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= 041904
(317 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1CA4|A Chain A, Structure Of Tnf Receptor Associated Factor 2 (Traf2)
pdb|1CA4|B Chain B, Structure Of Tnf Receptor Associated Factor 2 (Traf2)
pdb|1CA4|C Chain C, Structure Of Tnf Receptor Associated Factor 2 (Traf2)
pdb|1CA4|D Chain D, Structure Of Tnf Receptor Associated Factor 2 (Traf2)
pdb|1CA4|E Chain E, Structure Of Tnf Receptor Associated Factor 2 (Traf2)
pdb|1CA4|F Chain F, Structure Of Tnf Receptor Associated Factor 2 (Traf2)
pdb|1D00|A Chain A, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A 5-Residue Cd40 Peptide
pdb|1D00|B Chain B, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A 5-Residue Cd40 Peptide
pdb|1D00|C Chain C, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A 5-Residue Cd40 Peptide
pdb|1D00|D Chain D, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A 5-Residue Cd40 Peptide
pdb|1D00|E Chain E, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A 5-Residue Cd40 Peptide
pdb|1D00|F Chain F, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A 5-Residue Cd40 Peptide
pdb|1D00|G Chain G, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A 5-Residue Cd40 Peptide
pdb|1D00|H Chain H, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A 5-Residue Cd40 Peptide
pdb|1D0J|A Chain A, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A M4-1bb Peptide
pdb|1D0J|B Chain B, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A M4-1bb Peptide
pdb|1D0J|C Chain C, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A M4-1bb Peptide
pdb|1D0J|D Chain D, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A M4-1bb Peptide
pdb|1D0J|E Chain E, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A M4-1bb Peptide
pdb|1D0J|F Chain F, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A M4-1bb Peptide
Length = 168
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 39/150 (26%), Positives = 63/150 (42%), Gaps = 21/150 (14%)
Query: 180 WKVSNFSSLLDEFYESESFGCYK---WYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQ 236
WK+S+F+ E + + + Y + + +Y NG+G +G +SLF V +
Sbjct: 23 WKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFVVMK 82
Query: 237 SSIPPNTKLL-----TKYFLCVENQMNGKN------SEVEGEWLYTLTNR---AIGGRQF 282
PN LL K L + +Q N ++ +V N A G F
Sbjct: 83 G---PNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLF 139
Query: 283 MTLAKLKDPTEGYLVDDSCIIKAEVTLHGL 312
++K+ + Y+ DD+ IKA V L GL
Sbjct: 140 CPVSKM-EAKNSYVRDDAIFIKAIVDLTGL 168
>pdb|1CA9|A Chain A, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A Peptide From Tnf-R2
pdb|1CA9|B Chain B, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A Peptide From Tnf-R2
pdb|1CA9|C Chain C, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A Peptide From Tnf-R2
pdb|1CA9|D Chain D, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A Peptide From Tnf-R2
pdb|1CA9|E Chain E, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A Peptide From Tnf-R2
pdb|1CA9|F Chain F, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A Peptide From Tnf-R2
Length = 192
Score = 33.9 bits (76), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 39/150 (26%), Positives = 63/150 (42%), Gaps = 21/150 (14%)
Query: 180 WKVSNFSSLLDEFYESESFGCYK---WYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQ 236
WK+S+F+ E + + + Y + + +Y NG+G +G +SLF V +
Sbjct: 47 WKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFVVMK 106
Query: 237 SSIPPNTKLL-----TKYFLCVENQMNGKN------SEVEGEWLYTLTNR---AIGGRQF 282
