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= 012677
(458 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 = 96.3 bits (238), Expect = 4e-20, Method: Composition-based stats.
Identities = 36/73 (49%), Positives = 57/73 (78%)
Query: 77 PYEFRCPISGEIMTDPVVLANGQTFDRPCIQRWLDEGNRTCPQTRQVLSHTVLIPNHLVR 136
P FRCPIS E+M DPV+++ GQT++R IQ+WLD G++TCP++++ L H L PN++++
Sbjct: 6 PEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNYVLK 65
Query: 137 EMISQWCKEHGIE 149
+I+ WC+ +GIE
Sbjct: 66 SLIALWCESNGIE 78
>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 = 48.1 bits (113), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 77 PYEFRCPISGEIMTDPVVLANGQTFDRPCIQRWLDEGNRTCPQTRQVLSHTVLIPNHLVR 136
P EFR P+ +MTDPV L +G DR I R L + T P RQ L+ ++L P ++
Sbjct: 27 PDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHL-LNSPTDPFNRQTLTESMLEPVPELK 85
Query: 137 EMISQWCKE 145
E I W +E
Sbjct: 86 EQIQAWMRE 94
>pdb|2KR4|A Chain A, U-Box Domain Of The E3 Ubiquitin Ligase E4b
Length = 85
Score = 48.1 bits (113), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 77 PYEFRCPISGEIMTDPVVLANGQTFDRPCIQRWLDEGNRTCPQTRQVLSHTVLIPNHLVR 136
P EFR P+ +MTDPV L +G DR I R L + T P RQ+L+ ++L P ++
Sbjct: 12 PDEFRDPLMDTLMTDPVRLPSGTVMDRSIILRHL-LNSPTDPFNRQMLTESMLEPVPELK 70
Query: 137 EMISQWCKE 145
E I W +E
Sbjct: 71 EQIQAWMRE 79
>pdb|2F42|A Chain A, Dimerization And U-Box Domains Of Zebrafish C-Terminal Of
Hsp70 Interacting Protein
Length = 179
Score = 42.7 bits (99), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 36/64 (56%)
Query: 84 ISGEIMTDPVVLANGQTFDRPCIQRWLDEGNRTCPQTRQVLSHTVLIPNHLVREMISQWC 143
IS E+M +P + +G T+DR I+ L P TR L+ LIPN ++E+I +
Sbjct: 111 ISFELMREPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNLAMKEVIDAFI 170
Query: 144 KEHG 147
+E+G
Sbjct: 171 QENG 174
>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 = 4e-04, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 35/64 (54%)
Query: 84 ISGEIMTDPVVLANGQTFDRPCIQRWLDEGNRTCPQTRQVLSHTVLIPNHLVREMISQWC 143
IS E+M +P + +G T+DR I+ L P TR L+ LIPN ++E+I +
Sbjct: 10 ISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAMKEVIDAFI 69
Query: 144 KEHG 147
E+G
Sbjct: 70 SENG 73
>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 = 41.6 bits (96), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 35/64 (54%)
Query: 84 ISGEIMTDPVVLANGQTFDRPCIQRWLDEGNRTCPQTRQVLSHTVLIPNHLVREMISQWC 143
IS E+M +P + +G T+DR I+ L P TR L+ LIPN ++E+I +
Sbjct: 213 ISFELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQEQLIPNLAMKEVIDAFI 272
Query: 144 KEHG 147
E+G
Sbjct: 273 SENG 276
>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 = 41.2 bits (95), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%)
Query: 84 ISGEIMTDPVVLANGQTFDRPCIQRWLDEGNRTCPQTRQVLSHTVLIPNHLVREMISQWC 143
IS E+M +P + +G T+DR I+ L P TR L+ LIPN ++E+I +
Sbjct: 18 ISFELMAEPCITPSGITYDRKDIEEHLQRVGHFDPVTRSPLTQDQLIPNLAMKEVIDAFI 77
Query: 144 KEH 146
+E+
Sbjct: 78 QEN 80
>pdb|1WGM|A Chain A, Solution Structure Of The U-Box In Human Ubiquitin
Conjugation Factor E4a
Length = 98
Score = 36.6 bits (83), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 79 EFRCPISGEIMTDPVVLANGQ-TFDRPCIQRWLDEGNRTCPQTRQVLSHTVLIPNHLVRE 137
EF PI +M DPVVL + + T DR I R L ++T P R L+ + PN ++E
Sbjct: 22 EFLDPIMSTLMCDPVVLPSSRVTVDRSTIARHL-LSDQTDPFNRSPLTMDQIRPNTELKE 80
Query: 138 MISQWCKE 145
I +W E
Sbjct: 81 KIQRWLAE 88
>pdb|2ECV|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Tripartite Motif-Containing Protein 5
Length = 85
Score = 36.2 bits (82), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 5/66 (7%)
Query: 79 EFRCPISGEIMTDPVVLANGQTFDRPCI-----QRWLDEGNRTCPQTRQVLSHTVLIPNH 133
E CPI E++T P+ L G +F + C+ + LD+G +CP R + PN
Sbjct: 19 EVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRISYQPENIRPNR 78
Query: 134 LVREMI 139
V ++
Sbjct: 79 HVANIV 84
>pdb|3L11|A Chain A, Crystal Structure Of The Ring Domain Of Rnf168
Length = 115
Score = 35.4 bits (80), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 26/47 (55%)
Query: 79 EFRCPISGEIMTDPVVLANGQTFDRPCIQRWLDEGNRTCPQTRQVLS 125
E +C I EI+ +PV L T +PC Q +++ + CP R+ +S
Sbjct: 15 ECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRRRVS 61
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 33.9 bits (76), Expect = 0.22, Method: Composition-based stats.
