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= psy4078
(269 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1BW5|A Chain A, The Nmr Solution Structure Of The Homeodomain Of The Rat
Insulin Gene Enhancer Protein Isl-1, 50 Structures
Length = 66
Score = 126 bits (316), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 59/65 (90%), Positives = 61/65 (93%)
Query: 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
K TRVRTVLNEKQLHTLRTCY ANPRPDALMKEQLVEMT LSPRVIRVWFQNKRCKDKKR
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61
Query: 141 ALAMK 145
++ MK
Sbjct: 62 SIMMK 66
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 54.7 bits (130), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 28/67 (41%), Positives = 40/67 (59%), Gaps = 2/67 (2%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
SG GK R+RT QL T+++ + N PDA +QL + T L+ RV++VWFQN R
Sbjct: 3 SGSSGK--RMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARA 60
Query: 136 KDKKRAL 142
K ++ L
Sbjct: 61 KFRRNLL 67
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 30 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNL 67
R+RT QL T+++ + N PDA +QL + T L
Sbjct: 9 RMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGL 46
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 32/61 (52%)
Query: 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
GK R RT QL L + PD +EQL T+L+ ++VWFQN+R K +K
Sbjct: 7 GKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRK 66
Query: 140 R 140
R
Sbjct: 67 R 67
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 46.6 bits (109), Expect = 1e-05, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 33/61 (54%)
Query: 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
G R RT +QL L + N PD +E++ TNL+ +RVWF+N+R K +K
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 140 R 140
R
Sbjct: 61 R 61
Score = 29.6 bits (65), Expect = 1.7, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 21/44 (47%)
Query: 30 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVR 73
R RT +QL L + N PD +E++ TNL RVR
Sbjct: 5 RQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVR 48
>pdb|2L7F|P Chain P, Solution Structure Of The Pitx2 Homeodomain
pdb|2LKX|A Chain A, Nmr Structure Of The Homeodomain Of Pitx2 In Complex With
A Taatcc Dna Binding Site
Length = 68
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 33/61 (54%)
Query: 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
G R RT +QL L + N PD +E++ TNL+ +RVWF+N+R K +K
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 140 R 140
R
Sbjct: 61 R 61
Score = 29.6 bits (65), Expect = 1.8, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 21/44 (47%)
Query: 30 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVR 73
R RT +QL L + N PD +E++ TNL RVR
Sbjct: 5 RQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVR 48
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 2/64 (3%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
SG G+ R RT+ ++QL L + PD +EQL +L + VWF+N+R
Sbjct: 3 SGSSGR--RHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRA 60
Query: 136 KDKK 139
K ++
Sbjct: 61 KWRR 64
>pdb|2RGT|A Chain A, Crystal Structure Of Lhx3 Lim Domains 1 And 2 With The
Binding Domain Of Isl1
pdb|2RGT|B Chain B, Crystal Structure Of Lhx3 Lim Domains 1 And 2 With The
Binding Domain Of Isl1
Length = 169
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 18/28 (64%), Positives = 21/28 (75%)
Query: 166 PMVASSPVRHDSPIGMNALEVTSYQPPW 193
PMVA+SP RHD + N +EV SYQPPW
Sbjct: 142 PMVAASPERHDGGLQANPVEVQSYQPPW 169
>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
pdb|1FJL|B Chain B, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
pdb|1FJL|C Chain C, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
Length = 81
Score = 43.9 bits (102), Expect = 9e-05, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 33/60 (55%)
Query: 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
K R RT + QL L + PD +E+L + TNL+ I+VWFQN+R + +K+
Sbjct: 17 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 76
Score = 27.7 bits (60), Expect = 6.7, Method: Composition-based stats.
