Family Search for PF10076 (Phage_Mu_Gp48)

April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.

Running HMMer for PF10076

PF10076 hits 19 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

CD630_28990 YmfQ family protein from Clostridioides difficile 630
Aligns to 5:151 / 205 (71.7%), covers 97.3% of PF10076, 142.4 bits

• Clostridioides difficile strain-dependent and strain-independent adaptations to a microaerobic environment
  Weiss, Microbial genomics 2021
  • “...(Table S3). Prophage genes encompassed three main gene clusters: CD630_09450 CD630_09680 , CD630_13620 CD630_13730 and CD630_28990 CD630_29230 . Based on our RNA-seq data, these prophage genes remained integrated in the bacterial chromosome and are expressed at a low level, rather than being excised (Table S1). Prophage...”

Psyr_4586 tail protein, putative from Pseudomonas syringae pv. syringae B728a
Aligns to 12:197 / 199 (93.5%), covers 97.3% of PF10076, 100.9 bits

• Independent Co-Option of a Tailed Bacteriophage into a Killing Complex in Pseudomonas
  Hockett, mBio 2015
  • “...genomic sequence, complemented in trans on a replicative vector), R struct (deletion of Psyr_4592 through Psyr_4586, as well as the promoter of Psyr_4585), R rbp (deletion of Psyr_4584 and Psyr_4585), R rbp + pR rbp (Psyr_4584 and Psyr_4585 expressed from a constitutive promoter in pBAV226), and...”
  • “...genome release GOLD Project ID Gp004223). The upstream # symbol indicates the stop codon of Psyr_4586. (C) The asterisk indicates that the promoter of the gene is removed and the coding sequence is unaltered. a , R reg annotations are from IMG and R struct and...”
• Involvement of rppH in thermoregulation in Pseudomonas syringae
  Hockett, Journal of bacteriology 2014
  • “...Psyr_2828 NA NA NA Psyr_2831 Psyr_2832 Psyr_2845 Psyr_2846 Psyr_4586 Psyr_4587 Psyr_4588 Psyr_4589 NA NA NA NA NA NA NA NA Psyr_4590 Psyr_4591 Psyr_4592 NA...”

Pchl3084_1224 putative phage tail protein from Pseudomonas chlororaphis subsp. aureofaciens 30-84
Aligns to 12:199 / 199 (94.5%), covers 98.7% of PF10076, 99.0 bits

• The Phenazine 2-Hydroxy-Phenazine-1-Carboxylic Acid Promotes Extracellular DNA Release and Has Broad Transcriptomic Consequences in Pseudomonas chlororaphis 30-84
  Wang, PloS one 2016
  • “...6.7 Pchl3084_1222 phage protein, GP46 family 3.5 6.4 Pchl3084_1223 baseplate J family protein 3.2 6.1 Pchl3084_1224 hypothetical protein 3.2 6.0 Pchl3084_1225 hypothetical protein 3.3 6.7 Pchl3084_1226 hypothetical protein 3.1 6.1 Pchl3084_1227 putative phage tail protein 3.2 6.8 Pchl3084_1228 putative phage tail protein 3.3 7.0 Pchl3084_1229 putative...”

BUE60_01870 putative phage tail protein from Pseudomonas syringae pv. actinidiae
Aligns to 12:198 / 199 (94.0%), covers 94.0% of PF10076, 98.8 bits

• Phytotoxin synthesis genes and type III effector genes of Pseudomonas syringae pv. actinidiae biovar 6 are regulated by culture conditions
  Hirose, PeerJ 2020
  • “...4.633089 9.090263 4.33E08 6.26E05 0.843105 BUE60_04770 hypothetical protein 0.34373 7.61338 7.61338 8.059493 5.40E08 6.26E05 0.670986 BUE60_01870 phage tail protein 7.758212 6.587112 7.860501 8.547592 3.98E07 0.000384 0.541496 BUE60_06970 hypothetical protein 2.58953 0.8029 8.1928 8.386577 1.29E06 0.001067 0.864256 BUE60_14400 4a-hydroxytetrahydrobiopterin dehydratase 7.494481 7.602294 8.036372 8.691885 2.15E06 0.001554 0.56063...”

