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Conserved domains on  [gi|1907200815|ref|XP_036011251|]
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roundabout homolog 4 isoform X5 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 1-33 1.74e-09

Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, including T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, including butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E, and D strands in one sheet and A', G, F, C, C' and C" in the other. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other by strands G, F, C, and C'. Moreover, a C1-set Ig domain contains a short C' strand (three residues) and lacks A' and C" strand. Unlike other Ig domain sets, C2-set structures do not have a D strand. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


The actual alignment was detected with superfamily member cd05724:

Pssm-ID: 472250 [Multi-domain]  Cd Length: 87  Bit Score: 55.10  E-value: 1.74e-09
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1907200815   1 MVSRAEKNDSGTYMCMATNNAGQRESRAARVSI 33
Cdd:cd05724    55 LIAEARKSDEGTYKCVATNMVGERESRAARLSV 87
fn3 pfam00041
Fibronectin type III domain;
158-240 4.96e-07

Fibronectin type III domain;


:

Pssm-ID: 394996 [Multi-domain]  Cd Length: 85  Bit Score: 48.18  E-value: 4.96e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907200815 158 PPQGVTLRS-GNGSVFVSWAPPPaeSHNGVIRGYQV-WSLGNASLPAANWTVVGEQTQLEIATRLPGS-YCVQVAAVTGA 234
Cdd:pfam00041   2 APSNLTVTDvTSTSLTVSWTPPP--DGNGPITGYEVeYRPKNSGEPWNEITVPGTTTSVTLTGLKPGTeYEVRVQAVNGG 79


                  ....*.
gi 1907200815 235 GAGELS 240
Cdd:pfam00041  80 GEGPPS 85
FN3 super family cl27307
Fibronectin type 3 domain [General function prediction only];
64-243 8.20e-04

Fibronectin type 3 domain [General function prediction only];


The actual alignment was detected with superfamily member COG3401:

Pssm-ID: 442628 [Multi-domain]  Cd Length: 603  Bit Score: 43.07  E-value: 8.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907200815  64 KGPKPGPSVWLSWKVSGPAAPAESYTALFRTQRSPRDQGSPWTEVLLRG-LQSAKLGGLHWGQDYEFKVRPSSGRARGPD 142
Cdd:COG3401   141 YALGAGLYGVDGANASGTTASSVAGAGVVVSPDTSATAAVATTSLTVTStTLVDGGGDIEPGTTYYYRVAATDTGGESAP 220

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907200815 143 SNVLLLRLPEQVPSApPQGVTLRS-GNGSVFVSWAPPPAEShngvIRGYQVWSlgnASLPAANWTVVGEQTQLEI--ATR 219
Cdd:COG3401   221 SNEVSVTTPTTPPSA-PTGLTATAdTPGSVTLSWDPVTESD----ATGYRVYR---SNSGDGPFTKVATVTTTSYtdTGL 292

                         170       180
                  ....*....|....*....|....*.
gi 1907200815 220 LPG-SYCVQVAAVTGAG-AGELSTPV 243
Cdd:COG3401   293 TNGtTYYYRVTAVDAAGnESAPSNVV 318
 
Name Accession Description Interval E-value
IgI_2_Robo cd05724
Second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of ...
 1-33 1.74e-09

Second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of the Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (Robo1, Robo2, and Robo3), and three mammalian Slit homologs (Slit-1,Slit-2, Slit-3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. Robo1, Robo2, and Robo3 are expressed by commissural neurons in the vertebrate spinal cord and Slit-1, Slit-2, Slit-3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of Slit responsiveness, antagonizes Slit responsiveness in precrossing axons. The Slit-Robo interaction is mediated by the second leucine-rich repeat (LRR) domain of Slit and the two N-terminal Ig domains of Robo, Ig1 and Ig2. The primary Robo binding site for Slit-2 has been shown by surface plasmon resonance experiments and mutational analysis to be the Ig1 domain, while the Ig2 domain has been proposed to harbor a weak secondary binding site. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409389 [Multi-domain]  Cd Length: 87  Bit Score: 55.10  E-value: 1.74e-09
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1907200815   1 MVSRAEKNDSGTYMCMATNNAGQRESRAARVSI 33
Cdd:cd05724    55 LIAEARKSDEGTYKCVATNMVGERESRAARLSV 87
fn3 pfam00041
Fibronectin type III domain;
158-240 4.96e-07

Fibronectin type III domain;


Pssm-ID: 394996 [Multi-domain]  Cd Length: 85  Bit Score: 48.18  E-value: 4.96e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907200815 158 PPQGVTLRS-GNGSVFVSWAPPPaeSHNGVIRGYQV-WSLGNASLPAANWTVVGEQTQLEIATRLPGS-YCVQVAAVTGA 234
Cdd:pfam00041   2 APSNLTVTDvTSTSLTVSWTPPP--DGNGPITGYEVeYRPKNSGEPWNEITVPGTTTSVTLTGLKPGTeYEVRVQAVNGG 79


                  ....*.
gi 1907200815 235 GAGELS 240
Cdd:pfam00041  80 GEGPPS 85
FN3 cd00063
Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein ...
 158-243 3.85e-06

