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= 004925
(723 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 = 120 bits (300), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 105/463 (22%), Positives = 196/463 (42%), Gaps = 126/463 (27%)
Query: 239 LHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQI 298
L S+KW+ + +DEAH +K+ S+ +++ + + + + ++GTPLQN + EL +LV FL
Sbjct: 363 LGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLITGTPLQNNIKELAALVNFL-- 420
Query: 299 TPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRAMIL 358
P + ++ D + D E + H ++ F
Sbjct: 421 MPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPF-------------------------- 454
Query: 359 LKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNTYVQ 418
ILRR KK + +LP + + R L + +YY+++ +++ + +
Sbjct: 455 ---------ILRRLKKD--VEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAK 503
Query: 419 AGTVMNNYAHIFDLLTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQQVCGLCNDLADD 478
G + + +++ L++A +HPY
Sbjct: 504 GG-----HFSLLNIMNELKKASNHPY---------------------------------- 524
Query: 479 PVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFTANEGAGNRTSKTTIKGFKSSS 538
LFD++ + + K G G T + ++G
Sbjct: 525 --------------LFDNAEERVLQKF---------------GDGKMTRENVLRGL---- 551
Query: 539 ILNRIQLDEFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCV 598
SS K+ L +++ +++DG + ++FSQ LD++ L G+N
Sbjct: 552 ---------IMSSGKM-VLLDQLLTRLKKDGH-RVLIFSQMVRMLDILGDYLSIKGINFQ 600
Query: 599 QLVGSMSIPARDAAINRFTEDPDCK--IFLMSLKAGGVALNLTVASHVFLMDPWWNPAVE 656
+L G++ R +I+ F PD +FL+S +AGG+ +NL A V + D WNP +
Sbjct: 601 RLDGTVPSAQRRISIDHFNS-PDSNDFVFLLSTRAGGLGINLMTADTVVIFDSDWNPQAD 659
Query: 657 QQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEKKKLVFE 699
QA R HRIGQ + + R + ++T+EE +L+ + +KK++ E
Sbjct: 660 LQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLE-RARKKMILE 701
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 31/139 (22%), Positives = 58/139 (41%), Gaps = 44/139 (31%)
Query: 37 WLAWALKQEESAIRGGILADEMGMGKTIQAIA----LVLAKREIRGTIGELDASSSSSTG 92
W+A+ + ++ GILADEMG+GKT+Q +A L+ A+R+ I
Sbjct: 247 WMAFLWSKGDN----GILADEMGLGKTVQTVAFISWLIFARRQNGPHI------------ 290
Query: 93 LLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERS--------------A 138
++ P++ + W+ ++ + Y G+ + R
Sbjct: 291 --------IVVPLSTMPAWLDTFEKWAP--DLNCICYMGNQKSRDTIREYEFYTNPRAKG 340
Query: 139 KQFSEFDFVITTYSIIEAD 157
K+ +F+ ++TTY I D
Sbjct: 341 KKTMKFNVLLTTYEYILKD 359
>pdb|1Z6A|A Chain A, Sulfolobus Solfataricus Swi2SNF2 ATPASE CORE DOMAIN
Length = 500
Score = 95.9 bits (237), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 51/152 (33%), Positives = 82/152 (53%), Gaps = 1/152 (0%)
Query: 568 DGSAKGIVFSQFTSFLDLINYSLHKS-GVNCVQLVGSMSIPARDAAINRFTEDPDCKIFL 626
D K +F+QF +I + K L G +S RD I++F +P K +
Sbjct: 339 DEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIV 398
Query: 627 MSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEER 686
+S+KAGG +NLT A+ V D WWNPAVE QA DR++RIGQ + + + + + T+EE+
Sbjct: 399 LSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEK 458
Query: 687 ILKLQEKKKLVFEGTVGGSADAFGKLTEADMR 718
I +L K+ +F+ + +L+ ++R
Sbjct: 459 IDQLLAFKRSLFKDIISSGDSWITELSTEELR 490
Score = 70.5 bits (171), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 62/211 (29%), Positives = 99/211 (46%), Gaps = 44/211 (20%)
Query: 239 LHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQ- 297
L ++W+ I++DEA IK+ ++ KAV L+S Y+ AL+GTP++N+V +L+S++ FL
