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= psy15554
(339 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2R9R|B Chain B, Shaker Family Voltage Dependent Potassium Channel
(Kv1.2-Kv2.1 Paddle Chimera Channel) In Association With
Beta Subunit
pdb|2R9R|H Chain H, Shaker Family Voltage Dependent Potassium Channel
(Kv1.2-Kv2.1 Paddle Chimera Channel) In Association With
Beta Subunit
Length = 514
Score = 87.8 bits (216), Expect = 8e-18, Method: Compositional matrix adjust.
Identities = 52/131 (39%), Positives = 72/131 (54%), Gaps = 10/131 (7%)
Query: 85 TDPHAAFFYVELACNAWFTFELLVRAVVSPNIFQFIRSPVNVIDIIATLSFYTDILLQDK 144
TDP FF VE C WF+FE LVR P+ F + +N+IDI+A + +Y I L +
Sbjct: 238 TDP---FFIVETLCIIWFSFEFLVRFFACPSKAGFFTNIMNIIDIVAIIPYYVTIFLTES 294
Query: 145 VQQ-------SDILEFFSIIRILRLFKLTRHSPGLKILIHTFKASAKELTXXXXXXXXXX 197
+ +++ F I+RILR+FKL+RHS GL+IL T KAS +EL
Sbjct: 295 NKSVLQFQNVRRVVQIFRIMRILRIFKLSRHSKGLQILGQTLKASMRELGLLIFFLFIGV 354
Query: 198 XXXASLVYYAE 208
+S VY+AE
Sbjct: 355 ILFSSAVYFAE 365
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 38/107 (35%), Positives = 57/107 (53%), Gaps = 7/107 (6%)
Query: 209 RLQVSPNIFQFIRSPVNVIDIIATLSFYTDILLQDKVQQ-------SDILEFFSIIRILR 261
R P+ F + +N+IDI+A + +Y I L + + +++ F I+RILR
Sbjct: 259 RFFACPSKAGFFTNIMNIIDIVAIIPYYVTIFLTESNKSVLQFQNVRRVVQIFRIMRILR 318
Query: 262 LFKLTRHSPGLKILIHTFKASAKELTXXXXXXXXXXXXXASLVYYAE 308
+FKL+RHS GL+IL T KAS +EL +S VY+AE
Sbjct: 319 IFKLSRHSKGLQILGQTLKASMRELGLLIFFLFIGVILFSSAVYFAE 365
>pdb|3LNM|B Chain B, F233w Mutant Of The Kv2.1 Paddle-Kv1.2 Chimera Channel
pdb|3LNM|D Chain D, F233w Mutant Of The Kv2.1 Paddle-Kv1.2 Chimera Channel
Length = 514
Score = 85.9 bits (211), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 51/131 (38%), Positives = 72/131 (54%), Gaps = 10/131 (7%)
Query: 85 TDPHAAFFYVELACNAWFTFELLVRAVVSPNIFQFIRSPVNVIDIIATLSFYTDILLQDK 144
TDP FF VE C W++FE LVR P+ F + +N+IDI+A + +Y I L +
Sbjct: 238 TDP---FFIVETLCIIWWSFEFLVRFFACPSKAGFFTNIMNIIDIVAIIPYYVTIFLTES 294
Query: 145 VQQ-------SDILEFFSIIRILRLFKLTRHSPGLKILIHTFKASAKELTXXXXXXXXXX 197
+ +++ F I+RILR+FKL+RHS GL+IL T KAS +EL
Sbjct: 295 NKSVLQFQNVRRVVQIFRIMRILRIFKLSRHSKGLQILGQTLKASMRELGLLIFFLFIGV 354
Query: 198 XXXASLVYYAE 208
+S VY+AE
Sbjct: 355 ILFSSAVYFAE 365
Score = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 38/107 (35%), Positives = 57/107 (53%), Gaps = 7/107 (6%)
Query: 209 RLQVSPNIFQFIRSPVNVIDIIATLSFYTDILLQDKVQQ-------SDILEFFSIIRILR 261
R P+ F + +N+IDI+A + +Y I L + + +++ F I+RILR
Sbjct: 259 RFFACPSKAGFFTNIMNIIDIVAIIPYYVTIFLTESNKSVLQFQNVRRVVQIFRIMRILR 318
Query: 262 LFKLTRHSPGLKILIHTFKASAKELTXXXXXXXXXXXXXASLVYYAE 308
