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= psy9587
(236 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1Y8Q|A Chain A, Sumo E1 Activating Enzyme Sae1-Sae2-Mg-Atp Complex
pdb|1Y8Q|C Chain C, Sumo E1 Activating Enzyme Sae1-Sae2-Mg-Atp Complex
pdb|1Y8R|A Chain A, Sumo E1 Activating Enzyme Sae1-Sae2-Sumo1-Mg-Atp Complex
pdb|1Y8R|D Chain D, Sumo E1 Activating Enzyme Sae1-Sae2-Sumo1-Mg-Atp Complex
pdb|3KYC|A Chain A, Human Sumo E1 Complex With A Sumo1-Amp Mimic
pdb|3KYD|A Chain A, Human Sumo E1~sumo1-amp Tetrahedral Intermediate Mimic
Length = 346
Score = 89.7 bits (221), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 50/113 (44%), Positives = 70/113 (61%), Gaps = 2/113 (1%)
Query: 124 LTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAKSSEARAQNL 183
L +GAEIAKN+IL+GVK + +LD VT ED AQFL +G+NRA++S RAQNL
Sbjct: 44 LKGLGAEIAKNLILAGVKGLTMLDHEQVTPEDPG-AQFLIRTGSVGRNRAEASLERAQNL 102
Query: 184 NPNVEVTSNETKVDEISEEFVHGFDVVIATSCNPNQLIKIDDFCRSKSKISLF 236
NP V+V + +++ E F FD V T C+ + ++K+D C K+ I F
Sbjct: 103 NPMVDVKVDTEDIEKKPESFFTQFDAVCLTCCSRDVIVKVDQICH-KNSIKFF 154
>pdb|4II2|A Chain A, Crystal Structure Of Ubiquitin Activating Enzyme 1 (uba1)
In Complex With The Ub E2 Ubc4, Ubiquitin, And Atp/mg
pdb|4II3|A Chain A, Crystal Structure Of S. Pombe Ubiquitin Activating Enzyme
1 (uba1) In Complex With Ubiquitin And Atp/mg
pdb|4II3|C Chain C, Crystal Structure Of S. Pombe Ubiquitin Activating Enzyme
1 (uba1) In Complex With Ubiquitin And Atp/mg
Length = 1001
Score = 63.5 bits (153), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 39/100 (39%), Positives = 59/100 (59%), Gaps = 5/100 (5%)
Query: 127 VGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAKSSEARAQNLNPN 186
+G EIAKN+ L+GVKSV L D ED+++ FL +DIG RAK + ++ LN
Sbjct: 37 LGVEIAKNVCLAGVKSVTLYDPQPTRIEDLSSQYFLT-EDDIGVPRAKVTVSKLAELNQY 95
Query: 187 VEVTSNETKVDEISEEFVHGFDVVIATSCNPNQLIKIDDF 226
V V+ VDE+S E++ F V+ T + + ++I+DF
Sbjct: 96 VPVSV----VDELSTEYLKNFKCVVVTETSLTKQLEINDF 131
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 28/113 (24%), Positives = 52/113 (46%), Gaps = 13/113 (11%)
Query: 127 VGAEIAKNIILSGVKS-----VCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAKSSEARAQ 181
+G E+ KN + GV + + + D + K ++N QFL D+GK +++ +
Sbjct: 427 IGCEMLKNWAMMGVATGESGHISVTDMDSIEKSNLNR-QFLFRPRDVGKLKSECASTAVS 485
Query: 182 NLNPNV--EVTSNETKVDEISE-----EFVHGFDVVIATSCNPNQLIKIDDFC 227
+NP++ ++TS + +V SE EF +V N + +D C
Sbjct: 486 IMNPSLTGKITSYQERVGPESEGIFGDEFFEKLSLVTNALDNVEARMYVDRRC 538
>pdb|3CMM|A Chain A, Crystal Structure Of The Uba1-Ubiquitin Complex
pdb|3CMM|C Chain C, Crystal Structure Of The Uba1-Ubiquitin Complex
Length = 1015
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 38/107 (35%), Positives = 64/107 (59%), Gaps = 5/107 (4%)
Query: 124 LTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAKSSEARAQNL 183
L +G EIAKN++L+GVKS+ + D V D++T QF +DIG+ R + A+ L
Sbjct: 35 LKGLGVEIAKNVVLAGVKSMTVFDPEPVQLADLST-QFFLTEKDIGQKRGDVTRAKLAEL 93
Query: 184 NPNVEVTSNETKVDEISEEFVHGFDVVIAT-SCNPNQLIKIDDFCRS 229
N V V ++ +D++++ + F VV+AT + + +KI++FC S
Sbjct: 94 NAYVPVNVLDS-LDDVTQ--LSQFQVVVATDTVSLEDKVKINEFCHS 137
