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= psy4539
(84 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 95.9 bits (237), Expect = 5e-21, Method: Compositional matrix adjust.
Identities = 44/63 (69%), Positives = 51/63 (80%)
Query: 20 DERYKGIDKVMIERIENEIMDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLRR 79
DER K ++ MIE I NEIMD G PV W+DIAG+ FAK TI+E++VWPMLRPDIFTGLR
Sbjct: 56 DERLKNLEPKMIELIMNEIMDHGPPVNWEDIAGVEFAKATIKEIVVWPMLRPDIFTGLRG 115
Query: 80 PPK 82
PPK
Sbjct: 116 PPK 118
>pdb|3VFD|A Chain A, Human Spastin Aaa Domain
Length = 389
Score = 64.3 bits (155), Expect = 1e-11, Method: Composition-based stats.
Identities = 28/62 (45%), Positives = 42/62 (67%)
Query: 21 ERYKGIDKVMIERIENEIMDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLRRP 80
+ ++ +D + I NEI+D G V +DDIAG AKQ +QE+++ P LRP++FTGLR P
Sbjct: 88 KNFRNVDSNLANLIMNEIVDNGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAP 147
Query: 81 PK 82
+
Sbjct: 148 AR 149
>pdb|3B9P|A Chain A, Spastin
Length = 297
Score = 57.4 bits (137), Expect = 2e-09, Method: Composition-based stats.
Identities = 25/53 (47%), Positives = 38/53 (71%)
Query: 30 MIERIENEIMDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLRRPPK 82
+++ I +EI++ G V W DIAG AKQ +QE+++ P +RP++FTGLR P K
Sbjct: 3 LVQLILDEIVEGGAKVEWTDIAGQDVAKQALQEMVILPSVRPELFTGLRAPAK 55
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 30/47 (63%)
Query: 34 IENEIMDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLRRP 80
+ + I+ + V W+D+AGL AK+ ++E ++ P+ P +F G R+P
Sbjct: 37 LSSAILSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKP 83
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 30/47 (63%)
Query: 34 IENEIMDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLRRP 80
+ + I+ + V W+D+AGL AK+ ++E ++ P+ P +F G R+P
Sbjct: 22 LSSAILSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKP 68
>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 = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 32/53 (60%)
Query: 28 KVMIERIENEIMDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLRRP 80
K + +++ I+ + V W D+AGL AK+ ++E ++ P+ P +FTG R P
Sbjct: 114 KKLQNQLQGAIVIERPNVKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTP 166
>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b
Length = 322
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 24/36 (66%)
Query: 45 VTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLRRP 80
V W D+AGL AK+ ++E ++ P+ P +FTG R P
Sbjct: 9 VKWSDVAGLEGAKEALKEAVILPIKFPHLFTGKRTP 44
>pdb|3EIE|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The So4-Bound
State
Length = 322
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 28/43 (65%)
Query: 38 IMDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLRRP 80
I+ + V W+D+AGL AK+ ++E ++ P+ P +F G R+P
Sbjct: 8 ILSEKPNVKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKP 50
>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer
Length = 331
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 25/36 (69%)
Query: 45 VTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLRRP 80
V W+D+AGL AK+ ++E ++ P+ P +F G R+P
Sbjct: 24 VKWEDVAGLEGAKEALKEAVILPVKFPHLFKGNRKP 59
>pdb|1R7R|A Chain A, The Crystal Structure Of Murine P97VCP AT 3.6A
Length = 816
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 21/30 (70%)
Query: 45 VTWDDIAGLTFAKQTIQEVIVWPMLRPDIF 74
VTW+DI GL K+ +QE++ +P+ PD F
Sbjct: 474 VTWEDIGGLEDVKRELQELVQYPVEHPDKF 503
>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 = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 21/30 (70%)
Query: 45 VTWDDIAGLTFAKQTIQEVIVWPMLRPDIF 74
VTW+DI GL K+ +QE++ +P+ PD F
Sbjct: 474 VTWEDIGGLEDVKRELQELVQYPVEHPDKF 503
>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: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 45 VTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLRRPPK 82
VTW+DI GL K+ +QE++ +P+ PD F P
Sbjct: 12 VTWEDIGGLEDVKRELQELVQYPVEHPDKFLKFGMTPS 49
>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 437
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 29/45 (64%), Gaps = 2/45 (4%)
