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= 002905
(867 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2XA7|B Chain B, Ap2 Clathrin Adaptor Core In Active Complex With Cargo
Peptides
Length = 592
Score = 74.3 bits (181), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 98/471 (20%), Positives = 194/471 (41%), Gaps = 47/471 (9%)
Query: 21 EIKEALEGNDVPAKVDAMKKAIMLLLNGETLPQLFITIVRYVLPSEDHTIQKLLLLYLEI 80
E+K L + +A+KK I + G+ + LF +V + +++ ++KL+ LYL
Sbjct: 17 ELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVN-CMQTDNLELKKLVYLYLMN 75
Query: 81 IDKTDAKGRVLPEMILICQN-LRNNLQHPNEYIRGVTLRFLCRLNETEIIEPLIPSVLQN 139
K+ P+M ++ N + + PN IR + +R + + +I E L + +
Sbjct: 76 YAKSQ------PDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKC 129
Query: 140 LQHRHPYIRRNAILAVMAIYKL------PQG-----EQLLVDAPEMI--EKVLSTEQDPS 186
L+ PY+R+ A + V ++ + QG L+ D+ M+ V + +
Sbjct: 130 LKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISE 189
Query: 187 AKRNAFLMLFTCDQDRAINYLLTHVDRVSEWGELLQMVVLELIRKVCRTNXXXXXXXXXX 246
+ N+ L+ + IN LLT ++ +EWG Q+ +L+ + +
Sbjct: 190 SHPNSNLLDLN---PQNINKLLTALNECTEWG---QIFILDCLSNYNPKDDREAQSICER 243
Query: 247 XXSLLNAPSTAVIYECAGTLVSLSSAPTAIRAAANTYSQLL---------LSQSDNNVKL 297
L+ ++AV+ L+ + ++ Y+ LL L + V+
Sbjct: 244 VTPRLSHANSAVVLSAVKVLMKFLEL---LPKDSDYYNMLLKKLAPPLVTLLSGEPEVQY 300
Query: 298 IVLDRLNELRSSHRDIMVDLIMDVLRALNSPNLDIRRKTLDIVLELITPRNINXXXXXXX 357
+ L +N + +I+ I N P + ++ + LDI++ L + NI
Sbjct: 301 VALRNINLIVQKRPEILKQEIKVFFVKYNDP-IYVKLEKLDIMIRLASQANI-------A 352
Query: 358 XXXXXTQSGELEKNGEYRQMLIQAIHSCAIKFPEVASTVVHLLMDFLGDSNVASAIDVII 417
+ E + ++ + ++AI CAIK + A V L+D + + I+
Sbjct: 353 QVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIV 412
Query: 418 FVREIIEMNPKLRVSIITRLLDNFYQIRAARVCTCALWIIGEYCQSLSEVE 468
+R+I P SII L +N + +WI+GEY + + +
Sbjct: 413 VIRDIFRKYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNAD 463
>pdb|2VGL|B Chain B, Ap2 Clathrin Adaptor Core
pdb|2JKR|B Chain B, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
Phosphos)qikrllse
pdb|2JKR|E Chain E, Ap2 Clathrin Adaptor Core With Dileucine Peptide Rm(
Phosphos)qikrllse
pdb|2JKT|B Chain B, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
Phosphos)eikrllse Q To E Mutant
pdb|2JKT|E Chain E, Ap2 Clathrin Adaptor Core With Cd4 Dileucine Peptide Rm(
Phosphos)eikrllse Q To E Mutant
Length = 591
Score = 74.3 bits (181), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 98/471 (20%), Positives = 194/471 (41%), Gaps = 47/471 (9%)
Query: 21 EIKEALEGNDVPAKVDAMKKAIMLLLNGETLPQLFITIVRYVLPSEDHTIQKLLLLYLEI 80
