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= psy12306
(1643 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3OXQ|E Chain E, Crystal Structure Of Ca2+CAM-Cav1.2 Pre-IqIQ DOMAIN COMPLEX
pdb|3OXQ|F Chain F, Crystal Structure Of Ca2+CAM-Cav1.2 Pre-IqIQ DOMAIN COMPLEX
Length = 78
Score = 131 bits (330), Expect = 3e-30, Method: Composition-based stats.
Identities = 62/79 (78%), Positives = 73/79 (92%), Gaps = 1/79 (1%)
Query: 1251 ATLFAVVRTSLRIKTEGNIDDANAELRAVIKKIWKRTSNELLNQVVPPPGGEEEVTVGKF 1310
TLFA+VRT+LRIKTEGN++ AN ELRA+IKKIWKRTS +LL+QVV PP G++EVTVGKF
Sbjct: 1 GTLFALVRTALRIKTEGNLEQANEELRAIIKKIWKRTSMKLLDQVV-PPAGDDEVTVGKF 59
Query: 1311 YATFLIQDYFRRFKKRKEQ 1329
YATFLIQ+YFR+FKKRKEQ
Sbjct: 60 YATFLIQEYFRKFKKRKEQ 78
Score = 60.1 bits (144), Expect = 1e-08, Method: Composition-based stats.
Identities = 29/51 (56%), Positives = 36/51 (70%), Gaps = 11/51 (21%)
Query: 1459 VTLLRKISPPLGFGKLCPHRVACEEEVTVGKFYATFLIQDYFRRFKKRKEQ 1509
+ LL ++ PP G ++EVTVGKFYATFLIQ+YFR+FKKRKEQ
Sbjct: 39 MKLLDQVVPPAG-----------DDEVTVGKFYATFLIQEYFRKFKKRKEQ 78
>pdb|3G43|E Chain E, Crystal Structure Of The Calmodulin-Bound Cav1.2 C-Terminal
Regulatory Domain Dimer
pdb|3G43|F Chain F, Crystal Structure Of The Calmodulin-Bound Cav1.2 C-Terminal
Regulatory Domain Dimer
Length = 81
Score = 127 bits (320), Expect = 4e-29, Method: Composition-based stats.
Identities = 59/78 (75%), Positives = 73/78 (93%), Gaps = 1/78 (1%)
Query: 1251 ATLFAVVRTSLRIKTEGNIDDANAELRAVIKKIWKRTSNELLNQVVPPPGGEEEVTVGKF 1310
+TLFA+VRT+LRIKTEGN++ AN ELRA+IKKIWKRTS +LL+QVV PP G++EVTVGKF
Sbjct: 5 STLFALVRTALRIKTEGNLEQANEELRAIIKKIWKRTSMKLLDQVV-PPAGDDEVTVGKF 63
Query: 1311 YATFLIQDYFRRFKKRKE 1328
YATFLIQ+YFR+FKKR++
Sbjct: 64 YATFLIQEYFRKFKKREQ 81
Score = 55.5 bits (132), Expect = 3e-07, Method: Composition-based stats.
Identities = 26/50 (52%), Positives = 35/50 (70%), Gaps = 11/50 (22%)
Query: 1459 VTLLRKISPPLGFGKLCPHRVACEEEVTVGKFYATFLIQDYFRRFKKRKE 1508
+ LL ++ PP G ++EVTVGKFYATFLIQ+YFR+FKKR++
Sbjct: 43 MKLLDQVVPPAG-----------DDEVTVGKFYATFLIQEYFRKFKKREQ 81
>pdb|4DEY|B Chain B, Crystal Structure Of The Voltage Dependent Calcium Channel
Beta-2 Subunit In Complex With The Cav1.2 I-Ii Linker
Length = 106
Score = 105 bits (263), Expect = 1e-22, Method: Composition-based stats.
