Family Search for PF01933 (CofD)

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

Running HMMer for PF01933

PF01933 hits 43 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

GNGF_BACSU / O06974 Gluconeogenesis factor from Bacillus subtilis (strain 168) (see 2 papers)
BSU34760 gluconeogenesis factor from Bacillus subtilis subsp. subtilis str. 168
NP_391356 gluconeogenesis morphogenetic factor (UDP-sugar binding) from Bacillus subtilis subsp. subtilis str. 168
Aligns to 7:293 / 317 (90.5%), covers 99.7% of PF01933, 405.1 bits

• function: Required for morphogenesis under gluconeogenic growth conditions. Required, in gluconeogenic growth conditions, for the correct localization of PBP1 and hence for displaying a normal rod shape.
  disruption phenotype: Deletion leads to growth defects when cells are grown on minimal medium containing ribose, gluconate, citrate, fumarate or succinate, but does not affect growth and morphology on minimal medium containing glycolytic substrates such as glucose, sucrose or glycerol. Mutants exhibit media-dependent filamentous or L-shape-like aberrant morphologies.
• The Blueprint of a Minimal Cell: MiniBacillus
  Reuß, Microbiology and molecular biology reviews : MMBR 2016
  • “...3ZIH 4UG3 B. subtilis B. subtilis B. subtilis yvcK BSU34760 No 2HZB B. halodurans BSU34750 No 3HYI T. maritima BSU15420 No 2WUJ B. subtilis minC BSU28000 No...”
• YvcK of Bacillus subtilis is required for a normal cell shape and for growth on Krebs cycle intermediates and substrates of the pentose phosphate pathway.
  Görke, Microbiology (Reading, England) 2005 (PubMed)
  • GeneRIF: important role in carbon metabolism, probably in gluconeogenesis required for the synthesis of cell wall precursor molecules

alr2298 hypothetical protein from Nostoc sp. PCC 7120
Aligns to 139:426 / 456 (63.2%), covers 99.7% of PF01933, 404.7 bits

• Nitrogen-regulated antisense transcription in the adaptation to nitrogen deficiency in Nostoc sp. PCC 7120
  Brenes-Álvarez, PNAS nexus 2023
  • “...TU01655 petR-petP TU00909 4.56 5.50 nifV1 to alr1410 TU00910 asl1412all1411 TU01443 4.33 4.49 asl2299 TU01442 alr2298 TU00901 4.30 4.47 all1395asl1394 NtcA TU00899 alr1390 to PCC7120DELTA_RS32405 TU02336 4.01 3.59 alr3554 TU02337 all3556-ilvB TU02841 3.86 2.58 PCC7120DELTA_RS22895 TU02840 argJ2 TU02078 3.81 2.08 alr3195 E-DIF TU02079 asl3196 TU02080 all3197...”
• Anabaena sp. strain PCC 7120 hetY gene influences heterocyst development
  Yoon, Journal of bacteriology 2003
  • “...It also differed from that of another flanking gene, alr2298, which showed a low amount of message in nitrate-grown cells, none at 6 h, and then increasing...”

sll0154 hypothetical 35.6 kD protein from Synechocystis sp. PCC 6803
Aligns to 149:435 / 462 (62.1%), covers 100.0% of PF01933, 404.1 bits

• Identification of the key functional genes in salt-stress tolerance of Cyanobacterium Phormidium tenue using in silico analysis
  Shahbazi, 3 Biotech 2021
  • “...sll0821 hypothetical protein, ssr3188 mrgA, slr1894 cruE, sll0154 lspA, slr1366 pbpD, sll1167 fdp, slr0952 cbiO, sll0385 putative peptidase, sll1369 nrsB,...”
• The Biosynthetic pathway for synechoxanthin, an aromatic carotenoid synthesized by the euryhaline, unicellular cyanobacterium Synechococcus sp. strain PCC 7002
  Graham, Journal of bacteriology 2008
  • “...and that in Synechocystis sp. strain PCC 6803 is sll0154. CruE sequences resemble the CrtU sequences of green sulfur bacteria by having a Rieske iron/sulfur...”
• Use of transposon Tn5367 mutagenesis and a nitroimidazopyran-based selection system to demonstrate a requirement for fbiA and fbiB in coenzyme F(420) biosynthesis by Mycobacterium bovis BCG
  Choi, Journal of bacteriology 2001
  • “...against Synechocystis alone, a weak hit was obtained with SLL0154 (score 44; E 105). The -Blast analysis also revealed a homolog from a Nostoc sp. (also known...”
  • “...MJ1256 (Methanococcus) Vng1429c (Halobacterium) MTH1018 (Methanobacterium) SLL0154 (Synechocystis) AAC03105 (Anabaena) Score 575 450 315 126 112 96 83...”

BH3568 hypothetical protein from Bacillus halodurans C-125
Aligns to 6:292 / 322 (89.1%), covers 99.7% of PF01933, 403.4 bits

• Molecular insights into the biosynthesis of the F420 coenzyme
  Forouhar, The Journal of biological chemistry 2008
  • “...M. jannaschii, and M. tuberculosis, as well as the BH3568 protein from B. gen) and eluted in lysis buffer conhalodurans. The secondary structure elements are...”
  • “...nonF420-producing CofD homologs have been determined, including the BH3568 protein from Bacillus halodurans (PDB entries 2HZB and 2O2Z, 24% sequence identity to...”

2o2zA / Q9K706 Crystal structure of a protein member of the upf0052 family (bh3568) from bacillus halodurans at 2.60 a resolution
Aligns to 7:292 / 310 (92.3%), covers 99.7% of PF01933, 400.1 bits

• Ligand: nicotinamide-adenine-dinucleotide (2o2zA)

BC5155 hypothetical Cytosolic Protein from Bacillus cereus ATCC 14579
Aligns to 9:295 / 317 (90.5%), covers 99.0% of PF01933, 384.7 bits

• SigB modulates expression of novel SigB regulon members via Bc1009 in non-stressed and heat-stressed cells revealing its alternative roles in Bacillus cereus
  Yeak, BMC microbiology 2023
  • “...ABC transporter ATP-binding protein 1.6 1.8 E 60 BC1275 BC1275 Methyltransferase 1.6 1.6 QR 61 BC5155 YvcK hypothetical Cytosolic Protein 1.6 2.2 S 62 BC5103 YclP Ferric anguibactin transport ATP-binding protein 1.6 2.0 P 63 BC3203 BC3203 hypothetical protein 1.6 1.5 S 64 BC2303 DhbC Isochorismate...”

USA300HOU_0795 hypothetical protein from Staphylococcus aureus subsp. aureus USA300_TCH1516
SA0721 hypothetical protein from Staphylococcus aureus subsp. aureus N315
SAOUHSC_00788 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_0749 hypothetical protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
SAR0821 conserved hypothetical protein from Staphylococcus aureus subsp. aureus MRSA252
SACOL0831 hypothetical protein from Staphylococcus aureus subsp. aureus COL
Aligns to 6:291 / 331 (86.4%), covers 98.3% of PF01933, 380.1 bits

