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Conserved domains on  [gi|39575298|emb|CAE79466|]
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putative general secretion pathway protein J precursor [Bdellovibrio bacteriovorus HD100]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PulJ COG4795
Type II secretory pathway, PulJ/GspJ component [Intracellular trafficking, secretion, and ...
 1-80 8.38e-13

Type II secretory pathway, PulJ/GspJ component [Intracellular trafficking, secretion, and vesicular transport];


:

Pssm-ID: 443823 [Multi-domain]  Cd Length: 118  Bit Score: 63.88  E-value: 8.38e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39575298   1 MMMKHNRGFTMIELMITITILGTLTMLTAQAIQQAVKAKVKLQDQIDDVSRMRDGLRLLERDINLAYHYRDVEKELEQLM 80
Cdd:COG4795   3 RARRRQRGFTLLELLVALAIFALLLLAAYRGLDSVLRSRERLEQQAERLQELQRALALLERDLRQAGPRPDEGGDPEPAL 82
T2SSJ super family cl42010
Type II secretion system (T2SS), protein J; The T2SJ proteins are pseudopilins, which are ...
 160-249 2.01e-10

Type II secretion system (T2SS), protein J; The T2SJ proteins are pseudopilins, which are targeted to the membrane in E. Coli. T2SJ forms a complex with T2SI (pfam02501) and T2SK (pfam03934) which is part of the Type II secretion apparatus involved in the translocation of proteins across the outer membrane in E.coli. The T2SK-I-J complex has quasihelical characteriztics.


The actual alignment was detected with superfamily member pfam11612:

Pssm-ID: 455355  Cd Length: 137  Bit Score: 57.72  E-value: 2.01e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39575298   160 VGYALRDckslregggssKCLWRRSSPYVDLDVTKGGDEVALLENVSEFKLRYMGKGKqdWANDWRTDAQGDAatkgkFP 239
Cdd:pfam11612  57 VGYRLED-----------GRLERLTWPYLDGAVGQEPQVQVLLDGVESLRLRFLDDGQ--WQDRWPPAAADQA-----LP 118

                          90
                  ....*....|
gi 39575298   240 QAVEISLTVE 249
Cdd:pfam11612 119 RAVEITLELK 128
 
Name Accession Description Interval E-value
PulJ COG4795
Type II secretory pathway, PulJ/GspJ component [Intracellular trafficking, secretion, and ...
 1-80 8.38e-13

Type II secretory pathway, PulJ/GspJ component [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 443823 [Multi-domain]  Cd Length: 118  Bit Score: 63.88  E-value: 8.38e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39575298   1 MMMKHNRGFTMIELMITITILGTLTMLTAQAIQQAVKAKVKLQDQIDDVSRMRDGLRLLERDINLAYHYRDVEKELEQLM 80
Cdd:COG4795   3 RARRRQRGFTLLELLVALAIFALLLLAAYRGLDSVLRSRERLEQQAERLQELQRALALLERDLRQAGPRPDEGGDPEPAL 82
T2SSJ pfam11612
Type II secretion system (T2SS), protein J; The T2SJ proteins are pseudopilins, which are ...
 160-249 2.01e-10

Type II secretion system (T2SS), protein J; The T2SJ proteins are pseudopilins, which are targeted to the membrane in E. Coli. T2SJ forms a complex with T2SI (pfam02501) and T2SK (pfam03934) which is part of the Type II secretion apparatus involved in the translocation of proteins across the outer membrane in E.coli. The T2SK-I-J complex has quasihelical characteriztics.


Pssm-ID: 431959  Cd Length: 137  Bit Score: 57.72  E-value: 2.01e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39575298   160 VGYALRDckslregggssKCLWRRSSPYVDLDVTKGGDEVALLENVSEFKLRYMGKGKqdWANDWRTDAQGDAatkgkFP 239
Cdd:pfam11612  57 VGYRLED-----------GRLERLTWPYLDGAVGQEPQVQVLLDGVESLRLRFLDDGQ--WQDRWPPAAADQA-----LP 118

                          90
                  ....*....|
gi 39575298   240 QAVEISLTVE 249
Cdd:pfam11612 119 RAVEITLELK 128
N_methyl pfam07963
Prokaryotic N-terminal methylation motif; This short motif directs methylation of the ...
 3-29 1.04e-05

Prokaryotic N-terminal methylation motif; This short motif directs methylation of the conserved phenylalanine residue. It is most often found at the N-terminus of pilins and other proteins involved in secretion, see pfam00114, pfam05946, pfam02501 and pfam07596.


