Family Search for PF03653 (UPF0093)
April 2024: See Interactive Tools for Functional Annotation of Bacterial Genomes for advice on using these tools.
PF03653 hits 23 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
BDOA9_0112090 protoporphyrinogen oxidase HemJ from Bradyrhizobium sp. DOA9
Aligns to 2:144 / 144 (99.3%), covers 98.6% of PF03653, 205.6 bits
- Genome analysis of a novel Bradyrhizobium sp. DOA9 carrying a symbiotic plasmid
Okazaki, PloS one 2015 - “...conserved hypothetical proteins bll0636 and blr0637 [ 4 ]. The orthologs of these two genes, BDOA9_0112090 and BDOA9_0112080, were found at coordinates 1,313,579 to 1,313,070 and 1,312,684 to 1,311,839, respectively. The dif sequence, which is required to convert a dimer chromosome to monomers after aberrant DNA...”
RPA0297 conserved hypothetical protein from Rhodopseudomonas palustris CGA009
Aligns to 8:150 / 150 (95.3%), covers 98.6% of PF03653, 205.0 bits
bll0636 bll0636 from Bradyrhizobium japonicum USDA 110
Aligns to 1:140 / 140 (100.0%), covers 97.9% of PF03653, 203.1 bits
- Genome analysis of a novel Bradyrhizobium sp. DOA9 carrying a symbiotic plasmid
Okazaki, PloS one 2015 - “...B . japonicum USDA110, the putative replication origin was positioned between two conserved hypothetical proteins bll0636 and blr0637 [ 4 ]. The orthologs of these two genes, BDOA9_0112090 and BDOA9_0112080, were found at coordinates 1,313,579 to 1,313,070 and 1,312,684 to 1,311,839, respectively. The dif sequence, which...”
- Complete Genome Sequence of the Soybean Symbiont Bradyrhizobium japonicum Strain USDA6T
Kaneko, Genes 2011 - “...Bradyrhizobiaceae [ 10 ]. In the case of USDA110, the putative origin is positioned between bll0636 (conserved hypothetical protein) and blr0637 (conserved hypothetical protein). In USDA6 T , BJ6T06040 and BJ6T06050 were found to be orthologs of these two genes, respectively. This intergenic region showed a...”
PP0431 conserved hypothetical protein TIGR00701 from Pseudomonas putida KT2440
Aligns to 1:141 / 141 (100.0%), covers 97.9% of PF03653, 195.8 bits
HP1484 conserved hypothetical integral membrane protein from Helicobacter pylori 26695
Aligns to 4:148 / 148 (98.0%), covers 98.6% of PF03653, 190.1 bits
PA0661 hypothetical protein from Pseudomonas aeruginosa PAO1
Aligns to 1:140 / 140 (100.0%), covers 97.9% of PF03653, 185.3 bits
Cj0362 putative integral membrane protein from Campylobacter jejuni subsp. jejuni NCTC 11168
Aligns to 5:150 / 150 (97.3%), covers 99.3% of PF03653, 183.8 bits
- In Campylobacter jejuni, a new type of chaperone receives heme from ferrochelatase
Zamarreño, Frontiers in genetics 2023 - “...cj124 3), CgdH1 ( cj0992c ), CgdH2 ( cj0363c ), CgdH3( cj0580c ), PgdH2 ( cj0362 ), and PpfC ( cj0503c ) were amplified by PCR from genomic DNA, extracted according to the manufacturers instructions (QIAprep Spin Miniprep Kit), using the Phusion High-Fidelity DNA Polymerase (Thermo...”
- “...PgoX, PgdH1, and PgdH2. A search of the C. jejuni genome retrieved a PgdH2-like enzyme (Cj0362) that exhibits 39% and 38% identity with PgdH2 from Synechocystis sp. and Acinetobacter baylyi , respectively ( Figure 4A ). Despite our efforts to purify C. jejuni Cj0362 to homogeneity,...”
- Application of TraDIS to define the core essential genome of Campylobacter jejuni and Campylobacter coli
Stoakes, BMC microbiology 2023 - “...found to have functions, but have not been annotated as such (Cj1276c FtsX, Cj0801 MurJ, Cj0362 HemJ and Cj0313 LptF/G). Two genes, Cj0651 and Cj1637c, have no functional domains predicted but are annotated as an integral membrane protein and a periplasmic domain respectively. We performed a...”
