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= 002077
(972 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3MWY|W Chain W, Crystal Structure Of The Chromodomain-atpase Portion Of
The Yeast Chd1 Chromatin Remodeler
Length = 800
Score = 98.2 bits (243), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 52/128 (40%), Positives = 81/128 (63%), Gaps = 3/128 (2%)
Query: 819 KSIVFSQWTRMLDLVENSLNQHCIQYRRLDGTMSLPARDRAVKDFNT-DREITVMLMSLK 877
+ ++FSQ RMLD++ + L+ I ++RLDGT+ R ++ FN+ D V L+S +
Sbjct: 574 RVLIFSQMVRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTR 633
Query: 878 AGNLGLNMVAASHVILLDLWWNPTTEDQAVDRAHRIGQTRPVTVTRLTIRDTVEDRILKL 937
AG LG+N++ A V++ D WNP + QA+ RAHRIGQ V V RL +DTVE+ + L
Sbjct: 634 AGGLGINLMTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEV--L 691
Query: 938 QDDKRKMV 945
+ ++KM+
Sbjct: 692 ERARKKMI 699
Score = 32.3 bits (72), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 41/173 (23%), Positives = 71/173 (41%), Gaps = 40/173 (23%)
Query: 507 LAKVGWFRVVLDEAQTIKNHRTQVARACCSLR-AKRSTIK-IPISRNSLHGYKKLQAVLR 564
L + W + +DEA +KN + + + S + A R I P+ N K+L A++
Sbjct: 363 LGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLITGTPLQNN----IKELAALVN 418
Query: 565 AIML-RRTKGTFIDG------------------QPII----------NLPPKTISLTKVD 595
+M R T ID QP I +LP KT + +V+
Sbjct: 419 FLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKKDVEKSLPSKTERILRVE 478
Query: 596 FSKEEWAFYKKLESDSLKKFKAFADAGTVNQNYANILLMLLRLRQACDHPLLV 648
S + +YK + + + A A G + ++L ++ L++A +HP L
Sbjct: 479 LSDVQTEYYKNILTKNYSALTAGAKGG-----HFSLLNIMNELKKASNHPYLF 526
Score = 30.8 bits (68), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 298 GGILADDQGLGKTISIIALI 317
GILAD+ GLGKT+ +A I
Sbjct: 257 NGILADEMGLGKTVQTVAFI 276
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 94.4 bits (233), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 51/150 (34%), Positives = 81/150 (54%), Gaps = 3/150 (2%)
Query: 819 KSIVFSQWTRMLDLVENSLNQHC-IQYRRLDGTMSLPARDRAVKDFNTDREITVMLMSLK 877
K +F+Q+ M ++ N + + + L G +S RD + F + + +++S+K
Sbjct: 343 KIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVK 402
Query: 878 AGNLGLNMVAASHVILLDLWWNPTTEDQAVDRAHRIGQTRPVTVTRLTIRDTVEDRILKL 937
AG G+N+ +A+ VI D WWNP EDQA DR +RIGQTR V V +L T+E++I +L
Sbjct: 403 AGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQL 462
Query: 938 QDDKRKMVASAFGEDQGGGTASRLTVEDLR 967
KR + G + L+ E+LR
Sbjct: 463 LAFKRSLFKDIIS--SGDSWITELSTEELR 490
Score = 55.8 bits (133), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 68/269 (25%), Positives = 116/269 (43%), Gaps = 48/269 (17%)
Query: 387 TLVVCPASVLRQWARELEDKVPDKAALSVLIYHGGSRTKDPVELAKYDVVLTTYSIV--- 443
+LV+CP SVL+ W EL P L ++H + ++L YD++LTTY+++
Sbjct: 89 SLVICPLSVLKNWEEELSKFAPH---LRFAVFH---EDRSKIKLEDYDIILTTYAVLLRD 142
