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= 011171
(492 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2D8M|A Chain A, Solution Structure Of The First Brct Domain Of Dna-Repair
Protein Xrcc1
Length = 129
Score = 48.5 bits (114), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 40/84 (47%)
Query: 1 MESVVATVSGYHGTERFNLIKLISYSGASYVGTMSKSTTHLVCWKFEGEKHSLAKKFRTI 60
++ VV +SG+ R L GA Y ++ +THL+C K+S
Sbjct: 23 LQGVVVVLSGFQNPFRSELRDKALELGAKYRPDWTRDSTHLICAFANTPKYSQVLGLGGR 82
Query: 61 IVNHQWVEDCIKQHRRLPERPYML 84
IV +WV DC + RRLP + Y++
Sbjct: 83 IVRKEWVLDCHRMRRRLPSQRYLM 106
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 45.8 bits (107), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 46/98 (46%), Gaps = 9/98 (9%)
Query: 299 RDFPALLQRESQDGCSGIENSNGM-VKNTDRIEHVNRSSTSGELSCVICWTEFSSTRGVL 357
+DF A++Q ++++ E M + + + H+N EL C+IC +E+ L
Sbjct: 12 KDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMN-DVLENELQCIIC-SEYFIEAVTL 69
Query: 358 ACGHRFCYSCIQNWADHMASVRKISTCPLCKASFMSIT 395
C H FC CI W RKI CP+C+ S T
Sbjct: 70 NCAHSFCSYCINEWMK-----RKIE-CPICRKDIKSKT 101
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 46/98 (46%), Gaps = 9/98 (9%)
Query: 299 RDFPALLQRESQDGCSGIENSNGM-VKNTDRIEHVNRSSTSGELSCVICWTEFSSTRGVL 357
+DF A++Q ++++ E M + + + H+N EL C+IC +E+ L
Sbjct: 12 KDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMN-DVLENELQCIIC-SEYFIEAVTL 69
Query: 358 ACGHRFCYSCIQNWADHMASVRKISTCPLCKASFMSIT 395
C H FC CI W RKI CP+C+ S T
Sbjct: 70 NCAHSFCSYCINEWMK-----RKIE-CPICRKDIKSKT 101
>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 = 45.4 bits (106), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 46/98 (46%), Gaps = 9/98 (9%)
Query: 299 RDFPALLQRESQDGCSGIENSNGM-VKNTDRIEHVNRSSTSGELSCVICWTEFSSTRGVL 357
+DF A++Q ++++ E M + + + H+N EL C+IC +E+ L
Sbjct: 23 KDFEAIIQAKNKELEQTKEEKEKMQAQKEEVLSHMN-DVLENELQCIIC-SEYFIEAVTL 80
Query: 358 ACGHRFCYSCIQNWADHMASVRKISTCPLCKASFMSIT 395
C H FC CI W RKI CP+C+ S T
Sbjct: 81 NCAHSFCSYCINEWMK-----RKIE-CPICRKDIKSKT 112
>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 = 42.7 bits (99), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 32/67 (47%), Gaps = 8/67 (11%)
Query: 343 CVICWTEFSSTRGVLACGHRFCYSCIQNWADHMASVRKISTCPLCKASFMSI--TKVEDA 400
C IC + S+ L C H FCY CI W +R+ TCPLCK S+ T D+
Sbjct: 8 CPICLEDPSNYSMALPCLHAFCYVCITRW------IRQNPTCPLCKVPVESVVHTIESDS 61
Query: 401 ATSDQKI 407
DQ I
Sbjct: 62 EFGDQLI 68
>pdb|3EF1|A Chain A, The Structure Of Fcp1, An Essential Rna Polymerase Ii Ctd
Phosphatase
Length = 442
Score = 37.0 bits (84), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 27 GASYVGTMSKSTTHLVCWKFEGEKHSLAKKFRTI-IVNHQWVEDCIKQHRRLPERPYML 84
GA V S THL+ K EK A I +V W+ + + Q +RLPE Y+L
Sbjct: 383 GAEVVLDFSVPPTHLIAAKIRTEKVKKAVSMGNIKVVKLNWLTESLSQWKRLPESDYLL 441
>pdb|3EF0|A Chain A, The Structure Of Fcp1, An Essential Rna Polymerase Ii Ctd
Phosphatase
Length = 372
Score = 36.2 bits (82), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 27 GASYVGTMSKSTTHLVCWKFEGEKHSLAKKFRTI-IVNHQWVEDCIKQHRRLPERPYML 84
GA V S THL+ K EK A I +V W+ + + Q +RLPE Y+L
