Family Search for PF13274 (SocA_Panacea)

PF13274 hits 17 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

D11S_2261 DUF4065 domain-containing protein from Aggregatibacter phage S1249
Aligns to 29:128 / 146 (68.5%), covers 99.1% of PF13274, 87.3 bits

• Human Serum Mediated Bacteriophage Life Cycle Switch in Aggregatibacter actinomycetemcomitans Is Linked to Pyruvate Dehydrogenase Complex
  Tang-Siegel, Life (Basel, Switzerland) 2023
  • “...(ID: 8672828) up-regulated 10-fold and 67-aa D11S_2260 (ID: 8672829) up-regulated 5-fold, as well as 146-aa D11S_2261 (ID: 8672830, a homologue of antitoxin SocA) up-regulated 2-fold, and 217-aa phage anti-repressor D11S_2263 (ID:8672832) up-regulated 2-fold in human serum [ 35 ]. Those identified phage regulatory proteins contain helical...”
  • “...( 85 ) D11S_2237 ( 4 ) D11S_2262 ( 1 ) D11S_2208 ( 1 ) D11S_2261 ( 1 ) B 3 Malic enzyme ( 291 ) Citrate lysate ( 249 ) DdRP subunit (D11S_0064, 159 ) RpoB (D11S_0063, 145 ) ATP synthase F0-F1 ( 91 )...”

HSM_0245 Panacea domain-containing protein from Histophilus somni 2336
HSM_0245 hypothetical protein from Haemophilus somnus 2336
Aligns to 29:127 / 145 (68.3%), covers 99.1% of PF13274, 81.6 bits

• Identification and initial characterization of Hfq-associated sRNAs in Histophilus somni strain 2336
  Subhadra, PloS one 2023
  • “...Y - HSM_0213 HSM_0214 C [ 8 ] HS15 258962 259117 156 Y Y HSM_0244 HSM_0245 A [ 8 ] HS16 260385 260624 240 Y Y HSM_0245 HSM_0246 A [ 8 ] HS18 261354 261531 178 Y Y HSM_0246 HSM_0247 A [ 8 ] HS19 261807...”

BOP93_05630 Panacea domain-containing protein from Pseudomonas orientalis
Aligns to 29:136 / 162 (66.7%), covers 99.1% of PF13274, 80.7 bits

• Pseudomonas orientalis F9: A Potent Antagonist against Phytopathogens with Phytotoxic Effect in the Apple Flower
  Zengerer, Frontiers in microbiology 2018
  • “...the assembly. PHASTER ( Arndt et al., 2016 ) detected two intact prophages (Locus tags BOP93_05630 to BOP93_05745 and BOP93_13270 to BOP93_13665) and one questionable prophage (Locus tags BOP93_15105 to BOP93_15245) ( Table 2 ), while IslandViewer 3 ( Dhillon et al., 2015 ) detected a...”

HD1614 possible prophage ps3 protein01-like protein from Haemophilus ducreyi 35000HP
Aligns to 36:129 / 132 (71.2%), covers 97.4% of PF13274, 79.6 bits

• Haemophilus ducreyi Seeks Alternative Carbon Sources and Adapts to Nutrient Stress and Anaerobiosis during Experimental Infection of Human Volunteers
  Gangaiah, Infection and immunity 2016
  • “...HD_RS06150 guaA HD0250 HD0673 HD1089 HD1354 HD1362 HD1614 HD_RS00990 HD_RS02750 HD_RS04480 HD_RS05525 HD_RS05560 HD_RS06570 HD0458 HD0746 HD0926 HD1524 HD1893...”
  • “...1.5E04 HD0250 HD0673 HD1089 HD1354 HD1362 HD1614 Hypothetical protein Membrane protein Hypothetical protein Hypothetical protein Hypothetical protein...”

NCTC10931_00949 Panacea domain-containing protein from Neisseria gonorrhoeae
Aligns to 34:151 / 194 (60.8%), covers 95.6% of PF13274, 79.0 bits

• Comparative Proteomics of Extended-Spectrum Cephalosporin-Resistant Neisseria gonorrhoeae Isolates Demonstrates Altered Protein Synthesis, Metabolism, Substance Transport, and Membrane Permeability
  Diao, Frontiers in microbiology 2020
  • “...in virulence L 0 N 3.35 A0A1D3H2B5 vacB Ribonuclease R K 0 N 2.3 A0A1D3HIN9 NCTC10931_00949 Phage associated protein X 0 N 4.97 A0A1D3IB26 NCTC10931_02268 Aminotransferase E 0 N 1.74 A0A1D3IBY0 NCTC10931_00390 Type II restriction endonuclease Nla IV 0 N 2.68 A0A1D3IYI7 WHOF_00049C Uncharacterized protein 0...”