Query: 444 --TNEVPKQPSVDEEEADEKNGETYGLSSEFSVNKKRKKIXXXXXXXXXXXXXXXXXXID 501
EV + V +E + KN +T + + K + I
Sbjct: 143 TRLKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYR--------------------IA 182
Query: 502 YGCGPLAKVGWFRVVLDEAQTIKNHRTQ-VARACCSLRAKRSTIKIPISRNSLHGYKKLQ 560
P+ +D+ +I + + ++K +T PI + ++L+
Sbjct: 183 LTGTPIEN------KVDDLWSIMTFLNPGLLGSYSEFKSKFAT---PIKKGDNMAKEELK 233
Query: 561 AVLRAIMLRRTKGTFIDGQPIINLPPKTISLTKVDFSKEEWAFYKKLESDSLKKFKAFAD 620
A++ +LRRTK D I +LP K + + + E+ A YK E ++L F D
Sbjct: 234 AIISPFILRRTK---YDKAIINDLPDKIETNVYCNLTPEQAAMYKA-EVENL--FNNI-D 286
Query: 621 AGTVNQNYANILLMLLRLRQACDHPLLVK 649
+ T + IL LL+L+Q DHP L+K
Sbjct: 287 SVTGIKRKGMILSTLLKLKQIVDHPALLK 315
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 28/49 (57%), Gaps = 7/49 (14%)
Query: 271 LSVNLLKHQKIALAWMLQKETRSLHCLG-GI-LADDQGLGKTISIIALI 317
+ NL +Q +WM R ++ LG GI LADD GLGKT+ IA+
Sbjct: 34 IKANLRPYQIKGFSWM-----RFMNKLGFGICLADDMGLGKTLQTIAVF 77
>pdb|1Z5Z|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE C-Terminal Domain
pdb|1Z5Z|B Chain B, Sulfolobus Solfataricus Swi2SNF2 ATPASE C-Terminal Domain
Length = 271
Score = 93.2 bits (230), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 51/150 (34%), Positives = 81/150 (54%), Gaps = 3/150 (2%)
Query: 819 KSIVFSQWTRMLDLVENSLNQHC-IQYRRLDGTMSLPARDRAVKDFNTDREITVMLMSLK 877
K +F+Q+ M ++ N + + + L G +S RD + F + + +++S+K
Sbjct: 114 KIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVK 173
Query: 878 AGNLGLNMVAASHVILLDLWWNPTTEDQAVDRAHRIGQTRPVTVTRLTIRDTVEDRILKL 937
AG G+N+ +A+ VI D WWNP EDQA DR +RIGQTR V V +L T+E++I +L
Sbjct: 174 AGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQL 233
Query: 938 QDDKRKMVASAFGEDQGGGTASRLTVEDLR 967
KR + G + L+ E+LR
Sbjct: 234 LAFKRSLFKDIIS--SGDSWITELSTEELR 261
>pdb|1Z63|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COMPLEX
With Dsdna
pdb|1Z63|B Chain B, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE IN COMPLEX
With Dsdna
Length = 500
Score = 92.0 bits (227), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 50/150 (33%), Positives = 80/150 (53%), Gaps = 3/150 (2%)
Query: 819 KSIVFSQWTRMLDLVENSLNQHC-IQYRRLDGTMSLPARDRAVKDFNTDREITVMLMSLK 877
K +F+Q+ ++ N + + + L G +S RD + F + + +++S+K
Sbjct: 343 KIAIFTQFVDXGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIVLSVK 402
Query: 878 AGNLGLNMVAASHVILLDLWWNPTTEDQAVDRAHRIGQTRPVTVTRLTIRDTVEDRILKL 937
AG G+N+ +A+ VI D WWNP EDQA DR +RIGQTR V V +L T+E++I +L
Sbjct: 403 AGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEKIDQL 462
Query: 938 QDDKRKMVASAFGEDQGGGTASRLTVEDLR 967
KR + G + L+ E+LR
Sbjct: 463 LAFKRSLFKDIIS--SGDSWITELSTEELR 490
Score = 55.5 bits (132), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 68/269 (25%), Positives = 116/269 (43%), Gaps = 48/269 (17%)