Pden_0001 conserved hypothetical protein 701 from Paracoccus denitrificans PD1222
Aligns to 5:148 / 148 (97.3%), covers 96.6% of PF03653, 182.8 bits
RP883 unknown from Rickettsia prowazekii str. Madrid E
Aligns to 1:144 / 145 (99.3%), covers 100.0% of PF03653, 177.9 bits
CCNA_03877 hypothetical protein from Caulobacter crescentus NA1000
Aligns to 21:169 / 171 (87.1%), covers 97.9% of PF03653, 174.3 bits
hemJ / P72793 protoporphyrinogen oxidase monomer (EC 1.3.3.4) from Synechocystis sp. (strain PCC 6803 / Kazusa) (see 3 papers)
HEMJ_SYNY3 / P72793 Protoporphyrinogen IX oxidase; PPO; Protox; EC 1.3.99.- from Synechocystis sp. (strain PCC 6803 / Kazusa) (see 2 papers)
P72793 protoporphyrinogen oxidase (EC 1.3.3.4) from Synechocystis sp. (see paper)
slr1790 hypothetical protein from Synechocystis sp. PCC 6803
Aligns to 16:164 / 210 (71.0%), covers 98.6% of PF03653, 172.3 bits
- function: Catalyzes the oxidation of protoporphyrinogen IX to protoporphyrin IX. Is involved in the biosynthesis of tetrapyrrole molecules like heme and chlorophyll. Does not use oxygen or artificial electron acceptors such as menadione or benzoquinone. Is functionally coupled with coproporphyrinogen III oxidase (CPO) (PubMed:29925590). Is essential for growth (PubMed:20823222).
catalytic activity: 3 A + protoporphyrinogen IX = 3 AH2 + protoporphyrin IX (RHEA:62000)
cofactor: heme b (Binds 1 heme b (iron(II)-protoporphyrin IX) group per subunit.)
subunit: Homodimer. Can also form higher oligomers, most probably tetramers. Interacts with Sll1106, however it is unlikely that Sll1106 is required for PPO function.
disruption phenotype: Attempts to disrupt this gene in the wild-type background of Synechocystis only allow to obtain heteroplasmic disruptants. These cells accumulate a substantial amount of protoporphyrin IX. - Promoting Heme and Phycocyanin Biosynthesis in Synechocystis sp. PCC 6803 by Overexpression of Porphyrin Pathway Genes with Genetic Engineering
Cao, Marine drugs 2023 - “...6803, including hemA-syn (slr1808), hemB-syn (sll1994), hemC-syn (slr1887), hemE-syn (slr0536), hemF-syn (sll1185), hemH-syn (slr0839), hemJ-syn (slr1790), hemL-syn (sll0017), hemN-syn (sll1876), and glbn (slr2097), were amplified by PCR, and the promoter Pcpc560 (P) was connected with each of the heme genes to obtain the overlapped fragment P+gene....”
- The cyanobacterial protoporphyrinogen oxidase HemJ is a new b-type heme protein functionally coupled with coproporphyrinogen III oxidase
Skotnicová, The Journal of biological chemistry 2018 - “...nitrate by corresponding reductases (8). Most recently, the slr1790 gene from the cyanobacterium Synechocystis 6803 has been described as the third PPO and...”
- “...at the C terminus (HemJ.f), the hemJ gene (slr1790) was cloned into the pPD-CFLAG plasmid containing the Synechocystis 6803 psbAII promoter, a sequence encoding...”
- Patterns in evolutionary origins of heme, chlorophyll a and isopentenyl diphosphate biosynthetic pathways suggest non-photosynthetic periods prior to plastid replacements in dinoflagellates
Matsuo, PeerJ 2018 - “...is not registered in the current KEGG pathway, by using UPF0093 membrane protein encoded by slr1790 in Synechocystis sp. strain PCC 6803 (UniProtKB P72793) as the query. Both N-DVR and F-DVR are included in a single KOID (K19073), but the sequences deposited in the GenBank database...”
- The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels
Hernández-Prieto, G3 (Bethesda, Md.) 2017 - “...a HemY-like domain. A BLAST search, using the sequence for the Synechocystis HemJ (encoded by slr1790 ) ( Kato et al. 2010 ), returned AM1_2801 as being highly homologous to HemJ. Unlike AM1_5767 , the expression of AM1_2801 was not influenced by altered O 2 levels,...”
- Evolutionary Aspects and Regulation of Tetrapyrrole Biosynthesis in Cyanobacteria under Aerobic and Anaerobic Environments
Fujita, Life (Basel, Switzerland) 2015 - “...this protein uses menaquinone rather than oxygen as an electron acceptor [ 28 ]. HemJ (Slr1790) was recently found to be a third PPgen oxidase in Synechocystis 6803 [ 26 ]. The PPgen oxidase assay with a purified Slr1790-like homolog from R. sphaeroides in E. coli...”