Sbjct: 145 LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIMTFLNP 204
Query: 298 --ITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRA 355
+ YS + K ATPI+ G A
Sbjct: 205 GLLGSYSEFKSK-------------------------------FATPIKK-----GDNMA 228
Query: 356 MILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNT 415
LK ++ ILRRTK +A LP +I + +L +A Y+ +E + FN
Sbjct: 229 KEELKA-IISPFILRRTKYDKAIINDLPDKIETNVYCNLTPEQAAMYK---AEVENLFNN 284
Query: 416 YVQAGTVMNNYAHIFDLLTRLRQAVDHPYLV 446
+ + T + I L +L+Q VDHP L+
Sbjct: 285 -IDSVTGIKRKGMILSTLLKLKQIVDHPALL 314
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 40/139 (28%), Positives = 69/139 (49%), Gaps = 25/139 (17%)
Query: 22 DPPDLITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVL-AKREIRGTI 80
+P ++ L YQ + +W + G LAD+MG+GKT+Q IA+ AK+E
Sbjct: 30 EPYNIKANLRPYQIKGFSWMRFMNKLGF-GICLADDMGLGKTLQTIAVFSDAKKE----- 83
Query: 81 GELDASSSSSTGLLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERSAKQ 140
EL S LVICP++ + W E+++F + ++H +RS +
Sbjct: 84 NELTPS-------------LVICPLSVLKNWEEELSKFAP--HLRFAVFH---EDRSKIK 125
Query: 141 FSEFDFVITTYSIIEADYR 159
++D ++TTY+++ D R
Sbjct: 126 LEDYDIILTTYAVLLRDTR 144
>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 = 95.5 bits (236), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 51/152 (33%), Positives = 82/152 (53%), Gaps = 1/152 (0%)
Query: 568 DGSAKGIVFSQFTSFLDLINYSLHKS-GVNCVQLVGSMSIPARDAAINRFTEDPDCKIFL 626
D K +F+QF +I + K L G +S RD I++F +P K +
Sbjct: 339 DEGDKIAIFTQFVDXGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIV 398
Query: 627 MSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEER 686
+S+KAGG +NLT A+ V D WWNPAVE QA DR++RIGQ + + + + + T+EE+
Sbjct: 399 LSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEK 458
Query: 687 ILKLQEKKKLVFEGTVGGSADAFGKLTEADMR 718
I +L K+ +F+ + +L+ ++R
Sbjct: 459 IDQLLAFKRSLFKDIISSGDSWITELSTEELR 490
Score = 70.1 bits (170), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 62/211 (29%), Positives = 98/211 (46%), Gaps = 44/211 (20%)
Query: 239 LHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFLQ- 297
L ++W+ I++DEA IK+ ++ KAV L+S Y+ AL+GTP++N+V +L+S+ FL
Sbjct: 145 LKEVEWKYIVIDEAQNIKNPQTKIFKAVKELKSKYRIALTGTPIENKVDDLWSIXTFLNP 204
Query: 298 --ITPYSYYFCKDCDCKVLDYSSAECPNCPHNSVRHFCWWNRYVATPIQTHGNSYGGRRA 355
+ YS + K ATPI+ G A
Sbjct: 205 GLLGSYSEFKSK-------------------------------FATPIKK-----GDNXA 228
Query: 356 MILLKHKVLRSVILRRTKKGRAADLALPPRIVSLRRDSLDIREADYYESLYSESQAQFNT 415
LK ++ ILRRTK +A LP +I + +L +A Y+ +E + FN
Sbjct: 229 KEELKA-IISPFILRRTKYDKAIINDLPDKIETNVYCNLTPEQAAXYK---AEVENLFNN 284
Query: 416 YVQAGTVMNNYAHIFDLLTRLRQAVDHPYLV 446
+ + T + I L +L+Q VDHP L+
Sbjct: 285 -IDSVTGIKRKGXILSTLLKLKQIVDHPALL 314
Score = 51.6 bits (122), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 39/139 (28%), Positives = 68/139 (48%), Gaps = 25/139 (17%)
Query: 22 DPPDLITPLLRYQKEWLAWALKQEESAIRGGILADEMGMGKTIQAIALVL-AKREIRGTI 80
+P ++ L YQ + +W + G LAD+ G+GKT+Q IA+ AK+E
Sbjct: 30 EPYNIKANLRPYQIKGFSWXRFXNKLGF-GICLADDXGLGKTLQTIAVFSDAKKE----- 83
Query: 81 GELDASSSSSTGLLGIKATLVICPVAAVTQWVSEINRFTSVGSTKVLIYHGSNRERSAKQ 140
EL S LVICP++ + W E+++F + ++H +RS +
Sbjct: 84 NELTPS-------------LVICPLSVLKNWEEELSKFAP--HLRFAVFH---EDRSKIK 125
Query: 141 FSEFDFVITTYSIIEADYR 159
++D ++TTY+++ D R
Sbjct: 126 LEDYDIILTTYAVLLRDTR 144
>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 = 95.1 bits (235), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 51/152 (33%), Positives = 82/152 (53%), Gaps = 1/152 (0%)
