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= 025685
(249 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 45.4 bits (106), Expect = 3e-05, Method: Composition-based stats.
Identities = 23/48 (47%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 46 CAICLDKTVLQETALVKGCEHAYCATCILRWASYVRNPTCPQCKHPFE 93
C ICL+ AL C HA+C CI RW +NPTCP CK P E
Sbjct: 8 CPICLEDPSNYSMAL--PCLHAFCYVCITRWIR--QNPTCPLCKVPVE 51
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 45 VCAICLDKTVLQETALVKGCEHAYCATCILRWASYVRNPTCPQCK 89
+C ICLD +L+ T K C H +CA CI+ A N CP C+
Sbjct: 56 MCPICLD--MLKNTMTTKECLHRFCADCII-TALRSGNKECPTCR 97
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 35.4 bits (80), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 45 VCAICLDKTVLQETALVKGCEHAYCATCILRWASYVRNPTCPQCK 89
+C ICLD +L+ T K C H +CA CI+ A N CP C+
Sbjct: 55 MCPICLD--MLKNTMTTKECLHRFCADCIIT-ALRSGNKECPTCR 96
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 34.7 bits (78), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 25/45 (55%), Gaps = 3/45 (6%)
Query: 45 VCAICLDKTVLQETALVKGCEHAYCATCILRWASYVRNPTCPQCK 89
+C ICLD +L+ T K C H +CA CI+ A N CP C+
Sbjct: 36 MCPICLD--MLKNTMTTKECLHRFCADCIIT-ALRSGNKECPTCR 77
>pdb|1JM7|B Chain B, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 117
Score = 34.3 bits (77), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 53 TVLQETALVKGCEHAYCATCILRWASYVRNPTCPQCKHP--FEFLHVHRSLDGSI 105
+L+E + GCEH +C+ C+ S CP C P + L ++R LD I
Sbjct: 30 NILREPVCLGGCEHIFCSNCV----SDCIGTGCPVCYTPAWIQDLKINRQLDSMI 80
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 23/44 (52%), Gaps = 6/44 (13%)
Query: 46 CAICLDKTVLQETALVKGCEHAYCATCILRWASYVRNPTCPQCK 89
C IC+D L+ C H++C CI +W+ RN CP C+
Sbjct: 18 CCICMDG----RADLILPCAHSFCQKCIDKWSDRHRN--CPICR 55
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 28/46 (60%), Gaps = 4/46 (8%)
Query: 46 CAICLDKTVLQETALVKGCEHAYCATCILRWASYVRNPT-CPQCKH 90
C ICL+ +++E K C+H +C C+L+ + + P+ CP CK+
Sbjct: 24 CPICLE--LIKEPVSTK-CDHIFCKFCMLKLLNQKKGPSQCPLCKN 66
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 31.6 bits (70), Expect = 0.39, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 45 VCAICLDKTVLQETALVKGCEHAYCATCILRWASYVRNPTCPQC 88
+C+IC K L + + C H +C +CI+R Y CP+C
Sbjct: 17 LCSIC--KGYLIDATTITECLHTFCKSCIVRHFYYSNR--CPKC 56
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 31.6 bits (70), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 5/61 (8%)
Query: 46 CAICLDKTVLQETALVKGCEHAYCATCILRWASYVRNPTCPQCKHPFEFLHVHRSLDGSI 105
C IC + + A+ C H++C+ CI W R CP C+ + LD I
Sbjct: 56 CIICSEYFI---EAVTLNCAHSFCSYCINEWMK--RKIECPICRKDIKSKTYSLVLDNXI 110
Query: 106 S 106
+
Sbjct: 111 N 111
>pdb|3LRQ|A Chain A, Crystal Structure Of The U-Box Domain Of Human
Ubiquitin- Protein Ligase (E3), Northeast Structural
Genomics Consortium Target Hr4604d.
pdb|3LRQ|B Chain B, Crystal Structure Of The U-Box Domain Of Human
Ubiquitin- Protein Ligase (E3), Northeast Structural
Genomics Consortium Target Hr4604d.
pdb|3LRQ|C Chain C, Crystal Structure Of The U-Box Domain Of Human
Ubiquitin- Protein Ligase (E3), Northeast Structural
Genomics Consortium Target Hr4604d.
