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= psy918
(504 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 711 bits (1835), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 338/408 (82%), Positives = 376/408 (92%), Gaps = 1/408 (0%)
Query: 98 MSASALYILDVKGKVLISRNYRGDVEMGVIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYI 157
MSASA+Y+LD+KGKVLI RNYRGDV+M +E FMP+LMEKEEEGML+P+L F +I
Sbjct: 1 MSASAVYVLDLKGKVLICRNYRGDVDMSEVEHFMPILMEKEEEGMLSPILAHGGVRFMWI 60
Query: 158 KYNNLFIVSTTKKNANIALVFVFLNKIVRVFTEYFKEIEEESIRDNFVVIYELLDELIDF 217
K+NNL++V+T+KKNA ++LVF FL K+V+VF+EYFKE+EEESIRDNFV+IYELLDEL+DF
Sbjct: 61 KHNNLYLVATSKKNACVSLVFSFLYKVVQVFSEYFKELEEESIRDNFVIIYELLDELMDF 120
Query: 218 GYPQTTDSKILQEYITQEGHKLEI-QPRIPMAVTNAVSWRSEGIKYRKNEVFLDVIESVN 276
GYPQTTDSKILQE+ITQEGHKLE PR P VTNAVSWRSEGIKYRKNEVFLDVIE+VN
Sbjct: 121 GYPQTTDSKILQEFITQEGHKLETGAPRPPATVTNAVSWRSEGIKYRKNEVFLDVIEAVN 180
Query: 277 LLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVLFESTGRGKSKSVELEDVKFHQ 336
LL ++NGNVLRSEIVG+IKMRV+LSGMPELRLGLNDKVLF++TGRGKSKSVELEDVKFHQ
Sbjct: 181 LLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQ 240
Query: 337 CVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIERFVHSRVEYMIKAKSQ 396
CVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIE+ HSR+EYM+KAKSQ
Sbjct: 241 CVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIEKHSHSRIEYMVKAKSQ 300
Query: 397 FKRRSTANNVEIVIPVPADADSPKFKTTIGSVKYTPEQSAITWTIKSFPGGKEYLMRAHF 456
FKRRSTANNVEI IPVP DADSPKFKTT+GSVK+ PE S I W++KSFPGGKEYLMRAHF
Sbjct: 301 FKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPENSEIVWSVKSFPGGKEYLMRAHF 360
Query: 457 GLPSVENEDAEGKPPIQVKFEIPYFTTSGIQVRYLKIIEKSGYQALPW 504
GLPSVE ED EGKPPI VKFEIPYFTTSGIQVRYLKIIEKSGYQA+PW
Sbjct: 361 GLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKIIEKSGYQAIPW 408
>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 = 475 bits (1222), Expect = e-134, Method: Compositional matrix adjust.
Identities = 225/251 (89%), Positives = 239/251 (95%)
Query: 254 SWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDK 313
SWRSEGIKYRKNEVFLDVIE+VNLL ++NGNVLRSEIVG+IKMRV+LSGMPELRLGLNDK
Sbjct: 1 SWRSEGIKYRKNEVFLDVIEAVNLLVSANGNVLRSEIVGSIKMRVFLSGMPELRLGLNDK 60
Query: 314 VLFESTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLI 373
VLF++TGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLI
Sbjct: 61 VLFDNTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLI 120
Query: 374 WIESVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSVKYTPE 433
WIESVIE+ HSR+EYM+KAKSQFKRRSTANNVEI IPVP DADSPKFKTT+GSVK+ PE
Sbjct: 121 WIESVIEKHSHSRIEYMVKAKSQFKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPE 180
Query: 434 QSAITWTIKSFPGGKEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQVRYLKI 493
S I W++KSFPGGKEYLMRAHFGLPSVE ED EGKPPI VKFEIPYFTTSGIQVRYLKI
Sbjct: 181 NSEIVWSVKSFPGGKEYLMRAHFGLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKI 240
Query: 494 IEKSGYQALPW 504
IEKSGYQALPW
Sbjct: 241 IEKSGYQALPW 251
>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 = 462 bits (1188), Expect = e-130, Method: Compositional matrix adjust.
