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Conserved domains on  [gi|998177578|gb|KXH76976|]
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hypothetical protein AM326_12640 [Candidatus Thorarchaeota archaeon SMTZ-45]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SMC_N super family cl47134
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 4-236 4.65e-04

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.


The actual alignment was detected with superfamily member TIGR02169:

Pssm-ID: 481474 [Multi-domain]  Cd Length: 1164  Bit Score: 41.59  E-value: 4.65e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578     4 EKIDAVIEEIQEKVDKLSDELAT------LHAELKEFnSLPDMDKKIDDLTKSLKGIDsKKLDDIAKSVTDIDSAVKEVV 77
Cdd:TIGR02169  187 ERLDLIIDEKRQQLERLRREREKaeryqaLLKEKREY-EGYELLKEKEALERQKEAIE-RQLASLEEELEKLTEEISELE 264

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578    78 dsKESTVIIKKLDDILVSLAD-----SDAIPKKLEDLQNYIAGL----STMEDKVQDLAGQFEETKEIVGIIVRQLDDIE 148
Cdd:TIGR02169  265 --KRLEEIEQLLEELNKKIKDlgeeeQLRVKEKIGELEAEIASLersiAEKERELEDAEERLAKLEAEIDKLLAEIEELE 342

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578   149 RK---YNLAIDKVTEAV-------DLLSDFIQAQDAKSAEPSkpDKKPSREEEIEEKPKvkppDKTSLPSTIDALMDNLM 218
Cdd:TIGR02169  343 REieeERKRRDKLTEEYaelkeelEDLRAELEEVDKEFAETR--DELKDYREKLEKLKR----EINELKRELDRLQEELQ 416

                          250
                   ....*....|....*...
gi 998177578   219 SLVVPQTEATEMAEALEE 236
Cdd:TIGR02169  417 RLSEELADLNAAIAGIEA 434
 
Name Accession Description Interval E-value
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 4-236 4.65e-04

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: 41.59  E-value: 4.65e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578     4 EKIDAVIEEIQEKVDKLSDELAT------LHAELKEFnSLPDMDKKIDDLTKSLKGIDsKKLDDIAKSVTDIDSAVKEVV 77
Cdd:TIGR02169  187 ERLDLIIDEKRQQLERLRREREKaeryqaLLKEKREY-EGYELLKEKEALERQKEAIE-RQLASLEEELEKLTEEISELE 264

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578    78 dsKESTVIIKKLDDILVSLAD-----SDAIPKKLEDLQNYIAGL----STMEDKVQDLAGQFEETKEIVGIIVRQLDDIE 148
Cdd:TIGR02169  265 --KRLEEIEQLLEELNKKIKDlgeeeQLRVKEKIGELEAEIASLersiAEKERELEDAEERLAKLEAEIDKLLAEIEELE 342

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578   149 RK---YNLAIDKVTEAV-------DLLSDFIQAQDAKSAEPSkpDKKPSREEEIEEKPKvkppDKTSLPSTIDALMDNLM 218
Cdd:TIGR02169  343 REieeERKRRDKLTEEYaelkeelEDLRAELEEVDKEFAETR--DELKDYREKLEKLKR----EINELKRELDRLQEELQ 416

                          250
                   ....*....|....*...
gi 998177578   219 SLVVPQTEATEMAEALEE 236
Cdd:TIGR02169  417 RLSEELADLNAAIAGIEA 434
ATG17_like pfam04108
Autophagy protein ATG17-like domain; This domain is found in the autophagy-related proteins ...
 4-151 9.68e-04

Autophagy protein ATG17-like domain; This domain is found in the autophagy-related proteins ATG17 and ATG11, conserved across eukaryotes. ATG17 forms a complex with ATG29 and ATG31, critical for both PAS (preautophagosomal structure) formation and autophagy. Together with ATG13, it is required for ATG1 kinase activation. ATG11 is a scaffold protein required for the cytoplasm-to-vacuole targeting (Cvt) pathway during starvation and to recruit ATG proteins to the pre-autophagosome. It is also required for ATG1 kinase activation. In many eukaryotes, ATG11 (the orthologue in mammals is RB1-inducible coiled-coil protein 1 (RB1CC1) and in S. pombe is Taz1-interacting factor 1 (taf1)) is essential for bulk autophagy, except in S.cerevisiae. ATG17 and ATG11 are large similar proteins, both predicted to be almost entirely helical, containing conserved coiled-coil regions and lack obvious functional motifs.


