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Conserved domains on  [gi|1438323657|emb|SUG17806|]
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Inner membrane protein translocase component YidC long form [Salmonella enterica subsp. arizonae]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK01318 super family cl35152
membrane protein insertase; Provisional
 2-144 1.44e-51

membrane protein insertase; Provisional


The actual alignment was detected with superfamily member PRK01318:

Pssm-ID: 234942 [Multi-domain]  Cd Length: 521  Bit Score: 171.59  E-value: 1.44e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323657   2 KTDVLDLTINTRGGDVEQALLPAYPKELGSSEPFQLLETTPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAFVLADG 81
Cdd:PRK01318   44 ETDVLRLSIDTKGGRIDDLLLKKYKETLDSSPPVVLLSPSTEHPYFAQSGLTGADGPDNVPNPDRTLYTADGDSLVLADG 123

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1438323657  82 QNELQVPMTYTDAAGNTFTKTFVFKRGDYAVNVNYSVQNTGEKPLEISTFGSVKAIHQPASSS 144
Cdd:PRK01318  124 QNELPVTLTWTNGNGLTFTKTYTLDRGDYMFTVEYSVNNNSGAPVNLSPYGQLKRTGSSNFAS 186
 
Name Accession Description Interval E-value
PRK01318 PRK01318
membrane protein insertase; Provisional
 2-144 1.44e-51

membrane protein insertase; Provisional


Pssm-ID: 234942 [Multi-domain]  Cd Length: 521  Bit Score: 171.59  E-value: 1.44e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323657   2 KTDVLDLTINTRGGDVEQALLPAYPKELGSSEPFQLLETTPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAFVLADG 81
Cdd:PRK01318   44 ETDVLRLSIDTKGGRIDDLLLKKYKETLDSSPPVVLLSPSTEHPYFAQSGLTGADGPDNVPNPDRTLYTADGDSLVLADG 123

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1438323657  82 QNELQVPMTYTDAAGNTFTKTFVFKRGDYAVNVNYSVQNTGEKPLEISTFGSVKAIHQPASSS 144
Cdd:PRK01318  124 QNELPVTLTWTNGNGLTFTKTYTLDRGDYMFTVEYSVNNNSGAPVNLSPYGQLKRTGSSNFAS 186
YidC_periplas pfam14849
YidC periplasmic domain; This is the periplasmic domain of YidC, a bacterial membrane protein ...
 2-135 5.98e-49

YidC periplasmic domain; This is the periplasmic domain of YidC, a bacterial membrane protein which is required for the insertion and assembly of inner membrane proteins.


Pssm-ID: 464346  Cd Length: 266  Bit Score: 158.59  E-value: 5.98e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323657   2 KTDVLDLTINTRGGDVEQALLPAYPKELGS-SEPFQLLETTPQFIYQAQSGLTGRDGPDNPAngPRPLYNVEKDAFVLAD 80
Cdd:pfam14849   4 ETDVLRGSISLKGGRIDDLELKKYRETLDDdSPPVVLLSPSGGRTYVAQSGLIGAGGPDLPP--HDTVFTAEGGSYTLAD 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1438323657  81 GQNELQVPMTYTDAAGNTFTKTFVFKRGDYAVNVNYSVQNTGEKPLEISTFGSVK 135
Cdd:pfam14849  82 GTDELPVTLTWDNGNGVTFTKTYTFDRGSYLIDVTYEVENTSGAPVTLQPYGQLV 136
yidC_nterm TIGR03593
membrane protein insertase, YidC/Oxa1 family, N-terminal domain; Essentially all bacteria have ...
 2-146 1.04e-44

membrane protein insertase, YidC/Oxa1 family, N-terminal domain; Essentially all bacteria have a member of the YidC family, whose C-terminal domain is modeled by TIGR03592. The two copies are found in endospore-forming bacteria such as Bacillus subtilis appear redundant during vegetative growth, although the member designated spoIIIJ (stage III sporulation protein J) has a distinct role in spore formation. YidC, its mitochondrial homolog Oxa1, and its chloroplast homolog direct insertion into the bacterial/organellar inner (or only) membrane. This model describes an N-terminal sequence region, including a large periplasmic domain lacking in YidC members from Gram-positive species. The multifunctional YidC protein acts both with and independently of the Sec system. [Protein fate, Protein and peptide secretion and trafficking]