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 30 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLFLGRVR 73
R RT + QL L + PD +E+L + TNL R++
Sbjct: 20 RSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQ 63
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 29/53 (54%)
Query: 87 TVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
T + QL L+ ++AN P EQL + NL RVI VWFQN R K +K
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
SG G+ R RT QL L + PD M+E++ NL ++VWF+N+R
Sbjct: 3 SGSSGR--RERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRA 60
Query: 136 K 136
K
Sbjct: 61 K 61
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 41.2 bits (95), Expect = 6e-04, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 29/57 (50%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
R RT QL L ++ PD +E+L L+ I+VWFQN+R K +K+
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 30/56 (53%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
R+RT + +QL L Y + P M + + L RV++VWFQN R +++K
Sbjct: 19 RLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74
>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
pdb|3A01|F Chain F, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
Length = 67
Score = 40.8 bits (94), Expect = 7e-04, Method: Composition-based stats.
Identities = 21/60 (35%), Positives = 30/60 (50%)
Query: 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
K R RT QL L ++ PD +E+L L+ I+VWFQN+R K +K+
Sbjct: 5 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 64
>pdb|3MMK|A Chain A, The Structural Basis For Partial Redundancy In A Class Of
Transcription Factors, The Lim-Homeodomain Proteins, In
Neural Cell Type Specification
pdb|3MMK|B Chain B, The Structural Basis For Partial Redundancy In A Class Of
Transcription Factors, The Lim-Homeodomain Proteins, In
Neural Cell Type Specification
Length = 169
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 22/28 (78%)
Query: 166 PMVASSPVRHDSPIGMNALEVTSYQPPW 193
P+VA SP+ H++ + +A+EV +YQPPW
Sbjct: 142 PLVAGSPIGHENAVQGSAVEVQTYQPPW 169
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 39.3 bits (90), Expect = 0.002, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 28/56 (50%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
R RT + Q+ L + N P + E L + NL I++WFQN+R K K+
Sbjct: 3 RPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKR 58
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 30/58 (51%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRA 141
R RT +QL L + PD +E+L + L+ ++VWF N+R + +K+A
Sbjct: 4 RSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQA 61
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 79 DGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDK 138
DG+ T EK LR Y NP P K +L E T L+ + WF+N+R +D+
Sbjct: 493 DGEETSY--CFKEKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDR 550
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 32/63 (50%)
Query: 78 GDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKD 137
G G P+ +RT +QL L ++ N + ++ L+ +++WFQN+R K
Sbjct: 30 GLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQ 89
Query: 138 KKR 140
KKR
Sbjct: 90 KKR 92
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%)
Query: 86 RTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKRA 141
R + ++ Q++ L + A +E L M +L+P +++WFQN R K K++A
Sbjct: 6 RVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61
>pdb|2H1K|A Chain A, Crystal Structure Of The Pdx1 Homeodomain In Complex With
Dna
pdb|2H1K|B Chain B, Crystal Structure Of The Pdx1 Homeodomain In Complex With
Dna
Length = 63
Score = 37.4 bits (85), Expect = 0.010, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 29/60 (48%)
Query: 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
G R RT QL L + N + +L M NL+ R I++WFQN+R K KK
Sbjct: 1 GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 37.4 bits (85), Expect = 0.010, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 26/48 (54%)
Query: 93 QLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKKR 140
QL L ++ PD +E+L L+ I+VWFQN+R K +K+
Sbjct: 10 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|1HDD|D Chain D, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|2JWT|A Chain A, Solution Structure Of Engrailed Homeodomain Wt
Length = 61
Score = 36.6 bits (83), Expect = 0.013, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 30/56 (53%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
R RT + +QL L+ +N N ++QL L+ I++WFQNKR K KK
Sbjct: 5 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 36.6 bits (83), Expect = 0.014, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 30/56 (53%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
