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Conserved domains on  [gi|1724156097|ref|WP_146967977|]
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plasmid recombination protein [Leptotrichia hofstadii]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MobM_relaxase super family cl03088
relaxase domain of MobM and similar proteins; With some plasmids, recombination can occur in a ...
 7-48 1.38e-07

relaxase domain of MobM and similar proteins; With some plasmids, recombination can occur in a site-specific manner that is independent of RecA. In such cases, the recombination event requires another protein called Pre (plasmid recombination enzyme), also known as Mob (conjugative mobilization). The best characterized member of this family is encoded by the streptococcal plasmid pMV158 that recognizes the plasmid origin of transfer. MobM converts supercoiled plasmid DNA into relaxed DNA by cleaving a phosphodiester bond of a specific dinucleotide and remains bound to the 5'-end of the nick site.


The actual alignment was detected with superfamily member cd17242:

Pssm-ID: 470731  Cd Length: 196  Bit Score: 52.27  E-value: 1.38e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1724156097   7 LSLEKWEQYYKENLEFLSKKFGKNaRCVYAVIHFDESTPHLQ 48
Cdd:cd17242    88 LDPEEIEEFFKDALEFLKERFGEE-NIVSAVVHLDETTPHLH 128
EnvC super family cl34844
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 311-483 2.17e-06

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


The actual alignment was detected with superfamily member COG4942:

Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 50.15  E-value: 2.17e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 311 EAINKKIEDYSKgeKVEELIKNRDNLYFEIKTLETKASNLKSSINFLEKEQNSKNNEIRNLDEQIweKKMEAEKpyvvse 390
Cdd:COG4942    30 EQLQQEIAELEK--ELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEI--AELRAEL------ 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 391 RRKQELINEALNEARKRGDT------LMRNIKKDVEKEEAKNNAIKQDILDKGLQMERELQEINNKRRRLNDIYVDLEEK 464
Cdd:COG4942   100 EAQKEELAELLRALYRLGRQpplallLSPEDFLDAVRRLQYLKYLAPARREQAEELRADLAELAALRAELEAERAELEAL 179

                         170
                  ....*....|....*....
gi 1724156097 465 KRRRKAELEKLAQPIIQKE 483
Cdd:COG4942   180 LAELEEERAALEALKAERQ 198
 
Name Accession Description Interval E-value
MobM_relaxase cd17242
relaxase domain of MobM and similar proteins; With some plasmids, recombination can occur in a ...
 7-48 1.38e-07

relaxase domain of MobM and similar proteins; With some plasmids, recombination can occur in a site-specific manner that is independent of RecA. In such cases, the recombination event requires another protein called Pre (plasmid recombination enzyme), also known as Mob (conjugative mobilization). The best characterized member of this family is encoded by the streptococcal plasmid pMV158 that recognizes the plasmid origin of transfer. MobM converts supercoiled plasmid DNA into relaxed DNA by cleaving a phosphodiester bond of a specific dinucleotide and remains bound to the 5'-end of the nick site.


Pssm-ID: 410988  Cd Length: 196  Bit Score: 52.27  E-value: 1.38e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1724156097   7 LSLEKWEQYYKENLEFLSKKFGKNaRCVYAVIHFDESTPHLQ 48
Cdd:cd17242    88 LDPEEIEEFFKDALEFLKERFGEE-NIVSAVVHLDETTPHLH 128
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 311-483 2.17e-06

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 50.15  E-value: 2.17e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 311 EAINKKIEDYSKgeKVEELIKNRDNLYFEIKTLETKASNLKSSINFLEKEQNSKNNEIRNLDEQIweKKMEAEKpyvvse 390
Cdd:COG4942    30 EQLQQEIAELEK--ELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEI--AELRAEL------ 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 391 RRKQELINEALNEARKRGDT------LMRNIKKDVEKEEAKNNAIKQDILDKGLQMERELQEINNKRRRLNDIYVDLEEK 464
Cdd:COG4942   100 EAQKEELAELLRALYRLGRQpplallLSPEDFLDAVRRLQYLKYLAPARREQAEELRADLAELAALRAELEAERAELEAL 179

                         170
                  ....*....|....*....
gi 1724156097 465 KRRRKAELEKLAQPIIQKE 483
Cdd:COG4942   180 LAELEEERAALEALKAERQ 198
MobV NF041497
MobV family relaxase;
6-47 3.15e-06

MobV family relaxase;


