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= psy4625
(120 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 105 bits (261), Expect = 8e-24, Method: Compositional matrix adjust.
Identities = 51/60 (85%), Positives = 57/60 (95%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWFQNKRAKIKK++
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKST 60
>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 = 104 bits (260), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 51/59 (86%), Positives = 56/59 (94%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWFQNKRAKIKK+
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 61
>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 = 102 bits (255), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 50/59 (84%), Positives = 56/59 (94%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWF+NKRAKIKK+
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61
>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 = 102 bits (255), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 50/59 (84%), Positives = 56/59 (94%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWFQN+RAKIKK+
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKKS 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 = 102 bits (254), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 50/59 (84%), Positives = 55/59 (93%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWFQN RAKIKK+
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKKS 59
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 100 bits (248), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 48/59 (81%), Positives = 55/59 (93%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
EKRPRTAFS EQL+R K EF ENRYLTERRRQ+L++ELGLNEAQIKIWFQNKRAKI+++
Sbjct: 3 EKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRRS 61
>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 = 99.0 bits (245), Expect = 6e-22, Method: Compositional matrix adjust.
Identities = 48/62 (77%), Positives = 56/62 (90%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
S EKRPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQ+K WF+N RAKIKK
Sbjct: 2 SDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
Query: 74 AS 75
++
Sbjct: 62 ST 63
>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 = 99.0 bits (245), Expect = 7e-22, Method: Compositional matrix adjust.
Identities = 48/57 (84%), Positives = 53/57 (92%)
Query: 18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
RPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWF NKRAKIKK+
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKKS 57
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 97.4 bits (241), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 47/54 (87%), Positives = 51/54 (94%)
Query: 18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
RPRTAFS EQL+RLK EF ENRYLTERRRQ+L++ELGLNEAQIKIWFQNKRAKI
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 77.0 bits (188), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 37/43 (86%), Positives = 41/43 (95%)
Query: 32 KVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
K EF ENRYLTERRRQ+L++ELGLNEAQIKIWFQNKRAKIKK+
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 44
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 64.3 bits (155), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 31/61 (50%), Positives = 42/61 (68%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
S ++PRT +S QL+ L+ F + +YL R ELA LGL + Q+KIWFQNKR+KIKK
Sbjct: 5 SSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
Query: 74 A 74
+
Sbjct: 65 S 65
>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 = 62.4 bits (150), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 33/57 (57%), Positives = 40/57 (70%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
KR RT+++ Q L+ EF NRYLT RRR E+A+ L L E QIKIWFQN+R K KK
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 85
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 60.8 bits (146), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 30/59 (50%), Positives = 42/59 (71%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
K +R RTAF+ EQL L+ EF +YL+ R ++A+ L L+E Q+KIWFQN+RAK K+
Sbjct: 6 KSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKR 64
>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 = 60.5 bits (145), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 31/57 (54%), Positives = 39/57 (68%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
KR R ++ Q L+ EF NRY+T RRR ++AN L L+E QIKIWFQN+R K KK
Sbjct: 4 KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKK 60
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 59.3 bits (142), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 30/54 (55%), Positives = 38/54 (70%)
Query: 20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
RT F+ QL+ L+ EF N+YL+ RR E+A L LNE Q+KIWFQN+R K KK
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91
>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 = 59.3 bits (142), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 33/62 (53%), Positives = 40/62 (64%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
KR R ++ Q L+ EF NRYLT RRR E+A+ L L E QIKIWFQN+R K KK +
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62
Query: 77 QK 78
K
Sbjct: 63 TK 64
>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 = 59.3 bits (142), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 33/62 (53%), Positives = 40/62 (64%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
