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= 048433
(279 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 57.4 bits (137), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 26/58 (44%), Positives = 33/58 (56%)
Query: 201 SKKADGSTKSSEDELTCTICLEQVKCGELVRSLPCLHQFHANCIDPWLRQRGTCPVCK 258
S + G+ + L C +C E GE VR LPC H FH +CI PWL Q +CPVC+
Sbjct: 2 SSGSSGTEEHVGSGLECPVCKEDYALGESVRQLPCNHLFHDSCIVPWLEQHDSCPVCR 59
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 54.3 bits (129), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 32/50 (64%)
Query: 213 DELTCTICLEQVKCGELVRSLPCLHQFHANCIDPWLRQRGTCPVCKFRMG 262
++ C +C+ + +L+R LPC H+FHA C+D WL+ TCP+C+ G
Sbjct: 22 EQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADSG 71
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/43 (51%), Positives = 28/43 (65%)
Query: 217 CTICLEQVKCGELVRSLPCLHQFHANCIDPWLRQRGTCPVCKF 259
CTICL ++ GE VR LPC+H FH C+D WL CP+C+
Sbjct: 17 CTICLSILEEGEDVRRLPCMHLFHQVCVDQWLITNKKCPICRV 59
>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 = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 29/74 (39%), Positives = 38/74 (51%), Gaps = 7/74 (9%)
Query: 191 AATPEQSKQESKKADGSTKSSED------ELTCTICLEQVKCGELVRSLPCLHQFHANCI 244
A P SK ES A +ED E+ C IC + G++ LPC H FH C+
Sbjct: 12 VANPPASK-ESIDALPEILVTEDHGAVGQEMCCPICCSEYVKGDVATELPCHHYFHKPCV 70
Query: 245 DPWLRQRGTCPVCK 258
WL++ GTCPVC+
Sbjct: 71 SIWLQKSGTCPVCR 84
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 32/51 (62%), Gaps = 1/51 (1%)
Query: 210 SSEDELTCTICLEQVKCGELVRSLP-CLHQFHANCIDPWLRQRGTCPVCKF 259
+ +D + C +CL +++ GE R LP C H FHA C+D WL TCP+C+
Sbjct: 1 AMDDGVECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRL 51
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 44.3 bits (103), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 29/61 (47%), Gaps = 4/61 (6%)
Query: 201 SKKADGSTKSSEDELTCTICLEQVKCGELVRSLPCLHQFHANCIDPWLRQRGTCPVCKFR 260
S + G K DE C IC++ G LPC H F CID W + CP+C+ +
Sbjct: 2 SSGSSGRVKQLTDEEECCICMD----GRADLILPCAHSFCQKCIDKWSDRHRNCPICRLQ 57
Query: 261 M 261
M
Sbjct: 58 M 58
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 217 CTICLEQVKCGELVRSLPCLHQFHANCIDPWLRQRGTCPVCKFRMGSGWQENRESESDSS 276
C ICLE +LPCLH F CI W+RQ TCP+CK + S ES+S+
Sbjct: 8 CPICLEDP--SNYSMALPCLHAFCYVCITRWIRQNPTCPLCKVPVESV-VHTIESDSEFG 64
Query: 277 D 277
D
Sbjct: 65 D 65
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 11/72 (15%)
Query: 195 EQSKQESKKADGSTKSS--------EDELTCTICLEQVKCGELVRSLPCLHQFHANCIDP 246
EQ+K+E +K + E+EL C IC E E V +L C H F + CI+
Sbjct: 26 EQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYF--IEAV-TLNCAHSFCSYCINE 82
Query: 247 WLRQRGTCPVCK 258
W++++ CP+C+
Sbjct: 83 WMKRKIECPICR 94
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 11/72 (15%)
Query: 195 EQSKQESKKADGSTKSS--------EDELTCTICLEQVKCGELVRSLPCLHQFHANCIDP 246
EQ+K+E +K + E+EL C IC E E V +L C H F + CI+
Sbjct: 26 EQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYF--IEAV-TLNCAHSFCSYCINE 82