YmfQ / b1153 e14 prophage; DUF2313 domain-containing protein YmfQ from Escherichia coli K-12 substr. MG1655 (see 2 papers)
b1153 e14 prophage; conserved protein from Escherichia coli str. K-12 substr. MG1655
P75982 Uncharacterized protein YmfQ from Escherichia coli (strain K12)
Aligns to 10:193 / 194 (94.8%), covers 98.0% of PF10076, 97.9 bits

• Construction of an Escherichia coli Strain Lacking Fimbriae by Deleting 64 Genes and Its Application for Efficient Production of Poly(3-Hydroxybutyrate) and l-Threonine
  Qiao, Applied and environmental microbiology 2021
  • “...6.528019 Toxic peptide b4245 pyrB 6.523107 UMP biosynthesis b4034 malE 6.452172 Maltose ABC transporter protein b1153 ymfQ 6.209994 Uncharacterized protein b1977 asnT 6.209994 tRNA-Asn b3882 yihU 6.209994 NAD binding Downregulated b4009 rrlE 15.6541 23S ribosomal RNA b1544 ydfK 9.85026 Cold shock protein b1545 pinQ 9.77538 DNA...”
• The association of DNA damage response and nucleotide level modulation with the antibacterial mechanism of the anti-folate drug trimethoprim
  Sangurdekar, BMC genomics 2011
  • “...resistance; dimer of dimers with MoaD ybhN b0788 Function unknown yliE b0833 Function unknown ymfQ b1153 Function unknown yobG b1826 Function unknown yecN b1869 Function unknown crr b2417 Phosphocarrier protein for glucose of the PTS; Enzyme IIA(Glc); formerly EIII(glc) recJ b2892 Single-stranded DNA-specific exonuclease, 5'-3' ygjT...”
• Analysis of the lambdoid prophage element e14 in the E. coli K-12 genome
  Mehta, BMC microbiology 2004
  • “...represent the boundaries of the right major e14 deletion in Figure 1 . b1152 and b1153 are tail protein homologs of gene 47 and 48 proteins of phage Mu, which has a contractile tail. SfV phage tail proteins are their closest homologs and occur in similar...”
  • “...Probable pseudogene, phage portal YmfP b1152 993510714 259 (+) 0.58 - tail protein (baseplate?) YmfQ b1153 1070511289 194 (+) 0.57 SS(132) tail protein (baseplate?) YcfK b1154 1129311922 209 (+) 0.50 COG3299 tail fibre YmfS b1155 1192412337 137 (+) 0.42 PF02413, IPR003458 tail fibre assembly TfaE b1156...”
• Interfering with different steps of protein synthesis explored by transcriptional profiling of Escherichia coli K-12
  Sabina, Journal of bacteriology 2003
  • “...b1644 gapA ilvC b1565 lysC b2653 b1513 yagY yagU ymfM b0165 b1153 ycgX aceA gloB b1462 glnA yrfD serA gltA malS trpB gadA aroF smpA trpD b0651 b1596 b0263 b1320...”
  • “...b3774 b1565 b4024 b2653 b1513 b0292 b0287 b1148 b0165 b1153 b1161 b4015 b0212 b1462 b3870 b3395 b2913 b0720 b3571 b1261 b3517 b2601 b2617 b1263 0.01 0.02 0.02...”
• Definition of the Escherichia coli MC4100 genome by use of a DNA array
  Peters, Journal of bacteriology 2003
  • “...b1144, b1146, b1147, b1148, b1149, b1150, b1151, b1152, b1153, b1155, b2174a a Partially deleted gene. Downloaded from http://jb.asm.org/ on February 11, 2017...”
• Complete genomic sequence of SfV, a serotype-converting temperate bacteriophage of Shigella flexneri
  Allison, Journal of bacteriology 2002
  • “...1e-35 (43) AF083977 3e-34 (44) YmfQ (hypothetical protein b1153; 194 aa; E. coli prophage e14b) Putative phage protein YPO1251 (115 aa; Yersinia pestis)...”
  • “...attP, gtrA, gtrB Predicted ORF(s)a 7807-8892 b1149 9545-11238 b1152, b1153, (b1154) 7200-8640 % identify at nucleotide level 95 b b1148 b1149 b b 96 82 b...”
• The nucleotide sequence of Shiga toxin (Stx) 2e-encoding phage phiP27 is not related to other Stx phage genomes, but the modular genetic structure is conserved
  Recktenwald, Infection and immunity 2002
  • “...(E. coli) NP_050651; gp47, phage Mu (E. coli) P75982; hypothetical protein YmfQ, prophage E14 (E. coli) NP_050652; gp48, phage Mu (E. coli) A42463; hypothetical...”
• Molecular and biological analysis of eight genetic islands that distinguish Neisseria meningitidis from the closely related pathogen Neisseria gonorrhoeae
  Klee, Infection and immunity 2000
  • “...P08558 P31340 P44238 P44239 P44240 P54339 P44240 P75982 rth49 rth52 gpxA 760 279 177 Repressor protein Transcriptional regulatory protein HI1476 DNA-binding...”

