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= 042485
(332 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SHQ|A Chain A, Crystal Structure Of Ublcp1
Length = 320
Score = 295 bits (755), Expect = 2e-80, Method: Compositional matrix adjust.
Identities = 155/304 (50%), Positives = 198/304 (65%), Gaps = 5/304 (1%)
Query: 22 WSGKEYTVRVCGDDSVAELKRRICELTNVLPKRQKLLYPKIGNKLADDTVXXXXXXXXXX 81
WSGKEY V + D+V L+ I T V P+RQKLL K K A D V
Sbjct: 12 WSGKEYPVDLTDQDTVEVLRHEIFRKTQVRPERQKLLNLKYKGKTAADNVKISALELKPN 71
Query: 82 XXMTMIGTVEDEI---IVDPVDSPEIIDDFELGQEEAVDIKDKEVNKQKLRRRLSQYKIK 138
+ M+G+ E +I P + E++DDF+ E + V K++RR+ YKIK
Sbjct: 72 FKLMMVGSTEADIEDACSLPDNIGEVVDDFDDADEREESVAHSAVYLAKVQRRVRDYKIK 131
Query: 139 LRNPSREGKKLLVLDIDYTLFDHRSTAENPLQLMRPYLHEFLTAAYAEYDIMIWSATSMK 198
P REGKKLLVLDIDYTLFDHRS AE +LMRPYLHEFLT+AY +YDI+IWSATSM+
Sbjct: 132 ELAPPREGKKLLVLDIDYTLFDHRSPAETGTELMRPYLHEFLTSAYEDYDIVIWSATSMR 191
Query: 199 WVELKMEELGVLTNPNYKITALLDHLAMITVQSDSRGIFDCKPLGLIWDQFPEFYSSKNT 258
W+E KM LGV +N NYK+ LD AMI+V RG+ D KPLG+IW + + Y+S NT
Sbjct: 192 WIEEKMRLLGVASNDNYKVMFYLDSTAMISVHVPERGVVDVKPLGVIWALYKQ-YNSSNT 250
Query: 259 IMFDDLRRNFVMNPQNGLAIKPFRKAHANRDSDQELVKLTQYLLAIA-DLDDLSNLDHGR 317
IMFDD+RRNF+MNP++GL I+PFR+AH NR +D EL+KL+ YL IA D ++L+H +
Sbjct: 251 IMFDDIRRNFLMNPKSGLKIRPFRQAHLNRGTDTELLKLSDYLRKIAHHCPDFNSLNHRK 310
Query: 318 WEFY 321
WE Y
Sbjct: 311 WEHY 314
>pdb|1V5T|A Chain A, Solution Structure Of The Ubiquitin-Like Domain From
Mouse Hypothetical 8430435i17rik Protein
Length = 90
Score = 52.4 bits (124), Expect = 4e-07, Method: Composition-based stats.
Identities = 30/73 (41%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 20 VKWSGKEYTVRVCG-DDSVAELKRRICELTNVLPKRQKLLYPKIGNKLADDTVXXXXXXX 78
VKW G+EY+V DD+V +LK+ + LT VLP+RQKLL K+ K A++ V
Sbjct: 12 VKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKL 71
Query: 79 XXXXXMTMIGTVE 91
+ M+GT E
Sbjct: 72 KPNTKIMMMGTRE 84
>pdb|2KX3|A Chain A, The Solution Structure Of The Mutant Of Ubl Domain Of
Ublcp1, I5m
Length = 81
Score = 51.6 bits (122), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 20 VKWSGKEYTVRVCG-DDSVAELKRRICELTNVLPKRQKLLYPKIGNKLADDTVXXXXXXX 78
VKW G+EY+V DD+V +LK+ + LT VLP+RQKLL K+ K A++ V
Sbjct: 7 VKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKL 66
Query: 79 XXXXXMTMIGTVED 92
+ M+GT E+
Sbjct: 67 KPNTKIMMMGTREE 80
>pdb|2LGD|A Chain A, The High Resolution Structure Of Ubiquitin Like Domain
Of Ublcp1
Length = 83
Score = 51.2 bits (121), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 20 VKWSGKEYTVRVCG-DDSVAELKRRICELTNVLPKRQKLLYPKIGNKLADDTVXXXXXXX 78
VKW G+EY+V DD+V +LK+ + LT VLP+RQKLL K+ K A++ V
Sbjct: 9 VKWGGQEYSVTTLSEDDTVLDLKQFLKTLTGVLPERQKLLGLKVKGKPAENDVKLGALKL 68
