BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 012010
(473 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WGP|A Chain A, Solution Structure Of The Cnmp-Binding Domain From
Arabidopsis Thaliana Cyclic Nucleotide-Regulated Ion
Channel
Length = 137
Score = 89.0 bits (219), Expect = 5e-18, Method: Composition-based stats.
Identities = 45/123 (36%), Positives = 70/123 (56%), Gaps = 2/123 (1%)
Query: 271 VRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQS--SQILH 328
VR+VPLF++MD+ +L+ IC+R+K +FT+ + +EGDPV MLF++RG L+S +
Sbjct: 8 VRRVPLFENMDERLLDAICERLKPCLFTEKSYLVREGDPVNEMLFIIRGRLESVTTDGGR 67
Query: 329 NNIKSCCMLGPGNFSGDELLSWCLRRPFIERXXXXXXXXXXXXXXXAFGLEAEDVKYVTQ 388
+ + +L G+F GDELL+W L AF L A+++K+V
Sbjct: 68 SGFYNRSLLKEGDFCGDELLTWALDPKSGSNLPSSTRTVKALTEVEAFALIADELKFVAS 127
Query: 389 HFR 391
FR
Sbjct: 128 QFR 130
>pdb|3UKN|A Chain A, Structure Of The C-LinkerCNBHD OF ZELK CHANNELS IN C 2 2
21 SPACE Group
pdb|3UKN|B Chain B, Structure Of The C-LinkerCNBHD OF ZELK CHANNELS IN C 2 2
21 SPACE Group
pdb|3UKN|C Chain C, Structure Of The C-LinkerCNBHD OF ZELK CHANNELS IN C 2 2
21 SPACE Group
pdb|3UKT|B Chain B, Structure Of The C-LinkerCNBHD OF ZELK CHANNELS IN P1 21 1
SPACE Group
pdb|3UKT|A Chain A, Structure Of The C-LinkerCNBHD OF ZELK CHANNELS IN P1 21 1
SPACE Group
pdb|3UKT|C Chain C, Structure Of The C-LinkerCNBHD OF ZELK CHANNELS IN P1 21 1
SPACE Group
pdb|3UKT|D Chain D, Structure Of The C-LinkerCNBHD OF ZELK CHANNELS IN P1 21 1
SPACE Group
pdb|3UKV|B Chain B, Structure Of The C-LinkerCNBHD OF ZELK CHANNELS IN P 1 21
1 SPACE Group, Crystallized In The Presence Of Camp
pdb|3UKV|A Chain A, Structure Of The C-LinkerCNBHD OF ZELK CHANNELS IN P 1 21
1 SPACE Group, Crystallized In The Presence Of Camp
pdb|3UKV|C Chain C, Structure Of The C-LinkerCNBHD OF ZELK CHANNELS IN P 1 21
1 SPACE Group, Crystallized In The Presence Of Camp
pdb|3UKV|D Chain D, Structure Of The C-LinkerCNBHD OF ZELK CHANNELS IN P 1 21
1 SPACE Group, Crystallized In The Presence Of Camp
Length = 212
Score = 68.6 bits (166), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 40/148 (27%), Positives = 79/148 (53%), Gaps = 5/148 (3%)
Query: 202 SKKQAMQLKMRNIEWWMRKRQLPQGFRQRVRNYERQRWAAMRGVDECEMISNLPEGLRRD 261
S++ + ++++ ++R +LP+ QR+ + W+ G+D E++ + P+ LR D
Sbjct: 9 SRRSLYHTRTKDLKDFIRVHRLPKALAQRMLECFQTTWSVNNGIDVSELLKDFPDELRAD 68
Query: 262 IKYHLCLDLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHL 321
I HL +L+ Q+PLF+ L ++ +K+ GE + ++GD +Q + FV G
Sbjct: 69 IAMHLNKELL-QLPLFESASRGCLRSLSLIIKTSFCAPGEFLIRQGDALQAIYFVCSG-- 125
Query: 322 QSSQILHNNIKSCCMLGPGNFSGDELLS 349
S ++L +N +LG G+ G + L+
Sbjct: 126 -SMEVLKDNT-VLAILGKGDLIGSDSLT 151
>pdb|1Q3E|A Chain A, Hcn2j 443-645 In The Presence Of Cgmp
pdb|1Q3E|B Chain B, Hcn2j 443-645 In The Presence Of Cgmp
Length = 207
Score = 62.4 bits (150), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 35/121 (28%), Positives = 61/121 (50%), Gaps = 1/121 (0%)
Query: 199 ATTSKKQAMQLKMRNIEWWMRKRQLPQGFRQRVRNYERQRWAAMRGVDECEMISNLPEGL 258
A S ++ Q K + +E +M +LP FRQ++ +Y R+ + DE ++ L L
Sbjct: 3 AMDSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPL 61
Query: 259 RRDIKYHLCLDLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVR 318
R +I C LV +PLF + D + + ++K +F G+ I +EG ++M F+
Sbjct: 62 REEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQH 121
Query: 319 G 319
G
Sbjct: 122 G 122
>pdb|3FFQ|A Chain A, Hcn2i 443-640 Apo-State
pdb|3FFQ|B Chain B, Hcn2i 443-640 Apo-State
Length = 202