Query: 387 TLVVCPASVLRQWARELEDKVPDKAALSVLIYHGGSRTKDPVELAKYDVVLTTYSIV--- 443
+LV+CP SVL+ W EL P L ++H + ++L YD++LTTY+++
Sbjct: 89 SLVICPLSVLKNWEEELSKFAPH---LRFAVFH---EDRSKIKLEDYDIILTTYAVLLRD 142
Query: 444 --TNEVPKQPSVDEEEADEKNGETYGLSSEFSVNKKRKKIXXXXXXXXXXXXXXXXXXID 501
EV + V +E + KN +T + + K + I
Sbjct: 143 TRLKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYR--------------------IA 182
Query: 502 YGCGPLAKVGWFRVVLDEAQTIKNHRTQ-VARACCSLRAKRSTIKIPISRNSLHGYKKLQ 560
P+ +D+ +I + + ++K +T PI + ++L+
Sbjct: 183 LTGTPIEN------KVDDLWSIXTFLNPGLLGSYSEFKSKFAT---PIKKGDNXAKEELK 233
Query: 561 AVLRAIMLRRTKGTFIDGQPIINLPPKTISLTKVDFSKEEWAFYKKLESDSLKKFKAFAD 620
A++ +LRRTK D I +LP K + + + E+ A YK E ++L F D
Sbjct: 234 AIISPFILRRTK---YDKAIINDLPDKIETNVYCNLTPEQAAXYKA-EVENL--FNNI-D 286
Query: 621 AGTVNQNYANILLMLLRLRQACDHPLLVK 649
+ T + IL LL+L+Q DHP L+K
Sbjct: 287 SVTGIKRKGXILSTLLKLKQIVDHPALLK 315
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 91.3 bits (225), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 54/154 (35%), Positives = 84/154 (54%), Gaps = 5/154 (3%)
Query: 819 KSIVFSQWTRMLDLVENSLNQHCIQYRRLDGTMSLPARDRAVKDFN--TDREITVMLMSL 876
K ++ S +T+ LDL E Y RLDGTMS+ R + V+ FN + E ML S
Sbjct: 418 KVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSIKKRAKIVERFNNPSSPEFIFMLSS- 476
Query: 877 KAGNLGLNMVAASHVILLDLWWNPTTEDQAVDRAHRIGQTRPVTVTRLTIRDTVEDRILK 936
KAG GLN++ A+ +++ D WNP ++QA+ R R GQ + + RL T+E++IL+
Sbjct: 477 KAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWRDGQKKTCYIYRLLSTGTIEEKILQ 536
Query: 937 LQDDKRKMVASAFGEDQGGGTASRLTVEDLRYLF 970
Q K+ + + E+Q ++ +LR LF
Sbjct: 537 RQAHKKALSSCVVDEEQ--DVERHFSLGELRELF 568
Score = 32.7 bits (73), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 268 DGLLSVNLLKHQK--IALAWMLQKETRSLHCLGGILADDQGLGKTISIIALI 317
D +LS L HQ+ + W R + G I+AD+ GLGKT+ I LI
Sbjct: 49 DPVLSKVLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLI 100
>pdb|3DMQ|A Chain A, Crystal Structure Of Rapa, A Swi2SNF2 PROTEIN THAT
Recycles Rna Polymerase During Transcription
pdb|3DMQ|B Chain B, Crystal Structure Of Rapa, A Swi2SNF2 PROTEIN THAT
Recycles Rna Polymerase During Transcription
Length = 968
Score = 40.8 bits (94), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 35/70 (50%)
Query: 852 SLPARDRAVKDFNTDREITVMLMSLKAGNLGLNMVAASHVILLDLWWNPTTEDQAVDRAH 911
S+ RDRA F + +L+ + G+ G N ASH + DL +NP +Q + R
Sbjct: 539 SIIERDRAAAWFAEEDTGAQVLLCSEIGSEGRNFQFASHXVXFDLPFNPDLLEQRIGRLD 598
Query: 912 RIGQTRPVTV 921
RIGQ + +
Sbjct: 599 RIGQAHDIQI 608
>pdb|2LDR|A Chain A, Solution Structure Of Helix-Ring Domain Of Cbl-B In The
Tyr363 Phosphorylated Form
Length = 82
Score = 39.7 bits (91), Expect = 0.008, Method: Composition-based stats.