Identities = 56/84 (66%), Positives = 65/84 (77%), Gaps = 7/84 (8%)
Query: 154 SGEFSKEREKAKARGDFHKLREKQQIEEDLRGYLDWITQAEDIEPEGEERANHHDQ-KNK 212
SGEFSKEREKAKARGDF KLREKQQ+EEDL+GYLDWITQAEDI+PE E+ ++ +N
Sbjct: 2 SGEFSKEREKAKARGDFQKLREKQQLEEDLKGYLDWITQAEDIDPENEDEGMDEEKPRNM 61
Query: 213 S--SSETESADRLE---GD-EGEN 230
S +SETES + GD EGEN
Sbjct: 62 SMPTSETESVNTENVAGGDIEGEN 85
>pdb|4DXW|A Chain A, Crystal Structure Of Navrh, A Voltage-Gated Sodium Channel
pdb|4DXW|B Chain B, Crystal Structure Of Navrh, A Voltage-Gated Sodium Channel
pdb|4DXW|C Chain C, Crystal Structure Of Navrh, A Voltage-Gated Sodium Channel
pdb|4DXW|D Chain D, Crystal Structure Of Navrh, A Voltage-Gated Sodium Channel
Length = 229
Score = 62.4 bits (150), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 57/264 (21%), Positives = 121/264 (45%), Gaps = 54/264 (20%)
Query: 906 SQYFEYTIFCLIMINTLTLAMKFYRQPLFYADILDKMNMFFTTVFALEFVFKLAAFRFK- 964
++ F++T+ +I++N + + Y + + + ++ T F +E + + + K
Sbjct: 11 NRIFQFTVVSIIILNAVLIGATTYELDPLFLETIHLLDYGITIFFVIEILIRFIGEKQKA 70
Query: 965 NYFSDAWNVFDFVIVMGSFIDIFSDSPPHAAAKATIPGSHEQTSGRLSINFFRLFRVMRL 1024
++F WN+FD VIV S I I ++S S RL R+ R+
Sbjct: 71 DFFKSGWNIFDTVIVAISLIPIPNNS---------------------SFLVLRLLRIFRV 109
Query: 1025 IKLLSRGEGIRTLLWTFIKSFQALPYVALLIVMLFFIYAVIGMQVFGKIALVFGGGIHRN 1084
++L+S ++ ++ ++S + + +V+LL+ ++ +IYA +G +FG
Sbjct: 110 LRLISVIPELKQIIEAILESVRRVFFVSLLLFIILYIYATMGAILFGN---------DDP 160
Query: 1085 NNFQTFPQAVLVLFRSATGEAWQDIMLDCSNRPSEVKCDAASDGNPTNDDNVSCGSDIAY 1144
+ + +++ LF+ T +W+ +ML P + + S +
Sbjct: 161 SRWGDLGISLITLFQVLTLSSWETVML------------------PMQE--IYWWS---W 197
Query: 1145 PYFISFYVLCSFLIINLFVAVIMD 1168
YF SF ++CS I+NL +A+++D
Sbjct: 198 VYFFSFIIICSITILNLVIAILVD 221
Score = 44.7 bits (104), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 40/65 (61%), Gaps = 2/65 (3%)
Query: 89 NNGITNFDNFGLAMLTVFQCITLEGWTDVLYNIEDALGRTWQWTYFVSMVILGAFFVMNL 148
N+ + + + G++++T+FQ +TL W V+ +++ W W YF S +I+ + ++NL
Sbjct: 157 NDDPSRWGDLGISLITLFQVLTLSSWETVMLPMQEIYW--WSWVYFFSFIIICSITILNL 214
Query: 149 ILGVL 153
++ +L
Sbjct: 215 VIAIL 219
>pdb|4DEX|B Chain B, Crystal Structure Of The Voltage Dependent Calcium Channel
Beta-2 Subunit In Complex With The Cav2.2 I-Ii Linker
Length = 113
Score = 61.2 bits (147), Expect = 4e-09, Method: Composition-based stats.