Sbjct: 313 GAEVVLDFSVPPTHLIAAKIRTEKVKKAVSMGNIKVVKLNWLTESLSQWKRLPESDYLL 371
>pdb|2XNK|A Chain A, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
pdb|2XNK|B Chain B, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
pdb|2XNK|C Chain C, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
pdb|2XNK|D Chain D, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
Length = 292
Score = 35.0 bits (79), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 5 VATVSGYHGTERFNLIKLISYSGASYVGTMSKST-THLVCWKFEGEKHSLAKKFRTIIVN 63
+ V+G G +R + +L G Y G + + THL+ + +G+K+ AK++ V
Sbjct: 206 IICVTGLCGLDRKEVQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECAKRWNVHCVT 265
Query: 64 HQWVEDCIKQ 73
QW D I++
Sbjct: 266 TQWFFDSIEK 275
>pdb|3OLC|X Chain X, Crystal Structure Of The N-Terminal Region Of Topbp1
Length = 298
Score = 35.0 bits (79), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 5 VATVSGYHGTERFNLIKLISYSGASYVGTMSKST-THLVCWKFEGEKHSLAKKFRTIIVN 63
+ V+G G +R + +L G Y G + + THL+ + +G+K+ AK++ V
Sbjct: 204 IICVTGLCGLDRKEVQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECAKRWNVHCVT 263
Query: 64 HQWVEDCIKQ 73
QW D I++
Sbjct: 264 TQWFFDSIEK 273
>pdb|2XNH|A Chain A, Structure And Function Of The Rad9-Binding Region Of The
Dna Damage Checkpoint Adaptor Topbp1
Length = 287
Score = 35.0 bits (79), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 36/70 (51%), Gaps = 1/70 (1%)
Query: 5 VATVSGYHGTERFNLIKLISYSGASYVGTMSKST-THLVCWKFEGEKHSLAKKFRTIIVN 63
+ V+G G +R + +L G Y G + + THL+ + +G+K+ AK++ V
Sbjct: 204 IICVTGLCGLDRKEVQQLTVKHGGQYXGQLKXNECTHLIVQEPKGQKYECAKRWNVHCVT 263
Query: 64 HQWVEDCIKQ 73
QW D I++
Sbjct: 264 TQWFFDSIEK 273
>pdb|1WF6|A Chain A, The Third Brca1 C-Terminus (Brct) Domain Of Similar To
S.Pombe Rad4+CUT5+ PRODUCT
Length = 132
Score = 35.0 bits (79), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 10 GYHGTERFNLIKLISYSGASYVGTMSKSTTHLVCWKFEGEKHSLAKK--FRTIIVNHQWV 67
G+ G + L +LI+ G +++ TH++ ++ E K R +V +W+
Sbjct: 50 GFSGRKLDKLRRLINSGGGVRFNQLNEDVTHVIVGDYDDELKQFWNKSAHRPHVVGAKWL 109
Query: 68 EDCIKQHRRLPERPYM 83
+C + L E PY+
Sbjct: 110 LECFSKGYMLSEEPYI 125
>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 = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 5/54 (9%)
Query: 340 ELSCVICWTEFSSTRGVLACGHRFCYSCIQNWADHMASV--RKISTCPLCKASF 391
E++C IC E + L CGH FC +C+ A+H S+ + S+CP+C+ S+
Sbjct: 19 EVTCPICL-ELLTQPLSLDCGHSFCQACL--TANHKKSMLDKGESSCPVCRISY 69
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 33.5 bits (75), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 7/63 (11%)
Query: 332 VNRSSTSGELSCVICWTEFSSTRGVLACGHRFCYSCIQNWADHMASVRKIST-CPLCKAS 390
V+ S EL C IC +T C HRFC CI + ++R + CP C+
Sbjct: 46 VSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCI------ITALRSGNKECPTCRKK 99
Query: 391 FMS 393
+S
Sbjct: 100 LVS 102
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 33.1 bits (74), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 8/49 (16%)
Query: 343 CVICWTEFSSTR--GVLACGHRFCYSCIQNWADHMASVRKISTCPLCKA 389
CV+C +F S + VL C H F C+ W ++ TCP+C+A
