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= psy17420
(209 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 137 bits (344), Expect = 6e-33, Method: Compositional matrix adjust.
Identities = 73/209 (34%), Positives = 110/209 (52%), Gaps = 45/209 (21%)
Query: 1 YRDQAGRDADVIYRRAQQLLHQLGQPSSAITEAQVKLFCRNASFIHVIRGTLWGDHGQAA 60
YR++A +DA + +LL +GQ +I+E ++KL C N++F+ V+R
Sbjct: 349 YREKAKKDAAAVGNHVAKLLQSIGQAPESISEKELKLLCSNSAFLRVVR----------- 397
Query: 61 LESARICLINATGLGTECGPVNFCPVEXXXXXXXXXXXADEYDPRTSNARQISEALENGD 120
C + A+EY T N +I +++N D
Sbjct: 398 -----------------CRSL-----------------AEEYGLDTINKDEIISSMDNPD 423
Query: 121 GLLIYHVMLRGVDKFYTEHNTYPGEYDDQVEPDIVKLKSCISKLTAEWGCGVLSKDDYLH 180
++ ++MLR VD+F+ + YPG + QVE DI KLKSC++ E+G V+ KDDY+H
Sbjct: 424 NEIVLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVH 483
Query: 181 EICRYGGGELHAVSSFLGGCAAQEVIKIL 209
E CRYG E H +++FLGG AAQEVIKI+
Sbjct: 484 EFCRYGAAEPHTIAAFLGGAAAQEVIKII 512
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/26 (80%), Positives = 22/26 (84%)
Query: 52 LWGDHGQAALESARICLINATGLGTE 77
LWGDHGQ ALESA +CLINAT GTE
Sbjct: 22 LWGDHGQEALESAHVCLINATATGTE 47
>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 = 137 bits (344), Expect = 6e-33, Method: Compositional matrix adjust.
Identities = 73/209 (34%), Positives = 110/209 (52%), Gaps = 45/209 (21%)
Query: 1 YRDQAGRDADVIYRRAQQLLHQLGQPSSAITEAQVKLFCRNASFIHVIRGTLWGDHGQAA 60
YR++A +DA + +LL +GQ +I+E ++KL C N++F+ V+R
Sbjct: 346 YREKAKKDAAAVGNHVAKLLQSIGQAPESISEKELKLLCSNSAFLRVVR----------- 394
Query: 61 LESARICLINATGLGTECGPVNFCPVEXXXXXXXXXXXADEYDPRTSNARQISEALENGD 120
C + A+EY T N +I +++N D
Sbjct: 395 -----------------CRSL-----------------AEEYGLDTINKDEIISSMDNPD 420
Query: 121 GLLIYHVMLRGVDKFYTEHNTYPGEYDDQVEPDIVKLKSCISKLTAEWGCGVLSKDDYLH 180
++ ++MLR VD+F+ + YPG + QVE DI KLKSC++ E+G V+ KDDY+H
Sbjct: 421 NEIVLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVH 480
Query: 181 EICRYGGGELHAVSSFLGGCAAQEVIKIL 209
E CRYG E H +++FLGG AAQEVIKI+
Sbjct: 481 EFCRYGAAEPHTIAAFLGGAAAQEVIKII 509
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/26 (80%), Positives = 22/26 (84%)
Query: 52 LWGDHGQAALESARICLINATGLGTE 77
LWGDHGQ ALESA +CLINAT GTE
Sbjct: 19 LWGDHGQEALESAHVCLINATATGTE 44
>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 = 137 bits (344), Expect = 6e-33, Method: Compositional matrix adjust.
