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= 020816
(321 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GAO|A Chain A, Dcnl Complex With N-terminally Acetylated Nedd8 E2 Peptide
pdb|4GAO|B Chain B, Dcnl Complex With N-terminally Acetylated Nedd8 E2 Peptide
pdb|4GAO|D Chain D, Dcnl Complex With N-terminally Acetylated Nedd8 E2 Peptide
pdb|4GAO|G Chain G, Dcnl Complex With N-terminally Acetylated Nedd8 E2 Peptide
Length = 200
Score = 100 bits (248), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 42/99 (42%), Positives = 62/99 (62%)
Query: 82 MGDFSEFSRFYDFVFFMCRENGQKNITVSRAVTAWRLVLAGRFRLLNQWCDFVERNQRHN 141
+ D ++F FY F F + GQK + + AV W+LVL+GRF+ L+ W F+ + + +
Sbjct: 89 LKDTAKFKDFYQFTFTFAKNPGQKGLDLEMAVAYWKLVLSGRFKFLDLWNTFLMEHHKRS 148
Query: 142 ISEDTWQQVLAFSRCVHENLEGYDPEGAWPVLIDDFVEH 180
I DTW +L F + +++ YD EGAWPVLIDDFVE+
Sbjct: 149 IPRDTWNLLLDFGNMIADDMSNYDEEGAWPVLIDDFVEY 187
>pdb|3TDU|A Chain A, N-Terminal Acetylation Acts As An Avidity Enhancer Within
An Interconnected Multiprotein Complex: Structure Of A
Human Cul1whb- Dcn1p-Acetylated Ubc12n Complex
pdb|3TDU|B Chain B, N-Terminal Acetylation Acts As An Avidity Enhancer Within
An Interconnected Multiprotein Complex: Structure Of A
Human Cul1whb- Dcn1p-Acetylated Ubc12n Complex
pdb|3TDZ|A Chain A, N-Terminal Acetylation Acts As An Avidity Enhancer Within
An Interconnected Multiprotein Complex: Structure Of A
Human Cul1whb- Dcn1p-Stapled Acetylated Ubc12n Complex
pdb|3TDZ|B Chain B, N-Terminal Acetylation Acts As An Avidity Enhancer Within
An Interconnected Multiprotein Complex: Structure Of A
Human Cul1whb- Dcn1p-Stapled Acetylated Ubc12n Complex
Length = 200
Score = 96.7 bits (239), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 43/102 (42%), Positives = 63/102 (61%), Gaps = 1/102 (0%)
Query: 88 FSRFYDFVFFMCRENGQKNITVSRAVTAWRLVLAGRFRLLNQWCDFVERNQRHNISEDTW 147
F FY F F + GQK + + A+ W LVL GRF+ L+ W F+ + + +I +DTW
Sbjct: 95 FKDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTW 154
Query: 148 QQVLAFSRCVHENLEGYDPEGAWPVLIDDFVEHMY-RVSGSK 188
+L FS + +++ YD EGAWPVLIDDFVE +++G+K
Sbjct: 155 NLLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTK 196
>pdb|3KEV|A Chain A, X-Ray Crystal Structure Of A Dcun1 Domain-Containing
Protein From Galdieria Sulfuraria
Length = 199
Score = 93.6 bits (231), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 57/168 (33%), Positives = 91/168 (54%), Gaps = 8/168 (4%)
Query: 15 IYRRFCEIKSQNADVCIEDSYREDKESPKAKFSREALAELFNLVELTVHIRIFVFDELFK 74
+ R F +I+ +DV + K S +FS + VE ++++ ++L +
Sbjct: 29 LQRLFEDIQVDPSDVVTLVLAWKLKASSTXEFSEK------EFVEGLANLQVDSLEKLKR 82
Query: 75 LMSQL-DLMGDFSEFSRFYDFVFFMCRENGQKNITVSRAVTAWRLVLAGRFRLLNQWCDF 133
+S L + D S+F FY FVF +E Q+++ A W ++L GRF LL+ W +F
Sbjct: 83 KLSSLRKEIEDPSKFRAFYQFVFQYSKEPSQRSLPAETAXALWDVLLRGRFSLLDSWLEF 142
Query: 134 VERNQRHNISEDTWQQVLAFSRCVHENLEGYDPEGAWPVLIDDFVEHM 181
+ +N H+IS DTW + FS+ ++L YD GAWPVLIDDFV+ +
Sbjct: 143 L-KNNTHSISRDTWNLLYDFSQLSEKDLSDYDENGAWPVLIDDFVKWL 189
>pdb|4GBA|A Chain A, Dcnl Complex With N-terminally Acetylated Nedd8 E2 Peptide
pdb|4GBA|B Chain B, Dcnl Complex With N-terminally Acetylated Nedd8 E2 Peptide
Length = 221
Score = 59.3 bits (142), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 40/126 (31%), Positives = 59/126 (46%), Gaps = 5/126 (3%)