NGO1626 hypothetical protein, putative phage associated protein from Neisseria gonorrhoeae FA 1090
Aligns to 55:172 / 215 (54.9%), covers 95.6% of PF13274, 79.0 bits

• Global Network Analysis of Neisseria gonorrhoeae Identifies Coordination between Pathways, Processes, and Regulators Expressed during Human Infection
  McClure, mSystems 2020
  • “...genes were connected to two other genes, both of which were phage-associated genes (NGO1625 and NGO1626). A second cluster consisted of three genes involved in pilin biogenesis (NGO0096 to NGO0098 [ pilO , pilN , and pilM ]). These genes were connected to a hypothetical protein...”
  • “...associated rRNA 0.016 NGO1325 Carbohydrate metabolism Genetic information processing 0.016 NGO1616 Phage associated rRNA 0.022 NGO1626 Phage associated Energy metabolism 0.006 NGO1629 Phage associated Cellular processes/organismal systems/human disease 0.000 NGO1809 Genetic information processing Carbohydrate metabolism 0.001 NGO1823 Genetic information processing Carbohydrate metabolism 0.013 NGO1831 Genetic information...”
• Characterization of the dsDNA prophage sequences in the genome of Neisseria gonorrhoeae and visualization of productive bacteriophage
  Piekarowicz, BMC microbiology 2007
  • “...[ Azoarcus sp. EbN1] 25,42% on 365 NGO1614 15951991595750 88 NS NGO1625 15960261596241 138 NS NGO1626 15830281584182 215 conserved hypothetical protein CDS21 [Bacteriophage bIL311] (pfam GepA,) 29,48% on 116 NGO1627 15842321584498 133 hypothetical protein HP2p14 protein [ Haemophilus phage (pfam UPFO150 family) HP2] 34,54% on 129...”

SpyM3_1207 conserved hypothetical protein - phage associated from Streptococcus pyogenes MGAS315
Aligns to 26:139 / 174 (65.5%), covers 100.0% of PF13274, 74.3 bits

• Characterization of the dsDNA prophage sequences in the genome of Neisseria gonorrhoeae and visualization of productive bacteriophage
  Piekarowicz, BMC microbiology 2007
  • “...218 NGO1117 10710671071606 179 hypothetical protein CDS21 [Phage bIL311] GepA [phage-like] 37, 53% on 135, SpyM3_1207 [ S. pyogenes phage 315.4] 40, 66% on 71 NGO1118 10716071071966 119 NS NGO1119 10719831072201 72 NS NGO1132 10780871078281 64 hypothetical protein 33 [ Enterobacteria phage epsilon15] 68% on 44...”

MAG6440 Putative prophage protein (ps3) from Mycoplasma agalactiae PG2
Aligns to 25:118 / 150 (62.7%), covers 100.0% of PF13274, 71.2 bits

• The Integrative Conjugative Element (ICE) of Mycoplasma agalactiae: Key Elements Involved in Horizontal Dissemination and Influence of Coresident ICEs
  Baranowski, mBio 2018
  • “...significant (90%) similarity to a putative prophage gene product found in the chromosomes of PG2 (MAG6440) and 5632 (MAGa7400). The presence of this chromosomal cdsE homologue is puzzling, and its role in ICEA transfer remains to be confirmed. A minimal genome able to cope with multiple...”
• Genome-scale analysis of Mycoplasma agalactiae loci involved in interaction with host cells
  Skapski, PloS one 2011
  • “...H F 1 (1) 290 nt 761860 () HP (MAG6430) and putative prophage protein ps3 (MAG6440) NCR I F * 2 (2) 80 nt 843595 (+)/843634 (+) cmk (MAG7250) and HP (MAG7260) a NCRs were labeled with a letter based on their position in the genome...”
• Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome
  Sirand-Pugnet, PLoS genetics 2007
  • “...analysis of the M. agalactiae genome also revealed two genes encoding a putative prophage protein (MAG6440) and a phage family integrase (MAG5690). All of these genetic elements can be regarded as vestiges of potential shuttles that may have been involved in the transfer of genome fragments...”