Sbjct: 26 CVVCMCDFESRQLLRVLPCNHEFHAKCVDKW------LKANRTCPICRA 68
>pdb|3JVE|A Chain A, Crystal Structure Of The Sixth Brct Domain Of Topbp1
Length = 109
Score = 32.7 bits (73), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 43/88 (48%), Gaps = 9/88 (10%)
Query: 1 MESVVATVSGYHGTERFNLIKLISYSGASYVGTMSKSTTHLVCWKFEGEKHSLAKKFRTI 60
+ VV VS ++ L + + GA Y + ++ TH + ++G + ++++++
Sbjct: 18 LHKVVVCVSKKLSKKQSELNGIAASLGADYRWSFDETVTHFI---YQGRPNDTNREYKSV 74
Query: 61 ------IVNHQWVEDCIKQHRRLPERPY 82
IV+ W+ DC ++ + LPE Y
Sbjct: 75 KERGVHIVSEHWLLDCAQECKHLPESLY 102
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 32.7 bits (73), Expect = 0.53, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 27/63 (42%), Gaps = 12/63 (19%)
Query: 328 RIEHVNRSSTSGELSCVICWTEFSSTRGVLACGHRFCYSCIQNWADHMASVRKIST---C 384
R + + + L CV+C F ++ C H FC +CI VR + T C
Sbjct: 3 RTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCI---------VRYLETSKYC 53
Query: 385 PLC 387
P+C
Sbjct: 54 PIC 56
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 32.3 bits (72), Expect = 0.55, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 27/63 (42%), Gaps = 12/63 (19%)
Query: 328 RIEHVNRSSTSGELSCVICWTEFSSTRGVLACGHRFCYSCIQNWADHMASVRKIST---C 384
R + + + L CV+C F ++ C H FC +CI VR + T C
Sbjct: 3 RTTRIKITELNPHLMCVLCGGYFIDATTIIECLHSFCKTCI---------VRYLETSKYC 53
Query: 385 PLC 387
P+C
Sbjct: 54 PIC 56
>pdb|3PD7|A Chain A, Crystal Structure Of The Sixth Brct Domain Of Human Topbp1
pdb|3PD7|B Chain B, Crystal Structure Of The Sixth Brct Domain Of Human Topbp1
Length = 107
Score = 32.3 bits (72), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 20/88 (22%), Positives = 43/88 (48%), Gaps = 9/88 (10%)
Query: 1 MESVVATVSGYHGTERFNLIKLISYSGASYVGTMSKSTTHLVCWKFEGEKHSLAKKFRTI 60
+ VV VS ++ L + + GA Y + ++ TH + ++G + ++++++
Sbjct: 16 LHKVVVCVSKKLSKKQSELNGIAASLGADYRRSFDETVTHFI---YQGRPNDTNREYKSV 72
Query: 61 ------IVNHQWVEDCIKQHRRLPERPY 82
IV+ W+ DC ++ + LPE Y
Sbjct: 73 KERGVHIVSEHWLLDCAQECKHLPESLY 100
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 32.3 bits (72), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 33/112 (29%), Positives = 48/112 (42%), Gaps = 25/112 (22%)
Query: 338 SGELSCVICWTEFS----STRGVLA--CGHRFCYSCIQNWADHMASVRKISTCPLCKASF 391
SG +SC IC +S + R +++ CGH FC C+++ S++ +TCP C+
Sbjct: 5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRD------SLKNANTCPTCRK-- 56
Query: 392 MSITKVEDAATSDQKIYSQTIPCAWSTRDVFILPDGDSASVQPSLLEACIEC 443
K+ I S T+ C I DG S VQ L EC
Sbjct: 57 ----KINHKRYHPIYIGSGTVSCP-------ICMDGYSEIVQNGRLIVSTEC 97
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 12/57 (21%)
Query: 338 SGELSCVICWTEFS----STRGVLA--CGHRFCYSCIQNWADHMASVRKISTCPLCK 388
SG +SC IC +S + R +++ CGH FC C+++ S++ +TCP C+
Sbjct: 70 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRD------SLKNANTCPTCR 120
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 32.0 bits (71), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 32/70 (45%), Gaps = 8/70 (11%)
Query: 326 TDRIE-HVNRSSTSGELSCVICWTEFSSTRGVLACGHRFCYSCIQNWADHMASVRKIST- 383
TD +E V+ S EL C IC +T C HRFC CI + ++R +
