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Conserved domains on  [gi|1510945337|ref|WP_122942625|]
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resuscitation-promoting factor [Brachybacterium sp. EE-P12]

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 ...
 347-417 2.62e-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: 143.32  E-value: 2.62e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1510945337 347 WDRLAQCESGGNWSINTGNGYYGGIQFNQQTWAAYGGTKYASRADLATREQQIDIAKKVQANQGWGAWPSC 417
Cdd:pfam06737   5 WDAIAQCESGGNWAINTGNGYYGGLQFSQSTWDAYGGLGYAPSAAQASREQQIAVAEKLLATQGAGAWPTC 75
YabE COG3583
Uncharacterized conserved protein YabE, contains G5 and tandem DUF348 domains [Function ...
 2-423 9.60e-42

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


:

Pssm-ID: 442802 [Multi-domain]  Cd Length: 335  Bit Score: 150.40  E-value: 9.60e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337   2 KKTPWIVGAATVCVVAVGGGGTAFAMSNEAQISAYGEESAVRVFSQpTVGDLLAAQGIEVKDTDLVTPGLEELVTDGI-- 79
Cdd:COG3583     5 RRKLLLAAVAAVLVTLAGGGGAYAAAKKTVTLDVDGEERTVTTFAG-TVGEVLEEAGITVGEHDVVSPALDTPLTDGDtg 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337  80 --DIQVVQRTPVTITIDGEDQELLTTGDTVADALAEtdyeaegAKISPEPEtalddtdgqvsvvtqktvtfvgqygkdtf 157
Cdd:COG3583    84 elTITVKRAKPVTVVVDGKTRTVTTTATTVGEALAE-------AGITLGED----------------------------- 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337 158 dvtaltvgeamekvlgniedtDKADVPRDELLEDGETYTVQRIREKERTESEEIPFETKTVEDDSLTEGTTNTKTEGKVG 237
Cdd:COG3583   128 ---------------------DRVSPALDAPLTDGMTITVTRVTTKTVTEEEPIPFETVRKEDPSLPKGETKVVQEGVPG 186

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337 238 ETEKVYTDKVVDGEVTDSELVSEEVVAEPVTQVVVKGTKPAPEPEPEVEEAPSaqktekresdtksnrssersstedsds 317
Cdd:COG3583   187 VKEVTYRVTYENGKEVSREVVSEKVTKEPVDEVVAVGTKPRPAPAPVPAGSGS--------------------------- 239

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337 318 ssksesksestsdsgntgasapaaasggvwdrlaqcesgGNWSINTGNGYYGGIQFNQQTWAAYGGTKYASRADLATREQ 397
Cdd:COG3583   240 ---------------------------------------GGGGSSTGSGGYGGLAASSATTAASGGGTGAPGGGGAARPT 280

                         410       420
                  ....*....|....*....|....*.
gi 1510945337 398 QIDIAKKVQANQGWGAWPSCTSQLGI 423
Cdd:COG3583   281 AGAVAGVVVVGGGGGGGPGGGGGGGA 306
 
Name Accession Description Interval E-value
Transglycosylas pfam06737
Transglycosylase-like domain; This family of proteins are very likely to act as ...
 347-417 2.62e-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: 143.32  E-value: 2.62e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1510945337 347 WDRLAQCESGGNWSINTGNGYYGGIQFNQQTWAAYGGTKYASRADLATREQQIDIAKKVQANQGWGAWPSC 417
Cdd:pfam06737   5 WDAIAQCESGGNWAINTGNGYYGGLQFSQSTWDAYGGLGYAPSAAQASREQQIAVAEKLLATQGAGAWPTC 75
YabE COG3583
Uncharacterized conserved protein YabE, contains G5 and tandem DUF348 domains [Function ...
 2-423 9.60e-42

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


Pssm-ID: 442802 [Multi-domain]  Cd Length: 335  Bit Score: 150.40  E-value: 9.60e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337   2 KKTPWIVGAATVCVVAVGGGGTAFAMSNEAQISAYGEESAVRVFSQpTVGDLLAAQGIEVKDTDLVTPGLEELVTDGI-- 79
Cdd:COG3583     5 RRKLLLAAVAAVLVTLAGGGGAYAAAKKTVTLDVDGEERTVTTFAG-TVGEVLEEAGITVGEHDVVSPALDTPLTDGDtg 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337  80 --DIQVVQRTPVTITIDGEDQELLTTGDTVADALAEtdyeaegAKISPEPEtalddtdgqvsvvtqktvtfvgqygkdtf 157
Cdd:COG3583    84 elTITVKRAKPVTVVVDGKTRTVTTTATTVGEALAE-------AGITLGED----------------------------- 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337 158 dvtaltvgeamekvlgniedtDKADVPRDELLEDGETYTVQRIREKERTESEEIPFETKTVEDDSLTEGTTNTKTEGKVG 237
Cdd:COG3583   128 ---------------------DRVSPALDAPLTDGMTITVTRVTTKTVTEEEPIPFETVRKEDPSLPKGETKVVQEGVPG 186

