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Conserved domains on  [gi|699613445|ref|XP_009874501|]
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PREDICTED: ATPase family AAA domain-containing protein 5, partial [Apaloderma vittatum]

Protein Classification

DNA topoisomerase 2-like domain-containing protein( domain architecture ID 1000163)

DNA topoisomerase 2-like domain-containing protein; DNA topoisomerase 2 alters DNA topology by binding to two double-stranded DNA molecules, generating a double-stranded break in one of the strands, passing the intact strand through the broken strand, and religating the broken strand

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK04195 super family cl35251
replication factor C large subunit; Provisional
 1031-1146 1.30e-14

replication factor C large subunit; Provisional


The actual alignment was detected with superfamily member PRK04195:

Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 78.81  E-value: 1.30e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699613445 1031 WTEKYQPQDSSELVGNKKEIERLHSWLKEWKKradweeKRNQKgekedkehqdsldsldfkdnksdveeetslcnTVLIT 1110
Cdd:PRK04195    4 WVEKYRPKTLSDVVGNEKAKEQLREWIESWLK------GKPKK--------------------------------ALLLY 45

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 699613445 1111 GPPGVGKTAAVYACAQELGFKIFEVNASCQRSGRQI 1146
Cdd:PRK04195   46 GPPGVGKTSLAHALANDYGWEVIELNASDQRTADVI 81
PTZ00108 super family cl36510
DNA topoisomerase 2-like protein; Provisional
 405-773 1.37e-03

DNA topoisomerase 2-like protein; Provisional


The actual alignment was detected with superfamily member PTZ00108:

Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 43.88  E-value: 1.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699613445  405 TSEVVKCGVKRAP--GKQKQTVGKSLKEKEGLEDDIASNKGLESGVPEDRVDKYTHSSPENNRTKPKRPKKFQKKENRRK 482
Cdd:PTZ00108 1037 VKELKKLGYVRFKdiIKKKSEKITAEEEEGAEEDDEADDEDDEEELGAAVSYDYLLSMPIWSLTKEKVEKLNAELEKKEK 1116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699613445  483 KTSETKEMNVSDITNEDEDSGANVLTKENTLEVRlsspkvhELRRSSRQKKIKTSKNGTPKKSRIRNTFSEDElsgcalQ 562
Cdd:PTZ00108 1117 ELEKLKNTTPKDMWLEDLDKFEEALEEQEEVEEK-------EIAKEQRLKSKTKGKASKLRKPKLKKKEKKKK------K 1183

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699613445  563 TSTPKGSKRSLKKSNMYKAEVITVPFDGSspiRMRFTRIGATAKSNKAEAMKNEEFNPKNMKMSSTSKNISKAKQLIEKA 642
Cdd:PTZ00108 1184 SSADKSKKASVVGNSKRVDSDEKRKLDDK---PDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEF 1260

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699613445  643 KALQQNRSKVGEDLPAPVRRSSRQRALAEKKKLEESDESIIILDSSLSNATTTVQTTDRVPNVKQKNLRSLNDVLGKKPR 722
Cdd:PTZ00108 1261 SSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKKKSKTR 1340

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|.
gi 699613445  723 NLMVAKNSRGKLGHPPSFLGRNaqntagEPIVIFDESSQDASENSQDDDQF 773
Cdd:PTZ00108 1341 VKQASASQSSRLLRRPRKKKSD------SSSEDDDDSEVDDSEDEDDEDDE 1385
 
Name Accession Description Interval E-value
PRK04195 PRK04195
replication factor C large subunit; Provisional
 1031-1146 1.30e-14

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 78.81  E-value: 1.30e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699613445 1031 WTEKYQPQDSSELVGNKKEIERLHSWLKEWKKradweeKRNQKgekedkehqdsldsldfkdnksdveeetslcnTVLIT 1110
Cdd:PRK04195    4 WVEKYRPKTLSDVVGNEKAKEQLREWIESWLK------GKPKK--------------------------------ALLLY 45

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 699613445 1111 GPPGVGKTAAVYACAQELGFKIFEVNASCQRSGRQI 1146
Cdd:PRK04195   46 GPPGVGKTSLAHALANDYGWEVIELNASDQRTADVI 81
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 1107-1138 1.82e-07