Identities = 220/251 (87%), Positives = 234/251 (93%)
Query: 254 SWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDK 313
SWRSEGIKYRKNEVFLDVIE+VNLL ++NGNVLRSEIVG+IK RV+LSG PELRLGLNDK
Sbjct: 1 SWRSEGIKYRKNEVFLDVIEAVNLLVSANGNVLRSEIVGSIKXRVFLSGXPELRLGLNDK 60
Query: 314 VLFESTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLI 373
VLF++TGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFEL SYRLNTHVKPLI
Sbjct: 61 VLFDNTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELXSYRLNTHVKPLI 120
Query: 374 WIESVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSVKYTPE 433
WIESVIE+ HSR+EY +KAKSQFKRRSTANNVEI IPVP DADSPKFKTT+GSVK+ PE
Sbjct: 121 WIESVIEKHSHSRIEYXVKAKSQFKRRSTANNVEIHIPVPNDADSPKFKTTVGSVKWVPE 180
Query: 434 QSAITWTIKSFPGGKEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQVRYLKI 493
S I W++KSFPGGKEYL RAHFGLPSVE ED EGKPPI VKFEIPYFTTSGIQVRYLKI
Sbjct: 181 NSEIVWSVKSFPGGKEYLXRAHFGLPSVEAEDKEGKPPISVKFEIPYFTTSGIQVRYLKI 240
Query: 494 IEKSGYQALPW 504
IEKSGYQALPW
Sbjct: 241 IEKSGYQALPW 251
>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 = 325 bits (833), Expect = 3e-89, Method: Compositional matrix adjust.
Identities = 167/421 (39%), Positives = 255/421 (60%), Gaps = 19/421 (4%)
Query: 101 SALYILDVKGKVLISRNYRGDVEMGVIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIKYN 160
L+I + KG+VLISR YR D+ ++ F ++ ++ + +P+ + +F ++K +
Sbjct: 3 GGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQ-VRSPVTNIARTSFFHVKRS 61
Query: 161 NLFIVSTTKKNANIALVFVFLNKIVRVFTEYFKEIEEESIRDNFVVIYELLDELIDFGYP 220
N+++ + TK+N N A+VF FL K+ V YF +I EE+I++NFV+IYELLDE++DFGYP
Sbjct: 62 NIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYP 121
Query: 221 QTTDSKILQEYITQEGHKL-----EIQPRIPMAVTNAVSWRSEGIKYRKNEVFLDVIESV 275
Q +++ L+ +ITQ+G K E Q +I VT + WR EGIKYR+NE+FLDV+ESV
Sbjct: 122 QNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLESV 181
Query: 276 NLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVLFESTGRGKS--------KSV 327
NLL + G VL + + G + M+ YLSGMPE + G+NDK++ E G+G + +S+
Sbjct: 182 NLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQSI 241
Query: 328 ELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIERFVHSRV 387
++D FHQCVRLS+F+++R+ISFIPPDGEFELM YR + + ++ +++
Sbjct: 242 AIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTKL 301
Query: 388 EYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSVKYTPEQSAITWTIKSFPGG 447
E + KS FK A +E+ IP P + + G KY ++AI W IK G
Sbjct: 302 EVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKRMAGM 361
Query: 448 KEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQVRYLKIIEK----SGYQALP 503
KE + A L ++ +PPI + FE+P F SG++VRYLK+ E S + +
Sbjct: 362 KESQISAEIELLPTNDKKKWARPPISMNFEVP-FAPSGLKVRYLKVFEPKLNYSDHDVIK 420
Query: 504 W 504
W
Sbjct: 421 W 421
>pdb|2XA7|M Chain M, Ap2 Clathrin Adaptor Core In Active Complex With Cargo
Peptides
Length = 446
Score = 321 bits (822), Expect = 6e-88, Method: Compositional matrix adjust.