Pssm-ID: 427715 [Multi-domain]  Cd Length: 360  Bit Score: 40.45  E-value: 9.68e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578    4 EKIDAVIEEIQEKVDKLSDELATLHAEL----KEFNSLPDMDKKIDDLTKSLKGIDS--KKLDDIAKSVT-DIDSAVKEV 76
Cdd:pfam04108 119 DALKELIDELQAAQESLDSDLKRFDDDLrdlqKELESLSSPSESISLIPTLLKELESleEEMASLLESLTnHYDQCVTAV 198

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 998177578   77 VDSKEStviikKLDDILVSLADSDAIPKKLEDLQNYIAGLSTMEDKVQDLAGQFEETKEIVGIIVRQLDDIERKY 151
Cdd:pfam04108 199 KLTEGG-----RAEMLEVLENDARELDDVVPELQDRLDEMENNYERLQKLLEQKNSLIDELLSALQLIAEIQSRL 268
46 PHA02562
endonuclease subunit; Provisional
 4-162 2.43e-03

endonuclease subunit; Provisional


Pssm-ID: 222878 [Multi-domain]  Cd Length: 562  Bit Score: 39.23  E-value: 2.43e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578   4 EKIDAVIEEIQEKVDKLSDELATLHAELKEFNS-LPDMDKKIDDLTKSLKGIDSKKlddiAKSVTDIDSAVKEVVDSKES 82
Cdd:PHA02562 209 KKNGENIARKQNKYDELVEEAKTIKAEIEELTDeLLNLVMDIEDPSAALNKLNTAA----AKIKSKIEQFQKVIKMYEKG 284

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578  83 TVI------IKKLDDILVSLADS-DAIPKKLEDLQNYIAGLSTMED-------KVQDLAGQFEETKEIVGIIVRQLDDIE 148
Cdd:PHA02562 285 GVCptctqqISEGPDRITKIKDKlKELQHSLEKLDTAIDELEEIMDefneqskKLLELKNKISTNKQSLITLVDKAKKVK 364

                        170
                 ....*....|....
gi 998177578 149 RkynlAIDKVTEAV 162
Cdd:PHA02562 365 A----AIEELQAEF 374
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 69-125 7.43e-03

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 36.88  E-value: 7.43e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 998177578  69 IDSAVKEVVDSKESTVIIKKLDDILVSLADSDAIPKKLEDLQNYIA--GLSTMEDKVQD 125
Cdd:cd01645  144 VAQALEPFRKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLrwGLTIPPEKVQK 202
 
Name Accession Description Interval E-value
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 4-236 4.65e-04

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: 41.59  E-value: 4.65e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578     4 EKIDAVIEEIQEKVDKLSDELAT------LHAELKEFnSLPDMDKKIDDLTKSLKGIDsKKLDDIAKSVTDIDSAVKEVV 77
Cdd:TIGR02169  187 ERLDLIIDEKRQQLERLRREREKaeryqaLLKEKREY-EGYELLKEKEALERQKEAIE-RQLASLEEELEKLTEEISELE 264

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578    78 dsKESTVIIKKLDDILVSLAD-----SDAIPKKLEDLQNYIAGL----STMEDKVQDLAGQFEETKEIVGIIVRQLDDIE 148
Cdd:TIGR02169  265 --KRLEEIEQLLEELNKKIKDlgeeeQLRVKEKIGELEAEIASLersiAEKERELEDAEERLAKLEAEIDKLLAEIEELE 342

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578   149 RK---YNLAIDKVTEAV-------DLLSDFIQAQDAKSAEPSkpDKKPSREEEIEEKPKvkppDKTSLPSTIDALMDNLM 218
Cdd:TIGR02169  343 REieeERKRRDKLTEEYaelkeelEDLRAELEEVDKEFAETR--DELKDYREKLEKLKR----EINELKRELDRLQEELQ 416

                          250
                   ....*....|....*...
gi 998177578   219 SLVVPQTEATEMAEALEE 236
Cdd:TIGR02169  417 RLSEELADLNAAIAGIEA 434
ATG17_like pfam04108
Autophagy protein ATG17-like domain; This domain is found in the autophagy-related proteins ...
 4-151 9.68e-04

Autophagy protein ATG17-like domain; This domain is found in the autophagy-related proteins ATG17 and ATG11, conserved across eukaryotes. ATG17 forms a complex with ATG29 and ATG31, critical for both PAS (preautophagosomal structure) formation and autophagy. Together with ATG13, it is required for ATG1 kinase activation. ATG11 is a scaffold protein required for the cytoplasm-to-vacuole targeting (Cvt) pathway during starvation and to recruit ATG proteins to the pre-autophagosome. It is also required for ATG1 kinase activation. In many eukaryotes, ATG11 (the orthologue in mammals is RB1-inducible coiled-coil protein 1 (RB1CC1) and in S. pombe is Taz1-interacting factor 1 (taf1)) is essential for bulk autophagy, except in S.cerevisiae. ATG17 and ATG11 are large similar proteins, both predicted to be almost entirely helical, containing conserved coiled-coil regions and lack obvious functional motifs.


