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= 008250
(572 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 = 233 bits (594), Expect = 2e-61, Method: Compositional matrix adjust.
Identities = 110/124 (88%), Positives = 119/124 (95%)
Query: 337 VRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGGR 396
VRRVPLFENMDERLLDAICERLKPCLFT+ +Y+VREGDPV+EMLFIIRGRLESVTTDGGR
Sbjct: 8 VRRVPLFENMDERLLDAICERLKPCLFTEKSYLVREGDPVNEMLFIIRGRLESVTTDGGR 67
Query: 397 SGFFNRGFLKEGDFCGEELLTWALDPKSGVNLPSSTRTVRALKEVEAFALMAEELKFVAS 456
SGF+NR LKEGDFCG+ELLTWALDPKSG NLPSSTRTV+AL EVEAFAL+A+ELKFVAS
Sbjct: 68 SGFYNRSLLKEGDFCGDELLTWALDPKSGSNLPSSTRTVKALTEVEAFALIADELKFVAS 127
Query: 457 QFRR 460
QFRR
Sbjct: 128 QFRR 131
>pdb|3OTF|A Chain A, Structural Basis For The Camp-Dependent Gating In Human
Hcn4 Channel
Length = 220
Score = 72.0 bits (175), Expect = 8e-13, Method: Compositional matrix adjust.
Identities = 45/138 (32%), Positives = 73/138 (52%), Gaps = 7/138 (5%)
Query: 276 KRRDSEQWMHHRLLPPDLRERVRRYDQYKWLETRGVDEENLVQSLPKDLRRDIKRHLCLA 335
K + EQ+M LPPD R+R+ Y ++++ + + DEE+++ L + LR +I C
Sbjct: 11 KYKQVEQYMSFHKLPPDTRQRIHDYYEHRY-QGKMFDEESILGELSEPLREEIINFNCRK 69
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV +PLF N D + ++ +L+ +F YI+REG +M FI G + SV T G
Sbjct: 70 LVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQHGVV-SVLTKGN 128
Query: 396 RSGFFNRGFLKEGDFCGE 413
+ L +G + GE
Sbjct: 129 KE-----TKLADGSYFGE 141
>pdb|4HBN|A Chain A, Crystal Structure Of The Human Hcn4 Channel C-terminus
Carrying The S672r Mutation
Length = 205
Score = 71.6 bits (174), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 45/138 (32%), Positives = 73/138 (52%), Gaps = 7/138 (5%)
Query: 276 KRRDSEQWMHHRLLPPDLRERVRRYDQYKWLETRGVDEENLVQSLPKDLRRDIKRHLCLA 335
K + EQ+M LPPD R+R+ Y ++++ + + DEE+++ L + LR +I C
Sbjct: 11 KYKQVEQYMSFHKLPPDTRQRIHDYYEHRY-QGKMFDEESILGELSEPLREEIINFNCRK 69
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV +PLF N D + ++ +L+ +F YI+REG +M FI G + SV T G
Sbjct: 70 LVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQHG-VVSVLTKGN 128
Query: 396 RSGFFNRGFLKEGDFCGE 413
+ L +G + GE
Sbjct: 129 KE-----TKLADGSYFGE 141
>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 = 68.9 bits (167), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 42/138 (30%), Positives = 68/138 (49%), Gaps = 7/138 (5%)
Query: 276 KRRDSEQWMHHRLLPPDLRERVRRYDQYKWLETRGVDEENLVQSLPKDLRRDIKRHLCLA 335
K + EQ+M LP D+R+++ Y ++++ + + DEEN++ L LR +I C
Sbjct: 17 KYKQVEQYMSFHKLPADMRQKIHDYYEHRY-QGKIFDEENILSELNDPLREEIVNFNCRK 75
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV +PLF N D + A+ +L+ +F YI+REG +M FI G +T
Sbjct: 76 LVATMPLFANADPNFVTAMLSKLRFEVFQPGDYIIREGAVGKKMYFIQHGVAGVITKSSK 135
Query: 396 RSGFFNRGFLKEGDFCGE 413
L +G + GE
Sbjct: 136 EMK------LTDGSYFGE 147
