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= psy18020
(434 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2F0R|A Chain A, Crystallographic Structure Of Human Tsg101 Uev Domain
pdb|2F0R|B Chain B, Crystallographic Structure Of Human Tsg101 Uev Domain
Length = 159
Score = 91.7 bits (226), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 38/79 (48%), Positives = 53/79 (67%)
Query: 6 GLVYHIPVCIWLMDTHPDHAPICYVRPTADMRINVSQNVDHTGKIYSPYLHTWTPQNSKL 65
G Y+IP+C+WL+DT+P + PIC+V+PT+ M I ++VD GKIY PYLH W S L
Sbjct: 79 GNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDL 138
Query: 66 EGLIKTLASAFSALPPLYS 84
GLI+ + F PP++S
Sbjct: 139 LGLIQVMIVVFGDEPPVFS 157
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 24/55 (43%), Positives = 33/55 (60%)
Query: 101 IRPTADMRINVSQNVDHTGKIYSPYLHTWTAQNSKLEGLIKTLASAFSALPPLYS 155
++PT+ M I ++VD GKIY PYLH W S L GLI+ + F PP++S
Sbjct: 103 VKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFS 157
>pdb|3OBQ|A Chain A, Crystal Structure Of The Tsg101 Uev Domain In Complex With
A Human Hrs Psap Peptide
pdb|3OBS|A Chain A, Crystal Structure Of Tsg101 Uev Domain
pdb|3OBU|A Chain A, Crystal Structure Of The Tsg101 Uev Domain In Complex With
A Hiv-1 Ptap Peptide
pdb|3OBX|A Chain A, Crystal Structure Of The Tsg101 Uev Domain In Complex With
A Hiv-1 Gag P7a Mutant Peptide
Length = 146
Score = 91.3 bits (225), Expect = 8e-19, Method: Compositional matrix adjust.
Identities = 38/79 (48%), Positives = 53/79 (67%)
Query: 6 GLVYHIPVCIWLMDTHPDHAPICYVRPTADMRINVSQNVDHTGKIYSPYLHTWTPQNSKL 65
G Y+IP+C+WL+DT+P + PIC+V+PT+ M I ++VD GKIY PYLH W S L
Sbjct: 66 GNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDL 125
Query: 66 EGLIKTLASAFSALPPLYS 84
GLI+ + F PP++S
Sbjct: 126 LGLIQVMIVVFGDEPPVFS 144
Score = 55.8 bits (133), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 24/55 (43%), Positives = 33/55 (60%)
Query: 101 IRPTADMRINVSQNVDHTGKIYSPYLHTWTAQNSKLEGLIKTLASAFSALPPLYS 155
++PT+ M I ++VD GKIY PYLH W S L GLI+ + F PP++S
Sbjct: 90 VKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFS 144
>pdb|3P9G|A Chain A, Crystal Structure Of The Tsg101 Uev Domain In Complex With
Fa459 Peptide
pdb|3P9H|A Chain A, Crystal Structure Of The Tsg101 Uev Domain In Complex With
Fa258 Peptide
Length = 145
Score = 91.3 bits (225), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 38/79 (48%), Positives = 53/79 (67%)
Query: 6 GLVYHIPVCIWLMDTHPDHAPICYVRPTADMRINVSQNVDHTGKIYSPYLHTWTPQNSKL 65
G Y+IP+C+WL+DT+P + PIC+V+PT+ M I ++VD GKIY PYLH W S L
Sbjct: 65 GNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDL 124
Query: 66 EGLIKTLASAFSALPPLYS 84
GLI+ + F PP++S
Sbjct: 125 LGLIQVMIVVFGDEPPVFS 143
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 24/55 (43%), Positives = 33/55 (60%)
Query: 101 IRPTADMRINVSQNVDHTGKIYSPYLHTWTAQNSKLEGLIKTLASAFSALPPLYS 155
++PT+ M I ++VD GKIY PYLH W S L GLI+ + F PP++S
Sbjct: 89 VKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFS 143
>pdb|1KPP|A Chain A, Structure Of The Tsg101 Uev Domain
pdb|1KPQ|A Chain A, Structure Of The Tsg101 Uev Domain
pdb|1M4P|A Chain A, Structure Of The Tsg101 Uev Domain In Complex With A Hiv-1
Ptap "late Domain" Peptide, Dyana Ensemble
pdb|1M4Q|A Chain A, Structure Of The Tsg101 Uev Domain In Complex With A Hiv-1
Ptap "late Domain" Peptide, Cns Ensemble
Length = 145
Score = 91.3 bits (225), Expect = 9e-19, Method: Compositional matrix adjust.