Pssm-ID: 427715 [Multi-domain]  Cd Length: 360  Bit Score: 40.45  E-value: 9.68e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578    4 EKIDAVIEEIQEKVDKLSDELATLHAEL----KEFNSLPDMDKKIDDLTKSLKGIDS--KKLDDIAKSVT-DIDSAVKEV 76
Cdd:pfam04108 119 DALKELIDELQAAQESLDSDLKRFDDDLrdlqKELESLSSPSESISLIPTLLKELESleEEMASLLESLTnHYDQCVTAV 198

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 998177578   77 VDSKEStviikKLDDILVSLADSDAIPKKLEDLQNYIAGLSTMEDKVQDLAGQFEETKEIVGIIVRQLDDIERKY 151
Cdd:pfam04108 199 KLTEGG-----RAEMLEVLENDARELDDVVPELQDRLDEMENNYERLQKLLEQKNSLIDELLSALQLIAEIQSRL 268
46 PHA02562
endonuclease subunit; Provisional
 4-162 2.43e-03

endonuclease subunit; Provisional


Pssm-ID: 222878 [Multi-domain]  Cd Length: 562  Bit Score: 39.23  E-value: 2.43e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578   4 EKIDAVIEEIQEKVDKLSDELATLHAELKEFNS-LPDMDKKIDDLTKSLKGIDSKKlddiAKSVTDIDSAVKEVVDSKES 82
Cdd:PHA02562 209 KKNGENIARKQNKYDELVEEAKTIKAEIEELTDeLLNLVMDIEDPSAALNKLNTAA----AKIKSKIEQFQKVIKMYEKG 284

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578  83 TVI------IKKLDDILVSLADS-DAIPKKLEDLQNYIAGLSTMED-------KVQDLAGQFEETKEIVGIIVRQLDDIE 148
Cdd:PHA02562 285 GVCptctqqISEGPDRITKIKDKlKELQHSLEKLDTAIDELEEIMDefneqskKLLELKNKISTNKQSLITLVDKAKKVK 364

                        170
                 ....*....|....
gi 998177578 149 RkynlAIDKVTEAV 162
Cdd:PHA02562 365 A----AIEELQAEF 374
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 4-195 4.01e-03

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: 38.90  E-value: 4.01e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578     4 EKIDAVIEEIQEKVDKLSDELATLHAELKEFNS-LPDMDKKIDDLTKSLKGIDSKKLDDIAKSVTDIDSAVKEVVDSKES 82
Cdd:TIGR02169  733 EKLKERLEELEEDLSSLEQEIENVKSELKELEArIEELEEDLHKLEEALNDLEARLSHSRIPEIQAELSKLEEEVSRIEA 812

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 998177578    83 tvIIKKLDDILVSLADSDAI-PKKLEDLQNYIAGL----STMEDKVQDLAGQFEETKEIVGIIVRQLDDIERKYnlaIDK 157
Cdd:TIGR02169  813 --RLREIEQKLNRLTLEKEYlEKEIQELQEQRIDLkeqiKSIEKEIENLNGKKEELEEELEELEAALRDLESRL---GDL 887

                          170       180       190
                   ....*....|....*....|....*....|....*...
gi 998177578   158 VTEAVDLLSDFIQAQDAKSAEPSKPDKKPSREEEIEEK 195
Cdd:TIGR02169  888 KKERDELEAQLRELERKIEELEAQIEKKRKRLSELKAK 925
RT_Rtv cd01645
RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of ...
 69-125 7.43e-03

RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.


Pssm-ID: 238823 [Multi-domain]  Cd Length: 213  Bit Score: 36.88  E-value: 7.43e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 998177578  69 IDSAVKEVVDSKESTVIIKKLDDILVSLADSDAIPKKLEDLQNYIA--GLSTMEDKVQD 125
Cdd:cd01645  144 VAQALEPFRKQYPDIVIYHYMDDILIASDLEGQLREIYEELRQTLLrwGLTIPPEKVQK 202
 
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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