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= 014913
(416 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 = 80.1 bits (196), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 42/80 (52%), Positives = 53/80 (66%), Gaps = 5/80 (6%)
Query: 5 DVPTFFLCPISLAIMKDPVTVPTGITYDRESIEKWLFAGKNNTCPMTKQVLSSECELTPN 64
+ P +F CPISL +MKDPV V TG TY+R SI+KWL AG + TCP +++ L LTPN
Sbjct: 4 EFPEYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAG-HKTCPKSQETL-LHAGLTPN 61
Query: 65 HTLRRLIQSWCTLNASYGIE 84
+ L+ LI WC N GIE
Sbjct: 62 YVLKSLIALWCESN---GIE 78
>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 = 52.0 bits (123), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 4/76 (5%)
Query: 5 DVPTFFLCPISLAIMKDPVTVPTGITYDRESIEKWL-FAGKNNTCPMTKQVLSSECELTP 63
D+P + IS +M++P P+GITYDR+ IE+ L G N P+T+ L+ E +L P
Sbjct: 204 DIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFN--PVTRSPLTQE-QLIP 260
Query: 64 NHTLRRLIQSWCTLNA 79
N ++ +I ++ + N
Sbjct: 261 NLAMKEVIDAFISENG 276
>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 = 50.4 bits (119), Expect = 2e-06, Method: Composition-based stats.
Identities = 27/76 (35%), Positives = 45/76 (59%), Gaps = 4/76 (5%)
Query: 5 DVPTFFLCPISLAIMKDPVTVPTGITYDRESIEKWL-FAGKNNTCPMTKQVLSSECELTP 63
D+P + IS +M++P P+GITYDR+ IE+ L G N P+T+ L+ E +L P
Sbjct: 1 DIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHFN--PVTRSPLTQE-QLIP 57
Query: 64 NHTLRRLIQSWCTLNA 79
N ++ +I ++ + N
Sbjct: 58 NLAMKEVIDAFISENG 73
>pdb|2F42|A Chain A, Dimerization And U-Box Domains Of Zebrafish C-Terminal Of
Hsp70 Interacting Protein
Length = 179
Score = 46.2 bits (108), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 43/75 (57%), Gaps = 2/75 (2%)
Query: 5 DVPTFFLCPISLAIMKDPVTVPTGITYDRESIEKWLFAGKNNTCPMTKQVLSSECELTPN 64
++P + IS +M++P P+GITYDR+ IE+ L + P+T+ L+ + +L PN
Sbjct: 102 EIPDYLCGKISFELMREPCITPSGITYDRKDIEEHL-QRVGHFDPVTRSPLTQD-QLIPN 159
Query: 65 HTLRRLIQSWCTLNA 79
++ +I ++ N
Sbjct: 160 LAMKEVIDAFIQENG 174
>pdb|2QIZ|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 42/72 (58%), Gaps = 4/72 (5%)
Query: 1 MEEIDVPTFFLCPISLAIMKDPVTVP-TGITYDRESIEKWLFAGKNNTCPMTKQVLSSEC 59
+E DVP FL P+ IMKDPV +P + + DR +I+ L + ++T P + L E
Sbjct: 897 LEYGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLS--DSTDPFNRMPLKLE- 953
Query: 60 ELTPNHTLRRLI 71
++TPN LR+ I
Sbjct: 954 DVTPNEELRQKI 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 = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 42/72 (58%), Gaps = 4/72 (5%)
Query: 1 MEEIDVPTFFLCPISLAIMKDPVTVP-TGITYDRESIEKWLFAGKNNTCPMTKQVLSSEC 59
+E DVP FL P+ IMKDPV +P + + DR +I+ L + ++T P + L E
Sbjct: 883 LEYGDVPDEFLDPLMYTIMKDPVILPASKMNIDRSTIKAHLLS--DSTDPFNRMPLKLE- 939
Query: 60 ELTPNHTLRRLI 71
++TPN LR+ I
Sbjct: 940 DVTPNEELRQKI 951
>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 = 43.1 bits (100), Expect = 3e-04, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 5 DVPTFFLCPISLAIMKDPVTVPTGITYDRESIEKWLFAGKNNTCPMTKQVLSSECELTPN 64
++P + IS +M +P P+GITYDR+ IE+ L + P+T+ L+ + +L PN
Sbjct: 9 EIPDYLCGKISFELMAEPCITPSGITYDRKDIEEHL-QRVGHFDPVTRSPLTQD-QLIPN 66
Query: 65 HTLRRLIQSWCTLN 78
++ +I ++ N
Sbjct: 67 LAMKEVIDAFIQEN 80
>pdb|2QJ0|A Chain A, Structure Of The Yeast U-Box-Containing Ubiquitin Ligase
Ufd2p
Length = 982
Score = 42.0 bits (97), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 40/72 (55%), Gaps = 4/72 (5%)
Query: 1 MEEIDVPTFFLCPISLAIMKDPVTVP-TGITYDRESIEKWLFAGKNNTCPMTKQVLSSEC 59
+E DVP FL P+ I KDPV +P + DR +I+ L + ++T P + L E
Sbjct: 897 LEYGDVPDEFLDPLXYTIXKDPVILPASKXNIDRSTIKAHLLS--DSTDPFNRXPLKLE- 953
Query: 60 ELTPNHTLRRLI 71
++TPN LR+ I
Sbjct: 954 DVTPNEELRQKI 965
>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 = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 5 DVPTFFLCPISLAIMKDPVTVPTGITYDRESIEKWLFAGKNNTCPMTKQVLSSECELTPN 64
D P F P+ +M DPV +P+G DR I + L T P +Q L +E L P
Sbjct: 25 DAPDEFRDPLMDTLMTDPVRLPSGTIMDRSIILRHLLNSP--TDPFNRQTL-TESMLEPV 81
Query: 65 HTLRRLIQSW 74
L+ IQ+W
Sbjct: 82 PELKEQIQAW 91
>pdb|2KR4|A Chain A, U-Box Domain Of The E3 Ubiquitin Ligase E4b
Length = 85
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 5 DVPTFFLCPISLAIMKDPVTVPTGITYDRESIEKWLFAGKNNTCPMTKQVLSSECELTPN 64
D P F P+ +M DPV +P+G DR I + L + T P +Q+L +E L P
Sbjct: 10 DAPDEFRDPLMDTLMTDPVRLPSGTVMDRSIILRHLL--NSPTDPFNRQML-TESMLEPV 66
Query: 65 HTLRRLIQSW 74
L+ IQ+W
Sbjct: 67 PELKEQIQAW 76
>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 = 28.5 bits (62), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 3 EIDVP--TFFLCPISLAIMKDPVTVPTGITYDRESIEKWLFAGKNNTCPMTKQVLSSECE 60
E D P + + CPI L +++ V P G + + I K + + CP+ ++L +
Sbjct: 10 EFDPPLESKYECPICLMALREAVQTPCGHRFCKACIIKSI-RDAGHKCPVDNEILLEN-Q 67
Query: 61 LTPNHTLRRLIQS 73
L P++ +R I S
Sbjct: 68 LFPDNFAKREILS 80
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 0.131 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,890,361
Number of Sequences: 62578
Number of extensions: 334509
Number of successful extensions: 831
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 821
Number of HSP's gapped (non-prelim): 12
length of query: 416
length of database: 14,973,337
effective HSP length: 101
effective length of query: 315
effective length of database: 8,652,959
effective search space: 2725682085
effective search space used: 2725682085
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)