>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 = 68.6 bits (166), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 44/138 (31%), Positives = 71/138 (51%), Gaps = 7/138 (5%)
Query: 276 KRRDSEQWMHHRLLPPDLRERVRRYDQYKWLETRGVDEENLVQSLPKDLRRDIKRHLCLA 335
K + EQ+M LP D R+++ Y ++++ + + DE++++ L LR +I C
Sbjct: 14 KYKQVEQYMSFHKLPADFRQKIHDYYEHRY-QGKMFDEDSILGELNGPLREEIVNFNCRK 72
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV +PLF N D + A+ +LK +F YI+REG +M FI G + SV T G
Sbjct: 73 LVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHG-VVSVLTKGN 131
Query: 396 RSGFFNRGFLKEGDFCGE 413
+ L +G + GE
Sbjct: 132 KE-----MKLSDGSYFGE 144
>pdb|3U10|A Chain A, Tetramerization Dynamics Of The C-Terminus Underlies
Isoform-Specific Camp-Gating In Hcn Channels
Length = 210
Score = 68.6 bits (166), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 44/138 (31%), Positives = 71/138 (51%), Gaps = 7/138 (5%)
Query: 276 KRRDSEQWMHHRLLPPDLRERVRRYDQYKWLETRGVDEENLVQSLPKDLRRDIKRHLCLA 335
K + EQ+M LP D R+++ Y ++++ + + DE++++ L LR +I C
Sbjct: 17 KYKQVEQYMSFHKLPADFRQKIHDYYEHRY-QGKMFDEDSILGELNGPLREEIVNFNCRK 75
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV +PLF N D + A+ +LK +F YI+REG +M FI G + SV T G
Sbjct: 76 LVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHG-VVSVLTKGN 134
Query: 396 RSGFFNRGFLKEGDFCGE 413
+ L +G + GE
Sbjct: 135 KE-----MKLSDGSYFGE 147
>pdb|3FFQ|A Chain A, Hcn2i 443-640 Apo-State
pdb|3FFQ|B Chain B, Hcn2i 443-640 Apo-State
Length = 202
Score = 68.2 bits (165), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 44/138 (31%), Positives = 71/138 (51%), Gaps = 7/138 (5%)
Query: 276 KRRDSEQWMHHRLLPPDLRERVRRYDQYKWLETRGVDEENLVQSLPKDLRRDIKRHLCLA 335
K + EQ+M LP D R+++ Y ++++ + + DE++++ L LR +I C
Sbjct: 14 KYKQVEQYMSFHKLPADFRQKIHDYYEHRY-QGKMFDEDSILGELNGPLREEIVNFNCRK 72
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV +PLF N D + A+ +LK +F YI+REG +M FI G + SV T G
Sbjct: 73 LVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHG-VVSVLTKGN 131
Query: 396 RSGFFNRGFLKEGDFCGE 413
+ L +G + GE
Sbjct: 132 KE-----MKLSDGSYFGE 144
>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 = 67.8 bits (164), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 44/138 (31%), Positives = 71/138 (51%), Gaps = 7/138 (5%)
Query: 276 KRRDSEQWMHHRLLPPDLRERVRRYDQYKWLETRGVDEENLVQSLPKDLRRDIKRHLCLA 335
K + EQ+M LP D R+++ Y ++++ + + DE++++ L LR +I C
Sbjct: 12 KYKQVEQYMSFHKLPADFRQKIHDYYEHRY-QGKMFDEDSILGELNGPLREEIVNFNCRK 70
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV +PLF N D + A+ +LK +F YI+REG +M FI G + SV T G
Sbjct: 71 LVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHG-VVSVLTKGN 129
Query: 396 RSGFFNRGFLKEGDFCGE 413
+ L +G + GE
Sbjct: 130 KE-----MKLSDGSYFGE 142
>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 = 67.8 bits (164), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 44/138 (31%), Positives = 72/138 (52%), Gaps = 7/138 (5%)