Identities = 167/432 (38%), Positives = 255/432 (59%), Gaps = 30/432 (6%)
Query: 101 SALYILDVKGKVLISRNYRGDVEMGVIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIKYN 160
L+I + KG+VLISR YR D+ ++ F ++ ++ + +P+ + +F ++K +
Sbjct: 3 GGLFIYNHKGEVLISRVYRDDIGRNAVDAFRVNVIHARQQ-VRSPVTNIARTSFFHVKRS 61
Query: 161 NLFIVSTTKKNANIALVFVFLNKIVRVFTEYFKEIEEESIRDNFVVIYELLDELIDFGYP 220
N+++ + TK+N N A+VF FL K+ V YF +I EE+I++NFV+IYELLDE++DFGYP
Sbjct: 62 NIWLAAVTKQNVNAAMVFEFLYKMCDVMAAYFGKISEENIKNNFVLIYELLDEILDFGYP 121
Query: 221 QTTDSKILQEYITQEGHKL-----EIQPRIPMAVTNAVSWRSEGIKYRKNEVFLDVIESV 275
Q +++ L+ +ITQ+G K E Q +I VT + WR EGIKYR+NE+FLDV+ESV
Sbjct: 122 QNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLESV 181
Query: 276 NLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVLFESTGRGKS----------- 324
NLL + G VL + + G + M+ YLSGMPE + G+NDK++ E G+G +
Sbjct: 182 NLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSMEQKL 241
Query: 325 --------KSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIE 376
+S+ ++D FHQCVRLS+F+++R+ISFIPPDGEFELM YR + +
Sbjct: 242 ISEEDLGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVI 301
Query: 377 SVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSVKYTPEQSA 436
++ +++E + KS FK A +E+ IP P + + G KY ++A
Sbjct: 302 PLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENA 361
Query: 437 ITWTIKSFPGGKEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQVRYLKIIEK 496
I W IK G KE + A L ++ +PPI + FE+P F SG++VRYLK+ E
Sbjct: 362 IVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVP-FAPSGLKVRYLKVFEP 420
Query: 497 ----SGYQALPW 504
S + + W
Sbjct: 421 KLNYSDHDVIKW 432
>pdb|1BW8|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain),
Complexed With Egfr Internalization Peptide Fyralm
Length = 321
Score = 225 bits (573), Expect = 6e-59, Method: Compositional matrix adjust.
Identities = 116/288 (40%), Positives = 170/288 (59%), Gaps = 14/288 (4%)
Query: 221 QTTDSKILQEYITQEGHK-----LEIQPRIPMAVTNAVSWRSEGIKYRKNEVFLDVIESV 275
Q +++ L+ +ITQ+G K E Q +I VT + WR EGIKYR+NE+FLDV+ESV
Sbjct: 8 QNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLESV 67
Query: 276 NLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVLFESTGRGKS--------KSV 327
NLL + G VL + + G + M+ YLSGMPE + G+NDK++ E G+G + +S+
Sbjct: 68 NLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQSI 127
Query: 328 ELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIERFVHSRV 387
++D FHQCVRLS+F+++R+ISFIPPDGEFELM YR + + ++ +++
Sbjct: 128 AIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTKL 187
Query: 388 EYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSVKYTPEQSAITWTIKSFPGG 447
E + KS FK A +E+ IP P + + G KY ++AI W IK G
Sbjct: 188 EVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKRMAGM 247
Query: 448 KEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQVRYLKIIE 495
KE + A L ++ +PPI + FE+P F SG++VRYLK+ E
Sbjct: 248 KESQISAEIELLPTNDKKKWARPPISMNFEVP-FAPSGLKVRYLKVFE 294
>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 = 224 bits (572), Expect = 7e-59, Method: Compositional matrix adjust.