PN LL K L + +Q N ++ +V N A G F
Sbjct: 107 G---PNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLF 163
Query: 283 MTLAKLKDPTEGYLVDDSCIIKAEVTLHGL 312
++K+ + Y+ DD+ IKA V L GL
Sbjct: 164 CPVSKM-EAKNSYVRDDAIFIKAIVDLTGL 192
>pdb|1CZY|A Chain A, Crystal Structure Of The Complex Between The Traf Domain
Of Human Traf2 And An Lmp1 Binding Peptide
pdb|1CZY|B Chain B, Crystal Structure Of The Complex Between The Traf Domain
Of Human Traf2 And An Lmp1 Binding Peptide
pdb|1CZY|C Chain C, Crystal Structure Of The Complex Between The Traf Domain
Of Human Traf2 And An Lmp1 Binding Peptide
pdb|1D0A|A Chain A, Structure Of Tnf Receptor Associated Factor 2 (Traf2) In
Complex With A Human Ox40 Peptide
pdb|1D0A|B Chain B, Structure Of Tnf Receptor Associated Factor 2 (Traf2) In
Complex With A Human Ox40 Peptide
pdb|1D0A|C Chain C, Structure Of Tnf Receptor Associated Factor 2 (Traf2) In
Complex With A Human Ox40 Peptide
pdb|1D0A|D Chain D, Structure Of Tnf Receptor Associated Factor 2 (Traf2) In
Complex With A Human Ox40 Peptide
pdb|1D0A|E Chain E, Structure Of Tnf Receptor Associated Factor 2 (Traf2) In
Complex With A Human Ox40 Peptide
pdb|1D0A|F Chain F, Structure Of Tnf Receptor Associated Factor 2 (Traf2) In
Complex With A Human Ox40 Peptide
pdb|1D01|A Chain A, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A Human Cd30 Peptide
pdb|1D01|B Chain B, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A Human Cd30 Peptide
pdb|1D01|C Chain C, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A Human Cd30 Peptide
pdb|1D01|D Chain D, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A Human Cd30 Peptide
pdb|1D01|E Chain E, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A Human Cd30 Peptide
pdb|1D01|F Chain F, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A Human Cd30 Peptide
Length = 168
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 39/150 (26%), Positives = 62/150 (41%), Gaps = 21/150 (14%)
Query: 180 WKVSNFSSLLDEFYESESFGCYK---WYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQ 236
WK+S+F E + + + Y + + +Y NG+G +G +SLF V +
Sbjct: 23 WKISDFPRKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFVVMK 82
Query: 237 SSIPPNTKLL-----TKYFLCVENQMNGKN------SEVEGEWLYTLTNR---AIGGRQF 282
PN LL K L + +Q N ++ +V N A G F
Sbjct: 83 G---PNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLF 139
Query: 283 MTLAKLKDPTEGYLVDDSCIIKAEVTLHGL 312
++K+ + Y+ DD+ IKA V L GL
Sbjct: 140 CPVSKM-EAKNSYVRDDAIFIKAIVDLTGL 168
>pdb|1CZZ|A Chain A, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A 17-Residue Cd40 Peptide
pdb|1CZZ|B Chain B, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A 17-Residue Cd40 Peptide
pdb|1CZZ|C Chain C, Structure Of Tnf Receptor Associated Factor 2 In Complex
With A 17-Residue Cd40 Peptide
Length = 187
Score = 33.5 bits (75), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 39/150 (26%), Positives = 62/150 (41%), Gaps = 21/150 (14%)
Query: 180 WKVSNFSSLLDEFYESESFGCYK---WYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQ 236
WK+S+F E + + + Y + + +Y NG+G +G +SLF V +
Sbjct: 42 WKISDFPRKRQEAVAGRIPAIFSPAFYTSRYGYKMCLRIYLNGDGTGRGTHLSLFFVVMK 101
Query: 237 SSIPPNTKLL-----TKYFLCVENQMNGKN------SEVEGEWLYTLTNR---AIGGRQF 282
PN LL K L + +Q N ++ +V N A G F
Sbjct: 102 G---PNDALLRWPFNQKVTLMLLDQNNREHVIDAFRPDVTSSSFQRPVNDMNIASGCPLF 158
Query: 283 MTLAKLKDPTEGYLVDDSCIIKAEVTLHGL 312
++K+ + Y+ DD+ IKA V L GL
Sbjct: 159 CPVSKM-EAKNSYVRDDAIFIKAIVDLTGL 187
>pdb|1QSC|A Chain A, Crystal Structure Of The Traf Domain Of Traf2 In A Complex
