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= 006936
(625 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 = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 36/135 (26%), Positives = 68/135 (50%), Gaps = 7/135 (5%)
Query: 342 VSGQINCRAELEGMPDVSFPLTGLNSAHVEVLSFHPSAQVPEQGVDKQAVMFSPPLGNFV 401
+ G I+ +L GMPD+S L+ +N ++ +SFHP + ++ ++ + F PP GNF
Sbjct: 45 IQGVIDACIKLSGMPDLS--LSFMNPRLLDDVSFHPCIRF-KRWESERVLSFIPPDGNFR 101
Query: 402 LMRYQAICG--LGPPVKGFYQLSMVSEDEGAFLFKLCLMESYKAPLTMEFCNVTMLFPRR 459
L+ Y+ + PV + +S E+ F + + T+E VT+ P +
Sbjct: 102 LISYRVSSQNLVAIPVYVKHNISF-KENSSCGRFDITIGPKQNMGKTIEGITVTVHMP-K 159
Query: 460 RVVSFDGTPSIGTVS 474
V++ + TP+ G+ +
Sbjct: 160 VVLNMNLTPTQGSYT 174
>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 = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 47/215 (21%), Positives = 91/215 (42%), Gaps = 33/215 (15%)
Query: 295 SELPPQDLKQPAWKPYLYKGKQRLLFT-IHETVHAAMYDRDEIPDSLSVSGQINCRAELE 353
S++ Q Q W+ K ++ LF + E+V+ M + ++ S VSG++ ++ L
Sbjct: 28 SQITSQVTGQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVL-SAHVSGRVVMKSYLS 86
Query: 354 GMPDVSFPL-------------------TGLNSAHVEVLSFHPSAQVPEQGVDKQAVMFS 394
GMP+ F + +G S ++ +FH ++ + ++ ++ F
Sbjct: 87 GMPECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSER-SISFI 145
Query: 395 PPLGNFVLMRYQAICGLGPPVKGFYQLSMVSE-DEGAFLFKLCLMESYKAPLTMEFCNVT 453
PP G F LMRY+ + P F + +V E K+ + ++K L + V
Sbjct: 146 PPDGEFELMRYRTTKDIILP---FRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVR 202
Query: 454 MLFPRR----RVVSFDGTPSIGTVSNNEHSVEWKI 484
+ P +V+ G +E+++ WKI
Sbjct: 203 IPTPLNTSGVQVICMKGK---AKYKASENAIVWKI 234
>pdb|1BW8|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain),
Complexed With Egfr Internalization Peptide Fyralm
Length = 321
Score = 38.5 bits (88), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 47/215 (21%), Positives = 91/215 (42%), Gaps = 33/215 (15%)
Query: 295 SELPPQDLKQPAWKPYLYKGKQRLLFT-IHETVHAAMYDRDEIPDSLSVSGQINCRAELE 353
S++ Q Q W+ K ++ LF + E+V+ M + ++ S VSG++ ++ L
Sbjct: 35 SQITSQVTGQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVL-SAHVSGRVVMKSYLS 93
Query: 354 GMPDVSFPL-------------------TGLNSAHVEVLSFHPSAQVPEQGVDKQAVMFS 394
GMP+ F + +G S ++ +FH ++ + ++ ++ F
Sbjct: 94 GMPECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSER-SISFI 152
Query: 395 PPLGNFVLMRYQAICGLGPPVKGFYQLSMVSE-DEGAFLFKLCLMESYKAPLTMEFCNVT 453
PP G F LMRY+ + P F + +V E K+ + ++K L + V
Sbjct: 153 PPDGEFELMRYRTTKDIILP---FRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVR 209
Query: 454 MLFPRR----RVVSFDGTPSIGTVSNNEHSVEWKI 484
+ P +V+ G +E+++ WKI
Sbjct: 210 IPTPLNTSGVQVICMKGK---AKYKASENAIVWKI 241
>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 = 38.5 bits (88), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 47/216 (21%), Positives = 91/216 (42%), Gaps = 33/216 (15%)
Query: 294 SSELPPQDLKQPAWKPYLYKGKQRLLFT-IHETVHAAMYDRDEIPDSLSVSGQINCRAEL 352
S++ Q Q W+ K ++ LF + E+V+ M + ++ S VSG++ ++ L