Sbjct: 38 TDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCI------ITALRSGNKE 91
Query: 384 CPLCKASFMS 393
CP C+ +S
Sbjct: 92 CPTCRKKLVS 101
>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 = 32.0 bits (71), Expect = 0.73, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 8/54 (14%)
Query: 340 ELSCVICWTEF--SSTRGVLACGHRFCYSCIQNWADHMASVRKISTCPLCKASF 391
E+ C IC +E+ L C H F C+ W ++K TCP+C+ F
Sbjct: 40 EMCCPICCSEYVKGDVATELPCHHYFHKPCVSIW------LQKSGTCPVCRCMF 87
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 32.0 bits (71), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 340 ELSCVICWTEFSSTRGVLACGHRFCYSCIQNWADHMASVRKISTCPLC 387
E SC +C E+ ++ CGH FC +CI W + + + CP+C
Sbjct: 15 EASCSVC-LEYLKEPVIIECGHNFCKACITRWWEDL---ERDFPCPVC 58
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 32.0 bits (71), Expect = 0.82, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 12/50 (24%)
Query: 341 LSCVICWTEFSSTRGVLACGHRFCYSCIQNWADHMASVRKIST---CPLC 387
L CV+C F ++ C H FC +CI VR + T CP+C
Sbjct: 12 LMCVLCGGYFIDATTIIECLHSFCKTCI---------VRYLETSKYCPIC 52
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 31.6 bits (70), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 32/70 (45%), Gaps = 8/70 (11%)
Query: 326 TDRIE-HVNRSSTSGELSCVICWTEFSSTRGVLACGHRFCYSCIQNWADHMASVRKIST- 383
TD +E V+ S EL C IC +T C HRFC CI + ++R +
Sbjct: 19 TDGLEIVVSPRSLHSELMCPICLDMLKNTMTTKECLHRFCADCI------ITALRSGNKE 72
Query: 384 CPLCKASFMS 393
CP C+ +S
Sbjct: 73 CPTCRKKLVS 82
>pdb|3ASK|A Chain A, Structure Of Uhrf1 In Complex With Histone Tail
pdb|3ASK|B Chain B, Structure Of Uhrf1 In Complex With Histone Tail
pdb|3ASK|C Chain C, Structure Of Uhrf1 In Complex With Histone Tail
pdb|3ASK|D Chain D, Structure Of Uhrf1 In Complex With Histone Tail
Length = 226
Score = 31.6 bits (70), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 7/50 (14%)
Query: 439 ACIECRSQEPQDLLIRCHLCQSRCIHCYCMDPPL------DPWTCIHCKD 482
AC C ++ D + C C H YC+DPPL D W C C++
Sbjct: 176 ACHLCGGRQDPDKQLMCDECDM-AFHIYCLDPPLSSVPSEDEWYCPECRN 224
>pdb|4GY5|A Chain A, Crystal Structure Of The Tandem Tudor Domain And Plant
Homeodomain Of Uhrf1 With Histone H3k9me3
pdb|4GY5|B Chain B, Crystal Structure Of The Tandem Tudor Domain And Plant
Homeodomain Of Uhrf1 With Histone H3k9me3
pdb|4GY5|C Chain C, Crystal Structure Of The Tandem Tudor Domain And Plant
Homeodomain Of Uhrf1 With Histone H3k9me3
pdb|4GY5|D Chain D, Crystal Structure Of The Tandem Tudor Domain And Plant
Homeodomain Of Uhrf1 With Histone H3k9me3
Length = 241
Score = 31.6 bits (70), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 23/50 (46%), Gaps = 7/50 (14%)
Query: 439 ACIECRSQEPQDLLIRCHLCQSRCIHCYCMDPPL------DPWTCIHCKD 482
AC C ++ D + C C H YC+DPPL D W C C++
Sbjct: 192 ACHLCGGRQDPDKQLMCDECDM-AFHIYCLDPPLSSVPSEDEWYCPECRN 240
>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 = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 12/57 (21%)
Query: 338 SGELSCVICWTEFS----STRGVLA--CGHRFCYSCIQNWADHMASVRKISTCPLCK 388
SG +SC IC +S + R +++ CGH FC C+++ S++ +TCP C+
Sbjct: 8 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRD------SLKNANTCPTCR 58