Pssm-ID: 469385  Cd Length: 187  Bit Score: 47.95  E-value: 3.15e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1724156097   6 MLSLEKWEQYYKENLEFLSKKFGKNaRCVYAVIHFDESTPHL 47
Cdd:NF041497   96 LADPGELKEWFEDNYDFLADRYGEE-NIVSAVVHLDETTPHI 136
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 306-479 2.99e-05

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 47.37  E-value: 2.99e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097  306 KNVDFEAINKKIEDYSKGEKVEeliknrdnLYFEIKTLETKASNLKSSINFLEKEQNSKNNEIRNLDEQIWEKKMEAE-- 383
Cdd:TIGR02169  270 IEQLLEELNKKIKDLGEEEQLR--------VKEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEel 341

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097  384 KPYVVSERRKQELINEALNEARKRGDTLMRnikkDVEKEEAKNNAIKQDILDKGLQME---RELQEINNKRRRLNDIYVD 460
Cdd:TIGR02169  342 EREIEEERKRRDKLTEEYAELKEELEDLRA----ELEEVDKEFAETRDELKDYREKLEklkREINELKRELDRLQEELQR 417

                          170
                   ....*....|....*....
gi 1724156097  461 LEEKKRRRKAELEKLAQPI 479
Cdd:TIGR02169  418 LSEELADLNAAIAGIEAKI 436
PRK00409 PRK00409
recombination and DNA strand exchange inhibitor protein; Reviewed
 324-475 4.83e-05

recombination and DNA strand exchange inhibitor protein; Reviewed


Pssm-ID: 234750 [Multi-domain]  Cd Length: 782  Bit Score: 46.36  E-value: 4.83e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 324 EKVEELIKNRDNLYfeiKTLETKASNLKSSINFLEKEQNSKNNEIRNLDEQIWEKKMEAEKPYvvserrkqeliNEALNE 403
Cdd:PRK00409  516 EKLNELIASLEELE---RELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEA-----------QQAIKE 581

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1724156097 404 ARKRGDtlmRNIKKDVEKEEAKNNAIKqdildkglqmERELQEinnKRRRLNDIYVDLEEKKRRRKAELEKL 475
Cdd:PRK00409  582 AKKEAD---EIIKELRQLQKGGYASVK----------AHELIE---ARKRLNKANEKKEKKKKKQKEKQEEL 637
Mob_Pre pfam01076
Plasmid recombination enzyme; With some plasmids, recombination can occur in a site specific ...
 7-47 5.70e-04

Plasmid recombination enzyme; With some plasmids, recombination can occur in a site specific manner that is independent of RecA. In such cases, the recombination event requires another protein called Pre. Pre is a plasmid recombination enzyme. This protein is also known as Mob (conjugative mobilization). This family is also known as Mob-V. One of the family members, MobM, is encoded by a promiscuous plasmid actively involved in the spread of antibiotic resistance. Homologs of MobM are found in many plasmids and other mobile genetic elements of pathogenic bacteria, including S. aureus. MobM is a metal-dependent nuclease that uses histidine nitrogen for the nucleophilic attack on the scissile phosphate. Furthermore, in contrast to other DNA-processing enzymes, MobM is a histidine relaxase, a DNA-breaking and -joining enzyme, that operates through a phosphorus-nitrogen protein-DNA adduct for cell-to-cell DNA transfer. Mutational analysis indicate that the H(N/D)(Q/E)R N-terminal motif of MobM plays a crucial role in the cleavage and generation of stable DNA-protein adducts.


Pssm-ID: 395854  Cd Length: 195  Bit Score: 41.54  E-value: 5.70e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1724156097   7 LSLEKWEQYYKENLEFLSKKFGKNaRCVYAVIHFDESTPHL 47
Cdd:pfam01076  94 LTYEEAKEFFETAFQFFEERYGKE-NVLYAVVHLDEATPHM 133
ATG14 pfam10186
Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are ...
 310-453 1.98e-03

Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.