Score = 62.0 bits (149), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 35/121 (28%), Positives = 61/121 (50%), Gaps = 1/121 (0%)
Query: 199 ATTSKKQAMQLKMRNIEWWMRKRQLPQGFRQRVRNYERQRWAAMRGVDECEMISNLPEGL 258
A S ++ Q K + +E +M +LP FRQ++ +Y R+ + DE ++ L L
Sbjct: 3 AMDSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPL 61
Query: 259 RRDIKYHLCLDLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVR 318
R +I C LV +PLF + D + + ++K +F G+ I +EG ++M F+
Sbjct: 62 REEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQH 121
Query: 319 G 319
G
Sbjct: 122 G 122
>pdb|3OTF|A Chain A, Structural Basis For The Camp-Dependent Gating In Human
Hcn4 Channel
Length = 220
Score = 62.0 bits (149), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 34/120 (28%), Positives = 62/120 (51%), Gaps = 1/120 (0%)
Query: 200 TTSKKQAMQLKMRNIEWWMRKRQLPQGFRQRVRNYERQRWAAMRGVDECEMISNLPEGLR 259
+ S ++ Q K + +E +M +LP RQR+ +Y R+ + DE ++ L E LR
Sbjct: 1 SDSSRRQYQEKYKQVEQYMSFHKLPPDTRQRIHDYYEHRYQG-KMFDEESILGELSEPLR 59
Query: 260 RDIKYHLCLDLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRG 319
+I C LV +PLF + D + ++ +++ +F G+ I +EG ++M F+ G
Sbjct: 60 EEIINFNCRKLVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQHG 119
>pdb|2Q0A|A Chain A, Structure And Rearrangements In The Carboxy-Terminal
Region Of Spih Channels
pdb|2Q0A|B Chain B, Structure And Rearrangements In The Carboxy-Terminal
Region Of Spih Channels
Length = 200
Score = 61.6 bits (148), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 34/121 (28%), Positives = 61/121 (50%), Gaps = 1/121 (0%)
Query: 199 ATTSKKQAMQLKMRNIEWWMRKRQLPQGFRQRVRNYERQRWAAMRGVDECEMISNLPEGL 258
+ S ++ Q K + +E +M +LP FRQ++ +Y R+ + DE ++ L L
Sbjct: 1 GSDSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPL 59
Query: 259 RRDIKYHLCLDLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVR 318
R +I C LV +PLF + D + + ++K +F G+ I +EG ++M F+
Sbjct: 60 REEIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQH 119
Query: 319 G 319
G
Sbjct: 120 G 120
>pdb|4HBN|A Chain A, Crystal Structure Of The Human Hcn4 Channel C-terminus
Carrying The S672r Mutation
Length = 205
Score = 61.2 bits (147), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 34/120 (28%), Positives = 62/120 (51%), Gaps = 1/120 (0%)
Query: 200 TTSKKQAMQLKMRNIEWWMRKRQLPQGFRQRVRNYERQRWAAMRGVDECEMISNLPEGLR 259
+ S ++ Q K + +E +M +LP RQR+ +Y R+ + DE ++ L E LR
Sbjct: 1 SDSSRRQYQEKYKQVEQYMSFHKLPPDTRQRIHDYYEHRYQG-KMFDEESILGELSEPLR 59
Query: 260 RDIKYHLCLDLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRG 319
+I C LV +PLF + D + ++ +++ +F G+ I +EG ++M F+ G
Sbjct: 60 EEIINFNCRKLVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQHG 119
>pdb|3BPZ|A Chain A, Hcn2-I 443-460 E502k In The Presence Of Camp
pdb|3BPZ|B Chain B, Hcn2-I 443-460 E502k In The Presence Of Camp
pdb|3BPZ|C Chain C, Hcn2-I 443-460 E502k In The Presence Of Camp
pdb|3BPZ|D Chain D, Hcn2-I 443-460 E502k In The Presence Of Camp
Length = 202
Score = 61.2 bits (147), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 35/121 (28%), Positives = 60/121 (49%), Gaps = 1/121 (0%)
Query: 199 ATTSKKQAMQLKMRNIEWWMRKRQLPQGFRQRVRNYERQRWAAMRGVDECEMISNLPEGL 258
A S ++ Q K + +E +M +LP FRQ++ +Y R+ + DE ++ L L
Sbjct: 3 AMDSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPL 61
Query: 259 RRDIKYHLCLDLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVR 318
R I C LV +PLF + D + + ++K +F G+ I +EG ++M F+
Sbjct: 62 REKIVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQH 121
Query: 319 G 319
G
Sbjct: 122 G 122
>pdb|3U10|A Chain A, Tetramerization Dynamics Of The C-Terminus Underlies