Identities = 29/81 (35%), Positives = 50/81 (61%), Gaps = 5/81 (6%)
Query: 156 EFSKEREKAKARGDFHKLREKQQIEEDLRGYLDWITQAEDI-----EPEGEERANHHDQK 210
EF+KERE+ + R F KLR +QQIE +L GYL+WI +AE++ + EE++
Sbjct: 3 EFAKERERVENRRAFLKLRRQQQIERELNGYLEWIFKAEEVMLAEEDKNAEEKSPLDAVL 62
Query: 211 NKSSSETESADRLEGDEGENQ 231
+++++ D + +EGE++
Sbjct: 63 KRAATKKSRNDLIHAEEGEDR 83
>pdb|3RVY|A Chain A, Crystal Structure Of The Navab Voltage-Gated Sodium Channel
(Ile217cys, 2.7 A)
pdb|3RVY|B Chain B, Crystal Structure Of The Navab Voltage-Gated Sodium Channel
(Ile217cys, 2.7 A)
pdb|3RVZ|A Chain A, Crystal Structure Of The Navab Voltage-Gated Sodium Channel
(Ile217cys, 2.8 A)
pdb|3RVZ|B Chain B, Crystal Structure Of The Navab Voltage-Gated Sodium Channel
(Ile217cys, 2.8 A)
Length = 285
Score = 60.1 bits (144), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 70/306 (22%), Positives = 129/306 (42%), Gaps = 74/306 (24%)
Query: 891 IPKQRLQY-KIWWFVTSQYFEYTIFCLIMINTLTLAMK----FYRQPLFYADILDKMNMF 945
+P+ Y +I V S +F I LI++N +T+ ++ F + Y + +++ +
Sbjct: 13 VPRGSHMYLRITNIVESSFFTKFIIYLIVLNGITMGLETSKTFMQSFGVYTTLFNQIVI- 71
Query: 946 FTTVFALEFVFKLAAFRFKNYFSDAWNVFDFVIVMGSFIDIFSDSPPHAAAKATIPGSHE 1005
T+F +E + ++ R ++F D W++FDF +V A + +P S
Sbjct: 72 --TIFTIEIILRIYVHRI-SFFKDPWSLFDFFVV----------------AISLVPTS-- 110
Query: 1006 QTSGRLSINFFRLFRVMRLIKLLSRGEGIRTLLWTFIKSFQALPYVALLIVMLFFIYAVI 1065
SG R+ RV+RL +L++ +R ++ I + V L+ + F+I+A++
Sbjct: 111 --SG---FEILRVLRVLRLFRLVTAVPQMRKIVSALISVIPGMLSVIALMTLFFYIFAIM 165
Query: 1066 GMQVFGKIALVFGGGIHRNNNFQTFPQAVLVLFRSATGEAWQDIMLDCSNRPSEVKCDAA 1125
Q+FG+ F T ++ LF+ T E+W +
Sbjct: 166 ATQLFGE---------RFPEWFGTLGESFYTLFQVMTLESW-----------------SM 199
Query: 1126 SDGNPTNDDNVSCGSDIAYPY----FISFYVLCSFLIINLFVAVIMDNFDYLTRDWSILG 1181
P + YPY FI F + +F++INL VA+ +D L +
Sbjct: 200 GIVRPLME---------VYPYAWVFFIPFIFVVTFVMINLVVAICVDAMAILNQKEE--- 247
Query: 1182 PHHLDE 1187
H +DE
Sbjct: 248 QHIIDE 253
Score = 32.0 bits (71), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 42/91 (46%), Gaps = 9/91 (9%)
Query: 95 FDNFGLAMLTVFQCITLEGWTDVLYNIEDALGRT--WQWTYFVSMVILGAFFVMNLILGV 152
F G + T+FQ +TLE W+ I L + W +F+ + + F ++NL++ +
