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Conserved domains on  [gi|1245641790|gb|PCC40353|]
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resuscitation-promoting factor [Brachybacterium alimentarium]

Protein Classification

resuscitation-promoting factor( domain architecture ID 11466449)

resuscitation-promoting factor is a cell-wall glycosidase that cleaves cell-wall peptidoglycan; it stimulates resuscitation of dormant cells

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Transglycosylas pfam06737
Transglycosylase-like domain; This family of proteins are very likely to act as ...
 340-414 7.82e-42

Transglycosylase-like domain; This family of proteins are very likely to act as transglycosylase enzymes related to pfam00062 and pfam01464. These other families are weakly matched by this family, and include the known active site residues.


:

Pssm-ID: 399604 [Multi-domain]  Cd Length: 75  Bit Score: 142.17  E-value: 7.82e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1245641790 340 DGSVWDRLAQCESGGNWSINTGNGYYGGIQFNNQTWAAYGGTSYAARADLATREQQIAVAKKVQANQGWGAWPSC 414
Cdd:pfam06737   1 DNSNWDAIAQCESGGNWAINTGNGYYGGLQFSQSTWDAYGGLGYAPSAAQASREQQIAVAEKLLATQGAGAWPTC 75
YabE COG3583
Uncharacterized conserved protein YabE, contains G5 and tandem DUF348 domains [Function ...
 23-420 2.39e-36

Uncharacterized conserved protein YabE, contains G5 and tandem DUF348 domains [Function unknown];


:

Pssm-ID: 442802 [Multi-domain]  Cd Length: 335  Bit Score: 135.77  E-value: 2.39e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790  23 TAFAMSNEAALSVYGEQSMVRTFSQpTVGELLEAQGISLKDTDLVLPDTSAQITDGI----EIQIIQRTPVTVTVDGEEQ 98
Cdd:COG3583    26 AYAAAKKTVTLDVDGEERTVTTFAG-TVGEVLEEAGITVGEHDVVSPALDTPLTDGDtgelTITVKRAKPVTVVVDGKTR 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790  99 EVLTTGDTVADALDEvdydadgAAISPAPEteltgdsaevdvvtrktvtfkgqngqdtfdvtaltvddamkkvlgdiedt 178
Cdd:COG3583   105 TVTTTATTVGEALAE-------AGITLGED-------------------------------------------------- 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790 179 DKASVDRDSILEDGATITVKRVREAERTETEEIPFTTKTVEDDTLLEGKTKTKTEGKKGTAEKVFAETTVDGEVTESELV 258
Cdd:COG3583   128 DRVSPALDAPLTDGMTITVTRVTTKTVTEEEPIPFETVRKEDPSLPKGETKVVQEGVPGVKEVTYRVTYENGKEVSREVV 207

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790 259 SEETTAEPVTEVVLKGTKKAPQPEAPAETTsekssssdssssssneksekstksdskdsssrsserkstdsgssksapsv 338
Cdd:COG3583   208 SEKVTKEPVDEVVAVGTKPRPAPAPVPAGS-------------------------------------------------- 237

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790 339 sdgsvwdrlaqceSGGNWSINTGNGYYGGIQFNNQTWAAYGGTSYAARADLATREQQIAVAKKVQANQGWGAWPSCTSQL 418
Cdd:COG3583   238 -------------GSGGGGSSTGSGGYGGLAASSATTAASGGGTGAPGGGGAARPTAGAVAGVVVVGGGGGGGPGGGGGG 304


                  ..
gi 1245641790 419 GI 420
Cdd:COG3583   305 GA 306
 
Name Accession Description Interval E-value
Transglycosylas pfam06737
Transglycosylase-like domain; This family of proteins are very likely to act as ...
 340-414 7.82e-42

Transglycosylase-like domain; This family of proteins are very likely to act as transglycosylase enzymes related to pfam00062 and pfam01464. These other families are weakly matched by this family, and include the known active site residues.


