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= 001413
(1082 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WEO|A Chain A, Solution Structure Of Ring-Finger In The Catalytic
Subunit (Irx3) Of Cellulose Synthase
Length = 93
Score = 106 bits (265), Expect = 7e-23, Method: Compositional matrix adjust.
Identities = 44/69 (63%), Positives = 57/69 (82%)
Query: 13 KSIKNVGGQVCQICGDNVGKTVDGNPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTRY 72
K +KN+ GQ C+ICGD +G TV+G+ FVAC+ C FP CRPCYEYER++G Q+CPQCKTRY
Sbjct: 9 KPLKNLDGQFCEICGDQIGLTVEGDLFVACNECGFPACRPCYEYERREGTQNCPQCKTRY 68
Query: 73 KKHKGSPAI 81
K+ +GSP +
Sbjct: 69 KRLRGSPRV 77
>pdb|4HG6|A Chain A, Structure Of A Cellulose Synthase - Cellulose
Translocation Intermediate
Length = 802
Score = 48.5 bits (114), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/108 (25%), Positives = 51/108 (47%), Gaps = 6/108 (5%)
Query: 773 GWIYGSVTEDILTGFKMHARGWRSIYCMPKRPAFKGSAPINLSDRLNQVLRWALGSVEIL 832
G+ ++TED T ++H+RGW+S+Y R G P + + Q RWA G +++L
Sbjct: 334 GFAGETITEDAETALEIHSRGWKSLYI--DRAMIAGLQPETFASFIQQRGRWATGMMQML 391
Query: 833 FSRHCPIWYGYGGRLKFLERFAYVNTTIYPLTAIPLLMYCTLPAVCLL 880
++ G G +R Y+N+ + + +M+ P + L
Sbjct: 392 LLKNPLFRRGLG----IAQRLCYLNSMSFWFFPLVRMMFLVAPLIYLF 435
Score = 47.8 bits (112), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 41/128 (32%), Positives = 55/128 (42%), Gaps = 19/128 (14%)
Query: 521 LVYVSREKRPGFQHHKKAGAMNALVRVSAVLTNGPFLLNLDCDHYINNSKALREAMCFMM 580
+VY +RE+ H KAG M+A + G ++ D DH + R F+
Sbjct: 214 VVYSTRER----NEHAKAGNMSAALE----RLKGELVVVFDADHVPSRDFLARTVGYFVE 265
Query: 581 DPNLGKHVCYVQFPQRF---DGIDRN----DRYANRNTVFFDINLRGLDGIQGPVYVGTG 633
DP+L VQ P F D I RN DR N +F+ RGLD G + G+
Sbjct: 266 DPDL----FLVQTPHFFINPDPIQRNLALGDRCPPENEMFYGKIHRGLDRWGGAFFCGSA 321
Query: 634 CVFNRTAL 641
V R AL
Sbjct: 322 AVLRRRAL 329
>pdb|1UR6|B Chain B, Nmr Based Structural Model Of The Ubch5b-Cnot4 Complex
Length = 52
Score = 34.7 bits (78), Expect = 0.27, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 3/50 (6%)
Query: 23 CQICGDNVGKTVDGNPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTRY 72
C +C + + +D F C C + +CR C+ R D N CP C+ Y
Sbjct: 3 CPLCMEPL--EIDDINFFPC-TCGYQICRFCWHRIRTDENGLCPACRKPY 49
>pdb|1E4U|A Chain A, N-Terminal Ring Finger Domain Of Human Not-4
Length = 78
Score = 34.7 bits (78), Expect = 0.31, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 6/59 (10%)
Query: 23 CQICGDNVGKTVDGNPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTRYKKHKGSPAI 81
C +C + + +D F C C + +CR C+ R D N CP C+ Y + PA+
Sbjct: 14 CPLCMEPL--EIDDINFFPC-TCGYQICRFCWHRIRTDENGLCPACRKPYPE---DPAV 66
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 32.0 bits (71), Expect = 1.9, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 1/61 (1%)
Query: 19 GGQVCQICGDNVGKTVDGNPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTRYKKHKGS 78
G C IC D + V + C C C K+ N +CP C+ + +
Sbjct: 6 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINHKRYH 64
Query: 79 P 79
P
Sbjct: 65 P 65
Score = 32.0 bits (71), Expect = 1.9, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 1/61 (1%)
Query: 19 GGQVCQICGDNVGKTVDGNPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTRYKKHKGS 78
G C IC D + V + C C C K+ N +CP C+ + +
Sbjct: 71 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINHKRYH 129
Query: 79 P 79
P
Sbjct: 130 P 130
>pdb|3NG2|A Chain A, Crystal Structure Of The Rnf4 Ring Domain Dimer
pdb|3NG2|B Chain B, Crystal Structure Of The Rnf4 Ring Domain Dimer
Length = 71
Score = 32.0 bits (71), Expect = 1.9, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 22/61 (36%), Gaps = 1/61 (1%)
Query: 19 GGQVCQICGDNVGKTVDGNPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTRYKKHKGS 78
G C IC D + V + C C C K+ N +CP C+ + +
Sbjct: 9 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINHKRYH 67
Query: 79 P 79
P
Sbjct: 68 P 68
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 32.0 bits (71), Expect = 2.0, Method: Composition-based stats.
