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= psy11204
(161 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2RH0|A Chain A, Crystal Structure Of Nudc Domain-containing Protein 2
(13542905) From Mus Musculus At 1.95 A Resolution
pdb|2RH0|B Chain B, Crystal Structure Of Nudc Domain-containing Protein 2
(13542905) From Mus Musculus At 1.95 A Resolution
pdb|2RH0|C Chain C, Crystal Structure Of Nudc Domain-containing Protein 2
(13542905) From Mus Musculus At 1.95 A Resolution
pdb|2RH0|D Chain D, Crystal Structure Of Nudc Domain-containing Protein 2
(13542905) From Mus Musculus At 1.95 A Resolution
Length = 157
Score = 121 bits (304), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 62/148 (41%), Positives = 90/148 (60%), Gaps = 5/148 (3%)
Query: 7 FDEKGGVVKCPTPWGSWWQTLDEVFIEVILTDKVRSRDIAIKCTNTEISCTIAGKELFQG 66
F+E+ GVV C TPWG W+QTL+EVFIEV + R++DI + ++ + G+E+ +G
Sbjct: 2 FEERSGVVPCGTPWGQWYQTLEEVFIEVQVPPGTRAQDIQCGLQSRHVALAVGGREILKG 61
Query: 67 KLLDVVHGDEIIWTLENNGTLLNIVLPKAEFKGKEQIWNSLFVNSKENYATDPTIFHEMK 126
KL D DE WTLE+ + IVL K + + W SL + YA DP + + +
Sbjct: 62 KLFDSTIADEGTWTLEDR-KXVRIVLTKTK-RDAANCWTSLL---ESEYAADPWVQDQXQ 116
Query: 127 KKMDLEKFQIENPGFDFSRAKLAKCYDK 154
+K+ LE+FQ ENPGFDFS A+++ Y K
Sbjct: 117 RKLTLERFQKENPGFDFSGAEISGNYTK 144
>pdb|2O30|A Chain A, Nuclear Movement Protein From E. Cuniculi Gb-M1
pdb|2O30|B Chain B, Nuclear Movement Protein From E. Cuniculi Gb-M1
Length = 131
Score = 32.0 bits (71), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 45/91 (49%), Gaps = 6/91 (6%)
Query: 22 SWWQTLDEVFIEVILTDKVRSRDIAIKCTNTEISCTIAGKELFQGKLLDVVHGDEIIWTL 81
+W Q L+E+ I+ +T S I I+ +I G+ + G+LL V + W +
Sbjct: 8 TWDQELNEINIQFPVTGDADSSAIKIRXVGKKICVKNQGEIVIDGELLHEVDVSSLWWVI 67
Query: 82 ENNGTLLNIVLPKAEFKGKEQIWNSLFVNSK 112
NG ++++ + K + + W+SL V S+
Sbjct: 68 --NGDVVDVNVTKK----RNEWWDSLLVGSE 92
>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 = 26.9 bits (58), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 38 DKVRSRDIAIKCTNTEISCTIAGKELFQGKLLDVVHGDEIIWTLEN--NGTLLNIVLPKA 95
+ + +++ + C+N+ + + L + LD ++ DEII +++N N +L ++L
Sbjct: 370 ESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVLYLMLRAV 429
Query: 96 EFKGKEQ 102
+ K+Q
Sbjct: 430 DRFHKQQ 436
>pdb|1NUI|A Chain A, Crystal Structure Of The Primase Fragment Of Bacteriophage
T7 Primase- Helicase Protein
pdb|1NUI|B Chain B, Crystal Structure Of The Primase Fragment Of Bacteriophage
T7 Primase- Helicase Protein
Length = 255
Score = 26.9 bits (58), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 9/66 (13%)
Query: 21 GSWWQTLDEVFIEV---------ILTDKVRSRDIAIKCTNTEISCTIAGKELFQGKLLDV 71
G W +D V +V I++ KVR +D K T + S + GK L+ G V
Sbjct: 95 GYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHKSDALFGKHLWNGGKKIV 154
Query: 72 VHGDEI 77
V EI
Sbjct: 155 VTEGEI 160
>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 = 26.9 bits (58), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 38 DKVRSRDIAIKCTNTEISCTIAGKELFQGKLLDVVHGDEIIWTLEN--NGTLLNIVLPKA 95
+ + +++ + C+N+ + + L + LD ++ DEII +++N N +L ++L
Sbjct: 376 ESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVLYLMLRAV 435
Query: 96 EFKGKEQ 102
+ K+Q
Sbjct: 436 DRFHKQQ 442
>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 = 26.9 bits (58), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 38 DKVRSRDIAIKCTNTEISCTIAGKELFQGKLLDVVHGDEIIWTLEN--NGTLLNIVLPKA 95
+ + +++ + C+N+ + + L + LD ++ DEII +++N N +L ++L
Sbjct: 368 ESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVLYLMLRAV 427
