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= psy16107
(256 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1HJB|A Chain A, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN AND
CEBPBETA BZIP DIMERIC BOUND TO A DNA FRAGMENT FROM THE
Csf-1r Promoter
pdb|1HJB|B Chain B, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN AND
CEBPBETA BZIP DIMERIC BOUND TO A DNA FRAGMENT FROM THE
Csf-1r Promoter
pdb|1HJB|D Chain D, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN AND
CEBPBETA BZIP DIMERIC BOUND TO A DNA FRAGMENT FROM THE
Csf-1r Promoter
pdb|1HJB|E Chain E, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN AND
CEBPBETA BZIP DIMERIC BOUND TO A DNA FRAGMENT FROM THE
Csf-1r Promoter
Length = 87
Score = 81.3 bits (199), Expect = 5e-16, Method: Compositional matrix adjust.
Identities = 47/80 (58%), Positives = 57/80 (71%), Gaps = 3/80 (3%)
Query: 162 KNGKSVDKNTDEYKRRRERNNIAVRKSREKAKIRSRETXXXXXXXXXXNERLQKRIELLS 221
K K+VDK++DEYK RRERNNIAVRKSR+KAK+R+ ET NERLQK++E LS
Sbjct: 4 KAKKTVDKHSDEYKIRRERNNIAVRKSRDKAKMRNLETQHKVLELTAENERLQKKVEQLS 63
Query: 222 EELNVLRSLFTNVGVLPEHL 241
EL+ LR+LF LPE L
Sbjct: 64 RELSTLRNLFKQ---LPEPL 80
>pdb|1IO4|A Chain A, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN-
Cbfbeta Core Domain Heterodimer And CEBPBETA BZIP
Homodimer Bound To A Dna Fragment From The Csf-1r
Promoter
pdb|1IO4|B Chain B, Crystal Structure Of Runx-1AML1CBFALPHA RUNT DOMAIN-
Cbfbeta Core Domain Heterodimer And CEBPBETA BZIP
Homodimer Bound To A Dna Fragment From The Csf-1r
Promoter
pdb|1H88|A Chain A, Crystal Structure Of Ternary Protein-Dna Complex1
pdb|1H88|B Chain B, Crystal Structure Of Ternary Protein-Dna Complex1
pdb|1H8A|A Chain A, Crystal Structure Of Ternary Protein-Dna Complex3
pdb|1H8A|B Chain B, Crystal Structure Of Ternary Protein-Dna Complex3
pdb|1GU4|A Chain A, Crystal Structure Of CEBPBETA BZIP DIMERIC BOUND TO A
High Affinity Dna Fragment
pdb|1GU4|B Chain B, Crystal Structure Of CEBPBETA BZIP DIMERIC BOUND TO A
High Affinity Dna Fragment
pdb|1GU5|A Chain A, Crystal Structure Of CEBPBETA BZIP DIMERIC BOUND TO A
Dna Fragment From The Mim-1 Promoter
pdb|1GU5|B Chain B, Crystal Structure Of CEBPBETA BZIP DIMERIC BOUND TO A
Dna Fragment From The Mim-1 Promoter
pdb|1GTW|A Chain A, Crystal Structure Of CEBPBETA BZIP DIMERIC BOUND TO A
Dna Fragment From The Tom-1a Promoter
pdb|1GTW|B Chain B, Crystal Structure Of CEBPBETA BZIP DIMERIC BOUND TO A
Dna Fragment From The Tom-1a Promoter
Length = 78
Score = 80.5 bits (197), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 46/78 (58%), Positives = 56/78 (71%), Gaps = 3/78 (3%)
Query: 162 KNGKSVDKNTDEYKRRRERNNIAVRKSREKAKIRSRETXXXXXXXXXXNERLQKRIELLS 221
K K+VDK++DEYK RRERNNIAVRKSR+KAK+R+ ET NERLQK++E LS
Sbjct: 4 KAKKTVDKHSDEYKIRRERNNIAVRKSRDKAKMRNLETQHKVLELTAENERLQKKVEQLS 63
Query: 222 EELNVLRSLFTNVGVLPE 239
EL+ LR+LF LPE
Sbjct: 64 RELSTLRNLFKQ---LPE 78
>pdb|2E42|A Chain A, Crystal Structure Of CEBPBETA BZIP HOMODIMER V285A MUTANT
Bound To A High Affinity Dna Fragment
pdb|2E42|B Chain B, Crystal Structure Of CEBPBETA BZIP HOMODIMER V285A MUTANT
Bound To A High Affinity Dna Fragment
Length = 78
Score = 78.6 bits (192), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 45/78 (57%), Positives = 55/78 (70%), Gaps = 3/78 (3%)
Query: 162 KNGKSVDKNTDEYKRRRERNNIAVRKSREKAKIRSRETXXXXXXXXXXNERLQKRIELLS 221
K K+VDK++DEYK RRERNNIA RKSR+KAK+R+ ET NERLQK++E LS
Sbjct: 4 KAKKTVDKHSDEYKIRRERNNIAARKSRDKAKMRNLETQHKVLELTAENERLQKKVEQLS 63
Query: 222 EELNVLRSLFTNVGVLPE 239
EL+ LR+LF LPE
Sbjct: 64 RELSTLRNLFKQ---LPE 78
>pdb|2E43|A Chain A, Crystal Structure Of CEBPBETA BZIP HOMODIMER K269A MUTANT
Bound To A High Affinity Dna Fragment
pdb|2E43|B Chain B, Crystal Structure Of CEBPBETA BZIP HOMODIMER K269A MUTANT
Bound To A High Affinity Dna Fragment
Length = 78
