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= 015939
(398 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1T1H|A Chain A, Nmr Solution Structure Of The U Box Domain From Atpub14,
An Armadillo Repeat Containing Protein From Arabidopsis
Thaliana
Length = 78
Score = 84.7 bits (208), Expect = 8e-17, Method: Composition-based stats.
Identities = 36/66 (54%), Positives = 44/66 (66%)
Query: 11 PNLFRCPISLDVMKSPVSLCTGVTYDRSSIQHWLESGHDTCPATMQILSTKEFVPNLTLH 70
P FRCPISL++MK PV + TG TY+RSSIQ WL++GH TCP + + L PN L
Sbjct: 6 PEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNYVLK 65
Query: 71 RLIAHW 76
LIA W
Sbjct: 66 SLIALW 71
>pdb|2C2L|A Chain A, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
pdb|2C2L|B Chain B, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
pdb|2C2L|C Chain C, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
pdb|2C2L|D Chain D, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
Length = 281
Score = 43.1 bits (100), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 34/64 (53%)
Query: 10 VPNLFRCPISLDVMKSPVSLCTGVTYDRSSIQHWLESGHDTCPATMQILSTKEFVPNLTL 69
+P+ IS ++M+ P +G+TYDR I+ L+ P T L+ ++ +PNL +
Sbjct: 205 IPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAM 264
Query: 70 HRLI 73
+I
Sbjct: 265 KEVI 268
>pdb|2C2V|S Chain S, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
pdb|2C2V|T Chain T, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
pdb|2C2V|U Chain U, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
pdb|2C2V|V Chain V, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
Length = 78
Score = 42.7 bits (99), Expect = 3e-04, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 34/64 (53%)
Query: 10 VPNLFRCPISLDVMKSPVSLCTGVTYDRSSIQHWLESGHDTCPATMQILSTKEFVPNLTL 69
+P+ IS ++M+ P +G+TYDR I+ L+ P T L+ ++ +PNL +
Sbjct: 2 IPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAM 61
Query: 70 HRLI 73
+I
Sbjct: 62 KEVI 65
>pdb|2F42|A Chain A, Dimerization And U-Box Domains Of Zebrafish C-Terminal Of
Hsp70 Interacting Protein
Length = 179
Score = 42.4 bits (98), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 35/65 (53%), Gaps = 2/65 (3%)
Query: 10 VPNLFRCPISLDVMKSPVSLCTGVTYDRSSIQHWLES-GHDTCPATMQILSTKEFVPNLT 68
+P+ IS ++M+ P +G+TYDR I+ L+ GH P T L+ + +PNL
Sbjct: 103 IPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGH-FDPVTRSPLTQDQLIPNLA 161
Query: 69 LHRLI 73
+ +I
Sbjct: 162 MKEVI 166
>pdb|2OXQ|C Chain C, Structure Of The Ubch5 :chip U-Box Complex
pdb|2OXQ|D Chain D, Structure Of The Ubch5 :chip U-Box Complex
Length = 80
Score = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 32/64 (50%)
Query: 10 VPNLFRCPISLDVMKSPVSLCTGVTYDRSSIQHWLESGHDTCPATMQILSTKEFVPNLTL 69
+P+ IS ++M P +G+TYDR I+ L+ P T L+ + +PNL +
Sbjct: 10 IPDYLCGKISFELMAEPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNLAM 69
