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= psy1864
(232 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3RHW|A Chain A, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab And Ivermectin
pdb|3RHW|B Chain B, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab And Ivermectin
pdb|3RHW|C Chain C, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab And Ivermectin
pdb|3RHW|D Chain D, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab And Ivermectin
pdb|3RHW|E Chain E, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab And Ivermectin
pdb|3RI5|A Chain A, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Picrotoxin
pdb|3RI5|B Chain B, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Picrotoxin
pdb|3RI5|C Chain C, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Picrotoxin
pdb|3RI5|D Chain D, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Picrotoxin
pdb|3RI5|E Chain E, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Picrotoxin
pdb|3RIA|A Chain A, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Iodide.
pdb|3RIA|B Chain B, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Iodide.
pdb|3RIA|C Chain C, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Iodide.
pdb|3RIA|D Chain D, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Iodide.
pdb|3RIA|E Chain E, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Iodide.
pdb|3RIF|A Chain A, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Glutamate.
pdb|3RIF|B Chain B, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Glutamate.
pdb|3RIF|C Chain C, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Glutamate.
pdb|3RIF|D Chain D, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Glutamate.
pdb|3RIF|E Chain E, C. Elegans Glutamate-Gated Chloride Channel (Glucl) In
Complex With Fab, Ivermectin And Glutamate
Length = 347
Score = 116 bits (291), Expect = 9e-27, Method: Compositional matrix adjust.
Identities = 81/233 (34%), Positives = 107/233 (45%), Gaps = 62/233 (26%)
Query: 1 EYSVQLTFREQWLDERLKYN-DYDGRIKYLTLTEASRVWMPDLFFSNEKEGHFHNIIMPN 59
EYS QLT RE W+D+RL Y DG+ ++ LT H I MP+
Sbjct: 48 EYSAQLTLRESWIDKRLSYGVKGDGQPDFVILTVG------------------HQIWMPD 89
Query: 60 VYIRIHPQGSVLYSISDLDNMRQCEVHMTVPQTPRKNCCRSWLAKFPTRSKRIDVISRIT 119
+ N +Q H + +V+ RI
Sbjct: 90 TF---------------FPNEKQAYKHTI---------------------DKPNVLIRI- 112
Query: 120 FPLVFALFNLTYWSTISLTLSCPMNLKLYPLDRQSCSLKMASYGWTTDDLIFLWKEGDPV 179
+ Y ISL LSCPM L+ YP+D Q CS+ +ASY +TT D+ +LWKE P+
Sbjct: 113 ----HNDGTVLYSVRISLVLSCPMYLQYYPMDVQQCSIDLASYAYTTKDIEYLWKEHSPL 168
Query: 180 QVVKNL--HLPRFTLEKFYTDYCNSKTNTGAYSCLKVDLLFKREFSYYLIQIY 230
Q+ L LP F L T YC S TNTG YSCL+ + KREFS+YL+Q+Y
Sbjct: 169 QLKVGLSSSLPSFQLTNTSTTYCTSVTNTGIYSCLRTTIQLKREFSFYLLQLY 221
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 15/25 (60%), Positives = 21/25 (84%)
Query: 109 SKRIDVISRITFPLVFALFNLTYWS 133
SKR+D+ISR FP++F +FN+ YWS
Sbjct: 312 SKRVDLISRALFPVLFFVFNILYWS 336
>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 = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 8 FREQWLDERLKYNDYD-GRIKYLTLTEASRVWMPDLFFSNEKEGHF 52
R+QW+D RL++N D G IK + L + VW+PDL N +G F
Sbjct: 80 LRQQWIDVRLRWNPADYGGIKKIRL-PSDDVWLPDLVLYNNADGDF 124
>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 = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 8 FREQWLDERLKYNDYD-GRIKYLTLTEASRVWMPDLFFSNEKEGHF 52
R+QW+D RL++N D G IK + L + VW+PDL N +G F