• Pre-epidemic evolution of the MRSA USA300 clade and a molecular key for classification
  Bianco, Frontiers in cellular and infection microbiology 2023
  • “...USA300HOU_0191 (202764) , intergenic (265666) , USA300HOU_0397 (424978) , argS (670365) , intergenic (835434) , USA300HOU_0795 (850349) vwb (876702) , USA300HOU_0938 (982790) , oppD1 (990291) , ebh (1488257) , rluB (1611873) , comGA (1657533) , alaS (1723795) , tyrS (1843158) , USA300HOU_1746) 1877551) , intergenic (1978879)...”
• Insights Into the Impact of Small RNA SprC on the Metabolism and Virulence of Staphylococcus aureus
  Zhou, Frontiers in cellular and infection microbiology 2022
  • “...rsbV -67.3 SAOUHSC_02881 SA2351 -85.3 SAOUHSC_00871 dltc -66.1 SAOUHSC_01452 ald -84.9 SAOUHSC_03045 cspB -65.7 SAOUHSC_00788 SA0721 -84.4 SAOUHSC_03055 rpmH -61 SAOUHSC_01955 lukE -83.7 SAOUHSC_02853 SA2331 -59.8 SAOUHSC_01424 murG -83.6 SAOUHSC_01336 SA1176 -54.4 SAOUHSC_02329 thiM -82.9 All the mRNAs transcribed by DEGs with defined functions were predicted...”
• Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
  Anderson, FEMS immunology and medical microbiology 2010
  • “...SA0653 hypothetical protein sa_c7835s10216_x_at 4.2 2.5 2.5 SA0654 hypothetical protein sa_c8905s7823_a_at * 6.5 2.5 2.5 SA0721 hypothetical protein sa_c8928s7841_a_at * 4.5 2.5 2.5 SA0755 hypothetical protein sa_c8934s7849_a_at 7.5 2.5 2.5 SA0767 hypothetical protein sa_c8196s7173_a_at 12.2 2.5 stable SA0768 hypothetical protein sa_c8228s7205_a_at * 3.6 2.5 30 SA0777...”
  • “...SA0703 hypothetical protein sa_c8013s6998_a_at 26.8 2.5 2.5 SA0711 hypothetical protein sa_c8905s7823_a_at * 2.5 2.5 2.5 SA0721 hypothetical protein sa_c8079s7064_a_at 2.4 2.5 5 SA0734 hypothetical protein sa_c8131s7116_a_at 2.1 2.5 2.5 SA0749 hypothetical protein sa_c8147s7131_a_at 2.6 2.5 2.5 SA0752 hypothetical protein sa_c8151s7135_at 2.2 2.5 ND SA0753 hypothetical protein...”
• Insights Into the Impact of Small RNA SprC on the Metabolism and Virulence of Staphylococcus aureus
  Zhou, Frontiers in cellular and infection microbiology 2022
  • “...SAOUHSC_02300 rsbV -67.3 SAOUHSC_02881 SA2351 -85.3 SAOUHSC_00871 dltc -66.1 SAOUHSC_01452 ald -84.9 SAOUHSC_03045 cspB -65.7 SAOUHSC_00788 SA0721 -84.4 SAOUHSC_03055 rpmH -61 SAOUHSC_01955 lukE -83.7 SAOUHSC_02853 SA2331 -59.8 SAOUHSC_01424 murG -83.6 SAOUHSC_01336 SA1176 -54.4 SAOUHSC_02329 thiM -82.9 All the mRNAs transcribed by DEGs with defined functions were...”
• A new platform for ultra-high density Staphylococcus aureus transposon libraries
  Santiago, BMC genomics 2015
  • “...ruvA [ 31 - 34 ] Unknown SAOUHSC_00760 hypothetical protein [ 33 , 34 ] SAOUHSC_00788 hypothetical protein [ 31 , 33 , 34 ] * mprF aiso annotated as fmtC, and lcpA also annotated as msrR. Figure 6 Genes that influence fitness at high temperature....”
• Novel Pathways for Ameliorating the Fitness Cost of Gentamicin Resistant Small Colony Variants
  Vestergaard, Frontiers in microbiology 2016
  • “...compensation via membrane potential restoration was suppressed, however, selected for secondary mutations in fusA and SAUSA300_0749 . This study is the first to describe fitness compensatory events in SCVs with deletion mutations and adaptation of SCVs to continued exposure to gentamicin. Staphylococcus aureus evolution gentamicin resistance...”
  • “...the presence of gentamicin. All of the seven lineages contained mutations in either fusA and/or SAUSA300_0749 , while none of the lineages evolved without gentamicin contained mutations in these genes ( Figure 5 ). The gene fusA encodes the elongation factor G (EF-G) and mutations were...”
• The Staphylococcus aureus response to unsaturated long chain free fatty acids: survival mechanisms and virulence implications
  Kenny, PloS one 2009
  • “...protein 2.29 4.39E-03 SAR0733 conserved hypothetical protein 3.04 1.99E-03 SAR0734 conserved hypothetical protein 2.23 1.59E-03 SAR0821 conserved hypothetical protein 3.19 6.54E-03 SAR0825 conserved hypothetical protein 5.06 1.86E-03 SAR0840 putative membrane protein 5.25 2.63E-03 SAR0849 hypothetical protein 2.81 6.05E-03 SAR0850 hypothetical protein 2.94 6.81E-04 SAR0854 hypothetical protein...”
• Transcriptomic Adjustments of Staphylococcus aureus COL (MRSA) Forming Biofilms Under Acidic and Alkaline Conditions
  Efthimiou, Frontiers in microbiology 2019
  • “...| BAB83937.11 SepA multidrug resistance efflux pump 3.38 0.0023 General functions [transporters, DNA-RNA, general] ybhK SACOL0831 pir| B90736 probable structural protein 4.08 0.0340 not found ref | NP_337929.l| phosphate transport system regulator PhoU-related protein 3.35 0.0016 mdlB SACOL2430 502776-1 Predicted CDS, ABC transporter with ABC transporter...”

Eab7_2247 YvcK family protein from Exiguobacterium antarcticum B7
Aligns to 7:294 / 332 (86.7%), covers 99.7% of PF01933, 377.8 bits

• Functional annotation of hypothetical proteins from the Exiguobacterium antarcticum strain B7 reveals proteins involved in adaptation to extreme environments, including high arsenic resistance
  da, PloS one 2018
  • “...protein YflT 102 Eab7_2195 IPR024775 DinB superfamily protein 103 Eab7_2221 IPR027417 AAA ATPase domain 104 Eab7_2247 IPR002882 2-phospho-L-lactate transferase 105 Eab7_2260 IPR001478 PDZ domain 106 Eab7_2266 IPR003740 YitT_membrane Superfamily protein 107 Eab7_2301 IPR003740 YitT_membrane Superfamily protein 108 Eab7_2309 IPR007809 Flagellar biosynthesis protein FlgN 109 Eab7_2341 IPR003838...”

lp_0780 unknown from Lactobacillus plantarum WCFS1
Aligns to 13:304 / 333 (87.7%), covers 100.0% of PF01933, 358.8 bits

• Molecular insights into the biosynthesis of the F420 coenzyme
  Forouhar, The Journal of biological chemistry 2008
  • “...24% sequence identity to M. mazei CofD), the LP_0780 protein from Lactobacillus plantarum (PDB entry 2P0Y, 21% identity), and the SE_0549 protein from...”

lmo2473 conserved hypothetical protein from Listeria monocytogenes EGD-e
Aligns to 9:292 / 322 (88.2%), covers 100.0% of PF01933, 358.1 bits