Pssm-ID: 429756 [Multi-domain]  Cd Length: 27  Bit Score: 41.59  E-value: 1.04e-05
                          10        20
                  ....*....|....*....|....*..
gi 39575298     3 MKHNRGFTMIELMITITILGTLTMLTA 29
Cdd:pfam07963   1 MRKQRGFTLIELLVALAILAILLAAAL 27
IV_pilin_GFxxxE TIGR02532
prepilin-type N-terminal cleavage/methylation domain; This model describes many but not all ...
 6-29 3.93e-05

prepilin-type N-terminal cleavage/methylation domain; This model describes many but not all examples of the N-terminal region of bacterial proteins that resemble type IV pilins at their N-terminus, with a cleavage site G^FxxxE followed by a hydrophobic stretch. The new N-terminal residue, usually Phe, is methylated. Separate domains of the prepilin peptidase appear responsible for cleavage and methylation. Proteins with this N-terminal region include type IV pilins and other components of pilus biogenesis, competence proteins, and type II secretion proteins. Typically several proteins in a single operon have this N-terminal domain. The N-terminal cleavage and methylation site is described by PROSITE motif PS00409 as [KRHEQSTAG]-G-[FYLIVM]-[ST]-[LT]-[LIVP]-E-[LIVMFWSTAG](14). [Cell envelope, Surface structures, Protein fate, Protein and peptide secretion and trafficking]


Pssm-ID: 274182 [Multi-domain]  Cd Length: 24  Bit Score: 39.60  E-value: 3.93e-05
                          10        20
                  ....*....|....*....|....
gi 39575298     6 NRGFTMIELMITITILGTLTMLTA 29
Cdd:TIGR02532   1 QRGFTLIELLVVLAILGILALIAL 24
PRK10506 PRK10506
prepilin peptidase-dependent protein;
3-72 3.07e-03

prepilin peptidase-dependent protein;


Pssm-ID: 236704 [Multi-domain]  Cd Length: 162  Bit Score: 37.67  E-value: 3.07e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 39575298    3 MKHNRGFTMIELMITITILGtltMLTA------QAIQQAvkakVKLQDQiddVSRMRDGLRLLERDINlaYHYRDV 72
Cdd:PRK10506   5 MKKQRGYTLIELLVVMTIVS---ILSAwglygwQRWQQR----QRLWQT---AQQLLDFLLRLQEDAN--WHNRDH 68
 
Name Accession Description Interval E-value
PulJ COG4795
Type II secretory pathway, PulJ/GspJ component [Intracellular trafficking, secretion, and ...
 1-80 8.38e-13

Type II secretory pathway, PulJ/GspJ component [Intracellular trafficking, secretion, and vesicular transport];


Pssm-ID: 443823 [Multi-domain]  Cd Length: 118  Bit Score: 63.88  E-value: 8.38e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39575298   1 MMMKHNRGFTMIELMITITILGTLTMLTAQAIQQAVKAKVKLQDQIDDVSRMRDGLRLLERDINLAYHYRDVEKELEQLM 80
Cdd:COG4795   3 RARRRQRGFTLLELLVALAIFALLLLAAYRGLDSVLRSRERLEQQAERLQELQRALALLERDLRQAGPRPDEGGDPEPAL 82
T2SSJ pfam11612
Type II secretion system (T2SS), protein J; The T2SJ proteins are pseudopilins, which are ...
 160-249 2.01e-10

Type II secretion system (T2SS), protein J; The T2SJ proteins are pseudopilins, which are targeted to the membrane in E. Coli. T2SJ forms a complex with T2SI (pfam02501) and T2SK (pfam03934) which is part of the Type II secretion apparatus involved in the translocation of proteins across the outer membrane in E.coli. The T2SK-I-J complex has quasihelical characteriztics.


Pssm-ID: 431959  Cd Length: 137  Bit Score: 57.72  E-value: 2.01e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39575298   160 VGYALRDckslregggssKCLWRRSSPYVDLDVTKGGDEVALLENVSEFKLRYMGKGKqdWANDWRTDAQGDAatkgkFP 239
Cdd:pfam11612  57 VGYRLED-----------GRLERLTWPYLDGAVGQEPQVQVLLDGVESLRLRFLDDGQ--WQDRWPPAAADQA-----LP 118

                          90
                  ....*....|
gi 39575298   240 QAVEISLTVE 249
Cdd:pfam11612 119 RAVEITLELK 128
PulG COG2165
Type II secretory pathway, pseudopilin PulG [Cell motility, Intracellular trafficking, ...
 1-62 1.33e-09

Type II secretory pathway, pseudopilin PulG [Cell motility, Intracellular trafficking, secretion, and vesicular transport, Extracellular structures];