Pssm-ID: 399604 [Multi-domain]  Cd Length: 75  Bit Score: 142.17  E-value: 7.82e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1245641790 340 DGSVWDRLAQCESGGNWSINTGNGYYGGIQFNNQTWAAYGGTSYAARADLATREQQIAVAKKVQANQGWGAWPSC 414
Cdd:pfam06737   1 DNSNWDAIAQCESGGNWAINTGNGYYGGLQFSQSTWDAYGGLGYAPSAAQASREQQIAVAEKLLATQGAGAWPTC 75
YabE COG3583
Uncharacterized conserved protein YabE, contains G5 and tandem DUF348 domains [Function ...
 23-420 2.39e-36

Uncharacterized conserved protein YabE, contains G5 and tandem DUF348 domains [Function unknown];


Pssm-ID: 442802 [Multi-domain]  Cd Length: 335  Bit Score: 135.77  E-value: 2.39e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790  23 TAFAMSNEAALSVYGEQSMVRTFSQpTVGELLEAQGISLKDTDLVLPDTSAQITDGI----EIQIIQRTPVTVTVDGEEQ 98
Cdd:COG3583    26 AYAAAKKTVTLDVDGEERTVTTFAG-TVGEVLEEAGITVGEHDVVSPALDTPLTDGDtgelTITVKRAKPVTVVVDGKTR 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790  99 EVLTTGDTVADALDEvdydadgAAISPAPEteltgdsaevdvvtrktvtfkgqngqdtfdvtaltvddamkkvlgdiedt 178
Cdd:COG3583   105 TVTTTATTVGEALAE-------AGITLGED-------------------------------------------------- 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790 179 DKASVDRDSILEDGATITVKRVREAERTETEEIPFTTKTVEDDTLLEGKTKTKTEGKKGTAEKVFAETTVDGEVTESELV 258
Cdd:COG3583   128 DRVSPALDAPLTDGMTITVTRVTTKTVTEEEPIPFETVRKEDPSLPKGETKVVQEGVPGVKEVTYRVTYENGKEVSREVV 207

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790 259 SEETTAEPVTEVVLKGTKKAPQPEAPAETTsekssssdssssssneksekstksdskdsssrsserkstdsgssksapsv 338
Cdd:COG3583   208 SEKVTKEPVDEVVAVGTKPRPAPAPVPAGS-------------------------------------------------- 237

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790 339 sdgsvwdrlaqceSGGNWSINTGNGYYGGIQFNNQTWAAYGGTSYAARADLATREQQIAVAKKVQANQGWGAWPSCTSQL 418
Cdd:COG3583   238 -------------GSGGGGSSTGSGGYGGLAASSATTAASGGGTGAPGGGGAARPTAGAVAGVVVVGGGGGGGPGGGGGG 304


                  ..
gi 1245641790 419 GI 420
Cdd:COG3583   305 GA 306
RPF cd13925
core lysozyme-like domain of resuscitation-promoting factor proteins; Resuscitation-promoting ...
 342-414 1.39e-33

core lysozyme-like domain of resuscitation-promoting factor proteins; Resuscitation-promoting factor (RPF) proteins, found in various (G+C)-rich Gram-positive bacteria, act to reactivate cultures from stationary phase. This protein shares elements of the structural core of lysozyme and related proteins. Furthermore, it shares a conserved active site glutamate which is required for activity, and has a polysaccharide binding cleft that corresponds to the peptidoglycan binding cleft of lysozyme. Muralytic activity of Rpf in Micrococcus luteus correlates with resuscitation, supporting a mechanism dependent on cleavage of peptidoglycan by RPF.