Sbjct: 56 LRQQWIDVRLRWNPADYGGIKKIRL-PSDDVWLPDLVLYNNADGDF 100
>pdb|2QC1|B Chain B, Crystal Structure Of The Extracellular Domain Of The
Nicotinic Acetylcholine Receptor 1 Subunit Bound To
Alpha-Bungarotoxin At 1.9 A Resolution
Length = 212
Score = 33.9 bits (76), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 29/51 (56%), Gaps = 2/51 (3%)
Query: 3 SVQLTFREQWLDERLKYNDYD-GRIKYLTLTEASRVWMPDLFFSNEKEGHF 52
+ + ++QW+D LK+N D G +K + + + ++W PD+ N +G F
Sbjct: 52 TTNVRLKQQWVDYNLKWNPDDYGGVKKIHIP-SEKIWRPDVVLYNNADGDF 101
>pdb|2BG9|C Chain C, Refined Structure Of The Nicotinic Acetylcholine Receptor
At 4a Resolution
Length = 369
Score = 33.9 bits (76), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 48/226 (21%), Positives = 76/226 (33%), Gaps = 80/226 (35%)
Query: 12 WLDERLKYNDYDGRIKYLTLTEASRVWMPDLFFSNEKEGHFHNIIMPNVYIRIHPQGSVL 71
W D RL +N + + +W+PD+ N +G ++ NV +R P G V
Sbjct: 62 WYDHRLTWNASEYSDISILRLRPELIWIPDIVLQNNNDGQYNVAYFCNVLVR--PNGYV- 118
Query: 72 YSISDLDNMRQCEVHMTVPQTPRKNCCRSWLAKFPTRSKRIDVISRITFPLVFALFNLTY 131
+WL RS
Sbjct: 119 ----------------------------TWLPPAIFRS---------------------- 128
Query: 132 WSTISLTLSCPMNLKLYPLDRQSCSLKMASYGWTTD----DLIFLWKEGDPVQVVKN--- 184
SCP+N+ +P D Q+CSLK + + + DLI DP +N
Sbjct: 129 --------SCPINVLYFPFDWQNCSLKFTALNYNANEISMDLII-----DPEAFTENGEW 175
Query: 185 --LHLPRFTLEKFYTDYCNSKTNTGAYSCLKVDLLFKREFSYYLIQ 228
+H P + Y D + TN Y + L+ +R+ +Y+I
Sbjct: 176 EIIHKP--AKKNIYGDKFPNGTN---YQDVTFYLIIRRKPLFYVIN 216
>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 = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 31/158 (19%), Positives = 51/158 (32%), Gaps = 61/158 (38%)
Query: 12 WLDERLKYNDYDGRIKYLTLTEASRVWMPDLFFSNEKEGHFHNIIMPNVYIRIHPQGSVL 71
W D RL +N + + +W+PD+ N +G ++ NV +R P G V
Sbjct: 83 WYDHRLTWNASEYSDISILRLRPELIWIPDIVLQNNNDGQYNVAYFCNVLVR--PNGYV- 139
Query: 72 YSISDLDNMRQCEVHMTVPQTPRKNCCRSWLAKFPTRSKRIDVISRITFPLVFALFNLTY 131
+WL RS
Sbjct: 140 ----------------------------TWLPPAIFRS---------------------- 149
Query: 132 WSTISLTLSCPMNLKLYPLDRQSCSLKMASYGWTTDDL 169
SCP+N+ +P D Q+CSLK + + +++
Sbjct: 150 --------SCPINVLYFPFDWQNCSLKFTALNYNANEI 179
>pdb|2BG9|B Chain B, Refined Structure Of The Nicotinic Acetylcholine Receptor
At 4a Resolution
Length = 370
Score = 30.8 bits (68), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 1 EYSVQLTFREQWLDERLKYN--DYDGRIKYLTLTEASRVWMPDLFFSNEKEGHFHNIIMP 58
E + + W D RL+++ Y+G IK L++ + VW PD+ N +G F +
Sbjct: 49 EMTTSVFLNLAWTDYRLQWDPAAYEG-IKDLSI-PSDDVWQPDIVLMNNNDGSFEITLHV 106
Query: 59 NVYIR 63
NV ++
Sbjct: 107 NVLVQ 111
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 140 SCPMNLKLYPLDRQSCSLKMASYGWTTDDLIF 171
SC + + +P D Q+C++ SY + T ++I
Sbjct: 127 SCTIKVMYFPFDWQNCTMVFKSYTYDTSEVIL 158
>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 = 30.8 bits (68), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 33/65 (50%), Gaps = 4/65 (6%)
Query: 1 EYSVQLTFREQWLDERLKYND--YDGRIKYLTLTEASRVWMPDLFFSNEKEGHFHNIIMP 58
E + + W D RL+++ Y+G IK L++ + VW PD+ N +G F +
Sbjct: 73 EMTTSVFLNLAWTDYRLQWDPAAYEG-IKDLSI-PSDDVWQPDIVLMNNNDGSFEITLHV 130
Query: 59 NVYIR 63
NV ++
Sbjct: 131 NVLVQ 135
Score = 26.9 bits (58), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 10/32 (31%), Positives = 19/32 (59%)
Query: 140 SCPMNLKLYPLDRQSCSLKMASYGWTTDDLIF 171
SC + + +P D Q+C++ SY + T ++I
Sbjct: 151 SCTIKVMYFPFDWQNCTMVFKSYTYDTSEVIL 182
>pdb|2BG9|E Chain E, Refined Structure Of The Nicotinic Acetylcholine Receptor