Identities = 116/288 (40%), Positives = 170/288 (59%), Gaps = 14/288 (4%)
Query: 221 QTTDSKILQEYITQEGHK-----LEIQPRIPMAVTNAVSWRSEGIKYRKNEVFLDVIESV 275
Q +++ L+ +ITQ+G K E Q +I VT + WR EGIKYR+NE+FLDV+ESV
Sbjct: 1 QNSETGALKTFITQQGIKSQHQTKEEQSQITSQVTGQIGWRREGIKYRRNELFLDVLESV 60
Query: 276 NLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVLFESTGRGKS--------KSV 327
NLL + G VL + + G + M+ YLSGMPE + G+NDK++ E G+G + +S+
Sbjct: 61 NLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGTADETSKSGKQSI 120
Query: 328 ELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWIESVIERFVHSRV 387
++D FHQCVRLS+F+++R+ISFIPPDGEFELM YR + + ++ +++
Sbjct: 121 AIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRVIPLVREVGRTKL 180
Query: 388 EYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSVKYTPEQSAITWTIKSFPGG 447
E + KS FK A +E+ IP P + + G KY ++AI W IK G
Sbjct: 181 EVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASENAIVWKIKRMAGM 240
Query: 448 KEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQVRYLKIIE 495
KE + A L ++ +PPI + FE+P F SG++VRYLK+ E
Sbjct: 241 KESQISAEIELLPTNDKKKWARPPISMNFEVP-FAPSGLKVRYLKVFE 287
>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 = 211 bits (538), Expect = 6e-55, Method: Compositional matrix adjust.
Identities = 105/259 (40%), Positives = 153/259 (59%), Gaps = 9/259 (3%)
Query: 245 IPMAVTNAVSWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMP 304
+P + WR EGIKYR+NE+FLDV+ESVNLL + G VL + + G + M+ YLSGMP
Sbjct: 15 VPRGSHMQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMP 74
Query: 305 ELRLGLNDKVLFESTGRGKS--------KSVELEDVKFHQCVRLSRFENDRTISFIPPDG 356
E + G+NDK++ E G+G + +S+ ++D FHQCVRLS+F+++R+ISFIPPDG
Sbjct: 75 ECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDG 134
Query: 357 EFELMSYRLNTHVKPLIWIESVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADA 416
EFELM YR + + ++ +++E + KS FK A +E+ IP P +
Sbjct: 135 EFELMRYRTTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNT 194
Query: 417 DSPKFKTTIGSVKYTPEQSAITWTIKSFPGGKEYLMRAHFGLPSVENEDAEGKPPIQVKF 476
+ G KY ++AI W IK G KE + A L ++ +PPI + F
Sbjct: 195 SGVQVICMKGKAKYKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNF 254
Query: 477 EIPYFTTSGIQVRYLKIIE 495
E+P F SG++VRYLK+ E
Sbjct: 255 EVP-FAPSGLKVRYLKVFE 272
>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 = 211 bits (536), Expect = 9e-55, Method: Compositional matrix adjust.
Identities = 104/251 (41%), Positives = 151/251 (60%), Gaps = 9/251 (3%)
Query: 253 VSWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLND 312
+ WR EGIKYR+NE+FLDV+ESVNLL + G VL + + G + M+ YLSGMPE + G+ND
Sbjct: 9 IGWRREGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMND 68
Query: 313 KVLFESTGRGKS--------KSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYR 364
K++ E G+G + +S+ ++D FHQCVRLS+F+++R+ISFIPPDGEFELM YR
Sbjct: 69 KIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYR 128
Query: 365 LNTHVKPLIWIESVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTT 424
+ + ++ +++E + KS FK A +E+ IP P + +
Sbjct: 129 TTKDIILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICM 188
Query: 425 IGSVKYTPEQSAITWTIKSFPGGKEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTS 484
G KY ++AI W IK G KE + A L ++ +PPI + FE+P F S
Sbjct: 189 KGKAKYKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVP-FAPS 247
Query: 485 GIQVRYLKIIE 495
G++VRYLK+ E
Sbjct: 248 GLKVRYLKVFE 258
>pdb|1H6E|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain),
Complexed With Ctla-4 Internalization Peptide
Ttgvyvkmppt
Length = 288
Score = 204 bits (518), Expect = 1e-52, Method: Compositional matrix adjust.