Pssm-ID: 462986 [Multi-domain]  Cd Length: 347  Bit Score: 40.90  E-value: 1.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 310 FEAINKKIEDYSKGEKVEELIKNRDN---LYFEIKTLETKASNLKSSInfleKEQNSKNNEIR----NLDEQIWEKKME- 381
Cdd:pfam10186  26 VDLARLLSEKDSLKKKVEEALEGKEEgeqLEDNIGNKKLKLRLLKSEV----AISNERLNEIKdkldQLRREIAEKKKKi 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1724156097 382 AEKPYVVSERR-KQELINEALNEARKRgdtLMRNIKKDVEKEEAKNNAIKQDILDKGLQMERELQEINNKRRR 453
Cdd:pfam10186 102 EKLRSSLKQRRsDLESASYQLEERRAS---QLAKLQNSIKRIKQKWTALHSKTAESRSFLCRELAKLYGLRQV 171
 
Name Accession Description Interval E-value
MobM_relaxase cd17242
relaxase domain of MobM and similar proteins; With some plasmids, recombination can occur in a ...
 7-48 1.38e-07

relaxase domain of MobM and similar proteins; With some plasmids, recombination can occur in a site-specific manner that is independent of RecA. In such cases, the recombination event requires another protein called Pre (plasmid recombination enzyme), also known as Mob (conjugative mobilization). The best characterized member of this family is encoded by the streptococcal plasmid pMV158 that recognizes the plasmid origin of transfer. MobM converts supercoiled plasmid DNA into relaxed DNA by cleaving a phosphodiester bond of a specific dinucleotide and remains bound to the 5'-end of the nick site.


Pssm-ID: 410988  Cd Length: 196  Bit Score: 52.27  E-value: 1.38e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1724156097   7 LSLEKWEQYYKENLEFLSKKFGKNaRCVYAVIHFDESTPHLQ 48
Cdd:cd17242    88 LDPEEIEEFFKDALEFLKERFGEE-NIVSAVVHLDETTPHLH 128
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 311-483 2.17e-06

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 50.15  E-value: 2.17e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 311 EAINKKIEDYSKgeKVEELIKNRDNLYFEIKTLETKASNLKSSINFLEKEQNSKNNEIRNLDEQIweKKMEAEKpyvvse 390
Cdd:COG4942    30 EQLQQEIAELEK--ELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEI--AELRAEL------ 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 391 RRKQELINEALNEARKRGDT------LMRNIKKDVEKEEAKNNAIKQDILDKGLQMERELQEINNKRRRLNDIYVDLEEK 464
Cdd:COG4942   100 EAQKEELAELLRALYRLGRQpplallLSPEDFLDAVRRLQYLKYLAPARREQAEELRADLAELAALRAELEAERAELEAL 179

                         170
                  ....*....|....*....
gi 1724156097 465 KRRRKAELEKLAQPIIQKE 483
Cdd:COG4942   180 LAELEEERAALEALKAERQ 198
MobV NF041497
MobV family relaxase;
6-47 3.15e-06

MobV family relaxase;


Pssm-ID: 469385  Cd Length: 187  Bit Score: 47.95  E-value: 3.15e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1724156097   6 MLSLEKWEQYYKENLEFLSKKFGKNaRCVYAVIHFDESTPHL 47
Cdd:NF041497   96 LADPGELKEWFEDNYDFLADRYGEE-NIVSAVVHLDETTPHI 136
CwlO1 COG3883
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ...
 324-483 5.49e-06

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];


Pssm-ID: 443091 [Multi-domain]  Cd Length: 379  Bit Score: 49.06  E-value: 5.49e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 324 EKVEELIKNRDNLYFEIKTLETKASNLKSSINFLEKEQNSKNNEIRNLDEQIweKKMEAEkpyvVSERRKQ--------- 394
Cdd:COG3883    23 KELSELQAELEAAQAELDALQAELEELNEEYNELQAELEALQAEIDKLQAEI--AEAEAE----IEERREElgeraraly 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 395 -------------------ELIN--EALNEARKRGDTLMRNIKKD---VEKEEAKNNAIKQDILDKGLQMERELQEINNK 450
Cdd:COG3883    97 rsggsvsyldvllgsesfsDFLDrlSALSKIADADADLLEELKADkaeLEAKKAELEAKLAELEALKAELEAAKAELEAQ 176

                         170       180       190
                  ....*....|....*....|....*....|...
gi 1724156097 451 RRRLNDIYVDLEEKKRRRKAELEKLAQPIIQKE 483
Cdd:COG3883   177 QAEQEALLAQLSAEEAAAEAQLAELEAELAAAE 209
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 306-479 2.99e-05

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 47.37  E-value: 2.99e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097  306 KNVDFEAINKKIEDYSKGEKVEeliknrdnLYFEIKTLETKASNLKSSINFLEKEQNSKNNEIRNLDEQIWEKKMEAE-- 383
Cdd:TIGR02169  270 IEQLLEELNKKIKDLGEEEQLR--------VKEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEel 341