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337 238 ETEKVYTDKVVDGEVTDSELVSEEVVAEPVTQVVVKGTKPAPEPEPEVEEAPSaqktekresdtksnrssersstedsds 317
Cdd:COG3583   187 VKEVTYRVTYENGKEVSREVVSEKVTKEPVDEVVAVGTKPRPAPAPVPAGSGS--------------------------- 239

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337 318 ssksesksestsdsgntgasapaaasggvwdrlaqcesgGNWSINTGNGYYGGIQFNQQTWAAYGGTKYASRADLATREQ 397
Cdd:COG3583   240 ---------------------------------------GGGGSSTGSGGYGGLAASSATTAASGGGTGAPGGGGAARPT 280

                         410       420
                  ....*....|....*....|....*.
gi 1510945337 398 QIDIAKKVQANQGWGAWPSCTSQLGI 423
Cdd:COG3583   281 AGAVAGVVVVGGGGGGGPGGGGGGGA 306
RPF cd13925
core lysozyme-like domain of resuscitation-promoting factor proteins; Resuscitation-promoting ...
 347-417 5.88e-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: 118.64  E-value: 5.88e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1510945337 347 WDRLAQCESGGNWS-INTGNGYYGGIQFNQQTWAAYGGtkyASRADLATREQQIDIAKKVQANQGWGAWPSC 417
Cdd:cd13925     3 WDAIAQCESGGNWNaVNTGNGYYGGLQFLQGTWKSVGG---LGYPDDATRAEQITRAERLYARQGAGAWPCC 71
G5 pfam07501
G5 domain; This domain is found in a wide range of extracellular proteins. It is found ...
 202-276 3.28e-19

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: 81.44  E-value: 3.28e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1510945337 202 EKERTESEEIPFETKTVEDDSLTEGTTNTKTEGKVGETEKVYTDKVVDGEVTDSELVSEEVVAEPVTQVVVKGTK 276
Cdd:pfam07501   1 EKTVTEEEEIPFETVTKEDPSLPKGEEKVVQEGKPGEKEVTYKVTYVNGKEVSREVVSEEVTKEPVDEVVAVGTK 75
PspC_relate_1 NF033840
PspC-related protein choline-binding protein 1; Members of this family share C-terminal ...
 178-276 1.10e-03

PspC-related protein choline-binding protein 1; Members of this family share C-terminal homology to the choline-binding form of the pneumococcal surface antigen PspC, but not to its allelic LPXTG-anchored forms because they lack the choline-binding repeat region. Members of this family should not be confused with PspC itself, whose identity and function reflect regions N-terminal to the choline-binding region. See Iannelli, et al. (PMID: 11891047) for information about the different allelic forms of PspC.


Pssm-ID: 411409 [Multi-domain]  Cd Length: 648  Bit Score: 41.22  E-value: 1.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337 178 TDKADVPRDElledgETYTVQRIREKERTESEEIPFETKTVEDDSLTEGTTNTKTEGKVGETEKVYTDKV--VDGEVTDS 255
Cdd:NF033840  306 TEKVTVDRKE-----PTDTVIKVPAKSKVEEVLVPFATKYEADNDLSAGQEQEITLGKNGKTVTTITYDVdgKSGQVTES 380

                          90       100
                  ....*....|....*....|.
gi 1510945337 256 ELVSEEvvaEPVTQVVVKGTK 276
Cdd:NF033840  381 TLSQKE---DSQTRVVKKGTK 398
 
Name Accession Description Interval E-value
Transglycosylas pfam06737
Transglycosylase-like domain; This family of proteins are very likely to act as ...
 347-417 2.62e-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: 143.32  E-value: 2.62e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1510945337 347 WDRLAQCESGGNWSINTGNGYYGGIQFNQQTWAAYGGTKYASRADLATREQQIDIAKKVQANQGWGAWPSC 417
Cdd:pfam06737   5 WDAIAQCESGGNWAINTGNGYYGGLQFSQSTWDAYGGLGYAPSAAQASREQQIAVAEKLLATQGAGAWPTC 75
YabE COG3583
Uncharacterized conserved protein YabE, contains G5 and tandem DUF348 domains [Function ...
 2-423 9.60e-42

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


Pssm-ID: 442802 [Multi-domain]  Cd Length: 335  Bit Score: 150.40  E-value: 9.60e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337   2 KKTPWIVGAATVCVVAVGGGGTAFAMSNEAQISAYGEESAVRVFSQpTVGDLLAAQGIEVKDTDLVTPGLEELVTDGI-- 79
Cdd:COG3583     5 RRKLLLAAVAAVLVTLAGGGGAYAAAKKTVTLDVDGEERTVTTFAG-TVGEVLEEAGITVGEHDVVSPALDTPLTDGDtg 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337  80 --DIQVVQRTPVTITIDGEDQELLTTGDTVADALAEtdyeaegAKISPEPEtalddtdgqvsvvtqktvtfvgqygkdtf 157
Cdd:COG3583    84 elTITVKRAKPVTVVVDGKTRTVTTTATTVGEALAE-------AGITLGED----------------------------- 127