Pssm-ID: 274666  Cd Length: 366  Bit Score: 150.56  E-value: 1.04e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323657   2 KTDVLDLTINTRGGDVEQALLPAYPKELGS-SEPFQLLETTPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAFVLAD 80
Cdd:TIGR03593  79 ETDVLRASISTKGGDIDSLELKKYKETLDKdSPPVLLLSDGAERLYVAQSGLIGANGADLALPGHRTVWQAEGGEYTLTP 158

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1438323657  81 GQneLQVPMTYTDAAGNTFTKTFVFKRGDYAVNVNYSVQNTGEKPLEISTFGSVKAIHQPASSSRH 146
Cdd:TIGR03593 159 GQ--LPVTLTWDNSNGVTVTKTYTFDRDSYLIDVEYKVTNNGDAPVSLSLYGQLKRDLSPTEKSTY 222
EcYidC-like_peri cd19961
periplasmic beta-super sandwich fold domain of membrane protein insertase YidC from ...
 2-144 1.06e-34

periplasmic beta-super sandwich fold domain of membrane protein insertase YidC from Escherichia coli and similar domains; This subfamily is composed of Escherichia coli YidC and similar proteins. Membrane protein insertase YidC, also called foldase YidC or membrane integrase YidC, facilitates proper folding, insertion, and assembly of inner membrane proteins and complexes. Depending on the nature of the substrate, YidC functions in a Sec-independent (YidC only) or a Sec-dependent manner as part of a complex containing YidC, the SecYEG channel, and SecDFYajC. YidC belongs to the YidC/Oxa1/Alb3 protein family of insertases that contain a core domain of five transmembrane (TM) segments that is essential to insertase function. In addition to this core transmembrane domain, YidC from Gram-negative bacteria contain an extra transmembrane segment (TM1) at the N-terminus and a large periplasmic domain, located between TM1 and TM2, that adopts a beta-super sandwich fold that is found in sugar-binding proteins such as galactose mutarotase. This periplasmic domain may have a role in protein assembly: a region of YidC that binds to SecF maps to one edge of the beta-super sandwich.


Pssm-ID: 411000  Cd Length: 255  Bit Score: 121.65  E-value: 1.06e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323657   2 KTDVLDLTINTRGGDVEQALLPAYPKELGSSEPFQLLEttPQFIYQAQSGLTGRDGPDNPANgpRPLYNVEKDAFvlaDG 81
Cdd:cd19961     6 ETDLLKASISTKGGRIKSVELKKYKETLPDSKPVELLS--PDGPYVAQLGLIGADGPLIPTA--DLLFTADSGSY---EG 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1438323657  82 QNELQVPMTYTDAAGNTFTKTFVFKRGDYAVNVNYSVQNTGEKPLEISTFGSVKAIHQPASSS 144
Cdd:cd19961    79 GDSLTVTLTWTNGDGLTIEKTYTFDPDSYLIDVEVRVENNSSAPLSLSLYLQLQRKGGEPEGS 141
 
Name Accession Description Interval E-value
PRK01318 PRK01318
membrane protein insertase; Provisional
 2-144 1.44e-51

membrane protein insertase; Provisional


Pssm-ID: 234942 [Multi-domain]  Cd Length: 521  Bit Score: 171.59  E-value: 1.44e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323657   2 KTDVLDLTINTRGGDVEQALLPAYPKELGSSEPFQLLETTPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAFVLADG 81
Cdd:PRK01318   44 ETDVLRLSIDTKGGRIDDLLLKKYKETLDSSPPVVLLSPSTEHPYFAQSGLTGADGPDNVPNPDRTLYTADGDSLVLADG 123