Sbjct: 148 QSQITSQVTGQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVL-SAHVSGRVVMKSYL 206
Query: 353 EGMPDVSFPL-------------------TGLNSAHVEVLSFHPSAQVPEQGVDKQAVMF 393
GMP+ F + +G S ++ +FH ++ + ++ ++ F
Sbjct: 207 SGMPECKFGMNDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSER-SISF 265
Query: 394 SPPLGNFVLMRYQAICGLGPPVKGFYQLSMVSE-DEGAFLFKLCLMESYKAPLTMEFCNV 452
PP G F LMRY+ + P F + +V E K+ + ++K L + V
Sbjct: 266 IPPDGEFELMRYRTTKDIILP---FRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEV 322
Query: 453 TMLFPRR----RVVSFDGTPSIGTVSNNEHSVEWKI 484
+ P +V+ G +E+++ WKI
Sbjct: 323 RIPTPLNTSGVQVICMKGKAKYKA---SENAIVWKI 355
>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 = 37.4 bits (85), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 45/206 (21%), Positives = 87/206 (42%), Gaps = 33/206 (16%)
Query: 304 QPAWKPYLYKGKQRLLFT-IHETVHAAMYDRDEIPDSLSVSGQINCRAELEGMPDVSFPL 362
Q W+ K ++ LF + E+V+ M + ++ S VSG++ ++ L GMP+ F +
Sbjct: 8 QIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVL-SAHVSGRVVMKSYLSGMPECKFGM 66
Query: 363 -------------------TGLNSAHVEVLSFHPSAQVPEQGVDKQAVMFSPPLGNFVLM 403
+G S ++ +FH ++ + ++ ++ F PP G F LM
Sbjct: 67 NDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSER-SISFIPPDGEFELM 125
Query: 404 RYQAICGLGPPVKGFYQLSMVSE-DEGAFLFKLCLMESYKAPLTMEFCNVTMLFPRR--- 459
RY+ + P F + +V E K+ + ++K L + V + P
Sbjct: 126 RYRTTKDIILP---FRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSG 182
Query: 460 -RVVSFDGTPSIGTVSNNEHSVEWKI 484
+V+ G +E+++ WKI
Sbjct: 183 VQVICMKGK---AKYKASENAIVWKI 205
>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 = 37.4 bits (85), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 45/206 (21%), Positives = 87/206 (42%), Gaps = 33/206 (16%)
Query: 304 QPAWKPYLYKGKQRLLFT-IHETVHAAMYDRDEIPDSLSVSGQINCRAELEGMPDVSFPL 362
Q W+ K ++ LF + E+V+ M + ++ S VSG++ ++ L GMP+ F +
Sbjct: 22 QIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVL-SAHVSGRVVMKSYLSGMPECKFGM 80
Query: 363 -------------------TGLNSAHVEVLSFHPSAQVPEQGVDKQAVMFSPPLGNFVLM 403
+G S ++ +FH ++ + ++ ++ F PP G F LM
Sbjct: 81 NDKIVIEKQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSER-SISFIPPDGEFELM 139
Query: 404 RYQAICGLGPPVKGFYQLSMVSE-DEGAFLFKLCLMESYKAPLTMEFCNVTMLFPRR--- 459
RY+ + P F + +V E K+ + ++K L + V + P
Sbjct: 140 RYRTTKDIILP---FRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSG 196
Query: 460 -RVVSFDGTPSIGTVSNNEHSVEWKI 484
+V+ G +E+++ WKI
Sbjct: 197 VQVICMKGK---AKYKASENAIVWKI 219
>pdb|1H6E|A Chain A, Mu2 Adaptin Subunit (Ap50) Of Ap2 Adaptor (Second Domain),
Complexed With Ctla-4 Internalization Peptide
Ttgvyvkmppt
Length = 288
Score = 37.0 bits (84), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 41/194 (21%), Positives = 81/194 (41%), Gaps = 32/194 (16%)
Query: 315 KQRLLFTIHETVHAAMYDRDEIPDSLSVSGQINCRAELEGMPDVSFPL------------ 362
+ L + E+V+ M + ++ S VSG++ ++ L GMP+ F +
Sbjct: 23 RNELFLDVLESVNLLMSPQGQVL-SAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKG 81
Query: 363 -------TGLNSAHVEVLSFHPSAQVPEQGVDKQAVMFSPPLGNFVLMRYQAICGLGPPV 415
