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= 004271
(764 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 35/49 (71%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
++EQ+ ++ F E+ + E++RQQLS +LGL Q+K WFQN+R +IK
Sbjct: 11 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 35/49 (71%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
++EQ+ ++ F E+ + E++RQQLS +LGL Q+K WFQN+R +IK
Sbjct: 9 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>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 = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 34/49 (69%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
++EQ+ ++ F E+ + E++RQQLS +LGL Q+K WFQN R +IK
Sbjct: 9 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57
>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 = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 35/49 (71%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
++EQ+ ++ F E+ + E++RQQLS +LGL Q+K WF+N+R +IK
Sbjct: 11 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>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 = 46.6 bits (109), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 34/49 (69%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
++EQ+ ++ F E+ + E++RQQLS +LGL Q+K WFQN R +IK
Sbjct: 9 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 57
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 46.6 bits (109), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 34/48 (70%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQI 164
++EQ+ ++ F E+ + E++RQQLS +LGL Q+K WFQN+R +I
Sbjct: 7 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54
>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 = 45.8 bits (107), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 34/49 (69%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
++EQ+ ++ F E+ + E++RQQLS +LGL Q+K WF N+R +IK
Sbjct: 7 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 45.8 bits (107), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 34/49 (69%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
++EQ+ + F E+ + E++RQQLS +LGL Q+K WFQN+R +I+
Sbjct: 11 SSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIR 59
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 34/49 (69%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
T EQ+ +E LF+E+ +PD R+QL++++ L +V+ WF+NRR + +
Sbjct: 15 TDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/38 (52%), Positives = 28/38 (73%)
Query: 128 FKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
F E+ + E++RQQLS +LGL Q+K WFQN+R +IK
Sbjct: 5 FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>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 = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/49 (44%), Positives = 34/49 (69%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
++EQ+ ++ F E+ + E++RQQLS +LGL QVK WF+N R +IK
Sbjct: 12 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 44.3 bits (103), Expect = 3e-04, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 31/47 (65%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQ 163
T+ Q+ E+E F + +PD R++L+ ++GL +++ WFQNRR +
Sbjct: 7 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAK 53
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 31/47 (65%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQ 163
T+ Q+ E+E F + +PD R++L+ ++GL +++ WFQNRR +
Sbjct: 7 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAK 53
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 32/47 (68%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQ 163
T+ Q+ E+E +F+++ +PD R+QL+ + L +V+ WFQNRR +
Sbjct: 17 TSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAK 63
>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 = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 31/47 (65%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQ 163
T+ Q+ E+E F + +PD R++L+ ++GL +++ WFQNRR +
Sbjct: 14 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAK 60
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 18/46 (39%), Positives = 28/46 (60%)
Query: 120 QIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
Q+ E+E FK+ + +R+ L+ + L P QVK WFQN R ++K
Sbjct: 13 QVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMK 58
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 33/55 (60%)
Query: 119 EQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTIQERHEN 173
Q+R M++ F + +PD K +QL+++ GL R ++ WFQN R + + R EN
Sbjct: 17 HQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQEN 71
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 32/54 (59%)
Query: 116 HTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTIQE 169
+T Q E+E F + + +R ++++ L L RQVK WFQNRR ++K I +
Sbjct: 20 YTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK 73
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 18/47 (38%), Positives = 31/47 (65%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQ 163
TAEQ+ E+E F+ + +PD R++L+++ L +V+ WF NRR +
Sbjct: 10 TAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRAR 56
>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 = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 29/47 (61%)
Query: 119 EQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+Q+ + + +P PD ++QL + GL+PR ++ WFQN+R + K
Sbjct: 13 KQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDK 59
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 28/52 (53%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTIQ 168
T Q E+E F++ + +R+ L+ + L P QVK WFQN R + K Q
Sbjct: 20 TKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRAQ 71
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 116 HTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+T Q E+E F + + ++R +++ L L RQ+K WFQNRR ++K
Sbjct: 27 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLK 76
>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 = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 20/46 (43%), Positives = 27/46 (58%)
Query: 120 QIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
Q+ E+E FK+ + +R QL+ L L QVK WFQNRR + K
Sbjct: 13 QVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>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 = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 28/52 (53%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTIQ 168
T Q E+E F++ + +R+ L+ + L P QVK WFQN R + K Q
Sbjct: 17 TKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68
>pdb|1APL|C Chain C, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1APL|D Chain D, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1YRN|B Chain B, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1AKH|B Chain B, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 83
Score = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 23/57 (40%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 114 HRHTAEQIREMEALFK---ESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTI 167
HR T E +R +E+ F E+P+ D K + L K L+ Q+K W NRR + KTI