Query: 276 KRRDSEQWMHHRLLPPDLRERVRRYDQYKWLETRGVDEENLVQSLPKDLRRDIKRHLCLA 335
K + EQ+M LPPD R+R+ Y ++++ + + DEE+++ L + LR +I
Sbjct: 17 KYKQVEQYMSFHKLPPDTRQRIHDYYEHRY-QGKMFDEESILGELSEPLREEIINFNXRK 75
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV +PLF N D + ++ +L+ +F YI+REG +M FI G + SV T G
Sbjct: 76 LVASMPLFANADPNFVTSMLTKLRFEVFQPGDYIIREGTIGKKMYFIQHG-VVSVLTKGN 134
Query: 396 RSGFFNRGFLKEGDFCGE 413
+ L +G + GE
Sbjct: 135 KE-----TKLADGSYFGE 147
>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 = 67.8 bits (164), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 44/138 (31%), Positives = 70/138 (50%), Gaps = 7/138 (5%)
Query: 276 KRRDSEQWMHHRLLPPDLRERVRRYDQYKWLETRGVDEENLVQSLPKDLRRDIKRHLCLA 335
K + EQ+M LP D R+++ Y ++++ + + DE++++ L LR I C
Sbjct: 14 KYKQVEQYMSFHKLPADFRQKIHDYYEHRY-QGKMFDEDSILGELNGPLREKIVNFNCRK 72
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV +PLF N D + A+ +LK +F YI+REG +M FI G + SV T G
Sbjct: 73 LVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHG-VVSVLTKGN 131
Query: 396 RSGFFNRGFLKEGDFCGE 413
+ L +G + GE
Sbjct: 132 KE-----MKLSDGSYFGE 144
>pdb|2PTM|A Chain A, Structure And Rearrangements In The Carboxy-Terminal
Region Of Spih Channels
Length = 198
Score = 67.0 bits (162), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 34/123 (27%), Positives = 67/123 (54%), Gaps = 1/123 (0%)
Query: 272 EMRIKRRDSEQWMHHRLLPPDLRERVRRYDQYKWLETRGVDEENLVQSLPKDLRRDIKRH 331
+ R K + E++M +R LP LR ++ Y +Y++ + DE ++ + + + +R+D+ +
Sbjct: 9 QYREKLKQVEEYMQYRKLPSHLRNKILDYYEYRY-RGKMFDERHIFREVSESIRQDVANY 67
Query: 332 LCLALVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVT 391
C LV VP F D + + L+ +F + Y+++EG D M FI +G ++ +
Sbjct: 68 NCRDLVASVPFFVGADSNFVTRVVTLLEFEVFQPADYVIQEGTFGDRMFFIQQGIVDIIM 127
Query: 392 TDG 394
+DG
Sbjct: 128 SDG 130
>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 = 64.7 bits (156), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 46/143 (32%), Positives = 73/143 (51%), Gaps = 8/143 (5%)
Query: 276 KRRDSEQWMHHRLLPPDLRERVRRYDQYKWLETRGVDEENLVQSLPKDLRRDIKRHLCLA 335
K + EQ+M LP D R+++ Y ++++ + + DE++++ L LR +I
Sbjct: 16 KYKQVEQYMSFHKLPADFRQKIHDYYEHRY-QGKMFDEDSILGELNGPLREEIVNFNNRK 74
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV +PLF N D + A+ +LK +F YI+REG +M FI G + SV T G
Sbjct: 75 LVASMPLFANADPNFVTAMLTKLKFEVFQPGDYIIREGTIGKKMYFIQHG-VVSVLTKGN 133
Query: 396 RSGFFNRGFLKEGDFCGE-ELLT 417
+ L +G + GE LLT
Sbjct: 134 KE-----MKLSDGSYFGEISLLT 151
>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 = 62.4 bits (150), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 42/138 (30%), Positives = 67/138 (48%), Gaps = 7/138 (5%)
Query: 276 KRRDSEQWMHHRLLPPDLRERVRRYDQYKWLETRGVDEENLVQSLPKDLRRDIKRHLCLA 335
K + EQ+ LP D R+++ Y ++++ + + DE++++ L LR +I C
Sbjct: 14 KYKQVEQYXSFHKLPADFRQKIHDYYEHRY-QGKXFDEDSILGELNGPLREEIVNFNCRK 72
