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= 035818
(568 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1R28|A Chain A, Crystal Structure Of The B-Cell Lymphoma 6 (Bcl6) Btb
Domain To 2.2 Angstrom
pdb|1R28|B Chain B, Crystal Structure Of The B-Cell Lymphoma 6 (Bcl6) Btb
Domain To 2.2 Angstrom
pdb|1R29|A Chain A, Crystal Structure Of The B-cell Lymphoma 6 (bcl6) Btb
Domain To 1.3 Angstrom
pdb|1R2B|A Chain A, Crystal Structure Of The Bcl6 Btb Domain Complexed With A
Smrt Co-Repressor Peptide
pdb|1R2B|B Chain B, Crystal Structure Of The Bcl6 Btb Domain Complexed With A
Smrt Co-Repressor Peptide
pdb|3BIM|A Chain A, Crystal Structure Of The Bcl6 Btb Domain Dimer In Complex
With The Bcor Bbd Corepressor Peptide
pdb|3BIM|B Chain B, Crystal Structure Of The Bcl6 Btb Domain Dimer In Complex
With The Bcor Bbd Corepressor Peptide
pdb|3BIM|C Chain C, Crystal Structure Of The Bcl6 Btb Domain Dimer In Complex
With The Bcor Bbd Corepressor Peptide
pdb|3BIM|D Chain D, Crystal Structure Of The Bcl6 Btb Domain Dimer In Complex
With The Bcor Bbd Corepressor Peptide
pdb|3BIM|E Chain E, Crystal Structure Of The Bcl6 Btb Domain Dimer In Complex
With The Bcor Bbd Corepressor Peptide
pdb|3BIM|F Chain F, Crystal Structure Of The Bcl6 Btb Domain Dimer In Complex
With The Bcor Bbd Corepressor Peptide
pdb|3BIM|G Chain G, Crystal Structure Of The Bcl6 Btb Domain Dimer In Complex
With The Bcor Bbd Corepressor Peptide
pdb|3BIM|H Chain H, Crystal Structure Of The Bcl6 Btb Domain Dimer In Complex
With The Bcor Bbd Corepressor Peptide
pdb|3LBZ|A Chain A, Crystal Structure Of The Bcl6 Btb Domain Complexed With
The Molecule Inhibitor 79-6
pdb|3LBZ|B Chain B, Crystal Structure Of The Bcl6 Btb Domain Complexed With
The Molecule Inhibitor 79-6
Length = 127
Score = 40.4 bits (93), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 1/87 (1%)
Query: 4 DVAGDITIVVDGESFLLHKFPLVSRSGKIRKMVADAKDSNSSKLELHNIPGGPQTFELAV 63
D+ D+ IVV E F HK L++ SG + D N S + L + P+ F + +
Sbjct: 27 DILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKRNLSVINL-DPEINPEGFNILL 85
Query: 64 KFCYGMNFEITTTNVASLRCAAEYLEM 90
F Y + N+ ++ A YL+M
Sbjct: 86 DFMYTSRLNLREGNIMAVMATAMYLQM 112
>pdb|3E4U|A Chain A, Crystal Structure Of The Wild-Type Human Bcl6 BtbPOZ
DOMAIN
pdb|3E4U|B Chain B, Crystal Structure Of The Wild-Type Human Bcl6 BtbPOZ
DOMAIN
pdb|3E4U|C Chain C, Crystal Structure Of The Wild-Type Human Bcl6 BtbPOZ
DOMAIN
pdb|3E4U|D Chain D, Crystal Structure Of The Wild-Type Human Bcl6 BtbPOZ
DOMAIN
pdb|3E4U|E Chain E, Crystal Structure Of The Wild-Type Human Bcl6 BtbPOZ
DOMAIN
pdb|3E4U|F Chain F, Crystal Structure Of The Wild-Type Human Bcl6 BtbPOZ
DOMAIN
Length = 130
Score = 39.3 bits (90), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 40/87 (45%), Gaps = 1/87 (1%)
Query: 4 DVAGDITIVVDGESFLLHKFPLVSRSGKIRKMVADAKDSNSSKLELHNIPGGPQTFELAV 63
D+ D+ IVV E F HK L++ SG + D N S + L + P+ F + +
Sbjct: 30 DILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKCNLSVINL-DPEINPEGFCILL 88
Query: 64 KFCYGMNFEITTTNVASLRCAAEYLEM 90
F Y + N+ ++ A YL+M
Sbjct: 89 DFMYTSRLNLREGNIMAVMATAMYLQM 115
>pdb|3GA1|A Chain A, Crystal Structure Of The Human Nac1 Poz Domain
pdb|3GA1|B Chain B, Crystal Structure Of The Human Nac1 Poz Domain
Length = 129
Score = 37.0 bits (84), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 8/87 (9%)
Query: 8 DITIVVDGESFLLHKFPLVSRSGKIRKMVADAKDSNSSKLELHNIPGG--PQTFELAVKF 65
D+++VV G +F H+ L + S R + N+S+ + +P PQ+F+ + F
Sbjct: 35 DVSVVVKGHAFKAHRAVLAASSSYFRDLF------NNSRSAVVELPAAVQPQSFQQILSF 88
Query: 66 CYGMNFEITTTNVASLRCAAEYLEMTE 92
CY + + L A +L++ E