Sbjct: 7 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI 63
>pdb|1K61|A Chain A, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|B Chain B, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|C Chain C, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|D Chain D, Matalpha2 Homeodomain Bound To Dna
Length = 60
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 114 HRHTAEQIREMEALFK---ESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTI 167
HR T E +R +E+ F E+P+ D K + L K L+ Q+K W NRR + KTI
Sbjct: 3 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI 59
>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 = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 21/53 (39%), Positives = 27/53 (50%)
Query: 120 QIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTIQERHE 172
Q+ E+E F + +R L+K L L QVK WFQNRR + K Q E
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSE 67
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 31/52 (59%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTIQ 168
T+EQ+ E+E F + +R Q++ L L+ QVK WFQNRR + K I+
Sbjct: 15 TSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKRIK 66
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 19/52 (36%), Positives = 31/52 (59%)
Query: 116 HTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTI 167
+T Q E+E F + + +R ++++ L L RQVK WFQNRR ++K +
Sbjct: 8 YTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKM 59
>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 = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 33/49 (67%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+A Q+ E+E F+ + +PD R++L+++ L +++ WFQNRR +++
Sbjct: 26 SASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR 74
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 32/57 (56%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTIQERHEN 173
T+ QI E+E F + + + LS +L L QVK WF+NRR + K ++H++
Sbjct: 10 TSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQHKD 66
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 35/53 (66%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTIQE 169
T++Q++E+EA F+ + +PD R++++ L +V+ WF+NRR + + +E
Sbjct: 11 TSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE 63
>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 = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 35/53 (66%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTIQE 169
T++Q++E+EA F+ + +PD R++++ L +V+ WF+NRR + + +E
Sbjct: 11 TSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE 63
>pdb|1MNM|C Chain C, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
pdb|1MNM|D Chain D, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
Length = 87
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 3/56 (5%)
Query: 114 HRHTAEQIREMEALFK---ESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKT 166
HR T E +R +E+ F E+P+ D K + L K L+ Q+K W NRR + KT
Sbjct: 32 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 87
>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 = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 29/50 (58%)
Query: 116 HTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+T Q E+E F + + ++R +++ L L RQ+K WFQNRR + K
Sbjct: 3 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 52
>pdb|1LE8|B Chain B, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 83
Score = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 114 HRHTAEQIREMEALFK---ESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTI 167
HR T E +R +E+ F E+P+ D K + L K L+ Q+K W RR + KTI
Sbjct: 7 HRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTI 63
>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 = 38.9 bits (89), Expect = 0.011, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 29/50 (58%)
Query: 116 HTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+T Q E+E F + + ++R +++ L L RQ+K WFQNRR + K
Sbjct: 35 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 84
>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 = 38.9 bits (89), Expect = 0.012, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 29/50 (58%)
Query: 116 HTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+T Q E+E F + + ++R +++ L L RQ+K WFQNRR + K
Sbjct: 9 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 38.9 bits (89), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 33/50 (66%)
Query: 116 HTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+++ Q+ ++ F+++ + +R +L+ LGL QVK WFQN+R++IK
Sbjct: 14 YSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 63
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 38.9 bits (89), Expect = 0.012, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 29/50 (58%)
Query: 116 HTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+T Q E+E F + + ++R +++ L L RQ+K WFQNRR + K
Sbjct: 10 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 59
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 38.9 bits (89), Expect = 0.012, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 28/51 (54%)
Query: 115 RHTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
R T Q+R ++ F + +P + + +QLS L L R + WFQN R + +
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKAR 63
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 20/51 (39%), Positives = 32/51 (62%)
Query: 115 RHTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
R + +Q E+E F+ + +R++L+K L L+ RQVK WFQNRR + +
Sbjct: 13 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
>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 = 38.1 bits (87), Expect = 0.018, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 29/50 (58%)
Query: 116 HTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+T Q E+E F + + ++R +++ L L RQ+K WFQNRR + K
Sbjct: 9 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 58
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 38.1 bits (87), Expect = 0.019, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 31/52 (59%)
Query: 116 HTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTI 167
+T Q++E+E + + + +R+++S L+ RQV WFQNRR + K +
Sbjct: 8 YTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV 59
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 38.1 bits (87), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 32/49 (65%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
T Q+ +EALF ++ +PD R++++ ++ L +V+ WF+NRR + +
Sbjct: 15 TRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>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 = 38.1 bits (87), Expect = 0.020, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 29/50 (58%)
Query: 116 HTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+T Q E+E F + + ++R ++ L L+ RQ+K WFQNRR + K
Sbjct: 10 YTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSK 59
>pdb|2CQX|A Chain A, Solution Structure Of Rsgi Ruh-034, A Homeodomain From
Mouse Cdna
Length = 72
Score = 38.1 bits (87), Expect = 0.020, Method: Composition-based stats.
