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Conserved domains on  [gi|113681054|ref|NP_001038664|]
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small conductance calcium-activated potassium channel protein 1b isoform 2 [Danio rerio]

Protein Classification

potassium channel family protein( domain architecture ID 10545872)

potassium channel family protein spans the cell membrane to form a conduction pathway or pore, through which selective ions such as potassium, sodium, and calcium, translocate across cell membranes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CaMBD smart01053
Calmodulin binding domain; Small-conductance Ca2+-activated K+ channels (SK channels) are ...
 64-139 2.91e-40

Calmodulin binding domain; Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM). CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other.


:

Pssm-ID: 198121  Cd Length: 76  Bit Score: 132.92  E-value: 2.91e-40
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 113681054    64 DTQLCKRVKNTAANVLRETWLIYKHTKLVKKIDHAKVRKHQRKFLQAIHQLRSVKMEQRKLNDQANTLVDLAKTQN 139
Cdd:smart01053   1 DTQLTKRVKNAAANVLRETWLIYKHTKLVKKGDQGRLRKHQRKFLQAIHQFRSVKMKQRKLREQANSLVDLAKTQM 76
Ion_trans_2 pfam07885
Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
 1-50 1.93e-10

Ion channel; This family includes the two membrane helix type ion channels found in bacteria.


:

Pssm-ID: 462301 [Multi-domain]  Cd Length: 78  Bit Score: 55.35  E-value: 1.93e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 113681054    1 MWLISITFLSIGYGDMVPNTYCGKGVCLLTGIMGAGCTALVVAVVARKLE 50
Cdd:pfam07885  28 LYFSFVTLTTVGYGDIVPLTDAGRLFTIFYILIGIPLFAIFLAVLGRFLT 77
rad50 super family cl31018
rad50; All proteins in this family for which functions are known are involvedin recombination, ...
 99-212 3.67e-03

rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).


The actual alignment was detected with superfamily member TIGR00606:

Pssm-ID: 129694 [Multi-domain]  Cd Length: 1311  Bit Score: 38.10  E-value: 3.67e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113681054    99 KVRKHQRKFLQAIHQLRSVKMEQRKLNDQANTLVDLAKTQNVMYDLVSELQERSEELEKRIGHLETKLDSINSSLQALPg 178
Cdd:TIGR00606  748 ELRNKLQKVNRDIQRLKNDIEEQETLLGTIMPEEESAKVCLTDVTIMERFQMELKDVERKIAQQAAKLQGSDLDRTVQQ- 826

                           90       100       110
                   ....*....|....*....|....*....|....
gi 113681054   179 lLSQAIQQQQHHlLDGLTQRGFTLTRPSSQTSER 212
Cdd:TIGR00606  827 -VNQEKQEKQHE-LDTVVSKIELNRKLIQDQQEQ 858
 
Name Accession Description Interval E-value
CaMBD smart01053
Calmodulin binding domain; Small-conductance Ca2+-activated K+ channels (SK channels) are ...
 64-139 2.91e-40

Calmodulin binding domain; Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM). CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other.


Pssm-ID: 198121  Cd Length: 76  Bit Score: 132.92  E-value: 2.91e-40
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 113681054    64 DTQLCKRVKNTAANVLRETWLIYKHTKLVKKIDHAKVRKHQRKFLQAIHQLRSVKMEQRKLNDQANTLVDLAKTQN 139
Cdd:smart01053   1 DTQLTKRVKNAAANVLRETWLIYKHTKLVKKGDQGRLRKHQRKFLQAIHQFRSVKMKQRKLREQANSLVDLAKTQM 76
CaMBD pfam02888
Calmodulin binding domain; Small-conductance Ca2+-activated K+ channels (SK channels) are ...
 64-138 5.05e-40

Calmodulin binding domain; Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM). CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other.


Pssm-ID: 460739  Cd Length: 75  Bit Score: 132.41  E-value: 5.05e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 113681054   64 DTQLCKRVKNTAANVLRETWLIYKHTKLVKKIDHAKVRKHQRKFLQAIHQLRSVKMEQRKLNDQANTLVDLAKTQ 138
Cdd:pfam02888   1 DTQLTKELKNAAANVLRETWLIYKHTKLVKKRDQSRVRKHQRKLLQAIHTFRKVKMKQRKLRDQVNTMVDLSKMQ 75
Ion_trans_2 pfam07885
Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
 1-50 1.93e-10

Ion channel; This family includes the two membrane helix type ion channels found in bacteria.


Pssm-ID: 462301 [Multi-domain]  Cd Length: 78  Bit Score: 55.35  E-value: 1.93e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 113681054    1 MWLISITFLSIGYGDMVPNTYCGKGVCLLTGIMGAGCTALVVAVVARKLE 50
Cdd:pfam07885  28 LYFSFVTLTTVGYGDIVPLTDAGRLFTIFYILIGIPLFAIFLAVLGRFLT 77
rad50 TIGR00606
rad50; All proteins in this family for which functions are known are involvedin recombination, ...
 99-212 3.67e-03

rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).