Query: 247 WLRQRGTCPVCK 258
W++++ CP+C+
Sbjct: 83 WMKRKIECPICR 94
>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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 11/72 (15%)
Query: 195 EQSKQESKKADGSTKSS--------EDELTCTICLEQVKCGELVRSLPCLHQFHANCIDP 246
EQ+K+E +K + E+EL C IC E E V +L C H F + CI+
Sbjct: 37 EQTKEEKEKMQAQKEEVLSHMNDVLENELQCIICSEYF--IEAV-TLNCAHSFCSYCINE 93
Query: 247 WLRQRGTCPVCK 258
W++++ CP+C+
Sbjct: 94 WMKRKIECPICR 105
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 26/59 (44%)
Query: 201 SKKADGSTKSSEDELTCTICLEQVKCGELVRSLPCLHQFHANCIDPWLRQRGTCPVCKF 259
S + G K C +CLE K + + PC H FH C+ WL R CP+C
Sbjct: 2 SSGSSGKVKELNLHELCAVCLEDFKPRDELGICPCKHAFHRKCLIKWLEVRKVCPLCNM 60
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 30/100 (30%), Positives = 49/100 (49%), Gaps = 12/100 (12%)
Query: 174 GPASESVGSSIRQPSSSA---------ATPEQSKQESKKADGSTKSSEDELTCTICLEQV 224
G S++V ++ QP S TP+++ + + S +S EL C ICL+ +
Sbjct: 4 GSMSQAVQTNGTQPLSKTWELSLYELQRTPQEAITDGLEIVVSPRSLHSELMCPICLDML 63
Query: 225 KCGELVRSLPCLHQFHANCIDPWLRQ-RGTCPVCKFRMGS 263
K + + CLH+F A+CI LR CP C+ ++ S
Sbjct: 64 K--NTMTTKECLHRFCADCIITALRSGNKECPTCRKKLVS 101
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 193 TPEQSKQESKKADGSTKSSEDELTCTICLEQVKCGELVRSLPCLHQFHANCIDPWLRQ-R 251
TP+++ + + S +S EL C ICL+ +K + + CLH+F A+CI LR
Sbjct: 33 TPQEAITDGLEIVVSPRSLHSELMCPICLDMLK--NTMTTKECLHRFCADCIITALRSGN 90
Query: 252 GTCPVCKFRMGS 263
CP C+ ++ S
Sbjct: 91 KECPTCRKKLVS 102
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 193 TPEQSKQESKKADGSTKSSEDELTCTICLEQVKCGELVRSLPCLHQFHANCIDPWLRQ-R 251
TP+++ + + S +S EL C ICL+ +K + + CLH+F A+CI LR
Sbjct: 13 TPQEAITDGLEIVVSPRSLHSELMCPICLDMLK--NTMTTKECLHRFCADCIITALRSGN 70
Query: 252 GTCPVCKFRMGS 263
CP C+ ++ S
Sbjct: 71 KECPTCRKKLVS 82
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 36.6 bits (83), Expect = 0.017, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 215 LTCTICL----EQVKCGELVRSLPCLHQFHANCIDPWLRQRGTCPVCKFRM 261
++C IC+ E V+ G L+ S C H F + C+ L+ TCP C+ ++
Sbjct: 4 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54
>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 = 35.8 bits (81), Expect = 0.024, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 215 LTCTICL----EQVKCGELVRSLPCLHQFHANCIDPWLRQRGTCPVCKFRM 261
++C IC+ E V+ G L+ S C H F + C+ L+ TCP C+ ++
Sbjct: 11 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 33.9 bits (76), Expect = 0.091, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 12/55 (21%)
Query: 216 TCTICLEQV-----KCGELVRSLPCL-------HQFHANCIDPWLRQRGTCPVCK 258
TC IC QV +C + C+ H FH C+ W++Q CP+C+
Sbjct: 17 TCAICRVQVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQ 71
>pdb|1LDJ|B Chain B, Structure Of The Cul1-rbx1-skp1-f Boxskp2 Scf Ubiquitin
Ligase Complex
pdb|1LDK|C Chain C, Structure Of The Cul1-Rbx1-Skp1-F Boxskp2 Scf Ubiquitin
Ligase Complex
Length = 90
Score = 33.5 bits (75), Expect = 0.13, Method: Composition-based stats.
