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= 016792
(382 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 40.4 bits (93), Expect = 0.002, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 319 FHSIFVCPVSKEQTSDDN-PPMIMSCGHVLCRQSINKMSKNHSRTFKCPYC 368
+ CP+ E +++ P ++ CGH +CRQ + K+ + +CP+C
Sbjct: 12 LREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPFC 62
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 34.7 bits (78), Expect = 0.080, Method: Composition-based stats.
Identities = 12/31 (38%), Positives = 18/31 (58%)
Query: 338 PMIMSCGHVLCRQSINKMSKNHSRTFKCPYC 368
P+I+ CGH C+ I + ++ R F CP C
Sbjct: 28 PVIIECGHNFCKACITRWWEDLERDFPCPVC 58
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 33.5 bits (75), Expect = 0.22, Method: Composition-based stats.
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 324 VCPVSKEQTSDDNPPMIMSCGHVLCRQSINKMSKNHSRTFKCPYCPSDI 372
+CP+ + P+ + CGH C + I ++ + FKCP C + +
Sbjct: 22 ICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSV 67
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 32.3 bits (72), Expect = 0.45, Method: Composition-based stats.
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 324 VCPVSKEQTSDDNPPMIMSCGHVLCRQSINKMSKNHSRTFKCPYC 368
+CP+ + P+ + CGH C + I ++ + FKCP C
Sbjct: 22 ICPICLDILQK---PVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63
>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 = 0.62, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 325 CPVSKEQTSD--DNPPMIMS--CGHVLCRQSINKMSKNHSRTFKCPYCPSDIDAAQCRQL 380
CP+ + S+ N +I+S CGHV C Q + KN + CP C I+ + +
Sbjct: 13 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN---TCPTCRKKINHKRYHPI 69
Query: 381 Y 381
Y
Sbjct: 70 Y 70
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 31.2 bits (69), Expect = 0.95, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 325 CPVSKEQTSD--DNPPMIMS--CGHVLCRQSINKMSKNHSRTFKCPYCPSDIDAAQCRQL 380
CP+ + S+ N +I+S CGHV C Q + KN + CP C I+ + +
Sbjct: 6 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN---TCPTCRKKINHKRYHPI 62
Query: 381 Y 381
Y
Sbjct: 63 Y 63
>pdb|2YU4|A Chain A, Solution Structure Of The Sp-Ring Domain In Non-Smc
Element 2 Homolog (Mms21, S. Cerevisiae)
Length = 94
Score = 31.2 bits (69), Expect = 1.0, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 2/49 (4%)
Query: 321 SIFVCPVSKEQTSDDNPPMIMSCGHVLCRQSINKMSKNHSRTFKCPYCP 369
S F CP++KE+ P CGH +I +M ++ + K YCP
Sbjct: 6 SGFTCPITKEEMK--KPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCP 52
>pdb|2HXR|A Chain A, Structure Of The Ligand Binding Domain Of E. Coli Cynr, A
Transcriptional Regulator Controlling Cyanate Metabolism
pdb|2HXR|B Chain B, Structure Of The Ligand Binding Domain Of E. Coli Cynr, A
Transcriptional Regulator Controlling Cyanate Metabolism
pdb|3HFU|A Chain A, Crystal Structure Of The Ligand Binding Domain Of E. Coli
Cynr With Its Specific Effector Azide
pdb|3HFU|B Chain B, Crystal Structure Of The Ligand Binding Domain Of E. Coli
Cynr With Its Specific Effector Azide
pdb|3HFU|C Chain C, Crystal Structure Of The Ligand Binding Domain Of E. Coli
Cynr With Its Specific Effector Azide
pdb|3HFU|D Chain D, Crystal Structure Of The Ligand Binding Domain Of E. Coli
Cynr With Its Specific Effector Azide
Length = 238
Score = 30.4 bits (67), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 35/69 (50%), Gaps = 12/69 (17%)
Query: 241 YPQLVSQTNWVTVAEELTRQFCNLVGQSYESPLSVTIAA---GVQAL---PPLLKFMTVM 294