Identities = 73/209 (34%), Positives = 110/209 (52%), Gaps = 45/209 (21%)
Query: 1 YRDQAGRDADVIYRRAQQLLHQLGQPSSAITEAQVKLFCRNASFIHVIRGTLWGDHGQAA 60
YR++A +DA + +LL +GQ +I+E ++KL C N++F+ V+R
Sbjct: 343 YREKAKKDAAAVGNHVAKLLQSIGQAPESISEKELKLLCSNSAFLRVVR----------- 391
Query: 61 LESARICLINATGLGTECGPVNFCPVEXXXXXXXXXXXADEYDPRTSNARQISEALENGD 120
C + A+EY T N +I +++N D
Sbjct: 392 -----------------CRSL-----------------AEEYGLDTINKDEIISSMDNPD 417
Query: 121 GLLIYHVMLRGVDKFYTEHNTYPGEYDDQVEPDIVKLKSCISKLTAEWGCGVLSKDDYLH 180
++ ++MLR VD+F+ + YPG + QVE DI KLKSC++ E+G V+ KDDY+H
Sbjct: 418 NEIVLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVH 477
Query: 181 EICRYGGGELHAVSSFLGGCAAQEVIKIL 209
E CRYG E H +++FLGG AAQEVIKI+
Sbjct: 478 EFCRYGAAEPHTIAAFLGGAAAQEVIKII 506
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/26 (80%), Positives = 22/26 (84%)
Query: 52 LWGDHGQAALESARICLINATGLGTE 77
LWGDHGQ ALESA +CLINAT GTE
Sbjct: 21 LWGDHGQEALESAHVCLINATATGTE 46
>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 = 137 bits (344), Expect = 6e-33, Method: Compositional matrix adjust.
Identities = 73/209 (34%), Positives = 110/209 (52%), Gaps = 45/209 (21%)
Query: 1 YRDQAGRDADVIYRRAQQLLHQLGQPSSAITEAQVKLFCRNASFIHVIRGTLWGDHGQAA 60
YR++A +DA + +LL +GQ +I+E ++KL C N++F+ V+R
Sbjct: 341 YREKAKKDAAAVGNHVAKLLQSIGQAPESISEKELKLLCSNSAFLRVVR----------- 389
Query: 61 LESARICLINATGLGTECGPVNFCPVEXXXXXXXXXXXADEYDPRTSNARQISEALENGD 120
C + A+EY T N +I +++N D
Sbjct: 390 -----------------CRSL-----------------AEEYGLDTINKDEIISSMDNPD 415
Query: 121 GLLIYHVMLRGVDKFYTEHNTYPGEYDDQVEPDIVKLKSCISKLTAEWGCGVLSKDDYLH 180
++ ++MLR VD+F+ + YPG + QVE DI KLKSC++ E+G V+ KDDY+H
Sbjct: 416 NEIVLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVH 475
Query: 181 EICRYGGGELHAVSSFLGGCAAQEVIKIL 209
E CRYG E H +++FLGG AAQEVIKI+
Sbjct: 476 EFCRYGAAEPHTIAAFLGGAAAQEVIKII 504
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/26 (80%), Positives = 22/26 (84%)
Query: 52 LWGDHGQAALESARICLINATGLGTE 77
LWGDHGQ ALESA +CLINAT GTE
Sbjct: 19 LWGDHGQEALESAHVCLINATATGTE 44
>pdb|2NVU|A Chain A, Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a), A
Trapped Ubiquitin-Like Protein Activation Complex
Length = 536
Score = 136 bits (343), Expect = 6e-33, Method: Compositional matrix adjust.