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1438323657  82 QNELQVPMTYTDAAGNTFTKTFVFKRGDYAVNVNYSVQNTGEKPLEISTFGSVKAIHQPASSS 144
Cdd:PRK01318  124 QNELPVTLTWTNGNGLTFTKTYTLDRGDYMFTVEYSVNNNSGAPVNLSPYGQLKRTGSSNFAS 186
YidC_periplas pfam14849
YidC periplasmic domain; This is the periplasmic domain of YidC, a bacterial membrane protein ...
 2-135 5.98e-49

YidC periplasmic domain; This is the periplasmic domain of YidC, a bacterial membrane protein which is required for the insertion and assembly of inner membrane proteins.


Pssm-ID: 464346  Cd Length: 266  Bit Score: 158.59  E-value: 5.98e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323657   2 KTDVLDLTINTRGGDVEQALLPAYPKELGS-SEPFQLLETTPQFIYQAQSGLTGRDGPDNPAngPRPLYNVEKDAFVLAD 80
Cdd:pfam14849   4 ETDVLRGSISLKGGRIDDLELKKYRETLDDdSPPVVLLSPSGGRTYVAQSGLIGAGGPDLPP--HDTVFTAEGGSYTLAD 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1438323657  81 GQNELQVPMTYTDAAGNTFTKTFVFKRGDYAVNVNYSVQNTGEKPLEISTFGSVK 135
Cdd:pfam14849  82 GTDELPVTLTWDNGNGVTFTKTYTFDRGSYLIDVTYEVENTSGAPVTLQPYGQLV 136
yidC_nterm TIGR03593
membrane protein insertase, YidC/Oxa1 family, N-terminal domain; Essentially all bacteria have ...
 2-146 1.04e-44

membrane protein insertase, YidC/Oxa1 family, N-terminal domain; Essentially all bacteria have a member of the YidC family, whose C-terminal domain is modeled by TIGR03592. The two copies are found in endospore-forming bacteria such as Bacillus subtilis appear redundant during vegetative growth, although the member designated spoIIIJ (stage III sporulation protein J) has a distinct role in spore formation. YidC, its mitochondrial homolog Oxa1, and its chloroplast homolog direct insertion into the bacterial/organellar inner (or only) membrane. This model describes an N-terminal sequence region, including a large periplasmic domain lacking in YidC members from Gram-positive species. The multifunctional YidC protein acts both with and independently of the Sec system. [Protein fate, Protein and peptide secretion and trafficking]


Pssm-ID: 274666  Cd Length: 366  Bit Score: 150.56  E-value: 1.04e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323657   2 KTDVLDLTINTRGGDVEQALLPAYPKELGS-SEPFQLLETTPQFIYQAQSGLTGRDGPDNPANGPRPLYNVEKDAFVLAD 80
Cdd:TIGR03593  79 ETDVLRASISTKGGDIDSLELKKYKETLDKdSPPVLLLSDGAERLYVAQSGLIGANGADLALPGHRTVWQAEGGEYTLTP 158

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1438323657  81 GQneLQVPMTYTDAAGNTFTKTFVFKRGDYAVNVNYSVQNTGEKPLEISTFGSVKAIHQPASSSRH 146
Cdd:TIGR03593 159 GQ--LPVTLTWDNSNGVTVTKTYTFDRDSYLIDVEYKVTNNGDAPVSLSLYGQLKRDLSPTEKSTY 222
EcYidC-like_peri cd19961
periplasmic beta-super sandwich fold domain of membrane protein insertase YidC from ...
 2-144 1.06e-34

