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= 001690
(1028 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 47.0 bits (110), Expect = 5e-05, Method: Composition-based stats.
Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 5/49 (10%)
Query: 259 ESLVCPLCNELMEDPVAIVCGHSFERKAIQEHFQR-----GGKNCPTCR 302
E + CP+C EL+++PV+ C HSF R I +++ G NCP CR
Sbjct: 18 EEVTCPICLELLKEPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCR 66
>pdb|1T1H|A Chain A, Nmr Solution Structure Of The U Box Domain From Atpub14,
An Armadillo Repeat Containing Protein From Arabidopsis
Thaliana
Length = 78
Score = 45.8 bits (107), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 31/65 (47%)
Query: 259 ESLVCPLCNELMEDPVAIVCGHSFERKAIQEHFQRGGKNCPTCRQEXXXXXXXXXXXXRS 318
E CP+ ELM+DPV + G ++ER +IQ+ G K CP ++ +S
Sbjct: 7 EYFRCPISLELMKDPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLHAGLTPNYVLKS 66
Query: 319 SIEEW 323
I W
Sbjct: 67 LIALW 71
>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 = 40.4 bits (93), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 5/49 (10%)
Query: 259 ESLVCPLCNELMEDPVAIVCGHSFERKAI-----QEHFQRGGKNCPTCR 302
E + CP+C EL+ P+++ CGHSF + + + +G +CP CR
Sbjct: 18 EEVTCPICLELLTQPLSLDCGHSFCQACLTANHKKSMLDKGESSCPVCR 66
>pdb|2YSL|A Chain A, Solution Structure Of The Ring Domain (1-66) From
Tripartite Motif-containing Protein 31
Length = 73
Score = 40.0 bits (92), Expect = 0.006, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 28/46 (60%), Gaps = 2/46 (4%)
Query: 259 ESLVCPLCNELMEDPVAIVCGHSFERKAIQEHFQR--GGKNCPTCR 302
E ++CP+C ++++ PV I CGH+F K I + + G CP C+
Sbjct: 19 EEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLCK 64
>pdb|1EE5|A Chain A, Yeast Karyopherin (Importin) Alpha In A Complex With A
Nucleoplasmin Nls Peptide
Length = 424
Score = 39.7 bits (91), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 50/240 (20%), Positives = 106/240 (44%), Gaps = 12/240 (5%)
Query: 338 KINSDDQSRRKSALEEMKNIM--ELPQYAEKAAKAGLIPKLVEFLKDTR---LSTEAILK 392
++NSDD + SA + + I+ E + +AG++P+LVEF+++ + L EA
Sbjct: 9 QLNSDDMQEQLSATVKFRQILSREHRPPIDVVIQAGVVPRLVEFMRENQPEMLQLEAAW- 67
Query: 393 CLYFLAKYSDIHKEAIVEAGAVRRIVKQICKG--ETMPEAIEVLSELTKRETLGEKIGNT 450
L +A + + +V+A AV ++ + G E +AI L + T
Sbjct: 68 ALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQ 127
Query: 451 KDCITIMVSLLHNNNPNLSQKAHDVLQNLSHNTHFAVKMAEAGYFQPFVACFNRGSQETR 510
+ + ++ L ++N P+L + A L NL + P +A S +T
Sbjct: 128 CNAMEPILGLFNSNKPSLIRTATWTLSNLCRGKKPQPDWSVVSQALPTLAKLIY-SMDTE 186
Query: 511 ALMASALRNMRLDES---SIKTLKDRQFIHNVIQMLSSNSPVCKSACLKCIKTLIAHSKM 567
L+ + L + +I+ + D + ++++LS S + ++ L+ + ++ + +