• Vying for the control of inflammasomes: The cytosolic frontier of enteric bacterial pathogen-host interactions
  Sanchez-Garrido, Cellular microbiology 2020
  • “...release of its DNA and direct activation of the AIM2 inflammasome. A mutant lacking the lmo2473 gene lyses more in the cytosol of infected macrophages and hyperactivates the AIM2ASCcaspase1 inflammasome pathway (Sauer et al., 2010 ). AIM2 expression requires type I IFN signalling, consistent with which,...”
• AIM2 in health and disease: Inflammasome and beyond
  Kumari, Immunological reviews 2020
  • “...release or by suppressing the priming signals ( 134 137 ). Mutation in L. monocytogenes lmo2473 enhances bacterial lysis in the cytosol thus leading to increased AIM2 activation.( 138 ) Mtb has been reported to inhibit AIM2 inflammasome activation via its type VII secretion system ESX-1-mediated...”
• Evasion of inflammasome activation by microbial pathogens
  Ulland, The Journal of clinical investigation 2015
  • “...associated induction of host cell death. Mutation of lmo2473, a gene that encodes a protein of unknown function, resulted in L. monocytogenes that...”
  • “...linked to impaired cell wall integrity of the lmo2473 mutant, driving an increase in its intracellular lysis. Enhanced bacterial lysis resulted in an increase...”
• Listeria monocytogenes is resistant to lysozyme through the regulation, not the acquisition, of cell wall-modifying enzymes
  Burke, Journal of bacteriology 2014
  • “...lmo2515 lmo0290 lmo0971 lmo0973 lmo1741 lmo1745 lmo1746 lmo2219 lmo2473 lmo2768 pgdA pbpX rli31 degU walI dltD dltB virS virR Peptidoglycan deacetylase Putative...”
  • “...resistance or to the cell wall was unknown. lmo2473 encodes an uncharacterized protein that has been hypothesized to function in the synthesis of peptidoglycan...”
• Listeria monocytogenes induces IFNβ expression through an IFI16-, cGAS- and STING-dependent pathway
  Hansen, The EMBO journal 2014
  • “...infection with a L. monocytogenes mutant lacking the lmo2473 gene, and which lyses with increased frequency in the macrophage cytosol (Sauer et al, 2010),...”
• Listeria monocytogenes MDR transporters are involved in LTA synthesis and triggering of innate immunity during infection
  Tadmor, Frontiers in cellular and infection microbiology 2014
  • “...regulator spx family Regulation LMRG_01692.6 lmo2555 Glycosyl transferase LTA LMRG_01693.6 lmo2554 Galactosyl transferase LTA LMRG_01775.6 lmo2473 N/A unknown LMRG_01983.6 lmo2713 Cell wall bound protein, contains 1 GW-repeat Cell surface proteins LMRG_02415.6 lmo0170 Hypothetical protein Unknown LMRG_02642.6 lmo0220 Highly similar to cell division protein ftsH Cell division...”
• PrkC-mediated phosphorylation of overexpressed YvcK protein regulates PBP1 protein localization in Bacillus subtilis mreB mutant cells
  Foulquier, The Journal of biological chemistry 2014
  • “...essential (15). In Listeria monocytogenes, a mutation in lmo2473, the gene encoding the Rv1422 homolog, causes pyroptosis, followed by bacterial lysis in the...”
• Listeria monocytogenes triggers AIM2-mediated pyroptosis upon infrequent bacteriolysis in the macrophage cytosol
  Sauer, Cell host & microbe 2010
  • “...identify Listeria monocytogenes mutants that induced altered levels of host cell death. A mutation in lmo2473 resulted in hyper-stimulation of host cell death and IL-1 secretion (pyroptosis) following bacteriolysis in the macrophage cytosol. In addition, strains engineered to lyse in the cytosol by expression of both...”
  • “...death. The mutant with the most robust phenotype was identified as a transposon insertion in lmo2473 . Deletion of lmo2473 resulted in mutant bacteria that hyper-induced pyroptosis. Bacterial cell lysis caused either by the loss of lmo2473 , expression of bacteriophage holin and lysin or treatment...”
• More

LMOSA_4390 YvcK family protein from Listeria monocytogenes str. Scott A
Aligns to 9:292 / 322 (88.2%), covers 100.0% of PF01933, 356.9 bits

• The Natural Antimicrobial trans-Cinnamaldehyde Interferes with UDP-N-Acetylglucosamine Biosynthesis and Cell Wall Homeostasis in Listeria monocytogenes
  Sun, Foods (Basel, Switzerland) 2021
  • “...promoter, 7.5 kb, Km R [ 21 ] pIMK3-yvcK pIMK3 with yvcK gene (locus tag: LMOSA_4390) from Scott A pIMK3-glmU pIMK3 with glmU gene (locus tag: LMOSA_10910) from Scott A pIMK2-glmM pIMK2 with glmM gene (locus tag: LMOSA_1060) from Scott A pIMK2-glmS pIMK2 with glmS gene...”

LGG_00928 extracellular lipase/esterase precursor from Lactobacillus rhamnosus GG
DU507_04840, LGG_00928 uridine diphosphate-N-acetylglucosamine-binding protein YvcK from Lacticaseibacillus rhamnosus GG
Aligns to 18:311 / 342 (86.0%), covers 100.0% of PF01933, 354.6 bits

• A network-based approach to identify substrate classes of bacterial glycosyltransferases
  Sánchez-Rodríguez, BMC genomics 2014
  • “...predictions, two resulted from the screening with the Rossmann-fold domain (class I) ( LGG_01412 and LGG_00928 , see Table 2 ). The other novel predictions LGG_01195 (previously annotated as ABC transporter), LGG_00985 (previously annotated as integral membrane protein) and LGG_02347 (previously annotated as hypothetical protein were...”
• Ribosomal protein L4 of Lactobacillus rhamnosus LRB alters resistance to macrolides and other antibiotics
  Biswas, Molecular oral microbiology 2020
  • “...8.21 AXI93816 CutC (DU507_04540) 02 19.3 12.35 AXI94228 N-acetyltransferase (DU507_06850) 01 2.5 3.60 AXI93870 YvcK (DU507_04840) 02 6.1 3.07 AXI95791 Hydrolase (DU507_03460) 05 28.9 13.23 AXI94021 Hypothetical protein (DU507_05690) 03 12.0 10.51 AXI94794 Hydrolase (DU507_09985) 03 19.0 12.48 AXI94133 SufB (DU507_06315) 04 12.3 46.28 AXI95434 tRNA-ligase,...”

stu0832 hypothetical protein from Streptococcus thermophilus LMG 18311
Aligns to 6:298 / 324 (90.4%), covers 100.0% of PF01933, 351.2 bits

• Transcriptome analysis of adaptive heat shock response of Streptococcus thermophilus
  Li, PloS one 2011
  • “...many distant bacterial species. In addition, an operon consists of four hypothetical genes (stu0830, stu0831, stu0832 and stu0833) are increased with the expression level under the heat shock response. Among them, stu0830 is predicted to be a transmembrane protein with two transmembrane helices. These candidate unknown...”

SPy0653, SPy_0653 conserved hypothetical protein from Streptococcus pyogenes M1 GAS
Aligns to 6:298 / 325 (90.2%), covers 99.0% of PF01933, 344.5 bits

• Global Analysis and Comparison of the Transcriptomes and Proteomes of Group A Streptococcus Biofilms
  Freiberg, mSystems 2016
  • “...Hypothetical protein Spy0652 1.4 1.38 2.17 2.14 1.46 1.82 1.79 1.11 Predicted flavin-nucleotide-binding protein R Spy0653 czcD 3.04 2.94 1.82 3.18 3.08 1.96 2.53 2.43 1.31 Cobalt-zinc-cadmium resistance protein P Spy0716 3.93 3.98 2.6 2.5 2.55 1.17 2.15 2.19 0.82 Hypothetical protein Spy0787 1.02 0.95 1.05...”
• Mechanisms of group A Streptococcus resistance to reactive oxygen species
  Henningham, FEMS microbiology reviews 2015
  • “...etal. , 2011 ), demonstrated that mutants in a putative Zn 2+ efflux/activator system, czcD (Spy_0653) and gzcA (Spy_0654) resulted in increased susceptibility to Zn 2+ and clearance by innate immune cells in vitro and in a mouse model of soft-tissue infection (Ong etal. , 2014...”
• An antimicrobial role for zinc in innate immune defense against group A streptococcus
  Ong, The Journal of infectious diseases 2014 (PubMed)
  • “...mutants were constructed with deletions in the czcD gene (Spy0653; which encodes a putative zinc efflux pump) and adjacent gczA gene (Spy0654; which encodes a...”
  • “...addition to zinc uptake systems, GAS possesses czcD (Spy0653), which encodes a cation diffusion facilitator that is associated with resistance of cobalt, zinc,...”