Query: 568 DGSAKGIVFSQFTSFLDLINYSLHKS-GVNCVQLVGSMSIPARDAAINRFTEDPDCKIFL 626
D K +F+QF +I + K L G +S RD I++F +P K +
Sbjct: 110 DEGDKIAIFTQFVDMGKIIRNIIEKELNTEVPFLYGELSKKERDDIISKFQNNPSVKFIV 169
Query: 627 MSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEER 686
+S+KAGG +NLT A+ V D WWNPAVE QA DR++RIGQ + + + + + T+EE+
Sbjct: 170 LSVKAGGFGINLTSANRVIHFDRWWNPAVEDQATDRVYRIGQTRNVIVHKLISVGTLEEK 229
Query: 687 ILKLQEKKKLVFEGTVGGSADAFGKLTEADMR 718
I +L K+ +F+ + +L+ ++R
Sbjct: 230 IDQLLAFKRSLFKDIISSGDSWITELSTEELR 261
>pdb|1Z3I|X Chain X, Structure Of The Swi2SNF2 CHROMATIN REMODELING DOMAIN OF
EUKARYOTIC Rad54
Length = 644
Score = 90.9 bits (224), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 64/176 (36%), Positives = 87/176 (49%), Gaps = 2/176 (1%)
Query: 547 EFQSSTKIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSI 606
E Q S K+ L + I M S K ++ S +T LDL V+L G+MSI
Sbjct: 394 EPQLSGKMLVL-DYILAMTRTTTSDKVVLVSNYTQTLDLFEKLCRNRRYLYVRLDGTMSI 452
Query: 607 PARDAAINRFTEDPDCK-IFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHR 665
R + RF + IF++S KAGG LNL A+ + + DP WNPA ++QA R+ R
Sbjct: 453 KKRAKIVERFNNPSSPEFIFMLSSKAGGCGLNLIGANRLVMFDPDWNPANDEQAMARVWR 512
Query: 666 IGQYKPIRIVRFLIENTIEERILKLQEKKKLVFEGTVGGSADAFGKLTEADMRFLF 721
GQ K I R L TIEE+IL+ Q KK + V D + ++R LF
Sbjct: 513 DGQKKTCYIYRLLSTGTIEEKILQRQAHKKALSSCVVDEEQDVERHFSLGELRELF 568
Score = 41.6 bits (96), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 35/58 (60%)
Query: 239 LHSLKWERIILDEAHFIKDRRSNTAKAVLALESSYKWALSGTPLQNRVGELYSLVRFL 296
LH K +I DE H +K+ + T A+ ++ + + +SGTP+QN + E +SLV F+
Sbjct: 188 LHKGKVGLVICDEGHRLKNSDNQTYLALNSMNAQRRVLISGTPIQNDLLEYFSLVHFV 245
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 38/89 (42%), Gaps = 12/89 (13%)
Query: 51 GGILADEMGMGKTIQAIALVLAKREIRGTIGELDASSSSSTGLLGIKATLVICPVAAVTQ 110
G I+ADEMG+GKT+Q I L+ S I +V+ P + V
Sbjct: 81 GCIMADEMGLGKTLQCITLIWT------------LLKQSPDCKPEIDKVIVVSPSSLVRN 128
Query: 111 WVSEINRFTSVGSTKVLIYHGSNRERSAK 139
W +E+ ++ V I GS E +K
Sbjct: 129 WYNEVGKWLGGRVQPVAIDGGSKDEIDSK 157
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 16/47 (34%), Positives = 28/47 (59%), Gaps = 4/47 (8%)
Query: 469 CGLCNDLADDPVVTNCGHAFCKACL---FDSSA-SKFVAKCPTCSIP 511
C +C +L +PV +C H+FC+AC+ ++S+ + CP C +P
Sbjct: 22 CPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVP 68
>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 = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 469 CGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAK----CPTCSI 510
C +C +L P+ +CGH+FC+ACL + + K CP C I
Sbjct: 22 CPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCRI 67
>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human
Tripartite Motif Protein 34
Length = 79
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 469 CGLCNDLADDPVVTNCGHAFCKACLFDSSASKFV-----AKCPTCSIPLTVD-FTANEGA 522
C +C +L +P+ +CGH+ C+AC+ S+ + CP C I + + AN+
Sbjct: 15 CPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVCGISYSFEHLQANQHL 74
Query: 523 GN 524
N
Sbjct: 75 AN 76
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 464 HVQQVCGLCNDLADDPVVTNCGHAFCKACL---FDSSASKFVAKCPTC 508
V+ C +C + +PV+ CGH FCKAC+ ++ F CP C
Sbjct: 13 QVEASCSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDF--PCPVC 58
>pdb|2YSJ|A Chain A, Solution Structure Of The Ring Domain (1-56) From
Tripartite Motif-containing Protein 31
Length = 63
Score = 39.7 bits (91), Expect = 0.005, Method: Composition-based stats.