Isoform-Specific Camp-Gating In Hcn Channels
Length = 210
Score = 60.8 bits (146), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 34/118 (28%), Positives = 60/118 (50%), Gaps = 1/118 (0%)
Query: 202 SKKQAMQLKMRNIEWWMRKRQLPQGFRQRVRNYERQRWAAMRGVDECEMISNLPEGLRRD 261
S ++ Q K + +E +M +LP FRQ++ +Y R+ + DE ++ L LR +
Sbjct: 9 SSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPLREE 67
Query: 262 IKYHLCLDLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRG 319
I C LV +PLF + D + + ++K +F G+ I +EG ++M F+ G
Sbjct: 68 IVNFNCRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHG 125
>pdb|3U0Z|A Chain A, Tetramerization Dynamics Of The C-Terminus Underlies
Isoform-Specific Camp-Gating In Hcn Channels
pdb|3U0Z|B Chain B, Tetramerization Dynamics Of The C-Terminus Underlies
Isoform-Specific Camp-Gating In Hcn Channels
Length = 210
Score = 59.3 bits (142), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 33/118 (27%), Positives = 61/118 (51%), Gaps = 1/118 (0%)
Query: 202 SKKQAMQLKMRNIEWWMRKRQLPQGFRQRVRNYERQRWAAMRGVDECEMISNLPEGLRRD 261
S ++ Q K + +E +M +LP RQ++ +Y R+ + DE ++S L + LR +
Sbjct: 9 SSRRQYQEKYKQVEQYMSFHKLPADMRQKIHDYYEHRYQG-KIFDEENILSELNDPLREE 67
Query: 262 IKYHLCLDLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRG 319
I C LV +PLF + D + + +++ +F G+ I +EG ++M F+ G
Sbjct: 68 IVNFNCRKLVATMPLFANADPNFVTAMLSKLRFEVFQPGDYIIREGAVGKKMYFIQHG 125
>pdb|2PTM|A Chain A, Structure And Rearrangements In The Carboxy-Terminal
Region Of Spih Channels
Length = 198
Score = 58.9 bits (141), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 35/147 (23%), Positives = 71/147 (48%), Gaps = 4/147 (2%)
Query: 199 ATTSKKQAMQLKMRNIEWWMRKRQLPQGFRQRVRNYERQRWAAMRGVDECEMISNLPEGL 258
A S + + K++ +E +M+ R+LP R ++ +Y R+ + DE + + E +
Sbjct: 2 AMDSSSRQYREKLKQVEEYMQYRKLPSHLRNKILDYYEYRYRG-KMFDERHIFREVSESI 60
Query: 259 RRDIKYHLCLDLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVR 318
R+D+ + C DLV VP F D + + ++ +F + + +EG RM F+ +
Sbjct: 61 RQDVANYNCRDLVASVPFFVGADSNFVTRVVTLLEFEVFQPADYVIQEGTFGDRMFFIQQ 120
Query: 319 GHLQSSQILHNNIKSCCMLGPGNFSGD 345
G + I+ ++ L G++ G+
Sbjct: 121 GIV---DIIMSDGVIATSLSDGSYFGE 144
>pdb|3U11|A Chain A, Tetramerization Dynamics Of The C-Terminus Underlies
Isoform-Specific Camp-Gating In Hcn Channels
pdb|3U11|B Chain B, Tetramerization Dynamics Of The C-Terminus Underlies
Isoform-Specific Camp-Gating In Hcn Channels
Length = 210
Score = 57.4 bits (137), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 33/118 (27%), Positives = 60/118 (50%), Gaps = 1/118 (0%)
Query: 202 SKKQAMQLKMRNIEWWMRKRQLPQGFRQRVRNYERQRWAAMRGVDECEMISNLPEGLRRD 261
S ++ Q K + +E +M +LP RQR+ +Y R+ + DE ++ L E LR +
Sbjct: 9 SSRRQYQEKYKQVEQYMSFHKLPPDTRQRIHDYYEHRYQG-KMFDEESILGELSEPLREE 67
Query: 262 IKYHLCLDLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRG 319
I LV +PLF + D + ++ +++ +F G+ I +EG ++M F+ G
Sbjct: 68 IINFNXRKLVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQHG 125
>pdb|3ETQ|A Chain A, X-Ray Structure Of Cysteine-Free Fragment Of Mhcn2 C-
Terminal Region From Amino Acids 443-630 Including
C508n, C584s, And C601s Mutations
pdb|3ETQ|B Chain B, X-Ray Structure Of Cysteine-Free Fragment Of Mhcn2 C-
Terminal Region From Amino Acids 443-630 Including
C508n, C584s, And C601s Mutations
Length = 204
Score = 57.4 bits (137), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 60/121 (49%), Gaps = 1/121 (0%)
Query: 199 ATTSKKQAMQLKMRNIEWWMRKRQLPQGFRQRVRNYERQRWAAMRGVDECEMISNLPEGL 258
+ S ++ Q K + +E +M +LP FRQ++ +Y R+ + DE ++ L L