Sbjct: 178 FGTLGESFYTLFQVMTLESWS---MGIVRPLMEVYPYAWVFFIPFIFVVTFVMINLVVAI 234
Query: 153 LSGEFSKEREKAKARGDFHKLREKQQIEEDL 183
+ +K + H + E Q E+++
Sbjct: 235 CVDAMAILNQKEEQ----HIIDEVQSHEDNI 261
>pdb|3RW0|A Chain A, Crystal Structure Of The Navab Voltage-Gated Sodium Channel
(Met221cys, 2.95 A)
pdb|3RW0|B Chain B, Crystal Structure Of The Navab Voltage-Gated Sodium Channel
(Met221cys, 2.95 A)
Length = 285
Score = 57.4 bits (137), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 64/269 (23%), Positives = 115/269 (42%), Gaps = 62/269 (23%)
Query: 904 VTSQYFEYTIFCLIMINTLTLAMK----FYRQPLFYADILDKMNMFFTTVFALEFVFKLA 959
V S +F I LI++N +T ++ F + Y + +++ + T+F +E + ++
Sbjct: 27 VESSFFTKFIIYLIVLNGITXGLETSKTFXQSFGVYTTLFNQIVI---TIFTIEIILRIY 83
Query: 960 AFRFKNYFSDAWNVFDFVIVMGSFIDIFSDSPPHAAAKATIPGSHEQTSGRLSINFFRLF 1019
R ++F D W++FDF +V A + +P S SG R+
Sbjct: 84 VHRI-SFFKDPWSLFDFFVV----------------AISLVPTS----SG---FEILRVL 119
Query: 1020 RVMRLIKLLSRGEGIRTLLWTFIKSFQALPYVALLIVMLFFIYAVIGMQVFGKIALVFGG 1079
RV+RL +L++ R ++ I V L + F+I+A+ Q+FG+
Sbjct: 120 RVLRLFRLVTAVPQXRKIVSALISVIPGXLSVIALXTLFFYIFAIXATQLFGE------- 172
Query: 1080 GIHRNNNFQTFPQAVLVLFRSATGEAWQDIMLDCSNRPSEVKCDAASDGNPTNDDNVSCG 1139
F T ++ LF+ T E+W ++ RP + P
Sbjct: 173 --RFPEWFGTLGESFYTLFQVXTLESWSXGIV----RP-------LXEVYPY-------- 211
Query: 1140 SDIAYPYFISFYVLCSFLIINLFVAVIMD 1168
A+ +FI F + +F+ INL VA+I+D
Sbjct: 212 ---AWVFFIPFIFVVTFVXINLVVAIIVD 237
Score = 31.6 bits (70), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 41/91 (45%), Gaps = 9/91 (9%)
Query: 95 FDNFGLAMLTVFQCITLEGWTDVLYNIEDALGRT--WQWTYFVSMVILGAFFVMNLILGV 152
F G + T+FQ TLE W+ I L + W +F+ + + F +NL++ +
Sbjct: 178 FGTLGESFYTLFQVXTLESWSX---GIVRPLXEVYPYAWVFFIPFIFVVTFVXINLVVAI 234
Query: 153 LSGEFSKEREKAKARGDFHKLREKQQIEEDL 183
+ + +K + H + E Q E+++
Sbjct: 235 IVDACAILNQKEEQ----HIIDEVQSHEDNI 261
>pdb|4EKW|A Chain A, Crystal Structure Of The Navab Voltage-Gated Sodium Channel
(Wild- Type, 3.2 A)
pdb|4EKW|B Chain B, Crystal Structure Of The Navab Voltage-Gated Sodium Channel
(Wild- Type, 3.2 A)
pdb|4EKW|C Chain C, Crystal Structure Of The Navab Voltage-Gated Sodium Channel
(Wild- Type, 3.2 A)