Query: 70 HRLI 73
+I
Sbjct: 70 KEVI 73
>pdb|2KR4|A Chain A, U-Box Domain Of The E3 Ubiquitin Ligase E4b
Length = 85
Score = 36.2 bits (82), Expect = 0.029, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 33/74 (44%), Gaps = 3/74 (4%)
Query: 7 YIAVPNLFRCPISLDVMKSPVSLCTGVTYDRSSI-QHWLESGHDTCPATMQILSTKEFVP 65
Y P+ FR P+ +M PV L +G DRS I +H L S D P Q+L+ P
Sbjct: 8 YSDAPDEFRDPLMDTLMTDPVRLPSGTVMDRSIILRHLLNSPTD--PFNRQMLTESMLEP 65
Query: 66 NLTLHRLIAHWSHQ 79
L I W +
Sbjct: 66 VPELKEQIQAWMRE 79
>pdb|2KRE|A Chain A, Solution Structure Of E4bUFD2A U-Box Domain
pdb|3L1X|A Chain A, Crystal Structure Of U-Box Domain Of Human E4b Ubiquitin
Ligase
pdb|3L1Z|B Chain B, Crystal Structure Of The U-Box Domain Of Human E4b
Ubiquitin Ligase In Complex With Ubch5c E2 Ubiquitin
Conjugating Enzyme
Length = 100
Score = 35.4 bits (80), Expect = 0.058, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 35/79 (44%), Gaps = 4/79 (5%)
Query: 3 RQEL-YIAVPNLFRCPISLDVMKSPVSLCTGVTYDRSSI-QHWLESGHDTCPATMQILST 60
R E+ Y P+ FR P+ +M PV L +G DRS I +H L S D P Q L+
Sbjct: 18 RAEIDYSDAPDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHLLNSPTD--PFNRQTLTE 75
Query: 61 KEFVPNLTLHRLIAHWSHQ 79
P L I W +
Sbjct: 76 SMLEPVPELKEQIQAWMRE 94
>pdb|3IZ6|C Chain C, Localization Of The Small Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 195
Score = 31.6 bits (70), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 34/61 (55%)
Query: 206 ISLDNESKRRVLETENLLSALFDYLKLAEDQALNDAILSILITLSVYRSVKAQLVELGMV 265
++LD ++ RR+ E E LL + Y LA+ Q D +L++ + + R ++ + + GM
Sbjct: 62 LTLDEKNPRRIFEGEALLRRMNRYGLLADGQNKLDYVLALTVENFLARRLQTLVFKAGMA 121
Query: 266 Q 266
+
Sbjct: 122 K 122
>pdb|2QIZ|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 31.6 bits (70), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 7 YIAVPNLFRCPISLDVMKSPVSL-CTGVTYDRSSIQHWLESGHDTCPATMQILSTKEFVP 65
Y VP+ F P+ +MK PV L + + DRS+I+ L S T P L ++ P
Sbjct: 899 YGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSD-STDPFNRMPLKLEDVTP 957
Query: 66 NLTLHRLIAHWSHQ 79
N L + I + Q
Sbjct: 958 NEELRQKILCFKKQ 971
>pdb|3M62|A Chain A, Crystal Structure Of Ufd2 In Complex With The
Ubiquitin-Like (Ubl) Domain Of Rad23
pdb|3M63|A Chain A, Crystal Structure Of Ufd2 In Complex With The
Ubiquitin-Like (Ubl) Domain Of Dsk2
Length = 968
Score = 31.2 bits (69), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 7 YIAVPNLFRCPISLDVMKSPVSL-CTGVTYDRSSIQHWLESGHDTCPATMQILSTKEFVP 65
Y VP+ F P+ +MK PV L + + DRS+I+ L S T P L ++ P
Sbjct: 885 YGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSD-STDPFNRMPLKLEDVTP 943
Query: 66 NLTLHRLIAHWSHQ 79
N L + I + Q
Sbjct: 944 NEELRQKILCFKKQ 957
>pdb|1F1S|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase At 2.1 Angstrom Resolution.
