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Conserved domains on  [gi|937902929|dbj|BAS77983|]
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Os02g0260400 [Oryza sativa Japonica Group]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YidD pfam01809
Putative membrane protein insertion efficiency factor; This family consists of membrane ...
 47-98 8.24e-30

Putative membrane protein insertion efficiency factor; This family consists of membrane insertion efficiency factor proteins. They contain three conserved cysteine residues. Family members such as YidD may be involved in insertion of integral membrane proteins into the membrane by assisting YidC (membrane protein insertase). Some members of the yidD family have been previously thought to posses alpha-hemolysin activity, however no sufficient evidence was found to corroborate this idea. Secondary structure prediction indicated the presence of three alpha-helices in YidD. None of the three alpha-helices appeared sufficiently hydrophobic to serve as a transmembrane, suggesting a cytoplasmic localization for YidD. However, a closer examination of the alpha-helical wheel projection of the predicted first alpha-helix in YidD suggested an amphipathic structure in its N-terminal region which might be involved in membrane targeting.


:

Pssm-ID: 460342  Cd Length: 67  Bit Score: 101.30  E-value: 8.24e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 937902929   47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDP 98
Cdd:pfam01809  15 ISPLLPPSCRFYPTCSEYAIEAIEKHGALKGGWLALKRILRCHPFHPGGYDP 66
 
Name Accession Description Interval E-value
YidD pfam01809
Putative membrane protein insertion efficiency factor; This family consists of membrane ...
 47-98 8.24e-30

Putative membrane protein insertion efficiency factor; This family consists of membrane insertion efficiency factor proteins. They contain three conserved cysteine residues. Family members such as YidD may be involved in insertion of integral membrane proteins into the membrane by assisting YidC (membrane protein insertase). Some members of the yidD family have been previously thought to posses alpha-hemolysin activity, however no sufficient evidence was found to corroborate this idea. Secondary structure prediction indicated the presence of three alpha-helices in YidD. None of the three alpha-helices appeared sufficiently hydrophobic to serve as a transmembrane, suggesting a cytoplasmic localization for YidD. However, a closer examination of the alpha-helical wheel projection of the predicted first alpha-helix in YidD suggested an amphipathic structure in its N-terminal region which might be involved in membrane targeting.


Pssm-ID: 460342  Cd Length: 67  Bit Score: 101.30  E-value: 8.24e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 937902929   47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDP 98
Cdd:pfam01809  15 ISPLLPPSCRFYPTCSEYAIEAIEKHGALKGGWLALKRILRCHPFHPGGYDP 66
YidD COG0759
Membrane-anchored protein YidD, putatitve component of membrane protein insertase Oxa1/YidC ...
 47-99 2.72e-28

Membrane-anchored protein YidD, putatitve component of membrane protein insertase Oxa1/YidC/SpoIIIJ [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440522  Cd Length: 71  Bit Score: 97.50  E-value: 2.72e-28
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDPP 99
Cdd:COG0759   19 ISPLLGPRCRFYPTCSEYALEAIERHGLLKGSWLTLKRILRCHPWHPGGYDPV 71
PRK14386 PRK14386
membrane protein insertion efficiency factor YidD;
47-98 4.80e-20

membrane protein insertion efficiency factor YidD;


Pssm-ID: 172862  Cd Length: 106  Bit Score: 77.76  E-value: 4.80e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDP 98
Cdd:PRK14386  16 ISPLLGPRCRYIPTCSQYALEALQTHGAIKGVWLSSKRICRCHPWGGSGYDP 67
TIGR00278 TIGR00278
putative membrane protein insertion efficiency factor; This model describes a family, YidD, of ...
 47-99 5.81e-18

putative membrane protein insertion efficiency factor; This model describes a family, YidD, of small, non-essential proteins now suggested to improve YidC-dependent inner membrane protein insertion. A related protein is found in the temperature phage HP1 of Haemophilus influenzae. Annotation of some members of this family as hemolysins appears to represent propagation from an unpublished GenBank submission, L36462, attributed to Aeromonas hydrophila but a close match to E. coli. [Hypothetical proteins, Conserved]


Pssm-ID: 272995  Cd Length: 75  Bit Score: 71.72  E-value: 5.81e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 937902929   47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDPP 99
Cdd:TIGR00278  12 ISPFFPPSCRFYPTCSQYAIEALKTHGFLKGGWLTLKRILRCHPLHPGGNDPV 64
 