NMA1324 hypothetical protein NMA1324 from Neisseria meningitidis Z2491
Aligns to 5:186 / 186 (97.8%), covers 96.7% of PF10076, 97.8 bits

• Mu-like Prophage in serogroup B Neisseria meningitidis coding for surface-exposed antigens
  Masignani, Infection and immunity 2001
  • “...terminal) HI1521 HI1522 NMA1825 NMA1824 (N terminal) NMA1324 NMA1325 NMB1116 NMB1117 NMB1118 NMB1119 NMB1120 NB5 NMB1122 1131560-1132084 1132350-1132204 ()...”

Q9JZC6 Phage tail protein from Neisseria meningitidis serogroup B (strain MC58)
NMB1114 hypothetical protein from Neisseria meningitidis MC58
Aligns to 5:186 / 186 (97.8%), covers 96.7% of PF10076, 97.5 bits

• Towards New Drug Targets? Function Prediction of Putative Proteins of Neisseria meningitidis MC58 and Their Virulence Characterization
  Shahbaaz, Omics : a journal of integrative biology 2015
  • “...Q9JZL2 Q9JZE3 Q9JZE2 Q9JZD8 Q9JZD6 Q9JYB9 Q9JZE1 Q9JZD7 Q9JZC7 Q9JZC6 33. 34. Q9JYK2 Q9JYD6 35. Q9K0X0 36. P67259 37. 38. 39. 40. 41. 42. Q9K194 Q7DDP7 Q9JZG0...”
• Localized Hypermutation is the Major Driver of Meningococcal Genetic Variability during Persistent Asymptomatic Carriage
  Green, mBio 2020
  • “...35 NEIS0212 (V51), pilQ (V51), pglA (V51), uvrA (V54), gltX (V59), rpoC (V59), NMB0830 (V59), NMB1114 (V59), NMB122 0 (V59), sspA (V59), polA (V59) mutS (V69), NEIS1978 (V69), NEIS1339 (V93), NEIS0202 (V93), NEIS1009 (V93), pabBC (V93), NEIS1623 (V93), NEIS0202 (V96), secG (V96), iga (V96) mafB1 (V96),...”
• Mu-like Prophage in serogroup B Neisseria meningitidis coding for surface-exposed antigens
  Masignani, Infection and immunity 2001
  • “...NMA1319 (C terminal) NMA1320 NMA1321 NMA1322 NMA1323 NMB1114 NMB1115 1128580-1129137 1129151-1131121 186 657 gp48 MuS (N terminal) HI1521 HI1522 NMA1825 NMA1824...”

YP_008766883 baseplate wedge subunit from Shigella phage SfIV
Aligns to 10:193 / 194 (94.8%), covers 98.0% of PF10076, 97.3 bits

• A novel inducible prophage from the mycosphere inhabitant Paraburkholderia terrae BS437
  Pratama, Scientific reports 2017
  • “...37019 36423 199 Prophage tail protein Tail protein [ Shigella phage SfIV] 97 1E-25 35 YP_008766883 72 38189 37026 388 Phage FluMu protein gp47 Baseplate protein [ Shigella phage SfIV] 89 7E-34 32 YP_009147467 73 38637 38191 149 Bacteriophage protein GP46 Putative tail protein [ Salmonella...”

BP48_BPMU / Q9T1V1 Baseplate protein gp48; Gene product 48; gp48; Gene product R; gpR from Escherichia phage Mu (Bacteriophage Mu) (see 3 papers)
Aligns to 8:176 / 180 (93.9%), covers 98.7% of PF10076, 96.9 bits

• function: Component of the baseplate
  subunit: Part of a complex composed of three DNA circularization protein N, three baseplate hub protein gp44 and three sub-complex wedge (made of two copies of each baseplate protein gp46, gp47 and gp48) that forms the baseplate.
  disruption phenotype: No tail is synthesized.

STMUK_1983 putative phage tail protein from Salmonella enterica subsp. enterica serovar Typhimurium str. UK-1
Aligns to 9:187 / 195 (91.8%), covers 98.0% of PF10076, 92.9 bits

• Transcriptional Profiling of a Cross-Protective Salmonella enterica serovar Typhimurium UK-1 dam Mutant Identifies a Set of Genes More Transcriptionally Active Compared to Wild-Type, and Stably Transcribed across Biologically Relevant Microenvironments
  Miller, Pathogens (Basel, Switzerland) 2014
  • “...4.53 15.96 NP Hypothetical bacteriophage protein STMUK_1982 6.90 10.08 17.47 NP Putative phage tail-like protein STMUK_1983 8.27 11.74 15.83 NP Hypothetical bacteriophage protein STMUK_1984 8.06 9.40 15.30 NP Similar to tail protein STMUK_1985 6.32 7.46 25.19 NP Similar to tail protein STMUK_1986 4.91 10.49 18.11 NP...”