Sbjct: 89 CYTGRLSMNVGDQDLLMYTAGFLQIQE 115
>pdb|3M52|A Chain A, Crystal Structure Of The Btb Domain From The Miz-1ZBTB17
Transcription Regulator
pdb|3M52|B Chain B, Crystal Structure Of The Btb Domain From The Miz-1ZBTB17
Transcription Regulator
Length = 117
Score = 36.2 bits (82), Expect = 0.045, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 37/85 (43%), Gaps = 6/85 (7%)
Query: 8 DITIVVDGESFLLHKFPLVSRSGKIRKMVADAKDSNSSKLELHNIPGGPQTFELAVKFCY 67
D T VVDG F HK L + S + + D KD L++ N G Q E F Y
Sbjct: 27 DCTFVVDGVHFKAHKAVLAACSEYFKMLFVDQKD--VVHLDISNAAGLGQVLE----FMY 80
Query: 68 GMNFEITTTNVASLRCAAEYLEMTE 92
++ NV + A +L+M +
Sbjct: 81 TAKLSLSPENVDDVLAVATFLQMQD 105
>pdb|2Q81|A Chain A, Crystal Structure Of The Miz-1 BtbPOZ DOMAIN
pdb|2Q81|B Chain B, Crystal Structure Of The Miz-1 BtbPOZ DOMAIN
pdb|2Q81|C Chain C, Crystal Structure Of The Miz-1 BtbPOZ DOMAIN
pdb|2Q81|D Chain D, Crystal Structure Of The Miz-1 BtbPOZ DOMAIN
Length = 119
Score = 36.2 bits (82), Expect = 0.045, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 37/85 (43%), Gaps = 6/85 (7%)
Query: 8 DITIVVDGESFLLHKFPLVSRSGKIRKMVADAKDSNSSKLELHNIPGGPQTFELAVKFCY 67
D T VVDG F HK L + S + + D KD L++ N G Q E F Y
Sbjct: 29 DCTFVVDGVHFKAHKAVLAACSEYFKMLFVDQKD--VVHLDISNAAGLGQVLE----FMY 82
Query: 68 GMNFEITTTNVASLRCAAEYLEMTE 92
++ NV + A +L+M +
Sbjct: 83 TAKLSLSPENVDDVLAVATFLQMQD 107
>pdb|4GZ9|A Chain A, Mouse Neuropilin-1, Extracellular Domains 1-4 (A1a2b1b2)
pdb|4GZA|H Chain H, Complex Of Mouse Plexin A2 - Semaphorin 3a - Neuropilin-1
Length = 577
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 35/73 (47%), Gaps = 8/73 (10%)
Query: 307 DTVHRILINFLQRIEDEDNDDCGYES-EGLGSPGHGSLLKVGRLIDAYLAEIAPDPYLSL 365
+ RI+INF + ED D C Y+ E + G GRL + +IAP P +S
Sbjct: 44 EPYQRIMINFNPHFDLEDRD-CKYDYVEVIDGENEG-----GRLWGKFCGKIAPSPVVSS 97
Query: 366 QKFIAMLEILPDY 378
F+ ++ + DY
Sbjct: 98 GPFL-FIKFVSDY 109
>pdb|2IHC|A Chain A, Crystal Structure Of The Bric-A-Brac (Btb) Domain Of Human
Bach1
pdb|2IHC|B Chain B, Crystal Structure Of The Bric-A-Brac (Btb) Domain Of Human
Bach1
pdb|2IHC|C Chain C, Crystal Structure Of The Bric-A-Brac (Btb) Domain Of Human
Bach1
pdb|2IHC|D Chain D, Crystal Structure Of The Bric-A-Brac (Btb) Domain Of Human
Bach1
Length = 124
Score = 28.9 bits (63), Expect = 8.1, Method: Composition-based stats.
Identities = 23/89 (25%), Positives = 38/89 (42%), Gaps = 6/89 (6%)
Query: 4 DVAGDITIVVDGESFLLHKFPLVSRSGKIRKMVADAKDS--NSSKLELHNIPGGPQTFEL 61
DV D+TI V+G+ F H+ L + S + D N + E + G FE
Sbjct: 27 DVLCDVTIFVEGQRFRAHRSVLAACSSYFHSRIVGQADGELNITLPEEVTVKG----FEP 82
Query: 62 AVKFCYGMNFEITTTNVASLRCAAEYLEM 90
++F Y ++ NV + E+L +
Sbjct: 83 LIQFAYTAKLILSKENVDEVCKCVEFLSV 111
>pdb|2LCJ|A Chain A, Solution Nmr Structure Of Pab Polii Intein
Length = 185
Score = 28.9 bits (63), Expect = 8.7, Method: Composition-based stats.
Identities = 13/43 (30%), Positives = 25/43 (58%)
Query: 304 FDVDTVHRILINFLQRIEDEDNDDCGYESEGLGSPGHGSLLKV 346
F+V ++L++ L+ +E + ++E LGSP H LL++
Sbjct: 109 FEVKEGDKVLVSELELVEQSSSSQDNPKNENLGSPEHDQLLEI 151
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 0.135 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,885,490
Number of Sequences: 62578
Number of extensions: 640721
Number of successful extensions: 1363
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1356
Number of HSP's gapped (non-prelim): 17
length of query: 568
length of database: 14,973,337
effective HSP length: 104
effective length of query: 464
effective length of database: 8,465,225
effective search space: 3927864400
effective search space used: 3927864400
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)