Identities = 14/54 (25%), Positives = 28/54 (51%)
Query: 674 DLLSRLETSSAICCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCPAPRCK 727
+L + ++ +C +C++ +D + CGH+ C C + + D CP RC+
Sbjct: 17 ELXCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTAWQESDGQGCPFCRCE 70
>pdb|3VGO|A Chain A, Crystal Structure Of The N-Terminal Fragment Of Cbl-B
pdb|3VGO|B Chain B, Crystal Structure Of The N-Terminal Fragment Of Cbl-B
pdb|3VGO|C Chain C, Crystal Structure Of The N-Terminal Fragment Of Cbl-B
Length = 394
Score = 39.3 bits (90), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 28/54 (51%)
Query: 674 DLLSRLETSSAICCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCPAPRCK 727
+L + ++ +C +C++ +D + CGH+ C C + + D CP RC+
Sbjct: 329 ELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTAWQESDGQGCPFCRCE 382
>pdb|2K4D|A Chain A, E2-C-Cbl Recognition Is Necessary But Not Sufficient For
Ubiquitination Activity
Length = 83
Score = 38.1 bits (87), Expect = 0.022, Method: Composition-based stats.
Identities = 13/54 (24%), Positives = 28/54 (51%)
Query: 674 DLLSRLETSSAICCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCPAPRCK 727
+L + ++ +C +C++ +D + CGH+ C C + + + CP RC+
Sbjct: 15 ELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCE 68
>pdb|4A49|A Chain A, Structure Of Phosphotyr371-C-Cbl-Ubch5b Complex
Length = 84
Score = 37.7 bits (86), Expect = 0.028, Method: Composition-based stats.
Identities = 13/54 (24%), Positives = 28/54 (51%)
Query: 674 DLLSRLETSSAICCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCPAPRCK 727
+L + ++ +C +C++ +D + CGH+ C C + + + CP RC+
Sbjct: 18 ELXCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCE 71
>pdb|4A4B|A Chain A, Structure Of Modified Phosphotyr371-C-Cbl-Ubch5b-Zap-70
Complex
Length = 391
Score = 37.7 bits (86), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 13/55 (23%), Positives = 28/55 (50%)
Query: 673 IDLLSRLETSSAICCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCPAPRCK 727
+L + ++ +C +C++ +D + CGH+ C C + + + CP RC+
Sbjct: 324 FELXCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCE 378
>pdb|2Y1M|A Chain A, Structure Of Native C-Cbl
pdb|2Y1M|B Chain B, Structure Of Native C-Cbl
pdb|2Y1M|C Chain C, Structure Of Native C-Cbl
pdb|2Y1M|D Chain D, Structure Of Native C-Cbl
pdb|2Y1M|E Chain E, Structure Of Native C-Cbl
pdb|2Y1M|F Chain F, Structure Of Native C-Cbl
pdb|2Y1N|A Chain A, Structure Of C-Cbl-Zap-70 Peptide Complex
pdb|2Y1N|C Chain C, Structure Of C-Cbl-Zap-70 Peptide Complex
Length = 389
Score = 37.4 bits (85), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 28/54 (51%)
Query: 674 DLLSRLETSSAICCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCPAPRCK 727
+L + ++ +C +C++ +D + CGH+ C C + + + CP RC+
Sbjct: 323 ELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCE 376
>pdb|1FBV|A Chain A, Structure Of A Cbl-Ubch7 Complex: Ring Domain Function In
Ubiquitin-Protein Ligases
Length = 388
Score = 37.4 bits (85), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 28/54 (51%)
Query: 674 DLLSRLETSSAICCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCPAPRCK 727
+L + ++ +C +C++ +D + CGH+ C C + + + CP RC+
Sbjct: 323 ELYCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCE 376
>pdb|4A4C|A Chain A, Structure Of Phosphotyr371-C-Cbl-Ubch5b-Zap-70 Complex
Length = 391
Score = 37.4 bits (85), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 13/54 (24%), Positives = 28/54 (51%)
Query: 674 DLLSRLETSSAICCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCPAPRCK 727
+L + ++ +C +C++ +D + CGH+ C C + + + CP RC+
Sbjct: 325 ELXCEMGSTFQLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQGCPFCRCE 378
>pdb|2CSY|A Chain A, Solution Structure Of The Ring Domain Of The Zinc Finger
Protein 183-Like 1
Length = 81
Score = 34.7 bits (78), Expect = 0.27, Method: Composition-based stats.