Score = 35.8 bits (81), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 51/93 (54%), Gaps = 10/93 (10%)
Query: 115 KIYVYSTGPLTRVGAEIAKNIILSGVKS-----VCLLDSGVVTKEDVNTAQFLAPHEDIG 169
K+++ +G +G E+ KN L G+ S + + D+ + K ++N QFL +D+G
Sbjct: 427 KVFLVGSGA---IGCEMLKNWALLGLGSGSDGYIVVTDNDSIEKSNLNR-QFLFRPKDVG 482
Query: 170 KNRAKSSEARAQNLNPNVEVTSNETKVDEISEE 202
KN+++ + +NP+++ N K+D++ E
Sbjct: 483 KNKSEVAAEAVCAMNPDLKGKIN-AKIDKVGPE 514
>pdb|1TT5|A Chain A, Structure Of Appbp1-Uba3-Ubc12n26: A Unique E1-E2
Interaction Required For Optimal Conjugation Of The
Ubiquitin-Like Protein Nedd8
pdb|1TT5|C Chain C, Structure Of Appbp1-Uba3-Ubc12n26: A Unique E1-E2
Interaction Required For Optimal Conjugation Of The
Ubiquitin-Like Protein Nedd8
pdb|3DBH|A Chain A, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBH|C Chain C, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBH|E Chain E, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBH|G Chain G, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBL|A Chain A, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBL|C Chain C, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBL|E Chain E, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBL|G Chain G, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBR|A Chain A, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
pdb|3DBR|C Chain C, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
pdb|3DBR|E Chain E, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
pdb|3DBR|G Chain G, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
Length = 531
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 33/104 (31%), Positives = 52/104 (50%), Gaps = 4/104 (3%)
Query: 125 TRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAKSSEARAQNLN 184
T G EI KN++L G+ S ++D V+ ED FL IGKNRA+++ Q LN
Sbjct: 41 TATGTEILKNLVLPGIGSFTIIDGNQVSGEDAGNNFFLQ-RSSIGKNRAEAAMEFLQELN 99
Query: 185 PNVEVTSNETKVDEISE---EFVHGFDVVIATSCNPNQLIKIDD 225
+V + E + + + F F VV+AT + +++ D
Sbjct: 100 SDVSGSFVEESPENLLDNDPSFFCRFTVVVATQLPESTSLRLAD 143
>pdb|3GZN|A Chain A, Structure Of Nedd8-Activating Enzyme In Complex With Nedd8
And Mln4924
pdb|3GZN|C Chain C, Structure Of Nedd8-Activating Enzyme In Complex With Nedd8
And Mln4924
Length = 534
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 33/104 (31%), Positives = 52/104 (50%), Gaps = 4/104 (3%)
Query: 125 TRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAKSSEARAQNLN 184
T G EI KN++L G+ S ++D V+ ED FL IGKNRA+++ Q LN
Sbjct: 39 TATGTEILKNLVLPGIGSFTIIDGNQVSGEDAGNNFFLQ-RSSIGKNRAEAAMEFLQELN 97
Query: 185 PNVEVTSNETKVDEISE---EFVHGFDVVIATSCNPNQLIKIDD 225
+V + E + + + F F VV+AT + +++ D
Sbjct: 98 SDVSGSFVEESPENLLDNDPSFFCRFTVVVATQLPESTSLRLAD 141
>pdb|1YOV|A Chain A, Insights Into The Ubiquitin Transfer Cascade From The
Refined Structure Of The Activating Enzyme For Nedd8
pdb|1YOV|C Chain C, Insights Into The Ubiquitin Transfer Cascade From The
Refined Structure Of The Activating Enzyme For Nedd8
Length = 537
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 33/104 (31%), Positives = 52/104 (50%), Gaps = 4/104 (3%)
Query: 125 TRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAKSSEARAQNLN 184
T G EI KN++L G+ S ++D V+ ED FL IGKNRA+++ Q LN
