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= psy13031
(477 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1K8K|D Chain D, Crystal Structure Of Arp23 COMPLEX
pdb|1TYQ|D Chain D, Crystal Structure Of Arp23 COMPLEX WITH BOUND ATP AND
Calcium
pdb|1U2V|D Chain D, Crystal Structure Of Arp23 COMPLEX WITH BOUND ADP AND
Calcium
pdb|2P9I|D Chain D, Crystal Structure Of Bovine Arp23 COMPLEX CO-Crystallized
With Adp And Crosslinked With Gluteraldehyde
pdb|2P9K|D Chain D, Crystal Structure Of Bovine Arp23 COMPLEX CO-Crystallized
With Atp And Crosslinked With Glutaraldehyde
pdb|2P9L|D Chain D, Crystal Structure Of Bovine Arp23 COMPLEX
pdb|2P9N|D Chain D, Crystal Structure Of Bovine Arp23 COMPLEX CO-Crystallized
With Adp
pdb|2P9P|D Chain D, Crystal Structure Of Bovine Arp23 COMPLEX CO-Crystallized
With Adp
pdb|2P9S|D Chain D, Structure Of Bovine Arp23 COMPLEX CO-Crystallized With
AtpMG2+
pdb|2P9U|D Chain D, Crystal Structure Of Bovine Arp23 COMPLEX CO-Crystallized
With Amp-Pnp And Calcium
pdb|3DXK|D Chain D, Structure Of Bos Taurus Arp23 COMPLEX WITH BOUND INHIBITOR
Ck0944636
pdb|3DXM|D Chain D, Structure Of Bos Taurus Arp23 COMPLEX WITH BOUND INHIBITOR
Ck0993548
pdb|3RSE|D Chain D, Structural And Biochemical Characterization Of Two Binding
Sites For Nucleation Promoting Factor Wasp-Vca On Arp23
COMPLEX
pdb|3UKR|D Chain D, Crystal Structure Of Bos Taurus Arp2/3 Complex With Bound
Inhibitor Ck-666
pdb|3UKU|D Chain D, Structure Of Arp2/3 Complex With Bound Inhibitor Ck-869
pdb|3ULE|D Chain D, Structure Of Bos Taurus Arp2/3 Complex With Bound
Inhibitor Ck-869 And Atp
Length = 300
Score = 308 bits (790), Expect = 3e-84, Method: Compositional matrix adjust.
Identities = 168/300 (56%), Positives = 195/300 (65%), Gaps = 64/300 (21%)
Query: 178 SISLKFYKELEEHGADELLRREYGSLLSEPEPGYNVSVLINLEDVPSNWEEIVKKIGLSR 237
SISLKFYKEL+ HGADELL+R YGS L PE GYNVS+L +LE++P++ + IV
Sbjct: 58 SISLKFYKELQAHGADELLKRVYGSYLVNPESGYNVSLLYDLENLPASKDSIV------- 110
Query: 238 LQCVRTHQPGRCALKLGGDSQENRYVEAKADRVTVVFSTVFRDEDDVIIGKVFMQEFKEG 297
HQ G K + VF F+ F +E KEG
Sbjct: 111 ------HQAGML----------------KRNCFASVFEKYFQ----------FQEEGKEG 138
Query: 298 RRASHTAPQVLFSHKEPPLELRNTDARQGDNIGYITFGKYVEAKADRVTVVFSTVFRDED 357
+ + R+ + YVE+K DRVTVVFSTVF+D+D
Sbjct: 139 ENRA-------------VIHYRDDETM------------YVESKKDRVTVVFSTVFKDDD 173
Query: 358 DVIIGKVFMQEFKEGRRASHTAPQVLFSHKEPPLELRNTDARQGDNIGYITFVLFPRHTN 417
DV+IGKVFMQEFKEGRRASHTAPQVLFSH+EPPLEL++TDA GDNIGYITFVLFPRHTN
Sbjct: 174 DVVIGKVFMQEFKEGRRASHTAPQVLFSHREPPLELKDTDAAVGDNIGYITFVLFPRHTN 233
Query: 418 RVARENTINLIHMFRDYLHYHIKCSKAYIHSRMRAKTSDFLKVLNRARPEVKNTEKKTIT 477
AR+NTINLIH FRDYLHYHIKCSKAYIH+RMRAKTSDFLKVLNRARP+ + E KTIT
Sbjct: 234 ASARDNTINLIHTFRDYLHYHIKCSKAYIHTRMRAKTSDFLKVLNRARPDAEKKEMKTIT 293
Score = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/21 (76%), Positives = 20/21 (95%)
Query: 13 KPESVDITIADFDGVLFHISN 33
KPE+V++T ADFDGVL+HISN
Sbjct: 27 KPEAVEVTFADFDGVLYHISN 47
>pdb|3DWL|D Chain D, Crystal Structure Of Fission Yeast Arp2/3 Complex Lacking
The Arp2 Subunit
pdb|3DWL|I Chain I, Crystal Structure Of Fission Yeast Arp2/3 Complex Lacking
The Arp2 Subunit
Length = 317
Score = 159 bits (402), Expect = 3e-39, Method: Compositional matrix adjust.
