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= psy8938
(75 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer
Length = 331
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 35 NVSWEHIAGLDGTIKDLKQTVIFPIKHKEMFAKSK 69
NV WE +AGL+G + LK+ VI P+K +F ++
Sbjct: 23 NVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNR 57
>pdb|3EIE|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The So4-Bound
State
Length = 322
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 35 NVSWEHIAGLDGTIKDLKQTVIFPIKHKEMFAKSK 69
NV WE +AGL+G + LK+ VI P+K +F ++
Sbjct: 14 NVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNR 48
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 35 NVSWEHIAGLDGTIKDLKQTVIFPIKHKEMFAKSK 69
NV WE +AGL+G + LK+ VI P+K +F ++
Sbjct: 47 NVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNR 81
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 23/35 (65%)
Query: 35 NVSWEHIAGLDGTIKDLKQTVIFPIKHKEMFAKSK 69
NV WE +AGL+G + LK+ VI P+K +F ++
Sbjct: 32 NVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNR 66
>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 = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 20/31 (64%)
Query: 35 NVSWEHIAGLDGTIKDLKQTVIFPIKHKEMF 65
NV W +AGL+G + LK+ VI PIK +F
Sbjct: 130 NVKWSDVAGLEGAKEALKEAVILPIKFPHLF 160
>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b
Length = 322
Score = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 35 NVSWEHIAGLDGTIKDLKQTVIFPIKHKEMFAKSK 69
NV W +AGL+G + LK+ VI PIK +F +
Sbjct: 8 NVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKR 42
>pdb|3H4M|A Chain A, Aaa Atpase Domain Of The Proteasome- Activating
Nucleotidase
pdb|3H4M|B Chain B, Aaa Atpase Domain Of The Proteasome- Activating
Nucleotidase
pdb|3H4M|C Chain C, Aaa Atpase Domain Of The Proteasome- Activating
Nucleotidase
Length = 285
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 23/33 (69%)
Query: 35 NVSWEHIAGLDGTIKDLKQTVIFPIKHKEMFAK 67
NV +E I GL+ ++++++ V P+KH E+F K
Sbjct: 13 NVRYEDIGGLEKQMQEIREVVELPLKHPELFEK 45
>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A
Length = 816
Score = 33.9 bits (76), Expect = 0.022, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 25/38 (65%)
Query: 36 VSWEHIAGLDGTIKDLKQTVIFPIKHKEMFAKSKLTKA 73
V+WE I GL+ ++L++ V +P++H + F K +T +
Sbjct: 474 VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPS 511
>pdb|3CF1|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX
pdb|3CF1|B Chain B, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX
pdb|3CF1|C Chain C, Structure Of P97VCP IN COMPLEX WITH ADPADP.ALFX
pdb|3CF2|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
pdb|3CF2|B Chain B, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
pdb|3CF2|C Chain C, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
pdb|3CF2|D Chain D, Structure Of P97VCP IN COMPLEX WITH ADPAMP-Pnp
pdb|3CF3|A Chain A, Structure Of P97VCP IN COMPLEX WITH ADP
pdb|3CF3|B Chain B, Structure Of P97VCP IN COMPLEX WITH ADP
pdb|3CF3|C Chain C, Structure Of P97VCP IN COMPLEX WITH ADP
Length = 806
Score = 33.9 bits (76), Expect = 0.022, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 25/38 (65%)
Query: 36 VSWEHIAGLDGTIKDLKQTVIFPIKHKEMFAKSKLTKA 73
V+WE I GL+ ++L++ V +P++H + F K +T +
Sbjct: 474 VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPS 511
>pdb|3CF0|A Chain A, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
pdb|3CF0|B Chain B, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
pdb|3CF0|C Chain C, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
pdb|3CF0|D Chain D, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
pdb|3CF0|E Chain E, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
pdb|3CF0|F Chain F, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
pdb|3CF0|G Chain G, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
pdb|3CF0|H Chain H, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
