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= 018850
(349 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1E4U|A Chain A, N-Terminal Ring Finger Domain Of Human Not-4
Length = 78
Score = 62.8 bits (151), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 28/62 (45%), Positives = 38/62 (61%), Gaps = 1/62 (1%)
Query: 271 PSSCPICYEDLDYTDSSFLPCLCGFRLCLFCHKRI-LEEDGRCPGCRKPYEHDQVESEAI 329
P CP+C E L+ D +F PC CG+++C FC RI +E+G CP CRKPY D + +
Sbjct: 11 PVECPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPEDPAVYKPL 70
Query: 330 VQ 331
Q
Sbjct: 71 SQ 72
>pdb|1UR6|B Chain B, Nmr Based Structural Model Of The Ubch5b-Cnot4 Complex
Length = 52
Score = 61.2 bits (147), Expect = 8e-10, Method: Composition-based stats.
Identities = 26/50 (52%), Positives = 34/50 (68%), Gaps = 1/50 (2%)
Query: 274 CPICYEDLDYTDSSFLPCLCGFRLCLFCHKRI-LEEDGRCPGCRKPYEHD 322
CP+C E L+ D +F PC CG+++C FC RI +E+G CP CRKPY D
Sbjct: 3 CPLCMEPLEIDDINFFPCTCGYQICRFCWHRIRTDENGLCPACRKPYPED 52
>pdb|1CHC|A Chain A, Structure Of The C3hc4 Domain By 1h-Nuclear Magnetic
Resonance Spectroscopy; A New Structural Class Of Zinc-
Finger
Length = 68
Score = 35.8 bits (81), Expect = 0.040, Method: Composition-based stats.
Identities = 20/47 (42%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 274 CPICYEDLDYTDSSFLPCLCGFRLCLFCHKRILEEDGRCPGCRKPYE 320
CPIC ED S LPCL F C C R + ++ CP C+ P E
Sbjct: 8 CPICLEDPS-NYSMALPCLHAF--CYVCITRWIRQNPTCPLCKVPVE 51
>pdb|2ECM|A Chain A, Solution Structure Of The Ring Domain Of The Ring Finger
And Chy Zinc Finger Domain-Containing Protein 1 From Mus
Musculus
Length = 55
Score = 33.1 bits (74), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 27/49 (55%), Gaps = 4/49 (8%)
Query: 272 SSCPICYEDLDYTD--SSFLPCLCGFRLCLFCHKRILEEDGRCPGCRKP 318
S CPIC ED+ + + LPC G L C++ +L+E RCP C P
Sbjct: 6 SGCPICLEDIHTSRVVAHVLPC--GHLLHRTCYEEMLKEGYRCPLCSGP 52
>pdb|2JRJ|A Chain A, Solution Structure Of The Human Pirh2 Ring-H2 Domain.
Northeast Structural Genomics Consortium Target Ht2b
Length = 52
Score = 32.3 bits (72), Expect = 0.38, Method: Composition-based stats.
Identities = 16/43 (37%), Positives = 23/43 (53%)
Query: 273 SCPICYEDLDYTDSSFLPCLCGFRLCLFCHKRILEEDGRCPGC 315
+CPIC ED+ + CG L C++ +L+E RCP C
Sbjct: 7 NCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLC 49
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 32.0 bits (71), Expect = 0.50, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 273 SCPIC---YEDLDYTDSSFLPCLCGFRLCLFCHKRILEEDGRCPGCRKPYEHDQ 323
SCPIC Y ++ + CG C C + L+ CP CRK H +
Sbjct: 5 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR 58
>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 = 0.55, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 273 SCPIC---YEDLDYTDSSFLPCLCGFRLCLFCHKRILEEDGRCPGCRKPYEHDQ 323
SCPIC Y ++ + CG C C + L+ CP CRK H +
Sbjct: 12 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR 65
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 28.5 bits (62), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 22/52 (42%), Gaps = 3/52 (5%)
Query: 273 SCPIC---YEDLDYTDSSFLPCLCGFRLCLFCHKRILEEDGRCPGCRKPYEH 321
SCPIC Y ++ + CG C C + L+ CP CRK H
Sbjct: 17 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH 68
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 28.5 bits (62), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 25/63 (39%), Gaps = 3/63 (4%)
Query: 273 SCPIC---YEDLDYTDSSFLPCLCGFRLCLFCHKRILEEDGRCPGCRKPYEHDQVESEAI 329
SCPIC Y ++ + CG C C + L+ CP CRK H + I
Sbjct: 9 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI 68
Query: 330 VQG 332
G
Sbjct: 69 GSG 71
Score = 27.7 bits (60), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 3/60 (5%)
Query: 273 SCPIC---YEDLDYTDSSFLPCLCGFRLCLFCHKRILEEDGRCPGCRKPYEHDQVESEAI 329
SCPIC Y ++ + CG C C + L+ CP CRK H + I
Sbjct: 74 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI 133
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
0.314 0.130 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,370,042
Number of Sequences: 62578
Number of extensions: 348513
Number of successful extensions: 457
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 446
Number of HSP's gapped (non-prelim): 14
length of query: 349
length of database: 14,973,337
effective HSP length: 100
effective length of query: 249
effective length of database: 8,715,537
effective search space: 2170168713
effective search space used: 2170168713
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 bits)