Pssm-ID: 381607 [Multi-domain]  Cd Length: 71  Bit Score: 120.18  E-value: 1.39e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1245641790 342 SVWDRLAQCESGGNWS-INTGNGYYGGIQFNNQTWAAYGGTSYaarADLATREQQIAVAKKVQANQGWGAWPSC 414
Cdd:cd13925     1 SQWDAIAQCESGGNWNaVNTGNGYYGGLQFLQGTWKSVGGLGY---PDDATRAEQITRAERLYARQGAGAWPCC 71
G5 pfam07501
G5 domain; This domain is found in a wide range of extracellular proteins. It is found ...
 211-276 7.72e-10

G5 domain; This domain is found in a wide range of extracellular proteins. It is found tandemly repeated in up to 8 copies. It is found in the N-terminus of peptidases belonging to the M26 family which cleave human IgA. The domain is also found in proteins involved in metabolism of bacterial cell walls suggesting this domain may have an adhesive function.


Pssm-ID: 462185 [Multi-domain]  Cd Length: 75  Bit Score: 54.86  E-value: 7.72e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1245641790 211 IPFTTKTVEDDTLLEGKTKTKTEGKKGTAEKVFAETTVDGEVTESELVSEETTAEPVTEVVLKGTK 276
Cdd:pfam07501  10 IPFETVTKEDPSLPKGEEKVVQEGKPGEKEVTYKVTYVNGKEVSREVVSEEVTKEPVDEVVAVGTK 75
LYZ1 smart00263
Alpha-lactalbumin / lysozyme C;
344-411 2.89e-03

Alpha-lactalbumin / lysozyme C;


Pssm-ID: 197612  Cd Length: 127  Bit Score: 37.65  E-value: 2.89e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790  344 WDRLAQCESGGN-WSINTGNGY---YGGIQFNNQTWAAYGGTSYAARA-----------DLAtreQQIAVAKKVQANQGW 408
Cdd:smart00263  28 WVCLAFHESGYNtQATNYNNGGstdYGIFQINSKYWCNDGKTPGSVNAcgiscskllddDIT---DDVKCAKKIVSDQGI 104


                   ...
gi 1245641790  409 GAW 411
Cdd:smart00263 105 DAW 107
 
Name Accession Description Interval E-value
Transglycosylas pfam06737
Transglycosylase-like domain; This family of proteins are very likely to act as ...
 340-414 7.82e-42

Transglycosylase-like domain; This family of proteins are very likely to act as transglycosylase enzymes related to pfam00062 and pfam01464. These other families are weakly matched by this family, and include the known active site residues.


Pssm-ID: 399604 [Multi-domain]  Cd Length: 75  Bit Score: 142.17  E-value: 7.82e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1245641790 340 DGSVWDRLAQCESGGNWSINTGNGYYGGIQFNNQTWAAYGGTSYAARADLATREQQIAVAKKVQANQGWGAWPSC 414
Cdd:pfam06737   1 DNSNWDAIAQCESGGNWAINTGNGYYGGLQFSQSTWDAYGGLGYAPSAAQASREQQIAVAEKLLATQGAGAWPTC 75
YabE COG3583
Uncharacterized conserved protein YabE, contains G5 and tandem DUF348 domains [Function ...
 23-420 2.39e-36

Uncharacterized conserved protein YabE, contains G5 and tandem DUF348 domains [Function unknown];


Pssm-ID: 442802 [Multi-domain]  Cd Length: 335  Bit Score: 135.77  E-value: 2.39e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790  23 TAFAMSNEAALSVYGEQSMVRTFSQpTVGELLEAQGISLKDTDLVLPDTSAQITDGI----EIQIIQRTPVTVTVDGEEQ 98
Cdd:COG3583    26 AYAAAKKTVTLDVDGEERTVTTFAG-TVGEVLEEAGITVGEHDVVSPALDTPLTDGDtgelTITVKRAKPVTVVVDGKTR 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790  99 EVLTTGDTVADALDEvdydadgAAISPAPEteltgdsaevdvvtrktvtfkgqngqdtfdvtaltvddamkkvlgdiedt 178
Cdd:COG3583   105 TVTTTATTVGEALAE-------AGITLGED-------------------------------------------------- 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790 179 DKASVDRDSILEDGATITVKRVREAERTETEEIPFTTKTVEDDTLLEGKTKTKTEGKKGTAEKVFAETTVDGEVTESELV 258
Cdd:COG3583   128 DRVSPALDAPLTDGMTITVTRVTTKTVTEEEPIPFETVRKEDPSLPKGETKVVQEGVPGVKEVTYRVTYENGKEVSREVV 207