Query: 96 EFKGKEQ 102
+ K+Q
Sbjct: 428 DRFHKQQ 434
>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 = 26.9 bits (58), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 38 DKVRSRDIAIKCTNTEISCTIAGKELFQGKLLDVVHGDEIIWTLEN--NGTLLNIVLPKA 95
+ + +++ + C+N+ + + L + LD ++ DEII +++N N +L ++L
Sbjct: 373 ESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVLYLMLRAV 432
Query: 96 EFKGKEQ 102
+ K+Q
Sbjct: 433 DRFHKQQ 439
>pdb|2NVU|A Chain A, Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a), A
Trapped Ubiquitin-Like Protein Activation Complex
Length = 536
Score = 26.9 bits (58), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 15/67 (22%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 38 DKVRSRDIAIKCTNTEISCTIAGKELFQGKLLDVVHGDEIIWTLEN--NGTLLNIVLPKA 95
+ + +++ + C+N+ + + L + LD ++ DEII +++N N +L ++L
Sbjct: 375 ESISEKELKLLCSNSAFLRVVRCRSLAEEYGLDTINKDEIISSMDNPDNEIVLYLMLRAV 434
Query: 96 EFKGKEQ 102
+ K+Q
Sbjct: 435 DRFHKQQ 441
>pdb|1U0E|A Chain A, Crystal Structure Of Mouse Phosphoglucose Isomerase
pdb|1U0E|B Chain B, Crystal Structure Of Mouse Phosphoglucose Isomerase
pdb|1U0F|A Chain A, Crystal Structure Of Mouse Phosphoglucose Isomerase In
Complex With Glucose 6-Phosphate
pdb|1U0F|B Chain B, Crystal Structure Of Mouse Phosphoglucose Isomerase In
Complex With Glucose 6-Phosphate
pdb|1U0G|A Chain A, Crystal Structure Of Mouse Phosphoglucose Isomerase In
Complex With Erythrose 4-Phosphate
pdb|1U0G|B Chain B, Crystal Structure Of Mouse Phosphoglucose Isomerase In
Complex With Erythrose 4-Phosphate
Length = 564
Score = 26.9 bits (58), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 69 LDVVHGDEIIWTLEN--NGTLLNIVLPKAEFKGKEQIWNSLFVNSKENYATDPTIFH 123
L+ HG ++ +N N ++ +++ A+ +G E +++F SK NY D + H
Sbjct: 44 LNTNHGHILVDYSKNLVNKEVMQMLVELAKSRGVEAARDNMFSGSKINYTEDRAVLH 100
>pdb|1Q57|A Chain A, The Crystal Structure Of The Bifunctional
Primase-helicase Of Bacteriophage T7
pdb|1Q57|B Chain B, The Crystal Structure Of The Bifunctional
Primase-helicase Of Bacteriophage T7
pdb|1Q57|C Chain C, The Crystal Structure Of The Bifunctional
Primase-helicase Of Bacteriophage T7
pdb|1Q57|D Chain D, The Crystal Structure Of The Bifunctional
Primase-helicase Of Bacteriophage T7
pdb|1Q57|E Chain E, The Crystal Structure Of The Bifunctional
Primase-helicase Of Bacteriophage T7
pdb|1Q57|F Chain F, The Crystal Structure Of The Bifunctional
Primase-helicase Of Bacteriophage T7
pdb|1Q57|G Chain G, The Crystal Structure Of The Bifunctional
Primase-helicase Of Bacteriophage T7
Length = 503
Score = 26.2 bits (56), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 29/66 (43%), Gaps = 9/66 (13%)
Query: 21 GSWWQTLDEVFIEV---------ILTDKVRSRDIAIKCTNTEISCTIAGKELFQGKLLDV 71
G W +D V +V I++ KVR +D K T + S + GK L+ G V
Sbjct: 32 GYWIAKVDGVMYQVADYRDQNGNIVSQKVRDKDKNFKTTGSHKSDALFGKHLWNGGKKIV 91
Query: 72 VHGDEI 77
V EI
Sbjct: 92 VTEGEI 97
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
0.318 0.136 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,412,219
Number of Sequences: 62578
Number of extensions: 220173
Number of successful extensions: 441
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 425
Number of HSP's gapped (non-prelim): 17
length of query: 161
length of database: 14,973,337
effective HSP length: 91
effective length of query: 70
effective length of database: 9,278,739
effective search space: 649511730
effective search space used: 649511730
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)