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Conserved domains on  [gi|445925816|ref|WP_000003671|]
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MULTISPECIES: hydrogenase 1 maturation protease [Enterobacteriaceae]

Protein Classification

HyaD/HybD family hydrogenase maturation endopeptidase; hydrogenase maturation protease( domain architecture ID 10793362)

HyaD/HybD family hydrogenase maturation endopeptidase similar to Escherichia coli HybD that catalyzes the nickel-dependent cleavage of a short C-terminal peptide after a His or an Arg residue in the large subunit (pre-HybC) of hydrogenase 2| hydrogenase maturation protease similar to Thermococcus kodakarensis [NiFe] hydrogenase maturation protease HybD, which is involved in the cleavage of the C-terminal residues of [NiFe] hydrogenase large subunits by Ni recognition

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK10264 PRK10264
hydrogenase 1 maturation protease; Provisional
 1-195 4.31e-143

hydrogenase 1 maturation protease; Provisional


:

Pssm-ID: 182345  Cd Length: 195  Bit Score: 396.31  E-value: 4.31e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   1 MSEQRVVVMGLGNLLWADEGFGVRVAERLYAHYHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYA 80
Cdd:PRK10264   1 MSEQRVVVMGLGNLLWADEGFGVRVAERLYAHYHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816  81 GERIPAYLSAKKMSLHQNSFSEVLALADIRGHLPAHIALVGLQPAMLDDYGGSLSELAREQLPAAEQAALAQLAAWGIVP 160
Cdd:PRK10264  81 GERIPAYLSAKKMSLHQNSFSEVLALADIRGHLPAHIALVGLQPAMLDDYGGSLSELAREQLPAAEQAALAQLAAWGIVP 160

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 445925816 161 QPANESRCLNYDCLSMENYEGVRLRQYRMTQEEQG 195
Cdd:PRK10264 161 QPANESRCLNYDCLSMENYEGVRLRQYRMTLEEQG 195
 
Name Accession Description Interval E-value
PRK10264 PRK10264
hydrogenase 1 maturation protease; Provisional
 1-195 4.31e-143

hydrogenase 1 maturation protease; Provisional


Pssm-ID: 182345  Cd Length: 195  Bit Score: 396.31  E-value: 4.31e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   1 MSEQRVVVMGLGNLLWADEGFGVRVAERLYAHYHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYA 80
Cdd:PRK10264   1 MSEQRVVVMGLGNLLWADEGFGVRVAERLYAHYHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816  81 GERIPAYLSAKKMSLHQNSFSEVLALADIRGHLPAHIALVGLQPAMLDDYGGSLSELAREQLPAAEQAALAQLAAWGIVP 160
Cdd:PRK10264  81 GERIPAYLSAKKMSLHQNSFSEVLALADIRGHLPAHIALVGLQPAMLDDYGGSLSELAREQLPAAEQAALAQLAAWGIVP 160

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 445925816 161 QPANESRCLNYDCLSMENYEGVRLRQYRMTQEEQG 195
Cdd:PRK10264 161 QPANESRCLNYDCLSMENYEGVRLRQYRMTLEEQG 195
hupD TIGR00140
hydrogenase expression/formation protein; valid names: hupD, hynC, hoxM. C at 64 and 67 are ...
 23-157 7.23e-63

hydrogenase expression/formation protein; valid names: hupD, hynC, hoxM. C at 64 and 67 are believed to be metal binding. Postulated to be involved in processing or hydrogenase. Superfamily suggests that it is a peptidase/protease. [Protein fate, Protein modification and repair]


Pssm-ID: 129246  Cd Length: 134  Bit Score: 190.98  E-value: 7.23e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   23 VRVAERLYAHYHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYAGERIPAYLsAKKMSLHQNSFSE 102
Cdd:TIGR00140   1 VRLVEALQQRYAFPDNVTLLDGGTQGLYLLPLIESADRLIILDAVDYGLEPGTLYILRDEEVPKFL-AKKMSLHQTGFQE 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 445925816  103 VLALADIRGHLPAHIALVGLQPAMLDDYGGSLSELAREQLPAAEQAALAQLAAWG 157
Cdd:TIGR00140  80 VLALAELLGHLPKELVLIGVQPEELEDYGGSLSPEVAEAIPPAIEIALAQLAEWG 134
H2MP_MemB-H2up cd06062
Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer ...
 6-143 1.72e-62

Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD from E. coli is well studied in this group. Maturation of [NiFe] hydrogenases include proteolytic processing of large subunit, assembly with other subunits, and formation of the nickel metallocenter. Hydrogenase maturation endopeptidase (HybD) cleaves a short C-terminal peptide after a His or an Arg residue in the large subunit (pre-HybC) of hydrogenase 2 (hyb operon) in E. coli. This cleavage is nickel dependent. A variety of endopeptidases belong to this group that are similar in function and sequence homology. They include such proteins as HynC, HoxM, and HupD.