MAGa7400 putative prophage protein (ps3) from Mycoplasma agalactiae
Aligns to 25:118 / 150 (62.7%), covers 100.0% of PF13274, 70.5 bits

• The Integrative Conjugative Element (ICE) of Mycoplasma agalactiae: Key Elements Involved in Horizontal Dissemination and Influence of Coresident ICEs
  Baranowski, mBio 2018
  • “...to a putative prophage gene product found in the chromosomes of PG2 (MAG6440) and 5632 (MAGa7400). The presence of this chromosomal cdsE homologue is puzzling, and its role in ICEA transfer remains to be confirmed. A minimal genome able to cope with multiple ICEA copies. Unlike...”

NGO1117 hypothetical protein, putative phage associated protein from Neisseria gonorrhoeae FA 1090
Aligns to 28:120 / 179 (52.0%), covers 99.1% of PF13274, 69.4 bits

• Characterization of the dsDNA prophage sequences in the genome of Neisseria gonorrhoeae and visualization of productive bacteriophage
  Piekarowicz, BMC microbiology 2007
  • “...protein cI [Phage Aaphi23]37, 54% on 191, cI [ Pseudomonas phage D3]30, 44% on 218 NGO1117 10710671071606 179 hypothetical protein CDS21 [Phage bIL311] GepA [phage-like] 37, 53% on 135, SpyM3_1207 [ S. pyogenes phage 315.4] 40, 66% on 71 NGO1118 10716071071966 119 NS NGO1119 10719831072201 72...”

Cthe_1643 Uncharacterized phage-associated protein-like protein from Clostridium thermocellum ATCC 27405
Aligns to 187:280 / 332 (28.3%), covers 99.1% of PF13274, 69.1 bits

• Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress
  Wilson, Biotechnology for biofuels 2013
  • “...min 120 min Furfural stress Cthe_0211 Glycoside hydrolase family 16 2.22 3.56 2.41 2.87 D Cthe_1643 Phage-associated protein 2.12 4.49 2.41 2.77 F Cthe_1644 Hypothetical protein 2.26 4.07 2.27 2.79 F Cthe_2531 Sulfate ABC transporter, periplasmic sulfate-binding protein 1.87 3.19 3.58 3.99 F Cthe_2532 Sulfate ABC...”

NCgl0308 Panacea domain-containing protein from Corynebacterium glutamicum ATCC 13032
cg0378 putative phage-associated protein from Corynebacterium glutamicum ATCC 13032
Aligns to 29:125 / 148 (65.5%), covers 99.1% of PF13274, 68.8 bits

