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= 015513
(405 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 = 83.6 bits (205), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 40/77 (51%), Positives = 53/77 (68%), Gaps = 2/77 (2%)
Query: 5 EVPQYFICPISLQIMKDPVTAITGISYDRESIEKWLKTAKDTTCPVTKQPLPRDSGLTSN 64
E P+YF CPISL++MKDPV TG +Y+R SI+KWL A TCP +++ L +GLT N
Sbjct: 4 EFPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLD-AGHKTCPKSQETL-LHAGLTPN 61
Query: 65 HTLRRLIQAWCTHNGID 81
+ L+ LI WC NGI+
Sbjct: 62 YVLKSLIALWCESNGIE 78
>pdb|2F42|A Chain A, Dimerization And U-Box Domains Of Zebrafish C-Terminal Of
Hsp70 Interacting Protein
Length = 179
Score = 53.1 bits (126), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 5 EVPQYFICPISLQIMKDPVTAITGISYDRESIEKWLKTAKDTTCPVTKQPLPRDSGLTSN 64
E+P Y IS ++M++P +GI+YDR+ IE+ L+ PVT+ PL +D L N
Sbjct: 102 EIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFD-PVTRSPLTQDQ-LIPN 159
Query: 65 HTLRRLIQAWCTHNG 79
++ +I A+ NG
Sbjct: 160 LAMKEVIDAFIQENG 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 = 51.2 bits (121), Expect = 9e-07, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 44/75 (58%), Gaps = 2/75 (2%)
Query: 5 EVPQYFICPISLQIMKDPVTAITGISYDRESIEKWLKTAKDTTCPVTKQPLPRDSGLTSN 64
++P Y IS ++M++P +GI+YDR+ IE+ L+ PVT+ PL ++ L N
Sbjct: 1 DIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFN-PVTRSPLTQEQ-LIPN 58
Query: 65 HTLRRLIQAWCTHNG 79
++ +I A+ + NG
Sbjct: 59 LAMKEVIDAFISENG 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 = 51.2 bits (121), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 44/75 (58%), Gaps = 2/75 (2%)
Query: 5 EVPQYFICPISLQIMKDPVTAITGISYDRESIEKWLKTAKDTTCPVTKQPLPRDSGLTSN 64
++P Y IS ++M++P +GI+YDR+ IE+ L+ PVT+ PL ++ L N
Sbjct: 204 DIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFN-PVTRSPLTQEQ-LIPN 261
Query: 65 HTLRRLIQAWCTHNG 79
++ +I A+ + NG
Sbjct: 262 LAMKEVIDAFISENG 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 = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 26/74 (35%), Positives = 41/74 (55%), Gaps = 2/74 (2%)
Query: 5 EVPQYFICPISLQIMKDPVTAITGISYDRESIEKWLKTAKDTTCPVTKQPLPRDSGLTSN 64
E+P Y IS ++M +P +GI+YDR+ IE+ L+ PVT+ PL +D L N
Sbjct: 9 EIPDYLCGKISFELMAEPCITPSGITYDRKDIEEHLQRVGHFD-PVTRSPLTQDQ-LIPN 66
Query: 65 HTLRRLIQAWCTHN 78
++ +I A+ N
Sbjct: 67 LAMKEVIDAFIQEN 80
>pdb|2QIZ|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 36.6 bits (83), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 5 EVPQYFICPISLQIMKDPVT-AITGISYDRESIEKWLKTAKDTTCPVTKQPLPRDSGLTS 63
+VP F+ P+ IMKDPV + ++ DR +I+ L + D+T P + PL + +T
Sbjct: 901 DVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLS--DSTDPFNRMPLKLED-VTP 957
Query: 64 NHTLRRLI 71
N LR+ I
Sbjct: 958 NEELRQKI 965
>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 = 36.6 bits (83), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 5 EVPQYFICPISLQIMKDPVT-AITGISYDRESIEKWLKTAKDTTCPVTKQPLPRDSGLTS 63
+VP F+ P+ IMKDPV + ++ DR +I+ L + D+T P + PL + +T
Sbjct: 887 DVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLS--DSTDPFNRMPL-KLEDVTP 943
Query: 64 NHTLRRLI 71
N LR+ I
Sbjct: 944 NEELRQKI 951
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 34.7 bits (78), Expect = 0.089, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 4/49 (8%)
Query: 12 CPISLQIMKDPVTAITGISYDRESIEKWLKTAKDT----TCPVTKQPLP 56
CPI L+++K+PV+A S+ R I ++ ++T CPV + P P
Sbjct: 22 CPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYP 70
>pdb|2QJ0|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 5 EVPQYFICPISLQIMKDPVT-AITGISYDRESIEKWLKTAKDTTCPVTKQPLPRDSGLTS 63
+VP F+ P+ I KDPV + + DR +I+ L + D+T P + PL + +T
Sbjct: 901 DVPDEFLDPLXYTIXKDPVILPASKXNIDRSTIKAHLLS--DSTDPFNRXPLKLED-VTP 957
Query: 64 NHTLRRLI 71
N LR+ I
Sbjct: 958 NEELRQKI 965
>pdb|2YU4|A Chain A, Solution Structure Of The Sp-Ring Domain In Non-Smc
Element 2 Homolog (Mms21, S. Cerevisiae)
Length = 94