Sbjct: 42 TATGTEILKNLVLPGIGSFTIIDGNQVSGEDAGNNFFLQ-RSSIGKNRAEAAMEFLQELN 100
Query: 185 PNVEVTSNETKVDEISE---EFVHGFDVVIATSCNPNQLIKIDD 225
+V + E + + + F F VV+AT + +++ D
Sbjct: 101 SDVSGSFVEESPENLLDNDPSFFCRFTVVVATQLPESTSLRLAD 144
>pdb|1R4M|A Chain A, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4M|C Chain C, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4M|E Chain E, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4M|G Chain G, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4N|A Chain A, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
pdb|1R4N|C Chain C, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
pdb|1R4N|E Chain E, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
pdb|1R4N|G Chain G, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
Length = 529
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 33/104 (31%), Positives = 52/104 (50%), Gaps = 4/104 (3%)
Query: 125 TRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAKSSEARAQNLN 184
T G EI KN++L G+ S ++D V+ ED FL IGKNRA+++ Q LN
Sbjct: 39 TATGTEILKNLVLPGIGSFTIIDGNQVSGEDAGNNFFLQ-RSSIGKNRAEAAMEFLQELN 97
Query: 185 PNVEVTSNETKVDEISE---EFVHGFDVVIATSCNPNQLIKIDD 225
+V + E + + + F F VV+AT + +++ D
Sbjct: 98 SDVSGSFVEESPENLLDNDPSFFCRFTVVVATQLPESTSLRLAD 141
>pdb|2NVU|A Chain A, Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a), A
Trapped Ubiquitin-Like Protein Activation Complex
Length = 536
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 33/104 (31%), Positives = 52/104 (50%), Gaps = 4/104 (3%)
Query: 125 TRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAKSSEARAQNLN 184
T G EI KN++L G+ S ++D V+ ED FL IGKNRA+++ Q LN
Sbjct: 41 TATGTEILKNLVLPGIGSFTIIDGNQVSGEDAGNNFFLQ-RSSIGKNRAEAAMEFLQELN 99
Query: 185 PNVEVTSNETKVDEISE---EFVHGFDVVIATSCNPNQLIKIDD 225
+V + E + + + F F VV+AT + +++ D
Sbjct: 100 SDVSGSFVEESPENLLDNDPSFFCRFTVVVATQLPESTSLRLAD 143
>pdb|1TT5|B Chain B, Structure Of Appbp1-Uba3-Ubc12n26: A Unique E1-E2
Interaction Required For Optimal Conjugation Of The
Ubiquitin-Like Protein Nedd8
pdb|1TT5|D Chain D, Structure Of Appbp1-Uba3-Ubc12n26: A Unique E1-E2
Interaction Required For Optimal Conjugation Of The
Ubiquitin-Like Protein Nedd8
Length = 434
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 50/98 (51%), Gaps = 4/98 (4%)
Query: 115 KIYVYSTGPLTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAK 174
K+ V G L G E+ KN+ LSG + + ++D + ++N QFL +DIG+ +A+
Sbjct: 42 KVLVIGAGGL---GCELLKNLALSGFRQIHVIDMDTIDVSNLNR-QFLFRPKDIGRPKAE 97
Query: 175 SSEARAQNLNPNVEVTSNETKVDEISEEFVHGFDVVIA 212
+ + PN V + K+ + ++ F F +++
Sbjct: 98 VAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVC 135
>pdb|3DBL|B Chain B, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBL|D Chain D, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBL|F Chain F, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBL|H Chain H, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
Length = 434
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 50/97 (51%), Gaps = 4/97 (4%)
Query: 115 KIYVYSTGPLTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAK 174
K+ V G L G E+ KN+ LSG + + ++D + ++N QFL +DIG+ +A+
Sbjct: 42 KVLVIGAGGL---GCELLKNLALSGFRQIHVIDMDTIDVSNLNR-QFLFRPKDIGRPKAE 97
