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= 022029
(304 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4AUQ|B Chain B, Structure Of Birc7-Ubch5b-Ub Complex.
pdb|4AUQ|E Chain E, Structure Of Birc7-Ubch5b-Ub Complex
Length = 62
Score = 31.2 bits (69), Expect = 0.69, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 5/47 (10%)
Query: 216 SCKVTLTNTLSLVALSSCGHVFCKKCADKFMAVDKVCLVCNKPCKER 262
+CKV L +S+V CGH+ C +CA ++C +C P + R
Sbjct: 15 TCKVCLDRAVSIV-FVPCGHLVCAECAPGL----QLCPICRAPVRSR 56
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 31.2 bits (69), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 13/31 (41%), Positives = 19/31 (61%)
Query: 228 VALSSCGHVFCKKCADKFMAVDKVCLVCNKP 258
+ + C H F +KC K++ V KVC +CN P
Sbjct: 31 LGICPCKHAFHRKCLIKWLEVRKVCPLCNMP 61
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 30/83 (36%), Gaps = 15/83 (18%)
Query: 178 CPEGKEKLKLKSLFPVYFTXXXXXXXXXXXXXXXFICPSCKVTLTNTLS---LVALSSCG 234
CP ++K+ K P+Y CP C + + L+ + CG
Sbjct: 51 CPTCRKKINHKRYHPIYIGSGTVS------------CPICMDGYSEIVQNGRLIVSTECG 98
Query: 235 HVFCKKCADKFMAVDKVCLVCNK 257
HVFC +C + C C K
Sbjct: 99 HVFCSQCLRDSLKNANTCPTCRK 121
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 30.8 bits (68), Expect = 1.1, Method: Composition-based stats.
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 233 CGHVFCKKCADKFMAVDKVCLVCN-KPCKERNLVNVEKGGT 272
C H FCK C +++ K C +C+ + K R L+N+ T
Sbjct: 30 CLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDKT 70
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 229 ALSSCGHVFCKKCADKFMAVDKVCLVCNKPC-KERNLVNVEKGGT 272
+ C H FCK C +++ K C +C+ K R L+N+ T
Sbjct: 30 TIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDKT 74
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 229 ALSSCGHVFCKKCADKFMAVDKVCLVCNKPC-KERNLVNVEKGGT 272
+ C H FCK C +++ K C +C+ K R L+N+ T
Sbjct: 30 TIIECLHSFCKTCIVRYLETSKYCPICDVQVHKTRPLLNIRSDKT 74
>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 = 29.3 bits (64), Expect = 2.5, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 214 CPSCKVTLTNTLS---LVALSSCGHVFCKKCADKFMAVDKVCLVCNK 257
CP C + + L+ + CGHVFC +C + C C K
Sbjct: 13 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 59
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 29.3 bits (64), Expect = 3.0, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 20/47 (42%), Gaps = 3/47 (6%)
Query: 214 CPSCKVTLTNTLS---LVALSSCGHVFCKKCADKFMAVDKVCLVCNK 257
CP C + + L+ + CGHVFC +C + C C K
Sbjct: 6 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRK 52
>pdb|1G25|A Chain A, Solution Structure Of The N-Terminal Domain Of The Human
Tfiih Mat1 Subunit
Length = 65
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 214 CPSCKVTLTNTLSL-VALSSCGHVFCKKCAD-KFMAVDKVCLVCNKPCKERNL 264
CP CK T SL + ++ CGH C+ C D F+ C C P ++ N
Sbjct: 6 CPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGAGNCPECGTPLRKSNF 58
>pdb|3ZYQ|A Chain A, Crystal Structure Of The Tandem Vhs And Fyve Domains Of
Hepatocyte Growth Factor-Regulated Tyrosine Kinase
Substrate (Hgs-Hrs) At 1.48 A Resolution
pdb|4AVX|A Chain A, Hepatocyte Growth Factor-Regulated Tyrosine Kinase
Substrate (Hgs-Hrs) Bound To An Ip2 Compound At 1.68 A
Resolution
Length = 226
Score = 28.5 bits (62), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 214 CPSCKVTLTNTLSLVALSSCGHVFCKKCADKF-----MAVDKVCLVCNKPCKER 262
C C+V +CG +FC KC+ K+ ++K VC +PC E+
Sbjct: 167 CHRCRVQFGVMTRKHHCRACGQIFCGKCSSKYSTIPKFGIEKEVRVC-EPCYEQ 219
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 28.1 bits (61), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 28/42 (66%), Gaps = 1/42 (2%)
Query: 35 DSIKPFDACCLCLKPFIDPLCCQKGHIYCKECILECLLSQKK 76
++++ C +CL+ +P+ + HI+CK C+L+ LL+QKK
Sbjct: 16 NAMQKILECPICLELIKEPVSTKCDHIFCKFCMLK-LLNQKK 56
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 28.1 bits (61), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 214 CPSCKVTLTNTLSLVALSSCGHVFCKKCADKFMA 247
CP C + T L CGH C++C +K +A
Sbjct: 18 CPICMESFTEEQLRPKLLHCGHTICRQCLEKLLA 51
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 27.7 bits (60), Expect = 7.8, Method: Composition-based stats.
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 233 CGHVFCKKCADKFMAVDKVCLVC 255
C H FC+KC DK+ + C +C
Sbjct: 32 CAHSFCQKCIDKWSDRHRNCPIC 54
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 27.7 bits (60), Expect = 7.8, Method: Composition-based stats.
Identities = 10/26 (38%), Positives = 17/26 (65%)
Query: 42 ACCLCLKPFIDPLCCQKGHIYCKECI 67
+C +CL+ +P+ + GH +CK CI
Sbjct: 17 SCSVCLEYLKEPVIIECGHNFCKACI 42
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 27.7 bits (60), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 227 LVALSSCGHVFCKKCADKFMAVDKVCLVC 255
L+ + C H F KC DK++ ++ C +C
Sbjct: 38 LLRVLPCNHEFHAKCVDKWLKANRTCPIC 66
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 0.135 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,471,648
Number of Sequences: 62578
Number of extensions: 315973
Number of successful extensions: 659
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 617
Number of HSP's gapped (non-prelim): 64
length of query: 304
length of database: 14,973,337
effective HSP length: 98
effective length of query: 206
effective length of database: 8,840,693
effective search space: 1821182758
effective search space used: 1821182758
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: 51 (24.3 bits)