Score = 31.6 bits (70), Expect = 0.89, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 32/70 (45%), Gaps = 7/70 (10%)
Query: 10 FICPISLQIMKDPV-TAITGISYDRES----IEKWLKTAKDTTCPVT--KQPLPRDSGLT 62
F CPI+ + MK PV + G +Y+ ++ IE K K CP R S L
Sbjct: 8 FTCPITKEEMKKPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGCSHTDIRKSDLI 67
Query: 63 SNHTLRRLIQ 72
+ LRR I+
Sbjct: 68 QDEALRRAIE 77
>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 = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 1 MDEIEVPQYFICPISLQIMKDPVTAITGISYDRESIEKWLKTAKDTTCPVTKQPLPRDSG 60
+D + P F P+ +M DPV +G DR I + L + T P +Q L +S
Sbjct: 21 IDYSDAPDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHLLNS--PTDPFNRQTL-TESM 77
Query: 61 LTSNHTLRRLIQAW 74
L L+ IQAW
Sbjct: 78 LEPVPELKEQIQAW 91
>pdb|2IZV|A Chain A, Crystal Structure Of Socs-4 In Complex With Elongin-B And
Elongin-C At 2.55a Resolution
Length = 187
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 20/40 (50%)
Query: 49 PVTKQPLPRDSGLTSNHTLRRLIQAWCTHNGIDRIPTPKS 88
P+ PL R + H R +I T++GID +P P S
Sbjct: 125 PLLSTPLIRTFPFSLQHICRTVICNCTTYDGIDALPIPSS 164
>pdb|2KR4|A Chain A, U-Box Domain Of The E3 Ubiquitin Ligase E4b
Length = 85
Score = 28.5 bits (62), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 3/74 (4%)
Query: 1 MDEIEVPQYFICPISLQIMKDPVTAITGISYDRESIEKWLKTAKDTTCPVTKQPLPRDSG 60
+D + P F P+ +M DPV +G DR I + L + T P +Q L +S
Sbjct: 6 IDYSDAPDEFRDPLMDTLMTDPVRLPSGTVMDRSIILRHLLNSP--TDPFNRQML-TESM 62
Query: 61 LTSNHTLRRLIQAW 74
L L+ IQAW
Sbjct: 63 LEPVPELKEQIQAW 76
>pdb|4HSB|A Chain A, S. Pombe 3-methyladenine Dna Glycosylase-like Protein Mag2
Bound To Damaged Dna
Length = 217
Score = 28.5 bits (62), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 3/90 (3%)
Query: 298 LCSCADGRLKFRE-HAGAIAMVTKRLLRVSPATNDRAVHILSSISKFSATYEVVLEMLSV 356
L C +LK +E H A A + K++ S ++ S+SK +EM S+
Sbjct: 94 LHECGFSKLKSQEIHIVAEAALNKQIPSKSEIEKMSEEELMESLSKIKGVKRWTIEMYSI 153
Query: 357 GAVSKLCMVTQADCEKYLKDRAKEILRLHS 386
+ +L ++ D LK+ AKE L S
Sbjct: 154 FTLGRLDIMPADDS--TLKNEAKEFFGLSS 181
>pdb|4B21|A Chain A, Unprecedented Sculpting Of Dna At Abasic Sites By Dna
Glycosylase Homolog Mag2
pdb|4B22|A Chain A, Unprecedented Sculpting Of Dna At Abasic Sites By Dna
Glycosylase Homolog Mag2
pdb|4B23|A Chain A, Unprecedented Sculpting Of Dna At Abasic Sites By Dna
Glycoslase Homolog Mag2
pdb|4B24|A Chain A, Unprecedented Sculpting Of Dna At Abasic Sites By Dna
Glycoslase Homolog Mag2
Length = 232
Score = 28.1 bits (61), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 3/90 (3%)
Query: 298 LCSCADGRLKFRE-HAGAIAMVTKRLLRVSPATNDRAVHILSSISKFSATYEVVLEMLSV 356
L C +LK +E H A A + K++ S ++ S+SK +EM S+
Sbjct: 109 LHECGFSKLKSQEIHIVAEAALNKQIPSKSEIEKMSEEELMESLSKIKGVKRWTIEMYSI 168
Query: 357 GAVSKLCMVTQADCEKYLKDRAKEILRLHS 386
+ +L ++ D LK+ AKE L S
Sbjct: 169 FTLGRLDIMPADDS--TLKNEAKEFFGLSS 196
>pdb|2I7T|A Chain A, Structure Of Human Cpsf-73
pdb|2I7V|A Chain A, Structure Of Human Cpsf-73
Length = 459
Score = 28.1 bits (61), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 29/59 (49%), Gaps = 10/59 (16%)
Query: 142 IITSYKGNKT-------TGLE--EALRILSLVWSPSNENKALVDHHNQDLIGALMWVLQ 191
II +KG K GLE +AL + L+ P+ + L+ H + D GAL W LQ
Sbjct: 28 IILEFKGRKIMLDCGIHPGLEGMDALPYIDLI-DPAEIDLLLISHFHLDHCGALPWFLQ 85
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
0.319 0.132 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,716,217
Number of Sequences: 62578
Number of extensions: 396384
Number of successful extensions: 1175
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1168
Number of HSP's gapped (non-prelim): 17
length of query: 405
length of database: 14,973,337
effective HSP length: 101
effective length of query: 304
effective length of database: 8,652,959
effective search space: 2630499536
effective search space used: 2630499536
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: 53 (25.0 bits)