Query: 79 XXXXXMTMIGTVED 92
+ M+GT E+
Sbjct: 69 KPNTKIMMMGTREE 82
>pdb|2KD0|A Chain A, Nmr Solution Structure Of O64736 Protein From
Arabidopsis Thaliana. Northeast Structural Genomics
Consortium Mega Target Ar3445a
Length = 85
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 18/41 (43%), Positives = 28/41 (68%)
Query: 19 TVKWSGKEYTVRVCGDDSVAELKRRICELTNVLPKRQKLLY 59
TVK+ GK + V D +V +LK ++ +TNVLP+ QKL++
Sbjct: 16 TVKFGGKSIPLSVSPDCTVKDLKSQLQPITNVLPRGQKLIF 56
>pdb|2KAN|A Chain A, Solution Nmr Structure Of Ubiquitin-Like Domain Of
Arabidopsis Thaliana Protein At2g32350. Northeast
Structural Genomics Consortium Target Ar3433a
Length = 94
Score = 34.3 bits (77), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 31/51 (60%), Gaps = 2/51 (3%)
Query: 19 TVKWSGKEYTVRVCGDDSVAELKRRICELTNVLPKRQKLLYPKIGNKLADD 69
TVK+ K++TV V ++V+ LK +I + N KR +L Y G +LADD
Sbjct: 19 TVKFPSKQFTVEVDRTETVSSLKDKIHIVENTPIKRMQLYYS--GIELADD 67
>pdb|1BT0|A Chain A, Structure Of Ubiquitin-Like Protein, Rub1
Length = 76
Score = 31.6 bits (70), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 2/48 (4%)
Query: 22 WSGKEYTVRVCGDDSVAELKRRICELTNVLPKRQKLLYPKIGNKLADD 69
+GKE + + D++ +K R+ E + P +Q+L+Y G +LADD
Sbjct: 8 LTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYA--GKQLADD 53
>pdb|1V86|A Chain A, Solution Structure Of The Ubiquitin Domain From Mouse
D7wsu128e Protein
Length = 95
Score = 30.4 bits (67), Expect = 1.3, Method: Composition-based stats.
Identities = 13/38 (34%), Positives = 25/38 (65%)
Query: 22 WSGKEYTVRVCGDDSVAELKRRICELTNVLPKRQKLLY 59
W+ ++ V+V D + +ELK++I +T + P QK++Y
Sbjct: 24 WNKTKHDVKVPLDSTGSELKQKIHSITGLPPAMQKVMY 61
>pdb|2DZI|A Chain A, 2dziSOLUTION STRUCTURE OF THE N-Terminal Ubiquitin-Like
Domain In Human Ubiquitin-Like Protein 4a (Gdx)
Length = 81
Score = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 29/45 (64%), Gaps = 2/45 (4%)
Query: 24 GKEYTVRVCGDDSVAELKRRICELTNVLPKRQKLLYPKIGNKLAD 68
G+E +++V D+ V+ LK+ + E NV ++Q+LL+ G LAD
Sbjct: 17 GRECSLQVPEDELVSTLKQLVSEKLNVPVRQQRLLFK--GKALAD 59
>pdb|3DBL|I Chain I, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBL|J Chain J, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBL|K Chain K, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
pdb|3DBL|L Chain L, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190wt-Nedd8ala72gln)
Length = 88
Score = 29.3 bits (64), Expect = 3.0, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 23 SGKEYTVRVCGDDSVAELKRRICELTNVLPKRQKLLYPKIGNKLADD 69
+GKE + + D V +K R+ E + P++Q+L+Y G ++ D+
Sbjct: 21 TGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYS--GKQMNDE 65