Pssm-ID: 99873  Cd Length: 146  Bit Score: 190.36  E-value: 1.72e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   6 VVVMGLGNLLWADEGFGVRVAERLYAHYHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYAGERIP 85
Cdd:cd06062    1 ILVLGIGNILLADEGIGVHAVERLEENYSFPENVELIDGGTLGLELLPYIEEADRLIIVDAVDAGGPPGTVYRFEGEDVP 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 445925816  86 AYLSAkKMSLHQNSFSEVLALADIRGHLPAHIALVGLQPAMLdDYGGSLSELAREQLP 143
Cdd:cd06062   81 AFLSA-KLSAHQVGLLEVLALAELLGDLPPEIVLIGVQPESI-EWGLELSPEVAAALP 136
HycI pfam01750
Hydrogenase maturation protease; The family consists of hydrogenase maturation proteases. In E. ...
 23-143 3.65e-54

Hydrogenase maturation protease; The family consists of hydrogenase maturation proteases. In E. coli HypI the hydrogenase maturation protease is involved in processing of HypE the large subunit of hydrogenases 3, by cleavage of its C-terminal.


Pssm-ID: 396353  Cd Length: 130  Bit Score: 168.61  E-value: 3.65e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   23 VRVAERLYAHYHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYAGERIPAYLSAKKMSLHQNSFSE 102
Cdd:pfam01750   1 VRVVEELKRRYAFPENVTVIDGGTGGLYLVGYLEEYDKLIIVDAVDFGLEPGTVRIIDVDEVPKFLIAKKMSAHQLPLSE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 445925816  103 VLALADIRGHLPAHIALVGLQPAMLDDYGGSLSELAREQLP 143
Cdd:pfam01750  81 VLRLLEELGEIPKVVILCGVQPVILEDYGGGLSEEVKKAIP 121
HyaD COG0680
Ni,Fe-hydrogenase maturation factor [Energy production and conversion];
5-143 2.31e-48

Ni,Fe-hydrogenase maturation factor [Energy production and conversion];


Pssm-ID: 440444  Cd Length: 150  Bit Score: 154.57  E-value: 2.31e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   5 RVVVMGLGNLLWADEGFGVRVAERLYAHyHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYAGERI 84
Cdd:COG0680    3 KILVLGIGNPLRGDDGVGVRVAEALEER-ELPEGVEVIDGGTLGLELLELLEGADRVIIVDAVDSGAEPGTVRRLEPEEL 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 445925816  85 PAYlSAKKMSLHQNSFSEVLALADIRGHLPAHIALVGLQPAMLdDYGGSLSELAREQLP 143
Cdd:COG0680   82 PAG-DASKLSTHQLGLAELLALARLLGDLPEEVVLIGIEPESL-EFGEGLSPEVAAAVP 138
 
Name Accession Description Interval E-value
PRK10264 PRK10264
hydrogenase 1 maturation protease; Provisional
 1-195 4.31e-143

hydrogenase 1 maturation protease; Provisional


Pssm-ID: 182345  Cd Length: 195  Bit Score: 396.31  E-value: 4.31e-143
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   1 MSEQRVVVMGLGNLLWADEGFGVRVAERLYAHYHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYA 80
Cdd:PRK10264   1 MSEQRVVVMGLGNLLWADEGFGVRVAERLYAHYHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816  81 GERIPAYLSAKKMSLHQNSFSEVLALADIRGHLPAHIALVGLQPAMLDDYGGSLSELAREQLPAAEQAALAQLAAWGIVP 160
Cdd:PRK10264  81 GERIPAYLSAKKMSLHQNSFSEVLALADIRGHLPAHIALVGLQPAMLDDYGGSLSELAREQLPAAEQAALAQLAAWGIVP 160