Identities = 16/35 (45%), Positives = 26/35 (74%)
Query: 131 SPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+ +PDEK+ + LSKQL + R+++ WF++RR Q K
Sbjct: 31 TKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65
>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 = 37.7 bits (86), Expect = 0.025, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 28/50 (56%)
Query: 116 HTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+T Q+ E+E F + + +R +L+ L L R +K WFQNRR + K
Sbjct: 10 YTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWK 59
>pdb|3NAU|A Chain A, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And Homeoboxes
Protein 2, Homeodomain 2)
pdb|3NAU|B Chain B, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And Homeoboxes
Protein 2, Homeodomain 2)
Length = 66
Score = 37.7 bits (86), Expect = 0.026, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 28/47 (59%)
Query: 115 RHTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRR 161
+ T EQI ++A F +S PD+ + +L + GLA ++K WF + R
Sbjct: 10 KKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHR 56
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 37.4 bits (85), Expect = 0.030, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 30/49 (61%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
T QI +E +F+ + +P + L+++L L +++ WFQNRR ++K
Sbjct: 9 TQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLK 57
>pdb|1X2M|A Chain A, Solution Structure Of The Homeobox Domain Of Mouse Lag1
Longevity Assurance Homolog 6
Length = 64
Score = 37.4 bits (85), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 17/33 (51%), Positives = 22/33 (66%)
Query: 133 HPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
HPDEK+ + LSKQL R ++ WF+ RR Q K
Sbjct: 25 HPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 37.0 bits (84), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 31/52 (59%)
Query: 116 HTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTI 167
+T Q++E+E + + + +R+++S L+ RQV WFQNRR + K +
Sbjct: 14 YTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV 65
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 37.0 bits (84), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 23/38 (60%)
Query: 124 MEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRR 161
+E +F +SP P +Q ++ QLGL V+ WF NRR
Sbjct: 111 LETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRR 148
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 36.6 bits (83), Expect = 0.054, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 30/53 (56%)
Query: 113 YHRHTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+++ E + E +P+P E+ +++L+K+ G+ QV WF N+R + K
Sbjct: 8 FNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 36.2 bits (82), Expect = 0.063, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 4/55 (7%)
Query: 115 RHTAEQIREM--EALFKE--SPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
RH +Q E+ E + +P+P E+ +++L+K+ G+ QV WF N+R + K
Sbjct: 8 RHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 62
>pdb|3K2A|A Chain A, Crystal Structure Of The Homeobox Domain Of Human Homeobox
Protein Meis2
pdb|3K2A|B Chain B, Crystal Structure Of The Homeobox Domain Of Human Homeobox
Protein Meis2
Length = 67
Score = 36.2 bits (82), Expect = 0.063, Method: Composition-based stats.