Identities = 81/138 (58%), Positives = 104/138 (75%), Gaps = 4/138 (2%)
Query: 343 DRVTVVFSTVFRDEDDVIIGKVFMQEFKEGRR--ASHTAPQVLFSHKEPPLELRNTDARQ 400
DRVTVVFST FR+E D I GKVF+QEF + RR A TAPQVLFS+++PPLE+R+ Q
Sbjct: 174 DRVTVVFSTKFREETDRIFGKVFLQEFVDARRRPAIQTAPQVLFSYRDPPLEIRDIQGIQ 233
Query: 401 -GDNIGYITFVLFPRHTNRVARENTINLIHMFRDYLHYHIKCSKAYIHSRMRAKTSDFLK 459
GD+ G++TFVLF RH RE+ I+ I +FR+ LH+HIK SKAY+H RMR + +DF K
Sbjct: 234 KGDDFGFVTFVLFERHFTPQNREDCISHIQVFRNTLHFHIKASKAYMHQRMRKRVADFQK 293
Query: 460 VLNRARPEVKNTEKKTIT 477
VLNRA+P+V+ E+KT T
Sbjct: 294 VLNRAKPDVE-LERKTAT 310
Score = 114 bits (286), Expect = 9e-26, Method: Compositional matrix adjust.
Identities = 75/193 (38%), Positives = 103/193 (53%), Gaps = 38/193 (19%)
Query: 178 SISLKFYKELEEHGADELLRREYGSLLSEPEPGYNVSVLINLEDVPSNWEE--------- 228
S+S+K Y EL +G +LL++ YG+ + EPE GYN S+LI+L+ +P+ EE
Sbjct: 53 SLSMKCYPELVNYGTLDLLKQIYGAYVHEPEMGYNFSILIDLQQLPATDEEKEQLAMSIS 112
Query: 229 --------------IVKKIGLSRLQCVRTHQPGRCALKLGGDSQENRYVEAKA------- 267
K+ L+ L R L SQE + +
Sbjct: 113 MLKRNVLAAPFHRAFTKQAELADL--ARKDPENAPMLDKQATSQELMAIHYRDEETIVLW 170
Query: 268 ---DRVTVVFSTVFRDEDDVIIGKVFMQEFKEGRR--ASHTAPQVLFSHKEPPLELRNTD 322
DRVTVVFST FR+E D I GKVF+QEF + RR A TAPQVLFS+++PPLE+R+
Sbjct: 171 PEHDRVTVVFSTKFREETDRIFGKVFLQEFVDARRRPAIQTAPQVLFSYRDPPLEIRDIQ 230
Query: 323 ARQ-GDNIGYITF 334
Q GD+ G++TF
Sbjct: 231 GIQKGDDFGFVTF 243
Score = 33.5 bits (75), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 32/121 (26%), Positives = 51/121 (42%), Gaps = 29/121 (23%)
Query: 14 PESVDITIADFDGVLFHISNLSAAGATGAFVGTPAEVALIRMTADGRLPPAERRNYK--N 71
P S+D + DFDGV FHIS TP E I ++ + P E NY +
Sbjct: 24 PSSIDQVVTDFDGVTFHIS-------------TPEEKTKILISLSMKCYP-ELVNYGTLD 69
Query: 72 VFHALYRMTSQEGVLTLWRGTIPTMGR--AMVVNAAQLASYSQAK-QFLLSLSYFEENIF 128
+ +Y E P MG +++++ QL + + K Q +S+S + N+
Sbjct: 70 LLKQIYGAYVHE----------PEMGYNFSILIDLQQLPATDEEKEQLAMSISMLKRNVL 119
Query: 129 C 129
Sbjct: 120 A 120
>pdb|2LCK|A Chain A, Structure Of The Mitochondrial Uncoupling Protein 2
Determined By Nmr Molecular Fragment Replacement
Length = 303
Score = 77.8 bits (190), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 45/129 (34%), Positives = 65/129 (50%), Gaps = 5/129 (3%)
Query: 32 SNLSAAGATGAF---VGTPAEVALIRMTADGRLPPAERRNYKNVFHALYRMTSQEGVLTL 88
S L A TGA V P +V +R A R R Y++ A + +EG+ L
Sbjct: 106 SRLLAGSTTGALAVAVAQPTDVVKVRFQAQAR--AGGGRRYQSTVEAYKTIAREEGIRGL 163
Query: 89 WRGTIPTMGRAMVVNAAQLASYSQAKQFLLSLSYFEENIFCFFVSSMISAFITTVASMPV 148
W+GT P + R +VN A+L +Y K LL + +++ C F S+ + F TTV + PV
Sbjct: 164 WKGTSPNVARNAIVNCAELVTYDLIKDTLLKANLMTDDLPCHFTSAFGAGFCTTVIASPV 223
Query: 149 DIAKTRIQN 157
D+ KTR N
Sbjct: 224 DVVKTRYMN 232
>pdb|1OKC|A Chain A, Structure Of Mitochondrial AdpATP CARRIER IN COMPLEX WITH
Carboxyatractyloside
pdb|2C3E|A Chain A, The Bovine Mitochondrial Adp-Atp Carrier
Length = 297
Score = 39.7 bits (91), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/93 (23%), Positives = 41/93 (44%), Gaps = 4/93 (4%)
Query: 67 RNYKNVFHALYRMTSQEGVLTLWRGTIPTMGRAMVVNAAQLASYSQAKQFLLSLSYFEEN 126
+ YK + + R+ ++G L+ WRG + + R A A + KQ L +
Sbjct: 48 KQYKGIIDCVVRIPKEQGFLSFWRGNLANVIRYFPTQALNFAFKDKYKQIFLGGVDRHKQ 107
Query: 127 IFCFFVSSMISAFITTVASM----PVDIAKTRI 155
+ +F ++ S S+ P+D A+TR+
Sbjct: 108 FWRYFAGNLASGGAAGATSLCFVYPLDFARTRL 140
Score = 33.9 bits (76), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 34/130 (26%), Positives = 62/130 (47%), Gaps = 11/130 (8%)
Query: 30 HISNLSAAGATGAFVGTPAEVALIRMTAD-GRLPPAERRNYKNVFHALYRMTSQEGVLTL 88
++++ AAGAT P + A R+ AD G+ A +R + + + + ++ +G+ L
Sbjct: 115 NLASGGAAGATSLCFVYPLDFARTRLAADVGK--GAAQREFTGLGNCITKIFKSDGLRGL 172
Query: 89 WRGTIPTMGRAMVVNAAQLASYSQAKQFLLSLSYFEENIFCFFVSSMISAFITTVA---S 145
++G ++ ++ AA Y AK L +N+ VS MI+ +T VA S
Sbjct: 173 YQGFNVSVQGIIIYRAAYFGVYDTAKGMLPD----PKNVH-IIVSWMIAQTVTAVAGLVS 227
Query: 146 MPVDIAKTRI 155
P D + R+
Sbjct: 228 YPFDTVRRRM 237
>pdb|2CW7|A Chain A, Crystal Structure Of Intein Homing Endonuclease Ii
Length = 537
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 7/71 (9%)
Query: 362 GKVFMQEFKEGRRASHTAPQVLFSHKEPPL-ELRNTDARQGDNIGYITFVLFPRHTNRVA 420
GKV+ K GRR T+ LFS + L E+ + + GD V PR
Sbjct: 77 GKVYTIRLKSGRRIKITSGHSLFSVRNGELVEVTGDELKPGD------LVAVPRRLELPE 130
Query: 421 RENTINLIHMF 431
R + +NL+ +
Sbjct: 131 RNHVLNLVELL 141
>pdb|2CW8|A Chain A, Crystal Structure Of Intein Homing Endonuclease Ii
Length = 537
Score = 30.0 bits (66), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 7/71 (9%)
Query: 362 GKVFMQEFKEGRRASHTAPQVLFSHKEPPL-ELRNTDARQGDNIGYITFVLFPRHTNRVA 420
GKV+ K GRR T+ LFS + L E+ + + GD V PR
Sbjct: 77 GKVYTIRLKSGRRIKITSGHSLFSVRNGELVEVTGDELKPGD------LVAVPRRLELPE 130
Query: 421 RENTINLIHMF 431
R + +NL+ +
Sbjct: 131 RNHVLNLVELL 141
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
0.321 0.135 0.391
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,514,240
Number of Sequences: 62578
Number of extensions: 556752
Number of successful extensions: 1173
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1157
Number of HSP's gapped (non-prelim): 15
length of query: 477
length of database: 14,973,337
effective HSP length: 102
effective length of query: 375
effective length of database: 8,590,381
effective search space: 3221392875
effective search space used: 3221392875
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)