Sbjct: 187 TLVDACWAISYLSDGPQEAIQAVIDVRIPKRLVELLSHESTLVQTPALRAVGNIVTGNDL 246
>pdb|1BK5|A Chain A, Karyopherin Alpha From Saccharomyces Cerevisiae
pdb|1BK5|B Chain B, Karyopherin Alpha From Saccharomyces Cerevisiae
Length = 422
Score = 39.7 bits (91), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 50/240 (20%), Positives = 106/240 (44%), Gaps = 12/240 (5%)
Query: 338 KINSDDQSRRKSALEEMKNIM--ELPQYAEKAAKAGLIPKLVEFLKDTR---LSTEAILK 392
++NSDD + SA + + I+ E + +AG++P+LVEF+++ + L EA
Sbjct: 7 QLNSDDMQEQLSATVKFRQILSREHRPPIDVVIQAGVVPRLVEFMRENQPEMLQLEAAW- 65
Query: 393 CLYFLAKYSDIHKEAIVEAGAVRRIVKQICKG--ETMPEAIEVLSELTKRETLGEKIGNT 450
L +A + + +V+A AV ++ + G E +AI L + T
Sbjct: 66 ALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQ 125
Query: 451 KDCITIMVSLLHNNNPNLSQKAHDVLQNLSHNTHFAVKMAEAGYFQPFVACFNRGSQETR 510
+ + ++ L ++N P+L + A L NL + P +A S +T
Sbjct: 126 CNAMEPILGLFNSNKPSLIRTATWTLSNLCRGKKPQPDWSVVSQALPTLAKLIY-SMDTE 184
Query: 511 ALMASALRNMRLDES---SIKTLKDRQFIHNVIQMLSSNSPVCKSACLKCIKTLIAHSKM 567
L+ + L + +I+ + D + ++++LS S + ++ L+ + ++ + +
Sbjct: 185 TLVDACWAISYLSDGPQEAIQAVIDVRIPKRLVELLSHESTLVQTPALRAVGNIVTGNDL 244
>pdb|1BK6|A Chain A, Karyopherin Alpha (Yeast) + Sv40 T Antigen Nls
pdb|1BK6|B Chain B, Karyopherin Alpha (Yeast) + Sv40 T Antigen Nls
Length = 422
Score = 39.7 bits (91), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 50/240 (20%), Positives = 106/240 (44%), Gaps = 12/240 (5%)
Query: 338 KINSDDQSRRKSALEEMKNIM--ELPQYAEKAAKAGLIPKLVEFLKDTR---LSTEAILK 392
++NSDD + SA + + I+ E + +AG++P+LVEF+++ + L EA
Sbjct: 7 QLNSDDMQEQLSATVKFRQILSREHRPPIDVVIQAGVVPRLVEFMRENQPEMLQLEAAW- 65
Query: 393 CLYFLAKYSDIHKEAIVEAGAVRRIVKQICKG--ETMPEAIEVLSELTKRETLGEKIGNT 450
L +A + + +V+A AV ++ + G E +AI L + T
Sbjct: 66 ALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQ 125
Query: 451 KDCITIMVSLLHNNNPNLSQKAHDVLQNLSHNTHFAVKMAEAGYFQPFVACFNRGSQETR 510
+ + ++ L ++N P+L + A L NL + P +A S +T
Sbjct: 126 CNAMEPILGLFNSNKPSLIRTATWTLSNLCRGKKPQPDWSVVSQALPTLAKLIY-SMDTE 184
Query: 511 ALMASALRNMRLDES---SIKTLKDRQFIHNVIQMLSSNSPVCKSACLKCIKTLIAHSKM 567
L+ + L + +I+ + D + ++++LS S + ++ L+ + ++ + +
Sbjct: 185 TLVDACWAISYLSDGPQEAIQAVIDVRIPKRLVELLSHESTLVQTPALRAVGNIVTGNDL 244
>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 = 0.008, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 2/45 (4%)
Query: 259 ESLVCPLCNELMEDPVAIVCGHSFERKAIQEHFQR--GGKNCPTC 301
E ++CP+C ++++ PV I CGH+F K I + + G CP C
Sbjct: 19 EEVICPICLDILQKPVTIDCGHNFCLKCITQIGETSCGFFKCPLC 63
>pdb|1EE4|A Chain A, Crystal Structure Of Yeast Karyopherin (Importin) Alpha In
A Complex With A C-Myc Nls Peptide
pdb|1EE4|B Chain B, Crystal Structure Of Yeast Karyopherin (Importin) Alpha In
A Complex With A C-Myc Nls Peptide
