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Conserved domains on  [gi|1084452927|gb|OGN19387|]
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MAG: hypothetical protein A3F50_00565 [Candidatus Yanofskybacteria bacterium RIFCSPHIGHO2_12_FULL_44_29b]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Hop super family cl34242
Intein/homing endonuclease [Replication, recombination and repair, Mobilome: prophages, ...
 6-165 9.19e-15

Intein/homing endonuclease [Replication, recombination and repair, Mobilome: prophages, transposons];


The actual alignment was detected with superfamily member COG1372:

Pssm-ID: 440983 [Multi-domain]  Cd Length: 866  Bit Score: 77.24  E-value: 9.19e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084452927   6 KQLNNASWKKISELSAGMKIAVpdiEGGFSWDEVASIKPIGREEVWDIEVEDVHNFIGNDIFAHNTYANGGPAVqADVVA 85
Cdd:COG1372   422 RRLSRERLRRLALEDEALEALA---DSDVYWDEVVSIEPVGEEDVYDLTVPGTHNFVANGIVVHNSGGALDDVG-AAVLD 497

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084452927  86 YDPSGNIVKAGPADQPAGVMIGFGENGSVSYEFNGRASVKVSAENGPVKVGDRLTVSATMPGFAMKMTEAGQSIGLALAE 165
Cdd:COG1372   498 EDLLGGEPEEGEAGGAAEDKDRAKTGATTLAAGDLLVERDVEAEPEEIEDVISGEGRILERAALLAVALDELEDELEEAR 577
 
Name Accession Description Interval E-value
Hop COG1372
Intein/homing endonuclease [Replication, recombination and repair, Mobilome: prophages, ...
 6-165 9.19e-15

Intein/homing endonuclease [Replication, recombination and repair, Mobilome: prophages, transposons];


Pssm-ID: 440983 [Multi-domain]  Cd Length: 866  Bit Score: 77.24  E-value: 9.19e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084452927   6 KQLNNASWKKISELSAGMKIAVpdiEGGFSWDEVASIKPIGREEVWDIEVEDVHNFIGNDIFAHNTYANGGPAVqADVVA 85
Cdd:COG1372   422 RRLSRERLRRLALEDEALEALA---DSDVYWDEVVSIEPVGEEDVYDLTVPGTHNFVANGIVVHNSGGALDDVG-AAVLD 497

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084452927  86 YDPSGNIVKAGPADQPAGVMIGFGENGSVSYEFNGRASVKVSAENGPVKVGDRLTVSATMPGFAMKMTEAGQSIGLALAE 165
Cdd:COG1372   498 EDLLGGEPEEGEAGGAAEDKDRAKTGATTLAAGDLLVERDVEAEPEEIEDVISGEGRILERAALLAVALDELEDELEEAR 577
HintC smart00305
Hint (Hedgehog/Intein) domain C-terminal region; Hedgehog/Intein domain, C-terminal region. ...
 31-71 1.42e-09

Hint (Hedgehog/Intein) domain C-terminal region; Hedgehog/Intein domain, C-terminal region. Domain has been split to accommodate large insertions of endonucleases.


Pssm-ID: 197641  Cd Length: 46  Bit Score: 53.72  E-value: 1.42e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1084452927   31 EGGFSWDEVASIKPIGREEVWDIEVEDVHNFIGNDIFAHNT 71
Cdd:smart00305   1 EGDFRFVRVKSIEETEYTGVYDPTVTENHNFIANGILVHNC 41
PRK07773 PRK07773
replicative DNA helicase; Validated
 36-112 3.47e-08

replicative DNA helicase; Validated


Pssm-ID: 236093 [Multi-domain]  Cd Length: 886  Bit Score: 56.30  E-value: 3.47e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084452927  36 WDEVASIKPIGREEVWDIEVEDVHNFIGNDIFAHNTYANggpavQADVV-------AYDPSGNivKAGPADqpagVMIGF 108
Cdd:PRK07773  792 WDTVVSITSIGEEEVFDLTVPGTHNFVANGIIVHNSIEQ-----DADVVillyrpdYYDRDDP--RGGEAE----FIVAK 860


                  ....
gi 1084452927 109 GENG 112
Cdd:PRK07773  861 HRNG 864
Hint cd00081
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins ...
 9-70 3.02e-07

Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here.