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 10/38 (26%)
Query: 235 CLHQFHANCIDPWLRQRGTCPVCKFRMGSGWQENRESE 272
C H FH +CI WL+ R CP+ +NRE E
Sbjct: 57 CNHAFHFHCISRWLKTRQVCPL----------DNREWE 84
>pdb|2ECM|A Chain A, Solution Structure Of The Ring Domain Of The Ring Finger
And Chy Zinc Finger Domain-Containing Protein 1 From Mus
Musculus
Length = 55
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 217 CTICLEQVKCGELV-RSLPCLHQFHANCIDPWLRQRGTCPVC 257
C ICLE + +V LPC H H C + L++ CP+C
Sbjct: 8 CPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLC 49
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 32.7 bits (73), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 32/74 (43%), Gaps = 17/74 (22%)
Query: 200 ESKKADGSTKSSEDELT--CTICLEQVK--CGEL-------------VRSLPCLHQFHAN 242
E KK++ S +S+ D + C IC + C E V C H FH +
Sbjct: 15 EVKKSNASAQSAWDIVVDNCAICRNHIMDLCIECQANQASATSEECTVAWGVCNHAFHFH 74
Query: 243 CIDPWLRQRGTCPV 256
CI WL+ R CP+
Sbjct: 75 CISRWLKTRQVCPL 88
>pdb|2JRJ|A Chain A, Solution Structure Of The Human Pirh2 Ring-H2 Domain.
Northeast Structural Genomics Consortium Target Ht2b
Length = 52
Score = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 216 TCTICLEQVKCGELV-RSLPCLHQFHANCIDPWLRQRGTCPVC 257
C ICLE + +V LPC H H C + L++ CP+C
Sbjct: 7 NCPICLEDIHTSRVVAHVLPCGHLLHRTCYEEMLKEGYRCPLC 49
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 215 LTCTICL----EQVKCGELVRSLPCLHQFHANCIDPWLRQRGTCPVCKFRM 261
++C IC+ E V+ G L+ S C H F + C+ L+ TCP C+ ++
Sbjct: 16 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 215 LTCTICL----EQVKCGELVRSLPCLHQFHANCIDPWLRQRGTCPVCKFRM 261
++C IC+ E V+ G L+ S C H F + C+ L+ TCP C+ ++
Sbjct: 8 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 58
Score = 32.0 bits (71), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 215 LTCTICL----EQVKCGELVRSLPCLHQFHANCIDPWLRQRGTCPVCKFRM 261
++C IC+ E V+ G L+ S C H F + C+ L+ TCP C+ ++
Sbjct: 73 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 123
>pdb|1U6G|B Chain B, Crystal Structure Of The Cand1-Cul1-Roc1 Complex
pdb|2HYE|D Chain D, Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex
Length = 108
Score = 32.0 bits (71), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 10/38 (26%)
Query: 235 CLHQFHANCIDPWLRQRGTCPVCKFRMGSGWQENRESE 272
C H FH +CI WL+ R CP+ +NRE E
Sbjct: 75 CNHAFHFHCISRWLKTRQVCPL----------DNREWE 102
>pdb|3DPL|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation.