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097  384 KPYVVSERRKQELINEALNEARKRGDTLMRnikkDVEKEEAKNNAIKQDILDKGLQME---RELQEINNKRRRLNDIYVD 460
Cdd:TIGR02169  342 EREIEEERKRRDKLTEEYAELKEELEDLRA----ELEEVDKEFAETRDELKDYREKLEklkREINELKRELDRLQEELQR 417

                          170
                   ....*....|....*....
gi 1724156097  461 LEEKKRRRKAELEKLAQPI 479
Cdd:TIGR02169  418 LSEELADLNAAIAGIEAKI 436
PRK00409 PRK00409
recombination and DNA strand exchange inhibitor protein; Reviewed
 324-475 4.83e-05

recombination and DNA strand exchange inhibitor protein; Reviewed


Pssm-ID: 234750 [Multi-domain]  Cd Length: 782  Bit Score: 46.36  E-value: 4.83e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 324 EKVEELIKNRDNLYfeiKTLETKASNLKSSINFLEKEQNSKNNEIRNLDEQIWEKKMEAEKPYvvserrkqeliNEALNE 403
Cdd:PRK00409  516 EKLNELIASLEELE---RELEQKAEEAEALLKEAEKLKEELEEKKEKLQEEEDKLLEEAEKEA-----------QQAIKE 581

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1724156097 404 ARKRGDtlmRNIKKDVEKEEAKNNAIKqdildkglqmERELQEinnKRRRLNDIYVDLEEKKRRRKAELEKL 475
Cdd:PRK00409  582 AKKEAD---EIIKELRQLQKGGYASVK----------AHELIE---ARKRLNKANEKKEKKKKKQKEKQEEL 637
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 259-479 1.08e-04

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 45.40  E-value: 1.08e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 259 KSNKEITDFKRIFNIKKIIKDKLNQRqnnknfKKNLKKEIKLFDEVFKNVDFEAINKKIEDYSKGEKVEELIKNRDNLYF 338
Cdd:TIGR04523 437 KNNSEIKDLTNQDSVKELIIKNLDNT------RESLETQLKVLSRSINKIKQNLEQKQKELKSKEKELKKLNEEKKELEE 510

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 339 EIKTLETKASNLKSSINFLEKEQNSKNNEIRNLDEQIWEKKMEAEKPYVVSERRKQELINEALNEARKRGDTLMRNIKKD 418
Cdd:TIGR04523 511 KVKDLTKKISSLKEKIEKLESEKKEKESKISDLEDELNKDDFELKKENLEKEIDEKNKEIEELKQTQKSLKKKQEEKQEL 590

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1724156097 419 VEKEEAKNNAIKQDILDKG---LQMERELQEINNKRRRLNDIYVDLEEKKRRRKAELEKLAQPI 479
Cdd:TIGR04523 591 IDQKEKEKKDLIKEIEEKEkkiSSLEKELEKAKKENEKLSSIIKNIKSKKNKLKQEVKQIKETI 654
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 311-490 5.41e-04

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 43.12  E-value: 5.41e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097  311 EAINKKIEDYSkgEKVEELIKNRDNLYFEIKTLETKASNLKSSINFLEKEQNSKNNEIRNLDEQI---------WEKKME 381
Cdd:TIGR02168  242 EELQEELKEAE--EELEELTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKqilrerlanLERQLE 319

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097  382 AEKPYVVSERRKQELINEALNEARKRGDTLMRNIKKDVEKEEAKNNAIKqdildkglQMERELQEINNKRRRLNDIYVDL 461
Cdd:TIGR02168  320 ELEAQLEELESKLDELAEELAELEEKLEELKEELESLEAELEELEAELE--------ELESRLEELEEQLETLRSKVAQL 391

                          170       180       190
                   ....*....|....*....|....*....|.
gi 1724156097  462 EEKKRRRKAELEKLAQPI--IQKEVDNLVRE 490
Cdd:TIGR02168  392 ELQIASLNNEIERLEARLerLEDRRERLQQE 422
Mob_Pre pfam01076
Plasmid recombination enzyme; With some plasmids, recombination can occur in a site specific ...
 7-47 5.70e-04

Plasmid recombination enzyme; With some plasmids, recombination can occur in a site specific manner that is independent of RecA. In such cases, the recombination event requires another protein called Pre. Pre is a plasmid recombination enzyme. This protein is also known as Mob (conjugative mobilization). This family is also known as Mob-V. One of the family members, MobM, is encoded by a promiscuous plasmid actively involved in the spread of antibiotic resistance. Homologs of MobM are found in many plasmids and other mobile genetic elements of pathogenic bacteria, including S. aureus. MobM is a metal-dependent nuclease that uses histidine nitrogen for the nucleophilic attack on the scissile phosphate. Furthermore, in contrast to other DNA-processing enzymes, MobM is a histidine relaxase, a DNA-breaking and -joining enzyme, that operates through a phosphorus-nitrogen protein-DNA adduct for cell-to-cell DNA transfer. Mutational analysis indicate that the H(N/D)(Q/E)R N-terminal motif of MobM plays a crucial role in the cleavage and generation of stable DNA-protein adducts.