Name Accession Description Interval E-value
YidD pfam01809
Putative membrane protein insertion efficiency factor; This family consists of membrane ...
 47-98 8.24e-30

Putative membrane protein insertion efficiency factor; This family consists of membrane insertion efficiency factor proteins. They contain three conserved cysteine residues. Family members such as YidD may be involved in insertion of integral membrane proteins into the membrane by assisting YidC (membrane protein insertase). Some members of the yidD family have been previously thought to posses alpha-hemolysin activity, however no sufficient evidence was found to corroborate this idea. Secondary structure prediction indicated the presence of three alpha-helices in YidD. None of the three alpha-helices appeared sufficiently hydrophobic to serve as a transmembrane, suggesting a cytoplasmic localization for YidD. However, a closer examination of the alpha-helical wheel projection of the predicted first alpha-helix in YidD suggested an amphipathic structure in its N-terminal region which might be involved in membrane targeting.


Pssm-ID: 460342  Cd Length: 67  Bit Score: 101.30  E-value: 8.24e-30
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 937902929   47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDP 98
Cdd:pfam01809  15 ISPLLPPSCRFYPTCSEYAIEAIEKHGALKGGWLALKRILRCHPFHPGGYDP 66
YidD COG0759
Membrane-anchored protein YidD, putatitve component of membrane protein insertase Oxa1/YidC ...
 47-99 2.72e-28

Membrane-anchored protein YidD, putatitve component of membrane protein insertase Oxa1/YidC/SpoIIIJ [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440522  Cd Length: 71  Bit Score: 97.50  E-value: 2.72e-28
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDPP 99
Cdd:COG0759   19 ISPLLGPRCRFYPTCSEYALEAIERHGLLKGSWLTLKRILRCHPWHPGGYDPV 71
PRK14386 PRK14386
membrane protein insertion efficiency factor YidD;
47-98 4.80e-20

membrane protein insertion efficiency factor YidD;


Pssm-ID: 172862  Cd Length: 106  Bit Score: 77.76  E-value: 4.80e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDP 98
Cdd:PRK14386  16 ISPLLGPRCRYIPTCSQYALEALQTHGAIKGVWLSSKRICRCHPWGGSGYDP 67
PRK14370 PRK14370
hypothetical protein; Provisional
 47-97 3.87e-19

hypothetical protein; Provisional


Pssm-ID: 184651  Cd Length: 120  Bit Score: 76.04  E-value: 3.87e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYD 97
Cdd:PRK14370  24 ISPILPARCRYYPTCSNYGKQAIAWHGVGKGSLLLLKRIGRCHPLGGHGID 74
PRK14391 PRK14391
membrane protein insertion efficiency factor YidD;
47-99 7.55e-19

membrane protein insertion efficiency factor YidD;


Pssm-ID: 172867  Cd Length: 84  Bit Score: 74.30  E-value: 7.55e-19
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLgGHGYDPP 99
Cdd:PRK14391  16 ISPLLPPACRFTPTCSEYAAQAFQECGFFQAIQLSAWRILRCNPL-SQGFDDP 67
PRK14387 PRK14387
membrane protein insertion efficiency factor YidD;
47-99 1.11e-18

membrane protein insertion efficiency factor YidD;


Pssm-ID: 184655  Cd Length: 84  Bit Score: 73.82  E-value: 1.11e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDPP 99
Cdd:PRK14387  19 LSPLIGRQCRFTPSCSEYTAAALKDHGPLKGSWLGLRRICRCNPFGGSGYDPP 71
PRK14382 PRK14382
hypothetical protein; Provisional
 47-99 4.07e-18

hypothetical protein; Provisional


Pssm-ID: 172858  Cd Length: 68  Bit Score: 71.72  E-value: 4.07e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDPP 99
Cdd:PRK14382  16 ISPLYPSSCRFYPTCSTYAILSIEKYGALKGSLKAFWRILRCNPFSKGGVDYP 68
PRK14373 PRK14373
hypothetical protein; Provisional
 47-98 5.45e-18

hypothetical protein; Provisional


Pssm-ID: 172849  Cd Length: 73  Bit Score: 71.57  E-value: 5.45e-18
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDP 98
Cdd:PRK14373  20 ISPLIPPRCRYTPTCSQYAVEAVKKYGAFKGGRLAIKRIARCHPFGGHGHDP 71
TIGR00278 TIGR00278
putative membrane protein insertion efficiency factor; This model describes a family, YidD, of ...
 47-99 5.81e-18

putative membrane protein insertion efficiency factor; This model describes a family, YidD, of small, non-essential proteins now suggested to improve YidC-dependent inner membrane protein insertion. A related protein is found in the temperature phage HP1 of Haemophilus influenzae. Annotation of some members of this family as hemolysins appears to represent propagation from an unpublished GenBank submission, L36462, attributed to Aeromonas hydrophila but a close match to E. coli. [Hypothetical proteins, Conserved]


