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= 036454
(410 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3RG1|A Chain A, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|E Chain E, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|I Chain I, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|M Chain M, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|B Chain B, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|F Chain F, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|J Chain J, Crystal Structure Of The Rp105MD-1 Complex
pdb|3RG1|N Chain N, Crystal Structure Of The Rp105MD-1 Complex
Length = 612
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 32/94 (34%), Positives = 44/94 (46%), Gaps = 17/94 (18%)
Query: 130 ECPELRKLEV--NHVDV------FANLE---ELTLSKCIFTTWRQAQFHKLKILHFISDG 178
ECP+L L+V H+ V F NL L LS C+ T Q L+ L ++
Sbjct: 397 ECPQLELLDVAFTHLHVKAPHSPFQNLHLLRVLNLSHCLLDTSNQHLLAGLQDLRHLNLQ 456
Query: 179 SDFFQVG------LLQNIHNLEKLVLSTCEYKKI 206
+ FQ G LLQ + +LE L+LS+C I
Sbjct: 457 GNSFQDGSISKTNLLQMVGSLEILILSSCNLLSI 490
>pdb|3B2D|A Chain A, Crystal Structure Of Human Rp105MD-1 Complex
pdb|3B2D|B Chain B, Crystal Structure Of Human Rp105MD-1 Complex
Length = 603
Score = 33.5 bits (75), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 31/106 (29%), Positives = 50/106 (47%), Gaps = 20/106 (18%)
Query: 130 ECPELRKLEVN----HVDV----FANL---EELTLSKCIFTTWRQAQFHKLKILHFISDG 178
ECP+L L++ H++ F NL + L L+ C T Q L +L ++
Sbjct: 395 ECPQLELLDLAFTRLHINAPQSPFQNLHFLQVLNLTYCFLDTSNQHLLAGLPVLRHLNLK 454
Query: 179 SDFFQVG------LLQNIHNLEKLVLSTCEYKKIFSCEEVEEHAEG 218
+ FQ G LLQ + +LE L+LS+C + S ++ H+ G
Sbjct: 455 GNHFQDGTITKTNLLQTVGSLEVLILSSC---GLLSIDQQAFHSLG 497
>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 = 30.8 bits (68), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 264 ISLVPSSASFRNLTVLKVCNCWQLISLVTPQTAKTLVQL 302
ISLVP+S+ F L VL+V ++L++ V PQ K + L
Sbjct: 104 ISLVPTSSGFEILRVLRVLRLFRLVTAV-PQMRKIVSAL 141
>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 = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 264 ISLVPSSASFRNLTVLKVCNCWQLISLVTPQTAKTLVQL 302
ISLVP+S+ F L VL+V ++L++ V PQ K + L
Sbjct: 104 ISLVPTSSGFEILRVLRVLRLFRLVTAV-PQXRKIVSAL 141
>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 = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/39 (43%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 264 ISLVPSSASFRNLTVLKVCNCWQLISLVTPQTAKTLVQL 302
ISLVP+S+ F L VL+V ++L++ V PQ K + L
Sbjct: 104 ISLVPTSSGFEILRVLRVLRLFRLVTAV-PQXRKIVSAL 141
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
0.321 0.136 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,322,106
Number of Sequences: 62578
Number of extensions: 429800
Number of successful extensions: 1011
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1004
Number of HSP's gapped (non-prelim): 12
length of query: 410
length of database: 14,973,337
effective HSP length: 101
effective length of query: 309
effective length of database: 8,652,959
effective search space: 2673764331
effective search space used: 2673764331
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)