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 468 VCGLCNDLADDPVVTNCGHAFCKACLF---DSSASKFVAKCPTC 508
+C +C D+ PV +CGH FC C+ ++S F KCP C
Sbjct: 22 ICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFF--KCPLC 63
>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 = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 32/128 (25%), Positives = 53/128 (41%)
Query: 574 IVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSLKAGG 633
++ ++ + L L + G+ SI RD A F E+ L+ + G
Sbjct: 508 VICAKAATALQLEQVLREREGIRAAVFHEGXSIIERDRAAAWFAEEDTGAQVLLCSEIGS 567
Query: 634 VALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQYKPIRIVRFLIENTIEERILKLQEK 693
N ASH D +NP + +Q R+ RIGQ I+I +E T + +++ +
Sbjct: 568 EGRNFQFASHXVXFDLPFNPDLLEQRIGRLDRIGQAHDIQIHVPYLEKTAQSVLVRWYHE 627
Query: 694 KKLVFEGT 701
FE T
Sbjct: 628 GLDAFEHT 635
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 39.3 bits (90), Expect = 0.007, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 469 CGLCNDLADDPVVTNCGHAFCKACLFD-SSASKFVAKCPTCSIPLT 513
C +C +L +PV T C H FCK C+ + K ++CP C +T
Sbjct: 24 CPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDIT 69
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 39.3 bits (90), Expect = 0.007, Method: Composition-based stats.
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 468 VCGLCNDLADDPVVTNCGHAFCKACLF---DSSASKFVAKCPTC 508
+C +C D+ PV +CGH FC C+ ++S F KCP C
Sbjct: 22 ICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFF--KCPLC 63
>pdb|1RMD|A Chain A, Rag1 Dimerization Domain
Length = 116
Score = 38.5 bits (88), Expect = 0.012, Method: Composition-based stats.
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 469 CGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIP 511
C +C + DPV T+C H FC+ C+ + CP+C P
Sbjct: 26 CQICEHILADPVETSCKHLFCRICIL-RCLKVMGSYCPSCRYP 67
>pdb|3L11|A Chain A, Crystal Structure Of The Ring Domain Of Rnf168
Length = 115
Score = 37.4 bits (85), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 469 CGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTC 508
CG+C ++ +PV C H CK C F S+ K CP C
Sbjct: 18 CGICMEILVEPVTLPCNHTLCKPC-FQSTVEKASLCCPFC 56
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 35.4 bits (80), Expect = 0.10, Method: Composition-based stats.
Identities = 16/29 (55%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 480 VVTNCGHAFCKACLFDSSASKFVAKCPTC 508
V T CGH FC CL DS K CPTC
Sbjct: 28 VSTECGHVFCSQCLRDS--LKNANTCPTC 54
Score = 35.4 bits (80), Expect = 0.10, Method: Composition-based stats.
Identities = 16/29 (55%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 480 VVTNCGHAFCKACLFDSSASKFVAKCPTC 508
V T CGH FC CL DS K CPTC
Sbjct: 93 VSTECGHVFCSQCLRDS--LKNANTCPTC 119
>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 = 35.4 bits (80), Expect = 0.10, Method: Composition-based stats.
Identities = 16/29 (55%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 480 VVTNCGHAFCKACLFDSSASKFVAKCPTC 508
V T CGH FC CL DS K CPTC
Sbjct: 31 VSTECGHVFCSQCLRDS--LKNANTCPTC 57
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 35.4 bits (80), Expect = 0.10, Method: Composition-based stats.
Identities = 16/29 (55%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 480 VVTNCGHAFCKACLFDSSASKFVAKCPTC 508
V T CGH FC CL DS K CPTC
Sbjct: 24 VSTECGHVFCSQCLRDS--LKNANTCPTC 50
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 35.4 bits (80), Expect = 0.12, Method: Composition-based stats.