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790 259 SEETTAEPVTEVVLKGTKKAPQPEAPAETTsekssssdssssssneksekstksdskdsssrsserkstdsgssksapsv 338
Cdd:COG3583   208 SEKVTKEPVDEVVAVGTKPRPAPAPVPAGS-------------------------------------------------- 237

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790 339 sdgsvwdrlaqceSGGNWSINTGNGYYGGIQFNNQTWAAYGGTSYAARADLATREQQIAVAKKVQANQGWGAWPSCTSQL 418
Cdd:COG3583   238 -------------GSGGGGSSTGSGGYGGLAASSATTAASGGGTGAPGGGGAARPTAGAVAGVVVVGGGGGGGPGGGGGG 304


                  ..
gi 1245641790 419 GI 420
Cdd:COG3583   305 GA 306
RPF cd13925
core lysozyme-like domain of resuscitation-promoting factor proteins; Resuscitation-promoting ...
 342-414 1.39e-33

core lysozyme-like domain of resuscitation-promoting factor proteins; Resuscitation-promoting factor (RPF) proteins, found in various (G+C)-rich Gram-positive bacteria, act to reactivate cultures from stationary phase. This protein shares elements of the structural core of lysozyme and related proteins. Furthermore, it shares a conserved active site glutamate which is required for activity, and has a polysaccharide binding cleft that corresponds to the peptidoglycan binding cleft of lysozyme. Muralytic activity of Rpf in Micrococcus luteus correlates with resuscitation, supporting a mechanism dependent on cleavage of peptidoglycan by RPF.


Pssm-ID: 381607 [Multi-domain]  Cd Length: 71  Bit Score: 120.18  E-value: 1.39e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1245641790 342 SVWDRLAQCESGGNWS-INTGNGYYGGIQFNNQTWAAYGGTSYaarADLATREQQIAVAKKVQANQGWGAWPSC 414
Cdd:cd13925     1 SQWDAIAQCESGGNWNaVNTGNGYYGGLQFLQGTWKSVGGLGY---PDDATRAEQITRAERLYARQGAGAWPCC 71
G5 pfam07501
G5 domain; This domain is found in a wide range of extracellular proteins. It is found ...
 211-276 7.72e-10

G5 domain; This domain is found in a wide range of extracellular proteins. It is found tandemly repeated in up to 8 copies. It is found in the N-terminus of peptidases belonging to the M26 family which cleave human IgA. The domain is also found in proteins involved in metabolism of bacterial cell walls suggesting this domain may have an adhesive function.


Pssm-ID: 462185 [Multi-domain]  Cd Length: 75  Bit Score: 54.86  E-value: 7.72e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1245641790 211 IPFTTKTVEDDTLLEGKTKTKTEGKKGTAEKVFAETTVDGEVTESELVSEETTAEPVTEVVLKGTK 276
Cdd:pfam07501  10 IPFETVTKEDPSLPKGEEKVVQEGKPGEKEVTYKVTYVNGKEVSREVVSEEVTKEPVDEVVAVGTK 75
Lyz-like cd00442
lysozyme-like domains; This family contains several members, including soluble lytic ...
 343-401 2.20e-08

lysozyme-like domains; This family contains several members, including soluble lytic transglycosylases (SLT), goose egg-white lysozymes (GEWL), hen egg-white lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, chitosanases, and pesticin. Typical members are involved in the hydrolysis of beta-1,4- linked polysaccharides.