Identities = 14/57 (24%), Positives = 21/57 (36%), Gaps = 1/57 (1%)
Query: 23 CQICGDNVGKTVDGNPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTRYKKHKGSP 79
C IC D + V + C C C K+ N +CP C+ + + P
Sbjct: 6 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKKINHKRYHP 61
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 30.8 bits (68), Expect = 4.1, Method: Composition-based stats.
Identities = 14/53 (26%), Positives = 20/53 (37%), Gaps = 1/53 (1%)
Query: 19 GGQVCQICGDNVGKTVDGNPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTR 71
G C IC D + V + C C C K+ N +CP C+ +
Sbjct: 14 GTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN-TCPTCRKK 65
>pdb|2L43|A Chain A, Structural Basis For Histone Code Recognition By
Brpf2-Phd1 Finger
Length = 88
Score = 30.8 bits (68), Expect = 4.8, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 22 VCQICGDNVGKTVDGNPFVACDVCAFPVCRPCYEYER-KDGNQSCPQC 68
VC IC D G++ + N + CD+C V + CY +G C C
Sbjct: 27 VCSICMD--GESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHC 72
>pdb|2LDR|A Chain A, Solution Structure Of Helix-Ring Domain Of Cbl-B In The
Tyr363 Phosphorylated Form
Length = 82
Score = 30.4 bits (67), Expect = 5.0, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 7/53 (13%)
Query: 21 QVCQICGDNVGKTVDGNPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTRYK 73
Q+C+IC +N K V P C +C C ++ Q CP C+ K
Sbjct: 27 QLCKICAEN-DKDVKIEP------CGHLMCTSCLTAWQESDGQGCPFCRCEIK 72
>pdb|2KU3|A Chain A, Solution Structure Of Brd1 Phd1 Finger
Length = 71
Score = 30.4 bits (67), Expect = 5.2, Method: Composition-based stats.
Identities = 16/48 (33%), Positives = 23/48 (47%), Gaps = 3/48 (6%)
Query: 22 VCQICGDNVGKTVDGNPFVACDVCAFPVCRPCYEYER-KDGNQSCPQC 68
VC IC D G++ + N + CD+C V + CY +G C C
Sbjct: 18 VCSICMD--GESQNSNVILFCDMCNLAVHQECYGVPYIPEGQWLCRHC 63
>pdb|2K4D|A Chain A, E2-C-Cbl Recognition Is Necessary But Not Sufficient For
Ubiquitination Activity
Length = 83
Score = 30.0 bits (66), Expect = 6.5, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 7/53 (13%)
Query: 21 QVCQICGDNVGKTVDGNPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTRYK 73
Q+C+IC +N K V P C +C C ++ Q CP C+ K
Sbjct: 25 QLCKICAEN-DKDVKIEP------CGHLMCTSCLTSWQESEGQGCPFCRCEIK 70
>pdb|4A49|A Chain A, Structure Of Phosphotyr371-C-Cbl-Ubch5b Complex
Length = 84
Score = 30.0 bits (66), Expect = 7.7, Method: Composition-based stats.
Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 7/53 (13%)
Query: 21 QVCQICGDNVGKTVDGNPFVACDVCAFPVCRPCYEYERKDGNQSCPQCKTRYK 73
Q+C+IC +N K V P C +C C ++ Q CP C+ K
Sbjct: 28 QLCKICAEN-DKDVKIEP------CGHLMCTSCLTSWQESEGQGCPFCRCEIK 73
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 0.138 0.438
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 32,726,650
Number of Sequences: 62578
Number of extensions: 1378073
Number of successful extensions: 2811
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 2805
Number of HSP's gapped (non-prelim): 22
length of query: 1082
length of database: 14,973,337
effective HSP length: 109
effective length of query: 973
effective length of database: 8,152,335
effective search space: 7932221955
effective search space used: 7932221955
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: 57 (26.6 bits)