Identities = 15/41 (36%), Positives = 19/41 (46%), Gaps = 6/41 (14%)
Query: 686 CCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCPAPRC 726
C +C ++ VVT C H FC CA E+ PRC
Sbjct: 18 CFICRQAFQNPVVTKCRHYFCESCALEHFRA------TPRC 52
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 33.9 bits (76), Expect = 0.51, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 21/43 (48%)
Query: 684 AICCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCPAPRC 726
A C VC + ++ V+ CGH FC C + + + P P C
Sbjct: 16 ASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC 58
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 33.5 bits (75), Expect = 0.56, Method: Composition-based stats.
Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 697 VVTMCGHVFCYQCASEYITGDDNMCPAPRCK 727
V T CGHVFC QC + + + N CP R K
Sbjct: 24 VSTECGHVFCSQCLRDSLK-NANTCPTCRKK 53
>pdb|3VK6|A Chain A, Crystal Structure Of A Phosphotyrosine Binding Domain
Length = 101
Score = 33.5 bits (75), Expect = 0.62, Method: Composition-based stats.
Identities = 12/23 (52%), Positives = 13/23 (56%)
Query: 701 CGHVFCYQCASEYITGDDNMCPA 723
C HVFCY CA + D MCP
Sbjct: 20 CKHVFCYDCAILHEKKGDKMCPG 42
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 33.5 bits (75), Expect = 0.63, Method: Composition-based stats.
Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 697 VVTMCGHVFCYQCASEYITGDDNMCPAPRCK 727
V T CGHVFC QC + + + N CP R K
Sbjct: 28 VSTECGHVFCSQCLRDSLK-NANTCPTCRKK 57
Score = 33.5 bits (75), Expect = 0.63, Method: Composition-based stats.
Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 697 VVTMCGHVFCYQCASEYITGDDNMCPAPRCK 727
V T CGHVFC QC + + + N CP R K
Sbjct: 93 VSTECGHVFCSQCLRDSLK-NANTCPTCRKK 122
>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 = 33.1 bits (74), Expect = 0.70, Method: Composition-based stats.
Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 697 VVTMCGHVFCYQCASEYITGDDNMCPAPRCK 727
V T CGHVFC QC + + + N CP R K
Sbjct: 31 VSTECGHVFCSQCLRDSLK-NANTCPTCRKK 60
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 32.7 bits (73), Expect = 0.90, Method: Composition-based stats.
Identities = 15/31 (48%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 697 VVTMCGHVFCYQCASEYITGDDNMCPAPRCK 727
V T CGHVFC QC + + + N CP R K
Sbjct: 36 VSTECGHVFCSQCLRDSLK-NANTCPTCRKK 65
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 32.3 bits (72), Expect = 1.2, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 22/51 (43%)
Query: 685 ICCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCPAPRCKEQLGADVV 735
IC +C D + V CGH FC +C ++ P CK + + +
Sbjct: 22 ICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRKNAI 72
>pdb|3PEU|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1
H337r And Ip6
pdb|3PEV|A Chain A, S. Cerevisiae Dbp5 L327v C-Terminal Domain Bound To Gle1
And Ip6
Length = 188
Score = 32.0 bits (71), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 45/100 (45%), Gaps = 8/100 (8%)
Query: 820 SIVFSQWTRMLDLVENSLNQHCIQYRRLDGTMSLPARDRAVKDFNTDREITVMLMSLKAG 879
SI+F + +++ L + L G + RDR + DF R ++ ++ A
Sbjct: 39 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLA- 97
Query: 880 NLGLNMVAASHVILLDLWWNPTTEDQAVDRA---HRIGQT 916
G+++ S V+ DL PT + D A HRIG+T
Sbjct: 98 -RGIDIPTVSXVVNYDL---PTLANGQADPATYIHRIGRT 133
>pdb|3GFP|A Chain A, Structure Of The C-Terminal Domain Of The Dead-Box Protein
Dbp5
Length = 189
Score = 32.0 bits (71), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 45/100 (45%), Gaps = 8/100 (8%)
Query: 820 SIVFSQWTRMLDLVENSLNQHCIQYRRLDGTMSLPARDRAVKDFNTDREITVMLMSLKAG 879
SI+F + +++ L + L G + RDR + DF R ++ ++ A