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV PLF N D + A +LK +F YI+REG + FI G + SV T G
Sbjct: 73 LVASXPLFANADPNFVTAXLTKLKFEVFQPGDYIIREGTIGKKXYFIQHG-VVSVLTKGN 131
Query: 396 RSGFFNRGFLKEGDFCGE 413
+ L +G + GE
Sbjct: 132 KE-----XKLSDGSYFGE 144
>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 = 57.8 bits (138), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 42/172 (24%), Positives = 80/172 (46%), Gaps = 13/172 (7%)
Query: 276 KRRDSEQWMHHRLLPPDLRERVRRYDQYKWLETRGVDEENLVQSLPKDLRRDIKRHLCLA 335
+ +D + ++ LP L +R+ Q W G+D L++ P +LR DI HL
Sbjct: 17 RTKDLKDFIRVHRLPKALAQRMLECFQTTWSVNNGIDVSELLKDFPDELRADIAMHLNKE 76
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
L+ ++PLFE+ L ++ +K +++R+GD + + F+ G +E + +
Sbjct: 77 LL-QLPLFESASRGCLRSLSLIIKTSFCAPGEFLIRQGDALQAIYFVCSGSMEVLKDNTV 135
Query: 396 RSGFFNRGFLKEGDFCGEELLTWALDPKSGVNLPSSTR------TVRALKEV 441
+ L +GD G + LT K+ N+ + T +++ L+EV
Sbjct: 136 LA------ILGKGDLIGSDSLTKEQVIKTNANVKALTYCDLQYISLKGLREV 181
>pdb|4F8A|A Chain A, Cyclic Nucleotide Binding-Homology Domain From Mouse Eag1
Potassium Channel
Length = 160
Score = 43.5 bits (101), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 42/100 (42%), Gaps = 5/100 (5%)
Query: 314 ENLVQSLPKDLRRDIKRHLCLALVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREG 373
E ++Q PKD+R DI HL + + P F + L A+ + I G
Sbjct: 6 EKVLQICPKDMRADICVHLNRKVFKEHPAFRLASDGCLRALAMEFQTVHCAPGDLIYHAG 65
Query: 374 DPVDEMLFIIRGRLESVTTDG-----GRSGFFNRGFLKEG 408
+ VD + F++ G LE + D G+ F F KE
Sbjct: 66 ESVDSLCFVVSGSLEVIQDDEVVAILGKGDVFGDVFWKEA 105
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 33/125 (26%), Positives = 53/125 (42%), Gaps = 10/125 (8%)
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV VPLF+ + +L I L+ I R G+P D M F++ G + T
Sbjct: 229 LVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATP--- 285
Query: 396 RSGFFNRGFLKEGDFCGEELLTWALDPKSGVNLPSSTRTVRALKEVEAFALMAEELKFVA 455
N L G F GE L +P+S ++T ++ +L + F ++ +A
Sbjct: 286 -----NPVELGPGAFFGEMALISG-EPRSATVSAATTVSLLSLHSAD-FQMLCSSSPEIA 338
Query: 456 SQFRR 460
FR+
Sbjct: 339 EIFRK 343
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 40/87 (45%), Gaps = 4/87 (4%)
Query: 329 KRHLCLALVRRVPLFENMD--ERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGR 386
KR + + +V + E++D ERL + + L+P F D IV +G+P DE I+ G
Sbjct: 147 KRKMYEEFLSKVSILESLDKWERL--TVADALEPVQFEDGQKIVVQGEPGDEFFIILEGS 204
Query: 387 LESVTTDGGRSGFFNRGFLKEGDFCGE 413
+ F G L D+ GE
Sbjct: 205 AAVLQRRSENEEFVEVGRLGPSDYFGE 231
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 40/87 (45%), Gaps = 4/87 (4%)
Query: 329 KRHLCLALVRRVPLFENMD--ERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGR 386
KR + + +V + E++D ERL + + L+P F D IV +G+P DE I+ G
Sbjct: 149 KRKMYEEFLSKVSILESLDKWERL--TVADALEPVQFEDGQKIVVQGEPGDEFFIILEGS 206
Query: 387 LESVTTDGGRSGFFNRGFLKEGDFCGE 413
+ F G L D+ GE
Sbjct: 207 AAVLQRRSENEEFVEVGRLGPSDYFGE 233
