NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2019012054|ref|WP_208476291|]
View 

collagen-like protein, partial [Bacillus subtilis]

Protein Classification

collagen-like domain-containing protein( domain architecture ID 1903237)

collagen-like domain-containing protein such as collagens, which are extracellular structural proteins involved in formation of connective tissue structure

PubMed:  21421911|15837519

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
SPT5 super family cl34925
Transcription elongation factor SPT5 [Transcription];
3-139 2.00e-04

Transcription elongation factor SPT5 [Transcription];


The actual alignment was detected with superfamily member COG5164:

Pssm-ID: 444063 [Multi-domain]  Cd Length: 495  Bit Score: 40.01  E-value: 2.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019012054   3 GVTGVTGATGVTGPTGPTGSTGPTGATGETGATGVTGSTGSTGATGVTGETGPTGPTGVTG-----------ATGSTGPT 71
Cdd:COG5164    58 GNTGGTRPAGNQGATGPAQNQGGTTPAQNQGGTRPAGNTGGTTPAGDGGATGPPDDGGATGppddggsttppSGGSTTPP 137

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2019012054  72 GVTGVTGPTGATGATGTTGETGPTGATGPTGPTGATGATGTTGETGPTGATGPTGATGATGETGATGA 139
Cdd:COG5164   138 GDGGSTPPGPGSTGPGGSTTPPGDGGSTTPPGPGGSTTPPDDGGSTTPPNKGETGTDIPTGGTPRQGP 205
 
Name Accession Description Interval E-value
SPT5 COG5164
Transcription elongation factor SPT5 [Transcription];
3-139 2.00e-04

Transcription elongation factor SPT5 [Transcription];


Pssm-ID: 444063 [Multi-domain]  Cd Length: 495  Bit Score: 40.01  E-value: 2.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019012054   3 GVTGVTGATGVTGPTGPTGSTGPTGATGETGATGVTGSTGSTGATGVTGETGPTGPTGVTG-----------ATGSTGPT 71
Cdd:COG5164    58 GNTGGTRPAGNQGATGPAQNQGGTTPAQNQGGTRPAGNTGGTTPAGDGGATGPPDDGGATGppddggsttppSGGSTTPP 137

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2019012054  72 GVTGVTGPTGATGATGTTGETGPTGATGPTGPTGATGATGTTGETGPTGATGPTGATGATGETGATGA 139
Cdd:COG5164   138 GDGGSTPPGPGSTGPGGSTTPPGDGGSTTPPGPGGSTTPPDDGGSTTPPNKGETGTDIPTGGTPRQGP 205
Collagen pfam01391
Collagen triple helix repeat (20 copies); Members of this family belong to the collagen ...
 6-60 6.92e-03

Collagen triple helix repeat (20 copies); Members of this family belong to the collagen superfamily. Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The alignment contains 20 copies of the G-X-Y repeat that forms a triple helix. The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and hydroxy-proline. Collagens are post translationally modified by proline hydroxylase to form the hydroxy-proline residues. Defective hydroxylation is the cause of scurvy. Some members of the collagen superfamily are not involved in connective tissue structure but share the same triple helical structure. The family includes bacterial collagen-like triple-helix repeat proteins.


Pssm-ID: 460189 [Multi-domain]  Cd Length: 57  Bit Score: 32.85  E-value: 6.92e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2019012054   6 GVTGATGVTGPTGPTGSTGPTGATGETGATGVTGSTGSTGATGVTGETGPTGPTG 60
Cdd:pfam01391   1 GPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGEPGPPGPPGPPGPPGPPGAPGAPG 55
 
Name Accession Description Interval E-value
SPT5 COG5164
Transcription elongation factor SPT5 [Transcription];
3-139 2.00e-04

Transcription elongation factor SPT5 [Transcription];