Pssm-ID: 272995  Cd Length: 75  Bit Score: 71.72  E-value: 5.81e-18
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 937902929   47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDPP 99
Cdd:TIGR00278  12 ISPFFPPSCRFYPTCSQYAIEALKTHGFLKGGWLTLKRILRCHPLHPGGNDPV 64
PRK14369 PRK14369
membrane protein insertion efficiency factor YidD;
47-100 2.55e-17

membrane protein insertion efficiency factor YidD;


Pssm-ID: 184650  Cd Length: 119  Bit Score: 71.24  E-value: 2.55e-17
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNP--LGGHGYDPPR 100
Cdd:PRK14369  16 ISPLLGPVCKYYPSCSHYGYTAIDRHGAIKGTALTAWRILRCNPwsLGGVDHVPPR 71
PRK14383 PRK14383
membrane protein insertion efficiency factor YidD;
46-98 1.40e-15

membrane protein insertion efficiency factor YidD;


Pssm-ID: 237698 [Multi-domain]  Cd Length: 84  Bit Score: 65.75  E-value: 1.40e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 937902929  46 EISPLLPS-SCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDP 98
Cdd:PRK14383  18 VLSPRKPApTCRFSPTCSQYAVEAIERHGALKGGWLALWRVLRCNPLVPGGFDP 71
PRK14380 PRK14380
hypothetical protein; Provisional
 47-98 1.09e-14

hypothetical protein; Provisional


Pssm-ID: 184654  Cd Length: 81  Bit Score: 63.43  E-value: 1.09e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDP 98
Cdd:PRK14380  23 ISPLITPCCRYYPSCSEYADSAIKHYGVIKGLLMALNRLSRCHPWSKGGYDP 74
PRK14389 PRK14389
membrane protein insertion efficiency factor YidD;
47-98 1.21e-14

membrane protein insertion efficiency factor YidD;


Pssm-ID: 184656  Cd Length: 98  Bit Score: 63.80  E-value: 1.21e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDP 98
Cdd:PRK14389  17 LSPWLGSACRFEPTCSAYSLQALEQHGAAAGSYLTLRRLARCHPWCDGGHDP 68
PRK14379 PRK14379
membrane protein insertion efficiency factor YidD;
29-98 1.59e-14

membrane protein insertion efficiency factor YidD;


Pssm-ID: 237697  Cd Length: 95  Bit Score: 63.31  E-value: 1.59e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 937902929  29 NKRRILTMRVYCAAdegeISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDP 98
Cdd:PRK14379   2 RKILIFLVRVYQKF----ISPILPPSCRYYPTCSSYMIDALKKHGPILGLIMGLARILRCNPFIRGGVDP 67
PRK14378 PRK14378
membrane protein insertion efficiency factor YidD;
47-97 6.12e-12

membrane protein insertion efficiency factor YidD;


Pssm-ID: 237696  Cd Length: 103  Bit Score: 57.27  E-value: 6.12e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYD 97
Cdd:PRK14378  27 VSPFYGDVCRYYPSCSAYGLEAVQEHGLIFGGYLAVWRVCRCHPWAEGGID 77
PRK14375 PRK14375
membrane protein insertion efficiency factor YidD;
47-99 8.48e-12

membrane protein insertion efficiency factor YidD;


Pssm-ID: 172851  Cd Length: 70  Bit Score: 55.77  E-value: 8.48e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDPP 99
Cdd:PRK14375  10 ISPFIPARCRYYPTCSEYALEALKTHGILKGLYLTTRRLLRCHPLSKRDYYDL 62
PRK14388 PRK14388
membrane protein insertion efficiency factor YidD;
47-97 1.62e-11

membrane protein insertion efficiency factor YidD;


