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= psy3030
(116 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 = 67.4 bits (163), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 41/61 (67%)
Query: 20 PRQLTPEILSAFEGVRFIAQHIKDADKDNEIVEDWKYVSMVLDRFFLCVFTAACVLGTCG 79
P P++ SA EGV++IA+H+K ++ + E+WKYV+MV+D LCVF C++GT
Sbjct: 155 PLIKNPDVKSAIEGVKYIAEHMKSDEESSNAAEEWKYVAMVIDHILLCVFMLICIIGTVS 214
Query: 80 I 80
+
Sbjct: 215 V 215
>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 = 66.2 bits (160), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 41/61 (67%)
Query: 20 PRQLTPEILSAFEGVRFIAQHIKDADKDNEIVEDWKYVSMVLDRFFLCVFTAACVLGTCG 79
P P++ SA EGV++IA+H+K ++ + E+WKYV+MV+D LCVF C++GT
Sbjct: 389 PLIKNPDVKSAIEGVKYIAEHMKSDEESSNAAEEWKYVAMVIDHILLCVFMLICIIGTVS 448
Query: 80 I 80
+
Sbjct: 449 V 449
>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 = 64.7 bits (156), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 39/57 (68%)
Query: 24 TPEILSAFEGVRFIAQHIKDADKDNEIVEDWKYVSMVLDRFFLCVFTAACVLGTCGI 80
+P SA EGV++IA+H+K ++ + E+WKYV+MV+D LCVF C++GT +
Sbjct: 302 SPSTHSAIEGVKYIAEHMKSDEESSNAAEEWKYVAMVIDHILLCVFMLICIIGTVSV 358
>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 = 56.2 bits (134), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 40/65 (61%)
Query: 20 PRQLTPEILSAFEGVRFIAQHIKDADKDNEIVEDWKYVSMVLDRFFLCVFTAACVLGTCG 79
P L ++ A E +++IA+ ++ A + +++ +DW+YV+MV DR FL +F C +GT
Sbjct: 418 PVTLPQDLKEAVEAIKYIAEQLESASEFDDLKKDWQYVAMVADRLFLYIFITMCSIGTFS 477
Query: 80 IIFQA 84
I A
Sbjct: 478 IFLDA 482
>pdb|2BG9|B Chain B, Refined Structure Of The Nicotinic Acetylcholine Receptor
At 4a Resolution
Length = 370
Score = 55.8 bits (133), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 38/61 (62%)
Query: 24 TPEILSAFEGVRFIAQHIKDADKDNEIVEDWKYVSMVLDRFFLCVFTAACVLGTCGIIFQ 83
+P A E +++IA+ ++ A + +++ +DW+YV+MV DR FL +F C +GT I
Sbjct: 299 SPNTHEAVEAIKYIAEQLESASEFDDLKKDWQYVAMVADRLFLYIFITMCSIGTFSIFLD 358
Query: 84 A 84
A
Sbjct: 359 A 359
>pdb|1OED|B Chain B, Structure Of Acetylcholine Receptor Pore From Electron
Images
Length = 250
Score = 55.8 bits (133), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 40/65 (61%)
Query: 20 PRQLTPEILSAFEGVRFIAQHIKDADKDNEIVEDWKYVSMVLDRFFLCVFTAACVLGTCG 79
P L ++ A E +++IA+ ++ A + +++ +DW+YV+MV DR FL VF C +GT
Sbjct: 178 PVTLPQDLKEAVEAIKYIAEQLESASEFDDLKKDWQYVAMVADRLFLYVFFVICSIGTFS 237
Query: 80 IIFQA 84
I A
Sbjct: 238 IFLDA 242
>pdb|1OED|C Chain C, Structure Of Acetylcholine Receptor Pore From Electron
Images
Length = 260
Score = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 30/59 (50%)
Query: 22 QLTPEILSAFEGVRFIAQHIKDADKDNEIVEDWKYVSMVLDRFFLCVFTAACVLGTCGI 80
QL EI S + +I + IK+ + +E V +W V +DR + + T VLGT I
Sbjct: 190 QLHDEIKSGIDSTNYIVKQIKEKNAYDEEVGNWNLVGQTIDRLSMFIITPVMVLGTIFI 248
>pdb|4AQ5|C Chain C, Gating Movement In Acetylcholine Receptor Analysed By
Time- Resolved Electron Cryo-Microscopy (Closed Class)
pdb|4AQ9|C Chain C, Gating Movement In Acetylcholine Receptor Analysed By
Time-Resolved Electron Cryo-Microscopy (Open Class)
Length = 522
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 30/59 (50%)
Query: 22 QLTPEILSAFEGVRFIAQHIKDADKDNEIVEDWKYVSMVLDRFFLCVFTAACVLGTCGI 80
QL EI S + +I + IK+ + +E V +W V +DR + + T VLGT I
Sbjct: 435 QLHDEIKSGIDSTNYIVKQIKEKNAYDEEVGNWNLVGQTIDRLSMFIITPVMVLGTIFI 493
>pdb|2BG9|C Chain C, Refined Structure Of The Nicotinic Acetylcholine Receptor
At 4a Resolution
Length = 369
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 24 TPEILSAFEGVRFIAQHIKDADKDNEIVEDWKYVSMVLDRFFLCVFTAACVLGTCGI 80