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 445925816 161 QPANESRCLNYDCLSMENYEGVRLRQYRMTQEEQG 195
Cdd:PRK10264 161 QPANESRCLNYDCLSMENYEGVRLRQYRMTLEEQG 195
hupD TIGR00140
hydrogenase expression/formation protein; valid names: hupD, hynC, hoxM. C at 64 and 67 are ...
 23-157 7.23e-63

hydrogenase expression/formation protein; valid names: hupD, hynC, hoxM. C at 64 and 67 are believed to be metal binding. Postulated to be involved in processing or hydrogenase. Superfamily suggests that it is a peptidase/protease. [Protein fate, Protein modification and repair]


Pssm-ID: 129246  Cd Length: 134  Bit Score: 190.98  E-value: 7.23e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   23 VRVAERLYAHYHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYAGERIPAYLsAKKMSLHQNSFSE 102
Cdd:TIGR00140   1 VRLVEALQQRYAFPDNVTLLDGGTQGLYLLPLIESADRLIILDAVDYGLEPGTLYILRDEEVPKFL-AKKMSLHQTGFQE 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 445925816  103 VLALADIRGHLPAHIALVGLQPAMLDDYGGSLSELAREQLPAAEQAALAQLAAWG 157
Cdd:TIGR00140  80 VLALAELLGHLPKELVLIGVQPEELEDYGGSLSPEVAEAIPPAIEIALAQLAEWG 134
H2MP_MemB-H2up cd06062
Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer ...
 6-143 1.72e-62

Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD from E. coli is well studied in this group. Maturation of [NiFe] hydrogenases include proteolytic processing of large subunit, assembly with other subunits, and formation of the nickel metallocenter. Hydrogenase maturation endopeptidase (HybD) cleaves a short C-terminal peptide after a His or an Arg residue in the large subunit (pre-HybC) of hydrogenase 2 (hyb operon) in E. coli. This cleavage is nickel dependent. A variety of endopeptidases belong to this group that are similar in function and sequence homology. They include such proteins as HynC, HoxM, and HupD.


Pssm-ID: 99873  Cd Length: 146  Bit Score: 190.36  E-value: 1.72e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   6 VVVMGLGNLLWADEGFGVRVAERLYAHYHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYAGERIP 85
Cdd:cd06062    1 ILVLGIGNILLADEGIGVHAVERLEENYSFPENVELIDGGTLGLELLPYIEEADRLIIVDAVDAGGPPGTVYRFEGEDVP 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 445925816  86 AYLSAkKMSLHQNSFSEVLALADIRGHLPAHIALVGLQPAMLdDYGGSLSELAREQLP 143
Cdd:cd06062   81 AFLSA-KLSAHQVGLLEVLALAELLGDLPPEIVLIGVQPESI-EWGLELSPEVAAALP 136
HycI pfam01750
Hydrogenase maturation protease; The family consists of hydrogenase maturation proteases. In E. ...
 23-143 3.65e-54

Hydrogenase maturation protease; The family consists of hydrogenase maturation proteases. In E. coli HypI the hydrogenase maturation protease is involved in processing of HypE the large subunit of hydrogenases 3, by cleavage of its C-terminal.


Pssm-ID: 396353  Cd Length: 130  Bit Score: 168.61  E-value: 3.65e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   23 VRVAERLYAHYHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYAGERIPAYLSAKKMSLHQNSFSE 102
Cdd:pfam01750   1 VRVVEELKRRYAFPENVTVIDGGTGGLYLVGYLEEYDKLIIVDAVDFGLEPGTVRIIDVDEVPKFLIAKKMSAHQLPLSE 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 445925816  103 VLALADIRGHLPAHIALVGLQPAMLDDYGGSLSELAREQLP 143
Cdd:pfam01750  81 VLRLLEELGEIPKVVILCGVQPVILEDYGGGLSEEVKKAIP 121
hydrog_prot TIGR00072
hydrogenase maturation protease; HycI and HoxM are well-characterized as responsible for ...
 7-143 1.08e-53

hydrogenase maturation protease; HycI and HoxM are well-characterized as responsible for C-terminal protease activity on their respective hydrogenase large chains. A large number of homologous proteins appear responsible for the maturation of various forms of hydrogenase.