Length = 423
Score = 39.7 bits (91), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 50/240 (20%), Positives = 106/240 (44%), Gaps = 12/240 (5%)
Query: 338 KINSDDQSRRKSALEEMKNIM--ELPQYAEKAAKAGLIPKLVEFLKDTR---LSTEAILK 392
++NSDD + SA + + I+ E + +AG++P+LVEF+++ + L EA
Sbjct: 9 QLNSDDMQEQLSATVKFRQILSREHRPPIDVVIQAGVVPRLVEFMRENQPEMLQLEAAW- 67
Query: 393 CLYFLAKYSDIHKEAIVEAGAVRRIVKQICKG--ETMPEAIEVLSELTKRETLGEKIGNT 450
L +A + + +V+A AV ++ + G E +AI L + T
Sbjct: 68 ALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQ 127
Query: 451 KDCITIMVSLLHNNNPNLSQKAHDVLQNLSHNTHFAVKMAEAGYFQPFVACFNRGSQETR 510
+ + ++ L ++N P+L + A L NL + P +A S +T
Sbjct: 128 CNAMEPILGLFNSNKPSLIRTATWTLSNLCRGKKPQPDWSVVSQALPTLAKLIY-SMDTE 186
Query: 511 ALMASALRNMRLDES---SIKTLKDRQFIHNVIQMLSSNSPVCKSACLKCIKTLIAHSKM 567
L+ + L + +I+ + D + ++++LS S + ++ L+ + ++ + +
Sbjct: 187 TLVDACWAISYLSDGPQEAIQAVIDVRIPKRLVELLSHESTLVQTPALRAVGNIVTGNDL 246
>pdb|1UN0|A Chain A, Crystal Structure Of Yeast Karyopherin (Importin) Alpha In
Complex With A Nup2p N-Terminal Fragment
pdb|1UN0|B Chain B, Crystal Structure Of Yeast Karyopherin (Importin) Alpha In
Complex With A Nup2p N-Terminal Fragment
Length = 443
Score = 39.7 bits (91), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 50/240 (20%), Positives = 106/240 (44%), Gaps = 12/240 (5%)
Query: 338 KINSDDQSRRKSALEEMKNIM--ELPQYAEKAAKAGLIPKLVEFLKDTR---LSTEAILK 392
++NSDD + SA + + I+ E + +AG++P+LVEF+++ + L EA
Sbjct: 8 QLNSDDMQEQLSATVKFRQILSREHRPPIDVVIQAGVVPRLVEFMRENQPEMLQLEAAW- 66
Query: 393 CLYFLAKYSDIHKEAIVEAGAVRRIVKQICKG--ETMPEAIEVLSELTKRETLGEKIGNT 450
L +A + + +V+A AV ++ + G E +AI L + T
Sbjct: 67 ALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQ 126
Query: 451 KDCITIMVSLLHNNNPNLSQKAHDVLQNLSHNTHFAVKMAEAGYFQPFVACFNRGSQETR 510
+ + ++ L ++N P+L + A L NL + P +A S +T
Sbjct: 127 CNAMEPILGLFNSNKPSLIRTATWTLSNLCRGKKPQPDWSVVSQALPTLAKLIY-SMDTE 185
Query: 511 ALMASALRNMRLDES---SIKTLKDRQFIHNVIQMLSSNSPVCKSACLKCIKTLIAHSKM 567
L+ + L + +I+ + D + ++++LS S + ++ L+ + ++ + +
Sbjct: 186 TLVDACWAISYLSDGPQEAIQAVIDVRIPKRLVELLSHESTLVQTPALRAVGNIVTGNDL 245
>pdb|2C1T|A Chain A, Structure Of The Kap60p:nup2 Complex
pdb|2C1T|B Chain B, Structure Of The Kap60p:nup2 Complex
Length = 454
Score = 39.7 bits (91), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 50/240 (20%), Positives = 106/240 (44%), Gaps = 12/240 (5%)
Query: 338 KINSDDQSRRKSALEEMKNIM--ELPQYAEKAAKAGLIPKLVEFLKDTR---LSTEAILK 392
++NSDD + SA + + I+ E + +AG++P+LVEF+++ + L EA
Sbjct: 8 QLNSDDMQEQLSATVKFRQILSREHRPPIDVVIQAGVVPRLVEFMRENQPEMLQLEAAW- 66
Query: 393 CLYFLAKYSDIHKEAIVEAGAVRRIVKQICKG--ETMPEAIEVLSELTKRETLGEKIGNT 450
L +A + + +V+A AV ++ + G E +AI L + T