spr1423 Conserved hypothetical protein from Streptococcus pneumoniae R6
Aligns to 6:299 / 325 (90.5%), covers 100.0% of PF01933, 326.8 bits

• Gain- and Loss-of-Function Screens Coupled to Next-Generation Sequencing for Antibiotic Mode of Action and Resistance Studies in Streptococcus pneumoniae
  Gingras, Antimicrobial agents and chemotherapy 2019
  • “...of S. pneumoniae R6 from gene dpr (spr1430) to spr1423. Genes are represented by open arrows. The dpr probe used for hybridizing the Northern blot is indicated....”
• Whole genome sequencing of penicillin-resistant Streptococcus pneumoniae reveals mutations in penicillin-binding proteins and in a putative iron permease
  Fani, Genome biology 2011
  • “...Conserved hypothetical protein T597C SYN spr1272 N-Acetylglucosamine-6-phosphate isomerase G385A G129R spr1384 UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine ligase G996A M332I spr1423 Conserved hypothetical protein A673G M225V spr1453 Major facilitator superfamily transporter T91C F31L spr1465 Conserved hypothetical protein G419A G140E spr1517 Penicillin-binding protein 2b C1245A D415E C1184T A395V C1528A G665D G1303A G435S...”

MXAN_3230 hypothetical protein from Myxococcus xanthus DK 1622
Aligns to 7:300 / 325 (90.5%), covers 99.7% of PF01933, 319.3 bits

• Synthesis and assembly of a novel glycan layer in Myxococcus xanthus spores
  Holkenbrink, The Journal of biological chemistry 2014
  • “...ID MXAN_3225 MXAN_3226 MXAN_3227 MXAN_3228 MXAN_3229 MXAN_3230 MXAN_3231 MXAN_3232 MXAN_3233 Predicted function (predicted domain accession; expect value)a 33...”

YbhK / b0780 putative transferase YbhK from Escherichia coli K-12 substr. MG1655 (see 3 papers)
b0780 predicted transferase with NAD(P)-binding Rossmann-fold domain from Escherichia coli str. K-12 substr. MG1655
Aligns to 12:300 / 302 (95.7%), covers 95.5% of PF01933, 280.1 bits

• Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding
  Bonocora, PLoS genetics 2015
  • “...b0656 insH3 204 11.713 P OS05 815921 4 T TGGC AGGTTAA TTGC T 815934 - b0780 ybhK 45 10.111 P OS06 847290 6 C TGGC ACGATTT TT T C A 847290 - b0811 glnH 44 10.791 C OS07 882891 10 T TGGC GAAGAAA TTGC A 882888...”
• Combinatorial strategies for improving multiple-stress resistance in industrially relevant Escherichia coli strains
  Lennen, Applied and environmental microbiology 2014
  • “...5.03 5.02 4.55 4.14 3.97 b0109 b3095 b1961 b0677 b3860 b0780 b3149 b0125 b3054 b2144 b1987 b0435 b2435 b4472 b4220 b4221 b3529 nadC yqjA dcm nagA dsbA ybhK diaA...”

c0861 Hypothetical protein ybhK from Escherichia coli CFT073
Aligns to 32:320 / 322 (89.8%), covers 95.2% of PF01933, 279.6 bits

• Transposon-Sequencing Analysis Unveils Novel Genes Involved in the Generation of Persister Cells in Uropathogenic Escherichia coli
  Molina-Quiroz, Antimicrobial agents and chemotherapy 2016
  • “...ampicillin Protein Gene Mean SIa c0147 c0608 c0751 c0764 c0861 c0909 c0943 c1174 c1176 c1179 c1254 c1303 c1560 c1572 c1610 c1822 c1884 c1888 c1925 c1927 c1945...”

VV1197 conserved hypothetical protein from Vibrio vulnificus YJ016
Aligns to 9:294 / 296 (96.6%), covers 95.5% of PF01933, 272.1 bits

• Genome-wide SNP-genotyping array to study the evolution of the human pathogen Vibrio vulnificus biotype 3
  Raz, PloS one 2014
  • “...lysA, pntA, pyrC and tnaA ) [26] , five conserved hypothetical genes (VV0048, VV0178, VV0415, VV1197 and VV1483) [27] , the 16S rRNA gene [56] , and seven newly selected genes ( S3 Table ). PCRs, sequencing and result analyses of selected loci were performed as...”

STM0801 putative cytoplasmic protein from Salmonella typhimurium LT2
Aligns to 12:300 / 302 (95.7%), covers 95.5% of PF01933, 270.1 bits

• High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach
  Allard, BMC genomics 2012
  • “...C/A H/N 562 e,f 1) transcriptional regulator (PadR), 2) family methyl-accepting chemotaxis protein II ybhK STM0801 SEEM020_19330 G/A L 618 a1 conserved hypothetical protein STM0818 SEEM020_19410 G/T A/S 277 e,f 1) putative ABC-type multidrug transport system, 2) membrane permease predicted cation efflux pump yliD STM0851 SEEM020_19565...”

KPNIH1_08215 uridine diphosphate-N-acetylglucosamine-binding protein YvcK from Klebsiella pneumoniae subsp. pneumoniae KPNIH1
Aligns to 12:298 / 301 (95.3%), covers 94.5% of PF01933, 268.1 bits

• A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae
  Sim, Microbiome 2022
  • “...These 3 SNPs, which were present in all evolved strains, included a missense SNP in KPNIH1_08215 (hypothetical protein), a synonymous SNP in KPNIH1_09140 (lipid transporter ATP-binding/permease), and a synonymous SNP in KPNIH1_09495 (gamma-glutamylputrescine synthetase). SNPs were named according to the Human Genome Variation Society (HGVS) nomenclature...”

SCO1951 hypothetical protein from Streptomyces coelicolor A3(2)
Aligns to 48:334 / 363 (79.1%), covers 89.0% of PF01933, 248.7 bits

• Developmental biology of Streptomyces from the perspective of 100 actinobacterial genome sequences
  Chandra, FEMS microbiology reviews 2014
  • “...production in E. coli (NCBI conserved domain PRK05416; SCO1952); and a protein of unknown function (SCO1951) that is related to an enzyme of cytochrome F420 biosynthesis, LPPG:Fo 2-phospho-L-lactate transferase (pfam01933). There is also conspicuous synteny on the other side of whiA in actinobacteria (but this does...”