Pssm-ID: 272890  Cd Length: 145  Bit Score: 168.08  E-value: 1.08e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816    7 VVMGLGNLLWADEGFGVRVAERLYAHYHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYAGERIPA 86
Cdd:TIGR00072   1 LVLGIGNILRGDDGFGPRVAERLEERYEFPPGVEVLDGGTLGLELLDALEGADRVIVVDAVDSGAEPGTVRRLDGEDLPA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 445925816   87 YLsAKKMSLHQNSFSEVLALADIRGHLPAHIALVGLQPAMLdDYGGSLSELAREQLP 143
Cdd:TIGR00072  81 GL-GGKLSTHQLGLAEALALLELLGALPPEIVLLGIQPESL-EFGLGLSPEVAAAVP 135
HyaD COG0680
Ni,Fe-hydrogenase maturation factor [Energy production and conversion];
5-143 2.31e-48

Ni,Fe-hydrogenase maturation factor [Energy production and conversion];


Pssm-ID: 440444  Cd Length: 150  Bit Score: 154.57  E-value: 2.31e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   5 RVVVMGLGNLLWADEGFGVRVAERLYAHyHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYAGERI 84
Cdd:COG0680    3 KILVLGIGNPLRGDDGVGVRVAEALEER-ELPEGVEVIDGGTLGLELLELLEGADRVIIVDAVDSGAEPGTVRRLEPEEL 81

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 445925816  85 PAYlSAKKMSLHQNSFSEVLALADIRGHLPAHIALVGLQPAMLdDYGGSLSELAREQLP 143
Cdd:COG0680   82 PAG-DASKLSTHQLGLAELLALARLLGDLPEEVVLIGIEPESL-EFGEGLSPEVAAAVP 138
H2MP cd00518
Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases ...
 7-143 2.09e-46

Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). These enzymes belong to the peptidase family M52. Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE, the large subunit of hydrogenase 3. This cleavage is nickel dependent. This CD also includes such hydrogenase-processing proteins as HydD, HupW, and HoxW, as well as, proteins of the F420-reducing hydrogenase of methanogens (e.g., FrcD). Also included, is the Pyrococcus furiosus FrxA protein, a bifunctional endopeptidase/ sulfhydrogenase found in NADP-reducing hyperthermophiles.The Pyrococcus FrxA is not related to those found in Helicobacter pylori.


Pssm-ID: 99872 [Multi-domain]  Cd Length: 139  Bit Score: 149.23  E-value: 2.09e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   7 VVMGLGNLLWADEGFGVRVAERLYAHYHWPEyVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYAGERIPA 86
Cdd:cd00518    1 LVLGIGNPLRGDDGFGPAVAERLEERYLPPG-VEVIDGGTLGLELLDLLEGADRVIIVDAVDSGGEPGTVRRLEPEELPA 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 445925816  87 YLSAkkMSLHQNSFSEVLALADIRGHLPAHIALVGLQPAMLdDYGGSLSELAREQLP 143
Cdd:cd00518   80 YLSA--LSTHQLGLAELLALLRLLGGLPPEVVLIGIQPESL-ELGEGLSPEVAAAVP 133
hybD PRK10466
HyaD/HybD family hydrogenase maturation endopeptidase;
5-128 1.88e-30

HyaD/HybD family hydrogenase maturation endopeptidase;


Pssm-ID: 182481  Cd Length: 164  Bit Score: 109.40  E-value: 1.88e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   5 RVVVMGLGNLLWADEGFGVRVAERLYAHYHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLE-PGTLRTYAGER 83
Cdd:PRK10466   2 RILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNaPGTIMVLRDEE 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 445925816  84 IPAYLSaKKMSLHQNSFSEVLALADIRGHLPAHIALVGLQPAMLD 128
Cdd:PRK10466  82 VPALFT-NKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLE 125
H2MP_F420-Reduc cd06064
Endopeptidases belonging to F420-reducing hydrogenases group. These hydrogenases from ...
 7-125 2.43e-21

Endopeptidases belonging to F420-reducing hydrogenases group. These hydrogenases from methanogens are encoded by the fru, frc, or frh genes. Sequence comparison indicates that fruD and frcD gene products from Methanococcus voltae are similar to HycI protease of Escherichia coli and are putatively involved in the C-terminal processing of large subunits (FruA and FrcA respectively). FrhD (F420 reducing hydrogenase delta subunit) enzyme belongs to the gene cluster of 8-hydroxy-5-deazaflavin (F420) reducing hydrogenase (FRH) from the thermophilic methanogen Methanobacterium thermoautotrophicum delta H. FrhD subunit is putatively involved in the processing of the coenzyme F420 hydrogenase-processing. It is similar to those frhD genes found in Methanomicrobia and Methanobacteria. It is different from the FrhD conserved domain found in methyl viologen-reducing hydrogenase and F420-non-reducing hydrogenase iron-sulfur subunit D.


