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Conserved domains on  [gi|1540238428|emb|VEJ02920|]
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Uncharacterised protein [Porphyromonas cangingivalis]

Protein Classification

fibronectin type III domain-containing protein( domain architecture ID 10973489)

fibronectin type III (FN3) domain-containing protein may be involved in specific interactions with other molecules through its FN3 domain

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CBM6-CBM35-CBM36_like super family cl14880
Carbohydrate Binding Module 6 (CBM6) and CBM35_like superfamily; Carbohydrate binding module ...
 228-377 1.23e-25

Carbohydrate Binding Module 6 (CBM6) and CBM35_like superfamily; Carbohydrate binding module family 6 (CBM6, family 6 CBM), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36). These are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate targets, including mannan, xylan, beta-glucans, cellulose, agarose, and arabinans. These domains facilitate the strong binding of the appended catalytic modules to their dedicated, insoluble substrates. Many of these CBMs are associated with glycoside hydrolase (GH) domains. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. CBM36s are calcium-dependent xylan binding domains. CBM35s display conserved specificity through extensive sequence similarity, but divergent function through their appended catalytic modules. This alignment model also contains the C-terminal domains of bacterial insecticidal toxins, where they may be involved in determining insect specificity through carbohydrate binding functionality.


The actual alignment was detected with superfamily member cd14488:

Pssm-ID: 449372  Cd Length: 132  Bit Score: 103.15  E-value: 1.23e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540238428 228 IVDNDKSHFTKGEyvetdkGWETVSKGFGYTqslwkdnenpfksGTSRLHLSSTRKESEVRWHPTIVRDETLAVYVSYQS 307
Cdd:cd14488     4 VVDNSDAGFSASG------NWTTSTSIAGYY-------------GTDYRYAEPVKGSDPATFTFKIPATGSYEVYVWYPA 64

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540238428 308 FPNSVEDALYTVHHARGTSSFKVNQTMGGGTWIYLGSFPFEAGKRDQgISLSNISRDKGKVIsADAVKIG 377
Cdd:cd14488    65 NPNRNSAAPYVVETAGGTSTVRVDQTTGGGTWVSLGTFEFKAGDQNK-VTVSNWTTGGGYVI-ADAVRVV 132
AmiC super family cl34058
N-acetylmuramoyl-L-alanine amidase [Cell wall/membrane/envelope biogenesis];
473-598 1.00e-04

N-acetylmuramoyl-L-alanine amidase [Cell wall/membrane/envelope biogenesis];


The actual alignment was detected with superfamily member COG0860:

Pssm-ID: 440621  Cd Length: 204  Bit Score: 44.49  E-value: 1.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540238428 473 DLSLTLHTDAGVRENVDdvlGTLAIFntkwnqglYPSGMDRLMARELTDIVQSYIVRDVRVshnpdwKRRGMWDKNYSEA 552
Cdd:COG0860    95 DLFISIHANAAPNPSAR---GAEVYY--------YSGSQTSAESKKLAEAIQKELVKALGL------KDRGVKQANFYVL 157

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1540238428 553 TWGSVPGVLLELLSHQNFKDMCYGHDPAFKFTVARAIYKGILRYLS 598
Cdd:COG0860   158 RETDMPAVLVELGFISNPEDEALLKSPAYQQKLAEAIADGILRYFG 203
fn3 pfam00041
Fibronectin type III domain;
626-694 1.61e-04

Fibronectin type III domain;


:

Pssm-ID: 394996 [Multi-domain]  Cd Length: 85  Bit Score: 41.25  E-value: 1.61e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1540238428 626 ARLSWHPTQDSIEPtatPSHY-ILYTAIDEGYFDQGKIIKNTTTTVPIA---PGRNYRFKIVAANEGGVSFES 694
Cdd:pfam00041  16 LTVSWTPPPDGNGP---ITGYeVEYRPKNSGEPWNEITVPGTTTSVTLTglkPGTEYEVRVQAVNGGGEGPPS 85
 
