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= 019461
(340 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 7/51 (13%)
Query: 133 KCCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRSTVLCPHCRAVVQ 183
+C IC + + VT+ C H+FC+ C +EW++R E CP CR ++
Sbjct: 55 QCIICSEYFIEAVTL-NCAHSFCSYCINEWMKRKIE------CPICRKDIK 98
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 9/68 (13%)
Query: 116 QESSNQQLEISIDIE----HAKCCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRS 171
QE+ LEI + C ICL++ + +T CLH FC C LR ++
Sbjct: 34 QEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKE-- 91
Query: 172 TVLCPHCR 179
CP CR
Sbjct: 92 ---CPTCR 96
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 37.0 bits (84), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 7/51 (13%)
Query: 133 KCCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRSTVLCPHCRAVVQ 183
+C IC + + VT+ C H+FC+ C +EW++R E CP CR ++
Sbjct: 55 QCIICSEYFIEAVTL-NCAHSFCSYCINEWMKRKIE------CPICRKDIK 98
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 37.0 bits (84), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 5/46 (10%)
Query: 134 CCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRSTVLCPHCR 179
C ICL++ + +T CLH FC C LR ++ CP CR
Sbjct: 57 CPICLDMLKNTMTTKECLHRFCADCIITALRSGNKE-----CPTCR 97
>pdb|3L11|A Chain A, Crystal Structure Of The Ring Domain Of Rnf168
Length = 115
Score = 37.0 bits (84), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 47/92 (51%), Gaps = 15/92 (16%)
Query: 129 IEHAKCCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRSTVLCPHCRAVV----QF 184
+ +C IC+ I + VT+ PC H C CF +S +++++ CP CR V ++
Sbjct: 13 LSECQCGICMEILVEPVTL-PCNHTLCKPCF-----QSTVEKASLCCPFCRRRVSSWTRY 66
Query: 185 VGRNHYLHNIEQ-SILQAH----SSLRRSDEE 211
R + L N+E +I+Q H LR S +E
Sbjct: 67 HTRRNSLVNVELWTIIQKHYPRECKLRASGQE 98
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 37.0 bits (84), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 33/71 (46%), Gaps = 10/71 (14%)
Query: 118 SSNQQLEISIDIEHAKCCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRSTVLCPH 177
SS + + +CCIC++ D++ PC H+FC C +W R + CP
Sbjct: 2 SSGSSGRVKQLTDEEECCICMDGRADLIL--PCAHSFCQKCIDKWSDRHRN------CPI 53
Query: 178 CRAVVQFVGRN 188
CR +Q G N
Sbjct: 54 CR--LQMTGAN 62
>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 = 36.6 bits (83), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 7/51 (13%)
Query: 133 KCCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRSTVLCPHCRAVVQ 183
+C IC + + VT+ C H+FC+ C +EW++R E CP CR ++
Sbjct: 66 QCIICSEYFIEAVTL-NCAHSFCSYCINEWMKRKIE------CPICRKDIK 109
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 36.2 bits (82), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 9/68 (13%)
Query: 116 QESSNQQLEISIDIE----HAKCCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRS 171
QE+ LEI + C ICL++ + +T CLH FC C LR ++
Sbjct: 15 QEAITDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKE-- 72
Query: 172 TVLCPHCR 179
CP CR
Sbjct: 73 ---CPTCR 77
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 35.8 bits (81), Expect = 0.039, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 6/53 (11%)
Query: 131 HAKCCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRSTVLCPHCRAVVQ 183
H C +C + D T+ CLH+FC C +L S+ CP C V
Sbjct: 11 HLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSK------YCPICDVQVH 57
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 35.4 bits (80), Expect = 0.042, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 23/53 (43%), Gaps = 6/53 (11%)
Query: 131 HAKCCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRSTVLCPHCRAVVQ 183
H C +C + D T+ CLH+FC C +L S+ CP C V
Sbjct: 15 HLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSK------YCPICDVQVH 61
>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 = 35.4 bits (80), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 30/63 (47%), Gaps = 11/63 (17%)
Query: 133 KCCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRSTVLCPHCRAVVQFVGRNHYLH 192
+C ICL + PCLH FC C + W+R++ CP C+ V+ V +H
Sbjct: 7 RCPICLEDPSNYSMALPCLHAFCYVCITRWIRQNPT------CPLCKVPVESV-----VH 55
Query: 193 NIE 195
IE
Sbjct: 56 TIE 58
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 35.0 bits (79), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 22/48 (45%), Gaps = 6/48 (12%)
Query: 131 HAKCCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRSTVLCPHC 178
H C +C + D T+ CLH+FC C +L S+ CP C
Sbjct: 15 HLMCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSK------YCPIC 56
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 19/53 (35%), Gaps = 6/53 (11%)
Query: 131 HAKCCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRSTVLCPHCRAVVQ 183
+ C IC D T+ CLH FC C S CP C VV
Sbjct: 15 YILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNR------CPKCNIVVH 61
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 1/63 (1%)
Query: 130 EHAKCCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRSTVLCPHCRAVVQFVGRNH 189
E C ICL + + V+ A C H+FC C + ++ CP CR F