Identities = 15/33 (45%), Positives = 22/33 (66%)
Query: 132 PHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQI 164
P+P E+Q++QL++ GL QV WF N R +I
Sbjct: 24 PYPSEEQKKQLAQDTGLTILQVNNWFINARRRI 56
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 36.2 bits (82), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 30/50 (60%)
Query: 116 HTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
++ Q+RE+E + + + +R+++S L+ RQ+ WFQNRR + K
Sbjct: 14 YSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 63
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 36.2 bits (82), Expect = 0.073, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 30/53 (56%)
Query: 113 YHRHTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+++ E + E +P+P E+ +++L+K+ G+ QV WF N+R + K
Sbjct: 8 FNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>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 = 35.8 bits (81), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 29/52 (55%)
Query: 113 YHRHTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQI 164
Y EQ+R +E+ F ++P P +++ +L + + R++ WF RR ++
Sbjct: 11 YKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKV 62
>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 = 35.8 bits (81), Expect = 0.085, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 27/49 (55%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
T +Q+ +E F + + +R +L+ QL L +K WFQNRR + K
Sbjct: 9 TRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDK 57
>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 = 35.8 bits (81), Expect = 0.093, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 30/49 (61%)
Query: 120 QIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTIQ 168
Q+ ++ F++ + +Q Q+LS L L+ +QVK WFQN+R + K Q
Sbjct: 14 QLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ 62
>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 = 35.8 bits (81), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 28/42 (66%)
Query: 124 MEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+E +F+ + K++++++K+ G+ P QV+ WF N+R + K
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 35.0 bits (79), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 26/46 (56%)
Query: 120 QIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
Q+ E+E F + +R L+K L + QVK WFQNRRT+ +
Sbjct: 8 QVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWR 53
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 35.0 bits (79), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 30/49 (61%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
T EQI +E F+ + +PD R++L+ ++ L +++ WF NRR + +
Sbjct: 15 TQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWR 63
>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 = 35.0 bits (79), Expect = 0.15, Method: Composition-based stats.
Identities = 14/53 (26%), Positives = 30/53 (56%)
Query: 113 YHRHTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+ + +E + E +P+P E+ +++L+++ G+ QV WF N+R + K
Sbjct: 8 FSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 35.0 bits (79), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 27/51 (52%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTI 167
T Q+ +E F++ + +R + S L L QVK WFQNRR + K +
Sbjct: 8 TTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL 58
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of Human
Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 30/52 (57%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTIQ 168
+ EQ+ ++ F + P + + + L+K GL+ R+V+ WF +RR + ++
Sbjct: 16 SHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLK 67
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 24/35 (68%)
Query: 131 SPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+P+P E+ +++L+K+ G+ QV WF N+R + K
Sbjct: 27 NPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 27/43 (62%)
Query: 128 FKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTIQER 170
+ +P+P +++++L++ GL QV WF+NRR + + + +
Sbjct: 513 YAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEAK 555
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 34.3 bits (77), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 28/42 (66%)
Query: 124 MEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+E +F+ + K++++++K+ G+ P QV+ WF N+R + K
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 33.9 bits (76), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 124 MEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRR 161
+E +F + P P +Q ++ QLGL V+ WF NRR
Sbjct: 23 LETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRR 60
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 33.5 bits (75), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 28/42 (66%)
Query: 124 MEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+E +F+ + K++++++K+ G+ P QV+ WF N+R + K
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|3A01|A Chain A, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
pdb|3A01|E Chain E, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
Length = 93
Score = 33.5 bits (75), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 120 QIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK--TIQER 170
Q+ E+E F + + +R L++ L + QVK WFQNRRT+ + T +ER
Sbjct: 28 QVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEER 80
>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 = 33.1 bits (74), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 28/42 (66%)
