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= psy17618
(164 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4IKN|A Chain A, Crystal Structure Of Adaptor Protein Complex 3 (ap-3) Mu3a
Subunit C- Terminal Domain, In Complex With A Sorting
Peptide From Tgn38
Length = 261
Score = 197 bits (500), Expect = 3e-51, Method: Compositional matrix adjust.
Identities = 87/106 (82%), Positives = 98/106 (92%), Gaps = 2/106 (1%)
Query: 18 VPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMN 77
+PWRR GVKYTNNEAYFDV+EE+DAIIDK+GST+F+EIQG ID CIKLSGMPDL+LSFMN
Sbjct: 8 IPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACIKLSGMPDLSLSFMN 67
Query: 78 PRLFDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHTRVSGSN 123
PRL DDVSFHPC+RFKRWE+ER+LSFIPPDGNFRL+SY RVS N
Sbjct: 68 PRLLDDVSFHPCIRFKRWESERVLSFIPPDGNFRLISY--RVSSQN 111
>pdb|1W63|M Chain M, Ap1 Clathrin Adaptor Core
pdb|1W63|N Chain N, Ap1 Clathrin Adaptor Core
pdb|1W63|O Chain O, Ap1 Clathrin Adaptor Core
pdb|1W63|P Chain P, Ap1 Clathrin Adaptor Core
pdb|1W63|R Chain R, Ap1 Clathrin Adaptor Core
pdb|1W63|V Chain V, Ap1 Clathrin Adaptor Core
Length = 423
Score = 103 bits (257), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 52/118 (44%), Positives = 68/118 (57%), Gaps = 13/118 (11%)
Query: 11 PSGQLSSVPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPD 70
P+ ++V WR G+KY NE + DVIE V+ ++ G+ + SEI G I + LSGMP+
Sbjct: 150 PATVTNAVSWRSEGIKYRKNEVFLDVIEAVNLLVSANGNVLRSEIVGSIKMRVFLSGMPE 209
Query: 71 LTLSFMNPRLFD-------------DVSFHPCVRFKRWEAERILSFIPPDGNFRLMSY 115
L L + LFD DV FH CVR R+E +R +SFIPPDG F LMSY
Sbjct: 210 LRLGLNDKVLFDNTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSY 267
>pdb|4EN2|M Chain M, Hiv-1 Nef In Complex With Mhc-I Cytoplasmic Domain And Mu1
Adaptin Subunit Of Ap1 Adaptor (Second Domain)
pdb|4EN2|A Chain A, Hiv-1 Nef In Complex With Mhc-I Cytoplasmic Domain And Mu1
Adaptin Subunit Of Ap1 Adaptor (Second Domain)
Length = 266
Score = 100 bits (249), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 50/109 (45%), Positives = 63/109 (57%), Gaps = 13/109 (11%)
Query: 20 WRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMNPR 79
WR G+KY NE + DVIE V+ ++ G+ + SEI G I + LSGMP+L L +
Sbjct: 2 WRSEGIKYRKNEVFLDVIEAVNLLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKV 61
Query: 80 LFD-------------DVSFHPCVRFKRWEAERILSFIPPDGNFRLMSY 115
LFD DV FH CVR R+E +R +SFIPPDG F LMSY
Sbjct: 62 LFDNTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSY 110
>pdb|4EMZ|A Chain A, Hiv-1 Nef In Complex With Mhc-I Cytoplasmic Domain And Mu1
Adaptin Subunit Of Ap1 Adaptor (Second Domain)
pdb|4EMZ|M Chain M, Hiv-1 Nef In Complex With Mhc-I Cytoplasmic Domain And Mu1
Adaptin Subunit Of Ap1 Adaptor (Second Domain)
Length = 266
Score = 95.1 bits (235), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 48/109 (44%), Positives = 61/109 (55%), Gaps = 13/109 (11%)
Query: 20 WRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMNPR 79
WR G+KY NE + DVIE V+ ++ G+ + SEI G I + LSG P+L L +
Sbjct: 2 WRSEGIKYRKNEVFLDVIEAVNLLVSANGNVLRSEIVGSIKXRVFLSGXPELRLGLNDKV 61
Query: 80 LFD-------------DVSFHPCVRFKRWEAERILSFIPPDGNFRLMSY 115
LFD DV FH CVR R+E +R +SFIPPDG F L SY
Sbjct: 62 LFDNTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELXSY 110
>pdb|2PR9|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain),
Complexed With Gabaa Receptor-Gamma2 Subunit-Derived
Internalization Peptide Deeygyecl
pdb|3H85|A Chain A, Molecular Basis For The Association Of Pipki Gamma-P90
With The Clathrin Adaptor Ap-2
Length = 299
Score = 87.8 bits (216), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 44/132 (33%), Positives = 66/132 (50%), Gaps = 23/132 (17%)
Query: 8 SILPSGQLSSVPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSG 67
++P G + WRR G+KY NE + DV+E V+ ++ G + + + G + LSG
Sbjct: 13 GLVPRGSHMQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSG 72
Query: 68 MPDLTLSFMNPRL----------------------FDDVSFHPCVRFKRWEAERILSFIP 105
