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= 008382
(567 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WD2|A Chain A, Solution Structure Of The C-Terminal Ring From A Ring-Ibr-
Ring (Triad) Motif
Length = 60
Score = 68.6 bits (166), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 34/60 (56%), Positives = 39/60 (65%), Gaps = 4/60 (6%)
Query: 293 WILANSKPCPKCKRPIEKNQGCMHMTC-SPPCKFEFCWLCLGAWSDHGERTGGFYACNRY 351
WI AN+K CPKC IEK+ GC HM C + CK EFCW+CLG W HG +Y CNRY
Sbjct: 1 WIAANTKECPKCHVTIEKDGGCNHMVCRNQNCKAEFCWVCLGPWEPHGS---AWYNCNRY 57
>pdb|2ECW|A Chain A, Solution Structure Of The Zinc Finger, C3hc4 Type (Ring
Finger) Domain Tripartite Motif Protein 30
Length = 85
Score = 37.0 bits (84), Expect = 0.029, Method: Composition-based stats.
Identities = 24/54 (44%), Positives = 28/54 (51%), Gaps = 4/54 (7%)
Query: 140 ELTCGICFDTYSCDKVVSAACGHPFCRACWR-GYISATVNDGPG-CLMLRCPDP 191
E+TC IC + + VSA C H FCRAC Y S DG G C + R P P
Sbjct: 19 EVTCPICLELLK--EPVSADCNHSFCRACITLNYESNRNTDGKGNCPVCRVPYP 70
>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 = 32.3 bits (72), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 141 LTCGICFDTYSCDKVVSAACGHPFCRACWRGYISATVNDGPGCLMLRCPD 190
L CGICF+ ++ ++ C H +C C R ++S C+ + PD
Sbjct: 23 LRCGICFEYFNIAMII-PQCSHNYCSLCIRKFLSYKTQCPTCCVTVTEPD 71
>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 = 32.0 bits (71), Expect = 0.91, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 22/48 (45%), Gaps = 6/48 (12%)
Query: 141 LTCGICFDTYS-----CDKVVSAACGHPFCRACWRGYISATVNDGPGC 183
++C IC D YS +VS CGH FC C R + N P C
Sbjct: 11 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK-NANTCPTC 57
>pdb|4AP4|A Chain A, Rnf4 - Ubch5a - Ubiquitin Heterotrimeric Complex
Length = 133
Score = 31.6 bits (70), Expect = 1.2, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 22/48 (45%), Gaps = 6/48 (12%)
Query: 141 LTCGICFDTYS-----CDKVVSAACGHPFCRACWRGYISATVNDGPGC 183
++C IC D YS +VS CGH FC C R + N P C
Sbjct: 8 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK-NANTCPTC 54
Score = 31.6 bits (70), Expect = 1.2, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 22/48 (45%), Gaps = 6/48 (12%)
Query: 141 LTCGICFDTYS-----CDKVVSAACGHPFCRACWRGYISATVNDGPGC 183
++C IC D YS +VS CGH FC C R + N P C
Sbjct: 73 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK-NANTCPTC 119
>pdb|2XEU|A Chain A, Ring Domain
Length = 64
Score = 31.2 bits (69), Expect = 1.4, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 22/48 (45%), Gaps = 6/48 (12%)
Query: 141 LTCGICFDTYS-----CDKVVSAACGHPFCRACWRGYISATVNDGPGC 183
++C IC D YS +VS CGH FC C R + N P C
Sbjct: 4 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK-NANTCPTC 50
>pdb|2CT2|A Chain A, Solution Structure Of The Ring Domain Of The Tripartite
Motif Protein 32
Length = 88
Score = 31.2 bits (69), Expect = 1.7, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 27/51 (52%), Gaps = 8/51 (15%)
Query: 141 LTCGICFDTYSCDKVVSAA--CGHPFCRACWRGYISATVNDGPGCLMLRCP 189
L C IC ++++ +++ CGH CR C +++++N +RCP
Sbjct: 16 LECPICMESFTEEQLRPKLLHCGHTICRQCLEKLLASSING------VRCP 60
>pdb|2EA6|A Chain A, Solution Structure Of The Ring Domain Of The Human Ring
Finger Protein 4
Length = 69
Score = 30.8 bits (68), Expect = 1.9, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 22/48 (45%), Gaps = 6/48 (12%)
Query: 141 LTCGICFDTYS-----CDKVVSAACGHPFCRACWRGYISATVNDGPGC 183
++C IC D YS +VS CGH FC C R + N P C
Sbjct: 16 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK-NANTCPTC 62
>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 = 30.4 bits (67), Expect = 2.9, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 19/29 (65%), Gaps = 2/29 (6%)
Query: 140 ELTCGICFDTYSCDKVVSAACGHPFCRAC 168
E+TC IC + + + +S CGH FC+AC
Sbjct: 19 EVTCPICLELLT--QPLSLDCGHSFCQAC 45
>pdb|2EGP|A Chain A, Solution Structure Of The Ring-Finger Domain From Human
Tripartite Motif Protein 34
Length = 79
Score = 30.0 bits (66), Expect = 3.9, Method: Composition-based stats.
