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= 045986
(148 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1IYM|A Chain A, Ring-H2 Finger Domain Of El5
Length = 55
Score = 50.4 bits (119), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 28/49 (57%)
Query: 98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIYL 146
EC +CL E G+ R LP C H +H+ C+ W TCP+CR ++ +
Sbjct: 7 ECAVCLAELEDGEEARFLPRCGHGFHAECVDMWLGSHSTCPLCRLTVVV 55
>pdb|1X4J|A Chain A, Solution Structure Of Ring Finger In Ring Finger Protein
38
Length = 75
Score = 50.4 bits (119), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 38/61 (62%), Gaps = 2/61 (3%)
Query: 82 PAEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
P+ +++ + H + T CV+C+ +F S L R+LP C H +H+ C+ +W TCPICR
Sbjct: 10 PSYRFNPNNHQSEQT-LCVVCMCDFESRQLLRVLP-CNHEFHAKCVDKWLKANRTCPICR 67
Query: 142 S 142
+
Sbjct: 68 A 68
>pdb|2ECT|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Of Ring Finger Protein 126
Length = 78
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
EC +C E++ G+ R LP C H++H CI+ W +CP+CR S+
Sbjct: 17 ECPVCKEDYALGESVRQLP-CNHLFHDSCIVPWLEQHDSCPVCRKSL 62
>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 = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
C IC E+V GD+ LP C H +H C+ W TCP+CR
Sbjct: 43 CPICCSEYVKGDVATELP-CHHYFHKPCVSIWLQKSGTCPVCR 84
>pdb|2EP4|A Chain A, Solution Structure Of Ring Finger From Human Ring Finger
Protein 24
Length = 74
Score = 43.5 bits (101), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
C +CLE+F D I P CKH +H C+I+W CP+C +
Sbjct: 18 CAVCLEDFKPRDELGICP-CKHAFHRKCLIKWLEVRKVCPLCNMPV 62
>pdb|2KIZ|A Chain A, Solution Structure Of Arkadia Ring-H2 Finger Domain
Length = 69
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
+C ICL G+ R LP C H++H C+ +W CPICR I
Sbjct: 16 KCTICLSILEEGEDVRRLP-CMHLFHQVCVDQWLITNKKCPICRVDI 61
>pdb|4AYC|B Chain B, Rnf8 Ring Domain Structure
Length = 138
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
+C+IC E F+ + C H + S+CI W + CPICR I
Sbjct: 55 QCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDI 97
>pdb|4AYC|A Chain A, Rnf8 Ring Domain Structure
Length = 138
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
+C+IC E F+ + C H + S+CI W + CPICR I
Sbjct: 55 QCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDI 97
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 4/47 (8%)
Query: 98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
+C+IC E F+ + C H + S+CI W + CPICR I
Sbjct: 66 QCIICSEYFIEA----VTLNCAHSFCSYCINEWMKRKIECPICRKDI 108
>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 = 0.033, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 83 AEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSD---EFTCPI 139
+ G L N + + C +CLE ++ C H + CI RW+ D +F CP+
Sbjct: 2 SSGSSGALENLQVEASCSVCLEYLKE----PVIIECGHNFCKACITRWWEDLERDFPCPV 57
Query: 140 C 140
C
Sbjct: 58 C 58
>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 = 32.7 bits (73), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 3/42 (7%)
Query: 99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPIC 140
C IC E F ++ I+P C H Y S CI ++ S + CP C
Sbjct: 25 CGICFEYF---NIAMIIPQCSHNYCSLCIRKFLSYKTQCPTC 63
>pdb|2ECN|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 141
Length = 70
Score = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 22/44 (50%), Gaps = 5/44 (11%)
Query: 98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICR 141
EC IC++ G ILP C H + CI +W CPICR
Sbjct: 17 ECCICMD----GRADLILP-CAHSFCQKCIDKWSDRHRNCPICR 55
>pdb|1M2O|A Chain A, Crystal Structure Of The Sec23-Sar1 Complex
pdb|1M2O|C Chain C, Crystal Structure Of The Sec23-Sar1 Complex
pdb|1M2V|A Chain A, Crystal Structure Of The Yeast Sec2324 HETERODIMER
Length = 768
Score = 31.6 bits (70), Expect = 0.16, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 116 PFCKHVYHSHCIIRWFSDEFTCPICRSSIYL 146
P CK + + +C+I + ++CPIC S +L
Sbjct: 59 PHCKSILNPYCVIDPRNSSWSCPICNSRNHL 89
>pdb|2QTV|A Chain A, Structure Of Sec23-Sar1 Complexed With The Active Fragment
Of Sec31
Length = 772
Score = 31.6 bits (70), Expect = 0.16, Method: Composition-based stats.