ECs4988 hypothetical protein from Escherichia coli O157:H7 str. Sakai
Aligns to 10:178 / 186 (90.9%), covers 96.7% of PF10076, 81.8 bits

• Complete genomic sequence of SfV, a serotype-converting temperate bacteriophage of Shigella flexneri
  Allison, Journal of bacteriology 2002
  • “...protein YPO1251 (115 aa; Yersinia pestis) Hypothetical protein ECs4988 (186 aa; E. coli O157:H7 prophage Sp16a [Mu-like]) Hypothetical protein NMA1825 (188 aa;...”

CDR20291_1216 phage protein from Clostridium difficile R20291
CDR20291_1216 putative phage tail protein from Clostridioides difficile R20291
Aligns to 2:145 / 232 (62.1%), covers 87.3% of PF10076, 80.7 bits

• Clostridioides difficile LuxS mediates inter-bacterial interactions within biofilms
  Slater, Scientific reports 2019
  • “...phage cell wall hydrolase 7 CDR20291_1214 1.09972952 phage protein 8 CDR20291_1215 1.038498251 phage protein 9 CDR20291_1216 1.047731727 phage protein 10 CDR20291_1217 0.999294901 phage tail fiber protein 11 CDR20291_1218 0.898724949 hypothetical protein 12 CDR20291_1425 0.928686375 virulence-associated protein e 13 CDR20291_1432 1.243533992 phage terminase large subunit 14 CDR20291_1433...”

CD1372 phage protein from Clostridium difficile 630
CD630_13720, CDIF630erm_01530 putative phage tail protein from Clostridioides difficile 630
Aligns to 2:145 / 232 (62.1%), covers 87.3% of PF10076, 80.3 bits

• Novel high-molecular-weight, R-type bacteriocins of Clostridium difficile
  Gebhart, Journal of bacteriology 2012
  • “...CD1364 CD1365 CD1365A CD1366 CD1367 CD1368 CD1369 CD1370 CD1371 CD1372 CD1373 CD1374 CD1375 CD1376 CD1377 CD1378 168 106 65 146 147 354 142 447 55 817 140...”
• Iron Regulation in Clostridioides difficile
  Berges, Frontiers in microbiology 2018
  • “...0.02 -3.93 CD630_13700 CDIF630erm_01528 XkdS-like protein - -1.07 CD630_13710 CDIF630erm_01529 Baseplate assembly protein -1.33 -2.06 CD630_13720 CDIF630erm_01530 XkdT-like protein -1.27 -2.90 CD630_13740 CDIF630erm_01532 Beta-lactamase-inhibitor protein II 0.64 ON -1.58 DNA/RNA nucleotide metabolism CD630_02180 CDIF630erm_00340 purE 5-carboxyaminoimidazole ribonucleotide mutase 0.09 -0.24 2.12 0.80 CD630_02190 CDIF630erm_00341 purC Phosphoribosylaminoimidazolesuccino...”
  • “...-3.93 CD630_13700 CDIF630erm_01528 XkdS-like protein - -1.07 CD630_13710 CDIF630erm_01529 Baseplate assembly protein -1.33 -2.06 CD630_13720 CDIF630erm_01530 XkdT-like protein -1.27 -2.90 CD630_13740 CDIF630erm_01532 Beta-lactamase-inhibitor protein II 0.64 ON -1.58 DNA/RNA nucleotide metabolism CD630_02180 CDIF630erm_00340 purE 5-carboxyaminoimidazole ribonucleotide mutase 0.09 -0.24 2.12 0.80 CD630_02190 CDIF630erm_00341 purC Phosphoribosylaminoimidazolesuccino carboxamide...”

NMA1825 hypothetical protein from Neisseria meningitidis Z2491
Aligns to 5:185 / 188 (96.3%), covers 96.7% of PF10076, 74.7 bits

• Complete genomic sequence of SfV, a serotype-converting temperate bacteriophage of Shigella flexneri
  Allison, Journal of bacteriology 2002
  • “...E. coli O157:H7 prophage Sp16a [Mu-like]) Hypothetical protein NMA1825 (188 aa; Neisseria meningitidis Z2491) Gp48 (180 aa; E. coli phage Mu) AE000214 AJ414147...”
• Mu-like Prophage in serogroup B Neisseria meningitidis coding for surface-exposed antigens
  Masignani, Infection and immunity 2001
  • “...186 657 gp48 MuS (N terminal) HI1521 HI1522 NMA1825 NMA1824 (N terminal) NMA1324 NMA1325 NMB1116 NMB1117 NMB1118 NMB1119 NMB1120 NB5 NMB1122 1131560-1132084...”