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 2/29 (6%)
Query: 140 ELTCGICFDTYSCDKVVSAACGHPFCRAC 168
E+TC IC + + + +S CGH CRAC
Sbjct: 12 EVTCPICLELLT--EPLSLDCGHSLCRAC 38
>pdb|1WIM|A Chain A, Solution Structure Of The Ring Finger Domain Of The Human
Ubcm4-Interacting Protein 4
Length = 94
Score = 29.6 bits (65), Expect = 5.2, Method: Composition-based stats.
Identities = 17/77 (22%), Positives = 37/77 (48%), Gaps = 4/77 (5%)
Query: 143 CGICFDTYSCDKVVS-AACGHPFCRACWRGYISATVNDGPGCLMLRCPDPSCC--AAVGQ 199
C +C Y +++ + A C FC C + Y+ + +G + CPD +C + +
Sbjct: 8 CKLCLGEYPVEQMTTIAQCQCIFCTLCLKQYVELLIKEGLET-AISCPDAACPKQGHLQE 66
Query: 200 DMIDMLASDEDKKKYSR 216
+ I+ + + E ++Y +
Sbjct: 67 NEIECMVAAEIMQRYKK 83
>pdb|1A74|A Chain A, I-Ppol Homing EndonucleaseDNA COMPLEX
pdb|1A74|B Chain B, I-Ppol Homing EndonucleaseDNA COMPLEX
pdb|1IPP|A Chain A, Homing EndonucleaseDNA COMPLEX
pdb|1IPP|B Chain B, Homing EndonucleaseDNA COMPLEX
pdb|1A73|A Chain A, Intron-Encoded Endonuclease I-Ppoi Complexed With Dna
pdb|1A73|B Chain B, Intron-Encoded Endonuclease I-Ppoi Complexed With Dna
Length = 163
Score = 29.3 bits (64), Expect = 5.7, Method: Composition-based stats.
Identities = 10/21 (47%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 223 VEDNRKTKWCPAP--GCEHAI 241
++DN+ WCP P GC HA+
Sbjct: 116 LDDNKGRNWCPGPNGGCVHAV 136
>pdb|2O6M|A Chain A, H98q Mutant Of The Homing Endonuclease I-ppoi Complexed
With Dna
pdb|2O6M|B Chain B, H98q Mutant Of The Homing Endonuclease I-ppoi Complexed
With Dna
Length = 163
Score = 29.3 bits (64), Expect = 5.7, Method: Composition-based stats.
Identities = 10/21 (47%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 223 VEDNRKTKWCPAP--GCEHAI 241
++DN+ WCP P GC HA+
Sbjct: 116 LDDNKGRNWCPGPNGGCVHAV 136
>pdb|1CYQ|A Chain A, Intron Encoded Homing Endonuclease I-Ppoi (H98a)DNA HOMING
Site Complex
pdb|1CYQ|B Chain B, Intron Encoded Homing Endonuclease I-Ppoi (H98a)DNA HOMING
Site Complex
Length = 162
Score = 29.3 bits (64), Expect = 5.8, Method: Composition-based stats.
Identities = 10/21 (47%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 223 VEDNRKTKWCPAP--GCEHAI 241
++DN+ WCP P GC HA+
Sbjct: 115 LDDNKGRNWCPGPNGGCVHAV 135
>pdb|1CZ0|A Chain A, Intron Encoded Homing Endonuclease I-PpoiDNA COMPLEX
Lacking Catalytic Metal Ion
pdb|1CZ0|B Chain B, Intron Encoded Homing Endonuclease I-PpoiDNA COMPLEX
Lacking Catalytic Metal Ion
pdb|1EVX|A Chain A, Apo Crystal Structure Of The Homing Endonuclease, I-Ppoi
pdb|1EVX|B Chain B, Apo Crystal Structure Of The Homing Endonuclease, I-Ppoi
Length = 162
Score = 29.3 bits (64), Expect = 5.8, Method: Composition-based stats.
Identities = 10/21 (47%), Positives = 14/21 (66%), Gaps = 2/21 (9%)
Query: 223 VEDNRKTKWCPAP--GCEHAI 241
++DN+ WCP P GC HA+
Sbjct: 115 LDDNKGRNWCPGPNGGCVHAV 135
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
0.320 0.133 0.434
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,321,882
Number of Sequences: 62578
Number of extensions: 660920
Number of successful extensions: 1347
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 18
Number of HSP's that attempted gapping in prelim test: 1338
Number of HSP's gapped (non-prelim): 25
length of query: 567
length of database: 14,973,337
effective HSP length: 104
effective length of query: 463
effective length of database: 8,465,225
effective search space: 3919399175
effective search space used: 3919399175
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: 54 (25.4 bits)