+G S ++ +FH ++ + ++ ++ F PP G F LMRY+ + P
Sbjct: 82 TADETSKSGKQSIAIDDCTFHQCVRLSKFDSER-SISFIPPDGEFELMRYRTTKDIILP- 139
Query: 416 KGFYQLSMVSE-DEGAFLFKLCLMESYKAPLTMEFCNVTMLFPRR----RVVSFDGTPSI 470
F + +V E K+ + ++K L + V + P +V+ G
Sbjct: 140 --FRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGK--- 194
Query: 471 GTVSNNEHSVEWKI 484
+E+++ WKI
Sbjct: 195 AKYKASENAIVWKI 208
>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 = 36.2 bits (82), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 41/194 (21%), Positives = 81/194 (41%), Gaps = 32/194 (16%)
Query: 315 KQRLLFTIHETVHAAMYDRDEIPDSLSVSGQINCRAELEGMPDVSFPL------------ 362
+ L + E+V+ M + ++ S VSG++ ++ L GMP+ F +
Sbjct: 120 RNELFLDVLESVNLLMSPQGQVL-SAHVSGRVVMKSYLSGMPECKFGMNDKIVIEKQGKG 178
Query: 363 -------TGLNSAHVEVLSFHPSAQVPEQGVDKQAVMFSPPLGNFVLMRYQAICGLGPPV 415
+G S ++ +FH ++ + ++ ++ F PP G F LMRY+ + P
Sbjct: 179 TADETSKSGKQSIAIDDCTFHQCVRLSKFDSER-SISFIPPDGEFELMRYRTTKDIILP- 236
Query: 416 KGFYQLSMVSE-DEGAFLFKLCLMESYKAPLTMEFCNVTMLFPRR----RVVSFDGTPSI 470
F + +V E K+ + ++K L + V + P +V+ G
Sbjct: 237 --FRVIPLVREVGRTKLEVKVVIKSNFKPSLLAQKIEVRIPTPLNTSGVQVICMKGK--- 291
Query: 471 GTVSNNEHSVEWKI 484
+E+++ WKI
Sbjct: 292 AKYKASENAIVWKI 305
>pdb|2XA7|M Chain M, Ap2 Clathrin Adaptor Core In Active Complex With Cargo
Peptides
Length = 446
Score = 33.9 bits (76), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 33/154 (21%), Positives = 63/154 (40%), Gaps = 33/154 (21%)
Query: 294 SSELPPQDLKQPAWKPYLYKGKQRLLFT-IHETVHAAMYDRDEIPDSLSVSGQINCRAEL 352
S++ Q Q W+ K ++ LF + E+V+ M + ++ S VSG++ ++ L
Sbjct: 148 QSQITSQVTGQIGWRREGIKYRRNELFLDVLESVNLLMSPQGQVL-SAHVSGRVVMKSYL 206
Query: 353 EGMPDVSFPLT------------------------------GLNSAHVEVLSFHPSAQVP 382
GMP+ F + G S ++ +FH ++
Sbjct: 207 SGMPECKFGMNDKIVIEKQGKGTADETSKSMEQKLISEEDLGKQSIAIDDCTFHQCVRLS 266
Query: 383 EQGVDKQAVMFSPPLGNFVLMRYQAICGLGPPVK 416
+ ++ ++ F PP G F LMRY+ + P +
Sbjct: 267 KFDSER-SISFIPPDGEFELMRYRTTKDIILPFR 299
>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 = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 35/83 (42%), Gaps = 12/83 (14%)
Query: 342 VSGQINCRAELEGMPD--------VSFPLTGL---NSAHVEVLSFHPSAQVPEQGVDKQA 390
+ G I R L GMP+ V F TG S +E + FH ++ D+
Sbjct: 37 IVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQCVRLSRFENDR-T 95
Query: 391 VMFSPPLGNFVLMRYQAICGLGP 413
+ F PP G F LM Y+ + P
Sbjct: 96 ISFIPPDGEFELMSYRLNTHVKP 118
>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 = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 36/85 (42%), Gaps = 12/85 (14%)
Query: 342 VSGQINCRAELEGMPD--------VSFPLTGL---NSAHVEVLSFHPSAQVPEQGVDKQA 390
+ G I R L GMP+ V F TG S +E + FH ++ D+
Sbjct: 194 IVGSIKMRVFLSGMPELRLGLNDKVLFDNTGRGKSKSVELEDVKFHQCVRLSRFENDR-T 252
Query: 391 VMFSPPLGNFVLMRYQAICGLGPPV 415
+ F PP G F LM Y+ + P +
Sbjct: 253 ISFIPPDGEFELMSYRLNTHVKPLI 277
>pdb|1CP9|B Chain B, Crystal Structure Of Penicillin G Acylase From The Bro1
Mutant Strain Of Providencia Rettgeri