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 116 PFCKHVYHSHCIIRWFSDEFTCPICRSSIYL 146
P CK + + +C+I + ++CPIC S +L
Sbjct: 63 PHCKSILNPYCVIDPRNSSWSCPICNSRNHL 93
>pdb|3NG2|A Chain A, Crystal Structure Of The Rnf4 Ring Domain Dimer
pdb|3NG2|B Chain B, Crystal Structure Of The Rnf4 Ring Domain Dimer
Length = 71
Score = 31.6 bits (70), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 96 TSECVICLE---EFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
T C IC++ E V + C HV+ S C+ + TCP CR I
Sbjct: 10 TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 61
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 31.6 bits (70), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 96 TSECVICLE---EFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
T C IC++ E V + C HV+ S C+ + TCP CR I
Sbjct: 15 TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 66
>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 = 31.2 bits (69), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 23/46 (50%), Gaps = 3/46 (6%)
Query: 99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
C ICLE+ + LP C H + CI RW TCP+C+ +
Sbjct: 8 CPICLED--PSNYSMALP-CLHAFCYVCITRWIRQNPTCPLCKVPV 50
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 30.8 bits (68), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 96 TSECVICLE---EFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
T C IC++ E V + C HV+ S C+ + TCP CR I
Sbjct: 7 TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 58
Score = 30.8 bits (68), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 3/52 (5%)
Query: 96 TSECVICLE---EFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
T C IC++ E V + C HV+ S C+ + TCP CR I
Sbjct: 72 TVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 123
>pdb|3T8R|A Chain A, Crystal Structure Of Staphylococcus Aureus Cymr
Length = 143
Score = 30.4 bits (67), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 45 WARDLYQ-RMHDPEVGSFDVLRLWDRPLRHQRVIEKLPPAEK 85
A+ YQ R+ E+ + D++RL + P+ IE PPA+K
Sbjct: 63 GAKGGYQLRVPAEEISAGDIIRLLEGPITFVESIESEPPAQK 104
>pdb|3T8T|A Chain A, Crystal Structure Of Staphylococcus Aureus Cymr Oxidized
Form
Length = 143
Score = 30.4 bits (67), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 1/42 (2%)
Query: 45 WARDLYQ-RMHDPEVGSFDVLRLWDRPLRHQRVIEKLPPAEK 85
A+ YQ R+ E+ + D++RL + P+ IE PPA+K
Sbjct: 63 GAKGGYQLRVPAEEISAGDIIRLLEGPITFVESIESEPPAQK 104
>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 = 30.4 bits (67), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 16/42 (38%)
Query: 98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPI 139
EC S + C H +H HCI RW CP+
Sbjct: 55 ECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 96
>pdb|4A0K|B Chain B, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 117
Score = 30.4 bits (67), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 16/42 (38%)
Query: 98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPI 139
EC S + C H +H HCI RW CP+
Sbjct: 64 ECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 105
>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 = 30.4 bits (67), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 16/42 (38%)
Query: 98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPI 139
EC S + C H +H HCI RW CP+
Sbjct: 53 ECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 94
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 30.4 bits (67), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 3/50 (6%)
Query: 98 ECVICLE---EFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSI 144
C IC++ E V + C HV+ S C+ + TCP CR I
Sbjct: 5 SCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI 54
>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 = 30.0 bits (66), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 16/42 (38%)
Query: 98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPI 139
EC S + C H +H HCI RW CP+
Sbjct: 53 ECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 94
>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 = 30.0 bits (66), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 16/42 (38%)
Query: 98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPI 139
EC S + C H +H HCI RW CP+
Sbjct: 45 ECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 86
>pdb|2LGV|A Chain A, Rbx1
Length = 100
Score = 30.0 bits (66), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 16/42 (38%)
Query: 98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPI 139
EC S + C H +H HCI RW CP+
Sbjct: 47 ECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 88
>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 = 29.6 bits (65), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 24/52 (46%), Gaps = 2/52 (3%)
Query: 92 NKKFTSECVICLEEF-VSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRS 142
+S C ICLE+ S + +LP C H+ H C + + CP+C
Sbjct: 1 GSSGSSGCPICLEDIHTSRVVAHVLP-CGHLLHRTCYEEMLKEGYRCPLCSG 51
>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 = 29.6 bits (65), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 16/42 (38%)
Query: 98 ECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPI 139
EC S + C H +H HCI RW CP+
Sbjct: 37 ECQANQASATSEECTVAWGVCNHAFHFHCISRWLKTRQVCPL 78
>pdb|2ECL|A Chain A, Solution Structure Of The Ring Domain Of The Human
Ring-Box Protein 2
Length = 81
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/49 (24%), Positives = 20/49 (40%)
Query: 94 KFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRS 142
+ C+ C E D + C H +H+ C+ W CP+C+
Sbjct: 24 QVMDACLRCQAENKQEDCVVVWGECNHSFHNCCMSLWVKQNNRCPLCQQ 72
>pdb|3LRQ|A Chain A, Crystal Structure Of The U-Box Domain Of Human Ubiquitin-
Protein Ligase (E3), Northeast Structural Genomics
Consortium Target Hr4604d.