Query: 175 SSEARAQNLNPNVEVTSNETKVDEISEEFVHGFDVVI 211
+ + PN V + K+ + ++ F F +++
Sbjct: 98 VAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIV 134
>pdb|3DBH|B Chain B, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBH|D Chain D, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBH|F Chain F, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBH|H Chain H, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
Length = 434
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 50/97 (51%), Gaps = 4/97 (4%)
Query: 115 KIYVYSTGPLTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAK 174
K+ V G L G E+ KN+ LSG + + ++D + ++N QFL +DIG+ +A+
Sbjct: 42 KVLVIGAGGL---GCELLKNLALSGFRQIHVIDMDTIDVSNLNR-QFLFRPKDIGRPKAE 97
Query: 175 SSEARAQNLNPNVEVTSNETKVDEISEEFVHGFDVVI 211
+ + PN V + K+ + ++ F F +++
Sbjct: 98 VAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIV 134
>pdb|3DBR|B Chain B, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
pdb|3DBR|D Chain D, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
pdb|3DBR|F Chain F, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
pdb|3DBR|H Chain H, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
Length = 434
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 50/97 (51%), Gaps = 4/97 (4%)
Query: 115 KIYVYSTGPLTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAK 174
K+ V G L G E+ KN+ LSG + + ++D + ++N QFL +DIG+ +A+
Sbjct: 42 KVLVIGAGGL---GCELLKNLALSGFRQIHVIDMDTIDVSNLNR-QFLFRPKDIGRPKAE 97
Query: 175 SSEARAQNLNPNVEVTSNETKVDEISEEFVHGFDVVI 211
+ + PN V + K+ + ++ F F +++
Sbjct: 98 VAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIV 134
>pdb|3GZN|B Chain B, Structure Of Nedd8-Activating Enzyme In Complex With Nedd8
And Mln4924
pdb|3GZN|D Chain D, Structure Of Nedd8-Activating Enzyme In Complex With Nedd8
And Mln4924
Length = 463
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 50/98 (51%), Gaps = 4/98 (4%)
Query: 115 KIYVYSTGPLTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAK 174
K+ V G L G E+ KN+ LSG + + ++D + ++N QFL +DIG+ +A+
Sbjct: 71 KVLVIGAGGL---GCELLKNLALSGFRQIHVIDMDTIDVSNLNR-QFLFRPKDIGRPKAE 126
Query: 175 SSEARAQNLNPNVEVTSNETKVDEISEEFVHGFDVVIA 212
+ + PN V + K+ + ++ F F +++
Sbjct: 127 VAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVC 164
>pdb|1R4M|B Chain B, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4M|D Chain D, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4M|F Chain F, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4M|H Chain H, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4N|B Chain B, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
pdb|1R4N|D Chain D, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
pdb|1R4N|F Chain F, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
pdb|1R4N|H Chain H, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
Length = 431
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 50/97 (51%), Gaps = 4/97 (4%)
Query: 115 KIYVYSTGPLTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAK 174
K+ V G L G E+ KN+ LSG + + ++D + ++N QFL +DIG+ +A+
Sbjct: 39 KVLVIGAGGL---GCELLKNLALSGFRQIHVIDMDTIDVSNLNR-QFLFRPKDIGRPKAE 94
