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= psy3809
(112 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 = 167 bits (422), Expect = 2e-42, Method: Compositional matrix adjust.
Identities = 78/110 (70%), Positives = 90/110 (81%)
Query: 3 SYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEM 62
YSGADISI+VRDALMQPVR VQSATHF + GPS DP+ VDDLLTPCSP PGA+EM
Sbjct: 213 GYSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNHLVDDLLTPCSPGDPGAIEM 272
Query: 63 NFMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDFGQEG 112
+MDVP DKLLEP VSM +L+SL +KPTVN+ D++KL+KF EDFGQEG
Sbjct: 273 TWMDVPGDKLLEPVVSMSDMLRSLSNTKPTVNEHDLLKLKKFTEDFGQEG 322
>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 = 162 bits (411), Expect = 3e-41, Method: Composition-based stats.
Identities = 77/109 (70%), Positives = 91/109 (83%)
Query: 4 YSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDDLLTPCSPSTPGAVEMN 63
YSGADISI+VRDALMQPVR VQSATHF + GPS DP+ V+DLLTPCSP PGA+EM
Sbjct: 336 YSGADISIIVRDALMQPVRKVQSATHFKKVRGPSRADPNCIVNDLLTPCSPGDPGAIEMT 395
Query: 64 FMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDFGQEG 112
+MDVP DKLLEP VSM +L+SL ++KPTVN+ D++KL+KF EDFGQEG
Sbjct: 396 WMDVPGDKLLEPVVSMWDMLRSLSSTKPTVNEQDLLKLKKFTEDFGQEG 444
>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 = 116 bits (290), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 55/113 (48%), Positives = 80/113 (70%), Gaps = 12/113 (10%)
Query: 3 SYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDD---LLTPCSPSTPGA 59
YSG+DI++VV+DALMQP+R +QSATHF S T DD LTPCSP GA
Sbjct: 236 GYSGSDIAVVVKDALMQPIRKIQSATHFKDVS---------TEDDETRKLTPCSPGDDGA 286
Query: 60 VEMNFMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDFGQEG 112
+EM++ D+ +D+L EP +++ LK++++++PTVN+DD++K +F DFGQEG
Sbjct: 287 IEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTRDFGQEG 339
>pdb|3EIE|A Chain A, Crystal Structure Of S.Cerevisiae Vps4 In The So4-Bound
State
Length = 322
Score = 116 bits (290), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 55/113 (48%), Positives = 80/113 (70%), Gaps = 12/113 (10%)
Query: 3 SYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDD---LLTPCSPSTPGA 59
YSG+DI++VV+DALMQP+R +QSATHF S T DD LTPCSP GA
Sbjct: 218 GYSGSDIAVVVKDALMQPIRKIQSATHFKDVS---------TEDDETRKLTPCSPGDDGA 268
Query: 60 VEMNFMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDFGQEG 112
+EM++ D+ +D+L EP +++ LK++++++PTVN+DD++K +F DFGQEG
Sbjct: 269 IEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTRDFGQEG 321
>pdb|2RKO|A Chain A, Crystal Structure Of The Vps4p-Dimer
Length = 331
Score = 116 bits (290), Expect = 4e-27, Method: Compositional matrix adjust.
