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= psy3811
(89 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1XWI|A Chain A, Crystal Structure Of Vps4b
Length = 322
Score = 123 bits (309), Expect = 2e-29, Method: Compositional matrix adjust.
Identities = 58/77 (75%), Positives = 63/77 (81%)
Query: 3 SYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEM 62
YSGADISI+VRDALMQPVR VQSATHF + GPS DP+ VDDLLTPCSP PGA+EM
Sbjct: 213 GYSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNHLVDDLLTPCSPGDPGAIEM 272
Query: 63 NFMDVPSDKLLEPPVSM 79
+MDVP DKLLEP VSM
Sbjct: 273 TWMDVPGDKLLEPVVSM 289
>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 = 119 bits (299), Expect = 4e-28, Method: Composition-based stats.
Identities = 57/76 (75%), Positives = 63/76 (82%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
YSGADISI+VRDALMQPVR VQSATHF + GPS DP+ V+DLLTPCSP PGA+EM
Sbjct: 336 YSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNCIVNDLLTPCSPGDPGAIEMT 395
Query: 64 FMDVPSDKLLEPPVSM 79
+MDVP DKLLEP VSM
Sbjct: 396 WMDVPGDKLLEPVVSM 411
>pdb|3MHV|C Chain C, Crystal Structure Of Vps4 And Vta1
Length = 117
Score = 77.8 bits (190), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 37/76 (48%), Positives = 55/76 (72%), Gaps = 6/76 (7%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
YSG+DI++VV+DALMQP+R +QSATHF S + D ++ LTPCSP GA+EM+
Sbjct: 38 YSGSDIAVVVKDALMQPIRKIQSATHFKDVS--TEDDETRK----LTPCSPGDDGAIEMS 91
Query: 64 FMDVPSDKLLEPPVSM 79
+ D+ +D+L EP +++
Sbjct: 92 WTDIEADELKEPDLTI 107
>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 = 73.6 bits (179), Expect = 2e-14, Method: Composition-based stats.
Identities = 39/79 (49%), Positives = 54/79 (68%), Gaps = 12/79 (15%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDD---LLTPCSPSTPGAV 60
YSG+DI++VV+DALMQP+R +QSATHF S T DD LTPCSP GA+
Sbjct: 237 YSGSDIAVVVKDALMQPIRKIQSATHFKDVS---------TEDDETRKLTPCSPGDDGAI 287
Query: 61 EMNFMDVPSDKLLEPPVSM 79
EM++ D+ +D+L EP +++
Sbjct: 288 EMSWTDIEADELKEPDLTI 306
>pdb|3EIE|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The So4-Bound
State
Length = 322
Score = 73.2 bits (178), Expect = 3e-14, Method: Composition-based stats.
Identities = 39/79 (49%), Positives = 54/79 (68%), Gaps = 12/79 (15%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDD---LLTPCSPSTPGAV 60
YSG+DI++VV+DALMQP+R +QSATHF S T DD LTPCSP GA+
Sbjct: 219 YSGSDIAVVVKDALMQPIRKIQSATHFKDVS---------TEDDETRKLTPCSPGDDGAI 269
Query: 61 EMNFMDVPSDKLLEPPVSM 79
EM++ D+ +D+L EP +++
Sbjct: 270 EMSWTDIEADELKEPDLTI 288
>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer
Length = 331
Score = 73.2 bits (178), Expect = 4e-14, Method: Composition-based stats.
Identities = 39/79 (49%), Positives = 54/79 (68%), Gaps = 12/79 (15%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDD---LLTPCSPSTPGAV 60
YSG+DI++VV+DALMQP+R +QSATHF S T DD LTPCSP GA+
Sbjct: 228 YSGSDIAVVVKDALMQPIRKIQSATHFKDVS---------TEDDETRKLTPCSPGDDGAI 278
Query: 61 EMNFMDVPSDKLLEPPVSM 79
EM++ D+ +D+L EP +++
Sbjct: 279 EMSWTDIEADELKEPDLTI 297
>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 = 69.7 bits (169), Expect = 4e-13, Method: Composition-based stats.