pdb|4EKW|D Chain D, Crystal Structure Of The Navab Voltage-Gated Sodium Channel
(Wild- Type, 3.2 A)
Length = 285
Score = 57.4 bits (137), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 64/269 (23%), Positives = 115/269 (42%), Gaps = 62/269 (23%)
Query: 904 VTSQYFEYTIFCLIMINTLTLAMK----FYRQPLFYADILDKMNMFFTTVFALEFVFKLA 959
V S +F I LI++N +T ++ F + Y + +++ + T+F +E + ++
Sbjct: 27 VESSFFTKFIIYLIVLNGITXGLETSKTFXQSFGVYTTLFNQIVI---TIFTIEIILRIY 83
Query: 960 AFRFKNYFSDAWNVFDFVIVMGSFIDIFSDSPPHAAAKATIPGSHEQTSGRLSINFFRLF 1019
R ++F D W++FDF +V A + +P S SG R+
Sbjct: 84 VHRI-SFFKDPWSLFDFFVV----------------AISLVPTS----SG---FEILRVL 119
Query: 1020 RVMRLIKLLSRGEGIRTLLWTFIKSFQALPYVALLIVMLFFIYAVIGMQVFGKIALVFGG 1079
RV+RL +L++ R ++ I V L + F+I+A+ Q+FG+
Sbjct: 120 RVLRLFRLVTAVPQXRKIVSALISVIPGXLSVIALXTLFFYIFAIXATQLFGE------- 172
Query: 1080 GIHRNNNFQTFPQAVLVLFRSATGEAWQDIMLDCSNRPSEVKCDAASDGNPTNDDNVSCG 1139
F T ++ LF+ T E+W ++ RP + P
Sbjct: 173 --RFPEWFGTLGESFYTLFQVXTLESWSXGIV----RP-------LXEVYPY-------- 211
Query: 1140 SDIAYPYFISFYVLCSFLIINLFVAVIMD 1168
A+ +FI F + +F+ INL VA+I+D
Sbjct: 212 ---AWVFFIPFIFVVTFVXINLVVAIIVD 237
Score = 32.3 bits (72), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 21/91 (23%), Positives = 41/91 (45%), Gaps = 9/91 (9%)
Query: 95 FDNFGLAMLTVFQCITLEGWTDVLYNIEDALGRT--WQWTYFVSMVILGAFFVMNLILGV 152
F G + T+FQ TLE W+ I L + W +F+ + + F +NL++ +
Sbjct: 178 FGTLGESFYTLFQVXTLESWSX---GIVRPLXEVYPYAWVFFIPFIFVVTFVXINLVVAI 234
Query: 153 LSGEFSKEREKAKARGDFHKLREKQQIEEDL 183
+ + +K + H + E Q E+++
Sbjct: 235 IVDAXAILNQKEEQ----HIIDEVQSHEDNI 261
>pdb|2BE6|D Chain D, 2.0 A Crystal Structure Of The Cav1.2 Iq Domain-CaCAM
COMPLEX
pdb|2BE6|E Chain E, 2.0 A Crystal Structure Of The Cav1.2 Iq Domain-CaCAM
COMPLEX
pdb|2BE6|F Chain F, 2.0 A Crystal Structure Of The Cav1.2 Iq Domain-CaCAM
COMPLEX
Length = 37
Score = 57.4 bits (137), Expect = 7e-08, Method: Composition-based stats.
Identities = 26/32 (81%), Positives = 29/32 (90%)
Query: 1300 GGEEEVTVGKFYATFLIQDYFRRFKKRKEQEL 1331
G +EVTVGKFYATFLIQ+YFR+FKKRKEQ L
Sbjct: 1 GHMDEVTVGKFYATFLIQEYFRKFKKRKEQGL 32
Score = 56.6 bits (135), Expect = 1e-07, Method: Composition-based stats.