Sbjct: 67 ALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQ 126
Query: 451 KDCITIMVSLLHNNNPNLSQKAHDVLQNLSHNTHFAVKMAEAGYFQPFVACFNRGSQETR 510
+ + ++ L ++N P+L + A L NL + P +A S +T
Sbjct: 127 CNAMEPILGLFNSNKPSLIRTATWTLSNLCRGKKPQPDWSVVSQALPTLAKLIY-SMDTE 185
Query: 511 ALMASALRNMRLDES---SIKTLKDRQFIHNVIQMLSSNSPVCKSACLKCIKTLIAHSKM 567
L+ + L + +I+ + D + ++++LS S + ++ L+ + ++ + +
Sbjct: 186 TLVDACWAISYLSDGPQEAIQAVIDVRIPKRLVELLSHESTLVQTPALRAVGNIVTGNDL 245
>pdb|1WA5|B Chain B, Crystal Structure Of The Exportin Cse1p Complexed With Its
Cargo (Kap60p) And Rangtp
Length = 530
Score = 38.5 bits (88), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 50/240 (20%), Positives = 106/240 (44%), Gaps = 12/240 (5%)
Query: 338 KINSDDQSRRKSALEEMKNIM--ELPQYAEKAAKAGLIPKLVEFLKDTR---LSTEAILK 392
++NSDD + SA + + I+ E + +AG++P+LVEF+++ + L EA
Sbjct: 95 QLNSDDMQEQLSATVKFRQILSREHRPPIDVVIQAGVVPRLVEFMRENQPEMLQLEAAW- 153
Query: 393 CLYFLAKYSDIHKEAIVEAGAVRRIVKQICKG--ETMPEAIEVLSELTKRETLGEKIGNT 450
L +A + + +V+A AV ++ + G E +AI L + T
Sbjct: 154 ALTNIASGTSAQTKVVVDADAVPLFIQLLYTGSVEVKEQAIWALGNVAGDSTDYRDYVLQ 213
Query: 451 KDCITIMVSLLHNNNPNLSQKAHDVLQNLSHNTHFAVKMAEAGYFQPFVACFNRGSQETR 510
+ + ++ L ++N P+L + A L NL + P +A S +T
Sbjct: 214 CNAMEPILGLFNSNKPSLIRTATWTLSNLCRGKKPQPDWSVVSQALPTLAKLIY-SMDTE 272
Query: 511 ALMASALRNMRLDES---SIKTLKDRQFIHNVIQMLSSNSPVCKSACLKCIKTLIAHSKM 567
L+ + L + +I+ + D + ++++LS S + ++ L+ + ++ + +
Sbjct: 273 TLVDACWAISYLSDGPQEAIQAVIDVRIPKRLVELLSHESTLVQTPALRAVGNIVTGNDL 332
>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human
Tripartite Motif Protein 34
Length = 79
Score = 38.1 bits (87), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 6/49 (12%)
Query: 259 ESLVCPLCNELMEDPVAIVCGHSFERKAI-----QEHFQRGGK-NCPTC 301
E + CP+C EL+ +P+++ CGHS R I + GGK +CP C
Sbjct: 11 EEVTCPICLELLTEPLSLDCGHSLCRACITVSNKEAVTSMGGKSSCPVC 59
>pdb|1RMD|A Chain A, Rag1 Dimerization Domain
Length = 116
Score = 37.7 bits (86), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 24/45 (53%)
Query: 258 IESLVCPLCNELMEDPVAIVCGHSFERKAIQEHFQRGGKNCPTCR 302
++S+ C +C ++ DPV C H F R I + G CP+CR
Sbjct: 21 VKSISCQICEHILADPVETSCKHLFCRICILRCLKVMGSYCPSCR 65
>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 = 35.8 bits (81), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 24/46 (52%)
Query: 259 ESLVCPLCNELMEDPVAIVCGHSFERKAIQEHFQRGGKNCPTCRQE 304
+S +C C EL+ PV C H+ + +Q F+ +CP CR +
Sbjct: 77 QSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHD 122
>pdb|3FL2|A Chain A, Crystal Structure Of The Ring Domain Of The E3 Ubiquitin-
Protein Ligase Uhrf1
Length = 124
Score = 35.4 bits (80), Expect = 0.19, Method: Composition-based stats.