Sbjct: 18 EEVTCPICLELLKEPVS-ADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYPFGNLKP 76
Query: 190 YLH 192
LH
Sbjct: 77 NLH 79
>pdb|3NA7|A Chain A, 2.2 Angstrom Structure Of The Hp0958 Protein From
Helicobacter Pylori Ccug 17874
Length = 256
Score = 29.6 bits (65), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 266 NQTTVHLQCQGCGGMMPSRNDSVPQHCLGCDRA----FCGAYWHAQMVARSDSQP 316
N + V ++ Q CGG ND + L +CG +A+ S++QP
Sbjct: 190 NTSIVTIKKQACGGCFIRLNDKIYTEVLTSGDMITCPYCGRILYAEGAYESNAQP 244
>pdb|2ECV|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Tripartite Motif-Containing Protein 5
Length = 85
Score = 29.3 bits (64), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 130 EHAKCCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRSTVLCPHCRAVVQ 183
E C ICL + +++ C H+FC C + ++S + CP CR Q
Sbjct: 18 EEVTCPICLELLTQPLSLD-CGHSFCQACLTANHKKSMLDKGESSCPVCRISYQ 70
>pdb|2XOC|A Chain A, C-terminal Cysteine-rich Domain Of Human Chfr Bound To
Madpr
pdb|2XOC|B Chain B, C-terminal Cysteine-rich Domain Of Human Chfr Bound To
Madpr
pdb|2XOY|A Chain A, C-Terminal Cysteine-Rich Domain Of Human Chfr Bound To
P(1), P(2)-Diadenosine-5'-Pyrophosphate
pdb|2XOY|B Chain B, C-Terminal Cysteine-Rich Domain Of Human Chfr Bound To
P(1), P(2)-Diadenosine-5'-Pyrophosphate
pdb|2XOZ|A Chain A, C-Terminal Cysteine Rich Domain Of Human Chfr Bound To Amp
pdb|2XOZ|B Chain B, C-Terminal Cysteine Rich Domain Of Human Chfr Bound To Amp
Length = 261
Score = 28.9 bits (63), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 26/102 (25%), Positives = 34/102 (33%), Gaps = 27/102 (26%)
Query: 225 LVIRNGKKHRRKRAHSP---------------IDEESDSIELPCPQCGTEINGFHCNQTT 269
+V R ++RR+ A P D S S+ L T + + C
Sbjct: 23 VVCRQCPEYRRQAAQPPHCPAPEGEPGAPQALGDAPSTSVSL-----TTAVQDYVCPLQG 77
Query: 270 VHLQCQGCGGMMPSRN-------DSVPQHCLGCDRAFCGAYW 304
H C C MP R PQ C C + FC YW
Sbjct: 78 SHALCTCCFQPMPDRRVEREQDPRVAPQQCAVCLQPFCHLYW 119
>pdb|2L0B|A Chain A, Solution Nmr Structure Of Zinc Finger Domain Of E3
Ubiquitin-Protein Ligase Praja-1 From Homo Sapiens,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4710b
Length = 91
Score = 28.9 bits (63), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 34/74 (45%), Gaps = 14/74 (18%)
Query: 116 QESSNQQLEISIDIEHAK-----CC-ICLN--IWHDVVTVAPCLHNFCNGCFSEWLRRSQ 167
+ES + EI + +H CC IC + + DV T PC H F C S WL++S
Sbjct: 19 KESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCVSIWLQKSG 78
Query: 168 EKRSTVLCPHCRAV 181
CP CR +
Sbjct: 79 T------CPVCRCM 86
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 28.9 bits (63), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 8/53 (15%)
Query: 133 KCCICLNIWHDVVTV--APCLHNFCNGCFSEWLRRSQEKRSTVLCPHCRAVVQ 183
KC ICL+I + V PC+H F C +WL +++ CP CR ++
Sbjct: 16 KCTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKK------CPICRVDIE 62
>pdb|2XP0|A Chain A, C-Terminal Cysteine-Rich Domain Of Human Chfr
pdb|2XP0|B Chain B, C-Terminal Cysteine-Rich Domain Of Human Chfr
Length = 274
Score = 28.9 bits (63), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 26/102 (25%), Positives = 34/102 (33%), Gaps = 27/102 (26%)
Query: 225 LVIRNGKKHRRKRAHSP---------------IDEESDSIELPCPQCGTEINGFHCNQTT 269
+V R ++RR+ A P D S S+ L T + + C
Sbjct: 36 VVCRQCPEYRRQAAQPPHCPAPEGEPGAPQALGDAPSTSVSL-----TTAVQDYVCPLQG 90
Query: 270 VHLQCQGCGGMMPSRN-------DSVPQHCLGCDRAFCGAYW 304
H C C MP R PQ C C + FC YW
Sbjct: 91 SHALCTCCFQPMPDRRVEREQDPRVAPQQCAVCLQPFCHLYW 132
>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 = 7.1, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 4/45 (8%)
Query: 134 CCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRSTVLCPHC 178
C IC +I D V + C +++C+ C L S E CP C
Sbjct: 18 CLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHT----CPTC 58
>pdb|3ZTG|A Chain A, Solution Structure Of The Ring Finger-Like Domain Of
Retinoblastoma Binding Protein-6 (Rbbp6)
pdb|3ZTG|B Chain B, Solution Structure Of The Ring Finger-Like Domain Of
Retinoblastoma Binding Protein-6 (Rbbp6)
Length = 92
Score = 28.1 bits (61), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 4/45 (8%)
Query: 134 CCICLNIWHDVVTVAPCLHNFCNGCFSEWLRRSQEKRSTVLCPHC 178
C IC +I D V + C +++C+ C L S E CP C
Sbjct: 16 CLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHT----CPTC 56
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 0.132 0.418
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,833,015
Number of Sequences: 62578
Number of extensions: 380739
Number of successful extensions: 865
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 18
Number of HSP's successfully gapped in prelim test: 32
Number of HSP's that attempted gapping in prelim test: 842
Number of HSP's gapped (non-prelim): 53
length of query: 340
length of database: 14,973,337
effective HSP length: 99
effective length of query: 241
effective length of database: 8,778,115
effective search space: 2115525715
effective search space used: 2115525715
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: 52 (24.6 bits)