Score = 78.6 bits (192), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 45/78 (57%), Positives = 55/78 (70%), Gaps = 3/78 (3%)
Query: 162 KNGKSVDKNTDEYKRRRERNNIAVRKSREKAKIRSRETXXXXXXXXXXNERLQKRIELLS 221
K K+VD ++DEYK RRERNNIAVRKSR+KAK+R+ ET NERLQK++E LS
Sbjct: 4 KAKKTVDAHSDEYKIRRERNNIAVRKSRDKAKMRNLETQHKVLELTAENERLQKKVEQLS 63
Query: 222 EELNVLRSLFTNVGVLPE 239
EL+ LR+LF LPE
Sbjct: 64 RELSTLRNLFKQ---LPE 78
>pdb|1CI6|B Chain B, Transcription Factor Atf4-CEBP BETA BZIP HETERODIMER
Length = 63
Score = 68.6 bits (166), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 37/59 (62%), Positives = 44/59 (74%)
Query: 173 EYKRRRERNNIAVRKSREKAKIRSRETXXXXXXXXXXNERLQKRIELLSEELNVLRSLF 231
EYK RRERNNIAVRKSR+KAK+R+ ET NERLQK++E LS EL+ LR+LF
Sbjct: 2 EYKMRRERNNIAVRKSRDKAKMRNLETQHKVLELTAENERLQKKVEQLSRELSTLRNLF 60
>pdb|1H89|A Chain A, Crystal Structure Of Ternary Protein-Dna Complex2
pdb|1H89|B Chain B, Crystal Structure Of Ternary Protein-Dna Complex2
Length = 64
Score = 67.8 bits (164), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 40/67 (59%), Positives = 47/67 (70%), Gaps = 3/67 (4%)
Query: 173 EYKRRRERNNIAVRKSREKAKIRSRETXXXXXXXXXXNERLQKRIELLSEELNVLRSLFT 232
EYK RRERNNIAVRKSR+KAK+R+ ET NERLQK++E LS EL+ LR+LF
Sbjct: 1 EYKIRRERNNIAVRKSRDKAKMRNLETQHKVLELTAENERLQKKVEQLSRELSTLRNLFK 60
Query: 233 NVGVLPE 239
LPE
Sbjct: 61 Q---LPE 64
>pdb|1NWQ|A Chain A, Crystal Structure Of CEBPALPHA-Dna Complex
pdb|1NWQ|C Chain C, Crystal Structure Of CEBPALPHA-Dna Complex
Length = 62
Score = 61.2 bits (147), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 34/59 (57%), Positives = 43/59 (72%)
Query: 170 NTDEYKRRRERNNIAVRKSREKAKIRSRETXXXXXXXXXXNERLQKRIELLSEELNVLR 228
N++EY+ RRERNNIAVRKSR+KAK R+ ET N+RL+KR+E LS EL+ LR
Sbjct: 3 NSNEYRVRRERNNIAVRKSRDKAKQRNVETQQKVLELTSDNDRLRKRVEQLSRELDTLR 61
>pdb|2F0R|A Chain A, Crystallographic Structure Of Human Tsg101 Uev Domain
pdb|2F0R|B Chain B, Crystallographic Structure Of Human Tsg101 Uev Domain
Length = 159
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 33/73 (45%), Gaps = 6/73 (8%)
Query: 20 QEAMNVKKQQLTQHQHMKRYTDLA---DLNTPEISLDLQNLIDDSQFNEGLFTEILNQGQ 76
+M V + QL + +Y DL +N + DL+ ++D FN+G E++N
Sbjct: 12 MASMAVSESQLKKMVSKYKYRDLTVRETVNVITLYKDLKPVLDSYVFNDGSSRELMNLTG 71
Query: 77 GKPRQQFPARSNT 89
P P R NT
Sbjct: 72 TIP---VPYRGNT 81
>pdb|4B8J|A Chain A, Rimp_alpha1a
Length = 528
Score = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 161 RKNGKSVDKNTDEYKRRRERNNIAVRKS-REKAKIRSR 197
R+N V + +E +RRRE N + +RKS RE++ ++ R
Sbjct: 14 RRNRYKVAVDAEEGRRRREDNMVEIRKSRREESLLKKR 51
>pdb|1KPP|A Chain A, Structure Of The Tsg101 Uev Domain
pdb|1KPQ|A Chain A, Structure Of The Tsg101 Uev Domain
pdb|1M4P|A Chain A, Structure Of The Tsg101 Uev Domain In Complex With A
Hiv-1 Ptap "late Domain" Peptide, Dyana Ensemble
pdb|1M4Q|A Chain A, Structure Of The Tsg101 Uev Domain In Complex With A
Hiv-1 Ptap "late Domain" Peptide, Cns Ensemble
Length = 145
Score = 28.1 bits (61), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 32/70 (45%), Gaps = 6/70 (8%)
Query: 23 MNVKKQQLTQHQHMKRYTDLA---DLNTPEISLDLQNLIDDSQFNEGLFTEILNQGQGKP 79
M V + QL + +Y DL +N + DL+ ++D FN+G E++N P
Sbjct: 1 MAVSESQLKKMVSKYKYRDLTVRETVNVITLYKDLKPVLDSYVFNDGSSRELMNLTGTIP 60
Query: 80 RQQFPARSNT 89
P R NT
Sbjct: 61 ---VPYRGNT 67
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
0.311 0.127 0.356
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,969,695
Number of Sequences: 62578
Number of extensions: 254563
Number of successful extensions: 434
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 423
Number of HSP's gapped (non-prelim): 16
length of query: 256
length of database: 14,973,337
effective HSP length: 97
effective length of query: 159
effective length of database: 8,903,271
effective search space: 1415620089
effective search space used: 1415620089
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 50 (23.9 bits)