Identities = 14/46 (30%), Positives = 23/46 (50%)
Query: 259 ESLVCPLCNELMEDPVAIVCGHSFERKAIQEHFQRGGKNCPTCRQE 304
E+ C C EL+ P+ VC H+ + + F+ +CP CR +
Sbjct: 51 ETFQCICCQELVFRPITTVCQHNVCKDCLDRSFRAQVFSCPACRYD 96
>pdb|1JM7|A Chain A, Solution Structure Of The Brca1/bard1 Ring-domain
Heterodimer
Length = 112
Score = 35.0 bits (79), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 261 LVCPLCNELMEDPVAIVCGHSFERKAIQEHF--QRGGKNCPTCRQE 304
L CP+C EL+++PV+ C H F + + + ++G CP C+ +
Sbjct: 22 LECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKND 67
>pdb|2H0D|B Chain B, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 100
Score = 35.0 bits (79), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 261 LVCPLCNELMEDPVAIV-CGHSFERKAIQEHFQRGGKNCPTCRQE 304
L+CP+C +++++ + C H F I + G K CPTCR++
Sbjct: 35 LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKK 79
>pdb|2F42|A Chain A, Dimerization And U-Box Domains Of Zebrafish C-Terminal Of
Hsp70 Interacting Protein
Length = 179
Score = 34.7 bits (78), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 33/71 (46%), Gaps = 9/71 (12%)
Query: 232 MQLLYSTELVRRPQDEAIPTYCQVYPIESLVCPLCNELMEDPVAIVCGHSFERKAIQEHF 291
M L+S +R + E IP Y L + ELM +P G +++RK I+EH
Sbjct: 87 MDELFSQVDEKRKKRE-IPDY--------LCGKISFELMREPCITPSGITYDRKDIEEHL 137
Query: 292 QRGGKNCPTCR 302
QR G P R
Sbjct: 138 QRVGHFDPVTR 148
>pdb|3RPG|C Chain C, Bmi1RING1B-Ubch5c Complex Structure
Length = 121
Score = 34.7 bits (78), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 261 LVCPLCNELMEDPVAIV-CGHSFERKAIQEHFQRGGKNCPTCRQE 304
L+CP+C +++++ + C H F I + G K CPTCR++
Sbjct: 54 LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKK 98
>pdb|2CKL|B Chain B, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 165
Score = 34.7 bits (78), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 261 LVCPLCNELMEDPVAIV-CGHSFERKAIQEHFQRGGKNCPTCRQE 304
L+CP+C +++++ + C H F I + G K CPTCR++
Sbjct: 55 LMCPICLDMLKNTMTTKECLHRFCADCIITALRSGNKECPTCRKK 99
>pdb|2ECJ|A Chain A, Solution Structure Of The Ring Domain Of The Human
Tripartite Motif-Containing Protein 39
Length = 58
Score = 34.3 bits (77), Expect = 0.34, Method: Composition-based stats.
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 263 CPLCNELMEDPVAIVCGHSFERKAIQEHFQRGGKN--CPTC 301
C +C E +++PV I CGH+F + I ++ ++ CP C
Sbjct: 18 CSVCLEYLKEPVIIECGHNFCKACITRWWEDLERDFPCPVC 58
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 34.3 bits (77), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 261 LVCPLCNELMEDPVAIVCGHSFERKAIQEHFQRGGKNCPTCRQE 304
L C +C+E + V + C HSF I E +R + CP CR++
Sbjct: 54 LQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIE-CPICRKD 96
>pdb|4DB9|A Chain A, Designed Armadillo Repeat Protein (Yiiim3aiii)
pdb|4DB9|B Chain B, Designed Armadillo Repeat Protein (Yiiim3aiii)