- A novel "oxygen-induced" greening process in a cyanobacterial mutant lacking the transcriptional activator ChlR involved in low-oxygen adaptation of tetrapyrrole biosynthesis
Aoki, The Journal of biological chemistry 2014 - “...primer for hemN (sll1876) Forward primer for hemJ (slr1790) Reverse primer for hemJ (slr1790) Forward primer for chlD (slr1777) Reverse primer for chlD...”
- Identification of a gene essential for protoporphyrinogen IX oxidase activity in the cyanobacterium Synechocystis sp. PCC6803
Kato, Proceedings of the National Academy of Sciences of the United States of America 2010 - “...Protox. Several cell lines containing the tagged slr1790 locus exhibited acifluorfen sensitivity. The slr1790 gene encodes a putative membrane-spanning protein...”
- “...substantial amount of protoporphyrin IX, suggesting that the slr1790 gene is essential for growth and Protox activity of cells. We found that most cyanobacteria...”
- In Campylobacter jejuni, a new type of chaperone receives heme from ferrochelatase
Zamarreño, Frontiers in genetics 2023 - “...[Cj0362, UniProt (UP): Q0PBE8], with two previously studied protoporphyrinogen oxidases, PgoX from Synechocystis sp. (UP: P72793) and Acinetobacter baylyi , (UP: Q6FDT1), carried out using Clustal Omega and edited using Jalview 2.11.2.5. Dark blue boxes highlight residues with a percentage identity >80%. The lighter the blue...”
- Patterns in evolutionary origins of heme, chlorophyll a and isopentenyl diphosphate biosynthetic pathways suggest non-photosynthetic periods prior to plastid replacements in dinoflagellates
Matsuo, PeerJ 2018 - “...by using UPF0093 membrane protein encoded by slr1790 in Synechocystis sp. strain PCC 6803 (UniProtKB P72793) as the query. Both N-DVR and F-DVR are included in a single KOID (K19073), but the sequences deposited in the GenBank database were subjected to the initial survey as queries...”
ZMO1997 hypothetical protein from Zymomonas mobilis subsp. mobilis ZM4
Aligns to 8:151 / 151 (95.4%), covers 99.3% of PF03653, 168.2 bits
- Towards an informative mutant phenotype for every bacterial gene
Deutschbauer, Journal of bacteriology 2014 - “...for genes that were, in hindsight, annotated erroneously (ZMO1997 and ZMO1510). More often, we obtained a specific prediction by comparing the gene's phenotypes...”
- “...for catechol/protocatechualdehyde Annotation correction ZMO1510 ZMO1997 Misannotated as HemK family protein; actually a methyltransferase-modifying release...”
SYNPCC7002_A0644 hypothetical protein from Synechococcus sp. PCC 7002
Aligns to 9:157 / 204 (73.0%), covers 97.9% of PF03653, 166.9 bits
Synpcc7942_0849 conserved hypothetical protein from Synechococcus elongatus PCC 7942
Aligns to 8:156 / 203 (73.4%), covers 97.3% of PF03653, 166.4 bits
- Promoting Heme and Phycocyanin Biosynthesis in Synechocystis sp. PCC 6803 by Overexpression of Porphyrin Pathway Genes with Genetic Engineering
Cao, Marine drugs 2023 - “...7942, including hemA-syf (Synpcc7942_0504), hemB-syf (Synpcc7942_1792), hemC-syf (Synpcc7942_0967), hemE-syf (Synpcc7942_1086), hemF-syf (Synpcc7942_0674), hemH-syf (Synpcc7942_0137), hemJ-syf (Synpcc7942_0849), and hemL-syf (Synpcc7942_0645), were homologously recombined to obtain the overexpression plasmids of strain PCC 7942 heme synthesis genes. The two endogenous genes of strain PCC 6803, i.e., hemD-syn (sll0166) and...”
APH_1307 hypothetical protein from Anaplasma phagocytophilum HZ
Aligns to 4:146 / 147 (97.3%), covers 98.6% of PF03653, 162.6 bits
AM1_2801 hypothetical protein from Acaryochloris marina MBIC11017
Aligns to 1:147 / 189 (77.8%), covers 97.3% of PF03653, 161.1 bits
- The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels
Hernández-Prieto, G3 (Bethesda, Md.) 2017 - “...ChlB 1659 417 2684 1.99 0.69 AM1_4366 Uroporphyrin-III C-methyltransferase, CysG 195 92 430 1.08 1.14 AM1_2801 Protein with homology to HemJ 182 178 162 0.03 0.17 AM1_0467 O 2 -independent coproporphyrinogen III oxidase, HemN 6 822 5 6.88 0.22 AM1_1283 O 2 -independent coproporphyrinogen III oxidase,...”