• The role of the transcriptional repressor CssR in Corynebacterium glutamicum in response to phenolic compounds
  Zhang, Heliyon 2024
  • “...family transcriptional regulator 1.64 1.38E-03 NCgl0283 Glutaryl-COA dehydrogenase 2.29 1.55E-05 NCgl0295 Hypothetical protein 1.24 2.62E-03 NCgl0308 Uncharacterized phage-associated protein 1.59 3.82E-07 NCgl0328 Nitroreductase 1.45 7.61E-06 NCgl0348 Transposase 3.26 0.03 NCgl0354 Acetyltransferase 1.50 7.60E-06 NCgl0358 XRE family transcriptional regulator 1.4 5.28E-06 NCgl0393 Hypothetical protein 2.80 0.02 NCgl0400...”
• Overlapping SigH and SigE sigma factor regulons in Corynebacterium glutamicum
  Busche, Frontiers in microbiology 2022
  • “...-controlled. Coding sequence a Gene 35 and 10 a Distance from start codon (nt) Function cg0378 GGAACA-N 16 -CGTT 92 Putative phage-associated protein cg0986 b amtR GGAAAC-N 17 -CGTT 397 Transcriptional repressor of nitrogen metabolism, TetR family cg1121 GGAACT-N 16 -CGTT 36 Permease, MFS type cg1272...”
  • “...and 10 sequences GGAACN 18-19 GTT. Figure 7 Activity of / E -dependent promoters P cg0378 , P amtR , P cg1121 , P cg1277 , P1 clgR , P cg3309 , and P cg3344 determined by in vivo two-plasmid system (A,C,E,G,I,K,M) and in vitro transcription...”
• Thiol-based redox switches in prokaryotes
  Hillion, Biological chemistry 2015
  • “...cg2838 , cg2661 ), methionine sulfoxide reductases ( msrA , msrB ), phage-associated functions ( cg0378 ), the tRNA-(5-methylaminomethyl-2-thiouridylate)-methyltransferase ( cg1397 ), the ubiquitin-like proteasomal conjugation pathway ( pup ) and DNA damage repair enzymes ( uvrA, uvrD3 ) ( Busche et al, 2012 ; Ehira...”
  • “...sensitive, Zn-site of ZAS sigH-rshA trxB, trxB1, trxC mshC,mca mtr cg2838, cg2661 msrA, msrB pup cg0378 cg1397 sigM, hspR, cglR, sufR, whcA, whcE uvrA, uvrD3 RshA/SigH thioredoxin/thioredoxin reductase mycothiol biosynthesis and recycling MSH reductase dsbA -like thiol-disulfide oxidoreductases methionine sulfoxide reductases ubiquitin-like protein- conjugation phage-associated tRNA-(5-...”
• Protein S-mycothiolation functions as redox-switch and thiol protection mechanism in Corynebacterium glutamicum under hypochlorite stress
  Chi, Antioxidants & redox signaling 2014
  • “...were the rH-dependent phage-associated gene cg0378 (50-80fold) and the tRNA-(5-methylaminomethyl-2-thiouridylate)methyltransferase gene cg1397 (17-45-fold). The...”
• Transcriptional regulation of the operon encoding stress-responsive ECF sigma factor SigH and its anti-sigma factor RshA, and control of its regulatory network in Corynebacterium glutamicum
  Busche, BMC genomics 2012
  • “...formate dehydrogenase, FdhD-family 3.71 cg1397* trmU tRNA (5-methylaminomethyl-2-thiouridylate) -methyltransferase 3.71 cg2423 lipA Lipoyl synthetase 3.34 cg0378 Putative phage-associated protein 2.93 cg2411 Conserved hypothetical protein, HesB/YadR/YfhF family 2.81 cg1799* ribC Riboflavin synthase, alpha chain 2.73 cg2247 Hypothetical protein 2.41 cg1282 Conserved hypothetical protein 2.35 cg2127 Hypothetical protein...”
• The alternative sigma factor SigB of Corynebacterium glutamicum modulates global gene expression during transition from exponential growth to stationary phase
  Larisch, BMC genomics 2007
  • “...bioD dethiobiotin synthetase protein 1.32 0.76* cg1227 ABC-type cobalt transport system 1.58 1.48 FUNCTION UNKNOWN cg0378 putative phage-associated protein 1.14 1.61 SULFONATE (ESTER) METABOLISM AND TRANSPORT cg1147 ssuI reductase involved in sulfonate degradation -1.25 -1.70 cg1152 seuB sulfonate ester monoxygenase -1.35 -1.25 cg1153 seuC sulfonate ester...”

BruAb2_0400 hypothetical protein from Brucella abortus biovar 1 str. 9-941
Aligns to 33:137 / 185 (56.8%), covers 99.1% of PF13274, 63.4 bits

• Mechanism of Asp24 upregulation in Brucella abortus rough mutant with a disrupted O-antigen export system and effect of Asp24 in bacterial intracellular survival
  Tian, Infection and immunity 2014
  • “...BruAb1_1726 BruAb1_1726 BruAb1_1735 BruAb1_1735 BruAb2_0400 BruAb2_0400 BruAb2_0811 BruAb2_0811 BruAb2_1055 BruAb2_1055 BruAb1_1241 BruAb1_1241 BruAb1_0657...”
  • “...BruAb1_0035 BruAb1_1556 BruAb1_1726 BruAb1_1735 BruAb2_0400 BruAb2_0811 BruAb2_1055 BruAb1_1241 BruAb1_0657 BruAb1_0822 BruAb1_1878 BruAb1_1239 BruAb1_1255...”

HA1_08347 Panacea domain-containing protein from Clostridium perfringens F262
Aligns to 27:119 / 141 (66.0%), covers 99.1% of PF13274, 63.1 bits

• Genome sequencing and analysis of a type A Clostridium perfringens isolate from a case of bovine clostridial abomasitis
  Nowell, PloS one 2012
  • “...F262 included site-specific recombinases (HA1_01897, HA1_06197, HA1_00723, HA1_07162), unique phage-like proteins (HA1_08482, many in Contig_14, HA1_08347, HA1_13167, HA1_13212, HA1_13597), unique sigma factors (HA1_06057, HA1_13097) and unique predicted transcriptional regulators (HA1_06282, HA1_13192, HA1_13197, HA1_07182). The two large plasmid-associated fragments, pF262A and pF262B, contained no and three unique...”

