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= psy3209
(567 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GBY|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Xylose
pdb|4GBZ|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To D-Glucose
pdb|4GC0|A Chain A, The Structure Of The Mfs (Major Facilitator Superfamily)
Proton:xylose Symporter Xyle Bound To
6-Bromo-6-Deoxy-D-Glucose
Length = 491
Score = 74.3 bits (181), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 88/365 (24%), Positives = 157/365 (43%), Gaps = 34/365 (9%)
Query: 217 RLLSGIGKGVGFTVVPMYIAEITDKEIRGTLSTMFTGHLYGGILFSLCVGPYIQYQT--- 273
R++ GIG G+ + PMYIAE+ IRG L + + G L CV +I
Sbjct: 133 RIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDAS 192
Query: 274 -LN-------IILGVIPLVFFITFMF-IPETPYFHIIKDNNQVAAKKSLEWFKGKSQNIT 324
LN IP + F+ ++ +PE+P + ++ Q A+ L G + T
Sbjct: 193 WLNTDGWRYMFASECIPALLFLMLLYTVPESPRW-LMSRGKQEQAEGILRKIMGNTLA-T 250
Query: 325 EELDEIVLTTNENMKNKSGYRELVSNYSYRKALIIVLVTSFLQRLSGVSTILSYASTTLP 384
+ + EI + + K+G R L+ ++I ++ S Q+ G++ +L YA P
Sbjct: 251 QAVQEIKHSLDHG--RKTGGRLLMFGVG---VIVIGVMLSIFQQFVGINVVLYYA----P 301
Query: 385 EHHGLIG-RTECLIIFSVLLVVTNFACSPL----VDIAGRKTLNMLSAFLSSGVMIVLAA 439
E +G T+ ++ ++++ V N + L VD GRK L ++ A + M L
Sbjct: 302 EVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGT 361
Query: 440 CFYWNFDYWVSYLFTSLFGITYSLGIGIIPTTLLSELFPTNVKXXXXXXXXXXXXXXXXX 499
FY V+ L + +++ G + LLSE+FP ++
Sbjct: 362 AFYTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYF 421
Query: 500 XNKFYKIVQINFGLYYMFA------FYAICSGINVLFTFFFIFETKGKSFQQIQNILKKK 553
+ + ++ N L F Y + LF + F+ ETKGK+ ++++ + + +
Sbjct: 422 VSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALWEPE 481
Query: 554 TATTQ 558
T TQ
Sbjct: 482 TKKTQ 486
>pdb|2WZP|R Chain R, Structures Of Lactococcal Phage P2 Baseplate Shed Light On
A Novel Mechanism Of Host Attachment And Activation In
Siphoviridae
Length = 375
Score = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 432 GVMIVLAACFYWNFDYW-VSYLFTSLFGITYSLGIGIIPTTLLSELFP 478
G+ I A C N++ W YL+TS +T S+ +G I L E+ P
Sbjct: 31 GLPIPKARCQVINYELWETGYLYTSSATLTVSVEVGDIVQILFPEVVP 78
>pdb|2X54|Y Chain Y, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 1 Of 2)
pdb|2X54|Z Chain Z, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 1 Of 2)
pdb|2X54|0 Chain 0, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 1 Of 2)
pdb|2X5A|Y Chain Y, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 2 Of 2)
pdb|2X5A|Z Chain Z, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 2 Of 2)
pdb|2X5A|0 Chain 0, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Ca (Part 2 Of 2)
Length = 372
Score = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 432 GVMIVLAACFYWNFDYW-VSYLFTSLFGITYSLGIGIIPTTLLSELFP 478
G+ I A C N++ W YL+TS +T S+ +G I L E+ P
Sbjct: 31 GLPIPKARCQVINYELWETGYLYTSSATLTVSVEVGDIVQILFPEVVP 78
>pdb|2X53|Y Chain Y, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Sr
pdb|2X53|Z Chain Z, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Sr
pdb|2X53|1 Chain 1, Structure Of The Phage P2 Baseplate In Its Activated
Conformation With Sr
Length = 375
Score = 30.0 bits (66), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 432 GVMIVLAACFYWNFDYW-VSYLFTSLFGITYSLGIGIIPTTLLSELFP 478
G+ I A C N++ W YL+TS +T S+ +G I L E+ P
Sbjct: 31 GLPIPKARCQVINYELWETGYLYTSSATLTVSVEVGDIVQILFPEVVP 78
>pdb|1M5I|A Chain A, Crystal Structure Of The Coiled Coil Region 129-250 Of The
Tumor Suppressor Gene Product Apc
Length = 125
Score = 29.3 bits (64), Expect = 6.7, Method: Composition-based stats.
Identities = 11/38 (28%), Positives = 23/38 (60%)
Query: 310 KKSLEWFKGKSQNITEELDEIVLTTNENMKNKSGYREL 347
+K +W+ + QN+T+ +D + LT N +++ R+L
Sbjct: 27 EKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQL 64
>pdb|4IFD|J Chain J, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 1003
Score = 28.9 bits (63), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 286 FITFMFIPETPYFHIIKDNNQVAAKKSLEWFKGKSQNITEELDEIVLTTNENMKNKSGYR 345
F F+ P I D N A +K+ +W+ S+++ +VL TN+ + ++ +
Sbjct: 154 FSEHTFVERLPN-ETINDRNNRAIRKTCQWY---SEHLKPYDINVVLVTNDRLNREAATK 209
Query: 346 ELVSN 350
E+ SN
Sbjct: 210 EVESN 214
>pdb|2WP8|J Chain J, Yeast Rrp44 Nuclease
Length = 977
Score = 28.9 bits (63), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 286 FITFMFIPETPYFHIIKDNNQVAAKKSLEWFKGKSQNITEELDEIVLTTNENMKNKSGYR 345
F F+ P I D N A +K+ +W+ S+++ +VL TN+ + ++ +
Sbjct: 128 FSEHTFVERLPN-ETINDRNDRAIRKTCQWY---SEHLKPYDINVVLVTNDRLNREAATK 183
Query: 346 ELVSN 350
E+ SN
Sbjct: 184 EVESN 188
>pdb|1N4C|A Chain A, Nmr Structure Of The J-Domain And Clathrin Substrate
Binding Domain Of Bovine Auxilin
Length = 182
Score = 28.9 bits (63), Expect = 8.6, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 6/56 (10%)
Query: 311 KSLEWFKGKSQNITEELDEI--VLTTNENMKNKSGYRELVS----NYSYRKALIIV 360
K LEW +GK +NI L + VL E G +LV+ YRKA+++V
Sbjct: 90 KILEWIEGKERNIRALLSTMHTVLWAGETKWKPVGMADLVTPEQVKKVYRKAVLVV 145
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
0.324 0.139 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,507,499
Number of Sequences: 62578
Number of extensions: 598772
Number of successful extensions: 1594
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1588
Number of HSP's gapped (non-prelim): 12
length of query: 567
length of database: 14,973,337
effective HSP length: 104
effective length of query: 463
effective length of database: 8,465,225
effective search space: 3919399175
effective search space used: 3919399175
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (25.4 bits)