E+K L + +A+KK I + G+ + LF +V + +++ ++KL+ LYL
Sbjct: 17 ELKAELNNEKKEKRKEAVKKVIAAMTVGKDVSSLFPDVVN-CMQTDNLELKKLVYLYLMN 75
Query: 81 IDKTDAKGRVLPEMILICQN-LRNNLQHPNEYIRGVTLRFLCRLNETEIIEPLIPSVLQN 139
K+ P+M ++ N + + PN IR + +R + + +I E L + +
Sbjct: 76 YAKSQ------PDMAIMAVNSFVKDCEDPNPLIRALAVRTMGCIRVDKITEYLCEPLRKC 129
Query: 140 LQHRHPYIRRNAILAVMAIYKL------PQG-----EQLLVDAPEMI--EKVLSTEQDPS 186
L+ PY+R+ A + V ++ + QG L+ D+ M+ V + +
Sbjct: 130 LKDEDPYVRKTAAVCVAKLHDINAQMVEDQGFLDSLRDLIADSNPMVVANAVAALSEISE 189
Query: 187 AKRNAFLMLFTCDQDRAINYLLTHVDRVSEWGELLQMVVLELIRKVCRTNXXXXXXXXXX 246
+ N+ L+ + IN LLT ++ +EWG Q+ +L+ + +
Sbjct: 190 SHPNSNLLDLN---PQNINKLLTALNECTEWG---QIFILDCLSNYNPKDDREAQSICER 243
Query: 247 XXSLLNAPSTAVIYECAGTLVSLSSAPTAIRAAANTYSQLL---------LSQSDNNVKL 297
L+ ++AV+ L+ + ++ Y+ LL L + V+
Sbjct: 244 VTPRLSHANSAVVLSAVKVLMKFLEL---LPKDSDYYNMLLKKLAPPLVTLLSGEPEVQY 300
Query: 298 IVLDRLNELRSSHRDIMVDLIMDVLRALNSPNLDIRRKTLDIVLELITPRNINXXXXXXX 357
+ L +N + +I+ I N P + ++ + LDI++ L + NI
Sbjct: 301 VALRNINLIVQKRPEILKQEIKVFFVKYNDP-IYVKLEKLDIMIRLASQANI-------A 352
Query: 358 XXXXXTQSGELEKNGEYRQMLIQAIHSCAIKFPEVASTVVHLLMDFLGDSNVASAIDVII 417
+ E + ++ + ++AI CAIK + A V L+D + + I+
Sbjct: 353 QVLAELKEYATEVDVDFVRKAVRAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIV 412
Query: 418 FVREIIEMNPKLRVSIITRLLDNFYQIRAARVCTCALWIIGEYCQSLSEVE 468
+R+I P SII L +N + +WI+GEY + + +
Sbjct: 413 VIRDIFRKYPNKYESIIATLCENLDSLDEPDARAAMIWIVGEYAERIDNAD 463
>pdb|1W63|B Chain B, Ap1 Clathrin Adaptor Core
pdb|1W63|D Chain D, Ap1 Clathrin Adaptor Core
pdb|1W63|F Chain F, Ap1 Clathrin Adaptor Core
pdb|1W63|H Chain H, Ap1 Clathrin Adaptor Core
pdb|1W63|J Chain J, Ap1 Clathrin Adaptor Core
pdb|1W63|L Chain L, Ap1 Clathrin Adaptor Core
Length = 584
Score = 60.1 bits (144), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 90/443 (20%), Positives = 182/443 (41%), Gaps = 57/443 (12%)
Query: 48 GETLPQLFITIVRYVLPSEDHTIQKLLLLYLEIIDKTDAKGRVLPEMILICQN-LRNNLQ 106
G+ + LF +V + +++ ++KL+ LYL K+ P+M ++ N + +
Sbjct: 44 GKDVSALFPDVVN-CMQTDNLELKKLVYLYLMNYAKSQ------PDMAIMAVNTFVKDCE 96
Query: 107 HPNEYIRGVTLRFLCRLNETEIIEPLIPSVLQNLQHRHPYIRRNAILAVMAIYKL----- 161
PN IR + +R + + +I E L + + L+ PY+R+ A + V ++ +
Sbjct: 97 DPNPLIRALAVRTMGCIRVDKITEYLCEPLRKCLKDEDPYVRKTAAVCVAKLHDINAQMV 156
Query: 162 -PQG-----EQLLVDAPEMI--EKVLSTEQDPSAKRNAFLMLFTCDQDRAINYLLTHVDR 213
QG + L+ D+ M+ +V + + + ++ L+ + ++IN LLT ++
Sbjct: 157 EDQGFLDTLKDLISDSNPMVVANRVAALSEIAESHPSSNLLDL---KAQSINKLLTALNE 213