Pssm-ID: 172864  Cd Length: 82  Bit Score: 55.28  E-value: 1.62e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYD 97
Cdd:PRK14388  16 ISPLLGNNCRFHPTCSEYAKEAISMHGSIKGLWFTFKRIIKCQPFCDGGYD 66
PRK14371 PRK14371
hypothetical protein; Provisional
 30-98 2.57e-11

hypothetical protein; Provisional


Pssm-ID: 172847  Cd Length: 81  Bit Score: 54.93  E-value: 2.57e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 937902929  30 KRRILTMRVYCAAdegeISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDP 98
Cdd:PRK14371   3 KLALVPIQFYRYA----ISPLMASHCRFYPSCSCYAYEAIENHGLLRGGWLSVRRLGRCHPWNPGGYDP 67
PRK14372 PRK14372
membrane protein insertion efficiency factor YidD;
47-97 3.10e-11

membrane protein insertion efficiency factor YidD;


Pssm-ID: 172848  Cd Length: 97  Bit Score: 54.94  E-value: 3.10e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYD 97
Cdd:PRK14372  12 ISANTPPCCKYYPSCSNYAIEAIERFGAFKGGVLAVLRLLRCRPWSRGGID 62
PRK14384 PRK14384
hypothetical protein; Provisional
 53-97 3.59e-11

hypothetical protein; Provisional


Pssm-ID: 172860  Cd Length: 56  Bit Score: 53.91  E-value: 3.59e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 937902929  53 SSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYD 97
Cdd:PRK14384   2 SSCRFYPSCSCYAETALKRFGVIKGSGLTVWRLLRCHPFHPGGVD 46
PRK14381 PRK14381
membrane protein insertion efficiency factor YidD;
47-97 1.13e-10

membrane protein insertion efficiency factor YidD;


Pssm-ID: 172857  Cd Length: 103  Bit Score: 53.71  E-value: 1.13e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYD 97
Cdd:PRK14381  26 ISPLLGSPCRFFPSCSQYALQALKHHGCIMGLWLTIKRIGKCGPWHPGGID 76
PRK14377 PRK14377
membrane protein insertion efficiency factor YidD;
47-97 3.22e-09

membrane protein insertion efficiency factor YidD;


Pssm-ID: 172853  Cd Length: 104  Bit Score: 50.15  E-value: 3.22e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 937902929  47 ISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYD 97
Cdd:PRK14377  21 ISPFLGAPCRFFPTCSEYALVALKKHPLRKSLFLIAKRLLKCGPWCIGGID 71
PRK14376 PRK14376
membrane protein insertion efficiency factor YidD;
55-98 8.25e-09

membrane protein insertion efficiency factor YidD;


Pssm-ID: 237695  Cd Length: 176  Bit Score: 50.34  E-value: 8.25e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 937902929  55 CRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDP 98
Cdd:PRK14376  64 CRFEPSCSAYALTAVRRHGGVRGGLLAVRRLLRCQPLSAGGYDP 107
PRK14385 PRK14385
membrane protein insertion efficiency factor YidD;
33-98 6.03e-08

membrane protein insertion efficiency factor YidD;


Pssm-ID: 172861  Cd Length: 96  Bit Score: 46.74  E-value: 6.03e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 937902929  33 ILTMRVYcaadEGEISPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPL--GGHGYDP 98
Cdd:PRK14385  15 ILLIKIY----QNTLSKIVGFQCIYKPSCSNYALECLKKYNILTALILITLRIIRCNALfkGGNESLP 78
PRK14390 PRK14390
hypothetical protein; Provisional
 48-98 2.04e-07

hypothetical protein; Provisional


Pssm-ID: 172866  Cd Length: 63  Bit Score: 44.61  E-value: 2.04e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 937902929  48 SPLLPSSCRYVPTCSEYSMQAYKKYGVAKGTILTAWRLCRCNPLGGHGYDP 98
Cdd:PRK14390  10 SPFFGPRCRFIPSCSSYGYEAITRHGPWKGGWLTLRRLSRCHPLTPCGCDP 60
PRK14374 PRK14374
membrane protein insertion efficiency factor YidD;
48-100 5.10e-03

membrane protein insertion efficiency factor YidD;


Pssm-ID: 237694  Cd Length: 118  Bit Score: 33.89  E-value: 5.10e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 937902929  48 SPLLPSSCRYVPTCSEYSMQ--AYKKYGVAKGTIltAWRLCRCNPL--GGHGYDPPR 100
Cdd:PRK14374  25 SAFTFSSCRFYPTCSNYALWllCFENPLSAMGKI--AIRILSCNPFcsGGIAYPTTR 79
 
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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