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= psy17538
(164 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2OEW|A Chain A, Structure Of AlixAIP1 BRO1 DOMAIN
pdb|3C3O|A Chain A, Alix Bro1-Domain:chmip4a Co-Crystal Structure
pdb|3C3Q|A Chain A, Alix Bro1-domain:chmip4b Co-crystal Structure
pdb|3C3R|A Chain A, Alix Bro1 Chmp4c Complex
Length = 380
Score = 137 bits (344), Expect = 4e-33, Method: Compositional matrix adjust.
Identities = 72/167 (43%), Positives = 98/167 (58%), Gaps = 4/167 (2%)
Query: 1 MAEFLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEK 60
MA F++V LKK ++VD+ KPL I +P+ E+ SKLR AAV + +K
Sbjct: 22 MATFISVQLKKTSEVDLAKPLVKFIQQTYPSGGEEQAQYCRAAEELSKLRRAAVGRPLDK 81
Query: 61 HESSLEVIYSYYDHLVSLESKIFPATVN---IPFRWKDAFNKGSLFGGRISLTVCSLAWE 117
HE +LE + YYD + S+E K FP + N + F WKDAF+KGSLFGG + L + SL +E
Sbjct: 82 HEGALETLLRYYDQICSIEPK-FPFSENQICLTFTWKDAFDKGSLFGGSVKLALASLGYE 140
Query: 118 RVCVLFNXXXXXXXXXXXXXXDTDEGLKLAAKMLQSSAGIFNYLKST 164
+ CVLFN D DEGLK+AAK Q ++G F ++K T
Sbjct: 141 KSCVLFNCAALASQIAAEQNLDNDEGLKIAAKHYQFASGAFLHIKET 187
>pdb|2OEV|A Chain A, Crystal Structure Of AlixAIP1
Length = 705
Score = 136 bits (342), Expect = 6e-33, Method: Compositional matrix adjust.
Identities = 72/167 (43%), Positives = 98/167 (58%), Gaps = 4/167 (2%)
Query: 1 MAEFLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEK 60
MA F++V LKK ++VD+ KPL I +P+ E+ SKLR AAV + +K
Sbjct: 8 MATFISVQLKKTSEVDLAKPLVKFIQQTYPSGGEEQAQYCRAAEELSKLRRAAVGRPLDK 67
Query: 61 HESSLEVIYSYYDHLVSLESKIFPATVN---IPFRWKDAFNKGSLFGGRISLTVCSLAWE 117
HE +LE + YYD + S+E K FP + N + F WKDAF+KGSLFGG + L + SL +E
Sbjct: 68 HEGALETLLRYYDQICSIEPK-FPFSENQICLTFTWKDAFDKGSLFGGSVKLALASLGYE 126
Query: 118 RVCVLFNXXXXXXXXXXXXXXDTDEGLKLAAKMLQSSAGIFNYLKST 164
+ CVLFN D DEGLK+AAK Q ++G F ++K T
Sbjct: 127 KSCVLFNCAALASQIAAEQNLDNDEGLKIAAKHYQFASGAFLHIKET 173
>pdb|2XS1|A Chain A, Crystal Structure Of Alix In Complex With The Sivmac239
Pykevtedl Late Domain
pdb|2XS8|A Chain A, Crystal Structure Of Alix In Complex With The Sivagmtan-1
Aydparkll Late Domain
Length = 704
Score = 136 bits (342), Expect = 6e-33, Method: Compositional matrix adjust.