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: 45.95  E-value: 3.85e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907200815 158 PPQGVTLRS-GNGSVFVSWAPPPaeSHNGVIRGYQV-WSLGNASLPAANWTVVGEQTQLEIaTRL-PGS-YCVQVAAVTG 233
Cdd:cd00063     3 PPTNLRVTDvTSTSVTLSWTPPE--DDGGPITGYVVeYREKGSGDWKEVEVTPGSETSYTL-TGLkPGTeYEFRVRAVNG 79

                          90
                  ....*....|
gi 1907200815 234 AGAGELSTPV 243
Cdd:cd00063    80 GGESPPSESV 89
FN3 smart00060
Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, ...
 158-237 4.00e-05

Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.


Pssm-ID: 214495 [Multi-domain]  Cd Length: 83  Bit Score: 42.60  E-value: 4.00e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907200815  158 PPQGVTLRS-GNGSVFVSWAPPPAESHNGVIRGYQVwSLGNASLPAANWTVVGEQTQLEIaTRL-PGS-YCVQVAAVTGA 234
Cdd:smart00060   3 PPSNLRVTDvTSTSVTLSWEPPPDDGITGYIVGYRV-EYREEGSEWKEVNVTPSSTSYTL-TGLkPGTeYEFRVRAVNGA 80


                   ...
gi 1907200815  235 GAG 237
Cdd:smart00060  81 GEG 83
FN3 COG3401
Fibronectin type 3 domain [General function prediction only];
64-243 8.20e-04

Fibronectin type 3 domain [General function prediction only];


Pssm-ID: 442628 [Multi-domain]  Cd Length: 603  Bit Score: 43.07  E-value: 8.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907200815  64 KGPKPGPSVWLSWKVSGPAAPAESYTALFRTQRSPRDQGSPWTEVLLRG-LQSAKLGGLHWGQDYEFKVRPSSGRARGPD 142
Cdd:COG3401   141 YALGAGLYGVDGANASGTTASSVAGAGVVVSPDTSATAAVATTSLTVTStTLVDGGGDIEPGTTYYYRVAATDTGGESAP 220

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907200815 143 SNVLLLRLPEQVPSApPQGVTLRS-GNGSVFVSWAPPPAEShngvIRGYQVWSlgnASLPAANWTVVGEQTQLEI--ATR 219
Cdd:COG3401   221 SNEVSVTTPTTPPSA-PTGLTATAdTPGSVTLSWDPVTESD----ATGYRVYR---SNSGDGPFTKVATVTTTSYtdTGL 292

                         170       180
                  ....*....|....*....|....*.
gi 1907200815 220 LPG-SYCVQVAAVTGAG-AGELSTPV 243
Cdd:COG3401   293 TNGtTYYYRVTAVDAAGnESAPSNVV 318
I-set pfam07679
Immunoglobulin I-set domain;
2-28 7.31e-03

Immunoglobulin I-set domain;


Pssm-ID: 400151 [Multi-domain]  Cd Length: 90  Bit Score: 36.47  E-value: 7.31e-03
                          10        20
                  ....*....|....*....|....*..
gi 1907200815   2 VSRAEKNDSGTYMCMATNNAGQRESRA 28
Cdd:pfam07679  60 ISNVQPDDSGKYTCVATNSAGEAEASA 86
 
Name Accession Description Interval E-value
IgI_2_Robo cd05724
Second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of ...
 1-33 1.74e-09

Second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of the Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (Robo1, Robo2, and Robo3), and three mammalian Slit homologs (Slit-1,Slit-2, Slit-3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. Robo1, Robo2, and Robo3 are expressed by commissural neurons in the vertebrate spinal cord and Slit-1, Slit-2, Slit-3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of Slit responsiveness, antagonizes Slit responsiveness in precrossing axons. The Slit-Robo interaction is mediated by the second leucine-rich repeat (LRR) domain of Slit and the two N-terminal Ig domains of Robo, Ig1 and Ig2. The primary Robo binding site for Slit-2 has been shown by surface plasmon resonance experiments and mutational analysis to be the Ig1 domain, while the Ig2 domain has been proposed to harbor a weak secondary binding site. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


Pssm-ID: 409389 [Multi-domain]  Cd Length: 87  Bit Score: 55.10  E-value: 1.74e-09
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1907200815   1 MVSRAEKNDSGTYMCMATNNAGQRESRAARVSI 33
Cdd:cd05724    55 LIAEARKSDEGTYKCVATNMVGERESRAARLSV 87
fn3 pfam00041
Fibronectin type III domain;
158-240 4.96e-07

Fibronectin type III domain;


Pssm-ID: 394996 [Multi-domain]  Cd Length: 85  Bit Score: 48.18  E-value: 4.96e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907200815 158 PPQGVTLRS-GNGSVFVSWAPPPaeSHNGVIRGYQV-WSLGNASLPAANWTVVGEQTQLEIATRLPGS-YCVQVAAVTGA 234
Cdd:pfam00041   2 APSNLTVTDvTSTSLTVSWTPPP--DGNGPITGYEVeYRPKNSGEPWNEITVPGTTTSVTLTGLKPGTeYEVRVQAVNGG 79


