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Conserved domains on  [gi|1948758819|ref|WP_198409290|]
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hypothetical protein [Caballeronia insecticola]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SDH_sah super family cl26734
Serine dehydrogenase proteinase; This family of archaebacterial proteins, formerly known as ...
 25-192 5.77e-16

Serine dehydrogenase proteinase; This family of archaebacterial proteins, formerly known as DUF114, has been found to be a serine dehydrogenase proteinase distantly related to ClpP proteinases that belong to the serine proteinase superfamily. The family has a catalytic triad of Ser, Asp, His residues, which shows an altered residue ordering compared with the ClpP proteinases but similar to that of the carboxypeptidase clan.


The actual alignment was detected with superfamily member pfam01972:

Pssm-ID: 110924  Cd Length: 286  Bit Score: 74.88  E-value: 5.77e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948758819  25 STLKGEPVDLMLETNGGYTDATEKIVSILTAMTTDLRVIVPRRAKSNGTVIALTGREIVMGVHSELGPIDPNVvlgpGNv 104
Cdd:pfam01972  87 LTPKDMPIDLIIHTPGGLALAATQIAKALKEHKAKTTVIVPHYAMSGGTLIALAADEIIMDENAVLGPVDPQI----GQ- 161

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948758819 105 VPADLILKSAEKHPP--------LIAGFASLAVAQTKKLATAVLTSGMLKGAEPKVIEEIVNKISTRDHyhshgsVIDSR 176
Cdd:pfam01972 162 YPAASILKAVEKKGPkkiddqtlILADISKKAIKQMEEFVYNLLKDKYGEEKAKEIAKILTEGRWTHDY------PLTVE 235

                         170
                  ....*....|....*.
gi 1948758819 177 EAADLGLKIAHLPPED 192
Cdd:pfam01972 236 ELKELGLEVNTNVPEE 251
 
Name Accession Description Interval E-value
SDH_sah pfam01972
Serine dehydrogenase proteinase; This family of archaebacterial proteins, formerly known as ...
 25-192 5.77e-16

Serine dehydrogenase proteinase; This family of archaebacterial proteins, formerly known as DUF114, has been found to be a serine dehydrogenase proteinase distantly related to ClpP proteinases that belong to the serine proteinase superfamily. The family has a catalytic triad of Ser, Asp, His residues, which shows an altered residue ordering compared with the ClpP proteinases but similar to that of the carboxypeptidase clan.


Pssm-ID: 110924  Cd Length: 286  Bit Score: 74.88  E-value: 5.77e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948758819  25 STLKGEPVDLMLETNGGYTDATEKIVSILTAMTTDLRVIVPRRAKSNGTVIALTGREIVMGVHSELGPIDPNVvlgpGNv 104
Cdd:pfam01972  87 LTPKDMPIDLIIHTPGGLALAATQIAKALKEHKAKTTVIVPHYAMSGGTLIALAADEIIMDENAVLGPVDPQI----GQ- 161

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948758819 105 VPADLILKSAEKHPP--------LIAGFASLAVAQTKKLATAVLTSGMLKGAEPKVIEEIVNKISTRDHyhshgsVIDSR 176
Cdd:pfam01972 162 YPAASILKAVEKKGPkkiddqtlILADISKKAIKQMEEFVYNLLKDKYGEEKAKEIAKILTEGRWTHDY------PLTVE 235

                         170
                  ....*....|....*.
gi 1948758819 177 EAADLGLKIAHLPPED 192
Cdd:pfam01972 236 ELKELGLEVNTNVPEE 251
Clp_protease_NfeD_like cd07021
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ...
 30-159 2.82e-07

Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cleaving hydrophobic substrates. Difference in oligomeric form and catalytic residues between 1510-N (forming a dimer) and ClpP (forming a tetradecamer) shows a possible functional difference: 1510-N is likely to have a regulatory function while ClpP is involved in protein quality control.