Identities = 16/29 (55%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 480 VVTNCGHAFCKACLFDSSASKFVAKCPTC 508
V T CGH FC CL DS K CPTC
Sbjct: 36 VSTECGHVFCSQCLRDS--LKNANTCPTC 62
>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 = 34.7 bits (78), Expect = 0.17, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 4/82 (4%)
Query: 458 TEADAEHVQQVCGLCNDLADDPVVTNC-GHAFCKACLFDSSASKFVAKCPTCSIPLTVDF 516
+E D + +C +C D+ D VV C G+++C C+ + CPTC D
Sbjct: 5 SEDDPIPDELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCH---QNDV 61
Query: 517 TANEGAGNRTSKTTIKGFKSSS 538
+ + N+ + + FK+ +
Sbjct: 62 SPDALIANKFLRQAVNNFKNET 83
>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 = 0.21, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 2/43 (4%)
Query: 469 CGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIP 511
C +C +PVVT C H FC++C + + +C C P
Sbjct: 18 CFICRQAFQNPVVTKCRHYFCESCALEH--FRATPRCYICDQP 58
>pdb|2DJB|A Chain A, Solution Structure Of The Ring Domain Of The Human
Polycomb Group Ring Finger Protein 6
Length = 72
Score = 34.3 bits (77), Expect = 0.22, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 468 VCGLCND-LADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSI 510
+C +C L D +T C H FCK+C+ + +CP C+I
Sbjct: 17 LCSICKGYLIDATTITECLHTFCKSCIV--RHFYYSNRCPKCNI 58
>pdb|4DB2|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
pdb|4DB2|B Chain B, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
Length = 257
Score = 34.3 bits (77), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 29/118 (24%), Positives = 55/118 (46%), Gaps = 14/118 (11%)
Query: 554 IEALREEIRFMVERDGSAKGIVFS---QFTSFLDLINYSLHKSGVNCVQLVGSMSIPARD 610
+E ++++I+ ERD + K I+F+ +FTSFL I + K + ++ G ++ R
Sbjct: 20 VEHIKKQIK---ERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRT 76
Query: 611 AAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQ 668
+ + RF +D L+ G ++ V + V + + IHRIG+
Sbjct: 77 SLVKRFKKDESG--ILVCTDVGARGMDFPNVHEVLQI------GVPSELANYIHRIGR 126
>pdb|1Z6U|A Chain A, Np95-Like Ring Finger Protein Isoform B [homo Sapiens]
pdb|1Z6U|B Chain B, Np95-Like Ring Finger Protein Isoform B [homo Sapiens]
Length = 150
Score = 34.3 bits (77), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 21/41 (51%), Gaps = 1/41 (2%)
Query: 468 VCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTC 508
+C C +L PV T C H CK CL S ++ V CP C
Sbjct: 80 MCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQ-VFSCPAC 119
>pdb|4DB4|A Chain A, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric
Rna-Dna Duplex
pdb|4DB4|B Chain B, Mss116p Dead-Box Helicase Domain 2 Bound To A Chimaeric
Rna-Dna Duplex
Length = 256
Score = 34.3 bits (77), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 29/118 (24%), Positives = 55/118 (46%), Gaps = 14/118 (11%)
Query: 554 IEALREEIRFMVERDGSAKGIVFS---QFTSFLDLINYSLHKSGVNCVQLVGSMSIPARD 610
+E ++++I+ ERD + K I+F+ +FTSFL I + K + ++ G ++ R
Sbjct: 20 VEHIKKQIK---ERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRT 76
Query: 611 AAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQ 668
+ + RF +D L+ G ++ V + V + + IHRIG+
Sbjct: 77 SLVKRFKKDESG--ILVCTDVGARGMDFPNVHEVLQI------GVPSELANYIHRIGR 126
>pdb|4DB2|C Chain C, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
pdb|4DB2|D Chain D, Mss116p Dead-Box Helicase Domain 2 Bound To An Rna Duplex
Length = 257
Score = 34.3 bits (77), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 29/118 (24%), Positives = 55/118 (46%), Gaps = 14/118 (11%)
Query: 554 IEALREEIRFMVERDGSAKGIVFS---QFTSFLDLINYSLHKSGVNCVQLVGSMSIPARD 610
+E ++++I+ ERD + K I+F+ +FTSFL I + K + ++ G ++ R
Sbjct: 20 VEHIKKQIK---ERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRT 76
Query: 611 AAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQ 668
+ + RF +D L+ G ++ V + V + + IHRIG+
Sbjct: 77 SLVKRFKKDESG--ILVCTDVGARGMDFPNVHEVLQI------GVPSELANYIHRIGR 126
>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And
Amp-Pnp
Length = 579
Score = 34.3 bits (77), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 29/118 (24%), Positives = 55/118 (46%), Gaps = 14/118 (11%)
Query: 554 IEALREEIRFMVERDGSAKGIVFS---QFTSFLDLINYSLHKSGVNCVQLVGSMSIPARD 610
+E ++++I+ ERD + K I+F+ +FTSFL I + K + ++ G ++ R
Sbjct: 275 VEHIKKQIK---ERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRT 331
Query: 611 AAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQ 668