Query: 214 VSEWGELLQMVVLELIRKVCRTNXXXXXXXXXXXXSLLNAPSTAVIYECAGTLVS----- 268
+EW Q+ +L+ + + L+ ++AV+ L+
Sbjct: 214 CTEWA---QIFILDCLGNYMPKDDREAQSICERVTPRLSHANSAVVLSAVKVLMKFMEML 270
Query: 269 ---LSSAPTAIRAAANTYSQLLLSQSD------NNVKLIVLDRLNELRSSHRDIMVDLIM 319
L T ++ A LL ++ + N+ LIV R L+ + V
Sbjct: 271 SKDLDYYATLLKKLAPPLVTLLSAEPEPQYVPLRNINLIVQKRPEILKHEMKVFFV---- 326
Query: 320 DVLRALNSPNLDIRRKTLDIVLELITPRNINXXXXXXXXXXXXTQSGELEKNGEYRQMLI 379
N P + ++ + LDI++ L + NI + E + ++ + +
Sbjct: 327 ----KYNDP-IYVKLEKLDIMIRLASQANI-------AQVLAELKEYATEVDVDFVRKAV 374
Query: 380 QAIHSCAIKFPEVASTVVHLLMDFLGDSNVASAIDVIIFVREIIEMNPKLRVSIITRLLD 439
+AI CAIK + A V L+D + + I+ +++I P S+I L +
Sbjct: 375 RAIGRCAIKVEQSAERCVSTLLDLIQTKVNYVVQEAIVVIKDIFRKYPNKYESVIATLCE 434
Query: 440 NFYQIRAARVCTCALWIIGEYCQ 462
N +WI+GEY +
Sbjct: 435 NLDSDDEPEARAAMIWIVGEYAE 457
>pdb|2HPI|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
Not Homologous: X-Ray Structure Of Dna Polymerase Iii
pdb|2HPM|A Chain A, Eubacterial And Eukaryotic Replicative Dna Polymerases Are
Not Homologous: X-ray Structure Of Dna Polymerase Iii
Length = 1220
Score = 32.7 bits (73), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 10/86 (11%)
Query: 407 SNVASAIDVIIFVREIIEMNPKLRVSIITRLLDNFYQIRAARVCTCALWIIGEYCQSLSE 466
S+ A++V++F R ++PKL+ I +L + RV A+W + E ++
Sbjct: 1071 SDETGALEVVVFGRAYEGVSPKLKEDIPLLVLAEVEKGEELRVLAQAVWTLEEVLEAPKA 1130
Query: 467 V----------ENGIATIKQCLGELP 482
+ E G+A +K L E P
Sbjct: 1131 LEVEVDHALLDEKGVARLKSLLDEHP 1156
>pdb|3E0D|A Chain A, Insights Into The Replisome From The Crystral Structure Of
The Ternary Complex Of The Eubacterial Dna Polymerase Iii
Alpha-Subunit
pdb|3E0D|B Chain B, Insights Into The Replisome From The Crystral Structure Of
The Ternary Complex Of The Eubacterial Dna Polymerase Iii
Alpha-Subunit
Length = 1220
Score = 32.7 bits (73), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 39/86 (45%), Gaps = 10/86 (11%)
Query: 407 SNVASAIDVIIFVREIIEMNPKLRVSIITRLLDNFYQIRAARVCTCALWIIGEYCQSLSE 466
S+ A++V++F R ++PKL+ I +L + RV A+W + E ++
Sbjct: 1071 SDETGALEVVVFGRAYEGVSPKLKEDIPLLVLAEVEKGEELRVLAQAVWTLEEVLEAPKA 1130
Query: 467 V----------ENGIATIKQCLGELP 482
+ E G+A +K L E P
Sbjct: 1131 LEVEVDHALLDEKGVARLKSLLDEHP 1156
>pdb|3GB8|A Chain A, Crystal Structure Of Crm1SNURPORTIN-1 Complex
Length = 1071
Score = 30.8 bits (68), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 9/77 (11%)
Query: 128 IIEPLIPSVLQNLQHRHPYIRRNAILAVMAIYKLPQGEQLLVDAPEMIEKVLST------ 181
+ PL+ +VL + Q P R +L+ MAI G + + P++ + V
Sbjct: 776 FVPPLLDAVLIDYQRNVPAAREPEVLSTMAIIVNKLGGHITAEIPQIFDAVFECTLNMIN 835