R RT + +QL L+ +N N ++QL L+ I++WFQNKR K KK
Sbjct: 3 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 36.6 bits (83), Expect = 0.014, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 34/64 (53%), Gaps = 2/64 (3%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
SG G+ R+ ++ QL L Y AN + ++ T+LS R I +WFQN+R
Sbjct: 3 SGSSGRKKRIP--YSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRV 60
Query: 136 KDKK 139
K+KK
Sbjct: 61 KEKK 64
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 36.6 bits (83), Expect = 0.016, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 2/74 (2%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
SG G+ R RT ++Q+ L + PD +E+L +L I+VWF N+R
Sbjct: 3 SGSSGQ--RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRA 60
Query: 136 KDKKRALAMKQQLQ 149
K ++ Q+ Q
Sbjct: 61 KWRREEKLRNQRRQ 74
>pdb|2VI6|A Chain A, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|B Chain B, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|C Chain C, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|D Chain D, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|E Chain E, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|F Chain F, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|G Chain G, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|H Chain H, Crystal Structure Of The Nanog Homeodomain
Length = 62
Score = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 32/60 (53%)
Query: 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
G ++RTV ++ QL L+ + ++L + NLS + ++ WFQN+R K K+
Sbjct: 1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52e
Length = 59
Score = 35.4 bits (80), Expect = 0.031, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 30/56 (53%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
R RT + +QL L+ +N N ++QL L+ I++WFQN+R K KK
Sbjct: 3 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex
pdb|2HDD|B Chain B, Engrailed Homeodomain Q50k Variant Dna Complex
Length = 61
Score = 35.4 bits (80), Expect = 0.033, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 30/56 (53%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
R RT + +QL L+ +N N ++QL L+ I++WF+NKR K KK
Sbjct: 5 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 35.0 bits (79), Expect = 0.041, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 28/53 (52%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCK 136
R RT + +QL L+ +N N ++QL L+ I++WFQNKR K
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|1DU0|A Chain A, Engrailed Homeodomain Q50a Variant Dna Complex
pdb|1DU0|B Chain B, Engrailed Homeodomain Q50a Variant Dna Complex
Length = 57
Score = 35.0 bits (79), Expect = 0.044, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 29/56 (51%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
R RT + +QL L+ +N N ++QL L+ I++WF NKR K KK
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>pdb|1P7I|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52a
Length = 59
Score = 35.0 bits (79), Expect = 0.044, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 29/56 (51%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
R RT + +QL L+ +N N ++QL L+ I++WFQN R K KK
Sbjct: 3 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 35.0 bits (79), Expect = 0.049, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 29/64 (45%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
S GK R RT +QL L ++ + Q+ LS +++WFQN+R
Sbjct: 1 SAPGGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRA 60
Query: 136 KDKK 139
K K+
Sbjct: 61 KWKR 64
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 34.3 bits (77), Expect = 0.078, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 27/54 (50%)
Query: 86 RTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
R + QL L Y N + ++ TNLS R + +WFQN+R K+KK
Sbjct: 11 RVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 34.3 bits (77), Expect = 0.078, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 27/54 (50%)
Query: 86 RTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
R + QL L Y N + ++ TNLS R + +WFQN+R K+KK
Sbjct: 5 RVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 34.3 bits (77), Expect = 0.082, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 30/60 (50%)
Query: 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
G R RT + +QL + +N N ++QL L+ I++WFQNKR K ++
Sbjct: 1 GDEKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
>pdb|1NK2|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES
pdb|1NK3|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, MINIMIZED AVERAGE