CBO1743 phage protein from Clostridium botulinum A str. ATCC 3502
Aligns to 3:152 / 208 (72.1%), covers 94.0% of PF10076, 73.5 bits

• The cold-induced two-component system CBO0366/CBO0365 regulates metabolic pathways with novel roles in group I Clostridium botulinum ATCC 3502 cold tolerance
  Dahlsten, Applied and environmental microbiology 2014
  • “...cbo1730-cbo1735, cbo1737, Prophage 1 cbo1739-cbo1741, cbo1743, cbo1745, cbo1750 cbo2325-cbo2337, cbo2339-cbo2356, cbo2358-cbo2360, Prophage 2 cbo2367-cbo2372,...”

HI1521 hypothetical protein from Haemophilus influenzae Rd KW20
Aligns to 1:182 / 186 (97.8%), covers 96.0% of PF10076, 68.8 bits

• Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
  Shahbaaz, PloS one 2013
  • “...Mu-like prophageFluMu protein gp46 252. HP HI1520 950385 P44240 Mu-like prophageFluMu protein gp47 253. HP HI1521 950386 P44241 Mu-like prophageFluMu protein gp48 254. HP HI1522 950387 P44242 Mu-like prophageFluMu defective tail fiber protein 255. HP HI1522.1 950388 P71390 Mu-like prophage protein Com 256. HP HI1523 949672...”
• Mu-like Prophage in serogroup B Neisseria meningitidis coding for surface-exposed antigens
  Masignani, Infection and immunity 2001
  • “...1129151-1131121 186 657 gp48 MuS (N terminal) HI1521 HI1522 NMA1825 NMA1824 (N terminal) NMA1324 NMA1325 NMB1116 NMB1117 NMB1118 NMB1119 NMB1120 NB5...”
• Molecular and biological analysis of eight genetic islands that distinguish Neisseria meningitidis from the closely related pathogen Neisseria gonorrhoeae
  Klee, Infection and immunity 2000
  • “...(C terminus) Hypothetical protein YmfQ (27% identical to HI1521) HI1522 HI1523 Glutathione peroxidase H. influenzae H. influenzae N. meningitidis 623 296 177...”

P44241 Mu-like prophage FluMu protein gp48 from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Aligns to 1:164 / 168 (97.6%), covers 82.7% of PF10076, 60.6 bits

• Functional annotation of conserved hypothetical proteins from Haemophilus influenzae Rd KW20
  Shahbaaz, PloS one 2013
  • “...protein gp46 252. HP HI1520 950385 P44240 Mu-like prophageFluMu protein gp47 253. HP HI1521 950386 P44241 Mu-like prophageFluMu protein gp48 254. HP HI1522 950387 P44242 Mu-like prophageFluMu defective tail fiber protein 255. HP HI1522.1 950388 P71390 Mu-like prophage protein Com 256. HP HI1523 949672 P44243 D12...”

YPO1251 putative bacteriophage protein from Yersinia pestis CO92
Aligns to 1:112 / 115 (97.4%), covers 54.0% of PF10076, 48.1 bits

• Complete genomic sequence of SfV, a serotype-converting temperate bacteriophage of Shigella flexneri
  Allison, Journal of bacteriology 2002
  • “...aa; E. coli prophage e14b) Putative phage protein YPO1251 (115 aa; Yersinia pestis) Hypothetical protein ECs4988 (186 aa; E. coli O157:H7 prophage Sp16a...”

BCAL1562 hypothetical protein from Burkholderia cenocepacia J2315
Aligns to 6:194 / 199 (95.0%), covers 94.0% of PF10076, 47.5 bits

• Reciprocal regulation by the CepIR and CciIR quorum sensing systems in Burkholderia cenocepacia
  O'Grady, BMC genomics 2009
  • “...conserved hypothetical protein MST2014 2.0 NC NC BCAL1354 conserved hypothetical protein MST2020 NC NC -2.2 BCAL1562 hypothetical phage protein MST2024 NC 2.7 NC BCAL2871 sigma-E factor negative regulatory protein 1 RseA1 MST2036 NC NC NC BCAL2870 sigma-E factor regulatory protein RseB precursor 1 MucB1 downstream from...”

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