Identities = 38/79 (48%), Positives = 53/79 (67%), Gaps = 12/79 (15%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDD---LLTPCSPSTPGAV 60
YSG+DI++VV+DALMQP+R +QSATHF S T DD LTP SP GA+
Sbjct: 252 YSGSDIAVVVKDALMQPIRKIQSATHFKDVS---------TEDDETRKLTPSSPGDDGAI 302
Query: 61 EMNFMDVPSDKLLEPPVSM 79
EM++ D+ +D+L EP +++
Sbjct: 303 EMSWTDIEADELKEPDLTI 321
>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 = 28.5 bits (62), Expect = 0.95, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 27/44 (61%), Gaps = 2/44 (4%)
Query: 3 SYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVD 46
++SGAD++ + R+A + P+R +Q+A + T P V P +D
Sbjct: 285 AFSGADMTQLCREASLGPIRSLQTAD--IATITPDQVRPIAYID 326
>pdb|1AY9|A Chain A, Wild-Type Umud' From E. Coli
pdb|1AY9|B Chain B, Wild-Type Umud' From E. Coli
Length = 108
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 26 SATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMNFMDVPSD----KL-LEPPVSMM 80
SAT+FV+ SG S +D + DLL S T ++ V + KL L P V ++
Sbjct: 18 SATYFVKASGDSMIDGGISDGDLLIVDSAITASHGDIVIAAVDGEFTVKKLQLRPTVQLI 77
Query: 81 P 81
P
Sbjct: 78 P 78
>pdb|1UMU|A Chain A, Structure Determination Of Umud' By Mad Phasing Of The
Selenomethionyl Protein
pdb|1UMU|B Chain B, Structure Determination Of Umud' By Mad Phasing Of The
Selenomethionyl Protein
Length = 116
Score = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 7/66 (10%)
Query: 23 LVQ--SATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMNFMDVPSD----KL-LEP 75
L+Q SAT+FV+ SG S +D + DLL S T ++ V + KL L P
Sbjct: 20 LIQHPSATYFVKASGDSXIDGGISDGDLLIVDSAITASHGDIVIAAVDGEFTVKKLQLRP 79
Query: 76 PVSMMP 81
V ++P
Sbjct: 80 TVQLIP 85
>pdb|3B9P|A Chain A, Spastin
Length = 297
Score = 26.6 bits (57), Expect = 3.9, Method: Composition-based stats.
Identities = 8/19 (42%), Positives = 16/19 (84%)
Query: 4 YSGADISIVVRDALMQPVR 22
YSG+D++ + +DA ++P+R
Sbjct: 224 YSGSDLTALAKDAALEPIR 242
>pdb|1I4V|A Chain A, Solution Structure Of The Umud' Homodimer
pdb|1I4V|B Chain B, Solution Structure Of The Umud' Homodimer
Length = 115
Score = 26.2 bits (56), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 26 SATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMNFMDVPSD----KL-LEPPVSMM 80
SAT+FV+ SG S +D + DLL S T ++ V + KL L P V ++
Sbjct: 25 SATYFVKASGDSMIDGGISDGDLLIVDSAITASHGDIVIAAVDGEFTVKKLQLRPTVQLI 84
Query: 81 P 81
P
Sbjct: 85 P 85
>pdb|1ESC|A Chain A, The Molecular Mechanism Of Enantiorecognition By Esterases
pdb|1ESD|A Chain A, The Molecular Mechanism Of Enantiorecognition By Esterases
pdb|1ESE|A Chain A, The Molecular Mechanism Of Enantiorecognition By Esterases
Length = 306
Score = 25.4 bits (54), Expect = 7.6, Method: Composition-based stats.
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 50 TPCSPSTPGAVEMNFMDVPSDKL 72
T C + PG ++ F D+P D L
Sbjct: 195 TKCLTAAPGQTQLPFADIPQDAL 217
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
0.314 0.130 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,678,067
Number of Sequences: 62578
Number of extensions: 89925
Number of successful extensions: 123
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 107
Number of HSP's gapped (non-prelim): 13
length of query: 89
length of database: 14,973,337
effective HSP length: 56
effective length of query: 33
effective length of database: 11,468,969
effective search space: 378475977
effective search space used: 378475977
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: 45 (21.9 bits)