Pssm-ID: 238035 [Multi-domain]  Cd Length: 136  Bit Score: 49.57  E-value: 3.02e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1084452927   9 NNASWKKISELSAGMKIAVPDieggfsWDEVASIKPIGREE-VWDIEVEDVHNFIGNDIFAHN 70
Cdd:cd00081    80 GELKWVFASDLKPGDYVLVPV------LEKVKEIEEIEYTGgVYDLTVEDNHNFIANGVLVHN 136
Intein_splicing pfam14890
Intein splicing domain; Inteins are segments of protein which excise themselves from a ...
 30-70 7.28e-07

Intein splicing domain; Inteins are segments of protein which excise themselves from a precursor protein and mediate the rejoining of the remainder of the precursor (the extein). Most inteins consist of a splicing domain which is split into two segments by a homing endonuclease domain. This domain represents the splicing domain.


Pssm-ID: 434290 [Multi-domain]  Cd Length: 378  Bit Score: 51.31  E-value: 7.28e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1084452927  30 IEGGFSWDEVASIKPIGREE-VWDIEVEDVHNFIGNDIFAHN 70
Cdd:pfam14890 337 INSDVYWDKVKSIEVLDEEEyVYDLTVEGYHNFVANGIIVHN 378
intein_Cterm TIGR01443
intein C-terminal splicing region; This model represents the well-conserved C-terminal region ...
 49-69 1.91e-04

intein C-terminal splicing region; This model represents the well-conserved C-terminal region of a large number of inteins. It is based on interated search results, starting with a curated collection of intein N-terminal splicing regions from InBase, the New England Biolabs Intein Database, as presented on its web site. Inteins are regions encoded within proteins from which they remove themselves after translation in a self-splicing reaction, leaving the remainder of the coding region to form a complete, functional protein as if the intein were never there. Proteins with inteins include RecA, GyrA, ribonucleotide reductase, and others. Most inteins have a central region with putative endonuclease activity.


Pssm-ID: 213622 [Multi-domain]  Cd Length: 21  Bit Score: 38.56  E-value: 1.91e-04
                          10        20
                  ....*....|....*....|.
gi 1084452927  49 EVWDIEVEDVHNFIGNDIFAH 69
Cdd:TIGR01443   1 YVYDLTVEGNHNFIANGIVVH 21
 
Name Accession Description Interval E-value
Hop COG1372
Intein/homing endonuclease [Replication, recombination and repair, Mobilome: prophages, ...
 6-165 9.19e-15

Intein/homing endonuclease [Replication, recombination and repair, Mobilome: prophages, transposons];


Pssm-ID: 440983 [Multi-domain]  Cd Length: 866  Bit Score: 77.24  E-value: 9.19e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084452927   6 KQLNNASWKKISELSAGMKIAVpdiEGGFSWDEVASIKPIGREEVWDIEVEDVHNFIGNDIFAHNTYANGGPAVqADVVA 85
Cdd:COG1372   422 RRLSRERLRRLALEDEALEALA---DSDVYWDEVVSIEPVGEEDVYDLTVPGTHNFVANGIVVHNSGGALDDVG-AAVLD 497

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084452927  86 YDPSGNIVKAGPADQPAGVMIGFGENGSVSYEFNGRASVKVSAENGPVKVGDRLTVSATMPGFAMKMTEAGQSIGLALAE 165
Cdd:COG1372   498 EDLLGGEPEEGEAGGAAEDKDRAKTGATTLAAGDLLVERDVEAEPEEIEDVISGEGRILERAALLAVALDELEDELEEAR 577
HintC smart00305
Hint (Hedgehog/Intein) domain C-terminal region; Hedgehog/Intein domain, C-terminal region. ...
 31-71 1.42e-09

Hint (Hedgehog/Intein) domain C-terminal region; Hedgehog/Intein domain, C-terminal region. Domain has been split to accommodate large insertions of endonucleases.