pdb|4DB9|C Chain C, Designed Armadillo Repeat Protein (Yiiim3aiii)
pdb|4DB9|D Chain D, Designed Armadillo Repeat Protein (Yiiim3aiii)
pdb|4DB9|E Chain E, Designed Armadillo Repeat Protein (Yiiim3aiii)
pdb|4DB9|F Chain F, Designed Armadillo Repeat Protein (Yiiim3aiii)
Length = 210
Score = 33.9 bits (76), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 45/165 (27%), Positives = 79/165 (47%), Gaps = 13/165 (7%)
Query: 338 KINSDDQSRRKSALEEMKNIMELPQYAEKAA-KAGLIPKLVEFLK--DTRLSTEAILKCL 394
++NS DQ +SAL ++ I +A AG +P LV+ L + ++ EA L L
Sbjct: 20 QLNSPDQQELQSALRKLSQIASGGNEQIQAVIDAGALPALVQLLSSPNEQILQEA-LWAL 78
Query: 395 YFLAKYSDIHKEAIVEAGAVRRIVKQICKG--ETMPEAIEVLSELTKRETLGEKIGNTKD 452
+A + +A+++AGA+ +V+ + + + EA+ LS + E+I D
Sbjct: 79 SNIASGGNEQIQAVIDAGALPALVQLLSSPNEQILQEALWALSNIASGGN--EQIQAVID 136
Query: 453 --CITIMVSLLHNNNPNLSQKAHDVLQNLSHNTHF---AVKMAEA 492
+ +V LL + N + Q+A L N++ + AVK A A
Sbjct: 137 AGALPALVQLLSSPNEQILQEALWALSNIASGGNEQKQAVKEAGA 181
>pdb|3L11|A Chain A, Crystal Structure Of The Ring Domain Of Rnf168
Length = 115
Score = 33.9 bits (76), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 7/60 (11%)
Query: 244 PQDEAIPTYCQVYPIESLVCPLCNELMEDPVAIVCGHSFERKAIQEHFQRGGKNCPTCRQ 303
P+D AIP+ + C +C E++ +PV + C H+ + Q ++ CP CR+
Sbjct: 6 PKD-AIPS------LSECQCGICMEILVEPVTLPCNHTLCKPCFQSTVEKASLCCPFCRR 58
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 33.9 bits (76), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 261 LVCPLCNELMEDPVAIVCGHSFERKAIQEHFQRGGKNCPTCRQE 304
L C +C+E + V + C HSF I E +R + CP CR++
Sbjct: 54 LQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIE-CPICRKD 96
>pdb|4DB6|A Chain A, Designed Armadillo Repeat Protein (Yiiim3aii)
Length = 210
Score = 33.9 bits (76), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 46/169 (27%), Positives = 81/169 (47%), Gaps = 15/169 (8%)
Query: 338 KINSDDQSRRKSALEEMKNIMELPQYAEKAA-KAGLIPKLVEFLK--DTRLSTEAILKCL 394
++NS DQ +SAL ++ I +A AG +P LV+ L + ++ EA L L
Sbjct: 20 QLNSPDQQELQSALRKLSQIASGGNEQIQAVIDAGALPALVQLLSSPNEQILQEA-LWAL 78
Query: 395 YFLAKYSDIHKEAIVEAGAVRRIVKQICKG--ETMPEAIEVLSELTKRETLGEKIGNTKD 452
+A + +A+++AGA+ +V+ + + + EA+ LS + E+I D
Sbjct: 79 SNIASGGNEQIQAVIDAGALPALVQLLSSPNEQILQEALWALSNIASGGN--EQIQAVID 136
Query: 453 --CITIMVSLLHNNNPNLSQKAHDVLQNLSHNTH---FAVKMAEAGYFQ 496
+ +V LL + N + Q+A L N++ + AVK EAG +
Sbjct: 137 AGALPALVQLLSSPNEQILQEALWALSNIASGGNEQKQAVK--EAGALE 183
>pdb|2C2V|S Chain S, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
pdb|2C2V|T Chain T, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
pdb|2C2V|U Chain U, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
pdb|2C2V|V Chain V, Crystal Structure Of The Chip-Ubc13-Uev1a Complex
Length = 78
Score = 33.9 bits (76), Expect = 0.47, Method: Composition-based stats.