>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 = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 40/87 (45%), Gaps = 4/87 (4%)
Query: 329 KRHLCLALVRRVPLFENMD--ERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGR 386
KR + + +V + E++D ERL + + L+P F D IV +G+P DE I+ G
Sbjct: 151 KRKMYEEFLSKVSILESLDKWERL--TVADALEPVQFEDGQKIVVQGEPGDEFFIILEGS 208
Query: 387 LESVTTDGGRSGFFNRGFLKEGDFCGE 413
+ F G L D+ GE
Sbjct: 209 AAVLQRRSENEEFVEVGRLGPSDYFGE 235
>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 = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 39/147 (26%), Positives = 58/147 (39%), Gaps = 22/147 (14%)
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV VPLF+ + +L I L+ I R G+P D M F++ G + T
Sbjct: 16 LVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATP--- 72
Query: 396 RSGFFNRGFLKEGDFCGEELLTWALDPKSGVNLPSSTRTVRALKEVEAFALMAEELKFVA 455
N L G F GE L +P+S TV A V +L + + + +
Sbjct: 73 -----NPVELGPGAFFGEMALISG-EPRSA--------TVSAATTVSLLSLHSADFQMLC 118
Query: 456 SQFRRLHSRQVQHTFRFYSQQWRTWAA 482
S S ++ FR + + R AA
Sbjct: 119 SS-----SPEIAEIFRKTALERRGAAA 140
>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 = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 39/147 (26%), Positives = 58/147 (39%), Gaps = 22/147 (14%)
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV VPLF+ + +L I L+ I R G+P D M F++ G + T
Sbjct: 14 LVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATP--- 70
Query: 396 RSGFFNRGFLKEGDFCGEELLTWALDPKSGVNLPSSTRTVRALKEVEAFALMAEELKFVA 455
N L G F GE L +P+S TV A V +L + + + +
Sbjct: 71 -----NPVELGPGAFFGEMALISG-EPRSA--------TVSAATTVSLLSLHSADFQMLC 116
Query: 456 SQFRRLHSRQVQHTFRFYSQQWRTWAA 482
S S ++ FR + + R AA
Sbjct: 117 SS-----SPEIAEIFRKTALERRGAAA 138
>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 = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 33/77 (42%), Gaps = 3/77 (3%)
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDG- 394
LV VPLF+ + +L I L+ I R G+P D M F++ G + T +
Sbjct: 14 LVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATPNPV 73
Query: 395 --GRSGFFNRGFLKEGD 409
G FF L G+
Sbjct: 74 ELGPGAFFGEMALISGE 90
>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 = 37.7 bits (86), Expect = 0.015, Method: Composition-based stats.
Identities = 33/125 (26%), Positives = 54/125 (43%), Gaps = 10/125 (8%)
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV VPLF+ + +L I L+ I R G+P D M F++ G + T
Sbjct: 12 LVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATP--- 68
Query: 396 RSGFFNRGFLKEGDFCGEELLTWALDPKSGVNLPSSTRTVRALKEVEAFALMAEELKFVA 455
N L G F GE L + +P+S ++T ++ +L + F ++ +A
Sbjct: 69 -----NPVELGPGAFFGEMALI-SGEPRSATVSAATTVSLLSLHSAD-FQMLCSSSPEIA 121
Query: 456 SQFRR 460
FR+
Sbjct: 122 EIFRK 126
>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 = 37.7 bits (86), Expect = 0.016, Method: Composition-based stats.
