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= psy17845
(81 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1OED|A Chain A, Structure Of Acetylcholine Receptor Pore From Electron
Images
pdb|1OED|D Chain D, Structure Of Acetylcholine Receptor Pore From Electron
Images
Length = 227
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 25/35 (71%)
Query: 11 DTNHIVEDWKYVSMVLDRFFLCVFTAACVLGTCGI 45
++++ E+WKYV+MV+D LCVF C++GT +
Sbjct: 181 ESSNAAEEWKYVAMVIDHILLCVFMLICIIGTVSV 215
>pdb|2BG9|A Chain A, Refined Structure Of The Nicotinic Acetylcholine Receptor
At 4a Resolution.
pdb|2BG9|D Chain D, Refined Structure Of The Nicotinic Acetylcholine Receptor
At 4a Resolution
Length = 370
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 27/43 (62%)
Query: 3 GRQVVTHPDTNHIVEDWKYVSMVLDRFFLCVFTAACVLGTCGI 45
+ + ++++ E+WKYV+MV+D LCVF C++GT +
Sbjct: 316 AEHMKSDEESSNAAEEWKYVAMVIDHILLCVFMLICIIGTVSV 358
>pdb|4AQ5|A Chain A, Gating Movement In Acetylcholine Receptor Analysed By
Time- Resolved Electron Cryo-Microscopy (Closed Class)
pdb|4AQ5|D Chain D, Gating Movement In Acetylcholine Receptor Analysed By
Time- Resolved Electron Cryo-Microscopy (Closed Class)
pdb|4AQ9|A Chain A, Gating Movement In Acetylcholine Receptor Analysed By
Time-Resolved Electron Cryo-Microscopy (Open Class)
pdb|4AQ9|D Chain D, Gating Movement In Acetylcholine Receptor Analysed By
Time-Resolved Electron Cryo-Microscopy (Open Class)
Length = 461
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 27/43 (62%)
Query: 3 GRQVVTHPDTNHIVEDWKYVSMVLDRFFLCVFTAACVLGTCGI 45
+ + ++++ E+WKYV+MV+D LCVF C++GT +
Sbjct: 407 AEHMKSDEESSNAAEEWKYVAMVIDHILLCVFMLICIIGTVSV 449
>pdb|4AQ5|B Chain B, Gating Movement In Acetylcholine Receptor Analysed By
Time- Resolved Electron Cryo-Microscopy (Closed Class)
pdb|4AQ9|B Chain B, Gating Movement In Acetylcholine Receptor Analysed By
Time-Resolved Electron Cryo-Microscopy (Open Class)
Length = 493
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 27/47 (57%)
Query: 3 GRQVVTHPDTNHIVEDWKYVSMVLDRFFLCVFTAACVLGTCGIIFQA 49
Q+ + + + + +DW+YV+MV DR FL +F C +GT I A
Sbjct: 436 AEQLESASEFDDLKKDWQYVAMVADRLFLYIFITMCSIGTFSIFLDA 482
>pdb|2BG9|B Chain B, Refined Structure Of The Nicotinic Acetylcholine Receptor
At 4a Resolution
Length = 370
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 27/47 (57%)
Query: 3 GRQVVTHPDTNHIVEDWKYVSMVLDRFFLCVFTAACVLGTCGIIFQA 49
Q+ + + + + +DW+YV+MV DR FL +F C +GT I A
Sbjct: 313 AEQLESASEFDDLKKDWQYVAMVADRLFLYIFITMCSIGTFSIFLDA 359
>pdb|1OED|B Chain B, Structure Of Acetylcholine Receptor Pore From Electron
Images
Length = 250
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 27/47 (57%)
Query: 3 GRQVVTHPDTNHIVEDWKYVSMVLDRFFLCVFTAACVLGTCGIIFQA 49
Q+ + + + + +DW+YV+MV DR FL VF C +GT I A
Sbjct: 196 AEQLESASEFDDLKKDWQYVAMVADRLFLYVFFVICSIGTFSIFLDA 242
>pdb|2KSR|A Chain A, Nmr Structures Of Tm Domain Of The N-Acetylcholine
Receptor B2 Subunit
Length = 164
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 19/28 (67%)
Query: 21 YVSMVLDRFFLCVFTAACVLGTCGIIFQ 48
YV+MV+DR FL +F CV GT G+ Q
Sbjct: 131 YVAMVIDRLFLWIFVFVCVFGTIGMFLQ 158
>pdb|3QN3|A Chain A, Phosphopyruvate Hydratase From Campylobacter Jejuni.
pdb|3QN3|B Chain B, Phosphopyruvate Hydratase From Campylobacter Jejuni.
pdb|3QN3|C Chain C, Phosphopyruvate Hydratase From Campylobacter Jejuni.
pdb|3QN3|D Chain D, Phosphopyruvate Hydratase From Campylobacter Jejuni
Length = 417
Score = 28.5 bits (62), Expect = 1.1, Method: Composition-based stats.
Identities = 13/30 (43%), Positives = 19/30 (63%)
Query: 49 APSLYDNTAPIDIQMTRITQYGISSPPTVA 78
AP+L +NT PID+ MT I + G + +A
Sbjct: 211 APNLANNTEPIDLLMTCIKKAGYENRVKIA 240
>pdb|2LM2|A Chain A, Nmr Structures Of The Transmembrane Domains Of The Achr B2
Subunit
Length = 137
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 26 LDRFFLCVFTAACVLGTCGIIFQ 48
+DR FL +F CV GT G+ Q
Sbjct: 109 IDRLFLWIFVFVCVFGTIGMFLQ 131
>pdb|2LLY|A Chain A, Nmr Structures Of The Transmembrane Domains Of The Nachr
A4 Subunit
Length = 137
Score = 25.8 bits (55), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 26 LDRFFLCVFTAACVLGTCGIIFQAPSL 52
+DR FL +F C+LGT G +F P L
Sbjct: 109 IDRIFLWMFIIVCLLGTVG-LFLPPWL 134
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 0.447
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,486,751
Number of Sequences: 62578
Number of extensions: 79061
Number of successful extensions: 148
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 138
Number of HSP's gapped (non-prelim): 10
length of query: 81
length of database: 14,973,337
effective HSP length: 50
effective length of query: 31
effective length of database: 11,844,437
effective search space: 367177547
effective search space used: 367177547
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: 45 (21.9 bits)