Pssm-ID: 129694 [Multi-domain]  Cd Length: 1311  Bit Score: 38.10  E-value: 3.67e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113681054    99 KVRKHQRKFLQAIHQLRSVKMEQRKLNDQANTLVDLAKTQNVMYDLVSELQERSEELEKRIGHLETKLDSINSSLQALPg 178
Cdd:TIGR00606  748 ELRNKLQKVNRDIQRLKNDIEEQETLLGTIMPEEESAKVCLTDVTIMERFQMELKDVERKIAQQAAKLQGSDLDRTVQQ- 826

                           90       100       110
                   ....*....|....*....|....*....|....
gi 113681054   179 lLSQAIQQQQHHlLDGLTQRGFTLTRPSSQTSER 212
Cdd:TIGR00606  827 -VNQEKQEKQHE-LDTVVSKIELNRKLIQDQQEQ 858
GIM5 COG1730
Prefoldin subunit 5 [Posttranslational modification, protein turnover, chaperones];
145-189 6.69e-03

Prefoldin subunit 5 [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441336 [Multi-domain]  Cd Length: 145  Bit Score: 36.04  E-value: 6.69e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 113681054 145 VSELQERSEELEKRIGHLETKLDSINSSLQALPGLLSQAIQQQQH 189
Cdd:COG1730   97 IEYLEKRIKELEKALEKLEEELQELEEEYEELEQQLQQLQQQAQQ 141
 
Name Accession Description Interval E-value
CaMBD smart01053
Calmodulin binding domain; Small-conductance Ca2+-activated K+ channels (SK channels) are ...
 64-139 2.91e-40

Calmodulin binding domain; Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM). CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other.


Pssm-ID: 198121  Cd Length: 76  Bit Score: 132.92  E-value: 2.91e-40
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 113681054    64 DTQLCKRVKNTAANVLRETWLIYKHTKLVKKIDHAKVRKHQRKFLQAIHQLRSVKMEQRKLNDQANTLVDLAKTQN 139
Cdd:smart01053   1 DTQLTKRVKNAAANVLRETWLIYKHTKLVKKGDQGRLRKHQRKFLQAIHQFRSVKMKQRKLREQANSLVDLAKTQM 76
CaMBD pfam02888
Calmodulin binding domain; Small-conductance Ca2+-activated K+ channels (SK channels) are ...
 64-138 5.05e-40

Calmodulin binding domain; Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM). CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other.


Pssm-ID: 460739  Cd Length: 75  Bit Score: 132.41  E-value: 5.05e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 113681054   64 DTQLCKRVKNTAANVLRETWLIYKHTKLVKKIDHAKVRKHQRKFLQAIHQLRSVKMEQRKLNDQANTLVDLAKTQ 138
Cdd:pfam02888   1 DTQLTKELKNAAANVLRETWLIYKHTKLVKKRDQSRVRKHQRKLLQAIHTFRKVKMKQRKLRDQVNTMVDLSKMQ 75
Ion_trans_2 pfam07885
Ion channel; This family includes the two membrane helix type ion channels found in bacteria.
 1-50 1.93e-10

Ion channel; This family includes the two membrane helix type ion channels found in bacteria.


Pssm-ID: 462301 [Multi-domain]  Cd Length: 78  Bit Score: 55.35  E-value: 1.93e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 113681054    1 MWLISITFLSIGYGDMVPNTYCGKGVCLLTGIMGAGCTALVVAVVARKLE 50
Cdd:pfam07885  28 LYFSFVTLTTVGYGDIVPLTDAGRLFTIFYILIGIPLFAIFLAVLGRFLT 77
rad50 TIGR00606
rad50; All proteins in this family for which functions are known are involvedin recombination, ...
 99-212 3.67e-03

rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).


Pssm-ID: 129694 [Multi-domain]  Cd Length: 1311  Bit Score: 38.10  E-value: 3.67e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113681054    99 KVRKHQRKFLQAIHQLRSVKMEQRKLNDQANTLVDLAKTQNVMYDLVSELQERSEELEKRIGHLETKLDSINSSLQALPg 178
Cdd:TIGR00606  748 ELRNKLQKVNRDIQRLKNDIEEQETLLGTIMPEEESAKVCLTDVTIMERFQMELKDVERKIAQQAAKLQGSDLDRTVQQ- 826

                           90       100       110
                   ....*....|....*....|....*....|....
gi 113681054   179 lLSQAIQQQQHHlLDGLTQRGFTLTRPSSQTSER 212
Cdd:TIGR00606  827 -VNQEKQEKQHE-LDTVVSKIELNRKLIQDQQEQ 858
GIM5 COG1730
Prefoldin subunit 5 [Posttranslational modification, protein turnover, chaperones];
145-189 6.69e-03

Prefoldin subunit 5 [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441336 [Multi-domain]  Cd Length: 145  Bit Score: 36.04  E-value: 6.69e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 113681054 145 VSELQERSEELEKRIGHLETKLDSINSSLQALPGLLSQAIQQQQH 189
Cdd:COG1730   97 IEYLEKRIKELEKALEKLEEELQELEEEYEELEQQLQQLQQQAQQ 141
 
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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