Query: 75 LMSQLDLMGDFSEFSRFYDFVFFMCRENGQKNITVSRAVTAWRLVLA-GRFRLLNQWCDF 133
L+++ F + RF F F + E GQ+++ A+ W+LV +L+QW +F
Sbjct: 86 LLTEAKQEDKFKDLYRF-TFQFGLDSEEGQRSLHREIAIALWKLVFTQNNPPVLDQWLNF 144
Query: 134 VERNQR--HNISEDTWQQVLAFSRCVHENLEGYDPEGAWPVLIDDFVE-HMYRVSGSKEN 190
+ N IS DTW L F++ + +L Y + AWP L D FVE M R E
Sbjct: 145 LTENPSGIKGISRDTWNMFLNFTQVIGPDLSNYSEDEAWPSLFDTFVEWEMERRKREGEG 204
Query: 191 PGLFCS 196
G S
Sbjct: 205 RGALSS 210
>pdb|3BQ3|A Chain A, Crystal Structure Of S. Cerevisiae Dcn1
Length = 270
Score = 57.8 bits (138), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 51/108 (47%), Gaps = 9/108 (8%)
Query: 81 LMGDFSEFSRFYDFVFFMCRENGQKNITVSRAVTAWRLVLAGRF------RLLNQWCDFV 134
L D F++ Y++ F + + +K+I + W+L + LL W F+
Sbjct: 157 LHEDLQYFTQIYNYAFNLILDPNRKDIDTDEGIQYWKLFFQPEYPVRXEPDLLEAWFRFL 216
Query: 135 ERNQRHNISEDTWQQVLAFSR---CVHENLEGYDPEGAWPVLIDDFVE 179
+ IS+DTW+ +L F + + + + YD AWP +ID+F E
Sbjct: 217 RDEGKTTISKDTWRXLLLFFKRYPTIQKIISDYDETAAWPFIIDEFYE 264
>pdb|2IS9|A Chain A, Structure Of Yeast Dcn-1
Length = 204
Score = 57.4 bits (137), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 51/108 (47%), Gaps = 9/108 (8%)
Query: 81 LMGDFSEFSRFYDFVFFMCRENGQKNITVSRAVTAWRLVLAGRF------RLLNQWCDFV 134
L D F++ Y++ F + + +K+I + W+L + LL W F+
Sbjct: 91 LHEDLQYFTQIYNYAFNLILDPNRKDIDTDEGIQYWKLFFQPEYPVRMEPDLLEAWFRFL 150
Query: 135 ERNQRHNISEDTWQQVLAFSR---CVHENLEGYDPEGAWPVLIDDFVE 179
+ IS+DTW+ +L F + + + + YD AWP +ID+F E
Sbjct: 151 RDEGKTTISKDTWRMLLLFFKRYPTIQKIISDYDETAAWPFIIDEFYE 198
>pdb|3O2P|A Chain A, A Dual E3 Mechanism For Rub1 Ligation To Cdc53:
Dcn1(P)-Cdc53(Whb)
pdb|3O6B|A Chain A, A Dual E3 Mechanism For Rub1 Ligation To Cdc53:
Dcn1(P)-Cdc53(Whb) Low Resolution
pdb|3O6B|C Chain C, A Dual E3 Mechanism For Rub1 Ligation To Cdc53:
Dcn1(P)-Cdc53(Whb) Low Resolution
pdb|3O6B|E Chain E, A Dual E3 Mechanism For Rub1 Ligation To Cdc53:
Dcn1(P)-Cdc53(Whb) Low Resolution
pdb|3O6B|G Chain G, A Dual E3 Mechanism For Rub1 Ligation To Cdc53:
Dcn1(P)-Cdc53(Whb) Low Resolution
pdb|3O6B|I Chain I, A Dual E3 Mechanism For Rub1 Ligation To Cdc53:
Dcn1(P)-Cdc53(Whb) Low Resolution
pdb|3TDI|B Chain B, Yeast Cul1whb-Dcn1p Acetylated Ubc12n Complex
pdb|3TDI|A Chain A, Yeast Cul1whb-Dcn1p Acetylated Ubc12n Complex
Length = 202
Score = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 29/108 (26%), Positives = 51/108 (47%), Gaps = 9/108 (8%)
Query: 81 LMGDFSEFSRFYDFVFFMCRENGQKNITVSRAVTAWRLVLAGRF------RLLNQWCDFV 134
L D F++ Y++ F + + +K+I + W+L + LL W F+
Sbjct: 89 LHEDLQYFTQIYNYAFNLILDPNRKDIDTDEGIQYWKLFFQPEYPVRMEPDLLEAWFRFL 148
Query: 135 ERNQRHNISEDTWQQVLAFSR---CVHENLEGYDPEGAWPVLIDDFVE 179
+ IS+DTW+ +L F + + + + YD AWP +ID+F E
Sbjct: 149 RDEGKTTISKDTWRMLLLFFKRYPTIQKIISDYDETAAWPFIIDEFYE 196
>pdb|2VQQ|A Chain A, Structure Of Hdac4 Catalytic Domain (A Double Cysteine-To-
Alanine Mutant) Bound To A Trifluoromethylketone
Inhbitor
pdb|2VQQ|B Chain B, Structure Of Hdac4 Catalytic Domain (A Double Cysteine-To-
Alanine Mutant) Bound To A Trifluoromethylketone
Inhbitor
Length = 413
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 38/85 (44%), Gaps = 6/85 (7%)
Query: 240 PELTDHNHISKRSRQVARPVNQEENPPG---SSGDDCMEIVRHNSPLGSAKSPCAVEGCL 296
P + D +++ R V P+ E P SSG D +E H +PLG G L
Sbjct: 256 PPMGDAEYLAAF-RTVVMPIASEFAPDVVLVSSGFDAVE--GHPTPLGGYNLSARCFGYL 312
Query: 297 SKGFVGLFSARSYLQVDRGRRLSYI 321