Identities = 33/125 (26%), Positives = 54/125 (43%), Gaps = 10/125 (8%)
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV VPLF+ + +L I L+ I R G+P D M F++ G + T
Sbjct: 12 LVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATP--- 68
Query: 396 RSGFFNRGFLKEGDFCGEELLTWALDPKSGVNLPSSTRTVRALKEVEAFALMAEELKFVA 455
N L G F GE L + +P+S ++T ++ +L + F ++ +A
Sbjct: 69 -----NPVELGPGAFFGEMALI-SGEPRSATVSAATTVSLLSLHSAD-FQMLCSSSPEIA 121
Query: 456 SQFRR 460
FR+
Sbjct: 122 EIFRK 126
>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 = 37.4 bits (85), Expect = 0.022, Method: Composition-based stats.
Identities = 33/125 (26%), Positives = 54/125 (43%), Gaps = 10/125 (8%)
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLESVTTDGG 395
LV VPLF+ + +L I L+ I R G+P D M F++ G + T
Sbjct: 14 LVAAVPLFQKLGPAVLVEIVRALRARTVPAGAVICRIGEPGDRMFFVVEGSVSVATP--- 70
Query: 396 RSGFFNRGFLKEGDFCGEELLTWALDPKSGVNLPSSTRTVRALKEVEAFALMAEELKFVA 455
N L G F GE L + +P+S ++T ++ +L + F ++ +A
Sbjct: 71 -----NPVELGPGAFFGEMALI-SGEPESATVSAATTVSLLSLHSAD-FQMLCSSSPEIA 123
Query: 456 SQFRR 460
FR+
Sbjct: 124 EIFRK 128
>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 = 35.8 bits (81), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 42/89 (47%)
Query: 328 IKRHLCLALVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRL 387
IK + ++ VP F+++ E +L + + L+ + + YI+R+G D I +G++
Sbjct: 150 IKHTEYMEFLKSVPTFQSLPEEILSKLADVLEETHYENGEYIIRQGARGDTFFIISKGKV 209
Query: 388 ESVTTDGGRSGFFNRGFLKEGDFCGEELL 416
D L +GD+ GE+ L
Sbjct: 210 NVTREDSPNEDPVFLRTLGKGDWFGEKAL 238
>pdb|4DIN|B Chain B, Novel Localization And Quaternary Structure Of The Pka Ri
Beta Holoenzyme
Length = 381
Score = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 39/87 (44%), Gaps = 4/87 (4%)
Query: 329 KRHLCLALVRRVPLFENMD--ERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGR 386
KR + + +V + E+++ ERL + + L+P F D IV +G+P D+ I G
Sbjct: 242 KRKMYEEFLSKVSILESLEKWERL--TVADALEPVQFEDGEKIVVQGEPGDDFYIITEGT 299
Query: 387 LESVTTDGGRSGFFNRGFLKEGDFCGE 413
+ + G L D+ GE
Sbjct: 300 ASVLQRRSPNEEYVEVGRLGPSDYFGE 326
>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 = 33.1 bits (74), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 30/53 (56%)
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLE 388
++ R +F+ ++ + A+ ++L+P F + EG+P D + II G+++
Sbjct: 7 ILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVK 59
>pdb|3I59|A Chain A, Crystal Structure Of Mtbcrp In Complex With N6-Camp
Length = 249
Score = 33.1 bits (74), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 30/53 (56%)
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLE 388
++ R +F+ ++ + A+ ++L+P F + EG+P D + II G+++
Sbjct: 29 ILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVK 81
>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 = 33.1 bits (74), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 30/53 (56%)
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLE 388