Name Accession Description Interval E-value
CBM6-CBM35-CBM36_like_2 cd14488
uncharacterized members of the carbohydrate binding module 6 (CBM6) and CBM35_like superfamily; ...
 228-377 1.23e-25

uncharacterized members of the carbohydrate binding module 6 (CBM6) and CBM35_like superfamily; Carbohydrate binding module family 6 (CBM6, family 6 CBM), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36). These are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate targets, including mannan, xylan, beta-glucans, cellulose, agarose, and arabinans. These domains facilitate the strong binding of the appended catalytic modules to their dedicated, insoluble substrates. Many of these CBMs are associated with glycoside hydrolase (GH) domains. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. CBM36s are calcium-dependent xylan binding domains. CBM35s display conserved specificity through extensive sequence similarity, but divergent function through their appended catalytic modules.


Pssm-ID: 271154  Cd Length: 132  Bit Score: 103.15  E-value: 1.23e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540238428 228 IVDNDKSHFTKGEyvetdkGWETVSKGFGYTqslwkdnenpfksGTSRLHLSSTRKESEVRWHPTIVRDETLAVYVSYQS 307
Cdd:cd14488     4 VVDNSDAGFSASG------NWTTSTSIAGYY-------------GTDYRYAEPVKGSDPATFTFKIPATGSYEVYVWYPA 64

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540238428 308 FPNSVEDALYTVHHARGTSSFKVNQTMGGGTWIYLGSFPFEAGKRDQgISLSNISRDKGKVIsADAVKIG 377
Cdd:cd14488    65 NPNRNSAAPYVVETAGGTSTVRVDQTTGGGTWVSLGTFEFKAGDQNK-VTVSNWTTGGGYVI-ADAVRVV 132
AmiC COG0860
N-acetylmuramoyl-L-alanine amidase [Cell wall/membrane/envelope biogenesis];
473-598 1.00e-04

N-acetylmuramoyl-L-alanine amidase [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440621  Cd Length: 204  Bit Score: 44.49  E-value: 1.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540238428 473 DLSLTLHTDAGVRENVDdvlGTLAIFntkwnqglYPSGMDRLMARELTDIVQSYIVRDVRVshnpdwKRRGMWDKNYSEA 552
Cdd:COG0860    95 DLFISIHANAAPNPSAR---GAEVYY--------YSGSQTSAESKKLAEAIQKELVKALGL------KDRGVKQANFYVL 157

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1540238428 553 TWGSVPGVLLELLSHQNFKDMCYGHDPAFKFTVARAIYKGILRYLS 598
Cdd:COG0860   158 RETDMPAVLVELGFISNPEDEALLKSPAYQQKLAEAIADGILRYFG 203
fn3 pfam00041
Fibronectin type III domain;
626-694 1.61e-04

Fibronectin type III domain;


Pssm-ID: 394996 [Multi-domain]  Cd Length: 85  Bit Score: 41.25  E-value: 1.61e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1540238428 626 ARLSWHPTQDSIEPtatPSHY-ILYTAIDEGYFDQGKIIKNTTTTVPIA---PGRNYRFKIVAANEGGVSFES 694
Cdd:pfam00041  16 LTVSWTPPPDGNGP---ITGYeVEYRPKNSGEPWNEITVPGTTTSVTLTglkPGTEYEVRVQAVNGGGEGPPS 85
FN3 cd00063
Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein ...
 609-699 1.81e-03

Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.


Pssm-ID: 238020 [Multi-domain]  Cd Length: 93  Bit Score: 38.63  E-value: 1.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540238428 609 PLPVRQFSIDIDAEDALaRLSWHPTQDSIEPtatPSHYIL-YTAIDEGYFDQ--GKIIKNTTTTVP-IAPGRNYRFKIVA 684
Cdd:cd00063     1 PSPPTNLRVTDVTSTSV-TLSWTPPEDDGGP---ITGYVVeYREKGSGDWKEveVTPGSETSYTLTgLKPGTEYEFRVRA 76

                          90
                  ....*....|....*
gi 1540238428 685 ANEGGVSFESEELSC 699
Cdd:cd00063    77 VNGGGESPPSESVTV 91
MurNAc-LAA cd02696
N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, ...
 506-594 6.36e-03

