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= 009432
(535 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1K5C|A Chain A, Endopolygalacturonase I From Stereum Purpureum At 0.96 A
Resolution
pdb|1KCC|A Chain A, Endopolygalacturonase I From Stereum Purpureum Complexed
With A Galacturonate At 1.00 A Resolution.
pdb|1KCD|A Chain A, Endopolygalacturonase I From Stereum Purpureum Complexed
With Two Galacturonate At 1.15 A Resolution
Length = 335
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 38/81 (46%), Gaps = 5/81 (6%)
Query: 320 KDPAGCAARNVHGFTLDDIERMAGQWEEAPTLYLQLDI---KTLFHGD--DLKESGIKEV 374
KD AGC+A ++GFT+ + ++ T+ + DI KT G + +GI V
Sbjct: 12 KDIAGCSAVTLNGFTVPAGNTLVLNPDKGATVTMAGDITFAKTTLDGPLFTIDGTGINFV 71
Query: 375 EMDMDEDSDGLLAQQEKETNS 395
D D +G L K TN+
Sbjct: 72 GADHIFDGNGALYWDGKGTNN 92
>pdb|2QP9|X Chain X, Crystal Structure Of S.Cerevisiae Vps4
pdb|2QPA|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The Presence Of
Adp
pdb|2QPA|B Chain B, Crystal Structure Of S.Cerevisiae Vps4 In The Presence Of
Adp
pdb|2QPA|C Chain C, Crystal Structure Of S.Cerevisiae Vps4 In The Presence Of
Adp
Length = 355
Score = 30.4 bits (67), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 172 LKQPH--RATRPDHFAIILRGLPGSGKSYIAKML 203
+K PH + R I+L G PG+GKSY+AK +
Sbjct: 71 VKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAV 104
>pdb|3EIH|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The Presence Of
Atpgammas
pdb|3EIH|B Chain B, Crystal Structure Of S.Cerevisiae Vps4 In The Presence Of
Atpgammas
pdb|3EIH|C Chain C, Crystal Structure Of S.Cerevisiae Vps4 In The Presence Of
Atpgammas
Length = 340
Score = 30.0 bits (66), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 172 LKQPH--RATRPDHFAIILRGLPGSGKSYIAKML 203
+K PH + R I+L G PG+GKSY+AK +
Sbjct: 56 VKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAV 89
>pdb|3EIE|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The So4-Bound
State
Length = 322
Score = 30.0 bits (66), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 172 LKQPH--RATRPDHFAIILRGLPGSGKSYIAKML 203
+K PH + R I+L G PG+GKSY+AK +
Sbjct: 38 VKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAV 71
>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer
Length = 331
Score = 30.0 bits (66), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/34 (44%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 172 LKQPH--RATRPDHFAIILRGLPGSGKSYIAKML 203
+K PH + R I+L G PG+GKSY+AK +
Sbjct: 47 VKFPHLFKGNRKPTSGILLYGPPGTGKSYLAKAV 80
>pdb|3H0K|A Chain A, Crystal Structure Of An Adenylated Kinase Related Protein
From Sulfolobus Solfataricus To 3.25a
pdb|3H0K|B Chain B, Crystal Structure Of An Adenylated Kinase Related Protein
From Sulfolobus Solfataricus To 3.25a
Length = 178
Score = 29.3 bits (64), Expect = 5.7, Method: Composition-based stats.
Identities = 11/20 (55%), Positives = 17/20 (85%)
Query: 186 IILRGLPGSGKSYIAKMLRD 205
I++ G+PGSGKS AK+L++
Sbjct: 3 ILITGMPGSGKSEFAKLLKE 22
>pdb|3LW7|A Chain A, The Crystal Structure Of An Adenylate Kinase-Related
Protein Bound To Amp From Sulfolobus Solfataricus To
2.3a
pdb|3LW7|B Chain B, The Crystal Structure Of An Adenylate Kinase-Related
Protein Bound To Amp From Sulfolobus Solfataricus To
2.3a
Length = 179
Score = 28.9 bits (63), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 11/21 (52%), Positives = 17/21 (80%)
Query: 185 AIILRGLPGSGKSYIAKMLRD 205
I++ G+PGSGKS AK+L++
Sbjct: 3 VILITGMPGSGKSEFAKLLKE 23
>pdb|2ZAM|A Chain A, Crystal Structure Of Mouse Skd1VPS4B APO-Form
pdb|2ZAN|A Chain A, Crystal Structure Of Mouse Skd1VPS4B ATP-Form
pdb|2ZAO|A Chain A, Crystal Structure Of Mouse Skd1VPS4B ADP-Form
Length = 444
Score = 28.9 bits (63), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 172 LKQPHRAT--RPDHFAIILRGLPGSGKSYIAKML 203
+K PH T R I+L G PG+GKSY+AK +
Sbjct: 154 IKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAV 187
>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b
Length = 322
Score = 28.5 bits (62), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 172 LKQPHRAT--RPDHFAIILRGLPGSGKSYIAKML 203
+K PH T R I+L G PG+GKSY+AK +
Sbjct: 32 IKFPHLFTGKRTPWRGILLFGPPGTGKSYLAKAV 65
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
0.315 0.134 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,282,538
Number of Sequences: 62578
Number of extensions: 689515
Number of successful extensions: 1255
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1252
Number of HSP's gapped (non-prelim): 14
length of query: 535
length of database: 14,973,337
effective HSP length: 103
effective length of query: 432
effective length of database: 8,527,803
effective search space: 3684010896
effective search space used: 3684010896
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (25.4 bits)