>pdb|3DBH|I Chain I, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBH|J Chain J, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBH|K Chain K, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBH|L Chain L, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190ala-Nedd8ala72arg)
pdb|3DBR|I Chain I, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
pdb|3DBR|J Chain J, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
pdb|3DBR|K Chain K, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
pdb|3DBR|L Chain L, Structural Dissection Of A Gating Mechanism Preventing
Misactivation Of Ubiquitin By Nedd8's E1 (Appbp1-
Uba3arg190gln-Nedd8ala72arg)
Length = 88
Score = 29.3 bits (64), Expect = 3.2, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 23 SGKEYTVRVCGDDSVAELKRRICELTNVLPKRQKLLYPKIGNKLADD 69
+GKE + + D V +K R+ E + P++Q+L+Y G ++ D+
Sbjct: 21 TGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYS--GKQMNDE 65
>pdb|2NVU|I Chain I, Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a),
A Trapped Ubiquitin-Like Protein Activation Complex
pdb|2NVU|J Chain J, Structure Of Appbp1-Uba3~nedd8-Nedd8-Mgatp-Ubc12(C111a),
A Trapped Ubiquitin-Like Protein Activation Complex
Length = 81
Score = 29.3 bits (64), Expect = 3.3, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 23 SGKEYTVRVCGDDSVAELKRRICELTNVLPKRQKLLYPKIGNKLADD 69
+GKE + + D V +K R+ E + P++Q+L+Y G ++ D+
Sbjct: 14 TGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYS--GKQMNDE 58
>pdb|2OND|A Chain A, Crystal Structure Of The Hat-C Domain Of Murine Cstf-77
pdb|2OND|B Chain B, Crystal Structure Of The Hat-C Domain Of Murine Cstf-77
Length = 308
Score = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 44/88 (50%), Gaps = 12/88 (13%)
Query: 177 HEFLTAAYAEYDIMIWSATSMKWVELKMEELGVLTNPNYKITALLDHLAMITVQSDSRGI 236
H ++TAA EY + + K EL +++ G + P Y + A +D+L+ + +++R +
Sbjct: 169 HVYVTAALXEYYCSKDKSVAFKIFELGLKKYGDI--PEY-VLAYIDYLSHLNEDNNTRVL 225
Query: 237 FD---------CKPLGLIWDQFPEFYSS 255
F+ + G IW +F F S+
Sbjct: 226 FERVLTSGSLPPEKSGEIWARFLAFESN 253
>pdb|2OOE|A Chain A, Crystal Structure Of Hat Domain Of Murine Cstf-77
Length = 530
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 23/88 (26%), Positives = 44/88 (50%), Gaps = 12/88 (13%)
Query: 177 HEFLTAAYAEYDIMIWSATSMKWVELKMEELGVLTNPNYKITALLDHLAMITVQSDSRGI 236
H ++TAA EY + + K EL +++ G + P Y + A +D+L+ + +++R +
Sbjct: 391 HVYVTAALMEYYCSKDKSVAFKIFELGLKKYGDI--PEY-VLAYIDYLSHLNEDNNTRVL 447
Query: 237 FD---------CKPLGLIWDQFPEFYSS 255
F+ + G IW +F F S+
Sbjct: 448 FERVLTSGSLPPEKSGEIWARFLAFESN 475
>pdb|3DQV|A Chain A, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
pdb|3DQV|B Chain B, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
Length = 81
Score = 28.9 bits (63), Expect = 4.6, Method: Composition-based stats.