Sbjct: 5 GSDSSRRQYQEKYKQVEQYMSFHKLPADFRQKIHDYYEHRYQG-KMFDEDSILGELNGPL 63
Query: 259 RRDIKYHLCLDLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVR 318
R +I LV +PLF + D + + ++K +F G+ I +EG ++M F+
Sbjct: 64 REEIVNFNNRKLVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQH 123
Query: 319 G 319
G
Sbjct: 124 G 124
>pdb|1Q43|A Chain A, Hcn2i 443-640 In The Presence Of Camp, Selenomethionine
Derivative
pdb|1Q43|B Chain B, Hcn2i 443-640 In The Presence Of Camp, Selenomethionine
Derivative
pdb|1Q5O|A Chain A, Hcn2j 443-645 In The Presence Of Camp, Selenomethionine
Derivative
Length = 207
Score = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 57/121 (47%), Gaps = 1/121 (0%)
Query: 199 ATTSKKQAMQLKMRNIEWWMRKRQLPQGFRQRVRNYERQRWAAMRGVDECEMISNLPEGL 258
A S ++ Q K + +E + +LP FRQ++ +Y R+ + DE ++ L L
Sbjct: 3 AMDSSRRQYQEKYKQVEQYXSFHKLPADFRQKIHDYYEHRYQG-KXFDEDSILGELNGPL 61
Query: 259 RRDIKYHLCLDLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVR 318
R +I C LV PLF + D + ++K +F G+ I +EG ++ F+
Sbjct: 62 REEIVNFNCRKLVASXPLFANADPNFVTAXLTKLKFEVFQPGDYIIREGTIGKKXYFIQH 121
Query: 319 G 319
G
Sbjct: 122 G 122
>pdb|3BEH|A Chain A, Structure Of A Bacterial Cyclic Nucleotide Regulated Ion
Channel
pdb|3BEH|B Chain B, Structure Of A Bacterial Cyclic Nucleotide Regulated Ion
Channel
pdb|3BEH|C Chain C, Structure Of A Bacterial Cyclic Nucleotide Regulated Ion
Channel
pdb|3BEH|D Chain D, Structure Of A Bacterial Cyclic Nucleotide Regulated Ion
Channel
pdb|2ZD9|A Chain A, Structure Of A Bacterial Cyclic-Nucleotide Regulated Ion
Channel
pdb|2ZD9|B Chain B, Structure Of A Bacterial Cyclic-Nucleotide Regulated Ion
Channel
pdb|2ZD9|C Chain C, Structure Of A Bacterial Cyclic-Nucleotide Regulated Ion
Channel
pdb|2ZD9|D Chain D, Structure Of A Bacterial Cyclic-Nucleotide Regulated Ion
Channel
Length = 355
Score = 49.3 bits (116), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 29/79 (36%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 270 LVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQSSQILHN 329
LV VPLFQ + VL I +++ G VI + G+P RM FVV G + + N
Sbjct: 229 LVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVAT--PN 286
Query: 330 NIKSCCMLGPGNFSGDELL 348
++ LGPG F G+ L
Sbjct: 287 PVE----LGPGAFFGEMAL 301
>pdb|1U12|A Chain A, M. Loti Cyclic Nucleotide Binding Domain Mutant
pdb|1U12|B Chain B, M. Loti Cyclic Nucleotide Binding Domain Mutant
Length = 138
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 30/79 (37%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 270 LVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQSSQILHN 329
LV VPLFQ + VL I +++ G VI + G+P RM FVV G + S N
Sbjct: 12 LVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSV--SVATPN 69
Query: 330 NIKSCCMLGPGNFSGDELL 348
++ LGPG F G+ L
Sbjct: 70 PVE----LGPGAFFGEMAL 84
>pdb|1VP6|A Chain A, M.Loti Ion Channel Cylic Nucleotide Binding Domain
pdb|1VP6|C Chain C, M.Loti Ion Channel Cylic Nucleotide Binding Domain
Length = 138
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 30/79 (37%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 270 LVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQSSQILHN 329
LV VPLFQ + VL I +++ G VI + G+P RM FVV G + S N
Sbjct: 12 LVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSV--SVATPN 69
Query: 330 NIKSCCMLGPGNFSGDELL 348
++ LGPG F G+ L
Sbjct: 70 PVE----LGPGAFFGEMAL 84
>pdb|2K0G|A Chain A, Solution Structure Of A Bacterial Cyclic Nucleotide-
Activated K+ Channel Binding Domain In Complex With Camp
pdb|2KXL|A Chain A, Solution Structure Of A Bacterial Cyclic