pdb|3LRQ|D Chain D, Crystal Structure Of The U-Box Domain Of Human
Ubiquitin- Protein Ligase (E3), Northeast Structural
Genomics Consortium Target Hr4604d
Length = 100
Score = 30.8 bits (68), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 3/49 (6%)
Query: 46 CAICLDKTVLQETALVKGCEHAYCATCILRWASYVRNPTCPQCKHPFEF 94
C IC +K L++ L C C +CI RW + R CP C+ P +
Sbjct: 25 CFICXEK--LRDARLCPHCSKLCCFSCIRRWLTEQR-AQCPHCRAPLQL 70
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 30.8 bits (68), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 5/61 (8%)
Query: 46 CAICLDKTVLQETALVKGCEHAYCATCILRWASYVRNPTCPQCKHPFEFLHVHRSLDGSI 105
C IC + + A+ C H++C+ CI W R CP C+ + LD I
Sbjct: 56 CIICSEYFI---EAVTLNCAHSFCSYCINEWMK--RKIECPICRKDIKSKTYSLVLDNCI 110
Query: 106 S 106
+
Sbjct: 111 N 111
>pdb|4EPO|C Chain C, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|G Chain G, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|H Chain H, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|K Chain K, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
pdb|4EPO|L Chain L, Crystal Structure Of Rnf8 Bound To The Ubc13MMS2
HETERODIMER
Length = 149
Score = 30.4 bits (67), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 26/61 (42%), Gaps = 5/61 (8%)
Query: 46 CAICLDKTVLQETALVKGCEHAYCATCILRWASYVRNPTCPQCKHPFEFLHVHRSLDGSI 105
C IC + + A+ C H++C+ CI W R CP C+ + LD I
Sbjct: 67 CIICSEYFI---EAVTLNCAHSFCSYCINEWMK--RKIECPICRKDIKSKTYSLVLDNCI 121
Query: 106 S 106
+
Sbjct: 122 N 122
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 30.4 bits (67), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 25/47 (53%), Gaps = 2/47 (4%)
Query: 45 VCAICLDKTVLQETALVKGCEHAYCATCILRWASYVRNPTCPQCKHP 91
+CA+CL+ ++ + C+HA+ C+++W + CP C P
Sbjct: 17 LCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRK--VCPLCNMP 61
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 4/44 (9%)
Query: 46 CAICLDKTVLQETALVKGCEHAYCATCILRWASYV-RNPTCPQC 88
C++CL+ L+E +++ C H +C CI RW + R+ CP C
Sbjct: 18 CSVCLE--YLKEPVIIE-CGHNFCKACITRWWEDLERDFPCPVC 58
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 7/60 (11%)
Query: 46 CAICLDKTVLQETALVKGCEHAYCATCILRWASYVRNP----TCPQCKHPFEFLHVHRSL 101
C ICL+ L + + C H++C CI RN CP C+ P+ F ++ +L
Sbjct: 22 CPICLE---LLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLKPNL 78
>pdb|2Y43|A Chain A, Rad18 Ubiquitin Ligase Ring Domain Structure
pdb|2Y43|B Chain B, Rad18 Ubiquitin Ligase Ring Domain Structure
Length = 99
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 21/41 (51%), Gaps = 3/41 (7%)
Query: 46 CAICLDKTVLQETALVKGCEHAYCATCILRWASY-VRNPTC 85
C IC + ++ C H YC+ CI ++ SY + PTC
Sbjct: 25 CGICFE--YFNIAMIIPQCSHNYCSLCIRKFLSYKTQCPTC 63
>pdb|1RMD|A Chain A, Rag1 Dimerization Domain
Length = 116
Score = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 63 GCEHAYCATCILRWASYVRNPTCPQCKHP 91
C+H +C CILR V CP C++P
Sbjct: 40 SCKHLFCRICILRCLK-VMGSYCPSCRYP 67
>pdb|2YUR|A Chain A, Solution Structure Of The Ring Finger Of Human
Retinoblastoma-Binding Protein 6
Length = 74
Score = 28.1 bits (61), Expect = 5.4, Method: Composition-based stats.
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 45 VCAICLDKTVLQETALVKGCEHAYCATCILRWASYVRNPTCPQC 88
+C IC K ++ + ++ C ++YC CI TCP C
Sbjct: 17 LCLIC--KDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTC 58
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 26.9 bits (58), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 45 VCAICLDKTVLQETALVKGCEHAYCATCILRWASYVRNPTCPQCK 89
+C +C+ ++ V C H + A C+ +W R TCP C+
Sbjct: 25 LCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANR--TCPICR 67
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
0.320 0.133 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,066,700
Number of Sequences: 62578
Number of extensions: 200216
Number of successful extensions: 466
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 462
Number of HSP's gapped (non-prelim): 25
length of query: 249
length of database: 14,973,337
effective HSP length: 96
effective length of query: 153
effective length of database: 8,965,849
effective search space: 1371774897
effective search space used: 1371774897
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)