Identities = 104/259 (40%), Positives = 152/259 (58%), Gaps = 13/259 (5%)
Query: 258 EGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVLFE 317
EGIKYR+NE+FLDV+ESVNLL + G VL + + G + M+ YLSGMPE + G+NDK++ E
Sbjct: 17 EGIKYRRNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIE 76
Query: 318 STGRGKS--------KSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHV 369
G+G + +S+ ++D FHQCVRLS+F+++R+ISFIPPDGEFELM YR +
Sbjct: 77 KQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDI 136
Query: 370 KPLIWIESVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSVK 429
+ ++ +++E + KS FK A +E+ IP P + + G K
Sbjct: 137 ILPFRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAK 196
Query: 430 YTPEQSAITWTIKSFPGGKEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQVR 489
Y ++AI W IK G KE + A L ++ +PPI + FE+P F SG++VR
Sbjct: 197 YKASENAIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVP-FAPSGLKVR 255
Query: 490 YLKIIEK----SGYQALPW 504
YLK+ E S + + W
Sbjct: 256 YLKVFEPKLNYSDHDVIKW 274
>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 = 191 bits (484), Expect = 1e-48, Method: Compositional matrix adjust.
Identities = 96/240 (40%), Positives = 142/240 (59%), Gaps = 9/240 (3%)
Query: 264 KNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLNDKVLFESTGRGK 323
+NE+FLDV+ESVNLL + G VL + + G + M+ YLSGMPE + G+NDK++ E G+G
Sbjct: 120 RNELFLDVLESVNLLMSPQGQVLSAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKGT 179
Query: 324 S--------KSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVKPLIWI 375
+ +S+ ++D FHQCVRLS+F+++R+ISFIPPDGEFELM YR + +
Sbjct: 180 ADETSKSGKQSIAIDDCTFHQCVRLSKFDSERSISFIPPDGEFELMRYRTTKDIILPFRV 239
Query: 376 ESVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSVKYTPEQS 435
++ +++E + KS FK A +E+ IP P + + G KY ++
Sbjct: 240 IPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGKAKYKASEN 299
Query: 436 AITWTIKSFPGGKEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQVRYLKIIE 495
AI W IK G KE + A L ++ +PPI + FE+P F SG++VRYLK+ E
Sbjct: 300 AIVWKIKRMAGMKESQISAEIELLPTNDKKKWARPPISMNFEVP-FAPSGLKVRYLKVFE 358
>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 = 110 bits (274), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 69/246 (28%), Positives = 118/246 (47%), Gaps = 21/246 (8%)
Query: 253 VSWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLND 312
+ WR G+KY NE + DV+E ++ + + +G+ + +EI G I + LSGMP+L L +
Sbjct: 8 IPWRRAGVKYTNNEAYFDVVEEIDAIIDKSGSTVFAEIQGVIDACIKLSGMPDLSLSFMN 67
Query: 313 KVLFESTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTH--VK 370
L L+DV FH C+R R+E++R +SFIPPDG F L+SYR+++ V
Sbjct: 68 PRL-------------LDDVSFHPCIRFKRWESERVLSFIPPDGNFRLISYRVSSQNLVA 114
Query: 371 PLIWIESVI---ERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGS 427
++++ I E R + I K + T + + + +P + T GS
Sbjct: 115 IPVYVKHNISFKENSSCGRFDITIGPKQNMGK--TIEGITVTVHMPKVVLNMNLTPTQGS 172
Query: 428 VKYTPEQSAITWTIKSFPGGKEYLMRAHFGLPSVENEDAEGKPPIQVKFEIPYFTTSGIQ 487
+ P + W + K ++ L S + E P + ++F+I SG++
Sbjct: 173 YTFDPVTKVLAWDVGKITPQKLPSLKGLVNLQSGAPKPEE-NPNLNIQFKIQQLAISGLK 231
Query: 488 VRYLKI 493
V L +
Sbjct: 232 VNRLDM 237
>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 = 108 bits (270), Expect = 7e-24, Method: Compositional matrix adjust.