Nucleotide-Activated K+ Channel Binding Domain In The
Unliganded State
Length = 142
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 30/79 (37%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 270 LVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQSSQILHN 329
LV VPLFQ + VL I +++ G VI + G+P RM FVV G + S N
Sbjct: 16 LVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSV--SVATPN 73
Query: 330 NIKSCCMLGPGNFSGDELL 348
++ LGPG F G+ L
Sbjct: 74 PVE----LGPGAFFGEMAL 88
>pdb|3CO2|A Chain A, Mlotik1 Ion Channel Cyclic-Nucleotide Binding Domain
Mutant
pdb|3CO2|B Chain B, Mlotik1 Ion Channel Cyclic-Nucleotide Binding Domain
Mutant
pdb|3CO2|C Chain C, Mlotik1 Ion Channel Cyclic-Nucleotide Binding Domain
Mutant
pdb|3CO2|D Chain D, Mlotik1 Ion Channel Cyclic-Nucleotide Binding Domain
Mutant
Length = 140
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 30/79 (37%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 270 LVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQSSQILHN 329
LV VPLFQ + VL I +++ G VI + G+P RM FVV G + S N
Sbjct: 14 LVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSV--SVATPN 71
Query: 330 NIKSCCMLGPGNFSGDELL 348
++ LGPG F G+ L
Sbjct: 72 PVE----LGPGAFFGEMAL 86
>pdb|3CLP|A Chain A, M. Loti Cyclic-Nucleotide Binding Domain Mutant 2
pdb|3CLP|C Chain C, M. Loti Cyclic-Nucleotide Binding Domain Mutant 2
Length = 140
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 30/79 (37%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 270 LVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQSSQILHN 329
LV VPLFQ + VL I +++ G VI + G+P RM FVV G + S N
Sbjct: 14 LVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSV--SVATPN 71
Query: 330 NIKSCCMLGPGNFSGDELL 348
++ LGPG F G+ L
Sbjct: 72 PVE----LGPGAFFGEMAL 86
>pdb|3CL1|A Chain A, M. Loti Cyclic-Nucleotide Binding Domain, Cyclic-Gmp Bound
pdb|3CL1|B Chain B, M. Loti Cyclic-Nucleotide Binding Domain, Cyclic-Gmp Bound
Length = 140
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 30/79 (37%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 270 LVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQSSQILHN 329
LV VPLFQ + VL I +++ G VI + G+P RM FVV G + S N
Sbjct: 14 LVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSV--SVATPN 71
Query: 330 NIKSCCMLGPGNFSGDELL 348
++ LGPG F G+ L
Sbjct: 72 PVE----LGPGAFFGEMAL 86
>pdb|4F8A|A Chain A, Cyclic Nucleotide Binding-Homology Domain From Mouse Eag1
Potassium Channel
Length = 160
Score = 39.7 bits (91), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/91 (27%), Positives = 44/91 (48%), Gaps = 4/91 (4%)
Query: 255 PEGLRRDIKYHLCLDLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRML 314
P+ +R DI HL + ++ P F+ D L + +++ G++I G+ V +
Sbjct: 13 PKDMRADICVHLNRKVFKEHPAFRLASDGCLRALAMEFQTVHCAPGDLIYHAGESVDSLC 72
Query: 315 FVVRGHLQSSQILHNNIKSCCMLGPGNFSGD 345
FVV G L+ Q + + +LG G+ GD
Sbjct: 73 FVVSGSLEVIQ----DDEVVAILGKGDVFGD 99
>pdb|1ZYB|A Chain A, Crystal Structure Of Transcription Regulator From
Bacteroides Thetaiotaomicron Vpi-5482 At 2.15 A
Resolution
Length = 232
Score = 35.4 bits (80), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 268 LDLVRQVPLFQHMDDLVLENICDRVKSLIFTK---GEVITKEGDPVQRMLFVVRGHL 321
D + Q+PLFQ + +I D+VK L F K GE I K G+P ++ F+++G +
Sbjct: 17 FDTLLQLPLFQGLCHEDFTSILDKVK-LHFIKHKAGETIIKSGNPCTQLCFLLKGEI 72
>pdb|3R6S|A Chain A, Crystal Structure Of Glxr Transcription Factor From
Corynebacterium Glutamicum With Camp
pdb|3R6S|B Chain B, Crystal Structure Of Glxr Transcription Factor From