Pssm-ID: 197641  Cd Length: 46  Bit Score: 53.72  E-value: 1.42e-09
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1084452927   31 EGGFSWDEVASIKPIGREEVWDIEVEDVHNFIGNDIFAHNT 71
Cdd:smart00305   1 EGDFRFVRVKSIEETEYTGVYDPTVTENHNFIANGILVHNC 41
PRK07773 PRK07773
replicative DNA helicase; Validated
 36-112 3.47e-08

replicative DNA helicase; Validated


Pssm-ID: 236093 [Multi-domain]  Cd Length: 886  Bit Score: 56.30  E-value: 3.47e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084452927  36 WDEVASIKPIGREEVWDIEVEDVHNFIGNDIFAHNTYANggpavQADVV-------AYDPSGNivKAGPADqpagVMIGF 108
Cdd:PRK07773  792 WDTVVSITSIGEEEVFDLTVPGTHNFVANGIIVHNSIEQ-----DADVVillyrpdYYDRDDP--RGGEAE----FIVAK 860


                  ....
gi 1084452927 109 GENG 112
Cdd:PRK07773  861 HRNG 864
Hint cd00081
Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins ...
 9-70 3.02e-07

Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here.


Pssm-ID: 238035 [Multi-domain]  Cd Length: 136  Bit Score: 49.57  E-value: 3.02e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1084452927   9 NNASWKKISELSAGMKIAVPDieggfsWDEVASIKPIGREE-VWDIEVEDVHNFIGNDIFAHN 70
Cdd:cd00081    80 GELKWVFASDLKPGDYVLVPV------LEKVKEIEEIEYTGgVYDLTVEDNHNFIANGVLVHN 136
Intein_splicing pfam14890
Intein splicing domain; Inteins are segments of protein which excise themselves from a ...
 30-70 7.28e-07

Intein splicing domain; Inteins are segments of protein which excise themselves from a precursor protein and mediate the rejoining of the remainder of the precursor (the extein). Most inteins consist of a splicing domain which is split into two segments by a homing endonuclease domain. This domain represents the splicing domain.


Pssm-ID: 434290 [Multi-domain]  Cd Length: 378  Bit Score: 51.31  E-value: 7.28e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1084452927  30 IEGGFSWDEVASIKPIGREE-VWDIEVEDVHNFIGNDIFAHN 70
Cdd:pfam14890 337 INSDVYWDKVKSIEVLDEEEyVYDLTVEGYHNFVANGIIVHN 378
intein_Cterm TIGR01443
intein C-terminal splicing region; This model represents the well-conserved C-terminal region ...
 49-69 1.91e-04

intein C-terminal splicing region; This model represents the well-conserved C-terminal region of a large number of inteins. It is based on interated search results, starting with a curated collection of intein N-terminal splicing regions from InBase, the New England Biolabs Intein Database, as presented on its web site. Inteins are regions encoded within proteins from which they remove themselves after translation in a self-splicing reaction, leaving the remainder of the coding region to form a complete, functional protein as if the intein were never there. Proteins with inteins include RecA, GyrA, ribonucleotide reductase, and others. Most inteins have a central region with putative endonuclease activity.


Pssm-ID: 213622 [Multi-domain]  Cd Length: 21  Bit Score: 38.56  E-value: 1.91e-04
                          10        20
                  ....*....|....*....|.
gi 1084452927  49 EVWDIEVEDVHNFIGNDIFAH 69
Cdd:TIGR01443   1 YVYDLTVEGNHNFIANGIVVH 21
PRK14714 PRK14714
DNA-directed DNA polymerase II large subunit;
14-69 1.26e-03

DNA-directed DNA polymerase II large subunit;


Pssm-ID: 237798 [Multi-domain]  Cd Length: 1337  Bit Score: 41.60  E-value: 1.26e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1084452927   14 KKISELSAGMKIAVPD---IEGGFSWDEVASIKPIGREE--VWDIEVEDVHNFIGNDIFAH 69
Cdd:PRK14714  1026 KRAFEVKEGDAVPVPEgveETGVVLADEVVSIEYVESDDdfVYCLTVAEYHTVVANGIFTG 1086
 
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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