pdb|3LRQ|B Chain B, Crystal Structure Of The U-Box Domain Of Human Ubiquitin-
Protein Ligase (E3), Northeast Structural Genomics
Consortium Target Hr4604d.
pdb|3LRQ|C Chain C, Crystal Structure Of The U-Box Domain Of Human Ubiquitin-
Protein Ligase (E3), Northeast Structural Genomics
Consortium Target Hr4604d.
pdb|3LRQ|D Chain D, Crystal Structure Of The U-Box Domain Of Human Ubiquitin-
Protein Ligase (E3), Northeast Structural Genomics
Consortium Target Hr4604d
Length = 100
Score = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 24/49 (48%), Gaps = 4/49 (8%)
Query: 99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDE-FTCPICRSSIYL 146
C IC E+ R+ P C + CI RW +++ CP CR+ + L
Sbjct: 25 CFICXEKLRDA---RLCPHCSKLCCFSCIRRWLTEQRAQCPHCRAPLQL 70
>pdb|2VE7|A Chain A, Crystal Structure Of A Bonsai Version Of The Human Ndc80
Complex
pdb|2VE7|B Chain B, Crystal Structure Of A Bonsai Version Of The Human Ndc80
Complex
pdb|3IZ0|C Chain C, Human Ndc80 Bonsai Decorated Microtubule
pdb|3IZ0|E Chain E, Human Ndc80 Bonsai Decorated Microtubule
Length = 315
Score = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 15/26 (57%)
Query: 84 EKYDGHLHNKKFTSECVICLEEFVSG 109
E DG +HNK F + C E F+SG
Sbjct: 136 ETEDGIMHNKLFLDYTIKCYESFMSG 161
>pdb|2JRJ|A Chain A, Solution Structure Of The Human Pirh2 Ring-H2 Domain.
Northeast Structural Genomics Consortium Target Ht2b
Length = 52
Score = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 98 ECVICLEEF-VSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSS 143
C ICLE+ S + +LP C H+ H C + + CP+C S
Sbjct: 7 NCPICLEDIHTSRVVAHVLP-CGHLLHRTCYEEMLKEGYRCPLCMHS 52
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 27.7 bits (60), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 23/61 (37%), Gaps = 3/61 (4%)
Query: 83 AEKYDGHLHNKKFTSECVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFT---CPI 139
+ G+L + EC IC+E F L L C H C+ + + CP
Sbjct: 2 SSGSSGNLDALREVLECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSINGVRCPF 61
Query: 140 C 140
C
Sbjct: 62 C 62
>pdb|2NXY|A Chain A, Hiv-1 Gp120 Envelope Glycoprotein(S334a) Complexed With
Cd4 And Antibody 17b
Length = 317
Score = 27.3 bits (59), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 18/29 (62%), Gaps = 6/29 (20%)
Query: 44 IWARDLYQRMHDPEVGSFDVLRLWDRPLR 72
+W D+ ++MH+ D++ LWD+ L+
Sbjct: 13 MWKNDMVEQMHE------DIISLWDQSLK 35
>pdb|3RPG|B Chain B, Bmi1RING1B-Ubch5c Complex Structure
Length = 117
Score = 27.3 bits (59), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY 145
CV+C F+ D I+ C H + CI+R+ CPIC ++
Sbjct: 18 CVLCGGYFI--DATTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVH 61
>pdb|2NY4|A Chain A, Hiv-1 Gp120 Envelope Glycoprotein (K231c, T257s, E268c,
S334a, S375w) Complexed With Cd4 And Antibody 17b
Length = 317
Score = 26.9 bits (58), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 9/56 (16%)
Query: 44 IWARDLYQRMHDPEVGSFDVLRLWDRPLRHQRVIEKLPPAEKYDGHLHNKKFTSEC 99
+W D+ ++MH+ D++ LWD+ L+ KL P G + T C