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337 158 dvtaltvgeamekvlgniedtDKADVPRDELLEDGETYTVQRIREKERTESEEIPFETKTVEDDSLTEGTTNTKTEGKVG 237
Cdd:COG3583   128 ---------------------DRVSPALDAPLTDGMTITVTRVTTKTVTEEEPIPFETVRKEDPSLPKGETKVVQEGVPG 186

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337 238 ETEKVYTDKVVDGEVTDSELVSEEVVAEPVTQVVVKGTKPAPEPEPEVEEAPSaqktekresdtksnrssersstedsds 317
Cdd:COG3583   187 VKEVTYRVTYENGKEVSREVVSEKVTKEPVDEVVAVGTKPRPAPAPVPAGSGS--------------------------- 239

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337 318 ssksesksestsdsgntgasapaaasggvwdrlaqcesgGNWSINTGNGYYGGIQFNQQTWAAYGGTKYASRADLATREQ 397
Cdd:COG3583   240 ---------------------------------------GGGGSSTGSGGYGGLAASSATTAASGGGTGAPGGGGAARPT 280

                         410       420
                  ....*....|....*....|....*.
gi 1510945337 398 QIDIAKKVQANQGWGAWPSCTSQLGI 423
Cdd:COG3583   281 AGAVAGVVVVGGGGGGGPGGGGGGGA 306
RPF cd13925
core lysozyme-like domain of resuscitation-promoting factor proteins; Resuscitation-promoting ...
 347-417 5.88e-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: 118.64  E-value: 5.88e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1510945337 347 WDRLAQCESGGNWS-INTGNGYYGGIQFNQQTWAAYGGtkyASRADLATREQQIDIAKKVQANQGWGAWPSC 417
Cdd:cd13925     3 WDAIAQCESGGNWNaVNTGNGYYGGLQFLQGTWKSVGG---LGYPDDATRAEQITRAERLYARQGAGAWPCC 71
G5 pfam07501
G5 domain; This domain is found in a wide range of extracellular proteins. It is found ...
 202-276 3.28e-19

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: 81.44  E-value: 3.28e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1510945337 202 EKERTESEEIPFETKTVEDDSLTEGTTNTKTEGKVGETEKVYTDKVVDGEVTDSELVSEEVVAEPVTQVVVKGTK 276
Cdd:pfam07501   1 EKTVTEEEEIPFETVTKEDPSLPKGEEKVVQEGKPGEKEVTYKVTYVNGKEVSREVVSEEVTKEPVDEVVAVGTK 75
Lyz-like cd00442
lysozyme-like domains; This family contains several members, including soluble lytic ...
 346-404 1.39e-09

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: 53.57  E-value: 1.39e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1510945337 346 VWDRLAQCESGGNW--SINTGNGYYGGIQFNQQTWAAYGGTkyaSRADLATREQQIDIAKK 404
Cdd:cd00442     1 VLAAIIGQESGGNKpaNAGSGSGAAGLFQFMPGTWKAYGKN---SSSDLNDPEASIEAAAK 58
DUF348 pfam03990
G5-linked-Ubiquitin-like domain; This domain normally occurs as tandem repeats; however it is ...
 89-128 5.33e-05

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: 40.09  E-value: 5.33e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1510945337  89 VTITIDGEDQELLTTGDTVADALAETDYE-AEGAKISPEPE 128
Cdd:pfam03990   1 VTLTVDGKERTVTTTAGTVGDLLEEAGITlGEHDKVSPSLD 41
DUF348 pfam03990
G5-linked-Ubiquitin-like domain; This domain normally occurs as tandem repeats; however it is ...
 32-72 1.03e-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: 39.32  E-value: 1.03e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1510945337  32 QISAYGEESAVRVFSqPTVGDLLAAQGIEVKDTDLVTPGLE 72
Cdd:pfam03990   2 TLTVDGKERTVTTTA-GTVGDLLEEAGITLGEHDKVSPSLD 41
PspC_relate_1 NF033840
PspC-related protein choline-binding protein 1; Members of this family share C-terminal ...
 178-276 1.10e-03

PspC-related protein choline-binding protein 1; Members of this family share C-terminal homology to the choline-binding form of the pneumococcal surface antigen PspC, but not to its allelic LPXTG-anchored forms because they lack the choline-binding repeat region. Members of this family should not be confused with PspC itself, whose identity and function reflect regions N-terminal to the choline-binding region. See Iannelli, et al. (PMID: 11891047) for information about the different allelic forms of PspC.


Pssm-ID: 411409 [Multi-domain]  Cd Length: 648  Bit Score: 41.22  E-value: 1.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1510945337 178 TDKADVPRDElledgETYTVQRIREKERTESEEIPFETKTVEDDSLTEGTTNTKTEGKVGETEKVYTDKV--VDGEVTDS 255
Cdd:NF033840  306 TEKVTVDRKE-----PTDTVIKVPAKSKVEEVLVPFATKYEADNDLSAGQEQEITLGKNGKTVTTITYDVdgKSGQVTES 380

                          90       100
                  ....*....|....*....|.
gi 1510945337 256 ELVSEEvvaEPVTQVVVKGTK 276
Cdd:NF033840  381 TLSQKE---DSQTRVVKKGTK 398
 
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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