Pssm-ID: 99875  Cd Length: 150  Bit Score: 85.37  E-value: 2.43e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   7 VVMGLGNLLWADEGFGVRVAERLYAHYHWPEYVEIVDGGTQG----LNLLGYVESASHLLILDAIDYGLEPGTLRTYAGE 82
Cdd:cd06064    1 LVVGCGNILFGDDGFGPAVIEELEKLELLPDNVQVIDAGTGAphllFTLLDEESKPKKIIIVDAIDFGLEPGTLKKISVD 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 445925816  83 RIPaylSAKK--MSLHQnsFSEVLALADIRGHLPAHIALVGLQPA 125
Cdd:cd06064   81 ELP---PGKYydFDAHS--WPLADPLHELKDKYGIEIVVIGCQPK 120
H2MP_MemB-H2evol cd06067
Endopeptidases belonging to membrane-bound hydrogen evolving hydrogenase group. In hydrogenase ...
 7-140 2.42e-16

Endopeptidases belonging to membrane-bound hydrogen evolving hydrogenase group. In hydrogenase 3 from E coli, the maturation of the large subunit (HycE) requires the cleavage of a C-terminal peptide by the endopeptidase HycI, before the final formation of the [NiFe] metallocenter. HycI protease is a monomer and lacks characteristic signature motifs of serine, zinc, cysteine, or acid proteases and thus its cleavage reaction is not inhibited by conventional inhibitors of serine and metalloproteases. Such hydrogenases as those from Methanosarcina barkeri (EchCE) and Rhodospirillum rubrum (CooLH) also belong to this group of membrane-bound hydrogen evolving hydrogenase. Sequence comparison of the large subunits from related hydrogenase indicates that in contrast to EchE (358 amino acids) and CooH (361 amino acids), the large subunit HycE (569 amino acids) contains an extra carboxy-terminal stretch of 32 amino acids that is cleaved during the maturation process. In the absence of this C-terminal stretch, there is no homolog of endopeptidase HycI found in these two related hydrogenase.


Pssm-ID: 99877  Cd Length: 136  Bit Score: 71.81  E-value: 2.42e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   7 VVMGLGNLLWADEGFGVRVAERLYAHYHwpEYVEIVDGGTQGLNLLGYV--ESASHLLILDAIDYGLEPGTLRTYAGERI 84
Cdd:cd06067    1 VLLGVGNELRGDDGAGPLLAEKLEDLPN--PNWLVIDGGTVPENFTGKIreEKPDLIVIVDAADMGLEPGEIRIIDPEEI 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 445925816  85 PAYLsakkMSLHQNSFSEVLALadIRGHLPAHIALVGLQPAMLdDYGGSLSELARE 140
Cdd:cd06067   79 AEYF----FSTHTLPLSILIDY--LRESTGAEVIFLGIQPENL-EFGEPLSPEVKD 127
H2MP_like-1 cd06068
Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity ...
 8-143 3.77e-15

Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity to hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE (the large subunit of hydrogenases 3). This cleavage is nickel dependent.


Pssm-ID: 99878  Cd Length: 144  Bit Score: 68.90  E-value: 3.77e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   8 VMGLGNLLWADEGFGVRVAERLyAHYHWPEYVEIVDGGTQGLNLL-----GYvesaSHLLILDAIDYGLEPGTLRTYAGE 82
Cdd:cd06068    2 VAGVGNIFLGDDGFGVEVARRL-RPRQLPPGVRVADFGIRGIHLAyelldGY----DTLILVDAVPRGGEPGTLYVIELE 76

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 445925816  83 RIPAylSAKKMSLHQNSFSEVLALADIRGHLPAHIALVGLQPAMLDDyGGSLSELAREQLP 143
Cdd:cd06068   77 DVDA--APELLDAHGMNPDAVLALLRALGGTPPRVVVVGCEPADVDE-GIGLSEPVAAAVP 134
H2MP_Cyano-H2up cd06063
This group of endopeptidases include HupW enzymes that are specific to the cyanobacterial ...
 6-140 3.50e-14

This group of endopeptidases include HupW enzymes that are specific to the cyanobacterial hydrogenase and are involved in the C-terminal cleavage of the hydrogenase large subunit precursor protein. Cyanobacterial nickel-iron (NiFe)-hydrogenases are found exclusively in the N2-fixing strains and are encoded by hup (hydrogen uptake) genes. These uptake hydrogenases are heterodimers with a large (hupL) and small subunit (hupS) and catalyze the consumption of the H2 produced during N2 fixation. Sequence similarity shows that the putative metal-binding resides are well conserved in this group of hydrogen maturation proteases. This group also includes such proteins as the hydrogenase III from Aquifex aeolicus.