Query: 175 SSEARAQNLNPNVEVTSNETKVDEISEEFVHGFDVVI 211
+ + PN V + K+ + ++ F F +++
Sbjct: 95 VAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIV 131
>pdb|1YOV|B Chain B, Insights Into The Ubiquitin Transfer Cascade From The
Refined Structure Of The Activating Enzyme For Nedd8
pdb|1YOV|D Chain D, Insights Into The Ubiquitin Transfer Cascade From The
Refined Structure Of The Activating Enzyme For Nedd8
Length = 444
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 50/98 (51%), Gaps = 4/98 (4%)
Query: 115 KIYVYSTGPLTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAK 174
K+ V G L G E+ KN+ LSG + + ++D + ++N QFL +DIG+ +A+
Sbjct: 52 KVLVIGAGGL---GCELLKNLALSGFRQIHVIDMDTIDVSNLNR-QFLFRPKDIGRPKAE 107
Query: 175 SSEARAQNLNPNVEVTSNETKVDEISEEFVHGFDVVIA 212
+ + PN V + K+ + ++ F F +++
Sbjct: 108 VAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIVC 145
>pdb|2NVU|B Chain B, Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a), A
Trapped Ubiquitin-Like Protein Activation Complex
Length = 805
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 28/107 (26%), Positives = 54/107 (50%), Gaps = 7/107 (6%)
Query: 115 KIYVYSTGPLTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAK 174
K+ V G L G E+ KN+ LSG + + ++D + ++N QFL +DIG+ +A+
Sbjct: 413 KVLVIGAGGL---GCELLKNLALSGFRQIHVIDMDTIDVSNLNR-QFLFRPKDIGRPKAE 468
Query: 175 SSEARAQNLNPNVEVTSNETKVDEISEEFVHGFDVVIATSCNPNQLI 221
+ + PN V + K+ + ++ F F +++ C + +I
Sbjct: 469 VAAEFLNDRVPNCNVVPHFNKIQDFNDTFYRQFHIIV---CGLDSII 512
>pdb|3KYD|B Chain B, Human Sumo E1~sumo1-amp Tetrahedral Intermediate Mimic
Length = 551
Score = 35.0 bits (79), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 19/87 (21%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 127 VGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAKSSEARAQNLNPN 186
+G E+ KN++L+G + L+D + ++N QFL + +G+++A+ ++ P
Sbjct: 30 IGCELLKNLVLTGFSHIDLIDLDTIDVSNLNR-QFLFQKKHVGRSKAQVAKESVLQFYPK 88
Query: 187 VEVTSNETKV--DEISEEFVHGFDVVI 211
+ + + + + EF F +V+
Sbjct: 89 ANIVAYHDSIMNPDYNVEFFRQFILVM 115
>pdb|3VH1|A Chain A, Crystal Structure Of Saccharomyces Cerevisiae Atg7 (1-595)
Length = 598
Score = 34.3 bits (77), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 45/91 (49%), Gaps = 4/91 (4%)
Query: 115 KIYVYSTGPLTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAK 174
K+ + G L G +++ +I GV+ + +D+G V+ + Q L ED GK +A+
Sbjct: 329 KVLLLGAGTL---GCYVSRALIAWGVRKITFVDNGTVSYSN-PVRQALYNFEDCGKPKAE 384
Query: 175 SSEARAQNLNPNVEVTSNETKVDEISEEFVH 205
+ A + + P ++ T + + I + V+
Sbjct: 385 LAAASLKRIFPLMDATGVKLSIPMIGHKLVN 415
>pdb|3KYC|B Chain B, Human Sumo E1 Complex With A Sumo1-Amp Mimic
Length = 660
Score = 34.3 bits (77), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 19/87 (21%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 127 VGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAKSSEARAQNLNPN 186
+G E+ KN++L+G + L+D + ++N QFL + +G+++A+ ++ P
Sbjct: 48 IGCELLKNLVLTGFSHIDLIDLDTIDVSNLNR-QFLFQKKHVGRSKAQVAKESVLQFYPK 106
Query: 187 VEVTSNETKV--DEISEEFVHGFDVVI 211
+ + + + + EF F +V+
Sbjct: 107 ANIVAYHDSIMNPDYNVEFFRQFILVM 133
>pdb|1Y8Q|B Chain B, Sumo E1 Activating Enzyme Sae1-Sae2-Mg-Atp Complex