Length = 553
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 33/74 (44%), Gaps = 16/74 (21%)
Query: 269 SAMPFGTPVDLSYSNIFAIKVNGFPSSELPPQDLKQPAWKPYL-------YKGKQRLLFT 321
S FG VD IFA +V S E P L Q WK L KG+Q + F
Sbjct: 67 STAGFGDGVD-----IFAEQV----SPEDPNSYLHQGQWKKMLSRQETLNVKGEQPITFE 117
Query: 322 IHETVHAAMYDRDE 335
I+ TVH + RD+
Sbjct: 118 IYRTVHGNVVKRDK 131
>pdb|2POC|A Chain A, The Crystal Structure Of Isomerase Domain Of
Glucosamine-6-Phosphate Synthase From Candida Albicans
pdb|2POC|B Chain B, The Crystal Structure Of Isomerase Domain Of
Glucosamine-6-Phosphate Synthase From Candida Albicans
pdb|2POC|C Chain C, The Crystal Structure Of Isomerase Domain Of
Glucosamine-6-Phosphate Synthase From Candida Albicans
pdb|2POC|D Chain D, The Crystal Structure Of Isomerase Domain Of
Glucosamine-6-Phosphate Synthase From Candida Albicans
pdb|2PUT|A Chain A, The Crystal Structure Of Isomerase Domain Of
Glucosamine-6-Phosphate Synthase From Candida Albicans
pdb|2PUT|B Chain B, The Crystal Structure Of Isomerase Domain Of
Glucosamine-6-Phosphate Synthase From Candida Albicans
pdb|2PUT|C Chain C, The Crystal Structure Of Isomerase Domain Of
Glucosamine-6-Phosphate Synthase From Candida Albicans
pdb|2PUT|D Chain D, The Crystal Structure Of Isomerase Domain Of
Glucosamine-6-Phosphate Synthase From Candida Albicans
pdb|2PUV|A Chain A, The Crystal Structure Of Isomerase Domain Of
Glucosamine-6-Phosphate Synthase From Candida Albicans
pdb|2PUV|B Chain B, The Crystal Structure Of Isomerase Domain Of
Glucosamine-6-Phosphate Synthase From Candida Albicans
pdb|2PUV|C Chain C, The Crystal Structure Of Isomerase Domain Of
Glucosamine-6-Phosphate Synthase From Candida Albicans
pdb|2PUV|D Chain D, The Crystal Structure Of Isomerase Domain Of
Glucosamine-6-Phosphate Synthase From Candida Albicans
pdb|2PUW|A Chain A, The Crystal Structure Of Isomerase Domain Of
Glucosamine-6-phosphate Synthase From Candida Albicans
pdb|2PUW|B Chain B, The Crystal Structure Of Isomerase Domain Of
Glucosamine-6-phosphate Synthase From Candida Albicans
Length = 367
Score = 30.0 bits (66), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 7/61 (11%)
Query: 35 ACKTENESCIEDPIKYNVLPLVPTDSELASAFAERKR---REGSVRGFGVRVSQSTEGSD 91
AC T SC+ + L +P ELAS F +R+ R+ + V VSQS E +D
Sbjct: 57 ACGTSYHSCLATRSIFEELTEIPVSVELASDFLDRRSPVFRDDTC----VFVSQSGETAD 112
Query: 92 S 92
S
Sbjct: 113 S 113
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 0.135 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,127,478
Number of Sequences: 62578
Number of extensions: 699893
Number of successful extensions: 1177
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 1169
Number of HSP's gapped (non-prelim): 15
length of query: 625
length of database: 14,973,337
effective HSP length: 105
effective length of query: 520
effective length of database: 8,402,647
effective search space: 4369376440
effective search space used: 4369376440
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)