Pssm-ID: 441768 [Multi-domain]  Cd Length: 99  Bit Score: 54.53  E-value: 1.33e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 39575298   1 MMMKHNRGFTMIELMITITILGTLTMLTAQAIQQAVKaKVKLQDQIDDVSRMRDGLRLLERD 62
Cdd:COG2165   5 RRRRRQRGFTLIELLVVIAIIGILAALALPALQGARE-RARRAELRSNLRQIQQALERYRLD 65
FimT COG4970
Type IV pilus assembly protein FimT [Cell motility, Extracellular structures];
2-66 3.73e-09

Type IV pilus assembly protein FimT [Cell motility, Extracellular structures];


Pssm-ID: 443996 [Multi-domain]  Cd Length: 73  Bit Score: 52.16  E-value: 3.73e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 39575298   2 MMKHNRGFTMIELMITITILGTLTMLTAQAIQQAVKAkvklqdqiddvSRMRDGLRLLERDINLA 66
Cdd:COG4970   4 LRRRQRGFTLIELLVVLAILAILAAIAVPSFSSLIAR-----------QRLRAAANELAAALRLA 57
PilW COG4966
Type IV pilus assembly protein PilW [Cell motility, Extracellular structures];
3-66 3.50e-08

Type IV pilus assembly protein PilW [Cell motility, Extracellular structures];


Pssm-ID: 443992 [Multi-domain]  Cd Length: 158  Bit Score: 52.10  E-value: 3.50e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 39575298   3 MKHNRGFTMIELMITITILGTLTMLTAQAIQQAVKAKVKLQDQIDDVSRMRDGLRLLERDINLA 66
Cdd:COG4966   1 RRRQRGFTLVELMVALAIGLIVLAAVLQLFLSSRRSYRTQEALARLQENGRFALDLLSRDLRQA 64
PilE COG4968
Type IV pilus assembly protein PilE [Cell motility, Extracellular structures];
1-56 5.60e-08

Type IV pilus assembly protein PilE [Cell motility, Extracellular structures];


Pssm-ID: 443994 [Multi-domain]  Cd Length: 124  Bit Score: 50.46  E-value: 5.60e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 39575298   1 MMMKHNRGFTMIELMITITILGTLTMLTAQAIQQAVkAKVKLQDQIDDVSRMRDGL 56
Cdd:COG4968   4 RMRRRQRGFTLIELMIVVAIIGILAAIAIPSYQDYV-ERARRAEAKAALLELAQAQ 58
N_methyl pfam07963
Prokaryotic N-terminal methylation motif; This short motif directs methylation of the ...
 3-29 1.04e-05

Prokaryotic N-terminal methylation motif; This short motif directs methylation of the conserved phenylalanine residue. It is most often found at the N-terminus of pilins and other proteins involved in secretion, see pfam00114, pfam05946, pfam02501 and pfam07596.


Pssm-ID: 429756 [Multi-domain]  Cd Length: 27  Bit Score: 41.59  E-value: 1.04e-05
                          10        20
                  ....*....|....*....|....*..
gi 39575298     3 MKHNRGFTMIELMITITILGTLTMLTA 29
Cdd:pfam07963   1 MRKQRGFTLIELLVALAILAILLAAAL 27
IV_pilin_GFxxxE TIGR02532
prepilin-type N-terminal cleavage/methylation domain; This model describes many but not all ...
 6-29 3.93e-05

prepilin-type N-terminal cleavage/methylation domain; This model describes many but not all examples of the N-terminal region of bacterial proteins that resemble type IV pilins at their N-terminus, with a cleavage site G^FxxxE followed by a hydrophobic stretch. The new N-terminal residue, usually Phe, is methylated. Separate domains of the prepilin peptidase appear responsible for cleavage and methylation. Proteins with this N-terminal region include type IV pilins and other components of pilus biogenesis, competence proteins, and type II secretion proteins. Typically several proteins in a single operon have this N-terminal domain. The N-terminal cleavage and methylation site is described by PROSITE motif PS00409 as [KRHEQSTAG]-G-[FYLIVM]-[ST]-[LT]-[LIVP]-E-[LIVMFWSTAG](14). [Cell envelope, Surface structures, Protein fate, Protein and peptide secretion and trafficking]


Pssm-ID: 274182 [Multi-domain]  Cd Length: 24  Bit Score: 39.60  E-value: 3.93e-05
                          10        20
                  ....*....|....*....|....
gi 39575298     6 NRGFTMIELMITITILGTLTMLTA 29
Cdd:TIGR02532   1 QRGFTLIELLVVLAILGILALIAL 24
PilA COG4969
Type IV pilus assembly protein, major pilin PilA [Cell motility, Extracellular structures];
2-40 6.15e-05

Type IV pilus assembly protein, major pilin PilA [Cell motility, Extracellular structures];