++ R +F+ ++ + A+ ++L+P F + EG+P D + II G+++
Sbjct: 29 ILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVK 81
>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 = 32.7 bits (73), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 30/53 (56%)
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLE 388
++ R +F+ ++ + A+ ++L+P F + EG+P D + II G+++
Sbjct: 5 ILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVK 57
>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 = 32.7 bits (73), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 30/53 (56%)
Query: 336 LVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVREGDPVDEMLFIIRGRLE 388
++ R +F+ ++ + A+ ++L+P F + EG+P D + II G+++
Sbjct: 4 ILARAGIFQGVEPSAIAALTKQLQPVDFPRGHTVFAEGEPGDRLYIIISGKVK 56
>pdb|3CEG|A Chain A, Crystal Structure Of The Ubc Domain Of Baculoviral Iap
Repeat- Containing Protein 6
pdb|3CEG|B Chain B, Crystal Structure Of The Ubc Domain Of Baculoviral Iap
Repeat- Containing Protein 6
Length = 323
Score = 32.0 bits (71), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 387 LESVTTDGGRSGFFNRGFLKEGDFCGEELLTWALDPKSGVNLPSSTRTVRALKEVEAFAL 446
L ++ T GG S FN +G C L TW P+ N P ++ ++ L V++ L
Sbjct: 145 LVNLETTGGHSVRFNPNLYNDGKVCLSILNTWHGRPEEKWN-PQTSSFLQVLVSVQSLIL 203
Query: 447 MAE 449
+AE
Sbjct: 204 VAE 206
>pdb|2OZ6|A Chain A, Crystal Structure Of Virulence Factor Regulator From
Pseudomonas Aeruginosa In Complex With Camp
Length = 207
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 363 FTDSTYIVREGDPVDEMLFIIRGRLES-VTTDGGRSGFFNRGFLKEGDFCGE 413
+T + I+ GD + + FII+G + + D GR G+L GDF GE
Sbjct: 18 YTAKSTIIYAGDRCETLFFIIKGSVTILIEDDDGREMII--GYLNSGDFFGE 67
>pdb|3IDB|B Chain B, Crystal Structure Of (108-268)riib:c Holoenzyme Of Camp-
Dependent Protein Kinase
Length = 161
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 46/100 (46%), Gaps = 4/100 (4%)
Query: 312 DEENLVQSLPKDLRRDIKRHLCLALVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVR 371
+EE+ +S + D +R+ + + LF+N+D + + + + L + +++
Sbjct: 15 EEEDDAESRIIHPKTDDQRNRLQEACKDILLFKNLDPEQMSQVLDAMFEKLVKEGEHVID 74
Query: 372 EGDPVDEMLFIIRGRLE-SVTTDG-GR--SGFFNRGFLKE 407
+GD D I RG + V DG GR + NRG E
Sbjct: 75 QGDDGDNFYVIDRGTFDIYVKCDGVGRCVGNYDNRGSFGE 114
>pdb|3TNP|B Chain B, Structure And Allostery Of The Pka Riib Tetrameric
Holoenzyme
pdb|3TNP|E Chain E, Structure And Allostery Of The Pka Riib Tetrameric
Holoenzyme
Length = 416
Score = 30.8 bits (68), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 46/100 (46%), Gaps = 4/100 (4%)
Query: 312 DEENLVQSLPKDLRRDIKRHLCLALVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVR 371
+EE+ +S + D +R+ + + LF+N+D + + + + L + +++
Sbjct: 122 EEEDDAESRIIHPKTDDQRNRLQEACKDILLFKNLDPEQMSQVLDAMFEKLVKEGEHVID 181
Query: 372 EGDPVDEMLFIIRGRLE-SVTTDG-GR--SGFFNRGFLKE 407
+GD D I RG + V DG GR + NRG E
Sbjct: 182 QGDDGDNFYVIDRGTFDIYVKCDGVGRCVGNYDNRGSFGE 221
>pdb|3IDC|B Chain B, Crystal Structure Of (102-265)riib:c Holoenzyme Of Camp-