Structure
pdb|1VND|A Chain A, VndNK-2 Protein (Homeodomain), Nmr
Length = 77
Score = 33.9 bits (76), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 3/66 (4%)
Query: 77 GGDGKPTRVR---TVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNK 133
DG P + R + + Q + L + A +E L + L+P +++WFQN
Sbjct: 1 ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNH 60
Query: 134 RCKDKK 139
R K K+
Sbjct: 61 RYKTKR 66
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 33.9 bits (76), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 79 DGKPTRVR---TVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
DG P + R + + Q + L + A +E L + L+P +++WFQN R
Sbjct: 6 DGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRY 65
Query: 136 KDKK 139
K K+
Sbjct: 66 KTKR 69
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 27/56 (48%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
R RT + + +L T + +P+P + L V+RVWF N+R K K+
Sbjct: 98 RKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%)
Query: 97 LRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
L + N +P + + E N+ VIRVWF N+R K+K+
Sbjct: 116 LEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 29/60 (48%)
Query: 80 GKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
G+ + RT + L + + P+P A L + L V+RVWF N+R K+K+
Sbjct: 97 GRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKR 156
>pdb|3D1N|I Chain I, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|J Chain J, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|K Chain K, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|L Chain L, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|M Chain M, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|N Chain N, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|O Chain O, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|P Chain P, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
Length = 151
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 25/60 (41%)
Query: 75 VSGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKR 134
V G K + RT + + L + NP P + + N V+RVWF N+R
Sbjct: 86 VGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRR 145
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 29/59 (49%)
Query: 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
K + RTV + QL L + ++L + NLS + ++ WFQN+R K K+
Sbjct: 21 KKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR 79
>pdb|3RKQ|A Chain A, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
pdb|3RKQ|B Chain B, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
Length = 58
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 78 GDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKD 137
G KP R + ++ Q++ L + A ++QL + L+ +++WFQN+R K
Sbjct: 1 GRRKP---RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKS 57
Query: 138 K 138
K
Sbjct: 58 K 58
>pdb|1HF0|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1HF0|B Chain B, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1GT0|C Chain C, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 159
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 97 LRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
L + N +P + + + N+ VIRVWF N+R K+K+
Sbjct: 115 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEKR 157
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 32/63 (50%)
Query: 77 GGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCK 136
G + + + RT ++ L + + +P + ++ E NL V+RVWF N+R +
Sbjct: 82 GANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQR 141
Query: 137 DKK 139
+K+
Sbjct: 142 EKR 144
>pdb|2HOS|A Chain A, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOS|B Chain B, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOT|A Chain A, Phage Selected Homeodomain Bound To Modified Dna
pdb|2HOT|B Chain B, Phage Selected Homeodomain Bound To Modified Dna
Length = 63
Score = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 77 GGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCK 136
G D K R RT + +QL L+ +N N ++QL L+ ++ WF+N R K
Sbjct: 1 GSDEK--RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAK 58
Query: 137 DKK 139
KK
Sbjct: 59 IKK 61
>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna
pdb|1JGG|B Chain B, Even-Skipped Homeodomain Complexed To At-Rich Dna
Length = 60
Score = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 28/59 (47%), Gaps = 6/59 (10%)
Query: 84 RVRTVLNEKQLHTL-RTCYNAN--PRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
R RT QL L + Y N RP +L NL I+VWFQN+R KDK+
Sbjct: 3 RYRTAFTRDQLGRLEKEFYKENYVSRPRRC---ELAAQLNLPESTIKVWFQNRRMKDKR 58