+PQ+V + N ++ EL R+ S + L IA G++A+ PPLL+ V+
Sbjct: 153 HPQVVIEANSISAVLELIRR------TSLSTLLPAAIATQHDGLKAISLAPPLLERTAVL 206
Query: 295 AGKKQEWQS 303
+K WQ+
Sbjct: 207 LRRKNSWQT 215
>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 = 14/54 (25%), Positives = 23/54 (42%), Gaps = 3/54 (5%)
Query: 319 FHSIFVCPVSKEQTSDDNPPMIMSCGHVLCRQSINKMSKNHSRTFKCPYCPSDI 372
I CP+ E + P+ C H+ C+ + K+ +CP C +DI
Sbjct: 18 MQKILECPICLELIKE---PVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 68
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 29.6 bits (65), Expect = 3.1, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 7/53 (13%)
Query: 325 CPVSKEQTSD--DNPPMIMS--CGHVLCRQSINKMSKNHSRTFKCPYCPSDID 373
CP+ + S+ N +I+S CGHV C Q + KN + CP C I+
Sbjct: 18 CPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN---TCPTCRKKIN 67
>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human
Tripartite Motif Protein 34
Length = 79
Score = 29.6 bits (65), Expect = 3.1, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 7/48 (14%)
Query: 325 CPVSKEQTSDDNPPMIMSCGHVLCRQSINKMSKNHSRTF----KCPYC 368
CP+ E ++ P+ + CGH LCR I +K + CP C
Sbjct: 15 CPICLELLTE---PLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVC 59
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 29.3 bits (64), Expect = 3.4, Method: Composition-based stats.
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 3/35 (8%)
Query: 334 DDNPPMIMSCGHVLCRQSINKMSKNHSRTFKCPYC 368
D +I+ C H C++ I+K S H CP C
Sbjct: 23 DGRADLILPCAHSFCQKCIDKWSDRHR---NCPIC 54
>pdb|3E0J|B Chain B, X-Ray Structure Of The Complex Of Regulatory Subunits Of
Human Dna Polymerase Delta
pdb|3E0J|D Chain D, X-Ray Structure Of The Complex Of Regulatory Subunits Of
Human Dna Polymerase Delta
pdb|3E0J|F Chain F, X-Ray Structure Of The Complex Of Regulatory Subunits Of
Human Dna Polymerase Delta
pdb|3E0J|H Chain H, X-Ray Structure Of The Complex Of Regulatory Subunits Of
Human Dna Polymerase Delta
Length = 144
Score = 28.9 bits (63), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 34/78 (43%), Gaps = 11/78 (14%)
Query: 150 MYQILEAMKSGNLEPALKWAAANSDKLTQNGSDLQLKLHSLQFVEILRKGSREEALKYAR 209
+Y +E + N L S L QNG HS V ++R E+ L+ +
Sbjct: 41 LYDYVERKRKENSGAQLHVTYLVSGSLIQNG-------HSCHKVAVVR----EDKLEAVK 89
Query: 210 ANLAPFASNHVNEIQKLM 227
+ LA AS HV IQK M
Sbjct: 90 SKLAVTASIHVYSIQKAM 107
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 28.5 bits (62), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 35/75 (46%), Gaps = 13/75 (17%)
Query: 318 QFHSIFV------CPVSKEQTSD--DNPPMIMS--CGHVLCRQSINKMSKNHSRTFKCPY 367
++H I++ CP+ + S+ N +I+S CGHV C Q + KN + CP
Sbjct: 62 RYHPIYIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNAN---TCPT 118
Query: 368 CPSDIDAAQCRQLYF 382
C I+ + +Y
Sbjct: 119 CRKKINHKRYHPIYI 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
0.318 0.131 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,387,949
Number of Sequences: 62578
Number of extensions: 391209
Number of successful extensions: 1195
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 1189
Number of HSP's gapped (non-prelim): 27
length of query: 382
length of database: 14,973,337
effective HSP length: 101
effective length of query: 281
effective length of database: 8,652,959
effective search space: 2431481479
effective search space used: 2431481479
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: 52 (24.6 bits)