Dependent Protein Kinase
Length = 164
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 46/100 (46%), Gaps = 4/100 (4%)
Query: 312 DEENLVQSLPKDLRRDIKRHLCLALVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVR 371
+EE+ +S + D +R+ + + LF+N+D + + + + L + +++
Sbjct: 21 EEEDDAESRIIHPKTDDQRNRLQEACKDILLFKNLDPEQMSQVLDAMFEKLVKEGEHVID 80
Query: 372 EGDPVDEMLFIIRGRLE-SVTTDG-GR--SGFFNRGFLKE 407
+GD D I RG + V DG GR + NRG E
Sbjct: 81 QGDDGDNFYVIDRGTFDIYVKCDGVGRCVGNYDNRGSFGE 120
>pdb|3TNQ|A Chain A, Structure And Allostery Of The Pka Riib Tetrameric
Holoenzyme
Length = 416
Score = 30.8 bits (68), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 46/100 (46%), Gaps = 4/100 (4%)
Query: 312 DEENLVQSLPKDLRRDIKRHLCLALVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVR 371
+EE+ +S + D +R+ + + LF+N+D + + + + L + +++
Sbjct: 122 EEEDDAESRIIHPKTDDQRNRLQEACKDILLFKNLDPEQMSQVLDAMFEKLVKEGEHVID 181
Query: 372 EGDPVDEMLFIIRGRLE-SVTTDG-GR--SGFFNRGFLKE 407
+GD D I RG + V DG GR + NRG E
Sbjct: 182 QGDDGDNFYVIDRGTFDIYVKCDGVGRCVGNYDNRGSFGE 221
>pdb|1CX4|A Chain A, Crystal Structure Of A Deletion Mutant Of The Type Ii Beta
Regulatory Subunit Of Camp-Dependent Protein Kinase
Length = 305
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 25/100 (25%), Positives = 46/100 (46%), Gaps = 4/100 (4%)
Query: 312 DEENLVQSLPKDLRRDIKRHLCLALVRRVPLFENMDERLLDAICERLKPCLFTDSTYIVR 371
+EE+ +S + D +R+ + + LF+N+D + + + + L + +++
Sbjct: 11 EEEDDAESRIIHPKTDDQRNRLQEACKDILLFKNLDPEQMSQVLDAMFEKLVKEGEHVID 70
Query: 372 EGDPVDEMLFIIRGRLE-SVTTDG-GR--SGFFNRGFLKE 407
+GD D I RG + V DG GR + NRG E
Sbjct: 71 QGDDGDNFYVIDRGTFDIYVKCDGVGRCVGNYDNRGSFGE 110
>pdb|2NN6|D Chain D, Structure Of The Human Rna Exosome Composed Of Rrp41,
Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
Length = 237
Score = 28.9 bits (63), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 27/97 (27%), Positives = 40/97 (41%), Gaps = 26/97 (26%)
Query: 410 FCGEELLTWALDPKSGVNLPSSTRTVRALKEVEAFALMAEELKFVASQFRRLHS------ 463
FCG + ALD + L +++ + + V FAL + E K + S + L+S
Sbjct: 154 FCG---VACALDSDGTLVLDPTSKQEKEARAVLTFALDSVERKLLMSSTKGLYSDTELQQ 210
Query: 464 ------RQVQHTFRFYSQQWRTWAACFIQAAWRRYSK 494
QH FRFY + + RRYSK
Sbjct: 211 CLAAAQAASQHVFRFYRESLQ-----------RRYSK 236
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
0.325 0.137 0.430
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,077,149
Number of Sequences: 62578
Number of extensions: 569057
Number of successful extensions: 1671
Number of sequences better than 100.0: 41
Number of HSP's better than 100.0 without gapping: 37
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1614
Number of HSP's gapped (non-prelim): 48
length of query: 572
length of database: 14,973,337
effective HSP length: 104
effective length of query: 468
effective length of database: 8,465,225
effective search space: 3961725300
effective search space used: 3961725300
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)