Query: 39 MDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLR-RPPK 82
+QG+ +T+D I GLT + ++EVI P+ P+IF + +PPK
Sbjct: 173 FEQGE-ITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGIKPPK 216
>pdb|4B4T|K Chain K, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 428
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 20/30 (66%)
Query: 45 VTWDDIAGLTFAKQTIQEVIVWPMLRPDIF 74
VT+ D+ GL KQ I+E + P+++ D++
Sbjct: 169 VTYADVGGLDMQKQEIREAVELPLVQADLY 198
>pdb|4B4T|J Chain J, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 405
Score = 28.9 bits (63), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 13/32 (40%), Positives = 20/32 (62%)
Query: 46 TWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGL 77
T+D + GLT + I+EVI P+ P++F L
Sbjct: 146 TYDMVGGLTKQIKEIKEVIELPVKHPELFESL 177
>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 = 28.9 bits (63), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 39 MDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPDIF 74
+D+ V ++DI GL Q I+EV+ P+ P++F
Sbjct: 8 VDERPNVRYEDIGGLEKQMQEIREVVELPLKHPELF 43
>pdb|4B4T|I Chain I, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 437
Score = 28.9 bits (63), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 1/45 (2%)
Query: 39 MDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLR-RPPK 82
MD+ ++ DI GL Q I+E + P+ P+++ + +PPK
Sbjct: 173 MDKSPTESYSDIGGLESQIQEIKESVELPLTHPELYEEMGIKPPK 217
>pdb|4B4T|H Chain H, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 467
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 45 VTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGLR-RPPK 82
VT+ D+ G + ++EV+ P+L P+ F L PPK
Sbjct: 206 VTYSDVGGCKDQIEKLREVVELPLLSPERFATLGIDPPK 244
>pdb|2OHD|A Chain A, Crystal Structure Of Hypothetical Molybdenum Cofactor
Biosynthesis Protein C From Sulfolobus Tokodaii
pdb|2OHD|B Chain B, Crystal Structure Of Hypothetical Molybdenum Cofactor
Biosynthesis Protein C From Sulfolobus Tokodaii
pdb|2OHD|C Chain C, Crystal Structure Of Hypothetical Molybdenum Cofactor
Biosynthesis Protein C From Sulfolobus Tokodaii
pdb|2OHD|D Chain D, Crystal Structure Of Hypothetical Molybdenum Cofactor
Biosynthesis Protein C From Sulfolobus Tokodaii
pdb|2OHD|E Chain E, Crystal Structure Of Hypothetical Molybdenum Cofactor
Biosynthesis Protein C From Sulfolobus Tokodaii
pdb|2OHD|F Chain F, Crystal Structure Of Hypothetical Molybdenum Cofactor
Biosynthesis Protein C From Sulfolobus Tokodaii
Length = 151
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 29/51 (56%), Gaps = 3/51 (5%)
Query: 21 ERYKGIDKVMIERIENEIMDQGKPVTWDDIAGLTFAKQTIQEVIVWPMLRP 71
E Y + K IE+I+N+ +++G +T AG+ AK+T + + PM P
Sbjct: 22 EGYIKLRKETIEKIKNKEVEKGDVITVAKTAGILAAKKTPE---LIPMCHP 69
>pdb|2X8A|A Chain A, Human Nuclear Valosin Containing Protein Like (Nvl), C-
Terminal Aaa-Atpase Domain
Length = 274
Score = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 45 VTWDDIAGLTFAKQTIQEVIVWPMLRPDIFTGL 77
VTW DI L ++ + I+ P+ PD F L
Sbjct: 7 VTWADIGALEDIREELTMAILAPVRNPDQFKAL 39
>pdb|2Z61|A Chain A, Crystal Structure Of Mj0684 From Methanococcus Jannaschii
Reveals Its Similarity In The Active Site To Kynurenine
Aminotransferases
Length = 370
Score = 25.4 bits (54), Expect = 9.0, Method: Composition-based stats.
Identities = 11/41 (26%), Positives = 25/41 (60%)
Query: 3 VDMPSGPRGKELEPELEDERYKGIDKVMIERIENEIMDQGK 43
++ PS P G+ ++ E+ + Y+ I ++ + I N ++ +GK
Sbjct: 160 INSPSNPLGEVIDREIYEFAYENIPYIISDEIYNGLVYEGK 200
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
0.317 0.140 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,770,544
Number of Sequences: 62578
Number of extensions: 104591
Number of successful extensions: 262
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 241
Number of HSP's gapped (non-prelim): 21
length of query: 84
length of database: 14,973,337
effective HSP length: 52
effective length of query: 32
effective length of database: 11,719,281
effective search space: 375016992
effective search space used: 375016992
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)