Identities = 75/266 (28%), Positives = 131/266 (49%), Gaps = 19/266 (7%)
Query: 253 VSWRSEGIKYRKNEVFLDVIESVNLLANSNGNVLRSEIVGAIKMRVYLSGMPELRLGLND 312
+S RS+ + +KNEVFLDV+E +++L SNG++L+ ++ G I+++ +L E+R+GL +
Sbjct: 23 LSSRSD--QSQKNEVFLDVVERLSVLIASNGSLLKVDVQGEIRLKSFLPSGSEMRIGLTE 80
Query: 313 KV-LFESTGRGKSKSVELEDVKFHQCVRLSRFENDRTISFIPPDGEFELMSYRLNTHVK- 370
+ + +S RG + +++V FH V L FE+ R + PP GE +M Y+L+ +
Sbjct: 81 EFSVGKSELRGYGPGIRVDEVSFHSSVNLDEFESHRILRLQPPQGELTVMRYQLSDDLPS 140
Query: 371 --PLIWIESVIERFVHSRVEYMIKAKSQFKRRSTANNVEIVIPVPADADSPKFKTTIGSV 428
P SV R++ +K + +S A NV + +P+P S + +
Sbjct: 141 PLPFRLFPSVQWDRGSGRLQVYLKLRCDLLSKSQALNVRLHLPLPRGVVSLSQELSSPEQ 200
Query: 429 KYTPEQSAITWTIKSFPGGKEY-----------LMRAHFGLPSVENEDAEGKPPIQVKFE 477
K + A+ W + GG + GL + + G P + FE
Sbjct: 201 KAELAEGALRWDLPRVQGGSQLSGLFQMDVPGPPGPPSHGLSTSASPLGLG--PASLSFE 258
Query: 478 IPYFTTSGIQVRYLKIIEKSGYQALP 503
+P T SG+QVR+L++ + A P
Sbjct: 259 LPRHTCSGLQVRFLRLAFRPSGNANP 284
>pdb|1W63|Q Chain Q, Ap1 Clathrin Adaptor Core
pdb|1W63|S Chain S, Ap1 Clathrin Adaptor Core
pdb|1W63|T Chain T, Ap1 Clathrin Adaptor Core
pdb|1W63|U Chain U, Ap1 Clathrin Adaptor Core
pdb|1W63|W Chain W, Ap1 Clathrin Adaptor Core
pdb|1W63|X Chain X, Ap1 Clathrin Adaptor Core
Length = 158
Score = 35.8 bits (81), Expect = 0.055, Method: Composition-based stats.
Identities = 24/109 (22%), Positives = 50/109 (45%), Gaps = 2/109 (1%)
Query: 126 VIEKFMPLLMEKEEEGMLTPLLQTSDCTFAYIKYNNLFIVSTTKKNANIALVFVFLNKIV 185
++ + M +++ ++ + + L+ D Y +Y +L+ + N + +++ V
Sbjct: 31 MVRELMQVVLARKPK--MCSFLEWRDLKVVYKRYASLYFCCAIEGQDNELITLELIHRYV 88
Query: 186 RVFTEYFKEIEEESIRDNFVVIYELLDELIDFGYPQTTDSKILQEYITQ 234
+ +YF + E I NF Y +LDE + G Q T K + + I Q
Sbjct: 89 ELLDKYFGSVCELDIIFNFEKAYFILDEFLMGGDVQDTSKKSVLKAIEQ 137
>pdb|2VGL|S Chain S, Ap2 Clathrin Adaptor Core
pdb|2JKR|I Chain I, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
Phosphos)qikrllse
pdb|2JKR|S Chain S, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
Phosphos)qikrllse
pdb|2JKT|I Chain I, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
Phosphos)eikrllse Q To E Mutant
pdb|2JKT|S Chain S, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
Phosphos)eikrllse Q To E Mutant
pdb|2XA7|S Chain S, Ap2 Clathrin Adaptor Core In Active Complex With Cargo
Peptides
Length = 142
Score = 33.1 bits (74), Expect = 0.38, Method: Composition-based stats.
Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 1/78 (1%)
Query: 156 YIKYNNLFIVSTTKKNANIALVFVFLNKIVRVFTEYFKEIEEESIRDNFVVIYELLDELI 215
Y +Y L+ N N ++ V V EYF + E + NF +Y ++DE+
Sbjct: 59 YRRYAGLYFCICVDVNDNNLAYLEAIHNFVEVLNEYFHNVCELDLVFNFYKVYTVVDEMF 118
Query: 216 DFG-YPQTTDSKILQEYI 232
G +T+ +K+L++ +
Sbjct: 119 LAGEIRETSQTKVLKQLL 136
>pdb|3LVT|A Chain A, The Crystal Structure Of A Protein In The Glycosyl
Hydrolase Family 38 From Enterococcus Faecalis To 2.55a
Length = 899
Score = 30.4 bits (67), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 30/104 (28%), Positives = 42/104 (40%), Gaps = 12/104 (11%)
Query: 182 NKIVRVFTEYFKEIEEESIRDNFVVIYELLDELIDFGYPQTTDSKILQEYITQEGHKLEI 241
NK V +F E E E + V + + EL D+GY T +++ EY + G L
Sbjct: 725 NKGVTIFNEGLNEYEVLADGTIAVTLIRCVGELGDWGYFATPEAQCQGEYTFKYGLSLHG 784
Query: 242 QPRIPMAV-----------TNAVSWRSEGIKYRKNEVFLDVIES 274
+P A T A + R EG K N V+L E
Sbjct: 785 KPEERFATYQQAYSAQIPFTAATTARHEG-KLAPNHVYLTTAEG 827
>pdb|3SQL|A Chain A, Crystal Structure Of Glycoside Hydrolase From
Synechococcus
pdb|3SQL|B Chain B, Crystal Structure Of Glycoside Hydrolase From
Synechococcus
pdb|3SQM|A Chain A, Crystal Structure Of Glycoside Hydrolase From
Synechococcus Complexed With N-Acetyl-D-Glucosamine
pdb|3SQM|B Chain B, Crystal Structure Of Glycoside Hydrolase From
Synechococcus Complexed With N-Acetyl-D-Glucosamine
pdb|3SQM|C Chain C, Crystal Structure Of Glycoside Hydrolase From
Synechococcus Complexed With N-Acetyl-D-Glucosamine
pdb|3SQM|D Chain D, Crystal Structure Of Glycoside Hydrolase From
Synechococcus Complexed With N-Acetyl-D-Glucosamine
Length = 535
Score = 29.3 bits (64), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 433 EQSAITWTIKSFPGGKEYLMRAHFGLPSVENED 465
+Q A+ T K FPG + +H LP++ ++D
Sbjct: 186 QQYAVLTTAKHFPGHGDTATDSHLALPTISHDD 218
>pdb|1WQL|B Chain B, Cumene Dioxygenase (Cuma1a2) From Pseudomonas Fluorescens
Ip01
Length = 186
Score = 29.3 bits (64), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 6/61 (9%)
Query: 330 EDVKFHQCVRLSRFENDRTISFIPPDGE------FELMSYRLNTHVKPLIWIESVIERFV 383
+D+++ +R + ++ + ++PP G +E M R+ V L W E R
Sbjct: 50 QDIQYWMPIRTTHTSRNKAMEYVPPGGNAHFDETYESMRARIRARVSGLNWTEDPPSRSR 109
Query: 384 H 384
H
Sbjct: 110 H 110
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 0.136 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,336,231
Number of Sequences: 62578
Number of extensions: 599471
Number of successful extensions: 1343
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1291
Number of HSP's gapped (non-prelim): 32
length of query: 504
length of database: 14,973,337
effective HSP length: 103
effective length of query: 401
effective length of database: 8,527,803
effective search space: 3419649003
effective search space used: 3419649003
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: 54 (25.4 bits)