Sbjct: 40 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLA- 98
Query: 880 NLGLNMVAASHVILLDLWWNPTTEDQAVDRA---HRIGQT 916
G+++ S V+ DL PT + D A HRIG+T
Sbjct: 99 -RGIDIPTVSXVVNYDL---PTLANGQADPATYIHRIGRT 134
>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 = 32.0 bits (71), Expect = 1.9, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 2/45 (4%)
Query: 679 LETSSAICCVC-SDPPEDSVVTMCGHVFCYQCASEYITGDDNMCP 722
+ T + C +C DP S+ C H FCY C + +I + CP
Sbjct: 1 MATVAERCPICLEDPSNYSMALPCLHAFCYVCITRWIR-QNPTCP 44
>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3
pdb|3RRM|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Nup159, Gle1 H337r, Ip6
And Adp
pdb|3RRN|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Gle1 H337r And Ip6
Length = 395
Score = 31.6 bits (70), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 45/100 (45%), Gaps = 8/100 (8%)
Query: 820 SIVFSQWTRMLDLVENSLNQHCIQYRRLDGTMSLPARDRAVKDFNTDREITVMLMSLKAG 879
SI+F + +++ L + L G + RDR + DF R ++ ++ A
Sbjct: 246 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 305
Query: 880 NLGLNMVAASHVILLDLWWNPTTEDQAVDRA---HRIGQT 916
G+++ S V+ DL PT + D A HRIG+T
Sbjct: 306 --GIDIPTVSMVVNYDL---PTLANGQADPATYIHRIGRT 340
>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3
Length = 395
Score = 31.6 bits (70), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 45/100 (45%), Gaps = 8/100 (8%)
Query: 820 SIVFSQWTRMLDLVENSLNQHCIQYRRLDGTMSLPARDRAVKDFNTDREITVMLMSLKAG 879
SI+F + +++ L + L G + RDR + DF R ++ ++ A
Sbjct: 246 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLAR 305
Query: 880 NLGLNMVAASHVILLDLWWNPTTEDQAVDRA---HRIGQT 916
G+++ S V+ DL PT + D A HRIG+T
Sbjct: 306 --GIDIPTVSMVVNYDL---PTLANGQADPATYIHRIGRT 340
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 31.2 bits (69), Expect = 3.0, Method: Composition-based stats.
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 685 ICCVCSDPPEDSVVTMCGHVFCYQCASE 712
IC +C D + V CGH FC +C ++
Sbjct: 22 ICPICLDILQKPVTIDCGHNFCLKCITQ 49
>pdb|2KBF|A Chain A, Solution Structure Of Carboxyl-Terminal Domain Of Dbp5p
Length = 187
Score = 31.2 bits (69), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 27/100 (27%), Positives = 45/100 (45%), Gaps = 8/100 (8%)
Query: 820 SIVFSQWTRMLDLVENSLNQHCIQYRRLDGTMSLPARDRAVKDFNTDREITVMLMSLKAG 879
SI+F + +++ L + L G + RDR + DF R ++ ++ A
Sbjct: 38 SIIFVATKKTANVLYGKLKSEGHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNVLA- 96
Query: 880 NLGLNMVAASHVILLDLWWNPTTEDQAVDRA---HRIGQT 916
G+++ S V+ DL PT + D A HRIG+T
Sbjct: 97 -RGIDIPTVSMVVNYDL---PTLANGQADPATYIHRIGRT 132
>pdb|3HCT|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The P1
Space Group
pdb|3HCU|A Chain A, Crystal Structure Of Traf6 In Complex With Ubc13 In The C2
Space Group
pdb|3HCU|C Chain C, Crystal Structure Of Traf6 In Complex With Ubc13 In The C2
Space Group
Length = 118
Score = 31.2 bits (69), Expect = 3.3, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 18/37 (48%)
Query: 686 CCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCP 722
C +C ++V T CGH FC C + I + CP
Sbjct: 21 CPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCP 57
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 31.2 bits (69), Expect = 3.3, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 18/37 (48%)
Query: 686 CCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCP 722
C +C ++V T CGH FC C + I + CP
Sbjct: 9 CPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCP 45
>pdb|2ECY|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger)" Domain Of Tnf Receptor-Associated Factor 3
Length = 66
Score = 30.8 bits (68), Expect = 3.6, Method: Composition-based stats.