With A Peptide From The Cd40 Receptor
pdb|1QSC|B Chain B, Crystal Structure Of The Traf Domain Of Traf2 In A Complex
With A Peptide From The Cd40 Receptor
pdb|1QSC|C Chain C, Crystal Structure Of The Traf Domain Of Traf2 In A Complex
With A Peptide From The Cd40 Receptor
Length = 191
Score = 32.0 bits (71), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 39/150 (26%), Positives = 61/150 (40%), Gaps = 21/150 (14%)
Query: 180 WKVSNFSSLLDEFYESESFGCYK---WYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQ 236
WK+S+F+ E + + + Y + +Y NG+G +G +SLF V +
Sbjct: 46 WKISDFARKRQEAVAGRIPAIFSPAFYTSRYGYKXCLRIYLNGDGTGRGTHLSLFFVVXK 105
Query: 237 SSIPPNTKLL-----TKYFLCVENQMNGKN------SEVEGEWLYTLTNR---AIGGRQF 282
PN LL K L + +Q N ++ +V N A G F
Sbjct: 106 G---PNDALLRWPFNQKVTLXLLDQNNREHVIDAFRPDVTSSSFQRPVNDXNIASGCPLF 162
Query: 283 MTLAKLKDPTEGYLVDDSCIIKAEVTLHGL 312
++K + Y+ DD+ IKA V L GL
Sbjct: 163 CPVSK-XEAKNSYVRDDAIFIKAIVDLTGL 191
>pdb|1EY2|A Chain A, Human Homogentisate Dioxygenase With Fe(ii)
pdb|1EYB|A Chain A, Crystal Structure Of Apo Human Homogentisate Dioxygenase
Length = 471
Score = 32.0 bits (71), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 31/138 (22%), Positives = 50/138 (36%), Gaps = 27/138 (19%)
Query: 79 LPTGWEVNAITISFYSI--KFKTNILVSKVRNSTINVIVKHFHAMKSKYGVAKFIDLKTF 136
+P W + Y++ K++ + +K S NV+ H + KY + F + +
Sbjct: 255 IPIAWYEDRQVPGGYTVINKYQGKLFAAKQDVSPFNVVAWHGNYTPYKYNLKNFXVINSV 314
Query: 137 S----DP-----------LNGYLINDACVFGAEVFVVKNTFKGECLSMMHDPPTYYHTWK 181
+ DP G I D +F V TF+ P YYH
Sbjct: 315 AFDHADPSIFTVLTAKSVRPGVAIADFVIFPPRWGVADKTFR----------PPYYHRNC 364
Query: 182 VSNFSSLLDEFYESESFG 199
S F L+ YE++ G
Sbjct: 365 XSEFXGLIRGHYEAKQGG 382
>pdb|1F3V|B Chain B, Crystal Structure Of The Complex Between The N-Terminal
Domain Of Tradd And The Traf Domain Of Traf2
Length = 171
Score = 31.6 bits (70), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 39/150 (26%), Positives = 60/150 (40%), Gaps = 21/150 (14%)
Query: 180 WKVSNFSSLLDEFYESESFGCYK---WYANYSMDVKILLYPNGNGEAKGNCISLFLDVSQ 236
WK+S+F E + + + Y + +Y NG+G +G +SLF V +
Sbjct: 26 WKISDFPRKRQEAVAGRIPAIFSPAFYTSRYGYKXCLRIYLNGDGTGRGTHLSLFFVVXK 85
Query: 237 SSIPPNTKLL-----TKYFLCVENQMNGKN------SEVEGEWLYTLTNR---AIGGRQF 282
PN LL K L + +Q N ++ +V N A G F
Sbjct: 86 G---PNDALLRWPFNQKVTLXLLDQNNREHVIDAFRPDVTSSSFQRPVNDXNIASGCPLF 142
Query: 283 MTLAKLKDPTEGYLVDDSCIIKAEVTLHGL 312
++K + Y+ DD+ IKA V L GL
Sbjct: 143 CPVSK-XEAKNSYVRDDAIFIKAIVDLTGL 171
>pdb|2CR2|A Chain A, Solution Structure Of N-Terminal Domain Of Speckle-Type
Poz Protein
Length = 159
Score = 28.1 bits (61), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 1/67 (1%)
Query: 96 KFKTNILVSKVRNSTINVIVKHFHAMKSK-YGVAKFIDLKTFSDPLNGYLINDACVFGAE 154
KFK +IL +K + + + ++ K +G KFI D NG L +D E
Sbjct: 81 KFKFSILNAKGEETKAMESQRAYRFVQGKDWGFKKFIRRDFLLDEANGLLPDDKLTLFCE 140
Query: 155 VFVVKNT 161
V VV+++
Sbjct: 141 VSVVQDS 147
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
0.318 0.134 0.399
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,559,832
Number of Sequences: 62578
Number of extensions: 384614
Number of successful extensions: 780
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 770
Number of HSP's gapped (non-prelim): 15
length of query: 317
length of database: 14,973,337
effective HSP length: 99
effective length of query: 218
effective length of database: 8,778,115
effective search space: 1913629070
effective search space used: 1913629070
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)