pdb|1Y8Q|D Chain D, Sumo E1 Activating Enzyme Sae1-Sae2-Mg-Atp Complex
pdb|1Y8R|B Chain B, Sumo E1 Activating Enzyme Sae1-Sae2-Sumo1-Mg-Atp Complex
pdb|1Y8R|E Chain E, Sumo E1 Activating Enzyme Sae1-Sae2-Sumo1-Mg-Atp Complex
Length = 640
Score = 34.3 bits (77), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 19/87 (21%), Positives = 44/87 (50%), Gaps = 3/87 (3%)
Query: 127 VGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAKSSEARAQNLNPN 186
+G E+ KN++L+G + L+D + ++N QFL + +G+++A+ ++ P
Sbjct: 28 IGCELLKNLVLTGFSHIDLIDLDTIDVSNLNR-QFLFQKKHVGRSKAQVAKESVLQFYPK 86
Query: 187 VEVTSNETKV--DEISEEFVHGFDVVI 211
+ + + + + EF F +V+
Sbjct: 87 ANIVAYHDSIMNPDYNVEFFRQFILVM 113
>pdb|4GSL|A Chain A, Crystal Structure Of An Atg7-Atg3 Crosslinked Complex
pdb|4GSL|B Chain B, Crystal Structure Of An Atg7-Atg3 Crosslinked Complex
Length = 615
Score = 33.9 bits (76), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 45/91 (49%), Gaps = 4/91 (4%)
Query: 115 KIYVYSTGPLTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAK 174
K+ + G L G +++ +I GV+ + +D+G V+ + Q L ED GK +A+
Sbjct: 328 KVLLLGAGTL---GCYVSRALIAWGVRKITFVDNGTVSYSN-PVRQALYNFEDCGKPKAE 383
Query: 175 SSEARAQNLNPNVEVTSNETKVDEISEEFVH 205
+ A + + P ++ T + + I + V+
Sbjct: 384 LAAASLKRIFPLMDATGVKLSIPMIGHKLVN 414
>pdb|3VH2|A Chain A, Crystal Structure Of Saccharomyces Cerevisiae Atg7 (1-613)
Length = 616
Score = 33.9 bits (76), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 45/91 (49%), Gaps = 4/91 (4%)
Query: 115 KIYVYSTGPLTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAK 174
K+ + G L G +++ +I GV+ + +D+G V+ + Q L ED GK +A+
Sbjct: 329 KVLLLGAGTL---GCYVSRALIAWGVRKITFVDNGTVSYSN-PVRQALYNFEDCGKPKAE 384
Query: 175 SSEARAQNLNPNVEVTSNETKVDEISEEFVH 205
+ A + + P ++ T + + I + V+
Sbjct: 385 LAAASLKRIFPLMDATGVKLSIPMIGHKLVN 415
>pdb|4GSK|A Chain A, Crystal Structure Of An Atg7-Atg10 Crosslinked Complex
pdb|4GSK|B Chain B, Crystal Structure Of An Atg7-Atg10 Crosslinked Complex
Length = 615
Score = 33.9 bits (76), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 45/91 (49%), Gaps = 4/91 (4%)
Query: 115 KIYVYSTGPLTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAK 174
K+ + G L G +++ +I GV+ + +D+G V+ + Q L ED GK +A+
Sbjct: 328 KVLLLGAGTL---GCYVSRALIAWGVRKITFVDNGTVSYSN-PVRQALYNFEDAGKPKAE 383
Query: 175 SSEARAQNLNPNVEVTSNETKVDEISEEFVH 205
+ A + + P ++ T + + I + V+
Sbjct: 384 LAAASLKRIFPLMDATGVKLSIPMIGHKLVN 414
>pdb|3VH3|A Chain A, Crystal Structure Of Atg7ctd-Atg8 Complex
pdb|3VH4|A Chain A, Crystal Structure Of Atg7ctd-Atg8-Mgatp Complex
Length = 340
Score = 33.5 bits (75), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 44/90 (48%), Gaps = 4/90 (4%)
Query: 115 KIYVYSTGPLTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAK 174
K+ + G L G +++ +I GV+ + +D+G V+ + Q L ED GK +A+
Sbjct: 36 KVLLLGAGTL---GCYVSRALIAWGVRKITFVDNGTVSYSN-PVRQALYNFEDCGKPKAE 91
Query: 175 SSEARAQNLNPNVEVTSNETKVDEISEEFV 204
+ A + + P ++ T + + I + V
Sbjct: 92 LAAASLKRIFPLMDATGVKLSIPMIGHKLV 121
>pdb|3T7E|A Chain A, Atg8 Transfer From Atg7 To Atg3: A Distinctive E1-E2
Architecture And Mechanism In The Autophagy Pathway
Length = 344
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 44/90 (48%), Gaps = 4/90 (4%)