Identities = 25/29 (86%), Positives = 28/29 (96%)
Query: 1483 EEVTVGKFYATFLIQDYFRRFKKRKEQEL 1511
+EVTVGKFYATFLIQ+YFR+FKKRKEQ L
Sbjct: 4 DEVTVGKFYATFLIQEYFRKFKKRKEQGL 32
>pdb|1VYT|E Chain E, Beta3 Subunit Complexed With Aid
pdb|1VYT|F Chain F, Beta3 Subunit Complexed With Aid
Length = 25
Score = 53.9 bits (128), Expect = 7e-07, Method: Composition-based stats.
Identities = 22/25 (88%), Positives = 24/25 (96%)
Query: 171 HKLREKQQIEEDLRGYLDWITQAED 195
KLREKQQ+EEDL+GYLDWITQAED
Sbjct: 1 QKLREKQQLEEDLKGYLDWITQAED 25
>pdb|2F3Y|B Chain B, CalmodulinIQ DOMAIN COMPLEX
Length = 21
Score = 43.1 bits (100), Expect = 0.001, Method: Composition-based stats.
Identities = 19/21 (90%), Positives = 21/21 (100%)
Query: 1309 KFYATFLIQDYFRRFKKRKEQ 1329
KFYATFLIQ+YFR+FKKRKEQ
Sbjct: 1 KFYATFLIQEYFRKFKKRKEQ 21
Score = 43.1 bits (100), Expect = 0.001, Method: Composition-based stats.
Identities = 19/21 (90%), Positives = 21/21 (100%)
Query: 1489 KFYATFLIQDYFRRFKKRKEQ 1509
KFYATFLIQ+YFR+FKKRKEQ
Sbjct: 1 KFYATFLIQEYFRKFKKRKEQ 21
>pdb|1T0J|C Chain C, Crystal Structure Of A Complex Between Voltage-Gated
Calcium Channel Beta2a Subunit And A Peptide Of The
Alpha1c Subunit
Length = 20
Score = 42.0 bits (97), Expect = 0.003, Method: Composition-based stats.
Identities = 16/18 (88%), Positives = 18/18 (100%)
Query: 177 QQIEEDLRGYLDWITQAE 194
QQ+EEDL+GYLDWITQAE
Sbjct: 3 QQLEEDLKGYLDWITQAE 20
>pdb|2F3Z|B Chain B, CalmodulinIQ-Aa Domain Complex
Length = 21
Score = 39.3 bits (90), Expect = 0.020, Method: Composition-based stats.
Identities = 17/21 (80%), Positives = 19/21 (90%)
Query: 1309 KFYATFLIQDYFRRFKKRKEQ 1329
KFYATFL +YFR+FKKRKEQ
Sbjct: 1 KFYATFLAAEYFRKFKKRKEQ 21
Score = 39.3 bits (90), Expect = 0.020, Method: Composition-based stats.
Identities = 17/21 (80%), Positives = 19/21 (90%)
Query: 1489 KFYATFLIQDYFRRFKKRKEQ 1509
KFYATFL +YFR+FKKRKEQ
Sbjct: 1 KFYATFLAAEYFRKFKKRKEQ 21
>pdb|1T3L|B Chain B, Structural Analysis Of The Voltage-Dependent Calcium
Channel Beta Subunit Functional Core In Complex With
Alpha1 Interaction Domain
Length = 18
Score = 38.1 bits (87), Expect = 0.047, Method: Composition-based stats.