pdb|1I8Q|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase Complexed With Enzyme Product, Unsaturated
Disaccharide Hyaluronan
pdb|1LXM|A Chain A, Crystal Structure Of Streptococcus Agalactiae Hyaluronate
Lyase Complexed With Hexasaccharide Unit Of Hyaluronan
Length = 814
Score = 31.2 bits (69), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 38/87 (43%), Gaps = 8/87 (9%)
Query: 223 LSALFDYLKLAEDQALNDAILSILITLSVYR--------SVKAQLVELGMVQILTRILSD 274
LS + +Y AE + D I + +R ++ LV++G V+I+ +L
Sbjct: 216 LSLMNNYFTDAEIKTYTDPIEHFVPDAEYFRKTLVNPFKALGGNLVDMGRVKIIEGLLRK 275
Query: 275 SRTQILTVEKSIKMLSIVATCSEGRLA 301
T I S+K L AT +EG A
Sbjct: 276 DNTIIEKTSHSLKNLFTTATKAEGFYA 302
>pdb|2XZM|D Chain D, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
In Complex With Initiation Factor 1. This File Contains
The 40s Subunit And Initiation Factor For Molecule 1
pdb|2XZN|D Chain D, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
In Complex With Initiation Factor 1. This File Contains
The 40s Subunit And Initiation Factor For Molecule 2
Length = 181
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 29/130 (22%), Positives = 59/130 (45%), Gaps = 20/130 (15%)
Query: 206 ISLDNESKRRVLETENLLSALFDYLKLAEDQALNDAILSILITLSVYRSVKAQLVELGMV 265
++LD + RR+ E LL +F Y L+E + D +L + I + R ++ ++ +L +
Sbjct: 60 LTLDPKDPRRLFEGSALLRRMFKYGLLSEQERKLDYVLGLTIHKLMERRLQTRVFKLNLA 119
Query: 266 QILTRILSDSRTQILTVEKSIKMLS--------IVATCSEGRLALSEEASCAGRVVERVM 317
S +++L ++ IK+ +V T SE + + + G
Sbjct: 120 N------SIHHSRVLIRQRHIKVGKNLVNVPSFMVRTDSEKSIDFASTSPLGG------G 167
Query: 318 KVGKTAREDA 327
+ G+T R++A
Sbjct: 168 REGRTKRKNA 177
>pdb|3LPO|A Chain A, Crystal Structure Of The N-Terminal Domain Of
Sucrase-Isomal
pdb|3LPO|B Chain B, Crystal Structure Of The N-Terminal Domain Of
Sucrase-Isomal
pdb|3LPO|C Chain C, Crystal Structure Of The N-Terminal Domain Of
Sucrase-Isomal
pdb|3LPO|D Chain D, Crystal Structure Of The N-Terminal Domain Of
Sucrase-Isomal
pdb|3LPP|A Chain A, Crystal Complex Of N-Terminal Sucrase-Isomaltase With
Kotala
pdb|3LPP|B Chain B, Crystal Complex Of N-Terminal Sucrase-Isomaltase With
Kotala
pdb|3LPP|C Chain C, Crystal Complex Of N-Terminal Sucrase-Isomaltase With
Kotala
pdb|3LPP|D Chain D, Crystal Complex Of N-Terminal Sucrase-Isomaltase With
Kotala
Length = 898
Score = 31.2 bits (69), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 31 TGVTYDRSSIQH-WLESGHDTCPATMQILSTKEFVPNLTLHRLIAHWSHQLTVPEQEVR 88
T TY+R + QH W+ + P ++ P+ T I W+++ ++ QEV+
Sbjct: 407 TYATYERGNTQHVWINESDGSTPIIGEVWPGLTVYPDFTNPNCIDWWANECSIFHQEVQ 465
>pdb|3ZEY|6 Chain 6, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 190
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 29/122 (23%), Positives = 56/122 (45%), Gaps = 6/122 (4%)
Query: 206 ISLDNESKRRVLETENLLSALFDYLKLAEDQALNDAILSILITLSVYRSVKAQLVELGMV 265
++L RR+LE ++ Y L ED+ D +LS+ + + R ++ + + G+
Sbjct: 59 LTLPENHPRRLLEGSAIMRRCHGYGFLDEDKDKLDYVLSLTVPDILERRLQTVVFKHGLA 118