Corynebacterium Glutamicum With Camp
pdb|3R6S|C Chain C, Crystal Structure Of Glxr Transcription Factor From
Corynebacterium Glutamicum With Camp
pdb|3R6S|D Chain D, Crystal Structure Of Glxr Transcription Factor From
Corynebacterium Glutamicum With Camp
pdb|3R6S|E Chain E, Crystal Structure Of Glxr Transcription Factor From
Corynebacterium Glutamicum With Camp
pdb|3R6S|F Chain F, Crystal Structure Of Glxr Transcription Factor From
Corynebacterium Glutamicum With Camp
Length = 247
Score = 33.9 bits (76), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/78 (19%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 269 DLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQSSQILH 328
+++ + +FQ +D + N+ ++++ F +G I EG+P R+ + G ++ ++
Sbjct: 26 EILSRAGIFQGVDPTAVNNLIQDMETVRFPRGATIFDEGEPGDRLYIITSGKVKLARHAP 85
Query: 329 NNIKS-CCMLGPGNFSGD 345
+ ++ ++GP + G+
Sbjct: 86 DGRENLLTIMGPSDMFGE 103
>pdb|2PQQ|A Chain A, Structural Genomics, The Crystal Structure Of The
N-Terminal Domain Of A Transcriptional Regulator From
Streptomyces Coelicolor A3(2)
pdb|2PQQ|B Chain B, Structural Genomics, The Crystal Structure Of The
N-Terminal Domain Of A Transcriptional Regulator From
Streptomyces Coelicolor A3(2)
pdb|2PQQ|C Chain C, Structural Genomics, The Crystal Structure Of The
N-Terminal Domain Of A Transcriptional Regulator From
Streptomyces Coelicolor A3(2)
pdb|2PQQ|D Chain D, Structural Genomics, The Crystal Structure Of The
N-Terminal Domain Of A Transcriptional Regulator From
Streptomyces Coelicolor A3(2)
Length = 149
Score = 33.9 bits (76), Expect = 0.22, Method: Composition-based stats.
Identities = 15/54 (27%), Positives = 27/54 (50%)
Query: 269 DLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQ 322
D++R+ PLF +DD + + +G+ + EGDP R+ V G ++
Sbjct: 5 DVLRRNPLFAALDDEQSAELRASXSEVTLARGDTLFHEGDPGDRLYVVTEGKVK 58
>pdb|1O5L|A Chain A, Crystal Structure Of Transcriptional Regulator (Tm1171)
From Thermotoga Maritima At 2.30 A Resolution
Length = 213
Score = 33.5 bits (75), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 24/37 (64%)
Query: 293 KSLIFTKGEVITKEGDPVQRMLFVVRGHLQSSQILHN 329
K ++F KGE++ + DP++ +L ++ G L++ + N
Sbjct: 23 KVIVFRKGEIVKHQDDPIEDVLILLEGTLKTEHVSEN 59
>pdb|3SHR|A Chain A, Crystal Structure Of Cgmp-Dependent Protein Kinase Reveals
Novel Site Of Interchain Communication
pdb|3SHR|B Chain B, Crystal Structure Of Cgmp-Dependent Protein Kinase Reveals
Novel Site Of Interchain Communication
Length = 299
Score = 32.0 bits (71), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 19/89 (21%), Positives = 43/89 (48%), Gaps = 2/89 (2%)
Query: 262 IKYHLCLDLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHL 321
IK+ ++ ++ VP FQ + + +L + D ++ + GE I ++G + +G +
Sbjct: 150 IKHTEYMEFLKSVPTFQSLPEEILSKLADVLEETHYENGEYIIRQGARGDTFFIISKGKV 209
Query: 322 QSSQILHNNIKSCCM--LGPGNFSGDELL 348
++ N + LG G++ G++ L
Sbjct: 210 NVTREDSPNEDPVFLRTLGKGDWFGEKAL 238
>pdb|3PVB|B Chain B, Crystal Structure Of (73-244)ria:c Holoenzyme Of
Camp-Dependent Protein Kinase
Length = 160
Score = 30.8 bits (68), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 4/79 (5%)
Query: 276 LFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQSSQILHNNIKSCC 335
LF H+DD +I D + + F GE + ++GD + +G + ++ N +
Sbjct: 52 LFSHLDDNERSDIFDAMFPVSFIAGETVIQQGDEGDNFYVIDQGEMD----VYVNNEWAT 107
Query: 336 MLGPGNFSGDELLSWCLRR 354
+G G G+ L + R
Sbjct: 108 SVGEGGSFGELALIYGTPR 126
>pdb|1NE4|A Chain A, Crystal Structure Of Rp-Camp Binding R1a Subunit Of Camp-
Dependent Protein Kinase
pdb|1NE6|A Chain A, Crystal Structure Of Sp-Camp Binding R1a Subunit Of Camp-