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 51.83  E-value: 1.82e-07
                           10        20        30
                   ....*....|....*....|....*....|..
gi 699613445  1107 VLITGPPGVGKTAAVYACAQELGFKIFEVNAS 1138
Cdd:pfam00004    1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGS 32
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 1105-1138 3.41e-05

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 45.60  E-value: 3.41e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 699613445 1105 NTVLITGPPGVGKTAAVYACAQEL---GFKIFEVNAS 1138
Cdd:cd00009    20 KNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNAS 56
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 1107-1138 3.66e-04

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 44.90  E-value: 3.66e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 699613445 1107 VLITGPPGVGKTAAVYACAQELGFKIFEVNAS 1138
Cdd:COG0464   194 LLLYGPPGTGKTLLARALAGELGLPLIEVDLS 225
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 405-773 1.37e-03

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 43.88  E-value: 1.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699613445  405 TSEVVKCGVKRAP--GKQKQTVGKSLKEKEGLEDDIASNKGLESGVPEDRVDKYTHSSPENNRTKPKRPKKFQKKENRRK 482
Cdd:PTZ00108 1037 VKELKKLGYVRFKdiIKKKSEKITAEEEEGAEEDDEADDEDDEEELGAAVSYDYLLSMPIWSLTKEKVEKLNAELEKKEK 1116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699613445  483 KTSETKEMNVSDITNEDEDSGANVLTKENTLEVRlsspkvhELRRSSRQKKIKTSKNGTPKKSRIRNTFSEDElsgcalQ 562
Cdd:PTZ00108 1117 ELEKLKNTTPKDMWLEDLDKFEEALEEQEEVEEK-------EIAKEQRLKSKTKGKASKLRKPKLKKKEKKKK------K 1183

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699613445  563 TSTPKGSKRSLKKSNMYKAEVITVPFDGSspiRMRFTRIGATAKSNKAEAMKNEEFNPKNMKMSSTSKNISKAKQLIEKA 642
Cdd:PTZ00108 1184 SSADKSKKASVVGNSKRVDSDEKRKLDDK---PDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEF 1260

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699613445  643 KALQQNRSKVGEDLPAPVRRSSRQRALAEKKKLEESDESIIILDSSLSNATTTVQTTDRVPNVKQKNLRSLNDVLGKKPR 722
Cdd:PTZ00108 1261 SSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKKKSKTR 1340

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|.
gi 699613445  723 NLMVAKNSRGKLGHPPSFLGRNaqntagEPIVIFDESSQDASENSQDDDQF 773
Cdd:PTZ00108 1341 VKQASASQSSRLLRRPRKKKSD------SSSEDDDDSEVDDSEDEDDEDDE 1385
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 1105-1143 2.99e-03

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 40.05  E-value: 2.99e-03
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|..
gi 699613445   1105 NTVLITGPPGVGKTAAVYACAQEL---GFKIFEVNASCQRSG 1143
Cdd:smart00382    3 EVILIVGPPGSGKTTLARALARELgppGGGVIYIDGEDILEE 44
 
Name Accession Description Interval E-value
PRK04195 PRK04195
replication factor C large subunit; Provisional
 1031-1146 1.30e-14

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 78.81  E-value: 1.30e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699613445 1031 WTEKYQPQDSSELVGNKKEIERLHSWLKEWKKradweeKRNQKgekedkehqdsldsldfkdnksdveeetslcnTVLIT 1110
Cdd:PRK04195    4 WVEKYRPKTLSDVVGNEKAKEQLREWIESWLK------GKPKK--------------------------------ALLLY 45

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 699613445 1111 GPPGVGKTAAVYACAQELGFKIFEVNASCQRSGRQI 1146
Cdd:PRK04195   46 GPPGVGKTSLAHALANDYGWEVIELNASDQRTADVI 81
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 1107-1138 1.82e-07

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 51.83  E-value: 1.82e-07
                           10        20        30
                   ....*....|....*....|....*....|..
gi 699613445  1107 VLITGPPGVGKTAAVYACAQELGFKIFEVNAS 1138
Cdd:pfam00004    1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGS 32
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 1105-1138 3.41e-05

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 45.60  E-value: 3.41e-05
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 699613445 1105 NTVLITGPPGVGKTAAVYACAQEL---GFKIFEVNAS 1138
Cdd:cd00009    20 KNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNAS 56
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 1107-1138 3.66e-04