TP S + +I + IK+ + +E V +W V +DR + + T VLGT I
Sbjct: 301 TPSTHSGIDSTNYIVKQIKEKNAYDEEVGNWNLVGQTIDRLSMFIITPVMVLGTIFI 357
>pdb|2KSR|A Chain A, Nmr Structures Of Tm Domain Of The N-Acetylcholine
Receptor B2 Subunit
Length = 164
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/28 (53%), Positives = 19/28 (67%)
Query: 56 YVSMVLDRFFLCVFTAACVLGTCGIIFQ 83
YV+MV+DR FL +F CV GT G+ Q
Sbjct: 131 YVAMVIDRLFLWIFVFVCVFGTIGMFLQ 158
>pdb|4AQ5|E Chain E, Gating Movement In Acetylcholine Receptor Analysed By
Time- Resolved Electron Cryo-Microscopy (Closed Class)
pdb|4AQ9|E Chain E, Gating Movement In Acetylcholine Receptor Analysed By
Time-Resolved Electron Cryo-Microscopy (Open Class)
Length = 488
Score = 30.8 bits (68), Expect = 0.21, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 25/60 (41%)
Query: 23 LTPEILSAFEGVRFIAQHIKDADKDNEIVEDWKYVSMVLDRFFLCVFTAACVLGTCGIIF 82
PEI S E FIA+ K+ + E+W + V+D+ + LGT I
Sbjct: 408 FAPEIKSCVEACNFIAKSTKEQNDSGSENENWVLIGKVIDKACFWIALLLFSLGTLAIFL 467
>pdb|1OED|E Chain E, Structure Of Acetylcholine Receptor Pore From Electron
Images
Length = 260
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 25/56 (44%)
Query: 25 PEILSAFEGVRFIAQHIKDADKDNEIVEDWKYVSMVLDRFFLCVFTAACVLGTCGI 80
PEI S E FIA+ K+ + E+W + V+D+ + +GT I
Sbjct: 193 PEIKSCVEACNFIAKSTKEQNDSGSENENWVLIGKVIDKACFWIALLLFSIGTLAI 248
>pdb|2LM2|A Chain A, Nmr Structures Of The Transmembrane Domains Of The Achr B2
Subunit
Length = 137
Score = 28.5 bits (62), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 61 LDRFFLCVFTAACVLGTCGIIFQ 83
+DR FL +F CV GT G+ Q
Sbjct: 109 IDRLFLWIFVFVCVFGTIGMFLQ 131
>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: 84 APSLYDNTAPIDIQMTRITQYGISSPPTVA 113
AP+L +NT PID+ MT I + G + +A
Sbjct: 211 APNLANNTEPIDLLMTCIKKAGYENRVKIA 240
>pdb|2BG9|E Chain E, Refined Structure Of The Nicotinic Acetylcholine Receptor
At 4a Resolution
Length = 370
Score = 28.1 bits (61), Expect = 1.2, Method: Composition-based stats.
Identities = 16/59 (27%), Positives = 24/59 (40%)
Query: 24 TPEILSAFEGVRFIAQHIKDADKDNEIVEDWKYVSMVLDRFFLCVFTAACVLGTCGIIF 82
TP S E FIA+ K+ + E+W + V+D+ + LGT I
Sbjct: 303 TPNTHSCVEACNFIAKSTKEQNDSGSENENWVLIGKVIDKACFWIALLLFSLGTLAIFL 361
>pdb|2LIU|A Chain A, Nmr Structure Of Holo-Acpi Domain From Cura Module From
Lyngbya Majuscula
pdb|2LIW|A Chain A, Nmr Structure Of Hmg-Acpi Domain From Cura Module From
Lyngbya Majuscula
Length = 99
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 7/78 (8%)
Query: 18 VIPR--QLTPEI--LSAFEGVRFIAQHIKDA--DKDNEIVEDWKYVSMVLDRFFLCVFTA 71
++PR +TP++ ++ E + + Q + +A +++EI ED K+V + LD +T
Sbjct: 3 LVPRGSHMTPQVNQVNLSEIKQVLKQQLAEALYTEESEIAEDQKFVDLGLDSIVGVEWT- 61
Query: 72 ACVLGTCGIIFQAPSLYD 89
+ T + +A LYD
Sbjct: 62 TTINQTYNLNLKATKLYD 79
>pdb|2LLY|A Chain A, Nmr Structures Of The Transmembrane Domains Of The Nachr
A4 Subunit
Length = 137
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 61 LDRFFLCVFTAACVLGTCGIIFQAPSL 87
+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
0.324 0.138 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,497,105
Number of Sequences: 62578
Number of extensions: 128226
Number of successful extensions: 287
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 271
Number of HSP's gapped (non-prelim): 17
length of query: 116
length of database: 14,973,337
effective HSP length: 79
effective length of query: 37
effective length of database: 10,029,675
effective search space: 371097975
effective search space used: 371097975
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: 45 (21.9 bits)