                  ....*.
gi 1907200815 235 GAGELS 240
Cdd:pfam00041  80 GEGPPS 85
FN3 cd00063
Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein ...
 158-243 3.85e-06

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: 45.95  E-value: 3.85e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907200815 158 PPQGVTLRS-GNGSVFVSWAPPPaeSHNGVIRGYQV-WSLGNASLPAANWTVVGEQTQLEIaTRL-PGS-YCVQVAAVTG 233
Cdd:cd00063     3 PPTNLRVTDvTSTSVTLSWTPPE--DDGGPITGYVVeYREKGSGDWKEVEVTPGSETSYTL-TGLkPGTeYEFRVRAVNG 79

                          90
                  ....*....|
gi 1907200815 234 AGAGELSTPV 243
Cdd:cd00063    80 GGESPPSESV 89
FN3 smart00060
Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, ...
 158-237 4.00e-05

Fibronectin type 3 domain; One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins.


Pssm-ID: 214495 [Multi-domain]  Cd Length: 83  Bit Score: 42.60  E-value: 4.00e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907200815  158 PPQGVTLRS-GNGSVFVSWAPPPAESHNGVIRGYQVwSLGNASLPAANWTVVGEQTQLEIaTRL-PGS-YCVQVAAVTGA 234
Cdd:smart00060   3 PPSNLRVTDvTSTSVTLSWEPPPDDGITGYIVGYRV-EYREEGSEWKEVNVTPSSTSYTL-TGLkPGTeYEFRVRAVNGA 80


                   ...
gi 1907200815  235 GAG 237
Cdd:smart00060  81 GEG 83
FN3 COG3401
Fibronectin type 3 domain [General function prediction only];
64-243 8.20e-04

Fibronectin type 3 domain [General function prediction only];


Pssm-ID: 442628 [Multi-domain]  Cd Length: 603  Bit Score: 43.07  E-value: 8.20e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907200815  64 KGPKPGPSVWLSWKVSGPAAPAESYTALFRTQRSPRDQGSPWTEVLLRG-LQSAKLGGLHWGQDYEFKVRPSSGRARGPD 142
Cdd:COG3401   141 YALGAGLYGVDGANASGTTASSVAGAGVVVSPDTSATAAVATTSLTVTStTLVDGGGDIEPGTTYYYRVAATDTGGESAP 220

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907200815 143 SNVLLLRLPEQVPSApPQGVTLRS-GNGSVFVSWAPPPAEShngvIRGYQVWSlgnASLPAANWTVVGEQTQLEI--ATR 219
Cdd:COG3401   221 SNEVSVTTPTTPPSA-PTGLTATAdTPGSVTLSWDPVTESD----ATGYRVYR---SNSGDGPFTKVATVTTTSYtdTGL 292

                         170       180
                  ....*....|....*....|....*.
gi 1907200815 220 LPG-SYCVQVAAVTGAG-AGELSTPV 243
Cdd:COG3401   293 TNGtTYYYRVTAVDAAGnESAPSNVV 318
FN3 COG3401
Fibronectin type 3 domain [General function prediction only];
60-243 7.27e-03

Fibronectin type 3 domain [General function prediction only];


Pssm-ID: 442628 [Multi-domain]  Cd Length: 603  Bit Score: 39.99  E-value: 7.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907200815  60 PEPVKG-PKPGPSVWLSWKvSGPAAPAESYTaLFRTQrsprDQGSPWTEVLLRGLQSAKLGGLHWGQDYEFKVRPSSGR- 137
Cdd:COG3401   236 PTGLTAtADTPGSVTLSWD-PVTESDATGYR-VYRSN----SGDGPFTKVATVTTTSYTDTGLTNGTTYYYRVTAVDAAg 309

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907200815 138 ARGPDSNVLLLrLPEQVPSAPPQGVTL-RSGNGSVFVSWAPppaeSHNGVIRGYQVWSlgnASLPAANWTVVGE---QTQ 213
Cdd:COG3401   310 NESAPSNVVSV-TTDLTPPAAPSGLTAtAVGSSSITLSWTA----SSDADVTGYNVYR---STSGGGTYTKIAEtvtTTS 381

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1907200815 214 LEIATRLPG-SYCVQVAAVTGAG-AGELSTPV 243
Cdd:COG3401   382 YTDTGLTPGtTYYYKVTAVDAAGnESAPSEEV 413
I-set pfam07679
Immunoglobulin I-set domain;
2-28 7.31e-03

Immunoglobulin I-set domain;


Pssm-ID: 400151 [Multi-domain]  Cd Length: 90  Bit Score: 36.47  E-value: 7.31e-03
                          10        20
                  ....*....|....*....|....*..
gi 1907200815   2 VSRAEKNDSGTYMCMATNNAGQRESRA 28
Cdd:pfam07679  60 ISNVQPDDSGKYTCVATNSAGEAEASA 86
 
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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