Dependent Protein Kinase
Length = 283
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 23/47 (48%)
Query: 276 LFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQ 322
LF H+DD +I D + + F GE + ++GD + +G +
Sbjct: 42 LFSHLDDNERSDIFDAMFPVSFIAGETVIQQGDEGDNFYVIDQGEMD 88
>pdb|2QCS|B Chain B, A Complex Structure Between The Catalytic And Regulatory
Subunit Of Protein Kinase A That Represents The
Inhibited State
Length = 291
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 23/47 (48%)
Query: 276 LFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQ 322
LF H+DD +I D + + F GE + ++GD + +G +
Sbjct: 46 LFSHLDDNERSDIFDAMFPVSFIAGETVIQQGDEGDNFYVIDQGEMD 92
>pdb|1RL3|A Chain A, Crystal Structure Of Camp-free R1a Subunit Of Pka
pdb|1RL3|B Chain B, Crystal Structure Of Camp-free R1a Subunit Of Pka
pdb|1RGS|A Chain A, Regulatory Subunit Of Camp Dependent Protein Kinase
Length = 288
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 23/47 (48%)
Query: 276 LFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQ 322
LF H+DD +I D + + F GE + ++GD + +G +
Sbjct: 44 LFSHLDDNERSDIFDAMFPVSFIAGETVIQQGDEGDNFYVIDQGEMD 90
>pdb|3I54|A Chain A, Crystal Structure Of Mtbcrp In Complex With Camp
pdb|3I54|B Chain B, Crystal Structure Of Mtbcrp In Complex With Camp
pdb|3I54|C Chain C, Crystal Structure Of Mtbcrp In Complex With Camp
pdb|3I54|D Chain D, Crystal Structure Of Mtbcrp In Complex With Camp
pdb|3I59|B Chain B, Crystal Structure Of Mtbcrp In Complex With N6-Camp
Length = 249
Score = 30.0 bits (66), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 12/78 (15%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 269 DLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQSSQILH 328
+++ + +FQ ++ + + +++ + F +G + EG+P R+ ++ G ++ +
Sbjct: 28 EILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAP 87
Query: 329 NNIKS-CCMLGPGNFSGD 345
+ ++ ++GP + G+
Sbjct: 88 DGRENLLTIMGPSDMFGE 105
>pdb|3H3U|A Chain A, Crystal Structure Of Crp (Camp Receptor Protein) From
Mycoba Tuberculosis
pdb|3H3U|B Chain B, Crystal Structure Of Crp (Camp Receptor Protein) From
Mycoba Tuberculosis
Length = 224
Score = 29.6 bits (65), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 12/71 (16%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 276 LFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQSSQILHNNIKS-C 334
+FQ ++ + + +++ + F +G + EG+P R+ ++ G ++ + + ++
Sbjct: 10 IFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLL 69
Query: 335 CMLGPGNFSGD 345
++GP + G+
Sbjct: 70 TIMGPSDMFGE 80
>pdb|3MZH|A Chain A, Crystal Structure Of Camp Receptor Protein From
Mycobacterium Tuberculosis In Complex With Camp And Its
Dna Binding Element
pdb|3MZH|B Chain B, Crystal Structure Of Camp Receptor Protein From
Mycobacterium Tuberculosis In Complex With Camp And Its
Dna Binding Element
Length = 225
Score = 29.6 bits (65), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 12/71 (16%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 276 LFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQSSQILHNNIKS-C 334
+FQ ++ + + +++ + F +G + EG+P R+ ++ G ++ + + ++
Sbjct: 11 IFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLL 70
Query: 335 CMLGPGNFSGD 345
++GP + G+
Sbjct: 71 TIMGPSDMFGE 81
>pdb|3D0S|A Chain A, Camp Receptor Protein From M.Tuberculosis, Camp-Free Form
pdb|3D0S|B Chain B, Camp Receptor Protein From M.Tuberculosis, Camp-Free Form
pdb|4A2U|A Chain A, Crp(Cap) From Myco. Tuberculosis, With Camp
pdb|4A2U|B Chain B, Crp(Cap) From Myco. Tuberculosis, With Camp