Query: 124 MEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+E +F+ + K++++++K+ G+ P QV+ WF N+R + K
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 33.1 bits (74), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
T Q+ +E F++ + R L++ LGL+ QVK W+QNRR + K
Sbjct: 25 TELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 32.7 bits (73), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 27/49 (55%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
T Q+ E+E F + + +R +++ L L QVK WFQNRR + K
Sbjct: 42 TTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQK 90
>pdb|2CUF|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Hypothetical Protein Flj21616
Length = 95
Score = 32.3 bits (72), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 15/57 (26%)
Query: 124 MEALFKESPHPDEKQRQQLS-----------KQLGLAPR----QVKFWFQNRRTQIK 165
ME+ F E+ +PDE +R++++ K+L R +V WF NRR +IK
Sbjct: 22 MESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIK 78
>pdb|3THW|B Chain B, Human Mutsbeta Complexed With An Idl Of 4 Bases (Loop4)
And Adp
pdb|3THX|B Chain B, Human Mutsbeta Complexed With An Idl Of 3 Bases (Loop3)
And Adp
pdb|3THY|B Chain B, Human Mutsbeta Complexed With An Idl Of 2 Bases (Loop2)
And Adp
pdb|3THZ|B Chain B, Human Mutsbeta Complexed With An Idl Of 6 Bases (Loop6)
And Adp
Length = 918
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 33/122 (27%), Positives = 62/122 (50%), Gaps = 14/122 (11%)
Query: 567 SRKNLNDPGEPLGVILCAVSSVWLPVSPNVLFDFLRDEAHRNEWDI-MSNGGPVQTIANL 625
+++N+ D + G I + V P + V+FD +D A R+E + MS+ PV+ +
Sbjct: 158 NKENVRDKKK--GNIFIGIVGVQ-PATGEVVFDSFQDSASRSELETRMSSLQPVELLLPS 214
Query: 626 AKGQD------RGNAVNIQTMKSKENSMWLLQDSYTNAYESMV-VYAP--VDITGMQSVI 676
A + R +V++Q + + M + Y++A++++ YA VDI G Q +I
Sbjct: 215 ALSEQTEALIHRATSVSVQDDRIRVERMDNIYFEYSHAFQAVTEFYAKDTVDIKGSQ-II 273
Query: 677 TG 678
+G
Sbjct: 274 SG 275
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 32.0 bits (71), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 26/42 (61%)
Query: 128 FKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTIQE 169
F+ + +Q Q+LS L L+ +QVK WFQN+R + K Q+
Sbjct: 41 FQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK 82
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 27/45 (60%)
Query: 115 RHTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQN 159
R T +Q+R + F + P E+Q ++++ + GL + +K WF+N
Sbjct: 13 RITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN 57
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 31.2 bits (69), Expect = 2.3, Method: Composition-based stats.
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQ 163
T EQ+ + + +P K ++ ++GL R V+ WFQN R +
Sbjct: 25 TPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRAR 71
>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 = 30.4 bits (67), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 27/49 (55%)
Query: 117 TAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
T + I + A F+++P P ++ + +K+L V+ WF NRR +K
Sbjct: 101 TPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRRQTLK 149
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 30.0 bits (66), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 2/40 (5%)
Query: 127 LFKE--SPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQI 164
LF+ P+P E +++Q++ Q L QV WF N R +I
Sbjct: 26 LFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRI 65
>pdb|3NAR|A Chain A, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And Homeoboxes
Protein 1, Homeodomain 4)
pdb|3NAR|B Chain B, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And Homeoboxes
Protein 1, Homeodomain 4)
Length = 96
Score = 29.6 bits (65), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 27/51 (52%)
Query: 115 RHTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIK 165
+ T EQ+ +++ F + P ++ +L+K+ GLA + WF + R K
Sbjct: 31 KKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWK 81
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 29.3 bits (64), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 25/45 (55%)
Query: 124 MEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRRTQIKTIQ 168
+E F E P ++ +++++L L V+ WF NRR + K ++
Sbjct: 102 LERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRVK 146
>pdb|2LY9|A Chain A, Solution Nmr Structure Of Homeobox 2 Domain From Human
Zhx1 Repressor, Northeast Structural Genomics Consortium
(Nesg) Target Hr7907f
Length = 74
Score = 29.3 bits (64), Expect = 8.9, Method: Composition-based stats.
Identities = 13/47 (27%), Positives = 26/47 (55%)
Query: 115 RHTAEQIREMEALFKESPHPDEKQRQQLSKQLGLAPRQVKFWFQNRR 161
+ T EQ+ E++ + ++ P + + +L K GL ++K WF + R
Sbjct: 12 KKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTR 58
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 0.129 0.375
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,910,576
Number of Sequences: 62578
Number of extensions: 760007
Number of successful extensions: 1925
Number of sequences better than 100.0: 101
Number of HSP's better than 100.0 without gapping: 95
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1829
Number of HSP's gapped (non-prelim): 101
length of query: 764
length of database: 14,973,337
effective HSP length: 106
effective length of query: 658
effective length of database: 8,340,069
effective search space: 5487765402
effective search space used: 5487765402
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: 55 (25.8 bits)