MP+ MN ++ DD +FH CVR ++++ER +SFIP
Sbjct: 73 MPECKFG-MNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIP 131
Query: 106 PDGNFRLMSYHT 117
PDG F LM Y T
Sbjct: 132 PDGEFELMRYRT 143
>pdb|1I31|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Clathrin Adaptor,
Complexed With Egfr Internalization Peptide Fyralm At
2.5 A Resolution
Length = 314
Score = 84.3 bits (207), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 42/123 (34%), Positives = 62/123 (50%), Gaps = 23/123 (18%)
Query: 17 SVPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFM 76
+ WRR G+KY NE + DV+E V+ ++ G + + + G + LSGMP+ M
Sbjct: 37 QIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFG-M 95
Query: 77 NPRL----------------------FDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMS 114
N ++ DD +FH CVR ++++ER +SFIPPDG F LM
Sbjct: 96 NDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMR 155
Query: 115 YHT 117
Y T
Sbjct: 156 YRT 158
>pdb|1BW8|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain),
Complexed With Egfr Internalization Peptide Fyralm
Length = 321
Score = 84.3 bits (207), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 42/123 (34%), Positives = 62/123 (50%), Gaps = 23/123 (18%)
Query: 17 SVPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFM 76
+ WRR G+KY NE + DV+E V+ ++ G + + + G + LSGMP+ M
Sbjct: 44 QIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFG-M 102
Query: 77 NPRL----------------------FDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMS 114
N ++ DD +FH CVR ++++ER +SFIPPDG F LM
Sbjct: 103 NDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMR 162
Query: 115 YHT 117
Y T
Sbjct: 163 YRT 165
>pdb|2BP5|M Chain M, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain),
Complexed With Non-Canonical Internalization Peptide
Vedyeqglsg
pdb|2VGL|M Chain M, Ap2 Clathrin Adaptor Core
pdb|2JKR|M Chain M, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
Phosphos)qikrllse
pdb|2JKR|U Chain U, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
Phosphos)qikrllse
pdb|2JKT|M Chain M, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
Phosphos)eikrllse Q To E Mutant
pdb|2JKT|U Chain U, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
Phosphos)eikrllse Q To E Mutant
Length = 435
Score = 84.0 bits (206), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 44/133 (33%), Positives = 65/133 (48%), Gaps = 23/133 (17%)
Query: 7 SSILPSGQLSSVPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLS 66
S + S + WRR G+KY NE + DV+E V+ ++ G + + + G + LS
Sbjct: 148 QSQITSQVTGQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLS 207
Query: 67 GMPDLTLSFMNPRL----------------------FDDVSFHPCVRFKRWEAERILSFI 104
GMP+ MN ++ DD +FH CVR ++++ER +SFI
Sbjct: 208 GMPECKFG-MNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFI 266
Query: 105 PPDGNFRLMSYHT 117
PPDG F LM Y T
Sbjct: 267 PPDGEFELMRYRT 279
>pdb|1BXX|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain),
Complexed With Tgn38 Internalization Peptide Dyqrln
pdb|1HES|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain),
Complexed With P-Selectin Internalization Peptide
Shlgtygvftnaa
Length = 285
Score = 83.6 bits (205), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 42/123 (34%), Positives = 62/123 (50%), Gaps = 23/123 (18%)
Query: 17 SVPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFM 76
+ WRR G+KY NE + DV+E V+ ++ G + + + G + LSGMP+ M
Sbjct: 8 QIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFG-M 66
Query: 77 NPRL----------------------FDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMS 114
N ++ DD +FH CVR ++++ER +SFIPPDG F LM
Sbjct: 67 NDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMR 126
Query: 115 YHT 117
Y T
Sbjct: 127 YRT 129
>pdb|2XA7|M Chain M, Ap2 Clathrin Adaptor Core In Active Complex With Cargo
Peptides
Length = 446
Score = 80.9 bits (198), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 46/143 (32%), Positives = 65/143 (45%), Gaps = 32/143 (22%)