+ + RF +D L+ G ++ V + V + + IHRIG+
Sbjct: 332 SLVKRFKKDESG--ILVCTDVGARGMDFPNVHEVLQI------GVPSELANYIHRIGR 381
>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp
pdb|3I5Y|A Chain A, Structure Of Mss116p Bound To Ssrna Containing A Single
5-Bru And Amp- Pnp
pdb|3I61|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-beryllium
Fluoride
pdb|3I62|A Chain A, Structure Of Mss116p Bound To Ssrna And Adp-aluminum
Fluoride
Length = 563
Score = 34.3 bits (77), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 29/118 (24%), Positives = 55/118 (46%), Gaps = 14/118 (11%)
Query: 554 IEALREEIRFMVERDGSAKGIVFS---QFTSFLDLINYSLHKSGVNCVQLVGSMSIPARD 610
+E ++++I+ ERD + K I+F+ +FTSFL I + K + ++ G ++ R
Sbjct: 326 VEHIKKQIK---ERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRT 382
Query: 611 AAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQ 668
+ + RF +D L+ G ++ V + V + + IHRIG+
Sbjct: 383 SLVKRFKKDESG--ILVCTDVGARGMDFPNVHEVLQI------GVPSELANYIHRIGR 432
>pdb|3SQX|A Chain A, Structure Of Mss116p (Nte And C-Tail Double Deletion)
Bound To Ssrna And Amp-Pnp
Length = 512
Score = 33.9 bits (76), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 29/118 (24%), Positives = 55/118 (46%), Gaps = 14/118 (11%)
Query: 554 IEALREEIRFMVERDGSAKGIVFS---QFTSFLDLINYSLHKSGVNCVQLVGSMSIPARD 610
+E ++++I+ ERD + K I+F+ +FTSFL I + K + ++ G ++ R
Sbjct: 275 VEHIKKQIK---ERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRT 331
Query: 611 AAINRFTEDPDCKIFLMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQ 668
+ + RF +D L+ G ++ V + V + + IHRIG+
Sbjct: 332 SLVKRFKKDESG--ILVCTDVGARGMDFPNVHEVLQI------GVPSELANYIHRIGR 381
>pdb|2YUR|A Chain A, Solution Structure Of The Ring Finger Of Human
Retinoblastoma-Binding Protein 6
Length = 74
Score = 33.5 bits (75), Expect = 0.40, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 22/42 (52%), Gaps = 1/42 (2%)
Query: 468 VCGLCNDLADDPVVTNC-GHAFCKACLFDSSASKFVAKCPTC 508
+C +C D+ D VV C G+++C C+ + CPTC
Sbjct: 17 LCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTC 58
>pdb|2YJT|D Chain D, Crystal Structure Of E. Coli Dead-Box Protein Srmb Bound
To Regulator Of Ribonuclease Activity A (Rraa)
Length = 170
Score = 33.1 bits (74), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 26/99 (26%), Positives = 44/99 (44%), Gaps = 8/99 (8%)
Query: 570 SAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAAINRFTEDPDCKIFLMSL 629
+ + IVF + + + L ++G+N L G M R+ AI R TE + +
Sbjct: 30 ATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDV 89
Query: 630 KAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHRIGQ 668
A G+ ++ SHVF D + + +HRIG+
Sbjct: 90 AARGI--DIPDVSHVFNFD------MPRSGDTYLHRIGR 120
>pdb|3FL2|A Chain A, Crystal Structure Of The Ring Domain Of The E3 Ubiquitin-
Protein Ligase Uhrf1
Length = 124
Score = 33.1 bits (74), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 469 CGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTC 508
C C +L P+ T C H CK CL D S V CP C
Sbjct: 55 CICCQELVFRPITTVCQHNVCKDCL-DRSFRAQVFSCPAC 93
>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 = 33.1 bits (74), Expect = 0.62, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 9/67 (13%)
Query: 469 CGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTC-------SIPLTVDFTANEG 521
C +C++ + V NC H+FC C+ + K +CP C + L +D N+
Sbjct: 67 CIICSEYFIEAVTLNCAHSFCSYCINEWMKRKI--ECPICRKDIKSKTYSLVLDNCINKM 124
Query: 522 AGNRTSK 528
N +S+
Sbjct: 125 VNNLSSE 131
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 32.7 bits (73), Expect = 0.67, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 9/67 (13%)
Query: 469 CGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTC-------SIPLTVDFTANEG 521
C +C++ + V NC H+FC C+ + K +CP C + L +D N+
Sbjct: 56 CIICSEYFIEAVTLNCAHSFCSYCINEWMKRKI--ECPICRKDIKSKTYSLVLDNXINKM 113
Query: 522 AGNRTSK 528
N +S+
Sbjct: 114 VNNLSSE 120
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 32.7 bits (73), Expect = 0.74, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 31/67 (46%), Gaps = 9/67 (13%)
Query: 469 CGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTC-------SIPLTVDFTANEG 521
C +C++ + V NC H+FC C+ + K +CP C + L +D N+
Sbjct: 56 CIICSEYFIEAVTLNCAHSFCSYCINEWMKRKI--ECPICRKDIKSKTYSLVLDNCINKM 113
Query: 522 AGNRTSK 528
N +S+
Sbjct: 114 VNNLSSE 120
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 32.7 bits (73), Expect = 0.74, Method: Composition-based stats.