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 32.0 bits (71), Expect = 0.37, Method: Composition-based stats.
Identities = 22/64 (34%), Positives = 33/64 (51%), Gaps = 13/64 (20%)
Query: 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTN---LSPRVIRVWFQNKRCKDKK 139
TR +T+ EK+ HT L + + +EM + L+ R I++WFQN+R K KK
Sbjct: 28 TRYQTLELEKEFHT----------NHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77
Query: 140 RALA 143
A
Sbjct: 78 EIQA 81
>pdb|1HDP|A Chain A, Solution Structure Of A Pou-Specific Homeodomain: 3d-Nmr
Studies Of Human B-Cell Transcription Factor Oct-2
Length = 63
Score = 32.0 bits (71), Expect = 0.39, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 27/54 (50%)
Query: 86 RTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
RT + L + AN +P + + E ++ VIRVWF N+R K+K+
Sbjct: 5 RTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEKR 58
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 31.6 bits (70), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 26/59 (44%)
Query: 81 KPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
K R RTV E QL L + + L E LS ++ W+QN+R K KK
Sbjct: 16 KGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 167
Score = 31.6 bits (70), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 97 LRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
L + N +P + + + N+ VIRVWF N+R K+K+
Sbjct: 119 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 161
>pdb|1CQT|A Chain A, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
pdb|1CQT|B Chain B, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
Length = 163
Score = 30.8 bits (68), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 97 LRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
L + N +P + + + N+ VIRVWF N+R K+K+
Sbjct: 118 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 160
>pdb|1OCT|C Chain C, Crystal Structure Of The Oct-1 Pou Domain Bound To An
Octamer Site: Dna Recognition With Tethered Dna-Binding
Modules
Length = 156
Score = 30.8 bits (68), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 97 LRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
L + N +P + + + N+ VIRVWF N+R K+K+
Sbjct: 111 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 153
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 30.8 bits (68), Expect = 0.92, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 29/63 (46%)
Query: 77 GGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCK 136
G + + RT + L + N +P + + + N+ VIRVWF N+R K
Sbjct: 2 GSHMRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 61
Query: 137 DKK 139
+K+
Sbjct: 62 EKR 64
>pdb|2R5Y|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 88
Score = 30.8 bits (68), Expect = 0.93, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 30/62 (48%)
Query: 78 GDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKD 137
+G+ R RT Q L ++ N + ++ +L+ R I++WFQN+R K
Sbjct: 24 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKW 83
Query: 138 KK 139
KK
Sbjct: 84 KK 85
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 20/28 (71%)
Query: 112 KEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
+++L +M LS R ++ WFQN+R K ++
Sbjct: 37 RKRLAKMLQLSERQVKTWFQNRRAKWRR 64
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 30.4 bits (67), Expect = 1.1, Method: Composition-based stats.
Identities = 11/28 (39%), Positives = 20/28 (71%)
Query: 112 KEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
+ ++ + NL+ R +++WFQN+R K KK
Sbjct: 43 RYEVARLLNLTERQVKIWFQNRRMKMKK 70
>pdb|1MH3|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form I
pdb|1MH4|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form Ii
Length = 421
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 112 KEQLVEMTNLSPRVIRVWFQNKRCKDK 138
KE++ + ++P +RVWF NKR + K
Sbjct: 395 KEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 30.0 bits (66), Expect = 1.3, Method: Composition-based stats.
Identities = 11/28 (39%), Positives = 20/28 (71%)
Query: 112 KEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
+ ++ + NL+ R +++WFQN+R K KK
Sbjct: 31 RYEVARVLNLTERQVKIWFQNRRMKMKK 58
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 30.0 bits (66), Expect = 1.4, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 21/37 (56%)
Query: 103 ANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
+NP P KE+L + + ++ + WF NKR + KK
Sbjct: 26 SNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKK 62
>pdb|1SAN|A Chain A, The Des(1-6)antennapedia Homeodomain: Comparison Of The
Nmr Solution Structure And The Dna Binding Affinity With
The Intact Antennapedia Homeodomain
Length = 62
