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= 041408
(425 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 = 79.7 bits (195), Expect = 3e-15, Method: Composition-based stats.
Identities = 38/75 (50%), Positives = 48/75 (64%), Gaps = 3/75 (4%)
Query: 68 EIPEYFICPISLQIMKDPVTAITGITYDRESIEHWLFQGNNNAECPVTKQPLPKDLDLTP 127
E PEYF CPISL++MKDPV TG TY+R SI+ WL G+ CP +++ L LTP
Sbjct: 4 EFPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKT--CPKSQETL-LHAGLTP 60
Query: 128 NHTLRRLIQAWCADN 142
N+ L+ LI WC N
Sbjct: 61 NYVLKSLIALWCESN 75
>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 = 53.5 bits (127), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 32/89 (35%), Positives = 54/89 (60%), Gaps = 6/89 (6%)
Query: 57 LLFQMDD-HQDIEIPEYFICPISLQIMKDPVTAITGITYDRESIEHWLFQ-GNNNAECPV 114
L Q+D+ + +IP+Y IS ++M++P +GITYDR+ IE L + G+ N PV
Sbjct: 192 LFSQVDEKRKKRDIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFN---PV 248
Query: 115 TKQPLPKDLDLTPNHTLRRLIQAWCADNS 143
T+ PL ++ L PN ++ +I A+ ++N
Sbjct: 249 TRSPLTQE-QLIPNLAMKEVIDAFISENG 276
>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 = 30/77 (38%), Positives = 47/77 (61%), Gaps = 5/77 (6%)
Query: 68 EIPEYFICPISLQIMKDPVTAITGITYDRESIEHWLFQ-GNNNAECPVTKQPLPKDLDLT 126
EIP+Y IS ++M++P +GITYDR+ IE L + G+ + PVT+ PL +D L
Sbjct: 102 EIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFD---PVTRSPLTQD-QLI 157
Query: 127 PNHTLRRLIQAWCADNS 143
PN ++ +I A+ +N
Sbjct: 158 PNLAMKEVIDAFIQENG 174
>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 = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 46/76 (60%), Gaps = 5/76 (6%)
Query: 68 EIPEYFICPISLQIMKDPVTAITGITYDRESIEHWLFQ-GNNNAECPVTKQPLPKDLDLT 126
EIP+Y IS ++M +P +GITYDR+ IE L + G+ + PVT+ PL +D L
Sbjct: 9 EIPDYLCGKISFELMAEPCITPSGITYDRKDIEEHLQRVGHFD---PVTRSPLTQD-QLI 64
Query: 127 PNHTLRRLIQAWCADN 142
PN ++ +I A+ +N
Sbjct: 65 PNLAMKEVIDAFIQEN 80
>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 = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/77 (37%), Positives = 48/77 (62%), Gaps = 5/77 (6%)
Query: 68 EIPEYFICPISLQIMKDPVTAITGITYDRESIEHWLFQ-GNNNAECPVTKQPLPKDLDLT 126
+IP+Y IS ++M++P +GITYDR+ IE L + G+ N PVT+ PL ++ L
Sbjct: 1 DIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFN---PVTRSPLTQE-QLI 56
Query: 127 PNHTLRRLIQAWCADNS 143
PN ++ +I A+ ++N
Sbjct: 57 PNLAMKEVIDAFISENG 73
>pdb|2QIZ|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 8/80 (10%)
Query: 60 QMDDHQDIE---IPEYFICPISLQIMKDPVT-AITGITYDRESIEHWLFQGNNNAECPVT 115
+ D+ +D+E +P+ F+ P+ IMKDPV + + DR +I+ L + + P
Sbjct: 890 KADEEEDLEYGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDSTD---PFN 946
Query: 116 KQPLPKDLDLTPNHTLRRLI 135
+ PL K D+TPN LR+ I
Sbjct: 947 RMPL-KLEDVTPNEELRQKI 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 = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 44/80 (55%), Gaps = 8/80 (10%)
Query: 60 QMDDHQDIE---IPEYFICPISLQIMKDPVT-AITGITYDRESIEHWLFQGNNNAECPVT 115
+ D+ +D+E +P+ F+ P+ IMKDPV + + DR +I+ L + + P
Sbjct: 876 KADEEEDLEYGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLSDSTD---PFN 932
Query: 116 KQPLPKDLDLTPNHTLRRLI 135
+ PL K D+TPN LR+ I
Sbjct: 933 RMPL-KLEDVTPNEELRQKI 951
>pdb|2QJ0|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 8/80 (10%)
Query: 60 QMDDHQDIE---IPEYFICPISLQIMKDPVT-AITGITYDRESIEHWLFQGNNNAECPVT 115
+ D+ +D+E +P+ F+ P+ I KDPV + DR +I+ L + + P
Sbjct: 890 KADEEEDLEYGDVPDEFLDPLXYTIXKDPVILPASKXNIDRSTIKAHLLSDSTD---PFN 946
Query: 116 KQPLPKDLDLTPNHTLRRLI 135
+ PL K D+TPN LR+ I
Sbjct: 947 RXPL-KLEDVTPNEELRQKI 965
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 35.8 bits (81), Expect = 0.047, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 69 IPEYFICPISLQIMKDPVTAITGITYDRESIEHWLFQGNNNAE----CPVTKQPLPKDLD 124
I E CPI L+++K+PV+A ++ R I ++ N N + CPV + P P +
Sbjct: 16 IKEEVTCPICLELLKEPVSADCNHSFCRACIT-LNYESNRNTDGKGNCPVCRVPYPFG-N 73
Query: 125 LTPNHTLRRLIQ 136
L PN + +++
Sbjct: 74 LKPNLHVANIVE 85
>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 = 32.0 bits (71), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 68 EIPEYFICPISLQIMKDPVTAITGITYDRESIEHWLFQGNNNAECPVTKQPLPKDLDLTP 127
+ P+ F P+ +M DPV +G DR I L N+ P +Q L + + L P
Sbjct: 25 DAPDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHLL---NSPTDPFNRQTLTESM-LEP 80
Query: 128 NHTLRRLIQAW 138
L+ IQAW
Sbjct: 81 VPELKEQIQAW 91
>pdb|2KR4|A Chain A, U-Box Domain Of The E3 Ubiquitin Ligase E4b
Length = 85
Score = 30.8 bits (68), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 33/71 (46%), Gaps = 4/71 (5%)
Query: 68 EIPEYFICPISLQIMKDPVTAITGITYDRESIEHWLFQGNNNAECPVTKQPLPKDLDLTP 127
+ P+ F P+ +M DPV +G DR I L N+ P +Q L + + L P
Sbjct: 10 DAPDEFRDPLMDTLMTDPVRLPSGTVMDRSIILRHLL---NSPTDPFNRQMLTESM-LEP 65
Query: 128 NHTLRRLIQAW 138
L+ IQAW
Sbjct: 66 VPELKEQIQAW 76
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%)
Query: 75 CPISLQIMKDPVTAITGITYDRESIEHWLFQGNNNAECPVTKQPLPK 121
CPI L+++K+PV+ + + + L Q ++CP+ K + K
Sbjct: 24 CPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITK 70
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
0.323 0.136 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,195,783
Number of Sequences: 62578
Number of extensions: 369289
Number of successful extensions: 826
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 820
Number of HSP's gapped (non-prelim): 17
length of query: 425
length of database: 14,973,337
effective HSP length: 102
effective length of query: 323
effective length of database: 8,590,381
effective search space: 2774693063
effective search space used: 2774693063
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)