Query: 7 SSILPSGQLSSVPWRRTGVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLS 66
S + S + WRR G+KY NE + DV+E V+ ++ G + + + G + LS
Sbjct: 148 QSQITSQVTGQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLS 207
Query: 67 GMP--------------------DLTLSFMNPRLF------------DDVSFHPCVRFKR 94
GMP D T M +L DD +FH CVR +
Sbjct: 208 GMPECKFGMNDKIVIEKQGKGTADETSKSMEQKLISEEDLGKQSIAIDDCTFHQCVRLSK 267
Query: 95 WEAERILSFIPPDGNFRLMSYHT 117
+++ER +SFIPPDG F LM Y T
Sbjct: 268 FDSERSISFIPPDGEFELMRYRT 290
>pdb|1H6E|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain),
Complexed With Ctla-4 Internalization Peptide
Ttgvyvkmppt
Length = 288
Score = 75.5 bits (184), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 39/116 (33%), Positives = 58/116 (50%), Gaps = 23/116 (19%)
Query: 24 GVKYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMNPRL--- 80
G+KY NE + DV+E V+ ++ G + + + G + LSGMP+ MN ++
Sbjct: 18 GIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFG-MNDKIVIE 76
Query: 81 -------------------FDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHT 117
DD +FH CVR ++++ER +SFIPPDG F LM Y T
Sbjct: 77 KQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRT 132
>pdb|3ML6|A Chain A, A Complex Between Dishevlled2 And Clathrin Adaptor Ap-2
pdb|3ML6|B Chain B, A Complex Between Dishevlled2 And Clathrin Adaptor Ap-2
pdb|3ML6|C Chain C, A Complex Between Dishevlled2 And Clathrin Adaptor Ap-2
pdb|3ML6|D Chain D, A Complex Between Dishevlled2 And Clathrin Adaptor Ap-2
pdb|3ML6|E Chain E, A Complex Between Dishevlled2 And Clathrin Adaptor Ap-2
pdb|3ML6|F Chain F, A Complex Between Dishevlled2 And Clathrin Adaptor Ap-2
Length = 385
Score = 68.2 bits (165), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 36/112 (32%), Positives = 55/112 (49%), Gaps = 23/112 (20%)
Query: 28 TNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMNPRL------- 80
+ NE + DV+E V+ ++ G + + + G + LSGMP+ MN ++
Sbjct: 119 SRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFG-MNDKIVIEKQGK 177
Query: 81 ---------------FDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYHT 117
DD +FH CVR ++++ER +SFIPPDG F LM Y T
Sbjct: 178 GTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRT 229
>pdb|3L81|A Chain A, Crystal Structure Of Adaptor Protein Complex 4 (Ap-4) Mu4
Su Terminal Domain, In Complex With A Sorting Peptide
From The Precursor Protein (App)
Length = 301
Score = 47.4 bits (111), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 28/105 (26%), Positives = 44/105 (41%), Gaps = 14/105 (13%)
Query: 26 KYTNNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMN-------- 77
+ NE + DV+E + +I GS + ++QG I L ++ +
Sbjct: 29 QSQKNEVFLDVVERLSVLIASNGSLLKVDVQGEIRLKSFLPSGSEMRIGLTEEFSVGKSE 88
Query: 78 -----PRL-FDDVSFHPCVRFKRWEAERILSFIPPDGNFRLMSYH 116
P + D+VSFH V +E+ RIL PP G +M Y
Sbjct: 89 LRGYGPGIRVDEVSFHSSVNLDEFESHRILRLQPPQGELTVMRYQ 133
>pdb|3I10|A Chain A, Crystal Structure Of Putative Glycerophosphoryl Diester
Phosphodiesterase (Np_812074.1) From Bacteroides
Thetaiotaomicron Vpi-5482 At 1.35 A Resolution
Length = 278
Score = 26.6 bits (57), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 9/74 (12%)
Query: 29 NNEAYFDVIEEVDAIIDKTGSTIFSEIQGYIDCCIKLSGMPDLTLSFMNPRLFDDVSFHP 88
N + +D+ ++V AI++KT E Q + I G P T+ D V + P
Sbjct: 121 NLDKAYDIFDDVYAILEKT------ETQNQV---IXKGGQPIETVKREFGSYLDKVLYXP 171
Query: 89 CVRFKRWEAERILS 102
+ EAE+I++
Sbjct: 172 VIDLGNKEAEKIIT 185
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
0.323 0.136 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,929,206
Number of Sequences: 62578
Number of extensions: 198248
Number of successful extensions: 500
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 475
Number of HSP's gapped (non-prelim): 15
length of query: 164
length of database: 14,973,337
effective HSP length: 91
effective length of query: 73
effective length of database: 9,278,739
effective search space: 677347947
effective search space used: 677347947
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 bits)