- “...for the Synechocystis HemJ (encoded by slr1790 ) ( Kato et al. 2010 ), returned AM1_2801 as being highly homologous to HemJ. Unlike AM1_5767 , the expression of AM1_2801 was not influenced by altered O 2 levels, suggesting that the main pathway for the oxidation of...”
ACIAD0878 conserved hypothetical protein; putative membrane protein from Acinetobacter sp. ADP1
Aligns to 5:150 / 150 (97.3%), covers 97.9% of PF03653, 159.2 bits
WP_026851012 protoporphyrinogen oxidase HemJ from Gemmatimonas phototrophica
Aligns to 1:144 / 144 (100.0%), covers 98.6% of PF03653, 158.7 bits
- Gemmatimonas groenlandica sp. nov. Is an Aerobic Anoxygenic Phototroph in the Phylum Gemmatimonadetes
Zeng, Frontiers in microbiology 2020 - “...WP_075071451 WP_075071577 QJR35625 n. d. Protoporphyrinogen oxidase Protoporphyrinogen IX Protoporphyrin IX hemJ* (aerobic) hemG (anaerobic) WP_026851012 WP_053334334 QJR36952 QJR35626 Mg-protoporphyrin IX monomethyl ester oxidative cyclase Mg-protoporphyrin IX Divinylprotochlorophyllide acsF (aerobic) bchE (anaerobic) WP_082821546 WP_026851009 QJR35611 n. d. Oxidative stress response Bacteriophytochrome, two-component sensor histidine kinase Light...”
BP2372 putative conserved inner membrane protein from Bordetella pertussis Tohama I
Aligns to 1:140 / 140 (100.0%), covers 96.6% of PF03653, 152.6 bits
- A curated genome-scale metabolic model of Bordetella pertussis metabolism
Fyson, PLoS computational biology 2017 - “...present. In some other bacteria missing HemG/Y an alternative gene, hemJ , encodes this activity. BP2372 was identified as a potential hemJ homologue and was not associated with any other reaction in the model. Thus, the model was curated to include BP2372 as performing this step....”
FGG12_RS23205 CopD family protein from Cupriavidus campinensis
Aligns to 1:140 / 140 (100.0%), covers 96.6% of PF03653, 151.5 bits
Q9K166 Protoporphyrinogen IX oxidase from Neisseria meningitidis serogroup B (strain MC58)
Aligns to 1:142 / 142 (100.0%), covers 97.9% of PF03653, 148.6 bits
BCAL3369 hypothetical protein from Burkholderia cenocepacia J2315
Aligns to 1:140 / 140 (100.0%), covers 97.9% of PF03653, 136.4 bits
- Comparative analysis of the Burkholderia cenocepacia K56-2 essential genome reveals cell envelope functions that are uniquely required for survival in species of the genus Burkholderia
Gislason, Microbial genomics 2017 - “...a lethal phenotype: dxs (BCAM0911), hemE (BCAL0040), infB (BCAL1507), gyrB (BCAL0421), ubiB (BCAL0876), valS (BCAL1448), BCAL3369, and murJ (BCAL2764) [ 6467 ]. In addition, we confirmed the essentiality of genes previously characterized by our laboratory. These genes encode EtfAB, an essential electron transfer flavoprotein [ 68...”
- Candidate Essential Genes in Burkholderia cenocepacia J2315 Identified by Genome-Wide TraDIS
Wong, Frontiers in microbiology 2016 - “.... In addition, a number of essential genes ( dxs, hemE, infB, gyrB, ubiB, valS, BCAL3369 , and murJ ) previously validated by a conditional lethal phenotype were also deemed to be essential based on our TraDIS prediction ( Cardona et al., 2006 ; Ortega et...”
- High confidence prediction of essential genes in Burkholderia cenocepacia
Juhas, PloS one 2012 - “..., as well as the so far uncharacterized genes BCAL1882 , BCAL2769 , BCAL3142 and BCAL3369 has been confirmed experimentally in B. cenocepacia . Conclusions/Significance We report on the identification of essential genes using a novel bioinformatics strategy and provide bioinformatics and experimental evidence that the...”
- “...demonstrated to be essential in another organism, namely: infB, gyrB, ubiB, valS , BCAL3142 and BCAL3369 ( Figure S2 ). Gene essentiality is condition dependent. For example, while the referred DEG database lists 1617 E. coli MG1655 genes as essential, other experimentally more rigorous studies list...”
XOO1954 hypothetical protein from Xanthomonas oryzae pv. oryzae KACC10331
Aligns to 31:179 / 179 (83.2%), covers 98.6% of PF03653, 134.4 bits
Or search for genetic data about PF03653 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory