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= psy12912
(185 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2J9W|A Chain A, Structural Insight Into The Escrt-I-Ii Link And Its Role
In Mvb Trafficking
pdb|2J9W|B Chain B, Structural Insight Into The Escrt-I-Ii Link And Its Role
In Mvb Trafficking
Length = 102
Score = 124 bits (311), Expect = 3e-29, Method: Compositional matrix adjust.
Identities = 57/78 (73%), Positives = 69/78 (88%)
Query: 106 GNTSKCIADIVSLFITTMDKLRLDIKAMDELQPDLRDLMDTMNRLSILPSGFEGKEKVSG 165
GN ++CIADIVSLFIT MDKLRL+I+AMDE+QPDLR+LM+TMNR+S LP FEG+EKVS
Sbjct: 4 GNLNRCIADIVSLFITVMDKLRLEIRAMDEIQPDLRELMETMNRMSHLPPDFEGREKVSQ 63
Query: 166 WLTTLESMSASDELNETQ 183
WL L SMSASDEL+++Q
Sbjct: 64 WLQKLSSMSASDELDDSQ 81
>pdb|2F66|B Chain B, Structure Of The Escrt-I Endosomal Trafficking Complex
pdb|2F66|E Chain E, Structure Of The Escrt-I Endosomal Trafficking Complex
Length = 116
Score = 60.1 bits (144), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 32/103 (31%), Positives = 57/103 (55%), Gaps = 7/103 (6%)
Query: 5 EEVKLFTNT---KEREKFDNQADLYAVINTLQNLEKAYIRDCVTPKEYTAACSKLLVQYK 61
+EV LF N+ K++E + +++Y+++ TL ++EKAY++D + +YT KLL Q+K
Sbjct: 11 DEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFK 70
Query: 62 AAFKQVQGEE----YPTVEHFVKKYRLDCPSALERIREDRPIT 100
EE + ++E F Y + +A+ R+ PIT
Sbjct: 71 VYLNSQNKEEINKHFQSIEAFADTYNITASNAITRLERGIPIT 113
>pdb|2CAZ|B Chain B, Escrt-I Core
pdb|2CAZ|E Chain E, Escrt-I Core
Length = 155
Score = 59.3 bits (142), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 32/103 (31%), Positives = 57/103 (55%), Gaps = 7/103 (6%)
Query: 5 EEVKLFTNT---KEREKFDNQADLYAVINTLQNLEKAYIRDCVTPKEYTAACSKLLVQYK 61
+EV LF N+ K++E + +++Y+++ TL ++EKAY++D + +YT KLL Q+K
Sbjct: 28 DEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFK 87
Query: 62 AAFKQVQGEE----YPTVEHFVKKYRLDCPSALERIREDRPIT 100
EE + ++E F Y + +A+ R+ PIT
Sbjct: 88 VYLNSQNKEEINKHFQSIEAFCDTYNITASNAITRLERGIPIT 130
>pdb|2F6M|B Chain B, Structure Of A Vps23-C:vps28-N Subcomplex
pdb|2F6M|D Chain D, Structure Of A Vps23-C:vps28-N Subcomplex
Length = 109
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 29/96 (30%), Positives = 54/96 (56%), Gaps = 7/96 (7%)
Query: 5 EEVKLFTNT---KEREKFDNQADLYAVINTLQNLEKAYIRDCVTPKEYTAACSKLLVQYK 61
+EV LF N+ K++E + +++Y+++ TL ++EKAY++D + +YT KLL Q+K
Sbjct: 11 DEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFK 70
Query: 62 AAFKQVQGEE----YPTVEHFVKKYRLDCPSALERI 93
EE + ++E F Y + +A+ R+
Sbjct: 71 VYLNSQNKEEINKHFQSIEAFADTYNITASNAITRL 106
>pdb|2P22|B Chain B, Structure Of The Yeast Escrt-i Heterotetramer Core
Length = 118
Score = 55.1 bits (131), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 29/96 (30%), Positives = 54/96 (56%), Gaps = 7/96 (7%)
Query: 5 EEVKLFTNT---KEREKFDNQADLYAVINTLQNLEKAYIRDCVTPKEYTAACSKLLVQYK 61
+EV LF N+ K++E + +++Y+++ TL ++EKAY++D + +YT KLL Q+K
Sbjct: 20 DEVPLFDNSITSKDKEVIETLSEIYSIVITLDHVEKAYLKDSIDDTQYTNTVDKLLKQFK 79
Query: 62 AAFKQVQGEE----YPTVEHFVKKYRLDCPSALERI 93
EE + ++E F Y + +A+ R+
Sbjct: 80 VYLNSQNKEEINKHFQSIEAFADTYNITASNAITRL 115
>pdb|2J9V|A Chain A, 2 Angstrom X-Ray Structure Of The Yeast Escrt-I Vps28 C-
Terminus
Length = 99
Score = 53.5 bits (127), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 2/75 (2%)
Query: 109 SKCIADIVSLFITTMDKLRLDIKAMDELQPDLRDLMDTMNRLSILPSGFEGKEKVSGWLT 168
+K +A+ FIT MD L+L+ A D+L P L +L+ ++NR++ FE + K+ W+
Sbjct: 7 AKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVT--RDDFENRSKLIDWIV 64
Query: 169 TLESMSASDELNETQ 183
+ +S D L ETQ
Sbjct: 65 RINKLSIGDTLTETQ 79
>pdb|2J9U|A Chain A, 2 Angstrom X-Ray Structure Of The Yeast Escrt-I Vps28 C-
Terminus In Complex With The Nzf-N Domain From Escrt-Ii
pdb|2J9U|C Chain C, 2 Angstrom X-Ray Structure Of The Yeast Escrt-I Vps28 C-
Terminus In Complex With The Nzf-N Domain From Escrt-Ii
Length = 96
Score = 53.1 bits (126), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 2/75 (2%)
Query: 109 SKCIADIVSLFITTMDKLRLDIKAMDELQPDLRDLMDTMNRLSILPSGFEGKEKVSGWLT 168
+K +A+ FIT MD L+L+ A D+L P L +L+ ++NR++ FE + K+ W+
Sbjct: 4 AKYVAEATGNFITVMDALKLNYNAKDQLHPLLAELLISINRVT--RDDFENRSKLIDWIV 61
Query: 169 TLESMSASDELNETQ 183
+ +S D L ETQ
Sbjct: 62 RINKLSIGDTLTETQ 76
>pdb|2G3K|A Chain A, Crystal Structure Of The C-Terminal Domain Of Vps28
pdb|2G3K|B Chain B, Crystal Structure Of The C-Terminal Domain Of Vps28
pdb|2G3K|C Chain C, Crystal Structure Of The C-Terminal Domain Of Vps28
pdb|2G3K|D Chain D, Crystal Structure Of The C-Terminal Domain Of Vps28
pdb|2G3K|E Chain E, Crystal Structure Of The C-Terminal Domain Of Vps28
pdb|2G3K|F Chain F, Crystal Structure Of The C-Terminal Domain Of Vps28
pdb|2G3K|G Chain G, Crystal Structure Of The C-Terminal Domain Of Vps28
Length = 94
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 109 SKCIADIVSLFITTMDKLRLDIKAMDELQPDLRDLMDTMNRLSILPSGFEGKEKVSGWLT 168
+K +A+ FIT D L+L+ A D+L P L +L+ ++NR++ FE + K+ W+
Sbjct: 3 AKYVAEATGNFITVXDALKLNYNAKDQLHPLLAELLISINRVT--RDDFENRSKLIDWIV 60
Query: 169 TLESMSASDELNETQ 183
+ +S D L ETQ
Sbjct: 61 RINKLSIGDTLTETQ 75
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 0.132 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,154,859
Number of Sequences: 62578
Number of extensions: 198390
Number of successful extensions: 566
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 550
Number of HSP's gapped (non-prelim): 16
length of query: 185
length of database: 14,973,337
effective HSP length: 93
effective length of query: 92
effective length of database: 9,153,583
effective search space: 842129636
effective search space used: 842129636
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: 48 (23.1 bits)