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 44.90  E-value: 3.66e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 699613445 1107 VLITGPPGVGKTAAVYACAQELGFKIFEVNAS 1138
Cdd:COG0464   194 LLLYGPPGTGKTLLARALAGELGLPLIEVDLS 225
PTZ00108 PTZ00108
DNA topoisomerase 2-like protein; Provisional
 405-773 1.37e-03

DNA topoisomerase 2-like protein; Provisional


Pssm-ID: 240271 [Multi-domain]  Cd Length: 1388  Bit Score: 43.88  E-value: 1.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699613445  405 TSEVVKCGVKRAP--GKQKQTVGKSLKEKEGLEDDIASNKGLESGVPEDRVDKYTHSSPENNRTKPKRPKKFQKKENRRK 482
Cdd:PTZ00108 1037 VKELKKLGYVRFKdiIKKKSEKITAEEEEGAEEDDEADDEDDEEELGAAVSYDYLLSMPIWSLTKEKVEKLNAELEKKEK 1116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699613445  483 KTSETKEMNVSDITNEDEDSGANVLTKENTLEVRlsspkvhELRRSSRQKKIKTSKNGTPKKSRIRNTFSEDElsgcalQ 562
Cdd:PTZ00108 1117 ELEKLKNTTPKDMWLEDLDKFEEALEEQEEVEEK-------EIAKEQRLKSKTKGKASKLRKPKLKKKEKKKK------K 1183

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699613445  563 TSTPKGSKRSLKKSNMYKAEVITVPFDGSspiRMRFTRIGATAKSNKAEAMKNEEFNPKNMKMSSTSKNISKAKQLIEKA 642
Cdd:PTZ00108 1184 SSADKSKKASVVGNSKRVDSDEKRKLDDK---PDNKKSNSSGSDQEDDEEQKTKPKKSSVKRLKSKKNNSSKSSEDNDEF 1260

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 699613445  643 KALQQNRSKVGEDLPAPVRRSSRQRALAEKKKLEESDESIIILDSSLSNATTTVQTTDRVPNVKQKNLRSLNDVLGKKPR 722
Cdd:PTZ00108 1261 SSDDLSKEGKPKNAPKRVSAVQYSPPPPSKRPDGESNGGSKPSSPTKKKVKKRLEGSLAALKKKKKSEKKTARKKKSKTR 1340

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|.
gi 699613445  723 NLMVAKNSRGKLGHPPSFLGRNaqntagEPIVIFDESSQDASENSQDDDQF 773
Cdd:PTZ00108 1341 VKQASASQSSRLLRRPRKKKSD------SSSEDDDDSEVDDSEDEDDEDDE 1385
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 1105-1143 2.99e-03

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 40.05  E-value: 2.99e-03
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|..
gi 699613445   1105 NTVLITGPPGVGKTAAVYACAQEL---GFKIFEVNASCQRSG 1143
Cdd:smart00382    3 EVILIVGPPGSGKTTLARALARELgppGGGVIYIDGEDILEE 44
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
1105-1138 3.10e-03

Predicted ATPase, AAA+ superfamily [General function prediction only];


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 41.41  E-value: 3.10e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 699613445 1105 NTVLITGPPGVGKTAAVYACAQELGFKIFEVNAS 1138
Cdd:COG1223    36 RKILFYGPPGTGKTMLAEALAGELKLPLLTVRLD 69
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 1107-1137 3.26e-03

first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. This subfamily also includes the first of the two ATPase domains of NVL (nuclear VCP-like protein) 2, an isoform of NVL mainly present in the nucleolus, which is involved in ribosome biogenesis, in telomerase assembly and the regulation of telomerase activity, and in pre-rRNA processing. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410911 [Multi-domain]  Cd Length: 165  Bit Score: 40.35  E-value: 3.26e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 699613445 1107 VLITGPPGVGKTAAVYACAQELGFKIFEVNA 1137
Cdd:cd19503    37 VLLHGPPGTGKTLLARAVANEAGANFLSISG 67
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 1107-1138 8.52e-03

proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410889 [Multi-domain]  Cd Length: 158  Bit Score: 38.80  E-value: 8.52e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 699613445 1107 VLITGPPGVGKTAAVYACAQELGFKIFEVNAS 1138
Cdd:cd19481    29 ILLYGPPGTGKTLLAKALAGELGLPLIVVKLS 60
 
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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