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= psy14360
(471 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2NVU|B Chain B, Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a), A
Trapped Ubiquitin-Like Protein Activation Complex
Length = 805
Score = 36.6 bits (83), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 29/54 (53%)
Query: 211 EKYGPFKHPAFGETILRVSLVLLTCKLALVVVGSIGFGILCTYSLQFYVPVAII 264
E+ GPF HP F + + +L TCK+ ++ G +G +L +L + + +I
Sbjct: 388 ERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVI 441
>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 = 36.6 bits (83), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 29/54 (53%)
Query: 211 EKYGPFKHPAFGETILRVSLVLLTCKLALVVVGSIGFGILCTYSLQFYVPVAII 264
E+ GPF HP F + + +L TCK+ ++ G +G +L +L + + +I
Sbjct: 46 ERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVI 99
>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 = 36.2 bits (82), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 29/54 (53%)
Query: 211 EKYGPFKHPAFGETILRVSLVLLTCKLALVVVGSIGFGILCTYSLQFYVPVAII 264
E+ GPF HP F + + +L TCK+ ++ G +G +L +L + + +I
Sbjct: 17 ERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVI 70
>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 = 36.2 bits (82), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 29/54 (53%)
Query: 211 EKYGPFKHPAFGETILRVSLVLLTCKLALVVVGSIGFGILCTYSLQFYVPVAII 264
E+ GPF HP F + + +L TCK+ ++ G +G +L +L + + +I
Sbjct: 17 ERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVI 70
>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 = 36.2 bits (82), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 29/54 (53%)
Query: 211 EKYGPFKHPAFGETILRVSLVLLTCKLALVVVGSIGFGILCTYSLQFYVPVAII 264
E+ GPF HP F + + +L TCK+ ++ G +G +L +L + + +I
Sbjct: 17 ERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVI 70
>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 = 36.2 bits (82), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 29/54 (53%)
Query: 211 EKYGPFKHPAFGETILRVSLVLLTCKLALVVVGSIGFGILCTYSLQFYVPVAII 264
E+ GPF HP F + + +L TCK+ ++ G +G +L +L + + +I
Sbjct: 14 ERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVI 67
>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 = 36.2 bits (82), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 29/54 (53%)
Query: 211 EKYGPFKHPAFGETILRVSLVLLTCKLALVVVGSIGFGILCTYSLQFYVPVAII 264
E+ GPF HP F + + +L TCK+ ++ G +G +L +L + + +I
Sbjct: 27 ERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVI 80
>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 = 36.2 bits (82), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 29/54 (53%)
Query: 211 EKYGPFKHPAFGETILRVSLVLLTCKLALVVVGSIGFGILCTYSLQFYVPVAII 264
E+ GPF HP F + + +L TCK+ ++ G +G +L +L + + +I
Sbjct: 17 ERSGPFTHPDFEPSTESLQFLLDTCKVLVIGAGGLGCELLKNLALSGFRQIHVI 70
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
0.328 0.144 0.433
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,448,426
Number of Sequences: 62578
Number of extensions: 555418
Number of successful extensions: 1342
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1326
Number of HSP's gapped (non-prelim): 16
length of query: 471
length of database: 14,973,337
effective HSP length: 102
effective length of query: 369
effective length of database: 8,590,381
effective search space: 3169850589
effective search space used: 3169850589
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (25.0 bits)