Sbjct: 13 MWKNDMVEQMHE------DIISLWDQSLKP---CVKLTPLCVGAGSCNTSVITQAC 59
>pdb|2NY3|A Chain A, Hiv-1 Gp120 Envelope Glycoprotein (K231c, T257s, E267c,
S334a, S375w) Complexed With Cd4 And Antibody 17b
Length = 317
Score = 26.9 bits (58), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 9/56 (16%)
Query: 44 IWARDLYQRMHDPEVGSFDVLRLWDRPLRHQRVIEKLPPAEKYDGHLHNKKFTSEC 99
+W D+ ++MH+ D++ LWD+ L+ KL P G + T C
Sbjct: 13 MWKNDMVEQMHE------DIISLWDQSLKP---CVKLTPLCVGAGSCNTSVITQAC 59
>pdb|1GC1|G Chain G, Hiv-1 Gp120 Core Complexed With Cd4 And A Neutralizing
Human Antibody
Length = 321
Score = 26.9 bits (58), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 18/29 (62%), Gaps = 6/29 (20%)
Query: 44 IWARDLYQRMHDPEVGSFDVLRLWDRPLR 72
+W D+ ++MH+ D++ LWD+ L+
Sbjct: 17 MWKNDMVEQMHE------DIISLWDQSLK 39
>pdb|1G9M|G Chain G, Hiv-1 Hxbc2 Gp120 Envelope Glycoprotein Complexed With
Cd4 And Induced Neutralizing Antibody 17b
pdb|1RZJ|G Chain G, Hiv-1 Hxbc2 Gp120 Envelope Glycoprotein Complexed With
Cd4 And Induced Neutralizing Antibody 17b
Length = 321
Score = 26.9 bits (58), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 18/29 (62%), Gaps = 6/29 (20%)
Query: 44 IWARDLYQRMHDPEVGSFDVLRLWDRPLR 72
+W D+ ++MH+ D++ LWD+ L+
Sbjct: 17 MWKNDMVEQMHE------DIISLWDQSLK 39
>pdb|2NXZ|A Chain A, Hiv-1 Gp120 Envelope Glycoprotein (t257s, S334a, S375w)
Complexed With Cd4 And Antibody 17b
Length = 317
Score = 26.9 bits (58), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 18/29 (62%), Gaps = 6/29 (20%)
Query: 44 IWARDLYQRMHDPEVGSFDVLRLWDRPLR 72
+W D+ ++MH+ D++ LWD+ L+
Sbjct: 13 MWKNDMVEQMHE------DIISLWDQSLK 35
>pdb|2NY2|A Chain A, Hiv-1 Gp120 Envelope Glycoprotein (T123c, T257s, S334a,
S375w, G431c) Complexed With Cd4 And Antibody 17b
Length = 317
Score = 26.9 bits (58), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 18/29 (62%), Gaps = 6/29 (20%)
Query: 44 IWARDLYQRMHDPEVGSFDVLRLWDRPLR 72
+W D+ ++MH+ D++ LWD+ L+
Sbjct: 13 MWKNDMVEQMHE------DIISLWDQSLK 35
>pdb|2CKL|A Chain A, Ring1b-Bmi1 E3 Catalytic Domain Structure
Length = 108
Score = 26.9 bits (58), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY 145
CV+C F+ D I+ C H + CI+R+ CPIC ++
Sbjct: 18 CVLCGGYFI--DATTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVH 61
>pdb|3JWD|A Chain A, Structure Of Hiv-1 Gp120 With Gp41-Interactive Region:
Layered Architecture And Basis Of Conformational
Mobility
pdb|3JWD|B Chain B, Structure Of Hiv-1 Gp120 With Gp41-Interactive Region:
Layered Architecture And Basis Of Conformational
Mobility
Length = 379
Score = 26.6 bits (57), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 18/29 (62%), Gaps = 6/29 (20%)
Query: 44 IWARDLYQRMHDPEVGSFDVLRLWDRPLR 72
+W D+ ++MH+ D++ LWD+ L+
Sbjct: 65 MWKNDMVEQMHE------DIISLWDQSLK 87
>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 = 26.6 bits (57), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 6/53 (11%)