Score = 30.0 bits (66), Expect = 1.4, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 7/57 (12%)
Query: 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
TR +T+ EK+ H R Y R + ++ +L+ R I++WFQN+R K KK
Sbjct: 4 TRYQTLELEKEFHFNR--YLTRRR-----RIEIAHALSLTERQIKIWFQNRRMKWKK 53
>pdb|2DA5|A Chain A, Solution Structure Of The Second Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 3 (Triple Homeobox 1
Protein)
Length = 75
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
S G PT+ + E QL L + + NP P ++L T ++ R I WF +R
Sbjct: 2 SSGSSGPTKYKERAPE-QLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRK 60
Query: 136 K 136
K
Sbjct: 61 K 61
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 26/56 (46%)
Query: 84 RVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
R RT + + +L T + P+P + L V+RVWF N+R K K+
Sbjct: 10 RKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 65
>pdb|1FTZ|A Chain A, Nuclear Magnetic Resonance Solution Structure Of The Fushi
Tarazu Homeodomain From Drosophila And Comparison With
The Antennapedia Homeodomain
Length = 70
Score = 29.6 bits (65), Expect = 1.8, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 13/60 (21%)
Query: 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTN---LSPRVIRVWFQNKRCKDKK 139
TR +T+ EK+ H R + + + +++ N LS R I++WFQN+R K KK
Sbjct: 11 TRYQTLELEKEFHFNRY----------ITRRRRIDIANALSLSERQIKIWFQNRRMKSKK 60
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 29.6 bits (65), Expect = 2.0, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 7/57 (12%)
Query: 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
TR +T+ EK+ H R Y R + ++ +L+ R I++WFQN+R K KK
Sbjct: 11 TRYQTLELEKEFHFNR--YLTRRR-----RIEIAHALSLTERQIKIWFQNRRMKWKK 60
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 31/64 (48%), Gaps = 2/64 (3%)
Query: 76 SGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRC 135
SG G+ + RT+ + QL L+ + + +L L+ +++WFQNKR
Sbjct: 3 SGSSGR--KPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRS 60
Query: 136 KDKK 139
K KK
Sbjct: 61 KIKK 64
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 29.3 bits (64), Expect = 2.1, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 103 ANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
+NP P KE+L + ++ + WF NKR + KK
Sbjct: 25 SNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 29.3 bits (64), Expect = 2.2, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 103 ANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
+NP P KE+L + ++ + WF NKR + KK
Sbjct: 25 SNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 61
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 29.3 bits (64), Expect = 2.2, Method: Composition-based stats.
Identities = 15/39 (38%), Positives = 21/39 (53%)
Query: 101 YNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
+N N ++QL L+ I++WFQNKR K KK
Sbjct: 5 FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43
>pdb|1HOM|A Chain A, Determination Of The Three-Dimensional Structure Of The
Antennapedia Homeodomain From Drosophila In Solution By
1h Nuclear Magnetic Resonance Spectroscopy
Length = 68
Score = 29.3 bits (64), Expect = 2.3, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 13/60 (21%)
Query: 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTN---LSPRVIRVWFQNKRCKDKK 139
TR +T+ EK+ H R L + + +E+ + L+ R I++WFQN+R K KK
Sbjct: 10 TRYQTLELEKEFHFNRY----------LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 59
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 29.3 bits (64), Expect = 2.3, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 103 ANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
+NP P KE+L + ++ + WF NKR + KK
Sbjct: 27 SNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|1AHD|P Chain P, Determination Of The Nmr Solution Structure Of An
Antennapedia Homeodomain-Dna Complex
pdb|2HOA|A Chain A, Structure Determination Of The Antp(C39->s) Homeodomain
From Nuclear Magnetic Resonance Data In Solution Using A
Novel Strategy For The Structure Calculation With The
Programs Diana, Caliba, Habas And Glomsa
Length = 68
Score = 29.3 bits (64), Expect = 2.4, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 7/57 (12%)
Query: 83 TRVRTVLNEKQLHTLRTCYNANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
TR +T+ EK+ H R Y R + ++ +L+ R I++WFQN+R K KK
Sbjct: 10 TRYQTLELEKEFHFNR--YLTRRR-----RIEIAHALSLTERQIKIWFQNRRMKWKK 59
>pdb|2NZZ|A Chain A, Nmr Structure Analysis Of The Penetratin Conjugated Gas
(374-394) Peptide
pdb|2O00|A Chain A, Nmr Structure Analysis Of The Penetratin Conjugated Gas
(374-394) Peptide
Length = 37
Score = 28.9 bits (63), Expect = 3.4, Method: Composition-based stats.