SOCA_CAUVN / A0A0H3CCP8 Antitoxin SocA; Adapter protein SocA from Caulobacter vibrioides (strain NA1000 / CB15N) (Caulobacter crescentus) (see paper)
CC_3515 conserved hypothetical protein from Caulobacter crescentus CB15
CCNA_03630 hypothetical protein from Caulobacter crescentus NA1000
Aligns to 36:140 / 188 (55.9%), covers 99.1% of PF13274, 59.7 bits

• function: Antitoxin component of an atypical type II toxin-antitoxin (TA) system. Unlike most type II TA systems, neutralizes the toxic activity of cognate toxin SocB by acting as an adapter to promote its degradation by ClpXP; degradation is dependent on the N-terminus of ClpX.
  subunit: Interacts with cognate toxin SocB and with ClpX.
  disruption phenotype: Essential, it cannot be deleted unless the downstream gene for cognate toxin socB is also deleted. In depletion experiments the half-life of SocB is 19 minutes in the absence of SocA and about 2 minutes in its presence.
• An integrative method for identifying the over-annotated protein-coding genes in microbial genomes
  Yu, DNA research : an international journal for rapid publication of reports on genes and genomes 2011
  • “...PH1861, PHs009) and 16 (CC_0370, CC_0605, CC_0853, CC_1246, CC_1274, CC_1712, CC_2413, CC_2699, CC_2731, CC_2732, CC_2737, CC_3515, CC_3516, CC_3517, CC_3520, CC_3548) of the recognized non-coding ORFs listed in Supplementary Table S6 are detected as HGTs by the HGT database, 54 respectively. The predicting procedure employed in the...”
• Genome Comparisons of Wild Isolates of Caulobacter crescentus Reveal Rates of Inversion and Horizontal Gene Transfer
  Ely, Current microbiology 2019
  • “...CCNA_02841 Hypothetical protein absent absent CCNA_02844 parD3 antitoxin present absent CCNA_03274 Hypothetical protein present absent CCNA_03630 socA antitoxin protein absent absent Table 5. Genes present in the NA1000 or CB2 genomes, but not in both. Gene category NA1000 CB2 Hypothetical 121 198 Transposase 40 9 Toxin/antitoxin...”
• Conservation of the Essential Genome Among Caulobacter and Brevundimonas Species
  Scott, Current microbiology 2016
  • “...protein none CCNA_02841 hypothetical protein none CCNA_02844 antitoxin protein parD-3 K31 CCNA_03307 hypothetical protein none CCNA_03630 socA antitoxin protein none CCNA_03474 SpoVT-AbrB transcription factor, phd antitoxin CB4, K31 CCNA_00364 deoxyhypusine synthase All but DS20 CCNA_01211 hypothetical protein TK0059, CB4, K31 CCNA_01380 pole-organizing protein popZ TK0059, CB4,...”

D805_0077 type II toxin-antitoxin system antitoxin SocA domain-containing protein from Bifidobacterium thermophilum RBL67
Aligns to 3:99 / 131 (74.0%), covers 99.1% of PF13274, 58.3 bits

• Bifidobacterium thermophilum RBL67 impacts on growth and virulence gene expression of Salmonella enterica subsp. enterica serovar Typhimurium
  Tanner, BMC microbiology 2016
  • “...logCPM b FDR c D805_0058 Oligopeptide transport ATP-binding protein OppF (TC 3.A.1.5.1) 1.52 4.09 4E-06 D805_0077 hypothetical protein 1.17 6.36 4.8E-07 D805_0155 Transcriptional regulator, MarR family 1.95 6.80 1.2E-17 D805_0156 hypothetical protein 1.50 3.64 0.00401 D805_0157 Lipid A export ATP-binding/permease protein MsbA 1.17 8.10 6.2E-06 D805_0382...”

Amuc_2017 Uncharacterized phage-associated protein-like protein from Akkermansia muciniphila ATCC BAA-835
Aligns to 37:133 / 161 (60.2%), covers 100.0% of PF13274, 50.6 bits

• The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes
  van, PloS one 2011
  • “...presence of 9 predicted phage-related sequences (Amuc_0323, Amuc_0551, Amuc_1116, Amuc_1335, Amuc_1348, Amuc_1355, Amuc_1367, Amuc_1711 and Amuc_2017) suggests that A. muciniphila experienced frequent infection by bacteriophages. Recently, the human microbiota were found to be a natural reservoir for antibiotic resistance genes [27] . As a frequent and...”

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