Identities = 14/18 (77%), Positives = 16/18 (88%)
Query: 177 QQIEEDLRGYLDWITQAE 194
QQ+EEDLRGY+ WITQ E
Sbjct: 1 QQLEEDLRGYMSWITQGE 18
>pdb|2VAY|B Chain B, Calmodulin Complexed With Cav1.1 Iq Peptide
Length = 21
Score = 35.8 bits (81), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 15/21 (71%), Positives = 20/21 (95%)
Query: 1309 KFYATFLIQDYFRRFKKRKEQ 1329
KFYATFLIQ++FR+F KR+E+
Sbjct: 1 KFYATFLIQEHFRKFMKRQEE 21
Score = 35.8 bits (81), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 15/21 (71%), Positives = 20/21 (95%)
Query: 1489 KFYATFLIQDYFRRFKKRKEQ 1509
KFYATFLIQ++FR+F KR+E+
Sbjct: 1 KFYATFLIQEHFRKFMKRQEE 21
>pdb|4F4L|A Chain A, Open Channel Conformation Of A Voltage Gated Sodium
Channel
pdb|4F4L|B Chain B, Open Channel Conformation Of A Voltage Gated Sodium
Channel
pdb|4F4L|C Chain C, Open Channel Conformation Of A Voltage Gated Sodium
Channel
pdb|4F4L|D Chain D, Open Channel Conformation Of A Voltage Gated Sodium
Channel
Length = 112
Score = 35.8 bits (81), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 95 FDNFGLAMLTVFQCITLEGWT-DVLYNIEDALGRTWQWTYFVSMVILGAFFVMNLILGVL 153
F + ++ T+FQ +TLE W+ ++ + + W +F+ ++L F V+NL +G++
Sbjct: 36 FGDLSKSLYTLFQVMTLESWSMGIVRPVMNVHPN--AWVFFIPFIMLTTFTVLNLFIGII 93
Query: 154 --SGEFSKEREKAKARG 168
+ +KE+E+ G
Sbjct: 94 VDAMAITKEQEEEAKTG 110
Score = 30.8 bits (68), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 30/125 (24%), Positives = 55/125 (44%), Gaps = 45/125 (36%)
Query: 1051 VALLIVMLFFIYAVIGMQVFGKIALVFGGGIHRNNNFQTFPQ-------AVLVLFRSATG 1103
VA L+ ++F+I AV+ ++G TFP+ ++ LF+ T
Sbjct: 9 VAALLTVVFYIAAVMATNLYGA----------------TFPEWFGDLSKSLYTLFQVMTL 52
Query: 1104 EAWQDIMLDCSNRPSEVKCDAASDGNPTNDDNVSCGSDIAYPYFISFYVLCSFLIINLFV 1163
E+W ++ RP + +P A+ +FI F +L +F ++NLF+
Sbjct: 53 ESWSMGIV----RP-------VMNVHPN-----------AWVFFIPFIMLTTFTVLNLFI 90
Query: 1164 AVIMD 1168
+I+D
Sbjct: 91 GIIVD 95
Score = 30.4 bits (67), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 12/84 (14%)
Query: 786 FDDVAKAMLTLFTVSTFEGWPGLLYNSIDSNLENHGPIHNYRPIVATXXXXXXXXXAFFM 845
F D++K++ TLF V T E W ++ P+ N P F +
Sbjct: 36 FGDLSKSLYTLFQVMTLESW----------SMGIVRPVMNVHPNAWVFFIPFIMLTTFTV 85
Query: 846 VNIFVGFVI--VTFQNEGEQEYKN 867
+N+F+G ++ + E E+E K
Sbjct: 86 LNLFIGIIVDAMAITKEQEEEAKT 109
>pdb|2KAV|A Chain A, Solution Structure Of The Human Voltage-Gated Sodium
Channel, Brain Isoform (Nav1.2)
Length = 129
Score = 35.4 bits (80), Expect = 0.24, Method: Composition-based stats.