Pssm-ID: 443995 [Multi-domain]  Cd Length: 134  Bit Score: 42.00  E-value: 6.15e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 39575298   2 MMKHNRGFTMIELMITITILGTLTMLTAQAIQQAV-KAKV 40
Cdd:COG4969   1 MKKKQKGFTLIELMIVVAIIGILAAIAIPAYQDYVaRARV 40
PilV COG4967
Type IV pilus assembly protein PilV [Cell motility, Extracellular structures];
1-53 6.97e-05

Type IV pilus assembly protein PilV [Cell motility, Extracellular structures];


Pssm-ID: 443993 [Multi-domain]  Cd Length: 86  Bit Score: 40.74  E-value: 6.97e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 39575298   1 MMMKHNRGFTMIELMITITI-----LGTLTMLTA--QAIQQA---VKAKVKLQDQIDdvsRMR 53
Cdd:COG4967   5 RRRRRQRGFTLIEVLVALVIlsiglLGLAGLQAAslRSSQDArqrTQAALLAQDLLE---RLR 64
typeII_sec_gspG TIGR01710
type II secretion system protein G; This model represents GspG, protein G of the main terminal ...
 7-85 7.99e-05

type II secretion system protein G; This model represents GspG, protein G of the main terminal branch of the general secretion pathway, also called type II secretion. It transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis]


Pssm-ID: 130771 [Multi-domain]  Cd Length: 134  Bit Score: 41.64  E-value: 7.99e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 39575298     7 RGFTMIELMITITILGTLTMLTA-QAIQQAVKAKVKLQD-QIDDVSRMRDGLRLlerDInlaYHYRDVEKELEQLMKKKN 84
Cdd:TIGR01710   1 RGFTLLEIMVVLVILGLLAALVApKLFSQADKAKAQVAKaQIKALKNALDMYRL---DN---GRYPTEEQGLAALVTKPS 74


                  .
gi 39575298    85 T 85
Cdd:TIGR01710  75 G 75
ComGC COG4537
Competence protein ComGC [Mobilome: prophages, transposons];
2-47 2.43e-04

Competence protein ComGC [Mobilome: prophages, transposons];


Pssm-ID: 443603 [Multi-domain]  Cd Length: 108  Bit Score: 39.91  E-value: 2.43e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 39575298   2 MMKHNRGFTMIELMITITILGTLTMLT--------AQAIQQAVKAKVK-LQDQID 47
Cdd:COG4537   7 KLKKEKGFTLIEMLIVLLIISILLLIAvpnltkqrETAQEKGCEANIKmVQSQVE 61
gspJ TIGR01711
type II secretion system protein J; This model represents GspJ, one of two proteins highly ...
 7-63 1.89e-03

type II secretion system protein J; This model represents GspJ, one of two proteins highly conserved at their N-termini and described by pfam02501 but easily separable phylogenetically. The other is GspI. Both GspI and GspJ are proteins of the type II secretion pathway, or main terminal branch of the general secretion pathway. This pathway carries proteins across the outer membrane. Note that proteins of type II secretion are cryptic in E. coli K-12 - present but not yet demonstrated to act on any target.


Pssm-ID: 130772 [Multi-domain]  Cd Length: 192  Bit Score: 38.74  E-value: 1.89e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 39575298     7 RGFTMIELMITITILGTLTMLTAQAIQQavkakVKLQDQIDDV--SRMRDGLR---LLERDI 63
Cdd:TIGR01711   1 RGFTLLELLVAIAIFASLSLGAYQVLDS-----VMQSDEATRVqeARLRELQRamgAMERDL 57
PRK10506 PRK10506
prepilin peptidase-dependent protein;
3-72 3.07e-03

prepilin peptidase-dependent protein;


Pssm-ID: 236704 [Multi-domain]  Cd Length: 162  Bit Score: 37.67  E-value: 3.07e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 39575298    3 MKHNRGFTMIELMITITILGtltMLTA------QAIQQAvkakVKLQDQiddVSRMRDGLRLLERDINlaYHYRDV 72
Cdd:PRK10506   5 MKKQRGYTLIELLVVMTIVS---ILSAwglygwQRWQQR----QRLWQT---AQQLLDFLLRLQEDAN--WHNRDH 68
PRK10574 PRK10574
putative major pilin subunit; Provisional
 3-33 6.22e-03

putative major pilin subunit; Provisional


Pssm-ID: 236718 [Multi-domain]  Cd Length: 146  Bit Score: 36.55  E-value: 6.22e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 39575298    3 MKHNRGFTMIELMITITILGTLTMLTAQAIQ 33
Cdd:PRK10574   1 MDKQRGFTLIELMVVIAIIAILSAIGIPAYQ 31
 
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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