Identities = 72/167 (43%), Positives = 98/167 (58%), Gaps = 4/167 (2%)
Query: 1 MAEFLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEK 60
MA F++V LKK ++VD+ KPL I +P+ E+ SKLR AAV + +K
Sbjct: 7 MATFISVQLKKTSEVDLAKPLVKFIQQTYPSGGEEQAQYCRAAEELSKLRRAAVGRPLDK 66
Query: 61 HESSLEVIYSYYDHLVSLESKIFPATVN---IPFRWKDAFNKGSLFGGRISLTVCSLAWE 117
HE +LE + YYD + S+E K FP + N + F WKDAF+KGSLFGG + L + SL +E
Sbjct: 67 HEGALETLLRYYDQICSIEPK-FPFSENQICLTFTWKDAFDKGSLFGGSVKLALASLGYE 125
Query: 118 RVCVLFNXXXXXXXXXXXXXXDTDEGLKLAAKMLQSSAGIFNYLKST 164
+ CVLFN D DEGLK+AAK Q ++G F ++K T
Sbjct: 126 KSCVLFNCAALASQIAAEQNLDNDEGLKIAAKHYQFASGAFLHIKET 172
>pdb|2R02|A Chain A, Crystal Structure Of AlixAIP1 IN COMPLEX WITH THE HIV-1
Ypltsl Late Domain
pdb|2R03|A Chain A, Crystal Structure Of AlixAIP1 IN COMPLEX WITH THE YPDL
Late Domain
pdb|2R05|A Chain A, Crystal Structure Of AlixAIP1 IN COMPLEX WITH THE HIV-1
Yplasl Late Domain
Length = 697
Score = 134 bits (336), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 71/166 (42%), Positives = 97/166 (58%), Gaps = 4/166 (2%)
Query: 2 AEFLAVPLKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAAVWKVFEKH 61
A F++V LKK ++VD+ KPL I +P+ E+ SKLR AAV + +KH
Sbjct: 1 ATFISVQLKKTSEVDLAKPLVKFIQQTYPSGGEEQAQYCRAAEELSKLRRAAVGRPLDKH 60
Query: 62 ESSLEVIYSYYDHLVSLESKIFPATVN---IPFRWKDAFNKGSLFGGRISLTVCSLAWER 118
E +LE + YYD + S+E K FP + N + F WKDAF+KGSLFGG + L + SL +E+
Sbjct: 61 EGALETLLRYYDQICSIEPK-FPFSENQICLTFTWKDAFDKGSLFGGSVKLALASLGYEK 119
Query: 119 VCVLFNXXXXXXXXXXXXXXDTDEGLKLAAKMLQSSAGIFNYLKST 164
CVLFN D DEGLK+AAK Q ++G F ++K T
Sbjct: 120 SCVLFNCAALASQIAAEQNLDNDEGLKIAAKHYQFASGAFLHIKET 165
>pdb|3RAU|A Chain A, Crystal Structure Of The Hd-Ptp Bro1 Domain
pdb|3RAU|B Chain B, Crystal Structure Of The Hd-Ptp Bro1 Domain
Length = 363
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 43/172 (25%), Positives = 71/172 (41%), Gaps = 23/172 (13%)
Query: 2 AEFLAVP--------LKKPTDVDIIKPLKNLIALQFPNDNEKLDILNEKLNLFSKLRTAA 53
EF AVP LK+ D +K + N E + NE+L LR A
Sbjct: 1 GEFEAVPRMPMIWLDLKEAGDFHFQPAVKKFV---LKNYGENPEAYNEELKKLELLRQNA 57
Query: 54 VWKVFEKHESSLEVIYSYYDHLVSLESKIFPAT---VNIPFRWKDAFNKGSLFGGRISLT 110
V +V E V+ Y L L+S++ + +P W + +F G+ S+
Sbjct: 58 V-RVPRDFEGC-SVLRKYLGQLHYLQSRVPMGSGQEAAVPVTWTE------IFSGK-SVA 108
Query: 111 VCSLAWERVCVLFNXXXXXXXXXXXXXXDTDEGLKLAAKMLQSSAGIFNYLK 162
+ +E+ C+L+N ++EG+K++ Q +AG F YL+
Sbjct: 109 HEDIKYEQACILYNLGALHSMLGAMDKRVSEEGMKVSCTHFQCAAGAFAYLR 160
>pdb|1ZB1|A Chain A, Structure Basis For Endosomal Targeting By The Bro1 Domain
pdb|1ZB1|B Chain B, Structure Basis For Endosomal Targeting By The Bro1 Domain
Length = 392
Score = 27.7 bits (60), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 5/57 (8%)
Query: 69 YSYYDHLV-SLESKIFPATVNIPFRWKDAFNKGSLFGGRISLTVCSLAWERVCVLFN 124
YS+ +HL L SK + + + F W DA + G + T +LA+E+ C LFN
Sbjct: 76 YSFLEHLYFRLGSK--GSRLKMDFTWYDAEYSSAQKG--LKYTQHTLAFEKSCTLFN 128
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 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,357,286
Number of Sequences: 62578
Number of extensions: 151225
Number of successful extensions: 363
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 351
Number of HSP's gapped (non-prelim): 7
length of query: 164
length of database: 14,973,337
effective HSP length: 91
effective length of query: 73
effective length of database: 9,278,739
effective search space: 677347947
effective search space used: 677347947
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: 47 (22.7 bits)