrate binding.)
  subunit: The RNase H2 complex is a heterotrimer composed of the catalytic subunit RNASEH2A and the non-catalytic subunits RNASEH2B and RNASEH2C.

4py5A / E8T217 Thermovibrio ammonificans rnase h3 in complex with 19-mer RNA/DNA (see paper)
28% identity, 65% coverage

• Ligands: rna; dna; magnesium ion (4py5A)

New Search

Statistics

How It Works

PaperBLAST builds a database of protein sequences that are linked to scientific articles. These links come from automated text searches against the articles in EuropePMC and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot, BRENDA, CAZy (as made available by dbCAN), BioLiP, CharProtDB, MetaCyc, EcoCyc, TCDB, REBASE, the Fitness Browser, and a subset of the European Nucleotide Archive with the /experiment tag. Given this database and a protein sequence query, PaperBLAST uses protein-protein BLAST to find similar sequences with E < 0.001.

To build the database, we query EuropePMC with locus tags, with RefSeq protein identifiers, and with UniProt accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use queries of the form "locus_tag AND genus_name" to try to ensure that the paper is actually discussing that gene. Because EuropePMC indexes most recent biomedical papers, even if they are not open access, some of the links may be to papers that you cannot read or that our computers cannot read. We query each of these identifiers that appears in the open access part of EuropePMC, as well as every locus tag that appears in the 500 most-referenced genomes, so that a gene may appear in the PaperBLAST results even though none of the papers that mention it are open access. We also incorporate text-mined links from EuropePMC that link open access articles to UniProt or RefSeq identifiers. (This yields some additional links because EuropePMC uses different heuristics for their text mining than we do.)

For every article that mentions a locus tag, a RefSeq protein identifier, or a UniProt accession, we try to select one or two snippets of text that refer to the protein. If we cannot get access to the full text, we try to select a snippet from the abstract, but unfortunately, unique identifiers such as locus tags are rarely provided in abstracts.

PaperBLAST also incorporates manually-curated protein functions:

• Proteins from NCBI's RefSeq are included if a GeneRIF entry links the gene to an article in PubMed^®. GeneRIF also provides a short summary of the article's claim about the protein, which is shown instead of a snippet.
• Proteins from Swiss-Prot (the curated part of UniProt) are included if the curators identified experimental evidence for the protein's function (evidence code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that describe the protein's function are shown (with bold headings).
• Proteins from BRENDA, a curated database of enzymes, are included if they are linked to a paper in PubMed and their full sequence is known.
• Every protein from the non-redundant subset of BioLiP, a database of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself does not include descriptions of the proteins, those are taken from the Protein Data Bank. Descriptions from PDB rely on the original submitter of the structure and cannot be updated by others, so they may be less reliable. (For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every ligand is represented among a group of structures with similar sequences, but for PaperBLAST, we use the non-redundant set provided by BioLiP.)
• Every protein from EcoCyc, a curated database of the proteins in Escherichia coli K-12, is included, regardless of whether they are characterized or not.
• Proteins from the MetaCyc metabolic pathway database are included if they are linked to a paper in PubMed and their full sequence is known.
• Proteins from the Transport Classification Database (TCDB) are included if they have known substrate(s), have reference(s), and are not described as uncharacterized or putative. (Some of the references are not visible on the PaperBLAST web site.)
• Every protein from CharProtDB, a database of experimentally characterized protein annotations, is included.
• Proteins from the CAZy database of carbohydrate-active enzymes are included if they are associated with an Enzyme Classification number. Even though CAZy does not provide links from individual protein sequences to papers, these should all be experimentally-characterized proteins.
• Proteins from the REBASE database of restriction enzymes are included if they have known specificity.
• Every protein with an evidence-based reannotation (based on mutant phenotypes) in the Fitness Browser is included.
• Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators) with experimentally-determined DNA binding sites from the PRODORIC database of gene regulation in prokaryotes.
• Putative transcription factors from RegPrecise that have manually-curated predictions for their binding sites. These predictions are based on conserved putative regulatory sites across genomes that contain similar transcription factors, so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
• Coding sequence (CDS) features from the European Nucleotide Archive (ENA) are included if the /experiment tag is set (implying that there is experimental evidence for the annotation), the nucleotide entry links to paper(s) in PubMed, and the nucleotide entry is from the STD data class (implying that these are targeted annotated sequences, not from shotgun sequencing). Also, to filter out genes whose transcription or translation was detected, but whose function was not studied, nucleotide entries or papers with more than 25 such proteins are excluded. Descriptions from ENA rely on the original submitter of the sequence and cannot be updated by others, so they may be less reliable.

Except for GeneRIF and ENA, the curated entries include a short curated description of the protein's function. For entries from BioLiP, the protein's function may not be known beyond binding to the ligand. Many of these entries also link to articles in PubMed.

For more information see the PaperBLAST paper (mSystems 2017) or the code. You can download PaperBLAST's database here.

Changes to PaperBLAST since the paper was written:

• November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
• February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
• June 2022: incorporated some coding sequences from ENA with the /experiment tag.
• March 2022: incorporated BioLiP.
• April 2020: incorporated TCDB.
• April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
• February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
• January 2018: incorporated BRENDA.
• December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
• September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.

Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.

Secrets

PaperBLAST cannot provide snippets for many of the papers that are published in non-open-access journals. This limitation applies even if the paper is marked as "free" on the publisher's web site and is available in PubmedCentral or EuropePMC. If a journal that you publish in is marked as "secret," please consider publishing elsewhere.

Omissions from the PaperBLAST Database

Many important articles are missing from PaperBLAST, either because the article's full text is not in EuropePMC (as for many older articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an article that characterizes a protein's function but is missing from PaperBLAST, please notify the curators at UniProt or add an entry to GeneRIF. Entries in either of these databases will eventually be incorporated into PaperBLAST. Note that to add an entry to UniProt, you will need to find the UniProt identifier for the protein. If the protein is not already in UniProt, you can ask them to create an entry. To add an entry to GeneRIF, you will need an NCBI Gene identifier, but unfortunately many prokaryotic proteins in RefSeq do not have corresponding Gene identifers.

References

PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.

Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.

Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.

UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.

BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.

The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.

CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.

The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.

The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.

REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.

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