Query: 99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWF--SDEFTCPIC-RSSIYLDA 148
C+IC + ++P C + Y CI SDE TCP C ++ + DA
Sbjct: 16 CLICKDIMTDA---VVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA 65
>pdb|3JWO|A Chain A, Structure Of Hiv-1 Gp120 With Gp41-Interactive Region:
Layered Architecture And Basis Of Conformational
Mobility
Length = 357
Score = 26.6 bits (57), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 18/29 (62%), Gaps = 6/29 (20%)
Query: 44 IWARDLYQRMHDPEVGSFDVLRLWDRPLR 72
+W D+ ++MH+ D++ LWD+ L+
Sbjct: 62 MWKNDMVEQMHE------DIISLWDQSLK 84
>pdb|2H0D|A Chain A, Structure Of A Bmi-1-Ring1b Polycomb Group Ubiquitin
Ligase Complex
Length = 97
Score = 26.6 bits (57), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 23/47 (48%), Gaps = 3/47 (6%)
Query: 99 CVICLEEFVSGDLFRILPFCKHVYHSHCIIRWFSDEFTCPICRSSIY 145
CV+C F+ D I+ C H + CI+R+ CPIC ++
Sbjct: 14 CVLCGGYFI--DATTIIE-CLHSFCKTCIVRYLETSKYCPICDVQVH 57
>pdb|2YUR|A Chain A, Solution Structure Of The Ring Finger Of Human
Retinoblastoma-Binding Protein 6
Length = 74
Score = 26.6 bits (57), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 12/29 (41%), Positives = 15/29 (51%), Gaps = 2/29 (6%)
Query: 114 ILPFCKHVYHSHCIIRWF--SDEFTCPIC 140
++P C + Y CI SDE TCP C
Sbjct: 30 VIPCCGNSYCDECIRTALLESDEHTCPTC 58
>pdb|3RJQ|A Chain A, Crystal Structure Of Anti-Hiv Llama Vhh Antibody A12 In
Complex With C186 Gp120
Length = 382
Score = 26.2 bits (56), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 17/29 (58%), Gaps = 6/29 (20%)
Query: 44 IWARDLYQRMHDPEVGSFDVLRLWDRPLR 72
+W D+ ++MH+ D++ LWD L+
Sbjct: 76 MWKNDMVEQMHE------DIISLWDESLK 98
>pdb|3TGR|A Chain A, Crystal Structure Of Unliganded Hiv-1 Clade C Strain
C1086 Gp120 Core
pdb|3TGR|B Chain B, Crystal Structure Of Unliganded Hiv-1 Clade C Strain
C1086 Gp120 Core
pdb|3TGS|A Chain A, Crystal Structure Of Hiv-1 Clade C Strain C1086 Gp120
Core In Complex With Nbd-556
pdb|3TGS|B Chain B, Crystal Structure Of Hiv-1 Clade C Strain C1086 Gp120
Core In Complex With Nbd-556
Length = 358
Score = 26.2 bits (56), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 9/29 (31%), Positives = 17/29 (58%), Gaps = 6/29 (20%)
Query: 44 IWARDLYQRMHDPEVGSFDVLRLWDRPLR 72
+W D+ ++MH+ D++ LWD L+
Sbjct: 52 MWKNDMVEQMHE------DIISLWDESLK 74
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
0.331 0.145 0.494
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,310,789
Number of Sequences: 62578
Number of extensions: 158964
Number of successful extensions: 421
Number of sequences better than 100.0: 51
Number of HSP's better than 100.0 without gapping: 35
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 381
Number of HSP's gapped (non-prelim): 52
length of query: 148
length of database: 14,973,337
effective HSP length: 90
effective length of query: 58
effective length of database: 9,341,317
effective search space: 541796386
effective search space used: 541796386
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 47 (22.7 bits)