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= 041895
(206 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 36.2 bits (82), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 28/46 (60%), Gaps = 5/46 (10%)
Query: 137 CAICLKKFENIDNEATSLNCPCQFLYHHECIWRWLRELRNYSCPVC 182
CA+CL+ F+ D CPC+ +H +C+ +WL E+R CP+C
Sbjct: 18 CAVCLEDFKPRDELGI---CPCKHAFHRKCLIKWL-EVRKV-CPLC 58
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 35.0 bits (79), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 157 PCQFLYHHECIWRWLRELRNYSCPVCRKNFA 187
PC L+H CI WL + + SCPVCRK+
Sbjct: 35 PCNHLFHDSCIVPWLEQ--HDSCPVCRKSLT 63
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 35.0 bits (79), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 137 CAICLKKFENIDNEATSLNCPCQFLYHHECIWRWLRELRNYSCPVCRKNFAHGTEHFARS 196
C IC + F EA +LNC F + CI W++ R CP+CRK+ T
Sbjct: 56 CIICSEYF----IEAVTLNCAHSFCSY--CINEWMK--RKIECPICRKDIKSKTYSLVLD 107
Query: 197 PCRRRKLRN 205
C + + N
Sbjct: 108 NCINKMVNN 116
>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 = 34.7 bits (78), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 31/69 (44%), Gaps = 8/69 (11%)
Query: 137 CAICLKKFENIDNEATSLNCPCQFLYHHECIWRWLRELRNYSCPVCRKNFAHGTEHFARS 196
C IC + F EA +LNC F + CI W++ R CP+CRK+ T
Sbjct: 67 CIICSEYF----IEAVTLNCAHSFCSY--CINEWMK--RKIECPICRKDIKSKTYSLVLD 118
Query: 197 PCRRRKLRN 205
C + + N
Sbjct: 119 NCINKMVNN 127
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 34.3 bits (77), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 8/54 (14%)
Query: 137 CAICLKKFENIDNEATSLNCPCQFLYHHECIWRWLRELRNYSCPVCRKNFAHGT 190
C IC + F EA +LNC F + CI W++ R CP+CRK+ T
Sbjct: 56 CIICSEYF----IEAVTLNCAHSFCSY--CINEWMK--RKIECPICRKDIKSKT 101
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 33.1 bits (74), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 5/50 (10%)
Query: 137 CAICLKKFENIDNEATSLNCPCQFLYHHECIWRWLRELRNYSCPVCRKNF 186
C ICL E ++ PC L+H C+ +WL + N CP+CR +
Sbjct: 17 CTICLSILEEGEDVRRL---PCMHLFHQVCVDQWL--ITNKKCPICRVDI 61
>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 = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 27/50 (54%), Gaps = 5/50 (10%)
Query: 137 CAICLKKFENIDNEATSLNCPCQFLYHHECIWRWLRELRNYSCPVCRKNF 186
C IC ++ D AT L PC +H C+ WL+ ++ +CPVCR F
Sbjct: 43 CPICCSEYVKGDV-ATEL--PCHHYFHKPCVSIWLQ--KSGTCPVCRCMF 87
>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 = 31.2 bits (69), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 10/58 (17%)
Query: 137 CAICLKKFENIDNEATSLNCPCQFLYHHECIWRWLRELRNYSCPVCR---KNFAHGTE 191
C ICL+ N S+ PC + + CI RW+R+ N +CP+C+ ++ H E
Sbjct: 8 CPICLEDPSNY-----SMALPCLHAFCYVCITRWIRQ--NPTCPLCKVPVESVVHTIE 58
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 30.8 bits (68), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 157 PCQFLYHHECIWRWLRELRNYSCPVCRKN 185
PC +H +C+ +WL+ N +CP+CR +
Sbjct: 43 PCNHEFHAKCVDKWLKA--NRTCPICRAD 69
>pdb|3HLZ|A Chain A, Crystal Structure Of Bt_1490 (Np_810393.1) From
Bacteroides Thetaiotaomicron Vpi-5482 At 1.50 A
Resolution
pdb|3HLZ|B Chain B, Crystal Structure Of Bt_1490 (Np_810393.1) From
Bacteroides Thetaiotaomicron Vpi-5482 At 1.50 A
Resolution
Length = 269