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 469 CGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCP 506
C +C + V T CGH FCKAC+ S KCP
Sbjct: 9 CPICLMALREAVQTPCGHRFCKACII-KSIRDAGHKCP 45
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 32.7 bits (73), Expect = 0.79, Method: Composition-based stats.
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 469 CGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCP 506
C +C + V T CGH FCKAC+ S KCP
Sbjct: 28 CPICLMALREAVQTPCGHRFCKACII-KSIRDAGHKCP 64
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 32.7 bits (73), Expect = 0.81, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 466 QQVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDFTANEGAG 523
++ C +C D D ++ C H+FC+ C+ S CP C + +T ANE +G
Sbjct: 15 EEECCICMDGRAD-LILPCAHSFCQKCI--DKWSDRHRNCPICRLQMT---GANESSG 66
>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 = 32.3 bits (72), Expect = 0.85, Method: Composition-based stats.
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 469 CGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCP 506
C +C + V T CGH FCKAC+ S KCP
Sbjct: 21 CPICLMALREAVQTPCGHRFCKACII-KSIRDAGHKCP 57
>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 = 32.3 bits (72), Expect = 0.93, Method: Composition-based stats.
Identities = 16/38 (42%), Positives = 19/38 (50%), Gaps = 1/38 (2%)
Query: 469 CGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCP 506
C +C + V T CGH FCKAC+ S KCP
Sbjct: 21 CPICLMALREAVQTPCGHRFCKACII-KSIRDAGHKCP 57
>pdb|1JM7|B Chain B, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 117
Score = 32.0 bits (71), Expect = 1.3, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 5/44 (11%)
Query: 469 CGLCNDLADDPV-VTNCGHAFCKACLFDSSASKFVAKCPTCSIP 511
C C ++ +PV + C H FC C+ D + CP C P
Sbjct: 25 CSRCTNILREPVCLGGCEHIFCSNCVSDCIGT----GCPVCYTP 64
>pdb|4AUQ|B Chain B, Structure Of Birc7-Ubch5b-Ub Complex.
pdb|4AUQ|E Chain E, Structure Of Birc7-Ubch5b-Ub Complex
Length = 62
Score = 32.0 bits (71), Expect = 1.4, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 8/59 (13%)
Query: 456 GETEADAEHVQQ--VCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPL 512
G EA +Q+ C +C D A V CGH C C + + CP C P+
Sbjct: 1 GSVEAQLRRLQEERTCKVCLDRAVSIVFVPCGHLVCAEC------APGLQLCPICRAPV 53
>pdb|4A49|A Chain A, Structure Of Phosphotyr371-C-Cbl-Ubch5b Complex
Length = 84
Score = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 467 QVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTC------SIPLTVD 515
Q+C +C + D + CGH C +CL S+ CP C + P+ VD
Sbjct: 28 QLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQG-CPFCRCEIKGTEPIVVD 81
>pdb|1WP9|A Chain A, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|B Chain B, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|C Chain C, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|D Chain D, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|E Chain E, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
pdb|1WP9|F Chain F, Crystal Structure Of Pyrococcus Furiosus Hef Helicase
Domain
Length = 494
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 33/140 (23%), Positives = 62/140 (44%), Gaps = 11/140 (7%)
Query: 553 KIEALREEIRFMVERDGSAKGIVFSQFTSFLDLINYSLHKSGVNCVQLVGSMSIPARDAA 612
K++ L+E IR ++R ++K IVF+ + I L K G+ + VG S D
Sbjct: 344 KMDKLKEIIREQLQRKQNSKIIVFTNYRETAKKIVNELVKDGIKAKRFVGQAS-KENDRG 402
Query: 613 INRFTEDPDCKIF-------LMSLKAGGVALNLTVASHVFLMDPWWNPAVEQQAQDRIHR 665
+++ + F L++ G L++ V +P P+ + Q R R
Sbjct: 403 LSQREQKLILDEFARGEFNVLVATSVGEEGLDVPEVDLVVFYEPV--PSAIRSIQRR-GR 459
Query: 666 IGQYKPIRIVRFLIENTIEE 685
G++ P R++ + + T +E
Sbjct: 460 TGRHMPGRVIILMAKGTRDE 479
>pdb|2K4D|A Chain A, E2-C-Cbl Recognition Is Necessary But Not Sufficient For
Ubiquitination Activity
Length = 83
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 467 QVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTC------SIPLTVD 515
Q+C +C + D + CGH C +CL S+ CP C + P+ VD
Sbjct: 25 QLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQG-CPFCRCEIKGTEPIVVD 78
>pdb|4A4C|A Chain A, Structure Of Phosphotyr371-C-Cbl-Ubch5b-Zap-70 Complex
Length = 391