Identities = 73/209 (34%), Positives = 110/209 (52%), Gaps = 45/209 (21%)
Query: 1 YRDQAGRDADVIYRRAQQLLHQLGQPSSAITEAQVKLFCRNASFIHVIRGTLWGDHGQAA 60
YR++A +DA + +LL +GQ +I+E ++KL C N++F+ V+R
Sbjct: 348 YREKAKKDAAAVGNHVAKLLQSIGQAPESISEKELKLLCSNSAFLRVVR----------- 396
Query: 61 LESARICLINATGLGTECGPVNFCPVEXXXXXXXXXXXADEYDPRTSNARQISEALENGD 120
C + A+EY T N +I +++N D
Sbjct: 397 -----------------CRSL-----------------AEEYGLDTINKDEIISSMDNPD 422
Query: 121 GLLIYHVMLRGVDKFYTEHNTYPGEYDDQVEPDIVKLKSCISKLTAEWGCGVLSKDDYLH 180
++ ++MLR VD+F+ + YPG + QVE DI KLKSC++ E+G V+ KDDY+H
Sbjct: 423 NEIVLYLMLRAVDRFHKQQGRYPGVSNYQVEEDIGKLKSCLTGFLQEYGLSVMVKDDYVH 482
Query: 181 EICRYGGGELHAVSSFLGGCAAQEVIKIL 209
E CRYG E H +++FLGG AAQEVIKI+
Sbjct: 483 EFCRYGAAEPHTIAAFLGGAAAQEVIKII 511
Score = 49.7 bits (117), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 21/26 (80%), Positives = 22/26 (84%)
Query: 52 LWGDHGQAALESARICLINATGLGTE 77
LWGDHGQ ALESA +CLINAT GTE
Sbjct: 21 LWGDHGQEALESAHVCLINATATGTE 46
>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 = 39.7 bits (91), Expect = 0.001, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 43/84 (51%), Gaps = 2/84 (2%)
Query: 126 HVMLRGVDKFYTEHN-TYPGEYDDQVEPDIVKLKSCISKLTAE-WGCGVLSKDDYLHEIC 183
H+ + + +F HN P +D+ +++KL + +S E G GV +D + E+
Sbjct: 284 HLGFQALHQFAVRHNGELPRTMNDEDANELIKLVTDLSVQQPEVLGEGVDVNEDLIKELS 343
Query: 184 RYGGGELHAVSSFLGGCAAQEVIK 207
G++ V +F GG AQEV+K
Sbjct: 344 YQARGDIPGVVAFFGGLVAQEVLK 367
>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 = 35.4 bits (80), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 38/84 (45%), Gaps = 4/84 (4%)
Query: 125 YHVMLRGVDKFYTEHN-TYPGEYDDQVEPDIVKLKSCISKLTAEWGCGVLSKDDYLHEIC 183
YH+ + + F H + P +D D + K+ + V + + EI
Sbjct: 280 YHIAFQALSAFADAHEGSLPRPRNDI---DAAEFFEFCKKIASTLQFDVELDEKLIKEIS 336
Query: 184 RYGGGELHAVSSFLGGCAAQEVIK 207
G+L A+S+FLGG AQEV+K
Sbjct: 337 YQARGDLVAMSAFLGGAVAQEVLK 360
>pdb|4FOM|A Chain A, Crystal Structure Of Human Nectin-3 Full Ectodomain
(D1-D3)
Length = 308
Score = 30.8 bits (68), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 157 LKSCISKLTAEWGCGVLSKDDYLHEI----CRYGGGELHAVSSFLGGCAAQEVIKI 208
KS S+L +W G+L+ D+ LH + Y G + V++ LG + Q+VI I
Sbjct: 243 FKSVWSRLDGQWPDGLLASDNTLHFVHPLTFNYSGVYICKVTNSLGQRSDQKVIYI 298
>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 = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 52 LWGDHGQAALESARICLINATGLGTE 77
LWG Q L ++R+ L+ GLG E
Sbjct: 25 LWGLEAQKRLRASRVLLVGLKGLGAE 50
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 0.138 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,077,313
Number of Sequences: 62578
Number of extensions: 228038
Number of successful extensions: 470
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 451
Number of HSP's gapped (non-prelim): 22
length of query: 209
length of database: 14,973,337
effective HSP length: 94
effective length of query: 115
effective length of database: 9,091,005
effective search space: 1045465575
effective search space used: 1045465575
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: 49 (23.5 bits)