Query: 115 KIYVYSTGPLTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAK 174
K+ + G L G +++ +I GV+ + +D+G V+ + Q L ED GK +A+
Sbjct: 40 KVLLLGAGTL---GCYVSRALIAWGVRKITFVDNGTVSYSN-PVRQALYNFEDCGKPKAE 95
Query: 175 SSEARAQNLNPNVEVTSNETKVDEISEEFV 204
+ A + + P ++ T + + I + V
Sbjct: 96 LAAASLKRIFPLMDATGVKLSIPMIGHKLV 125
>pdb|3RUI|A Chain A, Crystal Structure Of Atg7c-Atg8 Complex
Length = 340
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 43/90 (47%), Gaps = 4/90 (4%)
Query: 115 KIYVYSTGPLTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAK 174
K+ + G L G +++ +I GV+ + +D+G V+ + Q L ED GK +A+
Sbjct: 36 KVLLLGAGTL---GCYVSRALIAWGVRKITFVDNGTVSYSN-PVRQALYNFEDCGKPKAE 91
Query: 175 SSEARAQNLNPNVEVTSNETKVDEISEEFV 204
+ A + + P + T + + I + V
Sbjct: 92 LAAASLKRIFPLXDATGVKLSIPXIGHKLV 121
>pdb|1ZUD|1 Chain 1, Structure Of This-Thif Protein Complex
pdb|1ZUD|3 Chain 3, Structure Of This-Thif Protein Complex
Length = 251
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 47/89 (52%), Gaps = 2/89 (2%)
Query: 124 LTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAKSSEARAQNL 183
L +G A + +GV ++ L D V ++ Q L EDI + +++ S+ R L
Sbjct: 36 LGGLGTPAALYLAGAGVGTLVLADDDDVHLSNLQR-QILFTTEDIDRPKSQVSQQRLTQL 94
Query: 184 NPNVEVTSNETKV-DEISEEFVHGFDVVI 211
NP++++T+ + ++ E ++ V DVV+
Sbjct: 95 NPDIQLTALQQRLTGEALKDAVARADVVL 123
>pdb|1ZFN|A Chain A, Structural Analysis Of Escherichia Coli Thif
pdb|1ZFN|B Chain B, Structural Analysis Of Escherichia Coli Thif
pdb|1ZFN|C Chain C, Structural Analysis Of Escherichia Coli Thif
pdb|1ZFN|D Chain D, Structural Analysis Of Escherichia Coli Thif
pdb|1ZKM|A Chain A, Structural Analysis Of Escherichia Coli Thif
pdb|1ZKM|B Chain B, Structural Analysis Of Escherichia Coli Thif
pdb|1ZKM|C Chain C, Structural Analysis Of Escherichia Coli Thif
pdb|1ZKM|D Chain D, Structural Analysis Of Escherichia Coli Thif
Length = 253
Score = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 47/89 (52%), Gaps = 2/89 (2%)
Query: 124 LTRVGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAKSSEARAQNL 183
L +G A + +GV ++ L D V ++ Q L EDI + +++ S+ R L
Sbjct: 38 LGGLGTPAALYLAGAGVGTLVLADDDDVHLSNLQR-QILFTTEDIDRPKSQVSQQRLTQL 96
Query: 184 NPNVEVTSNETKV-DEISEEFVHGFDVVI 211
NP++++T+ + ++ E ++ V DVV+
Sbjct: 97 NPDIQLTALQQRLTGEALKDAVARADVVL 125
>pdb|3BH2|A Chain A, Structural Studies Of Acetoacetate Decarboxylase
pdb|3BH2|B Chain B, Structural Studies Of Acetoacetate Decarboxylase
pdb|3BH2|C Chain C, Structural Studies Of Acetoacetate Decarboxylase
pdb|3BH2|D Chain D, Structural Studies Of Acetoacetate Decarboxylase
Length = 244
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 12/48 (25%), Positives = 23/48 (47%)
Query: 77 YKKKVCPRWELNPRPSAYRAHTVTLTTLHTNWAGSQSYKIYVYSTGPL 124
Y K+ P ++ +PR +T T+H W G +++ ++ PL
Sbjct: 166 YMLKIIPNYDGSPRICELINAKITDVTVHEAWTGPTRLQLFDHAMAPL 213
>pdb|1ADQ|A Chain A, Crystal Structure Of A Human Igm Rheumatoid Factor Fab In
Complex With Its Autoantigen Igg Fc
Length = 206
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 92 SAYRAHTVTLTTLHTNWAGSQSYKIYVYSTGPLTRVGAEIAK 133
S YR +V LT LH NW + YK V + G + + I+K
Sbjct: 61 STYRVVSV-LTVLHQNWLDGKEYKCKVSNKGLPSSIEKTISK 101
>pdb|3H5A|A Chain A, Crystal Structure Of E. Coli Mccb