GNGF_MYCTU / P9WMU5 Putative gluconeogenesis factor from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see paper)
NP_215938 hypothetical protein from Mycobacterium tuberculosis H37Rv
Rv1422 hypothetical protein from Mycobacterium tuberculosis H37Rv
WP_003407352 carbon utilization/virulence protein CuvA from Mycobacterium tuberculosis
Aligns to 5:297 / 342 (85.7%), covers 94.1% of PF01933, 247.8 bits

• function: Required for morphogenesis under gluconeogenic growth conditions.
• Mycobacterial gene cuvA is required for optimal nutrient utilization and virulence.
  Mir, Infection and immunity 2014
  • GeneRIF: Authors name this gene cuvA (carbon utilization and virulence protein A) and suggest a model in which deletion of cuvA leads to changes in nutrient uptake and/or metabolism that affect cell wall structure, morphology, and virulence.
• A proposed carbon-utilization and virulence protein A, CuvA (Rv1422), from Mycobacterium tuberculosis H37Rv: crystallization, X-ray diffraction analysis and ligand binding
  Jeong, Acta crystallographica. Section F, Structural biology communications 2020
  • “...protein A, CuvA (Rv1422), from Mycobacterium tuberculosis H37Rv: crystallization, X-ray diffraction analysis and ligand binding Yoon Chae Jeong and Ki Seog Lee*...”
  • “...of Korea Keywords: Mycobacterium tuberculosis; CuvA (Rv1422); bacterial adaptation; nutrient utilization; cell-wall precursor components. Department of Clinical...”
• Mycobacterial gene cuvA is required for optimal nutrient utilization and virulence
  Mir, Infection and immunity 2014
  • “...nutrient utilization and alterations in growth rate. M. tuberculosis Rv1422 is a conserved gene of unknown function that was found in a genetic screen to...”
  • “...interact with the mce4 cholesterol uptake locus. The Rv1422 protein is phosphorylated by the M. tuberculosis Ser/Thr kinases PknA and PknB, which regulate cell...”
• PrkC-mediated phosphorylation of overexpressed YvcK protein regulates PBP1 protein localization in Bacillus subtilis mreB mutant cells
  Foulquier, The Journal of biological chemistry 2014
  • “...shape and cell division (12). Interestingly, PknB phosphorylates Rv1422, a protein present in many bacteria, at the single yet non-conserved Thr-325 residue in...”
  • “...important functions. For example, in Staphylococcus aureus, the Rv1422 homolog is essential (15). In Listeria monocytogenes, a mutation in lmo2473, the gene...”
• Whole genome sequencing of Mycobacterium tuberculosis reveals slow growth and low mutation rates during latent infections in humans
  Colangeli, PloS one 2014
  • “...- - G Rv3586 - - - A A - - - - - G Rv1422 - - T - - - - - - - C lldD2 T - - - T T T T T T C fadE21 G - - - G G...”
• Mycobacterium tuberculosis Serine/Threonine Protein Kinases
  Prisic, Microbiology spectrum 2014
  • “...inhibits protein interactions ( 55 ) Rv0681 Transcriptional regulator In vitro (PknH) ( 116 ) Rv1422 Cell wall synthesis? In vitro (PknA and PknB), in vivo ( 17 ) Rvl747 ABC-transporter? Virulence factor In vitro (multiple kinases), in vivo, FHA domain interacts with kinases, activates (...”
• Eukaryote-like serine/threonine kinases and phosphatases in bacteria
  Pereira, Microbiology and molecular biology reviews : MMBR 2011
  • “...FtsZ GlmU GroEL1 KasA KasB MabA MurD PknB Rv1422 Wag31 Cell division Cell wall synthesis MurC PknB Cell division eSTK Pathogenesis Transaldolase; central...”
  • “...sigma factor; oxidative stress PBPA PknA RshA Rv0020c Rv1422 Rv1747 SigH Putative ABC transporter Mycolic acid biosynthesis Mycolic acid synthesis, cell wall...”
• Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases
  Prisic, Proceedings of the National Academy of Sciences of the United States of America 2010
  • “...defined M. tuberculosis phosphoproteins, including four STPKs, GarA, Rv1422, and FhaA (4, 8, 10). The MS/MS search algorithms that we used can identify the...”
  • “...at least two M. tuberculosis STPK substrates, GarA and Rv1422 (4, 23). The other implication is that other factors must contribute to in vivo substrate...”
• Phthiocerol dimycocerosate transport is required for resisting interferon-gamma-independent immunity
  Murry, The Journal of infectious diseases 2009
  • “...increased growth in iNOS / mice relative to wild-type mice at 4 weeks (Rv1224, Rv0326, Rv1422, and Rv3864; figure 1 ). None of these mutants was significantly overrepresented in iNOS / mice relative to wild-type mice at 3 weeks. The differences observed at these time points...”
  • “...to the stringent requirements used to identify reproducible attenuation and rescue. For example, mutations in Rv1422 consistently caused attenuation in mice and increased replication in iNOS / mice at 4 weeks but were not statistically significant at 3 weeks ( P =.055). Similarly, mutations in pstP...”
• More
• A proposed carbon-utilization and virulence protein A, CuvA (Rv1422), from Mycobacterium tuberculosis H37Rv: crystallization, X-ray diffraction analysis and ligand binding.
  Jeong, Acta crystallographica. Section F, Structural biology communications 2020
  • GeneRIF: A proposed carbon-utilization and virulence protein A, CuvA (Rv1422), from Mycobacterium tuberculosis H37Rv: crystallization, X-ray diffraction analysis and ligand binding.

Mb1457 CONSERVED HYPOTHETICAL PROTEIN from Mycobacterium bovis AF2122/97
Aligns to 5:297 / 342 (85.7%), covers 94.1% of PF01933, 246.7 bits

• Mutant analysis shows that alanine racemases from Pseudomonas aeruginosa and Escherichia coli are dimeric
  Strych, Journal of bacteriology 2002
  • “...(Table 1). The plasmids were transformed into E. coli MB1457 and verified by DNA sequence analysis. Some members of our group previously reported the cloning of...”
  • “...Source or reference Strains E. coli MG1655 BL21(DE3)/pLysS MB414 MB1457 MB1547 MB2859 MB2946 P. aeruginosa PAO1 lam rph-1 F ompT hsdSB(rB mB) gal dcm (DE3) Cmr...”

MSMEG_3080 hypothetical protein from Mycobacterium smegmatis str. MC2 155
Aligns to 5:296 / 354 (82.5%), covers 92.4% of PF01933, 244.1 bits

• Mycobacterial gene cuvA is required for optimal nutrient utilization and virulence
  Mir, Infection and immunity 2014
  • “...and M. tuberculosis cuvA deletion strains. To delete cuvA (MSMEG_3080) from M. smegmatis, a 1,008bp region (L arm) 5= to MSMEG_3080, including 6 codons of...”
  • “...Similarly, a 1,040-bp region (R arm) 3= to MSMEG_3080, including 100 bp of the MSMEG_3080 gene, was PCR amplified using primers MSMEG3080-cond-3 and...”
• LpqM, a mycobacterial lipoprotein-metalloproteinase, is required for conjugal DNA transfer in Mycobacterium smegmatis
  Nguyen, Journal of bacteriology 2009
  • “...had insertions in msmeg_0033, msmeg_1435, msmeg_1455, msmeg_3080, msmeg_4913, and msmeg_6128. Notably, four independent insertions were isolated in msmeg_4913,...”

CPS_2836 hypothetical protein from Colwellia psychrerythraea 34H
Aligns to 8:294 / 304 (94.4%), covers 95.5% of PF01933, 243.4 bits

• Subzero, saline incubations of Colwellia psychrerythraea reveal strategies and biomarkers for sustained life in extreme icy environments
  Mudge, Environmental microbiology 2021
  • “...Fig. 5B and C ), including a putative gluconeogenesis factor protein for regulating cell shape (CPS_2836), NAD kinase (NadK) which synthesizes NADP and acts as an essential reducing agent ( Spaans et al ., 2015 ), an ubiquinone kinase (UbiB) that functions under anaerobic conditions (...”

FQ188_04305 2-phospho-L-lactate transferase from Rhodococcus sp. ANT_H53B
Aligns to 3:319 / 324 (97.8%), covers 88.3% of PF01933, 208.8 bits

• Genome-Based Insights into the Production of Carotenoids by Antarctic Bacteria, Planococcus sp. ANT_H30 and Rhodococcus sp. ANT_H53B
  Styczynski, Molecules (Basel, Switzerland) 2020
  • “...2.7.7.68) (GenBank accession number: FQ188_05230), FO 2-phospho- l -lactate transferase (EC: 2.7.8.28) (GenBank accession number: FQ188_04305), and F420-0: l -glutamate ligase (EC: 6.3.2.31) (GenBank accession number: FQ188_04300)), involved in catalyzing a wide range of complex enzymatic redox reactions, which are widely distributed amongst archaeal methanogens and...”