pdb|4A2U|C Chain C, Crp(Cap) From Myco. Tuberculosis, With Camp
pdb|4A2U|D Chain D, Crp(Cap) From Myco. Tuberculosis, With Camp
pdb|4A2U|E Chain E, Crp(Cap) From Myco. Tuberculosis, With Camp
pdb|4A2U|F Chain F, Crp(Cap) From Myco. Tuberculosis, With Camp
pdb|4A2U|G Chain G, Crp(Cap) From Myco. Tuberculosis, With Camp
pdb|4A2U|H Chain H, Crp(Cap) From Myco. Tuberculosis, With Camp
Length = 227
Score = 29.6 bits (65), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 12/71 (16%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 276 LFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQSSQILHNNIKS-C 334
+FQ ++ + + +++ + F +G + EG+P R+ ++ G ++ + + ++
Sbjct: 13 IFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVKIGRRAPDGRENLL 72
Query: 335 CMLGPGNFSGD 345
++GP + G+
Sbjct: 73 TIMGPSDMFGE 83
>pdb|3OF1|A Chain A, Crystal Structure Of Bcy1, The Yeast Regulatory Subunit Of
Pka
Length = 246
Score = 29.6 bits (65), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 28/57 (49%)
Query: 269 DLVRQVPLFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHLQSSQ 325
DL++ +P+ + + + D + + I+ GE I +EGD + + G + S+
Sbjct: 125 DLLKSMPVLKSLTTYDRAKLADALDTKIYQPGETIIREGDQGENFYLIEYGAVDVSK 181
>pdb|3FHI|B Chain B, Crystal Structure Of A Complex Between The Catalytic And
Regulatory (Ri{alpha}) Subunits Of Pka
pdb|3IIA|A Chain A, Crystal Structure Of Apo (91-244) Ria Subunit Of
Camp-Dependent Protein Kinase
pdb|3PLQ|A Chain A, Crystal Structure Of Pka Type I Regulatory Subunit Bound
With Rp-8-Br- Camps
pdb|3PNA|A Chain A, Crystal Structure Of Camp Bound (91-244)ria Subunit Of
Camp-Dependent Protein Kinase
pdb|3PNA|B Chain B, Crystal Structure Of Camp Bound (91-244)ria Subunit Of
Camp-Dependent Protein Kinase
Length = 154
Score = 28.9 bits (63), Expect = 7.1, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 23/46 (50%)
Query: 276 LFQHMDDLVLENICDRVKSLIFTKGEVITKEGDPVQRMLFVVRGHL 321
LF H+DD +I D + + F GE + ++GD + +G +
Sbjct: 45 LFSHLDDNERSDIFDAMFPVSFIAGETVIQQGDEGDNFYVIDQGEM 90
>pdb|3KG2|A Chain A, Ampa Subtype Ionotropic Glutamate Receptor In Complex With
Competitive Antagonist Zk 200775
pdb|3KG2|B Chain B, Ampa Subtype Ionotropic Glutamate Receptor In Complex With
Competitive Antagonist Zk 200775
pdb|3KG2|C Chain C, Ampa Subtype Ionotropic Glutamate Receptor In Complex With
Competitive Antagonist Zk 200775
pdb|3KG2|D Chain D, Ampa Subtype Ionotropic Glutamate Receptor In Complex With
Competitive Antagonist Zk 200775
Length = 823
Score = 28.5 bits (62), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 14/72 (19%)
Query: 27 QNLSGYIFGTVWWGIVLNMIAYFVASHAAGACWYLLGIQRSAKCLREQCREMNGCDLRLL 86
++LSG I G VWW L +I+ + A+ AA L ++R + E + L
Sbjct: 585 RSLSGRIVGGVWWFFTLIIISSYTANLAA-----FLTVERMVSPI-ESAED--------L 630
Query: 87 SCKEPIYYGTTD 98
S + I YGT D
Sbjct: 631 SKQTEIAYGTLD 642
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.327 0.139 0.446
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,746,426
Number of Sequences: 62578
Number of extensions: 468613
Number of successful extensions: 1183
Number of sequences better than 100.0: 38
Number of HSP's better than 100.0 without gapping: 33
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1135
Number of HSP's gapped (non-prelim): 38
length of query: 473
length of database: 14,973,337
effective HSP length: 102
effective length of query: 371
effective length of database: 8,590,381
effective search space: 3187031351
effective search space used: 3187031351
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)