>pdb|2H6E|A Chain A, Crystal Structure Of The D-Arabinose Dehydrogenase From
Sulfolobus Solfataricus
Length = 344
Score = 31.2 bits (69), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 50/102 (49%), Gaps = 16/102 (15%)
Query: 13 GTER--FNLIKLISYSGASYVGTMSKSTTHLVCWKFEGEKHSLAKKFRTIIVNHQWVEDC 70
GTE +NL KL++ GA ++ EG++ SL + F T + N + +
Sbjct: 247 GTEETTYNLGKLLAQEGA------------IILVGMEGKRVSL-EAFDTAVWNKKLLGSN 293
Query: 71 IKQHRRLPERPYMLQSGQEIGPLLLEVPLFNMNSDRSNLDDN 112
L + + +SG+ I P +++VPL ++N +NLD+
Sbjct: 294 YGSLNDLEDVVRLSESGK-IKPYIIKVPLDDINKAFTNLDEG 334
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 31.2 bits (69), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 12/57 (21%)
Query: 338 SGELSCVICWTEFS----STRGVLA--CGHRFCYSCIQNWADHMASVRKISTCPLCK 388
SG +SC IC +S + R +++ CGH FC C+++ S++ +TCP C+
Sbjct: 13 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRD------SLKNANTCPTCR 63
>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human
Tripartite Motif Protein 34
Length = 79
Score = 30.8 bits (68), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 340 ELSCVICWTEFSSTRGVLACGHRFCYSCIQ-NWADHMASVRKISTCPLCKASF 391
E++C IC E + L CGH C +CI + + + S+ S+CP+C S+
Sbjct: 12 EVTCPICL-ELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISY 63
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 26/91 (28%), Positives = 37/91 (40%), Gaps = 18/91 (19%)
Query: 318 NSNGMVKNTDRIEHVNRSSTSGELSCVICWTEFSSTR---GVLACGHRFCYSCIQN-WAD 373
S+G N D + V L C IC F+ + +L CGH C C++ A
Sbjct: 1 GSSGSSGNLDALREV--------LECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLAS 52
Query: 374 HMASVRKISTCPLCK--ASFMSITKVEDAAT 402
+ VR CP C S+T++ D T
Sbjct: 53 SINGVR----CPFCSKITRITSLTQLTDNLT 79
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 6/33 (18%)
Query: 356 VLACGHRFCYSCIQNWADHMASVRKISTCPLCK 388
+L C H FC CI W+D + CP+C+
Sbjct: 29 ILPCAHSFCQKCIDKWSD------RHRNCPICR 55
>pdb|3L40|A Chain A, Crystal Structure Of S. Pombe Brc1 Brct5-Brct6 Domains
pdb|3L40|B Chain B, Crystal Structure Of S. Pombe Brc1 Brct5-Brct6 Domains
pdb|3L41|A Chain A, Crystal Structure Of S. Pombe Brc1 Brct5-Brct6 Domains
In Complex With Phosphorylated H2a
Length = 220
Score = 30.4 bits (67), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/87 (21%), Positives = 36/87 (41%), Gaps = 5/87 (5%)
Query: 4 VVATVSGYHGTERFNLIKLISYSGASYVGTMSKSTTHLVCWK-FEGEKHSLAKKFRTIIV 62
V T +GY + +K + S + + THL+ + K + + +V
Sbjct: 9 VYITFTGYDKKPSIDNLKKLDMS----ITSNPSKCTHLIAPRILRTSKFLCSIPYGPCVV 64
Query: 63 NHQWVEDCIKQHRRLPERPYMLQSGQE 89
W+ C+K H + E PY+L ++
Sbjct: 65 TMDWINSCLKTHEIVDEEPYLLNDPEK 91
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 30.4 bits (67), Expect = 2.3, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 22/51 (43%), Gaps = 4/51 (7%)
Query: 340 ELSCVICWTEFSSTRGVLACGHRFCYSCIQNWADHMASVRKISTCPLCKAS 390
E+ C IC + + CGH FC CI + K CPLCK S
Sbjct: 20 EVICPIC-LDILQKPVTIDCGHNFCLKCITQIGETSCGFFK---CPLCKTS 66
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 30.4 bits (67), Expect = 2.6, Method: Composition-based stats.
