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= 009502
(533 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YUC|A Chain A, Solution Structure Of The Traf-Type Zinc Finger Domains
(102-164) From Human Tnf Receptor Associated Factor 4
Length = 76
Score = 37.0 bits (84), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 6/54 (11%)
Query: 209 SAGHLEKHDSVCPFKIIPCEQKCPDTLMRRDMDRHCITVCQMKLANCPFYAVGC 262
S+GHL + C F +IPC +CP L RRD+ H C + C F GC
Sbjct: 5 SSGHL----NTCSFNVIPCPNRCPMKLSRRDLPAHLQHDCPKRRLKCEF--CGC 52
>pdb|2FKJ|A Chain A, The Crystal Structure Of Engineered Ospa
pdb|2FKJ|B Chain B, The Crystal Structure Of Engineered Ospa
pdb|2FKJ|C Chain C, The Crystal Structure Of Engineered Ospa
Length = 366
Score = 36.2 bits (82), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 46/166 (27%), Positives = 79/166 (47%), Gaps = 32/166 (19%)
Query: 376 EEGKINATDKVNEKEKISNKSKPNEGGKGNEQEKDSDGDVKEGKFTEGKNNGRKVSEEDR 435
E+GK + KV K+K S + K NE G+ +E +K++ D+
Sbjct: 82 EDGKTLVSKKVTSKDKSSTEEKFNEKGELSE---------------------KKITRADK 120
Query: 436 IHDEQNVNREGTIDGGKINNETRVNEEQKANEPG-----KVTKGEKVSEEGKANDTG--- 487
E+ N +G + KI + + E+K NE G K+T+ +K S E K N+ G
Sbjct: 121 SSTEEKFNEKGELSEKKITRADKSSTEEKFNEKGELSEKKITRADKSSTEEKFNEKGELS 180
Query: 488 --KVNKEVRASEGRKVSEERNINEGK-TNGVRVNEEEKINAEGKVN 530
K+ + ++S K +E+ ++E K T + + EEK N +G+V+
Sbjct: 181 EKKITRADKSSTEEKFNEKGELSEKKITRADKSSTEEKFNEKGEVS 226
>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 = 34.7 bits (78), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/31 (48%), Positives = 18/31 (58%)
Query: 199 CPNEGCNAKFSAGHLEKHDSVCPFKIIPCEQ 229
CPNEGC K HLE H + C F ++ C Q
Sbjct: 85 CPNEGCLHKMELRHLEDHQAHCEFALMDCPQ 115
>pdb|2FKG|A Chain A, The Crystal Structure Of Engineered Ospa
Length = 320
Score = 34.7 bits (78), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 32/99 (32%), Positives = 55/99 (55%), Gaps = 2/99 (2%)
Query: 376 EEGKINATDKVNEKEKISNKSKPNEGGKGNEQE-KDSDGDVKEGKFTE-GKNNGRKVSEE 433
E+GK + KV K+K S + K NE G+ +E++ +D E KF E G+ + +K++
Sbjct: 82 EDGKTLVSKKVTSKDKSSTEEKFNEKGELSEKKITRADKSSTEEKFNEKGELSEKKITRA 141
Query: 434 DRIHDEQNVNREGTIDGGKINNETRVNEEQKANEPGKVT 472
D+ E+ N +G + KI + + E+K NE G+V+
Sbjct: 142 DKSSTEEKFNEKGELSEKKITRADKSSTEEKFNEKGEVS 180
>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 = 0.67, Method: Compositional matrix adjust.
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 199 CPNEGCNAKFSAGHLEKHDSVCPFKII 225
CPNEGC K HLE H + C F ++
Sbjct: 85 CPNEGCLHKMELRHLEDHQAHCEFALL 111
>pdb|2YRE|A Chain A, Solution Structure Of The Zinc Finger Domains (1-87) From
Human F-Box Only Protein
Length = 100
Score = 32.0 bits (71), Expect = 0.79, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 3/43 (6%)
Query: 204 CNAKFSAGHLEKHDSVCPFKIIPCEQK---CPDTLMRRDMDRH 243
C A F + ++H +CPF+ +PC CP T+ R + H
Sbjct: 44 CGAVFHSCKADEHRLLCPFERVPCLNSDFGCPFTMARNKVAEH 86
>pdb|2HKD|A Chain A, The Crystal Structure Of Engineered Ospa
Length = 320
Score = 31.6 bits (70), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 30/98 (30%), Positives = 53/98 (54%), Gaps = 2/98 (2%)
Query: 377 EGKINATDKVNEKEKISNKSKPNEGGKGNEQE-KDSDGDVKEGKFTE-GKNNGRKVSEED 434
+G + KV K+K S + K NE G+ +E++ +D E KF E G+ + +K++ D
Sbjct: 83 DGSTLVSKKVTSKDKSSTEEKFNEKGELSEKKITRADKSSTEEKFNEKGELSEKKITRAD 142
Query: 435 RIHDEQNVNREGTIDGGKINNETRVNEEQKANEPGKVT 472
+ E+ N +G + KI + + E+K NE G+V+
Sbjct: 143 KSSTEEKFNEKGELSEKKITRADKSSTEEKFNEKGEVS 180
>pdb|2J7J|A Chain A, Invariance Of The Zinc Finger Module: A Comparison Of The
Free Structure With Those In Nucleic-Acid Complexes
Length = 85
Score = 30.0 bits (66), Expect = 3.7, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 174 HCNMKFNSEKELNEHML-HCGFISMICPNEGCNAKFS-AGHLEKHDSV 219
+C F +L H H + CP+EGC+ +FS L++H+ V
Sbjct: 8 NCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKV 55
>pdb|1UN6|B Chain B, The Crystal Structure Of A Zinc Finger - Rna Complex
Reveals Two Modes Of Molecular Recognition
pdb|1UN6|C Chain C, The Crystal Structure Of A Zinc Finger - Rna Complex
Reveals Two Modes Of Molecular Recognition
pdb|1UN6|D Chain D, The Crystal Structure Of A Zinc Finger - Rna Complex
Reveals Two Modes Of Molecular Recognition
pdb|2HGH|A Chain A, Transcription Factor Iiia Zinc Fingers 4-6 Bound To 5s
Rrna 55mer (Nmr Structure)
Length = 87
Score = 29.6 bits (65), Expect = 4.5, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 174 HCNMKFNSEKELNEHML-HCGFISMICPNEGCNAKFS-AGHLEKHDSV 219
+C F +L H H + CP+EGC+ +FS L++H+ V
Sbjct: 8 NCGKAFKKHNQLKVHQFSHTQQLPYECPHEGCDKRFSLPSRLKRHEKV 55
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
0.313 0.132 0.381
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,985,391
Number of Sequences: 62578
Number of extensions: 679415
Number of successful extensions: 1055
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 1006
Number of HSP's gapped (non-prelim): 39
length of query: 533
length of database: 14,973,337
effective HSP length: 103
effective length of query: 430
effective length of database: 8,527,803
effective search space: 3666955290
effective search space used: 3666955290
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 54 (25.4 bits)