At 4a Resolution
Length = 370
Score = 30.4 bits (67), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 23/52 (44%)
Query: 11 QWLDERLKYNDYDGRIKYLTLTEASRVWMPDLFFSNEKEGHFHNIIMPNVYI 62
QW D RL +N + L + +W+PD+ N +G F NV +
Sbjct: 58 QWNDYRLSWNTSEYEGIDLVRIPSELLWLPDVVLENNVDGQFEVAYYANVLV 109
>pdb|2GGO|A Chain A, Crystal Structure Of Glucose-1-Phosphate
Thymidylyltransferase From Sulfolobus Tokodaii
pdb|2GGQ|A Chain A, Complex Of Hypothetical Glucose-1-Phosphate
Thymidylyltransferase From Sulfolobus Tokodaii
Length = 401
Score = 30.4 bits (67), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 28/67 (41%), Gaps = 4/67 (5%)
Query: 41 DLFFSNEKEGHFHNIIM--PNVYIRIHPQGSVLYSISDLDNMRQCEVHMTVPQTPRKNCC 98
DLFFSNEKE NII N I + Y + LDN + P+ P N
Sbjct: 99 DLFFSNEKE--ICNIITLKENAIIGVKVSNPKDYGVLVLDNQNNLSKIIEKPEIPPSNLI 156
Query: 99 RSWLAKF 105
+ + K
Sbjct: 157 NAGIYKL 163
>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 = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 23/52 (44%)
Query: 11 QWLDERLKYNDYDGRIKYLTLTEASRVWMPDLFFSNEKEGHFHNIIMPNVYI 62
QW D RL +N + L + +W+PD+ N +G F NV +
Sbjct: 58 QWNDYRLSWNTSEYEGIDLVRIPSELLWLPDVVLENNVDGQFEVAYYANVLV 109
>pdb|2OAF|A Chain A, Crystal Structure Of Thioesterase Superfamily
(Yp_508616.1) From Jannaschia Sp. Ccs1 At 2.00 A
Resolution
pdb|2OAF|B Chain B, Crystal Structure Of Thioesterase Superfamily
(Yp_508616.1) From Jannaschia Sp. Ccs1 At 2.00 A
Resolution
Length = 151
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 168 DLIFLWKEGDPVQVVKNLHLPRFTLE 193
D+ W + DP ++ HLPRF LE
Sbjct: 20 DVRVTWGDCDPAKIAYTGHLPRFALE 45
>pdb|2WW8|A Chain A, Structure Of The Pilus Adhesin (Rrga) From Streptococcus
Pneumoniae
Length = 893
Score = 28.9 bits (63), Expect = 2.4, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 29/47 (61%), Gaps = 5/47 (10%)
Query: 46 NEKEGHFHNIIMPNVYIRIHPQGSV---LYSISDLDNMRQCEVHMTV 89
+EK G H + PN Y R+ P+G++ +Y +++LD+ Q + +TV
Sbjct: 166 SEKNGQ-HKALNPNPYERVIPEGTLSKRIYQVNNLDD-NQYGIELTV 210
>pdb|1IAG|A Chain A, First Structure Of A Snake Venom Metalloproteinase: A
Prototype For Matrix
Metalloproteinases(Slash)collagenases
Length = 202
Score = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 14/57 (24%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 152 RQSCSLKMASYGWTTDDLIFLWKEGDPVQVVKNLHLPRFTLEKFYT-DYCNSKTNTG 207
+ S S + S+G + ++ +WK D Q++ ++ + K YT CN +++ G
Sbjct: 68 QSSSSNTLNSFGEWRERVLLIWKRHDNAQLLTAINFEGKIIGKAYTSSMCNPRSSVG 124
>pdb|3CIH|A Chain A, Crystal Structure Of A Putative Alpha-Rhamnosidase From
Bacteroides Thetaiotaomicron
Length = 739
Score = 27.7 bits (60), Expect = 5.7, Method: Composition-based stats.
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 21 DYDGRIKYLTLTEASRVWMPDLFFSNEKEGHFHNII 56
D DG+ KY L A + + F++N+K+ HN +
Sbjct: 476 DKDGQQKYEKLASALKAKLEPTFWNNQKQAFVHNCV 511
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 0.139 0.449
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,251,394
Number of Sequences: 62578
Number of extensions: 293143
Number of successful extensions: 695
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 672
Number of HSP's gapped (non-prelim): 28
length of query: 232
length of database: 14,973,337
effective HSP length: 96
effective length of query: 136
effective length of database: 8,965,849
effective search space: 1219355464
effective search space used: 1219355464
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: 50 (23.9 bits)