Score = 31.6 bits (70), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 467 QVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTC------SIPLTVD 515
Q+C +C + D + CGH C +CL S+ CP C + P+ VD
Sbjct: 335 QLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQG-CPFCRCEIKGTEPIVVD 388
>pdb|1FBV|A Chain A, Structure Of A Cbl-Ubch7 Complex: Ring Domain Function In
Ubiquitin-Protein Ligases
Length = 388
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 467 QVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTC------SIPLTVD 515
Q+C +C + D + CGH C +CL S+ CP C + P+ VD
Sbjct: 333 QLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQG-CPFCRCEIKGTEPIVVD 386
>pdb|4A4B|A Chain A, Structure Of Modified Phosphotyr371-C-Cbl-Ubch5b-Zap-70
Complex
Length = 391
Score = 31.2 bits (69), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 467 QVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTC------SIPLTVD 515
Q+C +C + D + CGH C +CL S+ CP C + P+ VD
Sbjct: 335 QLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQG-CPFCRCEIKGTEPIVVD 388
>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 = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 467 QVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTC------SIPLTVD 515
Q+C +C + D + CGH C +CL S+ CP C + P+ VD
Sbjct: 333 QLCKICAENDKDVKIEPCGHLMCTSCLTSWQESEGQG-CPFCRCEIKGTEPIVVD 386
>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 = 30.8 bits (68), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 36/89 (40%), Gaps = 11/89 (12%)
Query: 433 LTRLRQAVDHPYLVVYSKTASLRGETEADAEHVQQVCGLCNDLADDPVVTNCGHAFCKAC 492
LT L + H ++ V + L E + Q+C +C + D + CGH C +C
Sbjct: 309 LTGLCEPTPHDHIKVTQEQYELYCEMGSTF----QLCKICAENDKDVKIEPCGHLMCTSC 364
Query: 493 LFDSSASKFVAKCPTC------SIPLTVD 515
L S CP C + P+ VD
Sbjct: 365 LTAWQESDGQG-CPFCRCEIKGTEPIIVD 392
>pdb|1G25|A Chain A, Solution Structure Of The N-Terminal Domain Of The Human
Tfiih Mat1 Subunit
Length = 65
Score = 30.4 bits (67), Expect = 3.4, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 480 VVTNCGHAFCKACLFDSSASKFVAKCPTCSIPL 512
+V CGH C++C+ D + CP C PL
Sbjct: 22 MVNVCGHTLCESCV-DLLFVRGAGNCPECGTPL 53
>pdb|2LDR|A Chain A, Solution Structure Of Helix-Ring Domain Of Cbl-B In The
Tyr363 Phosphorylated Form
Length = 82
Score = 30.4 bits (67), Expect = 3.7, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 7/55 (12%)
Query: 467 QVCGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTC------SIPLTVD 515
Q+C +C + D + CGH C +CL S CP C + P+ VD
Sbjct: 27 QLCKICAENDKDVKIEPCGHLMCTSCLTAWQESDGQG-CPFCRCEIKGTEPIIVD 80
>pdb|2D8T|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 146
Length = 71
Score = 30.4 bits (67), Expect = 3.8, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 19/48 (39%), Gaps = 2/48 (4%)
Query: 469 CGLCNDLADDPVVTNCGHAFCKACLFDSSASKFVAKCPTCSIPLTVDF 516
C +C PV C H FC C+ AS +C C + DF
Sbjct: 18 CAICLQTCVHPVSLPCKHVFCYLCV--KGASWLGKRCALCRQEIPEDF 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 = 3.9, Method: Composition-based stats.
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 479 PVVTNCGHAFCKACLFDSSASKFVA-KCPTCS 509
P + +CGH C+ CL AS +CP CS
Sbjct: 32 PKLLHCGHTICRQCLEKLLASSINGVRCPFCS 63
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 29.6 bits (65), Expect = 5.7, Method: Composition-based stats.
Identities = 15/45 (33%), Positives = 21/45 (46%), Gaps = 5/45 (11%)
Query: 468 VCGLCND-LADDPVVTNCGHAFCKACLFDS-SASKFVAKCPTCSI 510
+C LC D + C H+FCK C+ SK+ CP C +
Sbjct: 13 MCVLCGGYFIDATTIIECLHSFCKTCIVRYLETSKY---CPICDV 54
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
0.321 0.135 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,089,102
Number of Sequences: 62578
Number of extensions: 719761
Number of successful extensions: 1686
Number of sequences better than 100.0: 62
Number of HSP's better than 100.0 without gapping: 39
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 1616
Number of HSP's gapped (non-prelim): 85
length of query: 723
length of database: 14,973,337
effective HSP length: 106
effective length of query: 617
effective length of database: 8,340,069
effective search space: 5145822573
effective search space used: 5145822573
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: 55 (25.8 bits)