+K +GL R L ++ G L+ I
Sbjct: 313 TKQLMGLAGGRIVLALEGGHDLTAI 337
>pdb|2VQJ|A Chain A, Structure Of Hdac4 Catalytic Domain Bound To A
Trifluoromethylketone Inhbitor
pdb|2VQM|A Chain A, Structure Of Hdac4 Catalytic Domain Bound To A Hydroxamic
Acid Inhbitor
Length = 413
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 38/85 (44%), Gaps = 6/85 (7%)
Query: 240 PELTDHNHISKRSRQVARPVNQEENPPG---SSGDDCMEIVRHNSPLGSAKSPCAVEGCL 296
P + D +++ R V P+ E P SSG D +E H +PLG G L
Sbjct: 256 PPMGDAEYLAAF-RTVVMPIASEFAPDVVLVSSGFDAVE--GHPTPLGGYNLSARCFGYL 312
Query: 297 SKGFVGLFSARSYLQVDRGRRLSYI 321
+K +GL R L ++ G L+ I
Sbjct: 313 TKQLMGLAGGRIVLALEGGHDLTAI 337
>pdb|2VQO|A Chain A, Structure Of Hdac4 Catalytic Domain With A
Gain-Of-Function Muation Bound To A
Trifluoromethylketone Inhbitor
pdb|2VQO|B Chain B, Structure Of Hdac4 Catalytic Domain With A
Gain-Of-Function Muation Bound To A
Trifluoromethylketone Inhbitor
pdb|2VQV|A Chain A, Structure Of Hdac4 Catalytic Domain With A
Gain-Of-Function Mutation Bound To A Hydroxamic Acid
Inhibitor
pdb|2VQV|B Chain B, Structure Of Hdac4 Catalytic Domain With A
Gain-Of-Function Mutation Bound To A Hydroxamic Acid
Inhibitor
Length = 413
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 38/85 (44%), Gaps = 6/85 (7%)
Query: 240 PELTDHNHISKRSRQVARPVNQEENPPG---SSGDDCMEIVRHNSPLGSAKSPCAVEGCL 296
P + D +++ R V P+ E P SSG D +E H +PLG G L
Sbjct: 256 PPMGDAEYLAAF-RTVVMPIASEFAPDVVLVSSGFDAVE--GHPTPLGGYNLSARCFGYL 312
Query: 297 SKGFVGLFSARSYLQVDRGRRLSYI 321
+K +GL R L ++ G L+ I
Sbjct: 313 TKQLMGLAGGRIVLALEGGYDLTAI 337
>pdb|2VQW|G Chain G, Structure Of Inhibitor-Free Hdac4 Catalytic Domain (With
Gain-Of-Function Mutation His332tyr)
Length = 413
Score = 30.0 bits (66), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 38/85 (44%), Gaps = 6/85 (7%)
Query: 240 PELTDHNHISKRSRQVARPVNQEENPPG---SSGDDCMEIVRHNSPLGSAKSPCAVEGCL 296
P + D +++ R V P+ E P SSG D +E H +PLG G L
Sbjct: 256 PPMGDAEYLAAF-RTVVMPIASEFAPDVVLVSSGFDAVE--GHPTPLGGYNLSARCFGYL 312
Query: 297 SKGFVGLFSARSYLQVDRGRRLSYI 321
+K +GL R L ++ G L+ I
Sbjct: 313 TKQLMGLAGGRIVLALEGGYDLTAI 337
>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56
Length = 390
Score = 27.7 bits (60), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 63 HIRIFVFDELFKLMSQLDLMGDFSEFSRF 91
HI+ F+ DE K++ QLD+ D E R
Sbjct: 151 HIKHFILDEADKMLEQLDMRRDVQEIFRM 179
>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56
pdb|1T6N|B Chain B, Crystal Structure Of The N-Terminal Domain Of Human Uap56
Length = 220
Score = 27.7 bits (60), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 63 HIRIFVFDELFKLMSQLDLMGDFSEFSRF 91
HI+ F+ DE K++ QLD+ D E R
Sbjct: 158 HIKHFILDECDKMLEQLDMRRDVQEIFRM 186
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
0.321 0.136 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,746,061
Number of Sequences: 62578
Number of extensions: 405565
Number of successful extensions: 707
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 690
Number of HSP's gapped (non-prelim): 17
length of query: 321
length of database: 14,973,337
effective HSP length: 99
effective length of query: 222
effective length of database: 8,778,115
effective search space: 1948741530
effective search space used: 1948741530
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: 51 (24.3 bits)