Query: 182 ---EQDPSAKRNAFLML 195
E+ P + N FL+L
Sbjct: 836 KDFEEYPEHRTNFFLLL 852
>pdb|3GJX|A Chain A, Crystal Structure Of The Nuclear Export Complex Crm1-
Snurportin1-Rangtp
pdb|3GJX|D Chain D, Crystal Structure Of The Nuclear Export Complex Crm1-
Snurportin1-Rangtp
pdb|3NBY|A Chain A, Crystal Structure Of The Pki Nes-Crm1-Rangtp Nuclear
Export Complex
pdb|3NBY|D Chain D, Crystal Structure Of The Pki Nes-Crm1-Rangtp Nuclear
Export Complex
pdb|3NBZ|A Chain A, Crystal Structure Of The Hiv-1 Rev Nes-Crm1-Rangtp Nuclear
Export Complex (Crystal I)
pdb|3NBZ|D Chain D, Crystal Structure Of The Hiv-1 Rev Nes-Crm1-Rangtp Nuclear
Export Complex (Crystal I)
pdb|3NC0|A Chain A, Crystal Structure Of The Hiv-1 Rev Nes-Crm1-Rangtp Nuclear
Export Complex (Crystal Ii)
pdb|3NC0|D Chain D, Crystal Structure Of The Hiv-1 Rev Nes-Crm1-Rangtp Nuclear
Export Complex (Crystal Ii)
pdb|3NC1|A Chain A, Crystal Structure Of The Crm1-Rangtp Complex
Length = 1073
Score = 30.8 bits (68), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 9/77 (11%)
Query: 128 IIEPLIPSVLQNLQHRHPYIRRNAILAVMAIYKLPQGEQLLVDAPEMIEKVLST------ 181
+ PL+ +VL + Q P R +L+ MAI G + + P++ + V
Sbjct: 778 FVPPLLDAVLIDYQRNVPAAREPEVLSTMAIIVNKLGGHITAEIPQIFDAVFECTLNMIN 837
Query: 182 ---EQDPSAKRNAFLML 195
E+ P + N FL+L
Sbjct: 838 KDFEEYPEHRTNFFLLL 854
>pdb|1W9C|A Chain A, Proteolytic Fragment Of Crm1 Spanning Six C-Terminal Heat
Repeats
pdb|1W9C|B Chain B, Proteolytic Fragment Of Crm1 Spanning Six C-Terminal Heat
Repeats
Length = 321
Score = 30.4 bits (67), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 34/77 (44%), Gaps = 9/77 (11%)
Query: 128 IIEPLIPSVLQNLQHRHPYIRRNAILAVMAIYKLPQGEQLLVDAPEMIEKVLST------ 181
+ PL+ +VL + Q P R +L+ MAI G + + P++ + V
Sbjct: 70 FVPPLLDAVLIDYQRNVPAAREPEVLSTMAIIVNKLGGHITAEIPQIFDAVFECTLNMIN 129
Query: 182 ---EQDPSAKRNAFLML 195
E+ P + N FL+L
Sbjct: 130 KDFEEYPEHRTNFFLLL 146
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
0.320 0.135 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,318,262
Number of Sequences: 62578
Number of extensions: 833427
Number of successful extensions: 2010
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1995
Number of HSP's gapped (non-prelim): 16
length of query: 867
length of database: 14,973,337
effective HSP length: 107
effective length of query: 760
effective length of database: 8,277,491
effective search space: 6290893160
effective search space used: 6290893160
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: 56 (26.2 bits)