+FKL+RHS GL+IL T KAS +EL +S VY+AE
Sbjct: 319 IFKLSRHSKGLQILGQTLKASMRELGLLIFFLFIGVILFSSAVYFAE 365
>pdb|2A79|B Chain B, Mammalian Shaker Kv1.2 Potassium Channel- Beta Subunit
Complex
Length = 499
Score = 79.0 bits (193), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 49/135 (36%), Positives = 70/135 (51%), Gaps = 14/135 (10%)
Query: 85 TDPHAAFFYVELACNAWFTFELLVRAVVSPNIFQFIRSPVNVIDIIATLSFYTDILLQ-- 142
TDP FF VE C WF+FE LVR P+ F + +N+IDI+A + ++ + +
Sbjct: 219 TDP---FFIVETLCIIWFSFEFLVRFFACPSKAGFFTNIMNIIDIVAIIPYFITLGTELA 275
Query: 143 ---DKVQQSD------ILEFFSIIRILRLFKLTRHSPGLKILIHTFKASAKELTXXXXXX 193
+ QQ IL ++R+ R+FKL+RHS GL+IL T KAS +EL
Sbjct: 276 EKPEDAQQGQQAMSLAILRVIRLVRVFRIFKLSRHSKGLQILGQTLKASMRELGLLIFFL 335
Query: 194 XXXXXXXASLVYYAE 208
+S VY+AE
Sbjct: 336 FIGVILFSSAVYFAE 350
Score = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 35/111 (31%), Positives = 55/111 (49%), Gaps = 11/111 (9%)
Query: 209 RLQVSPNIFQFIRSPVNVIDIIATLSFYTDILLQ-----DKVQQSD------ILEFFSII 257
R P+ F + +N+IDI+A + ++ + + + QQ IL ++
Sbjct: 240 RFFACPSKAGFFTNIMNIIDIVAIIPYFITLGTELAEKPEDAQQGQQAMSLAILRVIRLV 299
Query: 258 RILRLFKLTRHSPGLKILIHTFKASAKELTXXXXXXXXXXXXXASLVYYAE 308
R+ R+FKL+RHS GL+IL T KAS +EL +S VY+AE
Sbjct: 300 RVFRIFKLSRHSKGLQILGQTLKASMRELGLLIFFLFIGVILFSSAVYFAE 350
>pdb|3LUT|B Chain B, A Structural Model For The Full-Length Shaker Potassium
Channel Kv1.2
Length = 499
Score = 79.0 bits (193), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 49/135 (36%), Positives = 70/135 (51%), Gaps = 14/135 (10%)
Query: 85 TDPHAAFFYVELACNAWFTFELLVRAVVSPNIFQFIRSPVNVIDIIATLSFYTDILLQ-- 142
TDP FF VE C WF+FE LVR P+ F + +N+IDI+A + ++ + +
Sbjct: 219 TDP---FFIVETLCIIWFSFEFLVRFFACPSKAGFFTNIMNIIDIVAIIPYFITLGTELA 275
Query: 143 ---DKVQQSD------ILEFFSIIRILRLFKLTRHSPGLKILIHTFKASAKELTXXXXXX 193
+ QQ IL ++R+ R+FKL+RHS GL+IL T KAS +EL
Sbjct: 276 EKPEDAQQGQQAMSLAILRVIRLVRVFRIFKLSRHSKGLQILGQTLKASMRELGLLIFFL 335
Query: 194 XXXXXXXASLVYYAE 208
+S VY+AE
Sbjct: 336 FIGVILFSSAVYFAE 350
Score = 55.1 bits (131), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 35/111 (31%), Positives = 55/111 (49%), Gaps = 11/111 (9%)
Query: 209 RLQVSPNIFQFIRSPVNVIDIIATLSFYTDILLQ-----DKVQQSD------ILEFFSII 257
R P+ F + +N+IDI+A + ++ + + + QQ IL ++
Sbjct: 240 RFFACPSKAGFFTNIMNIIDIVAIIPYFITLGTELAEKPEDAQQGQQAMSLAILRVIRLV 299
Query: 258 RILRLFKLTRHSPGLKILIHTFKASAKELTXXXXXXXXXXXXXASLVYYAE 308
R+ R+FKL+RHS GL+IL T KAS +EL +S VY+AE
Sbjct: 300 RVFRIFKLSRHSKGLQILGQTLKASMRELGLLIFFLFIGVILFSSAVYFAE 350
>pdb|3UVJ|A Chain A, Crystal Structure Of The Catalytic Domain Of The
Heterodimeric Human Soluble Guanylate Cyclase 1.