Pssm-ID: 381596 [Multi-domain]  Cd Length: 59  Bit Score: 50.49  E-value: 2.20e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1245641790 343 VWDRLAQCESGGNW--SINTGNGYYGGIQFNNQTWAAYGGTSyaaRADLATREQQIAVAKK 401
Cdd:cd00442     1 VLAAIIGQESGGNKpaNAGSGSGAAGLFQFMPGTWKAYGKNS---SSDLNDPEASIEAAAK 58
DUF348 pfam03990
G5-linked-Ubiquitin-like domain; This domain normally occurs as tandem repeats; however it is ...
 89-128 2.60e-06

G5-linked-Ubiquitin-like domain; This domain normally occurs as tandem repeats; however it is found as a single copy in the S. cerevisiae DNA-binding nuclear protein YCR593. This protein is involved in sporulation part of the SET3C complex, which is required to repress early/middle sporulation genes during meiosis. The bacterial proteins are likely to be involved in a cell wall function as they are found in conjunction with the pfam07501 domain, which is involved in various cell surface processes. This domain is also present in the resuscitation-promoting factors RpfB from Mycobacterium tuberculosis and Rpf2 from Corynebacterium glutamicum. These are factors that stimulate resuscitation of dormant cells. This domain has a beta grasp fold. Structural description of this domain revealed a structural conservation between these domains and ubiquitin, hence it is termed UBL-G5.


Pssm-ID: 461121 [Multi-domain]  Cd Length: 41  Bit Score: 43.95  E-value: 2.60e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1245641790  89 VTVTVDGEEQEVLTTGDTVADALDEVDYD-ADGAAISPAPE 128
Cdd:pfam03990   1 VTLTVDGKERTVTTTAGTVGDLLEEAGITlGEHDKVSPSLD 41
DUF348 pfam03990
G5-linked-Ubiquitin-like domain; This domain normally occurs as tandem repeats; however it is ...
 33-69 4.34e-04

G5-linked-Ubiquitin-like domain; This domain normally occurs as tandem repeats; however it is found as a single copy in the S. cerevisiae DNA-binding nuclear protein YCR593. This protein is involved in sporulation part of the SET3C complex, which is required to repress early/middle sporulation genes during meiosis. The bacterial proteins are likely to be involved in a cell wall function as they are found in conjunction with the pfam07501 domain, which is involved in various cell surface processes. This domain is also present in the resuscitation-promoting factors RpfB from Mycobacterium tuberculosis and Rpf2 from Corynebacterium glutamicum. These are factors that stimulate resuscitation of dormant cells. This domain has a beta grasp fold. Structural description of this domain revealed a structural conservation between these domains and ubiquitin, hence it is termed UBL-G5.


Pssm-ID: 461121 [Multi-domain]  Cd Length: 41  Bit Score: 37.78  E-value: 4.34e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1245641790  33 LSVYGEQSMVRTFSqPTVGELLEAQGISLKDTDLVLP 69
Cdd:pfam03990   3 LTVDGKERTVTTTA-GTVGDLLEEAGITLGEHDKVSP 38
LYZ1 smart00263
Alpha-lactalbumin / lysozyme C;
344-411 2.89e-03

Alpha-lactalbumin / lysozyme C;


Pssm-ID: 197612  Cd Length: 127  Bit Score: 37.65  E-value: 2.89e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1245641790  344 WDRLAQCESGGN-WSINTGNGY---YGGIQFNNQTWAAYGGTSYAARA-----------DLAtreQQIAVAKKVQANQGW 408
Cdd:smart00263  28 WVCLAFHESGYNtQATNYNNGGstdYGIFQINSKYWCNDGKTPGSVNAcgiscskllddDIT---DDVKCAKKIVSDQGI 104


                   ...
gi 1245641790  409 GAW 411
Cdd:smart00263 105 DAW 107
 
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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