pdb|3RTR|B Chain B, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|D Chain D, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|F Chain F, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|3RTR|H Chain H, A Ring E3-Substrate Complex Poised For Ubiquitin-Like
Protein Transfer: Structural Insights Into Cullin-Ring
Ligases
pdb|4F52|B Chain B, Structure Of A Glomulin-Rbx1-Cul1 Complex
pdb|4F52|D Chain D, Structure Of A Glomulin-Rbx1-Cul1 Complex
Length = 106
Score = 31.6 bits (70), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 10/38 (26%)
Query: 235 CLHQFHANCIDPWLRQRGTCPVCKFRMGSGWQENRESE 272
C H FH +CI WL+ R CP+ +NRE E
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPL----------DNREWE 100
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 31.6 bits (70), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 10/38 (26%)
Query: 235 CLHQFHANCIDPWLRQRGTCPVCKFRMGSGWQENRESE 272
C H FH +CI WL+ R CP+ +NRE E
Sbjct: 84 CNHAFHFHCISRWLKTRQVCPL----------DNREWE 111
>pdb|4A0C|D Chain D, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0C|F Chain F, Structure Of The Cand1-Cul4b-Rbx1 Complex
pdb|4A0L|F Chain F, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
pdb|4A0L|I Chain I, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 98
Score = 31.6 bits (70), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 10/38 (26%)
Query: 235 CLHQFHANCIDPWLRQRGTCPVCKFRMGSGWQENRESE 272
C H FH +CI WL+ R CP+ +NRE E
Sbjct: 65 CNHAFHFHCISRWLKTRQVCPL----------DNREWE 92
>pdb|3DQV|R Chain R, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
pdb|3DQV|Y Chain Y, Structural Insights Into Nedd8 Activation Of Cullin-Ring
Ligases: Conformational Control Of Conjugation
Length = 106
Score = 31.6 bits (70), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 10/38 (26%)
Query: 235 CLHQFHANCIDPWLRQRGTCPVCKFRMGSGWQENRESE 272
C H FH +CI WL+ R CP+ +NRE E
Sbjct: 73 CNHAFHFHCISRWLKTRQVCPL----------DNREWE 100
>pdb|2EYQ|A Chain A, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
pdb|2EYQ|B Chain B, Crystal Structure Of Escherichia Coli Transcription-Repair
Coupling Factor
Length = 1151
Score = 31.2 bits (69), Expect = 0.59, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 30/70 (42%), Gaps = 3/70 (4%)
Query: 135 FDELDYDTLRALDSDNTSTTPSMSEEEINSLPVHKYKVPGPASESVGSSIRQPSSSAATP 194
FD+ + D+LR D D+ T + E IN LP H++ A E S R P
Sbjct: 188 FDD-EIDSLRVFDVDSQRTLEEV--EAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDP 244
Query: 195 EQSKQESKKA 204
E Q+ K
Sbjct: 245 EHIYQQVSKG 254
>pdb|3HJH|A Chain A, A Rigid N-Terminal Clamp Restrains The Motor Domains Of
The Bacterial Transcription-Repair Coupling Factor
Length = 483
Score = 30.4 bits (67), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 30/70 (42%), Gaps = 3/70 (4%)
Query: 135 FDELDYDTLRALDSDNTSTTPSMSEEEINSLPVHKYKVPGPASESVGSSIRQPSSSAATP 194
FD+ + D+LR D D+ T + E IN LP H++ A E S R P
Sbjct: 185 FDD-EIDSLRVFDVDSQRTLEEV--EAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDP 241
Query: 195 EQSKQESKKA 204
E Q+ K
Sbjct: 242 EHIYQQVSKG 251
>pdb|2B2N|A Chain A, Structure Of Transcription-repair Coupling Factor
pdb|2B2N|B Chain B, Structure Of Transcription-repair Coupling Factor
Length = 344
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 30/70 (42%), Gaps = 3/70 (4%)
Query: 135 FDELDYDTLRALDSDNTSTTPSMSEEEINSLPVHKYKVPGPASESVGSSIRQPSSSAATP 194
FD+ + D+LR D D+ T + E IN LP H++ A E S R P
Sbjct: 185 FDD-EIDSLRVFDVDSQRTLEEV--EAINLLPAHEFPTDKAAIELFRSQWRDTFEVKRDP 241
Query: 195 EQSKQESKKA 204
E Q+ K
Sbjct: 242 EHIYQQVSKG 251
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 30.4 bits (67), Expect = 1.1, Method: Composition-based stats.
Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 9/53 (16%)
Query: 212 EDELTCTICLEQVKCGELVRSLPCLHQFHANCIDPWLRQ------RGTCPVCK 258
++E+TC ICLE +K E V S C H F CI +G CPVC+
Sbjct: 17 KEEVTCPICLELLK--EPV-SADCNHSFCRACITLNYESNRNTDGKGNCPVCR 66
>pdb|1UAA|A Chain A, E. Coli Rep HelicaseDNA COMPLEX
pdb|1UAA|B Chain B, E. Coli Rep HelicaseDNA COMPLEX
Length = 673
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 25/48 (52%)
Query: 187 PSSSAATPEQSKQESKKADGSTKSSEDELTCTICLEQVKCGELVRSLP 234
P S+ + +E + A ++ ELT T+C E+ + GELVR P
Sbjct: 579 PHQSSIDEDNIDEERRLAYVGITRAQKELTFTLCKERRQYGELVRPEP 626
>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 = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 2/49 (4%)
Query: 209 KSSEDELTCTICLEQVKCGELVRSLPCLHQFHANCIDPWLRQRGTCPVC 257
K+ +D L C IC E ++ C H + + CI +L + CP C
Sbjct: 17 KTIDDLLRCGICFEYFNIAMIIPQ--CSHNYCSLCIRKFLSYKTQCPTC 63
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 6/60 (10%)
Query: 201 SKKADGSTKSSEDELTCTICLEQVKCGELVRSLPCLHQFHANCIDPW---LRQRGTCPVC 257
S + G+ ++ + E +C++CLE +K E V + C H F CI W L + CPVC
Sbjct: 2 SSGSSGALENLQVEASCSVCLEYLK--EPV-IIECGHNFCKACITRWWEDLERDFPCPVC 58
>pdb|2PUY|A Chain A, Crystal Structure Of The Bhc80 Phd Finger
pdb|2PUY|B Chain B, Crystal Structure Of The Bhc80 Phd Finger
Length = 60
Score = 28.5 bits (62), Expect = 3.8, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 7/49 (14%)
Query: 217 CTICLEQVKCGELVRSLPCLHQFHANCIDPWLRQ--RGT--CPVCKFRM 261
C++C K G+L+ C +H +C+DP L+ +G CP C+ +M
Sbjct: 8 CSVCR---KSGQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQDQM 53
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 27.7 bits (60), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 233 LPCLHQFHANCIDPWLRQRGTCPVC 257
+ CLH F CI +L CP+C
Sbjct: 32 IECLHSFCKTCIVRYLETSKYCPIC 56
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 27.7 bits (60), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 233 LPCLHQFHANCIDPWLRQRGTCPVC 257
+ CLH F CI +L CP+C
Sbjct: 32 IECLHSFCKTCIVRYLETSKYCPIC 56
>pdb|2YQL|A Chain A, Solution Structure Of The Phd Domain In Phd Finger Protein
21a
Length = 56
Score = 27.3 bits (59), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 31/57 (54%), Gaps = 7/57 (12%)
Query: 206 GSTKSSEDELTCTICLEQVKCGELVRSLPCLHQFHANCIDPWLRQ--RG--TCPVCK 258
GS+ SS E C++C + G+L+ C +H +C+DP L+ +G CP C+
Sbjct: 1 GSSGSSGHEDFCSVCRKS---GQLLMCDTCSRVYHLDCLDPPLKTIPKGMWICPRCQ 54
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 27.3 bits (59), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 233 LPCLHQFHANCIDPWLRQRGTCPVC 257
+ CLH F CI +L CP+C
Sbjct: 28 IECLHSFCKTCIVRYLETSKYCPIC 52
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
0.316 0.130 0.390
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,768,622
Number of Sequences: 62578
Number of extensions: 215196
Number of successful extensions: 439
Number of sequences better than 100.0: 59
Number of HSP's better than 100.0 without gapping: 31
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 402
Number of HSP's gapped (non-prelim): 60
length of query: 279
length of database: 14,973,337
effective HSP length: 98
effective length of query: 181
effective length of database: 8,840,693
effective search space: 1600165433
effective search space used: 1600165433
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)