6uw3B / A0QTG2 The crystal structure of fbia from mycobacterium smegmatis, gdp bound form (see paper)
Aligns to 3:317 / 326 (96.6%), covers 87.6% of PF01933, 204.7 bits

• Ligands: guanosine-5'-diphosphate; calcium ion (6uw3B)

MSMEG_1830 lppg:fo 2-phospho-l-lactate transferase from Mycobacterium smegmatis str. MC2 155
Aligns to 3:317 / 327 (96.3%), covers 87.6% of PF01933, 204.7 bits

• Cellular and Structural Basis of Synthesis of the Unique Intermediate Dehydro-F₄₂₀-0 in Mycobacteria
  Grinter, mSystems 2020
  • “...that the strains were otherwise isogenic. MSMEG_1829 ( fbiB ), MSMEG_2392 ( fbiD ), and MSMEG_1830 ( fbiA ) deletion mutants were generated by using the same methods used for MSMEG_5126, using gene-specific primer combinations ( TableS3 ). Individual deletion mutants of fbiA , fbiB ,...”
• Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria
  Selengut, Journal of bacteriology 2010
  • “...the biosynthetic genes for CofC (MSMEG_2393), CofD (fbiA; MSMEG_1830), CofE (fbiB; MSMEG_1829), and the fusion protein CofGH (fbiC; MSMEG_5126), 62 of the top...”

fbiA / P9WP81 phosphoenolpyruvate transferase (EC 2.7.8.28) from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 2 papers)
FBIA_MYCTU / P9WP81 Phosphoenolpyruvate transferase; EPPG:FO PEP transferase; EC 2.7.8.28 from Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (see 3 papers)
Rv3261 PROBABLE F420 BIOSYNTHESIS PROTEIN FBIA from Mycobacterium tuberculosis H37Rv
Aligns to 3:318 / 331 (95.5%), covers 87.2% of PF01933, 198.8 bits

• function: Catalyzes the transfer of the phosphoenolpyruvate moiety from enoylpyruvoyl-2-diphospho-5'-guanosine (EPPG) to 7,8-didemethyl-8- hydroxy-5-deazariboflavin (FO) with the formation of dehydro coenzyme F420-0 and GMP.
  catalytic activity: 7,8-didemethyl-8-hydroxy-5-deazariboflavin + enolpyruvoyl-2- diphospho-5'-guanosine = dehydro coenzyme F420-0 + GMP + H(+) (RHEA:27510)
  cofactor: Mg(2+)
  subunit: Homodimer.
• Refined understanding of the impact of the Mycobacterium tuberculosis complex diversity on the intrinsic susceptibility to pretomanid
  Rupasinghe, Microbiology spectrum 2024 (no snippet)
• Designing molecular diagnostics for current tuberculosis drug regimens
  Georghiou, Emerging microbes & infections 2023
  • “...F 420 pathway enzymes, including ddn ( Rv3547 ), fgd1 ( Rv0407 ), fbiA ( Rv3261 ), fbiB ( Rv3262 ), and fbiC ( Rv1173 ), is expected to result in cross-resistance [ 5053 ]. However, 10-17% of phenotypically pretomanid-resistant isolates have no mutations in these...”
• Mechanism of Action, Resistance, Synergism, and Clinical Implications of Delamanid Against Multidrug-Resistant Mycobacterium tuberculosis
  Khoshnood, Frontiers in microbiology 2021
  • “...glucose-6-phosphate dehydrogenase (G6PD; FGD1, Rv0407), as well as four coenzymes, Fbi A (Rv3361), Fbi B (Rv3261), Fbi C (Rv1173), and Rv0132c ( Bashiri et al., 2010 ; Hartkoorn et al., 2014 ). All of these genes and coenzymes are involved in the synthesis and recycling of...”
• Recombinant Rv3261 protein of Mycobacterium tuberculosis induces apoptosis through a mitochondrion-dependent pathway in macrophages and inhibits intracellular bacterial growth
  Lee, Cellular immunology 2020 (PubMed)
  • “...Rv3261 protein of Mycobacterium tuberculosis induces apoptosis through a mitochondrion-dependent pathway in macrophages and inhibits intracellular bacterial growth Cellular Immunology Journal fla 00088749 354 104145...”
  • “...understood. In this study, we investigated protein Rv3261, isolated from an Mtb culture filtrate, for its apoptotic potential using multidimensional...”
• Adduct Formation of Delamanid with NAD in Mycobacteria
  Hayashi, Antimicrobial agents and chemotherapy 2020 (secret)
• Whole Genome Sequencing for the Analysis of Drug Resistant Strains of Mycobacterium tuberculosis: A Systematic Review for Bedaquiline and Delamanid
  Nieto, Antibiotics (Basel, Switzerland) 2020
  • “...to BDQ resistance [ 9 ]. Similarly, off-target mutations at ddn (Rv3547), fgd1 (Rv0407), fbiA (Rv3261), fbiB (Rv3262), and fbiC (Rv1173) were associated to DLM resistance [ 6 , 10 , 11 ]. Resistance mechanisms for BDQ and DLM can be found in previous reviews [...”
  • “...them naturally resistant to DLM and pretomanid [ 57 ]. In the same sense, fbiA (Rv3261), fbiB (Rv3262), and fbiC (Rv1173) are essential for the mycobacterial F 420 synthesis that together with the glucose-6-phosphate dehydrogenase encoded by fgd1 (Rv0407) complete the conversion of DLM to its...”
• Characterization of Genomic Variants Associated with Resistance to Bedaquiline and Delamanid in Naive Mycobacterium tuberculosis Clinical Strains
  Battaglia, Journal of clinical microbiology 2020 (secret)
• Integrating informatics tools and portable sequencing technology for rapid detection of resistance to anti-tuberculous drugs
  Phelan, Genome medicine 2019
  • “...Bedaquiline Rv0678 Rv0678 5 (0) 2 (1) Clofazimine Rv0678 Rv0678 5 (0) 2 (1) Delamanid Rv3261 fbiA 1 (0) 0 (0) Drugs which are new to the library are bolded; indels insertions and deletions, FQ fluoroquinolones, PAS para-aminosalicylic acid. *Number of mutations observed in the ~17k...”
• More

ML0759 conserved hypothetical protein from Mycobacterium leprae TN
Aligns to 49:353 / 379 (80.5%), covers 87.2% of PF01933, 197.2 bits

• Use of transposon Tn5367 mutagenesis and a nitroimidazopyran-based selection system to demonstrate a requirement for fbiA and fbiB in coenzyme F(420) biosynthesis by Mycobacterium bovis BCG
  Choi, Journal of bacteriology 2001
  • “...of the arrangement of these homologs (the M. leprae homolog, ML0759, which was the same size as Rv3261, is listed in Table 2 but was omitted from Fig. 4...”
  • “...Homolog (organism) Rv3261 (M. tuberculosis) ML0759 (M. leprae) CAB88920 (Streptomyces) AF0917 (Archaeoglobus) MJ1256 (Methanococcus) Vng1429c (Halobacterium)...”

MAP_RS17350 2-phospho-L-lactate transferase from Mycobacterium avium subsp. paratuberculosis K-10
Aligns to 3:325 / 337 (95.8%), covers 86.9% of PF01933, 191.2 bits

• Diagnostic Sequences That Distinguish M. avium Subspecies Strains
  Bannantine, Frontiers in veterinary science 2020
  • “...PCR and Taq-based PCR. This gene encodes a hypothetical protein and is immediately upstream of MAP_RS17350 in Map K-10, but with a significant 27-amino acid overlap in these coding sequences. MAP_RS17350 is annotated as a frameshifted non-functional protein that contains several internal stop codons. The primers...”
  • “...MAP_RS22905 coding sequence while the reverse primer binds within the coding sequence that overlaps with MAP_RS17350. In the non- Map strains (as well as other Map strains) there is a single protein that is functional and encompasses the sequence that corresponds to MAP_RS22905 and MAP_RS17350. Therefore,...”