pdb|3UVJ|C Chain C, Crystal Structure Of The Catalytic Domain Of The
Heterodimeric Human Soluble Guanylate Cyclase 1
Length = 225
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/33 (63%), Positives = 23/33 (69%)
Query: 1 VVNFLNDLYTLFDRIIKGYDVYKVETIGDAYMV 33
V+ LN LYT FD+ DVYKVETIGDAY V
Sbjct: 37 VITMLNALYTRFDQQCGELDVYKVETIGDAYCV 69
>pdb|2WZ1|A Chain A, Structure Of The Catalytic Domain Of Human Soluble
Guanylate Cyclase 1 Beta 3.
pdb|2WZ1|B Chain B, Structure Of The Catalytic Domain Of Human Soluble
Guanylate Cyclase 1 Beta 3
Length = 219
Score = 42.4 bits (98), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/39 (53%), Positives = 25/39 (64%), Gaps = 3/39 (7%)
Query: 1 VVNFLNDLYTLFDRII---KGYDVYKVETIGDAYMVILA 36
+VN LNDLYT FD + K VYKVET+GD YM +
Sbjct: 39 IVNLLNDLYTRFDTLTDSRKNPFVYKVETVGDKYMTVSG 77
>pdb|3ET6|A Chain A, The Crystal Structure Of The Catalytic Domain Of A
Eukaryotic Guanylate Cyclase
Length = 190
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/36 (55%), Positives = 26/36 (72%), Gaps = 1/36 (2%)
Query: 1 VVNFLNDLYTLFDRIIKGY-DVYKVETIGDAYMVIL 35
V + L++LY FD I+ Y +YKVETIGDAYMV+
Sbjct: 32 VXSLLDELYQRFDAAIEEYPQLYKVETIGDAYMVVC 67
>pdb|3ET6|B Chain B, The Crystal Structure Of The Catalytic Domain Of A
Eukaryotic Guanylate Cyclase
Length = 190
Score = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/36 (55%), Positives = 26/36 (72%), Gaps = 1/36 (2%)
Query: 1 VVNFLNDLYTLFDRIIKGY-DVYKVETIGDAYMVIL 35
V + L++LY FD I+ Y +YKVETIGDAYMV+
Sbjct: 32 VXSLLDELYQRFDAAIEEYPQLYKVETIGDAYMVVC 67
>pdb|3UVJ|B Chain B, Crystal Structure Of The Catalytic Domain Of The
Heterodimeric Human Soluble Guanylate Cyclase 1.
pdb|3UVJ|D Chain D, Crystal Structure Of The Catalytic Domain Of The
Heterodimeric Human Soluble Guanylate Cyclase 1
Length = 220
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/39 (51%), Positives = 24/39 (61%), Gaps = 3/39 (7%)
Query: 1 VVNFLNDLYTLFDRII---KGYDVYKVETIGDAYMVILA 36
+VN LNDLYT FD + K VYKVET+ D YM +
Sbjct: 40 IVNLLNDLYTRFDTLTDSRKNPFVYKVETVCDKYMTVSG 78
>pdb|1YK9|A Chain A, Crystal Structure Of A Mutant Form Of The Mycobacterial
Adenylyl Cyclase Rv1625c
Length = 204
Score = 35.4 bits (80), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 23/33 (69%)
Query: 2 VNFLNDLYTLFDRIIKGYDVYKVETIGDAYMVI 34
V FL+ LY+ FD ++ + + K+E GD+YMV+
Sbjct: 34 VRFLDRLYSAFDELVDQHGLEKIEVSGDSYMVV 66
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
0.328 0.141 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,628,789
Number of Sequences: 62578
Number of extensions: 238225
Number of successful extensions: 665
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 636
Number of HSP's gapped (non-prelim): 20
length of query: 339
length of database: 14,973,337
effective HSP length: 99
effective length of query: 240
effective length of database: 8,778,115
effective search space: 2106747600
effective search space used: 2106747600
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: 52 (24.6 bits)