Pssm-ID: 395854  Cd Length: 195  Bit Score: 41.54  E-value: 5.70e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1724156097   7 LSLEKWEQYYKENLEFLSKKFGKNaRCVYAVIHFDESTPHL 47
Cdd:pfam01076  94 LTYEEAKEFFETAFQFFEERYGKE-NVLYAVVHLDEATPHM 133
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 336-477 8.66e-04

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 42.62  E-value: 8.66e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 336 LYFEIKTLETKASNLKSSINFLEKEQNSKNNEIRNLDEQIwekkmeaekpyvVSERRKQELINEALNEARKRgdtlMRNI 415
Cdd:COG1196   230 LLLKLRELEAELEELEAELEELEAELEELEAELAELEAEL------------EELRLELEELELELEEAQAE----EYEL 293

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1724156097 416 KKDVEKEEAKNNAIKQDILDKGLQMERELQEINNKRRRLNDIYVDLEEKKRRRKAELEKLAQ 477
Cdd:COG1196   294 LAELARLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEE 355
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 315-490 1.28e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 41.97  E-value: 1.28e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097  315 KKIEDYSKGEKVEELIKNRDNLYFEIKTLETKASNLKSSINFLEKEQNSKNNEIRNLDEQIWEKKMEAEKPYVVSERRKQ 394
Cdd:TIGR02168  272 LRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAELEEKLEELKE 351

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097  395 ELinEALNEARKRGDTLMRNIKKDVEKEEAKNNAIKQDILdkglQMERELQEINNKRRRLNDIYVDLEEKKRRRKAELEK 474
Cdd:TIGR02168  352 EL--ESLEAELEELEAELEELESRLEELEEQLETLRSKVA----QLELQIASLNNEIERLEARLERLEDRRERLQQEIEE 425

                          170
                   ....*....|....*.
gi 1724156097  475 LAQPIIQKEVDNLVRE 490
Cdd:TIGR02168  426 LLKKLEEAELKELQAE 441
ATG14 pfam10186
Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are ...
 310-453 1.98e-03

Vacuolar sorting 38 and autophagy-related subunit 14; The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex.


Pssm-ID: 462986 [Multi-domain]  Cd Length: 347  Bit Score: 40.90  E-value: 1.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 310 FEAINKKIEDYSKGEKVEELIKNRDN---LYFEIKTLETKASNLKSSInfleKEQNSKNNEIR----NLDEQIWEKKME- 381
Cdd:pfam10186  26 VDLARLLSEKDSLKKKVEEALEGKEEgeqLEDNIGNKKLKLRLLKSEV----AISNERLNEIKdkldQLRREIAEKKKKi 101

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1724156097 382 AEKPYVVSERR-KQELINEALNEARKRgdtLMRNIKKDVEKEEAKNNAIKQDILDKGLQMERELQEINNKRRR 453
Cdd:pfam10186 102 EKLRSSLKQRRsDLESASYQLEERRAS---QLAKLQNSIKRIKQKWTALHSKTAESRSFLCRELAKLYGLRQV 171
DR0291 COG1579
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ...
 339-503 4.34e-03

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];


Pssm-ID: 441187 [Multi-domain]  Cd Length: 236  Bit Score: 39.14  E-value: 4.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 339 EIKTLETKASNLKSSINFLEKEQNSKNNEIRNLDEQIWEKKMEAEkpyvvSERRKQELINEALNEARKRGDtlMRNIKKD 418
Cdd:COG1579    25 RLKELPAELAELEDELAALEARLEAAKTELEDLEKEIKRLELEIE-----EVEARIKKYEEQLGNVRNNKE--YEALQKE 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 419 VEKEEAKNNAIKQDILDKGLQMERELQEINNKRRRLNDIYVDLEEKKRRRKAELEKlaqpiIQKEVDNLVREHLRYYEVT 498
Cdd:COG1579    98 IESLKRRISDLEDEILELMERIEELEEELAELEAELAELEAELEEKKAELDEELAE-----LEAELEELEAEREELAAKI 172