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 79 EFRCPISGEIMTDPVVLANGQTFDRPCIQRWLDEGNRTCP 118
E C + E + +PV++ G F + CI RW ++ R P
Sbjct: 15 EASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFP 54
>pdb|3HCT|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The P1
Space Group
pdb|3HCU|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The C2
Space Group
pdb|3HCU|C Chain C, Crystal Structure Of Traf6 In Complex With Ubc13 In The C2
Space Group
Length = 118
Score = 31.6 bits (70), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 79 EFRCPISGEIMTDPVVLANGQTFDRPCIQRWLDEGNRTCPQTRQVLSHTVLIPNHLV-RE 137
++ CPI + + V G F + CI + + + CP ++L L P++ RE
Sbjct: 18 KYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKRE 77
Query: 138 MIS 140
++S
Sbjct: 78 ILS 80
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 30.8 bits (68), Expect = 1.4, Method: Composition-based stats.
Identities = 14/61 (22%), Positives = 27/61 (44%)
Query: 79 EFRCPISGEIMTDPVVLANGQTFDRPCIQRWLDEGNRTCPQTRQVLSHTVLIPNHLVREM 138
++ CPI + + V G F + CI + + + CP ++L L P++ +
Sbjct: 25 KYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKRE 84
Query: 139 I 139
I
Sbjct: 85 I 85
>pdb|3HCS|A Chain A, Crystal Structure Of The N-Terminal Domain Of Traf6
pdb|3HCS|B Chain B, Crystal Structure Of The N-Terminal Domain Of Traf6
Length = 170
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 1/63 (1%)
Query: 79 EFRCPISGEIMTDPVVLANGQTFDRPCIQRWLDEGNRTCPQTRQVLSHTVLIPNHLV-RE 137
++ CPI + + V G F + CI + + + CP ++L L P++ RE
Sbjct: 18 KYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAKRE 77
Query: 138 MIS 140
++S
Sbjct: 78 ILS 80
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 30.4 bits (67), Expect = 2.2, Method: Composition-based stats.
Identities = 13/58 (22%), Positives = 26/58 (44%)
Query: 79 EFRCPISGEIMTDPVVLANGQTFDRPCIQRWLDEGNRTCPQTRQVLSHTVLIPNHLVR 136
++ CPI + + V G F + CI + + + CP ++L L P++ +
Sbjct: 6 KYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPDNFAK 63
>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 = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 77 PYEFRCPISGEIMTDPVVL-ANGQTFDRPCIQRWLDEGNRTCPQTRQVLSHTVLIPNHLV 135
P EF P+ IM DPV+L A+ DR I+ L + T P R L + PN +
Sbjct: 889 PDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHL-LSDSTDPFNRMPLKLEDVTPNEEL 947
Query: 136 REMISQWCKE 145
R+ I + K+
Sbjct: 948 RQKILCFKKQ 957
>pdb|2QIZ|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 30.0 bits (66), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 2/70 (2%)
Query: 77 PYEFRCPISGEIMTDPVVL-ANGQTFDRPCIQRWLDEGNRTCPQTRQVLSHTVLIPNHLV 135
P EF P+ IM DPV+L A+ DR I+ L + T P R L + PN +
Sbjct: 903 PDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHL-LSDSTDPFNRMPLKLEDVTPNEEL 961
Query: 136 REMISQWCKE 145
R+ I + K+
Sbjct: 962 RQKILCFKKQ 971
>pdb|3J08|A Chain A, High Resolution Helical Reconstruction Of The Bacterial
P-Type Atpase Copper Transporter Copa
pdb|3J08|B Chain B, High Resolution Helical Reconstruction Of The Bacterial
P-Type Atpase Copper Transporter Copa
Length = 645