MAP3374 hypothetical protein from Mycobacterium avium subsp. paratuberculosis str. k10
Aligns to 9:331 / 343 (94.2%), covers 86.9% of PF01933, 191.1 bits

• The ability of Mycobacterium avium subsp. paratuberculosis to enter bovine epithelial cells is influenced by preexposure to a hyperosmolar environment and intracellular passage in bovine mammary epithelial cells
  Patel, Infection and immunity 2006
  • “...4.33 4.33 4.25 MAP2652c MAP2524c MAP0462 MAP0369 MAP1758c MAP3374 MAP0392c MAP4310c 4.02 3.89 3.79 3.72 3.56 3.43 3.23 3.08 Function(s) or characteristic(s)...”

cofD / Q58653 LPPG:Fo 2-phospho-L-lactate transferase subunit (EC 2.7.8.28) from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (see 3 papers)
COFD_METJA / Q58653 2-phospho-L-lactate transferase; LPPG:FO 2-phospho-L-lactate transferase; EC 2.7.8.28 from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) (see paper)
Q58653 2-phospho-L-lactate transferase (EC 2.7.8.28) from Methanocaldococcus jannaschii (see paper)
MJ1256 conserved hypothetical protein from Methanocaldococcus jannaschii DSM 2661
Aligns to 5:300 / 311 (95.2%), covers 88.6% of PF01933, 171.4 bits

• function: Catalyzes the transfer of the 2-phospholactate moiety from (2S)-lactyl-2-diphospho-5'-guanosine to 7,8-didemethyl-8-hydroxy-5- deazariboflavin (FO) with the formation of oxidized coenzyme F420-0 and GMP.
  catalytic activity: (2S)-lactyl-2-diphospho-5'-guanosine + 7,8-didemethyl-8- hydroxy-5-deazariboflavin = GMP + H(+) + oxidized coenzyme F420-0 (RHEA:63444)
  cofactor: Mg(2+)
  subunit: Homodimer.
• Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
  Pfeiffer, Genes 2021
  • “...MM_1874 Q8PVT6 [ 201 ] [ 196 ] 18252724 31469543 4a HVO_2479 (cont.) yes 32% MJ1256 Q58653 [ 202 ] 11888293 4a HVO_1936 cofE yes 47% AF_2256 O28028 [ 203 ] 17669425 4a HVO_1936 (cont.) yes 38% MJ0768 Q58178 [ 204 ] 12911320 4b HVO_0433 npdG...”
• Molecular insights into the biosynthesis of the F420 coenzyme
  Forouhar, The Journal of biological chemistry 2008
  • “...mg/liter of culture. Cloning, expression, and purification of MJ1256 from MethCofD protein was carried out as part of the high throughput protein production...”
  • “...to Northeast ously (20). The D50A mutant of MJ1256 was created with the Structural Genomics Consortium Target MaR46. The full- QuikChange site-directed...”
• Structure of an amide bond forming F(420):gamma-glutamyl ligase from Archaeoglobus fulgidus -- a member of a new family of non-ribosomal peptide synthases
  Nocek, Journal of molecular biology 2007
  • “...using recombinantly produced MJ1117 gene product and CofD (MJ1256) 27 from M. jannaschii . Each 1ml reaction mixture contained 50mM TrisHCl (pH 7.5), 0.1mM...”
• Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
  Pfeiffer, Genes 2021
  • “...Q8PVT6 [ 201 ] [ 196 ] 18252724 31469543 4a HVO_2479 (cont.) yes 32% MJ1256 Q58653 [ 202 ] 11888293 4a HVO_1936 cofE yes 47% AF_2256 O28028 [ 203 ] 17669425 4a HVO_1936 (cont.) yes 38% MJ0768 Q58178 [ 204 ] 12911320 4b HVO_0433 npdG yes...”

AF0917 conserved hypothetical protein from Archaeoglobus fulgidus DSM 4304
Aligns to 1:293 / 296 (99.0%), covers 91.0% of PF01933, 169.9 bits

• Use of transposon Tn5367 mutagenesis and a nitroimidazopyran-based selection system to demonstrate a requirement for fbiA and fbiB in coenzyme F(420) biosynthesis by Mycobacterium bovis BCG
  Choi, Journal of bacteriology 2001
  • “...ML0759 (M. leprae) CAB88920 (Streptomyces) AF0917 (Archaeoglobus) MJ1256 (Methanococcus) Vng1429c (Halobacterium) MTH1018 (Methanobacterium) SLL0154...”

Q8PVT6 2-phospho-L-lactate transferase (EC 2.7.8.28) from Methanosarcina mazei (see paper)
Aligns to 1:299 / 303 (98.7%), covers 87.9% of PF01933, 162.3 bits

• Improved production of the non-native cofactor F₄₂₀ in Escherichia coli
  Shah, Scientific reports 2021
  • “...described in Bashiri et al . 18 . The pathway consists of CofD (Accession number: Q8PVT6), CofE (A0QTG1), CofC (A0QUZ4) and CofGH (NC_008596) genes under the control of the tetracycline-inducible promoter BBa_R0040 56 and the artificial terminator BBa_B1006 57 . The F 420 biosynthesis operon had...”
• Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea.
  Pfeiffer, Genes 2021
  • “...[ 195 ] [ 196 ] 18260642 30952857 31469543 4a HVO_2479 cofD yes 39% MM_1874 Q8PVT6 [ 201 ] [ 196 ] 18252724 31469543 4a HVO_2479 (cont.) yes 32% MJ1256 Q58653 [ 202 ] 11888293 4a HVO_1936 cofE yes 47% AF_2256 O28028 [ 203 ] 17669425...”

3c3dA / Q8PVT6 Crystal structure of 2-phospho-(s)-lactate transferase from methanosarcina mazei in complex with fo and phosphate. Northeast structural genomics consortium target mar46 (see paper)
Aligns to 1:302 / 306 (98.7%), covers 88.3% of PF01933, 162.3 bits

• Ligands: phosphate ion; 1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2h)-yl)-d-ribitol (3c3dA)

cofD / E5ASS0 3-phospho-(R)-glycerate transferase (EC 2.7.8.28) from Mycetohabitans rhizoxinica (strain DSM 19002 / CIP 109453 / HKI 454) (see paper)
Aligns to 4:304 / 328 (91.8%), covers 90.3% of PF01933, 154.7 bits

YNB1_YEAST / P53980 Uncharacterized protein YNL011C from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see paper)
YNL011C Putative protein of unknown function; YNL011C is not an essential gene from Saccharomyces cerevisiae
Aligns to 3:440 / 444 (98.6%), covers 94.1% of PF01933, 145.3 bits