pdb|3H5A|B Chain B, Crystal Structure Of E. Coli Mccb
pdb|3H5A|C Chain C, Crystal Structure Of E. Coli Mccb
pdb|3H5A|D Chain D, Crystal Structure Of E. Coli Mccb
Length = 358
Score = 27.3 bits (59), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 23/105 (21%), Positives = 53/105 (50%), Gaps = 7/105 (6%)
Query: 127 VGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAKSSEARAQNLNPN 186
+G ++ + SG+ + L+D+ + ++ T Q L +D+GKN K+ + + L N
Sbjct: 126 IGNHVSVILATSGIGEIILIDNDQIENTNL-TRQVLFSEDDVGKN--KTEVIKRELLKRN 182
Query: 187 VEVTSNETKVDEISEEFVHGF---DVVIATSCNPNQLIK-IDDFC 227
E++ +E ++ +H D+ + ++ +P LI ++ +C
Sbjct: 183 SEISVSEIALNINDYTDLHKVPEADIWVVSADHPFNLINWVNKYC 227
>pdb|3H5N|A Chain A, Crystal Structure Of E. Coli Mccb + Atp
pdb|3H5N|B Chain B, Crystal Structure Of E. Coli Mccb + Atp
pdb|3H5N|C Chain C, Crystal Structure Of E. Coli Mccb + Atp
pdb|3H5N|D Chain D, Crystal Structure Of E. Coli Mccb + Atp
pdb|3H5R|A Chain A, Crystal Structure Of E. Coli Mccb + Succinimide
pdb|3H5R|B Chain B, Crystal Structure Of E. Coli Mccb + Succinimide
pdb|3H5R|C Chain C, Crystal Structure Of E. Coli Mccb + Succinimide
pdb|3H5R|D Chain D, Crystal Structure Of E. Coli Mccb + Succinimide
pdb|3H9G|A Chain A, Crystal Structure Of E. Coli Mccb + Mcca-N7isoasn
pdb|3H9G|B Chain B, Crystal Structure Of E. Coli Mccb + Mcca-N7isoasn
pdb|3H9G|C Chain C, Crystal Structure Of E. Coli Mccb + Mcca-N7isoasn
pdb|3H9G|D Chain D, Crystal Structure Of E. Coli Mccb + Mcca-N7isoasn
pdb|3H9J|A Chain A, Crystal Structure Of E. Coli Mccb + Ampcpp + Semet Mcca
pdb|3H9J|B Chain B, Crystal Structure Of E. Coli Mccb + Ampcpp + Semet Mcca
pdb|3H9J|C Chain C, Crystal Structure Of E. Coli Mccb + Ampcpp + Semet Mcca
pdb|3H9J|D Chain D, Crystal Structure Of E. Coli Mccb + Ampcpp + Semet Mcca
pdb|3H9Q|A Chain A, Crystal Structure Of E. Coli Mccb + Semet Mcca
pdb|3H9Q|B Chain B, Crystal Structure Of E. Coli Mccb + Semet Mcca
pdb|3H9Q|C Chain C, Crystal Structure Of E. Coli Mccb + Semet Mcca
pdb|3H9Q|D Chain D, Crystal Structure Of E. Coli Mccb + Semet Mcca
Length = 353
Score = 27.3 bits (59), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 23/105 (21%), Positives = 53/105 (50%), Gaps = 7/105 (6%)
Query: 127 VGAEIAKNIILSGVKSVCLLDSGVVTKEDVNTAQFLAPHEDIGKNRAKSSEARAQNLNPN 186
+G ++ + SG+ + L+D+ + ++ T Q L +D+GKN K+ + + L N
Sbjct: 129 IGNHVSVILATSGIGEIILIDNDQIENTNL-TRQVLFSEDDVGKN--KTEVIKRELLKRN 185
Query: 187 VEVTSNETKVDEISEEFVHGF---DVVIATSCNPNQLIK-IDDFC 227
E++ +E ++ +H D+ + ++ +P LI ++ +C
Sbjct: 186 SEISVSEIALNINDYTDLHKVPEADIWVVSADHPFNLINWVNKYC 230
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
0.314 0.129 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,856,566
Number of Sequences: 62578
Number of extensions: 275631
Number of successful extensions: 574
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 534
Number of HSP's gapped (non-prelim): 38
length of query: 236
length of database: 14,973,337
effective HSP length: 96
effective length of query: 140
effective length of database: 8,965,849
effective search space: 1255218860
effective search space used: 1255218860
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)