Score = 29.6 bits (65), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 133 HLVREMISQWCKEHGIELPKPIKD---TDEDVVTDASRSHLNSLLEKMSSSLSDQKEAAK 189
H + E I + EHGIEL +P K E VV D L+E ++S++ E A
Sbjct: 370 HPIAEAIVKKALEHGIELGEPEKVEVIAGEGVVADGILVGNKRLMEDFGVAVSNEVELAL 429
Query: 190 E 190
E
Sbjct: 430 E 430
>pdb|3J09|A Chain A, High Resolution Helical Reconstruction Of The Bacterial
P-Type Atpase Copper Transporter Copa
pdb|3J09|B Chain B, High Resolution Helical Reconstruction Of The Bacterial
P-Type Atpase Copper Transporter Copa
Length = 723
Score = 29.6 bits (65), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 133 HLVREMISQWCKEHGIELPKPIKD---TDEDVVTDASRSHLNSLLEKMSSSLSDQKEAAK 189
H + E I + EHGIEL +P K E VV D L+E ++S++ E A
Sbjct: 448 HPIAEAIVKKALEHGIELGEPEKVEVIAGEGVVADGILVGNKRLMEDFGVAVSNEVELAL 507
Query: 190 E 190
E
Sbjct: 508 E 508
>pdb|1RMD|A Chain A, Rag1 Dimerization Domain
Length = 116
Score = 28.9 bits (63), Expect = 6.2, Method: Composition-based stats.
Identities = 24/91 (26%), Positives = 36/91 (39%), Gaps = 5/91 (5%)
Query: 82 CPISGEIMTDPVVLANGQTFDRPCIQRWLDEGNRTCPQTRQVLSHTVLIPNHLVREMISQ 141
C I I+ DPV + F R CI R L CP R P L + S
Sbjct: 26 CQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCRY-----PCFPTDLESPVKSF 80
Query: 142 WCKEHGIELPKPIKDTDEDVVTDASRSHLNS 172
+ + + P +D +E+V + H++S
Sbjct: 81 LNILNSLMVKCPAQDCNEEVSLEKYNHHVSS 111
>pdb|4DB9|A Chain A, Designed Armadillo Repeat Protein (Yiiim3aiii)
pdb|4DB9|B Chain B, Designed Armadillo Repeat Protein (Yiiim3aiii)
pdb|4DB9|C Chain C, Designed Armadillo Repeat Protein (Yiiim3aiii)
pdb|4DB9|D Chain D, Designed Armadillo Repeat Protein (Yiiim3aiii)
pdb|4DB9|E Chain E, Designed Armadillo Repeat Protein (Yiiim3aiii)
pdb|4DB9|F Chain F, Designed Armadillo Repeat Protein (Yiiim3aiii)
Length = 210
Score = 28.5 bits (62), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 33/156 (21%), Positives = 76/156 (48%), Gaps = 6/156 (3%)
Query: 297 GAMTPLIDLLEEGHPLAMKDVASAIFSLCILLENKRRAV-HAGAVRVILRKIM---ENSL 352
GA+ L+ LL + +++ A+ ++ + +AV AGA+ +++ + E L
Sbjct: 54 GALPALVQLLSSPNEQILQEALWALSNIASGGNEQIQAVIDAGALPALVQLLSSPNEQIL 113
Query: 353 VDELLAILAMLSSHQDAIEEIGELGAIPCLLRIIRESTCERNKENCAAILYNICFTDRTR 412
+ L A+ + S + I+ + + GA+P L++++ S E+ + L NI +
Sbjct: 114 QEALWALSNIASGGNEQIQAVIDAGALPALVQLLS-SPNEQILQEALWALSNIA-SGGNE 171
Query: 413 TREIMEEENANGTLSRLAENGTSRAKRKANGILERL 448
++ ++E A L +L + + +++A LE++
Sbjct: 172 QKQAVKEAGAEPALEQLQSSPNEKIQKEAQEALEKI 207
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 0.135 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,928,357
Number of Sequences: 62578
Number of extensions: 451431
Number of successful extensions: 1321
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1302
Number of HSP's gapped (non-prelim): 35
length of query: 458
length of database: 14,973,337
effective HSP length: 102
effective length of query: 356
effective length of database: 8,590,381
effective search space: 3058175636
effective search space used: 3058175636
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: 53 (25.0 bits)