pdb|3CF0|I Chain I, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
pdb|3CF0|J Chain J, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
pdb|3CF0|K Chain K, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
pdb|3CF0|L Chain L, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
pdb|3CF0|M Chain M, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
pdb|3CF0|N Chain N, Structure Of D2 Subdomain Of P97VCP IN COMPLEX WITH ADP
Length = 301
Score = 33.9 bits (76), Expect = 0.024, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 25/38 (65%)
Query: 36 VSWEHIAGLDGTIKDLKQTVIFPIKHKEMFAKSKLTKA 73
V+WE I GL+ ++L++ V +P++H + F K +T +
Sbjct: 12 VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPS 49
>pdb|4B4T|I Chain I, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 437
Score = 32.7 bits (73), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 33/65 (50%), Gaps = 12/65 (18%)
Query: 22 MSIASHLVDPADINVS-----------WEHIAGLDGTIKDLKQTVIFPIKHKEMFAKSKL 70
MSI L D AD VS + I GL+ I+++K++V P+ H E++ + +
Sbjct: 154 MSIVGVLQDDADPMVSVMKMDKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGI 213
Query: 71 TKAPK 75
K PK
Sbjct: 214 -KPPK 217
>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 405
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 10/29 (34%), Positives = 20/29 (68%)
Query: 37 SWEHIAGLDGTIKDLKQTVIFPIKHKEMF 65
+++ + GL IK++K+ + P+KH E+F
Sbjct: 146 TYDMVGGLTKQIKEIKEVIELPVKHPELF 174
>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 437
Score = 29.6 bits (65), Expect = 0.49, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 9/76 (11%)
Query: 8 KTLKINMDSFTDHEMSIASHLVDPADIN--------VSWEHIAGLDGTIKDLKQTVIFPI 59
K +++ +D T M I DP N ++++ I GL I++L++ + P+
Sbjct: 142 KGVRVTLDITTLTIMRILPRETDPLVYNMTSFEQGEITFDGIGGLTEQIRELREVIELPL 201
Query: 60 KHKEMFAKSKLTKAPK 75
K+ E+F + + K PK
Sbjct: 202 KNPEIFQRVGI-KPPK 216
>pdb|4B4T|M Chain M, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 434
Score = 28.5 bits (62), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 1/39 (2%)
Query: 37 SWEHIAGLDGTIKDLKQTVIFPIKHKEMFAKSKLTKAPK 75
++ + GLD I++L + ++ P+K + F K +APK
Sbjct: 179 TYSDVGGLDKQIEELVEAIVLPMKRADKF-KDMGIRAPK 216
>pdb|3DM5|A Chain A, Structures Of Srp54 And Srp19, The Two Proteins Assembling
The Ribonucleic Core Of The Signal Recognition Particle
From The Archaeon Pyrococcus Furiosus.
pdb|3DM5|B Chain B, Structures Of Srp54 And Srp19, The Two Proteins Assembling
The Ribonucleic Core Of The Signal Recognition Particle
From The Archaeon Pyrococcus Furiosus
Length = 443
Score = 27.3 bits (59), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 8/53 (15%)
Query: 3 AERKLKTLKINMDSFTDHEMSIASHLVDPADINVSW-EHIAGLDGT-IKDLKQ 53
E +LK K+ MDS T+ E L++P IN S + IA GT KD+K+
Sbjct: 368 GEERLKKFKVIMDSMTEEE------LLNPEIINYSRIKRIARGSGTSTKDVKE 414
>pdb|3D8B|A Chain A, Crystal Structure Of Human Fidgetin-Like Protein 1 In
Complex With Adp
pdb|3D8B|B Chain B, Crystal Structure Of Human Fidgetin-Like Protein 1 In
Complex With Adp
Length = 357
Score = 27.3 bits (59), Expect = 2.5, Method: Composition-based stats.
Identities = 10/30 (33%), Positives = 20/30 (66%)
Query: 36 VSWEHIAGLDGTIKDLKQTVIFPIKHKEMF 65
V+WE IAG++ +K+ V++P+ ++F
Sbjct: 81 VNWEDIAGVEFAKATIKEIVVWPMLRPDIF 110
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 0.369
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,092,311
Number of Sequences: 62578
Number of extensions: 66166
Number of successful extensions: 200
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 184
Number of HSP's gapped (non-prelim): 17
length of query: 75
length of database: 14,973,337
effective HSP length: 44
effective length of query: 31
effective length of database: 12,219,905
effective search space: 378817055
effective search space used: 378817055
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: 45 (21.9 bits)