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 11/49 (22%), Positives = 28/49 (57%)
Query: 61 DLERDKGNYSFFKTEPVPYKLQLQMFKDISNFAKDALANAIAKNDSSTI 109
+ E +G++ F+ + ++ FK +++ KDA+ + +NDS+++
Sbjct: 24 EFEDGEGSFLFYNPDVWTGNFRISAFKGNASYGKDAIRQELKENDSASL 72
>pdb|3IZ3|B Chain B, Cryoem Structure Of Cytoplasmic Polyhedrosis Virus
pdb|3IZ3|C Chain C, Cryoem Structure Of Cytoplasmic Polyhedrosis Virus
pdb|3J17|B Chain B, Structure Of A Transcribing Cypovirus By Cryo-Electron
Microscopy
pdb|3J17|C Chain C, Structure Of A Transcribing Cypovirus By Cryo-Electron
Microscopy
Length = 1333
Score = 27.3 bits (59), Expect = 6.0, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 38 GILEPDLPNPSDHLAHCLMLSLFDLERDKG 67
G L P+L DH+ CLML+ + R +G
Sbjct: 395 GALRPELAFDHDHIIRCLMLAAANYPRLEG 424
>pdb|3CNF|A Chain A, 3.88 Angstrom Structure Of Cytoplasmic Polyhedrosis Virus
By Cryo-Electron Microscopy
pdb|3CNF|B Chain B, 3.88 Angstrom Structure Of Cytoplasmic Polyhedrosis Virus
By Cryo-Electron Microscopy
pdb|3IZX|B Chain B, 3.1 Angstrom Cryoem Structure Of Cytoplasmic Polyhedrosis
Virus
pdb|3IZX|C Chain C, 3.1 Angstrom Cryoem Structure Of Cytoplasmic Polyhedrosis
Virus
Length = 1333
Score = 27.3 bits (59), Expect = 6.0, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 17/30 (56%)
Query: 38 GILEPDLPNPSDHLAHCLMLSLFDLERDKG 67
G L P+L DH+ CLML+ + R +G
Sbjct: 395 GALRPELAFDHDHIIRCLMLAAANYPRLEG 424
>pdb|2YUR|A Chain A, Solution Structure Of The Ring Finger Of Human
Retinoblastoma-Binding Protein 6
Length = 74
Score = 27.3 bits (59), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 137 CAICLKKFENIDNEATSLNCPCQFLYHHECIWRWLRELRNYSCPVCRKN 185
C IC ++I +A + C C Y ECI L E ++CP C +N
Sbjct: 18 CLIC----KDIMTDAVVIPC-CGNSYCDECIRTALLESDEHTCPTCHQN 61
>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 = 26.9 bits (58), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 24/49 (48%), Gaps = 5/49 (10%)
Query: 137 CAICLKKFENIDNEATSLNCPCQFLYHHECIWRWLRELRNYSCPVCRKN 185
C IC ++I +A + C C Y ECI L E ++CP C +N
Sbjct: 16 CLIC----KDIMTDAVVIPC-CGNSYCDECIRTALLESDEHTCPTCHQN 59
>pdb|1I0E|A Chain A, Crystal Structure Of Creatine Kinase From Human Muscle
pdb|1I0E|B Chain B, Crystal Structure Of Creatine Kinase From Human Muscle
pdb|1I0E|C Chain C, Crystal Structure Of Creatine Kinase From Human Muscle
pdb|1I0E|D Chain D, Crystal Structure Of Creatine Kinase From Human Muscle
Length = 381
Score = 26.9 bits (58), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 42 PDLPNPSDHLAHCLMLSLFDLERDKGNYSFFKTEPV 77
PDL ++H+A L L L+ RDK S F + V
Sbjct: 21 PDLSKHNNHMAKVLTLELYKKLRDKETPSGFTVDDV 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
0.326 0.139 0.450
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,891,959
Number of Sequences: 62578
Number of extensions: 211260
Number of successful extensions: 595
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 586
Number of HSP's gapped (non-prelim): 26
length of query: 206
length of database: 14,973,337
effective HSP length: 94
effective length of query: 112
effective length of database: 9,091,005
effective search space: 1018192560
effective search space used: 1018192560
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 bits)