Identities = 38/79 (48%), Positives = 53/79 (67%)
Query: 6 GLVYHIPVCIWLMDTHPDHAPICYVRPTADMRINVSQNVDHTGKIYSPYLHTWTPQNSKL 65
G Y+IP+C+WL+DT+P + PIC+V+PT+ M I ++VD GKIY PYLH W S L
Sbjct: 65 GNTYNIPICLWLLDTYPYNPPICFVKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDL 124
Query: 66 EGLIKTLASAFSALPPLYS 84
GLI+ + F PP++S
Sbjct: 125 LGLIQVMIVVFGDEPPVFS 143
Score = 55.8 bits (133), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 24/55 (43%), Positives = 33/55 (60%)
Query: 101 IRPTADMRINVSQNVDHTGKIYSPYLHTWTAQNSKLEGLIKTLASAFSALPPLYS 155
++PT+ M I ++VD GKIY PYLH W S L GLI+ + F PP++S
Sbjct: 89 VKPTSSMTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVMIVVFGDEPPVFS 143
>pdb|1S1Q|A Chain A, Tsg101(Uev) Domain In Complex With Ubiquitin
pdb|1S1Q|C Chain C, Tsg101(Uev) Domain In Complex With Ubiquitin
Length = 145
Score = 87.4 bits (215), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 39/92 (42%), Positives = 56/92 (60%), Gaps = 8/92 (8%)
Query: 1 MTNLSGLV--------YHIPVCIWLMDTHPDHAPICYVRPTADMRINVSQNVDHTGKIYS 52
+ NL+G + Y+IP+C+WL+DT+P + PIC+V+PT+ I ++VD GKIY
Sbjct: 52 LXNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVKPTSSXTIKTGKHVDANGKIYL 111
Query: 53 PYLHTWTPQNSKLEGLIKTLASAFSALPPLYS 84
PYLH W S L GLI+ F PP++S
Sbjct: 112 PYLHEWKHPQSDLLGLIQVXIVVFGDEPPVFS 143
Score = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 31/55 (56%)
Query: 101 IRPTADMRINVSQNVDHTGKIYSPYLHTWTAQNSKLEGLIKTLASAFSALPPLYS 155
++PT+ I ++VD GKIY PYLH W S L GLI+ F PP++S
Sbjct: 89 VKPTSSXTIKTGKHVDANGKIYLPYLHEWKHPQSDLLGLIQVXIVVFGDEPPVFS 143
>pdb|3IV1|A Chain A, Coiled-Coil Domain Of Tumor Susceptibility Gene 101
pdb|3IV1|B Chain B, Coiled-Coil Domain Of Tumor Susceptibility Gene 101
pdb|3IV1|C Chain C, Coiled-Coil Domain Of Tumor Susceptibility Gene 101
pdb|3IV1|D Chain D, Coiled-Coil Domain Of Tumor Susceptibility Gene 101
pdb|3IV1|E Chain E, Coiled-Coil Domain Of Tumor Susceptibility Gene 101
pdb|3IV1|F Chain F, Coiled-Coil Domain Of Tumor Susceptibility Gene 101
pdb|3IV1|G Chain G, Coiled-Coil Domain Of Tumor Susceptibility Gene 101
pdb|3IV1|H Chain H, Coiled-Coil Domain Of Tumor Susceptibility Gene 101
Length = 78
Score = 59.3 bits (142), Expect = 4e-09, Method: Composition-based stats.