Query: 266 QIL--TRILSDSRTQILTVEKSIKMLS--IVATCSEGRLALSEEASCAGRVVERVMKVGK 321
+ + +R+L R + V K I + IV SE +A ++ + RV +V +
Sbjct: 119 KSVHHSRVLIQQRH--IAVAKQIVTIPSFIVRVSSEHHIAFADASPFGNGRPGRVKRVKR 176
Query: 322 TA 323
A
Sbjct: 177 NA 178
>pdb|3SXU|B Chain B, Structure Of The E. Coli Ssb-Dna Polymerase Iii Interface
Length = 138
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 32/78 (41%), Gaps = 3/78 (3%)
Query: 264 MVQILTRILSDSRTQIL--TVEKSIKMLSIVATCSEGRLALSEEASCAGRVVERVMKVGK 321
+V + R L+ S Q+L T EK I ML + C+ RL E S G V
Sbjct: 54 LVSDVLRALTVSPDQVLQLTPEK-IAMLPQGSHCNSWRLGTDEPLSLEGAQVASPALTDL 112
Query: 322 TAREDAVVVIWSMCCVYK 339
A A +W C Y+
Sbjct: 113 RANPTARAALWQQICTYE 130
>pdb|3B48|A Chain A, Crystal Structure Of Unknown Function Protein Ef1359
pdb|3B48|B Chain B, Crystal Structure Of Unknown Function Protein Ef1359
pdb|3B48|C Chain C, Crystal Structure Of Unknown Function Protein Ef1359
pdb|3B48|D Chain D, Crystal Structure Of Unknown Function Protein Ef1359
pdb|3B48|E Chain E, Crystal Structure Of Unknown Function Protein Ef1359
pdb|3B48|F Chain F, Crystal Structure Of Unknown Function Protein Ef1359
Length = 135
Score = 28.5 bits (62), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 33/98 (33%), Positives = 45/98 (45%), Gaps = 23/98 (23%)
Query: 191 GNLDSKIGS--IKILDSISLDNESKRRVLETENLLSAL------FDYLKLAEDQALNDAI 242
G D +GS KI+D+I+ + +S R L +L SA+ FD L+ EDQ +
Sbjct: 41 GTSDGSLGSDPXKIIDTIN-EADSDREFLIFADLGSAVLSSELAFDXLE--EDQQKH--- 94
Query: 243 LSILITLSVYRSVKAQLVELGMVQILTRILSDSRTQIL 280
Y V A LVE +T +SD TQIL
Sbjct: 95 ---------YHLVDAPLVEGAFASAITAGVSDDLTQIL 123
>pdb|2CJS|A Chain A, Structural Basis For A Munc13-1 Dimeric - Munc13-1 - Rim
Heterodimer Switch: C2-domains As Versatile Protein-
Protein Interaction Modules
pdb|2CJS|B Chain B, Structural Basis For A Munc13-1 Dimeric - Munc13-1 - Rim
Heterodimer Switch: C2-domains As Versatile Protein-
Protein Interaction Modules
Length = 167
Score = 28.1 bits (61), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 6/51 (11%)
Query: 42 HWLESGHDTCPATMQILSTKEFVPNLTLHRLI--AHWSHQLTVPEQEVRVW 90
WL A +I TK + T HR++ AH+ L +PE+E R W
Sbjct: 107 EWLTLDSQAIMADSEICGTK----DPTFHRILLDAHFELPLDIPEEEARYW 153
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 0.135 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,661,187
Number of Sequences: 62578
Number of extensions: 343072
Number of successful extensions: 904
Number of sequences better than 100.0: 54
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 43
Number of HSP's that attempted gapping in prelim test: 864
Number of HSP's gapped (non-prelim): 84
length of query: 398
length of database: 14,973,337
effective HSP length: 101
effective length of query: 297
effective length of database: 8,652,959
effective search space: 2569928823
effective search space used: 2569928823
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)