Identities = 15/35 (42%), Positives = 20/35 (57%)
Query: 268 ELMEDPVAIVCGHSFERKAIQEHFQRGGKNCPTCR 302
ELM +P G +++RK I+EH QR G P R
Sbjct: 13 ELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTR 47
>pdb|2QMX|B Chain B, The Crystal Structure Of L-Phe Inhibited Prephenate
Dehydratase From Chlorobium Tepidum Tls
pdb|2QMX|A Chain A, The Crystal Structure Of L-Phe Inhibited Prephenate
Dehydratase From Chlorobium Tepidum Tls
Length = 283
Score = 33.9 bits (76), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 24/100 (24%), Positives = 41/100 (41%)
Query: 371 GLIPKLVEFLKDTRLSTEAILKCLYFLAKYSDIHKEAIVEAGAVRRIVKQICKGETMPEA 430
GL VE +A+++C F A + I EA + + V + + A
Sbjct: 90 GLPGASVETATKAXSHPQALVQCHNFFATHPQIRAEAAYDTAGSAKXVAESRDKSALAIA 149
Query: 431 IEVLSELTKRETLGEKIGNTKDCITIMVSLLHNNNPNLSQ 470
+ EL + L E + + + IT + H NNP++S
Sbjct: 150 SKRAGELYGLDILKENLADEEWNITRFFCIAHENNPDISH 189
>pdb|2YUR|A Chain A, Solution Structure Of The Ring Finger Of Human
Retinoblastoma-Binding Protein 6
Length = 74
Score = 33.9 bits (76), Expect = 0.52, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 10/61 (16%)
Query: 245 QDEAIPTYCQVYPIESLVCPLCNELMEDPVAI-VCGHSFERKAIQEHFQRGGKN-CPTCR 302
+D+ IP + L+C +C ++M D V I CG+S+ + I+ ++ CPTC
Sbjct: 8 EDDPIP--------DELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCH 59
Query: 303 Q 303
Q
Sbjct: 60 Q 60
>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 = 33.5 bits (75), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 261 LVCPLCNELMEDPVAIVCGHSFERKAIQEHFQRGGKNCPTCRQE 304
L C +C+E + V + C HSF I E +R + CP CR++
Sbjct: 65 LQCIICSEYFIEAVTLNCAHSFCSYCINEWMKRKIE-CPICRKD 107
>pdb|2ECI|A Chain A, Solution Structure Of The Ring Domain Of The Human Tnf
Receptor-Associated Factor 6 Protein
Length = 86
Score = 33.1 bits (74), Expect = 0.72, Method: Composition-based stats.
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 257 PIES-LVCPLCNELMEDPVAIVCGHSFERKAIQEHFQRGGKNCP 299
P+ES CP+C + + V CGH F + I + + G CP
Sbjct: 21 PLESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCP 64
>pdb|2C2L|A Chain A, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
pdb|2C2L|B Chain B, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
pdb|2C2L|C Chain C, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
pdb|2C2L|D Chain D, Crystal Structure Of The Chip U-Box E3 Ubiquitin Ligase
Length = 281
Score = 32.7 bits (73), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%)
Query: 268 ELMEDPVAIVCGHSFERKAIQEHFQRGGKNCPTCR 302
ELM +P G +++RK I+EH QR G P R
Sbjct: 216 ELMREPCITPSGITYDRKDIEEHLQRVGHFNPVTR 250
>pdb|2OXQ|C Chain C, Structure Of The Ubch5 :chip U-Box Complex
pdb|2OXQ|D Chain D, Structure Of The Ubch5 :chip U-Box Complex
Length = 80
Score = 32.7 bits (73), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 20/35 (57%)
Query: 268 ELMEDPVAIVCGHSFERKAIQEHFQRGGKNCPTCR 302
ELM +P G +++RK I+EH QR G P R
Sbjct: 21 ELMAEPCITPSGITYDRKDIEEHLQRVGHFDPVTR 55
>pdb|4A61|A Chain A, Parm From Plasmid R1 In Complex With Amppnp
Length = 326
Score = 32.3 bits (72), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 37/69 (53%), Gaps = 5/69 (7%)
Query: 11 GIAVLQELWNRVALQAVDIASETRDV--VLGKDSLQGFSRTIGELSTLMQSLDVKKIESV 68
G VLQEL R +L +D+ T D+ V+GK L G S+ G+ S+L SL ++
Sbjct: 159 GYEVLQELDERDSLLIIDLGGTTLDISQVMGK--LSGISKIYGD-SSLGVSLVTSAVKDA 215
Query: 69 IGLEFTKAA 77
+ L TK +
Sbjct: 216 LSLARTKGS 224
>pdb|2JMD|A Chain A, Solution Structure Of The Ring Domain Of Human Traf6
Length = 63
Score = 32.3 bits (72), Expect = 1.4, Method: Composition-based stats.
Identities = 12/37 (32%), Positives = 18/37 (48%)
Query: 263 CPLCNELMEDPVAIVCGHSFERKAIQEHFQRGGKNCP 299
CP+C + + V CGH F + I + + G CP
Sbjct: 9 CPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCP 45
>pdb|2CSY|A Chain A, Solution Structure Of The Ring Domain Of The Zinc Finger
Protein 183-Like 1
Length = 81
Score = 31.6 bits (70), Expect = 2.7, Method: Composition-based stats.