N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino acids in certain cell wall glycopeptides. These proteins are Zn-dependent peptidases with highly conserved residues involved in cation co-ordination. MurNAc-LAA in this family is one of several peptidoglycan hydrolases (PGHs) found in bacterial and bacteriophage or prophage genomes that are involved in the degradation of the peptidoglycan. In Escherichia coli, there are five MurNAc-LAAs present: AmiA, AmiB, AmiC and AmiD that are periplasmic, and AmpD that is cytoplasmic. Three of these (AmiA, AmiB and AmiC) belong to this family, the other two (AmiD and AmpD) do not. E. coli AmiA, AmiB and AmiC play an important role in cleaving the septum to release daughter cells after cell division. In general, bacterial MurNAc-LAAs are members of the bacterial autolytic system and carry a signal peptide in their N-termini that allows their transport across the cytoplasmic membrane. However, the bacteriophage MurNAc-LAAs are endolysins since these phage-encoded enzymes break down bacterial peptidoglycan at the terminal stage of the phage reproduction cycle. As opposed to autolysins, almost all endolysins have no signal peptides and their translocation through the cytoplasmic membrane is thought to proceed with the help of phage-encoded holin proteins. The amidase catalytic module is fused to another functional module (cell wall binding module or CWBM) either at the N- or C-terminus, which is responsible for high affinity binding of the protein to the cell wall.


Pssm-ID: 119407 [Multi-domain]  Cd Length: 172  Bit Score: 38.68  E-value: 6.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540238428 506 LYPSGmDRLMARELTDIVQSYIVRdvrvshNPDWKRRGMWDKNYSEATWGSVPGVLLEL--LSHQNfkDMCYGHDPAFKF 583
Cdd:cd02696    91 YYYSG-SSEESKRLAEAIQKELVK------ALGLRNRGVKQANLYVLRNTKMPAVLVELgfISNPE--DAKLLNSPEYQD 161

                          90
                  ....*....|.
gi 1540238428 584 TVARAIYKGIL 594
Cdd:cd02696   162 KIAEAIAEGIL 172
 
Name Accession Description Interval E-value
CBM6-CBM35-CBM36_like_2 cd14488
uncharacterized members of the carbohydrate binding module 6 (CBM6) and CBM35_like superfamily; ...
 228-377 1.23e-25

uncharacterized members of the carbohydrate binding module 6 (CBM6) and CBM35_like superfamily; Carbohydrate binding module family 6 (CBM6, family 6 CBM), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36). These are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate targets, including mannan, xylan, beta-glucans, cellulose, agarose, and arabinans. These domains facilitate the strong binding of the appended catalytic modules to their dedicated, insoluble substrates. Many of these CBMs are associated with glycoside hydrolase (GH) domains. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. CBM36s are calcium-dependent xylan binding domains. CBM35s display conserved specificity through extensive sequence similarity, but divergent function through their appended catalytic modules.


Pssm-ID: 271154  Cd Length: 132  Bit Score: 103.15  E-value: 1.23e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540238428 228 IVDNDKSHFTKGEyvetdkGWETVSKGFGYTqslwkdnenpfksGTSRLHLSSTRKESEVRWHPTIVRDETLAVYVSYQS 307
Cdd:cd14488     4 VVDNSDAGFSASG------NWTTSTSIAGYY-------------GTDYRYAEPVKGSDPATFTFKIPATGSYEVYVWYPA 64

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540238428 308 FPNSVEDALYTVHHARGTSSFKVNQTMGGGTWIYLGSFPFEAGKRDQgISLSNISRDKGKVIsADAVKIG 377
Cdd:cd14488    65 NPNRNSAAPYVVETAGGTSTVRVDQTTGGGTWVSLGTFEFKAGDQNK-VTVSNWTTGGGYVI-ADAVRVV 132
AmiC COG0860
N-acetylmuramoyl-L-alanine amidase [Cell wall/membrane/envelope biogenesis];
473-598 1.00e-04

N-acetylmuramoyl-L-alanine amidase [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440621  Cd Length: 204  Bit Score: 44.49  E-value: 1.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540238428 473 DLSLTLHTDAGVRENVDdvlGTLAIFntkwnqglYPSGMDRLMARELTDIVQSYIVRDVRVshnpdwKRRGMWDKNYSEA 552
Cdd:COG0860    95 DLFISIHANAAPNPSAR---GAEVYY--------YSGSQTSAESKKLAEAIQKELVKALGL------KDRGVKQANFYVL 157