Identities = 11/19 (57%), Positives = 14/19 (73%)
Query: 124 RVIRVWFQNKRCKDKKRAL 142
R I++WFQN+R K KKR
Sbjct: 1 RQIKIWFQNRRMKWKKRVF 19
>pdb|2F9Y|B Chain B, The Crystal Structure Of The Carboxyltransferase Subunit
Of Acc From Escherichia Coli
Length = 304
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 45/88 (51%), Gaps = 10/88 (11%)
Query: 91 EKQLHTLRTC-----YNANPRPDALMKE-QLVEM-TNLSPRVIRVWFQNKRCKDKKRALA 143
E+ L C A R +L+ E LVE+ + L P+ + + +K+ KD+ LA
Sbjct: 40 ERNLEVCPKCDHHMRMTARNRLHSLLDEGSLVELGSELEPKDVLKFRDSKKYKDR---LA 96
Query: 144 MKQQLQQEKDGRKMGYGSMQGIPMVASS 171
Q+ EKD + G++ G+P+VA++
Sbjct: 97 SAQKETGEKDALVVMKGTLYGMPVVAAA 124
>pdb|1B8I|B Chain B, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
pdb|2R5Y|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 63
Score = 28.5 bits (62), Expect = 3.9, Method: Composition-based stats.
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 103 ANPRPDALMKEQLVEMTNLSPRVIRVWFQNKRCKDKK 139
+NP P KE+L ++ + WF NKR + KK
Sbjct: 25 SNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 61
>pdb|3ZTG|A Chain A, Solution Structure Of The Ring Finger-Like Domain Of
Retinoblastoma Binding Protein-6 (Rbbp6)
pdb|3ZTG|B Chain B, Solution Structure Of The Ring Finger-Like Domain Of
Retinoblastoma Binding Protein-6 (Rbbp6)
Length = 92
Score = 28.5 bits (62), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 2/67 (2%)
Query: 50 NPRPDALMKEQLVEMTNLFLGRVRKVSGGDGKPTRVRTVLNEKQLHTLRTCYNANPRPDA 109
+P PD L+ L+ + V G +RT L E HT TC+ + PDA
Sbjct: 8 DPIPDELL--CLICKDIMTDAVVIPCCGNSYCDECIRTALLESDEHTCPTCHQNDVSPDA 65
Query: 110 LMKEQLV 116
L+ + +
Sbjct: 66 LIANKFL 72
Score = 27.7 bits (60), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 31 VRTVLNEKQLHTLRTCYNANPRPDALMKEQLV 62
+RT L E HT TC+ + PDAL+ + +
Sbjct: 41 IRTALLESDEHTCPTCHQNDVSPDALIANKFL 72
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 28.5 bits (62), Expect = 4.5, Method: Composition-based stats.
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 112 KEQLVEMTNLSPRVIRVWFQNKRCKDK 138
KE++ + ++P +RVWF NKR + K
Sbjct: 27 KEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|2L9R|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Homeobox
Protein Nkx-3.1 From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6470a
Length = 69
Score = 28.1 bits (61), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 10/29 (34%), Positives = 19/29 (65%)
Query: 115 LVEMTNLSPRVIRVWFQNKRCKDKKRALA 143
L + L+ +++WFQN+R K K++ L+
Sbjct: 37 LAKNLKLTETQVKIWFQNRRYKTKRKQLS 65
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 27.7 bits (60), Expect = 6.2, Method: Composition-based stats.
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 112 KEQLVEMTNLSPRVIRVWFQNKRCKDK 138
KE++ + ++P +RVWF NKR + K
Sbjct: 35 KEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1YRN|A Chain A, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1F43|A Chain A, Solution Structure Of The Mata1 Homeodomain
Length = 61
Score = 27.7 bits (60), Expect = 6.8, Method: Composition-based stats.
Identities = 11/27 (40%), Positives = 18/27 (66%)
Query: 112 KEQLVEMTNLSPRVIRVWFQNKRCKDK 138
KE++ + ++P +RVWF NKR + K
Sbjct: 35 KEEVAKKCGITPLQVRVWFINKRMRSK 61
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
0.315 0.130 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,162,361
Number of Sequences: 62578
Number of extensions: 253829
Number of successful extensions: 564
Number of sequences better than 100.0: 84
Number of HSP's better than 100.0 without gapping: 80
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 469
Number of HSP's gapped (non-prelim): 98
length of query: 269
length of database: 14,973,337
effective HSP length: 97
effective length of query: 172
effective length of database: 8,903,271
effective search space: 1531362612
effective search space used: 1531362612
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)