periplasmic beta-super sandwich fold domain of membrane protein insertase YidC from Escherichia coli and similar domains; This subfamily is composed of Escherichia coli YidC and similar proteins. Membrane protein insertase YidC, also called foldase YidC or membrane integrase YidC, facilitates proper folding, insertion, and assembly of inner membrane proteins and complexes. Depending on the nature of the substrate, YidC functions in a Sec-independent (YidC only) or a Sec-dependent manner as part of a complex containing YidC, the SecYEG channel, and SecDFYajC. YidC belongs to the YidC/Oxa1/Alb3 protein family of insertases that contain a core domain of five transmembrane (TM) segments that is essential to insertase function. In addition to this core transmembrane domain, YidC from Gram-negative bacteria contain an extra transmembrane segment (TM1) at the N-terminus and a large periplasmic domain, located between TM1 and TM2, that adopts a beta-super sandwich fold that is found in sugar-binding proteins such as galactose mutarotase. This periplasmic domain may have a role in protein assembly: a region of YidC that binds to SecF maps to one edge of the beta-super sandwich.


Pssm-ID: 411000  Cd Length: 255  Bit Score: 121.65  E-value: 1.06e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323657   2 KTDVLDLTINTRGGDVEQALLPAYPKELGSSEPFQLLEttPQFIYQAQSGLTGRDGPDNPANgpRPLYNVEKDAFvlaDG 81
Cdd:cd19961     6 ETDLLKASISTKGGRIKSVELKKYKETLPDSKPVELLS--PDGPYVAQLGLIGADGPLIPTA--DLLFTADSGSY---EG 78

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1438323657  82 QNELQVPMTYTDAAGNTFTKTFVFKRGDYAVNVNYSVQNTGEKPLEISTFGSVKAIHQPASSS 144
Cdd:cd19961    79 GDSLTVTLTWTNGDGLTIEKTYTFDPDSYLIDVEVRVENNSSAPLSLSLYLQLQRKGGEPEGS 141
YidC_peri cd19960
periplasmic beta-super sandwich fold domain of membrane protein insertase YidC from ...
 2-117 1.98e-17

periplasmic beta-super sandwich fold domain of membrane protein insertase YidC from Gram-negative bacteria and similar domains; Membrane protein insertase YidC, also called foldase YidC or membrane integrase YidC, facilitates proper folding, insertion, and assembly of inner membrane proteins and complexes. Depending on the nature of the substrate, YidC functions in a Sec-independent (YidC only) or a Sec-dependent manner as part of a complex containing YidC, the SecYEG channel, and SecDFYajC. YidC belongs to the YidC/Oxa1/Alb3 protein family of insertases that contains a core domain of five transmembrane (TM) segments that is essential to insertase function. In addition to this core transmembrane domain, YidC from Gram-negative bacteria contain an extra transmembrane segment (TM1) at the N-terminus and a large periplasmic domain, located between TM1 and TM2, that adopts a beta-super sandwich fold that is found in sugar-binding proteins such as galactose mutarotase. This periplasmic domain may have a role in protein assembly: a region of YidC that binds to SecF maps to one edge of the beta-super sandwich. Other members of the YidC/Oxa1/Alb3 family include YidC1/YidC2 from gram-positive bacteria as well as eukaryotic members such as mitochondrial Oxa1/Oxa2 (or Cox18) and chloroplastic Alb3/Alb4; they are not part of this hierarchy as they do not possess the periplasmic domain.


Pssm-ID: 410999  Cd Length: 233  Bit Score: 76.14  E-value: 1.98e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438323657   2 KTDVLDLTINTRGgDVEQALLPAYPKElgSSEPFQLLETTPQfiyqAQSGLTGRDGPD--NPANGPRPLYNVEKDafvLA 79
Cdd:cd19960     6 KSKDFELTIDTLG-RISQFYLKDKKYK--NEDGKQLELISPQ----APKPLEIRFSDPalNEEAFKTPYTASVSE---ID 75

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1438323657  80 DGQNELQVPMTYTDAaGNTFTKTFVFKR-GDYAVNVNYS 117
Cdd:cd19960    76 LESGPQSVVLTQTLS-GLTVTKTITFYPdGHYDVKVKLS 113
 
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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