                  ....*
gi 1724156097 499 DKDIL 503
Cdd:COG1579   173 PPELL 177
PRK12704 PRK12704
phosphodiesterase; Provisional
 374-492 4.74e-03

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 39.76  E-value: 4.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 374 QIWEKKMEAEKPYVVSERRKQELINEALNEARKRGDTLMRNIKKDVEKEEAKNNAIKQDILDKGLQMERELQEINNKRRR 453
Cdd:PRK12704   32 KIKEAEEEAKRILEEAKKEAEAIKKEALLEAKEEIHKLRNEFEKELRERRNELQKLEKRLLQKEENLDRKLELLEKREEE 111

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1724156097 454 LNDIYVDLEEKKRrrkaELEKLaqpiiQKEVDNLVREHL 492
Cdd:PRK12704  112 LEKKEKELEQKQQ----ELEKK-----EEELEELIEEQL 141
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
324-493 5.26e-03

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 39.75  E-value: 5.26e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 324 EKVEELIKNRDNLYFEIKTLETKASNLKSSINFLEKEQNSKNNEIRNLDEQIwekkmEAEKPYVVSERRKQELIN----- 398
Cdd:COG4717    74 KELEEELKEAEEKEEEYAELQEELEELEEELEELEAELEELREELEKLEKLL-----QLLPLYQELEALEAELAElperl 148

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 399 EALNEARKRGDTLMRNIKKDVEKEEAKNNAIKQDILDKGLQMERELQEINNKRRRLNDIYVDLEEKKRRRKAELEKLAQP 478
Cdd:COG4717   149 EELEERLEELRELEEELEELEAELAELQEELEELLEQLSLATEEELQDLAEELEELQQRLAELEEELEEAQEELEELEEE 228

                         170
                  ....*....|....*
gi 1724156097 479 IIQKEVDNLVREHLR 493
Cdd:COG4717   229 LEQLENELEAAALEE 243
PRK05771 PRK05771
V-type ATP synthase subunit I; Validated
 245-481 5.42e-03

V-type ATP synthase subunit I; Validated


Pssm-ID: 235600 [Multi-domain]  Cd Length: 646  Bit Score: 39.91  E-value: 5.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 245 LNEFKNYETDFKVRKSNKEITDFKRIFNIKKIIKDKLNqrqnnKNFKKNLKKEIKLFDEVFKNVDFEAInkKIEdyskgE 324
Cdd:PRK05771   33 IEDLKEELSNERLRKLRSLLTKLSEALDKLRSYLPKLN-----PLREEKKKVSVKSLEELIKDVEEELE--KIE-----K 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 325 KVEELIKNRDNLYFEIKTLETKASNLKSSINF---LEKEQNSKNNEIR--NLDEQIWEK-KMEAEKPYVVSERRKQELIN 398
Cdd:PRK05771  101 EIKELEEEISELENEIKELEQEIERLEPWGNFdldLSLLLGFKYVSVFvgTVPEDKLEElKLESDVENVEYISTDKGYVY 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 399 EALnearkrgdTLMRNIKKDVEKEEAKNNAIKQDILDKGLQMERelqeINNKRRRLNDIYVDLEEKKRRRKAELEKLAQP 478
Cdd:PRK05771  181 VVV--------VVLKELSDEVEEELKKLGFERLELEEEGTPSEL----IREIKEELEEIEKERESLLEELKELAKKYLEE 248


                  ...
gi 1724156097 479 IIQ 481
Cdd:PRK05771  249 LLA 251
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 339-483 6.74e-03

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 39.72  E-value: 6.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1724156097 339 EIKTLETKASNLKSSINFLEKEQNSKNNEIRNLDEQIWEKKMEAEKpyvvsERRKQELINEALN-------EARKRGDTL 411
Cdd:pfam17380 436 EVRRLEEERAREMERVRLEEQERQQQVERLRQQEEERKRKKLELEK-----EKRDRKRAEEQRRkilekelEERKQAMIE 510

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1724156097 412 MRNIKKDVEKE-EAKNNAIKQDILDKGLQMERELQ-EINNKRRRLNDIYVDLEEKKRRRKAELEK-LAQPIIQKE 483
Cdd:pfam17380 511 EERKRKLLEKEmEERQKAIYEEERRREAEEERRKQqEMEERRRIQEQMRKATEERSRLEAMEREReMMRQIVESE 585
 
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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