Identities = 32/74 (43%), Positives = 48/74 (64%)
Query: 276 SLKSAVEDKIRRKMNEQKVQAQEEIEILKQTENELNQGKFKLARMFERIDKEKAELERSI 335
SL SAV DK+R + E+ +AQ E+ LK+TE +L +G KL R+D+E AE++++I
Sbjct: 3 SLISAVSDKLRWRXKEEXDRAQAELNALKRTEEDLKKGHQKLEEXVTRLDQEVAEVDKNI 62
Query: 336 SFLKEKETELDEIL 349
LK+K+ EL L
Sbjct: 63 ELLKKKDEELSSAL 76
>pdb|2P22|A Chain A, Structure Of The Yeast Escrt-i Heterotetramer Core
Length = 174
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 29/48 (60%)
Query: 373 QILNTFTEEAATEDTIYYMGEALRRGVIDLEVYLKQVRSLSRKQFMFR 420
Q+ N ++ A DTI + L RG I L+ ++KQ R L+R+QF+ R
Sbjct: 116 QLYNLVAQDYALTDTIECLSRMLHRGTIPLDTFVKQGRELARQQFLVR 163
>pdb|2CAZ|A Chain A, Escrt-I Core
pdb|2CAZ|D Chain D, Escrt-I Core
Length = 82
Score = 41.6 bits (96), Expect = 8e-04, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 29/48 (60%)
Query: 373 QILNTFTEEAATEDTIYYMGEALRRGVIDLEVYLKQVRSLSRKQFMFR 420
Q+ N ++ A DTI + L RG I L+ ++KQ R L+R+QF+ R
Sbjct: 24 QLYNLVAQDYALTDTIECLSRMLHRGTIPLDTFVKQGRELARQQFLVR 71
>pdb|2F66|A Chain A, Structure Of The Escrt-I Endosomal Trafficking Complex
pdb|2F66|D Chain D, Structure Of The Escrt-I Endosomal Trafficking Complex
pdb|2F6M|A Chain A, Structure Of A Vps23-C:vps28-N Subcomplex
pdb|2F6M|C Chain C, Structure Of A Vps23-C:vps28-N Subcomplex
Length = 65
Score = 41.6 bits (96), Expect = 9e-04, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 29/48 (60%)
Query: 373 QILNTFTEEAATEDTIYYMGEALRRGVIDLEVYLKQVRSLSRKQFMFR 420
Q+ N ++ A DTI + L RG I L+ ++KQ R L+R+QF+ R
Sbjct: 7 QLYNLVAQDYALTDTIEALSRMLHRGTIPLDTFVKQGRELARQQFLVR 54
>pdb|3R3Q|A Chain A, Crystal Structure Of The Yeast Vps23 Uev Domain
pdb|3R42|A Chain A, Crystal Structure Of The Yeast Vps23 Uev Domain In Complex
With A Vps27 Psdp Peptide
Length = 162
Score = 30.4 bits (67), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 6/72 (8%)
Query: 9 YHIPVCIWLMDTHPDHAPICYVR------PTADMRINVSQNVDHTGKIYSPYLHTWTPQN 62
+ IPV +W+ +P P + T + + + +D G I P LH W P
Sbjct: 81 HSIPVIMWVPSMYPVKPPFISINLENFDMNTISSSLPIQEYIDSNGWIALPILHAWDPAA 140
Query: 63 SKLEGLIKTLAS 74
L +++ L S
Sbjct: 141 MNLIMVVQELMS 152
>pdb|1UZX|A Chain A, A Complex Of The Vps23 Uev With Ubiquitin
Length = 169
Score = 30.0 bits (66), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 29/72 (40%), Gaps = 6/72 (8%)
Query: 9 YHIPVCIWLMDTHPDHAPICYVR------PTADMRINVSQNVDHTGKIYSPYLHTWTPQN 62
+ IPV W+ +P P + T + + + +D G I P LH W P
Sbjct: 87 HSIPVIXWVPSXYPVKPPFISINLENFDXNTISSSLPIQEYIDSNGWIALPILHCWDPAA 146
Query: 63 SKLEGLIKTLAS 74
L +++ L S
Sbjct: 147 XNLIXVVQELXS 158
>pdb|3Q8T|A Chain A, Crystal Structure Of The Coiled Coil Domain Of Beclin 1,
An Essential Autophagy Protein
pdb|3Q8T|B Chain B, Crystal Structure Of The Coiled Coil Domain Of Beclin 1,
An Essential Autophagy Protein
Length = 96
Score = 28.1 bits (61), Expect = 8.7, Method: Composition-based stats.
Identities = 15/52 (28%), Positives = 31/52 (59%)
Query: 298 EEIEILKQTENELNQGKFKLARMFERIDKEKAELERSISFLKEKETELDEIL 349
+E+E +++ + + K+ ER+D+E+A+ +R S K ++ ELD+ L
Sbjct: 25 QELEDVEKNRKVVAENLEKVQAEAERLDQEEAQYQREYSEFKRQQLELDDEL 76
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
0.316 0.130 0.377
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,515,701
Number of Sequences: 62578
Number of extensions: 327992
Number of successful extensions: 1084
Number of sequences better than 100.0: 31
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 912
Number of HSP's gapped (non-prelim): 64
length of query: 434
length of database: 14,973,337
effective HSP length: 102
effective length of query: 332
effective length of database: 8,590,381
effective search space: 2852006492
effective search space used: 2852006492
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)