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 699 TMCGHVFCYQCASEYITGDDNMCPAPRCKEQLGADVVF 736
T CGH FC C + ++ C A C+E + D VF
Sbjct: 31 TECGHRFCESCMAALLSSSSPKCTA--CQESIVKDKVF 66
>pdb|3TOJ|A Chain A, Structure Of The Spry Domain Of Human Ash2l
pdb|3TOJ|B Chain B, Structure Of The Spry Domain Of Human Ash2l
Length = 213
Score = 30.8 bits (68), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 40/84 (47%), Gaps = 12/84 (14%)
Query: 837 LNQHCIQYRRLDGTMSLPARDRAVKDFNTDREITVMLMSLKAGNLGLNMVAASHVILLDL 896
L + C+ R L L DRA + +D +TV+ G G +MV ASH +
Sbjct: 4 LYRACLYERVL-----LALHDRAPQLKISDDRLTVV------GEKGYSMVRASHGVRKGA 52
Query: 897 WWNPTTEDQ-AVDRAHRIGQTRPV 919
W+ T D+ D A R+G ++P+
Sbjct: 53 WYFEITVDEMPPDTAARLGWSQPL 76
>pdb|3HCS|A Chain A, Crystal Structure Of The N-Terminal Domain Of Traf6
pdb|3HCS|B Chain B, Crystal Structure Of The N-Terminal Domain Of Traf6
Length = 170
Score = 30.8 bits (68), Expect = 4.0, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 18/37 (48%)
Query: 686 CCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCP 722
C +C ++V T CGH FC C + I + CP
Sbjct: 21 CPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCP 57
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 30.8 bits (68), Expect = 4.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 18/37 (48%)
Query: 686 CCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCP 722
C +C ++V T CGH FC C + I + CP
Sbjct: 28 CPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCP 64
>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 = 30.8 bits (68), Expect = 4.2, Method: Composition-based stats.
Identities = 16/65 (24%), Positives = 33/65 (50%), Gaps = 3/65 (4%)
Query: 685 ICCVCSDPPEDSVVT-MCGHVFCYQCA-SEYITGDDNMCPAPRCKEQLGADVVFSKTTLK 742
+C +C D D+VV CG+ +C +C + + D++ CP + + D + + L+
Sbjct: 15 LCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCH-QNDVSPDALIANKFLR 73
Query: 743 NCVSD 747
V++
Sbjct: 74 QAVNN 78
>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 = 5.3, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 686 CCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCPAPRCKEQLGADVVFSKTTLKNCV 745
C +CS+ ++V C H FC C +E++ P C++ + + L NC+
Sbjct: 67 CIICSEYFIEAVTLNCAHSFCSYCINEWMK---RKIECPICRKDIKSKTY--SLVLDNCI 121
Query: 746 S 746
+
Sbjct: 122 N 122
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 30.0 bits (66), Expect = 6.7, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 5/61 (8%)
Query: 686 CCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCPAPRCKEQLGADVVFSKTTLKNCV 745
C +CS+ ++V C H FC C +E++ P C++ + + L NC+
Sbjct: 56 CIICSEYFIEAVTLNCAHSFCSYCINEWMK---RKIECPICRKDIKSKTY--SLVLDNCI 110
Query: 746 S 746
+
Sbjct: 111 N 111
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 29.6 bits (65), Expect = 7.5, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 20/45 (44%)
Query: 686 CCVCSDPPEDSVVTMCGHVFCYQCASEYITGDDNMCPAPRCKEQL 730
C +C + ++ V T C H+FC C + + P CK +
Sbjct: 24 CPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDI 68
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 0.132 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,789,242
Number of Sequences: 62578
Number of extensions: 1019180
Number of successful extensions: 2005
Number of sequences better than 100.0: 46
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 1958
Number of HSP's gapped (non-prelim): 62
length of query: 972
length of database: 14,973,337
effective HSP length: 108
effective length of query: 864
effective length of database: 8,214,913
effective search space: 7097684832
effective search space used: 7097684832
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: 56 (26.2 bits)