Pssm-ID: 132932 [Multi-domain]  Cd Length: 178  Bit Score: 49.12  E-value: 2.82e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948758819  30 EPVDLMLETNGGYTDATEKIVSILTAmtTDLRVI--VPRRAKSNGTVIALTGREIVMGvhselgpidPNVVLGPGNVVPA 107
Cdd:cd07021    31 DAVVLDIDTPGGRVDSALEIVDLILN--SPIPTIayVNDRAASAGALIALAADEIYMA---------PGATIGAAEPIPG 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1948758819 108 DLILKSAEKhppliagFASLAVAQTKKLATAvltsgmlKGAEPKVIEEIVNK 159
Cdd:cd07021   100 DGNGAADEK-------VQSYWRAKMRAAAEK-------KGRDPDIAEAMVDK 137
NfeD COG1030
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ...
 28-108 4.08e-04

Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440653 [Multi-domain]  Cd Length: 413  Bit Score: 41.00  E-value: 4.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948758819  28 KGEPVDLMLETNGGYTDATEKIVSILTAmtTDLRVIV----PRRAKSNGTVIALTGREIVMGVHSELGPIDPnVVLGPGN 103
Cdd:COG1030    56 GADAVVLELDTPGGLVDSAREIVDAILA--SPVPVIVyvasGARAASAGAYILLASHIAAMAPGTNIGAATP-VQIGGGI 132


                  ....*
gi 1948758819 104 VVPAD 108
Cdd:COG1030   133 DEAME 137
 
Name Accession Description Interval E-value
SDH_sah pfam01972
Serine dehydrogenase proteinase; This family of archaebacterial proteins, formerly known as ...
 25-192 5.77e-16

Serine dehydrogenase proteinase; This family of archaebacterial proteins, formerly known as DUF114, has been found to be a serine dehydrogenase proteinase distantly related to ClpP proteinases that belong to the serine proteinase superfamily. The family has a catalytic triad of Ser, Asp, His residues, which shows an altered residue ordering compared with the ClpP proteinases but similar to that of the carboxypeptidase clan.


Pssm-ID: 110924  Cd Length: 286  Bit Score: 74.88  E-value: 5.77e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948758819  25 STLKGEPVDLMLETNGGYTDATEKIVSILTAMTTDLRVIVPRRAKSNGTVIALTGREIVMGVHSELGPIDPNVvlgpGNv 104
Cdd:pfam01972  87 LTPKDMPIDLIIHTPGGLALAATQIAKALKEHKAKTTVIVPHYAMSGGTLIALAADEIIMDENAVLGPVDPQI----GQ- 161

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948758819 105 VPADLILKSAEKHPP--------LIAGFASLAVAQTKKLATAVLTSGMLKGAEPKVIEEIVNKISTRDHyhshgsVIDSR 176
Cdd:pfam01972 162 YPAASILKAVEKKGPkkiddqtlILADISKKAIKQMEEFVYNLLKDKYGEEKAKEIAKILTEGRWTHDY------PLTVE 235

                         170
                  ....*....|....*.
gi 1948758819 177 EAADLGLKIAHLPPED 192
Cdd:pfam01972 236 ELKELGLEVNTNVPEE 251
Clp_protease_NfeD_like cd07021
Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation ...
 30-159 2.82e-07

Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease; Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cleaving hydrophobic substrates. Difference in oligomeric form and catalytic residues between 1510-N (forming a dimer) and ClpP (forming a tetradecamer) shows a possible functional difference: 1510-N is likely to have a regulatory function while ClpP is involved in protein quality control.


Pssm-ID: 132932 [Multi-domain]  Cd Length: 178  Bit Score: 49.12  E-value: 2.82e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948758819  30 EPVDLMLETNGGYTDATEKIVSILTAmtTDLRVI--VPRRAKSNGTVIALTGREIVMGvhselgpidPNVVLGPGNVVPA 107
Cdd:cd07021    31 DAVVLDIDTPGGRVDSALEIVDLILN--SPIPTIayVNDRAASAGALIALAADEIYMA---------PGATIGAAEPIPG 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1948758819 108 DLILKSAEKhppliagFASLAVAQTKKLATAvltsgmlKGAEPKVIEEIVNK 159
Cdd:cd07021   100 DGNGAADEK-------VQSYWRAKMRAAAEK-------KGRDPDIAEAMVDK 137
NfeD COG1030
Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein ...
 28-108 4.08e-04

Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440653 [Multi-domain]  Cd Length: 413  Bit Score: 41.00  E-value: 4.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1948758819  28 KGEPVDLMLETNGGYTDATEKIVSILTAmtTDLRVIV----PRRAKSNGTVIALTGREIVMGVHSELGPIDPnVVLGPGN 103
Cdd:COG1030    56 GADAVVLELDTPGGLVDSAREIVDAILA--SPVPVIVyvasGARAASAGAYILLASHIAAMAPGTNIGAATP-VQIGGGI 132


                  ....*
gi 1948758819 104 VVPAD 108
Cdd:COG1030   133 DEAME 137
 
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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