Pssm-ID: 99874  Cd Length: 146  Bit Score: 66.65  E-value: 3.50e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   6 VVVMGLGNLLWADEGFGVRVAERLYAhYHWPEYVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTYAGERIP 85
Cdd:cd06063    1 LTIIGCGNLNRGDDGVGPILIRRLQA-YLLPPHVRLVDCGTAGMEVMFRARGAKQLIIIDASSTGSEPGAVFEVPGEELE 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 445925816  86 AyLSAKKMSLHQNSFSEVLALAD--IRGHLPAHIAlVGLQPAMLDDYGGSLSELARE 140
Cdd:cd06063   80 A-LPEPSYNLHDFRWDHALAAGRkiFGDDFPKDVT-VYLIEAKSLDFGLELSPPVKQ 134
hycI TIGR00142
hydrogenase maturation protease HycI; Hydrogenase maturation protease is a protease that is ...
 7-136 3.10e-11

hydrogenase maturation protease HycI; Hydrogenase maturation protease is a protease that is involved in the C-terminal processing of HycE,the large subunit of hydrogenase 3 from E.Coli. This protein seems to be found in E.Coli and in Archaea. [Protein fate, Protein modification and repair]


Pssm-ID: 129247  Cd Length: 146  Bit Score: 58.70  E-value: 3.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816    7 VVMGLGNLLWADEGFGVRVAERLYAHYHWPEYVeIVDGGTQGLNLLGYVES--ASHLLILDAIDYGLEPGTLRTYAGERI 84
Cdd:TIGR00142   2 VLLCVGNELMGDDGAGPYLAEKCAAAPKEENWV-VINAGTVPENFTVAIRElrPTHILIVDATDMGLNPGEVRIIDDDII 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 445925816   85 PAYLsakkMSLHQNSFSEVLALadIRGHLPAHIALVGLQPAMLdDYGGSLSE 136
Cdd:TIGR00142  81 EMYS----MSTHNMPLSYLVDY--LKEDINGEIIFLGIQPDIV-GFYYPMSQ 125
H2MP_like-2 cd06070
Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity ...
 8-128 3.37e-10

Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity to hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE (the large subunit of hydrogenases 3). This cleavage is nickel dependent.


Pssm-ID: 99879  Cd Length: 140  Bit Score: 55.90  E-value: 3.37e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   8 VMGLGNLLWADEGFGVRVAERLyAHYHwpeyVEIVDGGTQGLNLLGYVESASHLLILDAIDYGLEPGTLRTyagERIPAY 87
Cdd:cd06070    2 IIGVGNRLYGDDGFGSCLAEAL-EQCG----APVFDGGLDGFGLLSHLENYDIVIFIDVAVIDEDVGVFKI---TPEPAS 73

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 445925816  88 LS---AKKMSLHQNSFSEVLALADIRGHLP-AHIalVGLQPAMLD 128
Cdd:cd06070   74 VAeqiSFETDAHRLGPAHLLLLLKSSGRRPkAYI--VGVKPESIE 116
H2MP_NAD-link-bidir cd06066
Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of ...
 7-143 1.19e-04

Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of endopeptidases are highly specific carboxyl-terminal protease (HoxW protease) which releases a 24-amino-acid peptide from HoxH prior to progression of subunit assembly. These bidirectional hydrogenases are heteropentamers encoded by the hox (hydrogen oxidation) genes, in which complex HoxEFU shows the diaphorase activity, and HoxYH constitutes the NiFe-hydrogenase.


Pssm-ID: 99876  Cd Length: 139  Bit Score: 40.27  E-value: 1.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816   7 VVMGLGNLLWADEGFGVRVAERLyAHYHWPEyVEIVDGG--TQGLNLLgyVESASHLLILDAiDYGLEPGtlrTYAGERI 84
Cdd:cd06066    1 LVIGYGNPLRGDDGLGPAVAERI-EEWLLPG-VEVLAVHqlTPELAED--LAGADRVIFIDA-SLGGSPA---PFRIVRL 72

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 445925816  85 PAyLSAKKMSLHQNSFSEVLALA-DIRGHLPAhiALVGLQPAMLDDYGGSLSELAREQLP 143
Cdd:cd06066   73 EP-RRDSSFTSHALSPAALLALAqALYGHAPP--AWLLTIPGYNFELGEPLSPAAEAALA 129
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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