• Systematic profiling of ale yeast protein dynamics across fermentation and repitching
  Garge, G3 (Bethesda, Md.) 2024 (no snippet)
• A widespread inversion polymorphism conserved among Saccharomyces species is caused by recurrent homogenization of a sporulation gene family
  Salzberg, PLoS genetics 2022
  • “...in spores [ 63 , 64 ]. We integrated these markers into the non-essential gene YNL011C , which is located between the FF region and the centromere of chromosome XIV, to make parental base strains LS022 ( MAT a ynl011c :: P DIT1 -GFP ) and...”
• Evolutionary rescue of phosphomannomutase deficiency in yeast models of human disease
  Vignogna, eLife 2022
  • “...we observe multiple independent mutations in the known SEC53 -interactors RPN5 , SRP1 , and YNL011C in sec53 populations, which could have positive genetic interactions with sec53 ( Figure 2 ). We find a high probability that the mutational spectrum of PGM1 (five missense mutations, 0...”
• A Genome-Wide Screen for Genes Affecting Spontaneous Direct-Repeat Recombination in Saccharomyces cerevisiae
  Novarina, G3 (Bethesda, Md.) 2020
  • “...8.3 YEL014C 22.9 RAD55 29.2 BUD20 32.1 BDF1 11.1 CDC40 23.1 SNO1 29.2 RPS16A 32.6 YNL011C 12.5 MDM34 23.4 SPE2 29.2 SWI6 12.8 OST4 23.5 SPT21 29.2 URA1 13.2 YOL013W-B 24.0 TCD1 29.2 YGR272C 13.2 YCK1 24.3 TPM1 29.2 BUD19 13.3 KNH1 25.0 YDR157W 29.2 UGO1...”
• Genetic Networks Required to Coordinate Chromosome Replication by DNA Polymerases α, δ, and ε in Saccharomyces cerevisiae
  Dubarry, G3 (Bethesda, Md.) 2015
  • “...:: :MRC1 Pol CFD1 GPI15 INO2 PKR1 PMR1 PRE8 PRI1 RAD51 RAD54 RAD55 RFC5 RMI1 YNL011C Pol AIM4 ARC18 ARP4 ARP6 ATG21 ATO2 AZF1 BEM1 BET3 BFA1 BPH1 BRE2 BUB2 BUD27 CAT5 CDC21 CDC33 CHK1 CHS5 CKB1 CKB2 CLB2 CLB5 DCC1 DCR2 DEG1 DFG16 DIA2 DPB11...”
• Most, but not all, yeast strains in the deletion library contain the [PIN(+)] prion
  Manogaran, Yeast (Chichester, England) 2010
  • “...] cells YBL107C YDR491C YIL041W (GVP36) YMR307W (GAS1) YBR001C ( NTH2 ) YDR506C YIL073C (SPO22) YNL011C YBR010W ( HHT1 ) YDR552C ( SPS2 ) YJL003W (COX16) YNL109W YBR044C ( TCM62 ) YER141W ( COX15 ) YJL007C YNL141W (AAH1) YBR114W ( RAD16 ) YFL033C ( RIM15 )...”
• Combining chemical genomics screens in yeast to reveal spectrum of effects of chemical inhibition of sphingolipid biosynthesis
  Kemmer, BMC microbiology 2009
  • “...PRP11 SIR2 2.04 1.72 NST1 RHO2 2.03 3.02 SDS22 ACP1 3.09 1.71 1.95 2.60 SPO1 YNL011C YNL010W IDP3 ASI3 3.88 2.15 3.11 YHR162W SOL3 DNA2 2.92 2.99 YML081W DUS1 YML079W CPR3 1.75 2.81 EBS1 UME6 MSS4 YDR210W 2.35 2.43 Syntenic regions enriched after treatment with motuporamines....”
• Cumulative mutations affecting sterol biosynthesis in the yeast Saccharomyces cerevisiae result in synthetic lethality that is suppressed by alterations in sphingolipid profiles
  Valachovic, Genetics 2006
  • “...HDA3 RPN9 IES1 SSN2 BCK2 RDN25-1 RDN37-1 TAR1 YNL011C YNL010W M2-7A: erg2upc2ecm22 M6-3B: erg6upc2ecm22 MH1-3B: hap1upc2ecm22 M28-2D: erg28upc2ecm22 1 1 -- -- 1...”

HVO_2479 LPPG:Fo 2-phospho-L-lactate transferase from Haloferax volcanii DS2
Aligns to 2:325 / 330 (98.2%), covers 86.9% of PF01933, 143.3 bits

• Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea
  Pfeiffer, Genes 2021
  • “...MJ0887 Q58297 [ 194 ] [ 195 ] [ 196 ] 18260642 30952857 31469543 4a HVO_2479 cofD yes 39% MM_1874 Q8PVT6 [ 201 ] [ 196 ] 18252724 31469543 4a HVO_2479 (cont.) yes 32% MJ1256 Q58653 [ 202 ] 11888293 4a HVO_1936 cofE yes 47% AF_2256...”

A9WAV7 Gluconeogenesis factor from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)
Aligns to 152:329 / 391 (45.5%), covers 54.8% of PF01933, 139.2 bits

• Deciphering the functional role of hypothetical proteins from Chloroflexus aurantiacs J-10-f1 using bioinformatics approach
  Thakur, Molecular biology research communications 2020
  • “...protein M like A9WEQ6 Carbohydrate binding domain containing protein Cthe_2159 A9WAF1 O antigen ligase related A9WAV7 LPPG:FO 2 phospho L lactate transferaseCofD/UPF0052 A9WBQ0 Glycoside hydrolase family 30 A9WBU0 Glycoside hydrolase superfamily A9WCD7 Peptidase C11, clostripain A9WCF4 PDZ superfamily A9WD37 Putative zincin peptidase A9WD59 4Fe4S_Fe-S-bd, NarG like...”
  • “...4 22015 20.02 stable 95.06 0.208 A9WAF1 511 58050.12 10.05 125820 45.72 unstable 121.14 0.683 A9WAV7 391 43267.39 6.16 37485 40.53 unstable 119.67 0.225 A9WBQ0 461 50401.05 4.59 92485 42.22 unstable 88.29 0.005 A9WCD7 907 97634.61 4.58 99615 39.74 stable 98.29 0.009 A9WCF4 511 57752.24 5.23...”

An14g06550 uncharacterized protein from Aspergillus niger
Aligns to 11:446 / 509 (85.7%), covers 82.4% of PF01933, 137.9 bits

• Genomic analysis of the secretion stress response in the enzyme-producing cell factory Aspergillus niger
  Guillemette, BMC genomics 2007
  • “...0.1 An18g06120 similar to secreted protein vc33_1 1.9 0.2 *-1.1 0.1 2.2 0.1 *1.0 0.05 An14g06550 hypothetical protein 2.1 0.3 *1.2 0.1 2.8 0.6 *1.2 0.1 An15g02650 hypothetical protein 2.8 1.5 *1.1 0.2 2.8 0.6 *1.1 0.1 An11g10800 similar to probable isochorismatase 2.3 0.3 *1.0 0.002...”

AT2G34090 MEE18 (maternal effect embryo arrest 18) from Arabidopsis thaliana
Aligns to 54:421 / 445 (82.7%), covers 94.8% of PF01933, 136.4 bits

• The tomato chloroplast stromal proteome compendium elucidated by leveraging a plastid protein-localization prediction Atlas
  Bhattacharya, Frontiers in plant science 2023
  • “...Solyc05g024330 Unknown Protein Solyc06g042980 Uncharacterized protein At3g12590 Solyc12g056350 Unknown Protein At2g32500 Solyc02g076950 UPF0052 domain protein At2g34090 A All primary data for the novel proteins are found in Table S2A . An expanded version of Table3 is found in Table S2C . Table S2C includes # of...”
• Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing
  Chen, BMC genomics 2018
  • “...pollen germination; plasma membrane component gma-circRNA1432 Glyma.10G217200 AT1G76850 pollen germination; pollen tube growth gma-circRNA1856 Glyma.13G230500 AT2G34090 pollen gametogenesis; pollen germination; pollen tube-embryo sac interactions gma-circRNA2481 Glyma.18G164900 AT5G48720 pollen development; DNA repair; male meiosis gma-circRNA2791 Glyma.20G182800 AT3G10380 pollen germination; pollen tube growth gma-circRNA1934 Glyma.14G119800 AT1G43850 flower development;...”

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