Pssm-ID: 444063 [Multi-domain]  Cd Length: 495  Bit Score: 40.01  E-value: 2.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019012054   3 GVTGVTGATGVTGPTGPTGSTGPTGATGETGATGVTGSTGSTGATGVTGETGPTGPTGVTG-----------ATGSTGPT 71
Cdd:COG5164    58 GNTGGTRPAGNQGATGPAQNQGGTTPAQNQGGTRPAGNTGGTTPAGDGGATGPPDDGGATGppddggsttppSGGSTTPP 137

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2019012054  72 GVTGVTGPTGATGATGTTGETGPTGATGPTGPTGATGATGTTGETGPTGATGPTGATGATGETGATGA 139
Cdd:COG5164   138 GDGGSTPPGPGSTGPGGSTTPPGDGGSTTPPGPGGSTTPPDDGGSTTPPNKGETGTDIPTGGTPRQGP 205
SPT5 COG5164
Transcription elongation factor SPT5 [Transcription];
14-139 2.47e-04

Transcription elongation factor SPT5 [Transcription];


Pssm-ID: 444063 [Multi-domain]  Cd Length: 495  Bit Score: 39.63  E-value: 2.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019012054  14 TGPTGPtGSTGPTGATGETGATGVTGSTGSTGATGVTGETGPTGPTGVTGATGSTGPTGVTGVTGPTGATGATGTTGETG 93
Cdd:COG5164     1 TGLYGP-GKTGPSDPGGVTTPAGSQGSTKPAQNQGSTRPAGNTGGTRPAQNQGSTTPAGNTGGTRPAGNQGATGPAQNQG 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2019012054  94 PTGATGPTGPTGATGATGTTGETGPTGATGPTGATGATGETGATGA 139
Cdd:COG5164    80 GTTPAQNQGGTRPAGNTGGTTPAGDGGATGPPDDGGATGPPDDGGS 125
SPT5 COG5164
Transcription elongation factor SPT5 [Transcription];
2-139 6.36e-04

Transcription elongation factor SPT5 [Transcription];


Pssm-ID: 444063 [Multi-domain]  Cd Length: 495  Bit Score: 38.47  E-value: 6.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2019012054   2 TGVTGVTGATGVTGPTGPTGSTGPTGATGETGATGVTGST---GSTGATGVTGETGPTGPTGVTGATGSTGPTGVTGVTG 78
Cdd:COG5164    15 GGVTTPAGSQGSTKPAQNQGSTRPAGNTGGTRPAQNQGSTtpaGNTGGTRPAGNQGATGPAQNQGGTTPAQNQGGTRPAG 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2019012054  79 PTGATGATGTTGETGPTGATGPTGPTGATGATGTTGETGPTGATGPTGATGATGETGATGA 139
Cdd:COG5164    95 NTGGTTPAGDGGATGPPDDGGATGPPDDGGSTTPPSGGSTTPPGDGGSTPPGPGSTGPGGS 155
Collagen pfam01391
Collagen triple helix repeat (20 copies); Members of this family belong to the collagen ...
 6-60 6.92e-03

Collagen triple helix repeat (20 copies); Members of this family belong to the collagen superfamily. Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The alignment contains 20 copies of the G-X-Y repeat that forms a triple helix. The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and hydroxy-proline. Collagens are post translationally modified by proline hydroxylase to form the hydroxy-proline residues. Defective hydroxylation is the cause of scurvy. Some members of the collagen superfamily are not involved in connective tissue structure but share the same triple helical structure. The family includes bacterial collagen-like triple-helix repeat proteins.


Pssm-ID: 460189 [Multi-domain]  Cd Length: 57  Bit Score: 32.85  E-value: 6.92e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2019012054   6 GVTGATGVTGPTGPTGSTGPTGATGETGATGVTGSTGSTGATGVTGETGPTGPTG 60
Cdd:pfam01391   1 GPPGPPGPPGPPGPPGPPGPPGPPGPPGPPGEPGPPGPPGPPGPPGPPGAPGAPG 55
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH