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= psy4828
(448 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1HO8|A Chain A, Crystal Structure Of The Regulatory Subunit H Of The
V-Type Atpase Of Saccharomyces Cerevisiae
Length = 480
Score = 119 bits (299), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 80/252 (31%), Positives = 127/252 (50%), Gaps = 38/252 (15%)
Query: 226 SGRVNFQIQYQLIFCLWVLTFNPKLADRMNKFNVIPTLADILSDSVKEKNLIEKPTEPAL 285
S + Q+QY + +W+LTFNP A+ + V L+D L D +K + K T
Sbjct: 237 SNHLGIQLQYHSLLLIWLLTFNPVFANEL----VQKYLSDFL-DLLK----LVKITIKEK 287
Query: 286 AKENCIAMV----------QSKVLKQLSIL----------EQRKFDDEDIVEDVQFLNEK 325
CI+++ KV+KQL +L +RK+ DE++ +D+ L E
Sbjct: 288 VSRLCISIILQCCSTRVKQHKKVIKQLLLLGNALPTVQSLSERKYSDEELRQDISNLKEI 347
Query: 326 LQASVQDLSSFDEYKTEVKSGRLEWSPVHRSAQFWRENAPRLHEKNYELLKSLIHLLE-- 383
L+ Q+L+SFDEY E+ S L WSP H FW +N + NY++ + LI LL+
Sbjct: 348 LENEYQELTSFDEYVAELDSKLLCWSPPHVDNGFWSDNIDEFKKDNYKIFRQLIELLQAK 407
Query: 384 -------TSRDPLVLSVASYDIGEYVRHCPRGKHVIEQLGGKQLVMQLLSHEDPNVRYEA 436
++ +++ VA DI V P V+++ GGK +M+LL+H D V+YEA
Sbjct: 408 VRNGDVNAKQEKIIIQVALNDITHVVELLPESIDVLDKTGGKADIMELLNHSDSRVKYEA 467
Query: 437 LLAVQKLMVHNW 448
L A Q ++ + +
Sbjct: 468 LKATQAIIGYTF 479
>pdb|1XM9|A Chain A, Structure Of The Armadillo Repeat Domain Of Plakophilin 1
Length = 457
Score = 33.5 bits (75), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 44/87 (50%), Gaps = 2/87 (2%)
Query: 180 LKDQLKLANNDYMQSVARCLQ-MMLRIDEYRIAFINVDGIRTLLSVLSGRVNFQIQYQLI 238
L D L+ N + Q+ A L+ ++ R ++ +GIR +S+L N +IQ QL
Sbjct: 49 LVDLLRSPNQNVQQAAAGALRNLVFRSTTNKLETRRQNGIREAVSLLRRTGNAEIQKQLT 108
Query: 239 FCLWVLTFNPKLADRMNKFNVIPTLAD 265
LW L+ +L + + + +P LAD
Sbjct: 109 GLLWNLSSTDELKEEL-IADALPVLAD 134
>pdb|1WXU|A Chain A, Solution Structure Of The Sh3 Domain Of Mouse
Peroxisomal Biogenesis Factor 13
Length = 93
Score = 32.0 bits (71), Expect = 0.76, Method: Composition-based stats.
Identities = 11/35 (31%), Positives = 21/35 (60%)
Query: 45 NWNTYQQSQMISKEDYDFITVFDTASSAKRAEMLN 79
NW + + ++++ +YDF+ V D S + +MLN
Sbjct: 9 NWASGEDDHVVARAEYDFVAVSDEEISFRAGDMLN 43
>pdb|4DBA|A Chain A, Designed Armadillo Repeat Protein (Yiim3aii)
pdb|4DBA|B Chain B, Designed Armadillo Repeat Protein (Yiim3aii)
pdb|4DBA|C Chain C, Designed Armadillo Repeat Protein (Yiim3aii)
pdb|4DBA|D Chain D, Designed Armadillo Repeat Protein (Yiim3aii)
Length = 210
Score = 30.0 bits (66), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 375 LKSLIHLLETSRDPLVLSVASYDIGEYVRHCPRGKHVIEQLGGKQLVMQLLSHEDPNVRY 434
L +L+ LL +S + +L A + + K +++ G + + QL SHE+ ++
Sbjct: 140 LPALVQLL-SSPNEQILQEALWALSNIASGGNEQKQAVKEAGALEKLEQLQSHENEKIQK 198
Query: 435 EALLAVQKLMVH 446
EA A++KL H
Sbjct: 199 EAQEALEKLQSH 210
>pdb|4DB8|A Chain A, Designed Armadillo-Repeat Protein
pdb|4DB8|B Chain B, Designed Armadillo-Repeat Protein
pdb|4DB8|C Chain C, Designed Armadillo-Repeat Protein
pdb|4DB8|D Chain D, Designed Armadillo-Repeat Protein
Length = 252
Score = 29.6 bits (65), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 375 LKSLIHLLETSRDPLVLSVASYDIGEYVRHCPRGKHVIEQLGGKQLVMQLLSHEDPNVRY 434
L +L+ LL +S + +L A + + K +++ G + + QL SHE+ ++
Sbjct: 182 LPALVQLL-SSPNEQILQEALWALSNIASGGNEQKQAVKEAGALEKLEQLQSHENEKIQK 240
Query: 435 EALLAVQKLMVH 446
EA A++KL H
Sbjct: 241 EAQEALEKLQSH 252
>pdb|4DB6|A Chain A, Designed Armadillo Repeat Protein (Yiiim3aii)
Length = 210
Score = 29.3 bits (64), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 375 LKSLIHLLETSRDPLVLSVASYDIGEYVRHCPRGKHVIEQLGGKQLVMQLLSHEDPNVRY 434
L +L+ LL +S + +L A + + K +++ G + + QL SHE+ ++
Sbjct: 140 LPALVQLL-SSPNEQILQEALWALSNIASGGNEQKQAVKEAGALEKLEQLQSHENEKIQK 198
Query: 435 EALLAVQKLMVH 446
EA A++KL H
Sbjct: 199 EAQEALEKLQSH 210
>pdb|2VS3|A Chain A, The Binding Of Udp-Galactose By An Active Site Mutant Of
Alpha-1,3 Galactosyltransferase (Alpha3gt)
pdb|2VS3|B Chain B, The Binding Of Udp-Galactose By An Active Site Mutant Of
Alpha-1,3 Galactosyltransferase (Alpha3gt)
Length = 289
Score = 28.9 bits (63), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 16/71 (22%), Positives = 35/71 (49%), Gaps = 1/71 (1%)
Query: 121 EIFKEYSQTKREPVCSQFLNLLNGSDGFIINMTAKIIAKIACWSVDLLNPSDLNFY-LTW 179
E FK + K+ + +Q+ N + + F++N KI++ CW + P+D+ ++W
Sbjct: 218 ECFKGILKDKKNDIEAQWHNESHLNKYFLLNKPTKILSPEYCWDYHIGLPADIKLVKMSW 277
Query: 180 LKDQLKLANND 190
+ + N+
Sbjct: 278 QTKEYNVVRNN 288
>pdb|2OEW|A Chain A, Structure Of AlixAIP1 BRO1 DOMAIN
pdb|3C3O|A Chain A, Alix Bro1-Domain:chmip4a Co-Crystal Structure
pdb|3C3Q|A Chain A, Alix Bro1-domain:chmip4b Co-crystal Structure
pdb|3C3R|A Chain A, Alix Bro1 Chmp4c Complex
Length = 380
Score = 28.5 bits (62), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 264 ADILSDSVKE---KNLIEKPTEPALAKENCIAMVQSKVLKQLSILEQRKFDDEDIVEDVQ 320
AD D+ K+ K+ + K P LA ++CI ++ + + +Q+KF +E + +Q
Sbjct: 242 ADYFGDAFKQCQYKDTLPKEVFPVLAAKHCIMQANAEYHQSILAKQQKKFGEE--IARLQ 299
Query: 321 FLNEKLQASVQDLSSFDEY 339
E ++ S +DEY
Sbjct: 300 HAAELIKTVA---SRYDEY 315
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
0.319 0.133 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,188,252
Number of Sequences: 62578
Number of extensions: 477949
Number of successful extensions: 1383
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 1365
Number of HSP's gapped (non-prelim): 28
length of query: 448
length of database: 14,973,337
effective HSP length: 102
effective length of query: 346
effective length of database: 8,590,381
effective search space: 2972271826
effective search space used: 2972271826
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)