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 23 SGKEYTVRVCGDDSVAELKRRICELTNVLPKRQKLLY 59
+GKE + + D V +K R+ E + P++Q+L+Y
Sbjct: 14 TGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIY 50
>pdb|2BKR|B Chain B, Nedd8 Nedp1 Complex
Length = 77
Score = 28.5 bits (62), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 22 WSGKEYTVRVCGDDSVAELKRRICELTNVLPKRQKLLYPKIGNKLADD 69
+GKE + + D V +K R+ E + P++Q+L+Y G ++ D+
Sbjct: 9 LTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYS--GKQMNDE 54
>pdb|1NDD|B Chain B, Structure Of Nedd8
pdb|1NDD|A Chain A, Structure Of Nedd8
pdb|1NDD|C Chain C, Structure Of Nedd8
pdb|1NDD|D Chain D, Structure Of Nedd8
pdb|1R4M|I Chain I, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4M|J Chain J, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4M|K Chain K, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4M|L Chain L, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
pdb|1R4N|I Chain I, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
pdb|1R4N|J Chain J, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
pdb|1R4N|K Chain K, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
pdb|1R4N|L Chain L, Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
With Atp
pdb|1XT9|B Chain B, Crystal Structure Of Den1 In Complex With Nedd8
pdb|2KO3|A Chain A, Nedd8 Solution Structure
Length = 76
Score = 28.5 bits (62), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 22 WSGKEYTVRVCGDDSVAELKRRICELTNVLPKRQKLLYPKIGNKLADD 69
+GKE + + D V +K R+ E + P++Q+L+Y G ++ D+
Sbjct: 8 LTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYS--GKQMNDE 53
>pdb|3GZN|I Chain I, Structure Of Nedd8-Activating Enzyme In Complex With
Nedd8 And Mln4924
pdb|3GZN|J Chain J, Structure Of Nedd8-Activating Enzyme In Complex With
Nedd8 And Mln4924
Length = 82
Score = 28.5 bits (62), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 22 WSGKEYTVRVCGDDSVAELKRRICELTNVLPKRQKLLYPKIGNKLADD 69
+GKE + + D V +K R+ E + P++Q+L+Y G ++ D+
Sbjct: 14 LTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYS--GKQMNDE 59
>pdb|4HCP|B Chain B, Crystal Structure Of Burkholderia Pseudomallei Effector
Protein Chbp In Complex With Nedd8
Length = 78
Score = 28.5 bits (62), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 22 WSGKEYTVRVCGDDSVAELKRRICELTNVLPKRQKLLYPKIGNKLADD 69
+GKE + + D V +K R+ E + P++Q+L+Y G ++ D+
Sbjct: 10 LTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYS--GKQMNDE 55
>pdb|1SIF|A Chain A, Crystal Structure Of A Multiple Hydrophobic Core Mutant
Of Ubiquitin
Length = 88
Score = 28.1 bits (61), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 22 WSGKEYTVRVCGDDSVAELKRRICELTNVLPKRQKLLYPKIGNKLAD 68
+GK +TV + D++ LK +I + + P +Q+L++ G +L D
Sbjct: 17 LTGKTFTVEMEPSDTIENLKAKIQDKEGIPPDQQRLIFA--GKQLED 61
>pdb|1WGG|A Chain A, Solution Structure Of The N-Terminal Ubiquitin-Like
Domain Of Mouse Ubiquitin Specific Protease 14 (Usp14)
Length = 96
Score = 28.1 bits (61), Expect = 7.4, Method: Composition-based stats.
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 19 TVKWSGKEYT-VRVCGDDSVAELKRRICELTNVLPKRQKLLYPKIGNKLADD 69
TVKW +++ V + D+ K ++ LT V P RQK++ G L DD
Sbjct: 11 TVKWGKEKFEGVELNTDEPPMVFKAQLFALTGVQPARQKVMVK--GGTLKDD 60
>pdb|4F8C|B Chain B, Structure Of The Cif:nedd8 Complex - Yersinia
Pseudotuberculosis Cycle Inhibiting Factor In Complex
With Human Nedd8
pdb|4F8C|D Chain D, Structure Of The Cif:nedd8 Complex - Yersinia
Pseudotuberculosis Cycle Inhibiting Factor In Complex
With Human Nedd8
pdb|4FBJ|B Chain B, Structure Of The Cif:nedd8 Complex - Photorhabdus
Luminescens Cycle Inhibiting Factor In Complex With
Human Nedd8
Length = 88
Score = 28.1 bits (61), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 27/48 (56%), Gaps = 2/48 (4%)
Query: 22 WSGKEYTVRVCGDDSVAELKRRICELTNVLPKRQKLLYPKIGNKLADD 69
+GKE + + D V +K R+ E + P++Q+L+Y G ++ D+
Sbjct: 8 LTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYS--GKQMNDE 53
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 0.137 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,143,576
Number of Sequences: 62578
Number of extensions: 352713
Number of successful extensions: 922
Number of sequences better than 100.0: 30
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 898
Number of HSP's gapped (non-prelim): 30
length of query: 332
length of database: 14,973,337
effective HSP length: 99
effective length of query: 233
effective length of database: 8,778,115
effective search space: 2045300795
effective search space used: 2045300795
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: 52 (24.6 bits)