Identities = 25/95 (26%), Positives = 45/95 (47%), Gaps = 6/95 (6%)
Query: 1168 DNFDYLTRDWS-ILGPHHLDEFIRLWSEYDPDAKGRIKHLDVVTLLRKISPPLGFGKLCP 1226
+NF T + + L + F +W ++DPDA I+ + + PPL K P
Sbjct: 24 ENFSVATEESAEPLSEDDFEMFYEVWEKFDPDATQFIEFAKLSDFADALDPPLLIAK--P 81
Query: 1227 HRVACKRLVSMNMPLNSDGTVLFNATLFAVVRTSL 1261
++V +L++M++P+ S + LFA + L
Sbjct: 82 NKV---QLIAMDLPMVSGDRIHCLDILFAFTKRVL 113
>pdb|2KBI|A Chain A, Solution Nmr Structure Of The C-Terminal Ef-Hand Domain Of
Human Cardiac Sodium Channel Nav1.5
Length = 97
Score = 33.5 bits (75), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 46/95 (48%), Gaps = 6/95 (6%)
Query: 1168 DNFDYLTRDWS-ILGPHHLDEFIRLWSEYDPDAKGRIKHLDVVTLLRKISPPLGFGKLCP 1226
+NF T + + L D F +W ++DP+A I++ + +S PL K P
Sbjct: 5 ENFSVATEESTEPLSEDDFDMFYEIWEKFDPEATQFIEYSVLSDFADALSEPLRIAK--P 62
Query: 1227 HRVACKRLVSMNMPLNSDGTVLFNATLFAVVRTSL 1261
++++ L++M++P+ S + LFA + L
Sbjct: 63 NQIS---LINMDLPMVSGDRIHCMDILFAFTKRVL 94
>pdb|4DCK|A Chain A, Crystal Structure Of The C-Terminus Of Voltage-Gated Sodium
Channel In Complex With Fgf13 And Cam
Length = 168
Score = 33.1 bits (74), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 46/95 (48%), Gaps = 6/95 (6%)
Query: 1168 DNFDYLTRDWS-ILGPHHLDEFIRLWSEYDPDAKGRIKHLDVVTLLRKISPPLGFGKLCP 1226
+NF T + + L D F +W ++DP+A I++ + +S PL K P
Sbjct: 1 ENFSVATEESTEPLSEDDFDMFYEIWEKFDPEATQFIEYSVLSDFADALSEPLRIAK--P 58
Query: 1227 HRVACKRLVSMNMPLNSDGTVLFNATLFAVVRTSL 1261
++++ L++M++P+ S + LFA + L
Sbjct: 59 NQIS---LINMDLPMVSGDRIHCMDILFAFTKRVL 90
>pdb|2KR6|A Chain A, Solution Structure Of Presenilin-1 Ctf Subunit
Length = 176
Score = 31.2 bits (69), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 189 WITQAEDIEPEGEERANHHDQKNKSSSETESADRL-EGDEGENQESW 234
W+ + +PE + R + + + N S+E ES D + E D+G E W
Sbjct: 3 WLVNMAEGDPEAQRRVSKNSKYNAESTERESQDTVAENDDGGFSEEW 49
>pdb|3L2P|A Chain A, Human Dna Ligase Iii Recognizes Dna Ends By Dynamic
Switching Between Two Dna Bound States
Length = 579
Score = 31.2 bits (69), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 31/73 (42%)
Query: 1418 DNFDYLTRDWSILGPHHLDEFIRLWSEYDPDAKGRIKHLDVVTLLRKISPPLGFGKLCPH 1477
D+F Y +R + PH + F + P I +V+ + K PL FG L H
Sbjct: 267 DHFSYFSRSLKPVLPHKVAHFKDYIPQAFPGGHSMILDSEVLLIDNKTGKPLPFGTLGVH 326
Query: 1478 RVACEEEVTVGKF 1490
+ A ++ V F
Sbjct: 327 KKAAFQDANVCLF 339
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 0.140 0.431
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 45,309,239
Number of Sequences: 62578
Number of extensions: 1815259
Number of successful extensions: 4682
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 4614
Number of HSP's gapped (non-prelim): 65
length of query: 1643
length of database: 14,973,337
effective HSP length: 112
effective length of query: 1531
effective length of database: 7,964,601
effective search space: 12193804131
effective search space used: 12193804131
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: 58 (26.9 bits)