Identities = 55/113 (48%), Positives = 80/113 (70%), Gaps = 12/113 (10%)
Query: 3 SYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDD---LLTPCSPSTPGA 59
YSG+DI++VV+DALMQP+R +QSATHF S T DD LTPCSP GA
Sbjct: 227 GYSGSDIAVVVKDALMQPIRKIQSATHFKDVS---------TEDDETRKLTPCSPGDDGA 277
Query: 60 VEMNFMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDFGQEG 112
+EM++ D+ +D+L EP +++ LK++++++PTVN+DD++K +F DFGQEG
Sbjct: 278 IEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTRDFGQEG 330
>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 = 113 bits (282), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 54/113 (47%), Positives = 79/113 (69%), Gaps = 12/113 (10%)
Query: 3 SYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDD---LLTPCSPSTPGA 59
YSG+DI++VV+DALMQP+R +QSATHF S T DD LTP SP GA
Sbjct: 251 GYSGSDIAVVVKDALMQPIRKIQSATHFKDVS---------TEDDETRKLTPSSPGDDGA 301
Query: 60 VEMNFMDVPSDKLLEPPVSMHHILKSLETSKPTVNDDDMVKLRKFMEDFGQEG 112
+EM++ D+ +D+L EP +++ LK++++++PTVN+DD++K +F DFGQEG
Sbjct: 302 IEMSWTDIEADELKEPDLTIKDFLKAIKSTRPTVNEDDLLKQEQFTRDFGQEG 354
>pdb|3MHV|C Chain C, Crystal Structure Of Vps4 And Vta1
Length = 117
Score = 82.8 bits (203), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 41/90 (45%), Positives = 61/90 (67%), Gaps = 12/90 (13%)
Query: 3 SYSGADISIVVRDALMQPVRLVQSATHFVRTSGPSPVDPSKTVDD---LLTPCSPSTPGA 59
YSG+DI++VV+DALMQP+R +QSATHF S T DD LTPCSP GA
Sbjct: 37 GYSGSDIAVVVKDALMQPIRKIQSATHFKDVS---------TEDDETRKLTPCSPGDDGA 87
Query: 60 VEMNFMDVPSDKLLEPPVSMHHILKSLETS 89
+EM++ D+ +D+L EP +++ LK+++++
Sbjct: 88 IEMSWTDIEADELKEPDLTIKDFLKAIKST 117
>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 = 29.3 bits (64), Expect = 0.58, 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|2Z0Q|A Chain A, Crystal Structure Of Dh-Ph Domain Of Rhogef3(Xpln)
Length = 352
Score = 29.3 bits (64), Expect = 0.64, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 45 VDDLLTPC--SPSTPGAVEMNFMDVPSDKLLEPPVSMHHILKSLETSKP 91
V D L C SP + NF+D+P +L++ P+ + IL+ P
Sbjct: 131 VQDFLQRCLESPFSRKLDLWNFLDIPRSRLVKYPLLLREILRHTPNDNP 179
>pdb|3EO2|A Chain A, Crystal Structure Of The Rhogef Domain Of Human
Neuroepithelial Cell- Transforming Gene 1 Protein
Length = 231
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 45 VDDLLTPC--SPSTPGAVEMNFMDVPSDKLLEPPVSMHHILKSLETSKPTVN 94
V D L C SP + +F+D+P +L++ P+ + ILK P V
Sbjct: 144 VQDFLQRCLESPFSRKLDLWSFLDIPRSRLVKYPLLLKEILKHTPKEHPDVQ 195
>pdb|3B9P|A Chain A, Spastin
Length = 297
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 8/20 (40%), Positives = 16/20 (80%)
Query: 3 SYSGADISIVVRDALMQPVR 22
YSG+D++ + +DA ++P+R
Sbjct: 223 GYSGSDLTALAKDAALEPIR 242
>pdb|1OPO|A Chain A, The Structure Of Carnation Mottle Virus
pdb|1OPO|B Chain B, The Structure Of Carnation Mottle Virus
pdb|1OPO|C Chain C, The Structure Of Carnation Mottle Virus
Length = 348
Score = 25.4 bits (54), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 20/44 (45%)
Query: 52 CSPSTPGAVEMNFMDVPSDKLLEPPVSMHHILKSLETSKPTVND 95
CS T G V + F D SD V + + K +ET+ T D
Sbjct: 143 CSFETNGRVALGFNDDASDTPPTTKVGFYDLGKHVETAAQTAKD 186
>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 = 8.5, Method: Compositional matrix adjust.
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 50 TPCSPSTPGAVEMNFMDVPSDKL 72
T C + PG ++ F D+P D L
Sbjct: 195 TKCLTAAPGQTQLPFADIPQDAL 217
>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 = 25.4 bits (54), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 26 SATHFVRTSGPSPVDPSKTVDDLL 49
SAT+FV+ SG S +D + DLL
Sbjct: 25 SATYFVKASGDSXIDGGISDGDLL 48
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 0.132 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,368,321
Number of Sequences: 62578
Number of extensions: 121433
Number of successful extensions: 267
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 248
Number of HSP's gapped (non-prelim): 14
length of query: 112
length of database: 14,973,337
effective HSP length: 76
effective length of query: 36
effective length of database: 10,217,409
effective search space: 367826724
effective search space used: 367826724
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)