Identities = 16/51 (31%), Positives = 22/51 (43%), Gaps = 9/51 (17%)
Query: 341 LSCVICWTEFS---STRGVLACGHRFCYSCIQNWADHMASVRKISTCPLCK 388
+ C +C E R + CGH F C+ W + STCPLC+
Sbjct: 6 VECAVCLAELEDGEEARFLPRCGHGFHAECVDMW------LGSHSTCPLCR 50
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 30.4 bits (67), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 8/63 (12%)
Query: 343 CVICWTEFSS--TRGVLACGHRFCYSCIQNWADHMASVRKISTCPLCKASFMSITKVEDA 400
C +C +F G+ C H F C+ W + VRK+ CPLC + + ++
Sbjct: 18 CAVCLEDFKPRDELGICPCKHAFHRKCLIKWLE----VRKV--CPLCNMPVLQLAQLSGP 71
Query: 401 ATS 403
++
Sbjct: 72 SSG 74
>pdb|2EBW|A Chain A, Solution Structure Of The Brct Domain From Human Dna
Repair Protein Rev1
Length = 97
Score = 29.6 bits (65), Expect = 3.9, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 35/82 (42%), Gaps = 3/82 (3%)
Query: 4 VVATVSGYHGTERFNLIKLISYSGASYVGTMSKS-TTHLVCWKFEGEKHSLAKKFRTIIV 62
V V+GY L KL+ G Y S+S TTH++ K K + ++
Sbjct: 16 VAIYVNGYTDPSAEELRKLMMLHGGQYHVYYSRSKTTHIIATNLPNAKIKELKGEK--VI 73
Query: 63 NHQWVEDCIKQHRRLPERPYML 84
+W+ + IK R L PY L
Sbjct: 74 RPEWIVESIKAGRLLSYIPYQL 95
>pdb|2KWJ|A Chain A, Solution Structures Of The Double Phd Fingers Of Human
Transcriptional Protein Dpf3 Bound To A Histone Peptide
Containing Acetylation At Lysine 14
pdb|2KWK|A Chain A, Solution Structures Of The Double Phd Fingers Of Human
Transcriptional Protein Dpf3b Bound To A H3 Peptide Wild
Type
pdb|2KWN|A Chain A, Solution Structure Of The Double Phd (Plant Homeodomain)
Fingers Of Human Transcriptional Protein Dpf3b Bound To
A Histone H4 Peptide Containing Acetylation At Lysine 16
pdb|2KWO|A Chain A, Solution Structure Of The Double Phd (Plant Homeodomain)
Fingers Of Human Transcriptional Protein Dpf3b Bound To
A Histone H4 Peptide Containing N-Terminal Acetylation
At Serine 1
Length = 114
Score = 28.9 bits (63), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 29/51 (56%), Gaps = 6/51 (11%)
Query: 438 EACIECRSQEPQDLLIRCHLCQSRCIHCYCMDPPL-DP----WTCIHCKDL 483
++CI C + E D L+ C C R H YC++PP+ +P W+C C +L
Sbjct: 59 KSCILCGTSENDDQLLFCDDCD-RGYHMYCLNPPVAEPPEGSWSCHLCWEL 108
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 0.132 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,373,174
Number of Sequences: 62578
Number of extensions: 513401
Number of successful extensions: 1073
Number of sequences better than 100.0: 60
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 46
Number of HSP's that attempted gapping in prelim test: 1053
Number of HSP's gapped (non-prelim): 64
length of query: 492
length of database: 14,973,337
effective HSP length: 103
effective length of query: 389
effective length of database: 8,527,803
effective search space: 3317315367
effective search space used: 3317315367
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: 53 (25.0 bits)