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1540238428 553 TWGSVPGVLLELLSHQNFKDMCYGHDPAFKFTVARAIYKGILRYLS 598
Cdd:COG0860   158 RETDMPAVLVELGFISNPEDEALLKSPAYQQKLAEAIADGILRYFG 203
fn3 pfam00041
Fibronectin type III domain;
626-694 1.61e-04

Fibronectin type III domain;


Pssm-ID: 394996 [Multi-domain]  Cd Length: 85  Bit Score: 41.25  E-value: 1.61e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1540238428 626 ARLSWHPTQDSIEPtatPSHY-ILYTAIDEGYFDQGKIIKNTTTTVPIA---PGRNYRFKIVAANEGGVSFES 694
Cdd:pfam00041  16 LTVSWTPPPDGNGP---ITGYeVEYRPKNSGEPWNEITVPGTTTSVTLTglkPGTEYEVRVQAVNGGGEGPPS 85
FN3 cd00063
Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein ...
 609-699 1.81e-03

Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases.


Pssm-ID: 238020 [Multi-domain]  Cd Length: 93  Bit Score: 38.63  E-value: 1.81e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540238428 609 PLPVRQFSIDIDAEDALaRLSWHPTQDSIEPtatPSHYIL-YTAIDEGYFDQ--GKIIKNTTTTVP-IAPGRNYRFKIVA 684
Cdd:cd00063     1 PSPPTNLRVTDVTSTSV-TLSWTPPEDDGGP---ITGYVVeYREKGSGDWKEveVTPGSETSYTLTgLKPGTEYEFRVRA 76

                          90
                  ....*....|....*
gi 1540238428 685 ANEGGVSFESEELSC 699
Cdd:cd00063    77 VNGGGESPPSESVTV 91
MurNAc-LAA cd02696
N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, ...
 506-594 6.36e-03

N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino acids in certain cell wall glycopeptides. These proteins are Zn-dependent peptidases with highly conserved residues involved in cation co-ordination. MurNAc-LAA in this family is one of several peptidoglycan hydrolases (PGHs) found in bacterial and bacteriophage or prophage genomes that are involved in the degradation of the peptidoglycan. In Escherichia coli, there are five MurNAc-LAAs present: AmiA, AmiB, AmiC and AmiD that are periplasmic, and AmpD that is cytoplasmic. Three of these (AmiA, AmiB and AmiC) belong to this family, the other two (AmiD and AmpD) do not. E. coli AmiA, AmiB and AmiC play an important role in cleaving the septum to release daughter cells after cell division. In general, bacterial MurNAc-LAAs are members of the bacterial autolytic system and carry a signal peptide in their N-termini that allows their transport across the cytoplasmic membrane. However, the bacteriophage MurNAc-LAAs are endolysins since these phage-encoded enzymes break down bacterial peptidoglycan at the terminal stage of the phage reproduction cycle. As opposed to autolysins, almost all endolysins have no signal peptides and their translocation through the cytoplasmic membrane is thought to proceed with the help of phage-encoded holin proteins. The amidase catalytic module is fused to another functional module (cell wall binding module or CWBM) either at the N- or C-terminus, which is responsible for high affinity binding of the protein to the cell wall.


Pssm-ID: 119407 [Multi-domain]  Cd Length: 172  Bit Score: 38.68  E-value: 6.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540238428 506 LYPSGmDRLMARELTDIVQSYIVRdvrvshNPDWKRRGMWDKNYSEATWGSVPGVLLEL--LSHQNfkDMCYGHDPAFKF 583
Cdd:cd02696    91 YYYSG-SSEESKRLAEAIQKELVK------ALGLRNRGVKQANLYVLRNTKMPAVLVELgfISNPE--DAKLLNSPEYQD 161

                          90
                  ....*....|.
gi 1540238428 584 TVARAIYKGIL 594
Cdd:cd02696   162 KIAEAIAEGIL 172
 
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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