Identities = 14/41 (34%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 263 CPLCNELMEDPVAIVCGHSFERKAIQEHFQRGGKNCPTCRQ 303
C +C + ++PV C H F EHF R C C Q
Sbjct: 18 CFICRQAFQNPVVTKCRHYFCESCALEHF-RATPRCYICDQ 57
>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 = 31.2 bits (69), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 10/61 (16%)
Query: 245 QDEAIPTYCQVYPIESLVCPLCNELMEDPVAI-VCGHSFERKAIQEHFQRGGKN-CPTCR 302
+D+ IP + L+C +C ++M D V I CG+S+ + I+ ++ CPTC
Sbjct: 6 EDDPIP--------DELLCLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCH 57
Query: 303 Q 303
Q
Sbjct: 58 Q 58
>pdb|3K3S|A Chain A, Crystal Structure Of Altronate Hydrolase (Fragment 1-84)
From Shigella Flexneri.
pdb|3K3S|B Chain B, Crystal Structure Of Altronate Hydrolase (Fragment 1-84)
From Shigella Flexneri.
pdb|3K3S|C Chain C, Crystal Structure Of Altronate Hydrolase (Fragment 1-84)
From Shigella Flexneri.
pdb|3K3S|D Chain D, Crystal Structure Of Altronate Hydrolase (Fragment 1-84)
From Shigella Flexneri.
pdb|3K3S|E Chain E, Crystal Structure Of Altronate Hydrolase (Fragment 1-84)
From Shigella Flexneri.
pdb|3K3S|F Chain F, Crystal Structure Of Altronate Hydrolase (Fragment 1-84)
From Shigella Flexneri.
pdb|3K3S|G Chain G, Crystal Structure Of Altronate Hydrolase (Fragment 1-84)
From Shigella Flexneri.
pdb|3K3S|H Chain H, Crystal Structure Of Altronate Hydrolase (Fragment 1-84)
From Shigella Flexneri
Length = 105
Score = 30.8 bits (68), Expect = 3.7, Method: Composition-based stats.
Identities = 15/29 (51%), Positives = 19/29 (65%)
Query: 830 AKQRAASALADLSQSTSVSVSNATLTAKQ 858
A A ALADL++ T VSV N T+T +Q
Sbjct: 29 ALDNVAVALADLAEGTEVSVDNQTVTLRQ 57
>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 = 30.4 bits (67), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 257 PIES-LVCPLCNELMEDPVAIVCGHSFERKAIQEHFQRGGKNCPT 300
P+ES CP+C + + V CGH F + I + + G CP
Sbjct: 14 PLESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPV 58
>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 = 29.6 bits (65), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 1/45 (2%)
Query: 257 PIES-LVCPLCNELMEDPVAIVCGHSFERKAIQEHFQRGGKNCPT 300
P+ES CP+C + + V CGH F + I + + G CP
Sbjct: 14 PLESKYECPICLMALREAVQTPCGHRFCKACIIKSIRDAGHKCPV 58
>pdb|4A62|A Chain A, Parm From R1 Plasmid In Complex With Peptide From C-
Terminus Of Parr
pdb|4A62|B Chain B, Parm From R1 Plasmid In Complex With Peptide From C-
Terminus Of Parr
Length = 320
Score = 29.6 bits (65), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 11 GIAVLQELWNRVALQAVDIASETRDV--VLGKDSLQGFSRTIGELSTLMQSLDVKKIESV 68
G VLQEL +L +D+ T D+ V+GK L G S+ G+ S+L SL ++
Sbjct: 153 GYEVLQELDEADSLLIIDLGGTTLDISQVMGK--LSGISKIYGD-SSLGVSLVTSAVKDA 209
Query: 69 IGLEFTKAA 77
+ L TK +
Sbjct: 210 LSLARTKGS 218
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
0.319 0.132 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,827,480
Number of Sequences: 62578
Number of extensions: 755373
Number of successful extensions: 2199
Number of sequences better than 100.0: 49
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 27
Number of HSP's that attempted gapping in prelim test: 2170
Number of HSP's gapped (non-prelim): 56
length of query: 1028
length of database: 14,973,337
effective HSP length: 109
effective length of query: 919
effective length of database: 8,152,335
effective search space: 7491995865
effective search space used: 7491995865
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)