KR R ++ Q L+ EF NRYLT RRR E+A+ L L E QIKIWFQN+R K KK +
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 62
Query: 77 QK 78
K
Sbjct: 63 TK 64
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 59.3 bits (142), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 32/57 (56%), Positives = 38/57 (66%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
KR R ++ Q L+ EF NRYLT RRR E+A+ L L E QIKIWFQN+R K KK
Sbjct: 4 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 60
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 59.3 bits (142), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 30/57 (52%), Positives = 38/57 (66%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+R R ++ Q L+ EF N YLT RRR E+A+ L L E QIKIWFQN+R K+KK
Sbjct: 21 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77
>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 = 58.2 bits (139), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 29/57 (50%), Positives = 41/57 (71%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+R RTAF+ +QL RL+ EF + Y++ RR ELA +L L E+ IK+WFQN+R K K+
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58
>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 = 57.4 bits (137), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 31/57 (54%), Positives = 38/57 (66%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
KR RTA++ QL L+ EF N+Y++ RR ELA L L E IKIWFQN+R K KK
Sbjct: 4 KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
>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 = 55.8 bits (133), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 30/57 (52%), Positives = 37/57 (64%)
Query: 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK 78
++ Q L+ EF NRYLT RRR E+A+ L L E QIKIWFQN+R K KK + K
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK 58
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 55.5 bits (132), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 26/57 (45%), Positives = 39/57 (68%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
++PRT F+ QL L+ +F + +YL+ R E ++ L L E Q+KIWFQN+RAK K+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 54.7 bits (130), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 39/61 (63%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
+R RT F+ Q++ L+ F + RYLT R +L+ +L L AQ+KIWF+N+R + K S
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62
Query: 77 Q 77
Q
Sbjct: 63 Q 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 = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/59 (45%), Positives = 40/59 (67%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
K++R RT F+ QL L+ F+ Y R+ELA ++GL EA+I++WFQN+RAK +K
Sbjct: 5 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 63
>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 = 53.9 bits (128), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 38/59 (64%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
K++R RT FS QL L+ F +Y R+ELA L EA+I++WFQN+RA+++K
Sbjct: 17 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 75
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/59 (45%), Positives = 37/59 (62%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
++ R ++ Q L+ EF N YLT RR E+A L L E Q+KIWFQN+R K+KK +
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN 60
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/62 (43%), Positives = 38/62 (61%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
++ R ++ Q L+ EF N YLT RR E+A L L E Q+KIWFQN+R K+KK +
Sbjct: 14 RKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINK 73
Query: 77 QK 78
+
Sbjct: 74 DR 75
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 52.4 bits (124), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/65 (44%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
K+++ RT FS QL L F +YL+ ++ QEL+N L L+ Q+K WFQN+R K K+
Sbjct: 21 KKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR- 79
Query: 75 SGQKN 79
QKN
Sbjct: 80 -WQKN 83
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 52.4 bits (124), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 37/56 (66%)
Query: 18 RPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
R RT F+ QL L+ F+ Y R+ELA ++GL EA+I++WFQN+RAK +K
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56
>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 = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 46/77 (59%), Gaps = 2/77 (2%)
Query: 3 SRRIKSGKDKRS--KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQI 60
+RRI R+ K K+PRT+F+ Q++ L+ F + +YL R LA L + +AQ+
Sbjct: 2 ARRIGHPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQV 61
Query: 61 KIWFQNKRAKIKKASGQ 77
K WFQN+R K ++ + +
Sbjct: 62 KTWFQNRRTKWRRQTAE 78
>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 = 52.0 bits (123), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 39/58 (67%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+++ RT FS QL LK F + +YL+ ++ QEL++ L L+ Q+K WFQN+R K K+
Sbjct: 3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/63 (42%), Positives = 40/63 (63%)
Query: 12 KRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
K K +R RT F+ QL L+ F + +YL+ R +LA LGL++ Q+K W+QN+R K
Sbjct: 13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKW 72
Query: 72 KKA 74
KK+
Sbjct: 73 KKS 75
>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 = 51.2 bits (121), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 35/56 (62%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72
++PR FS Q+ L+ F + RYL+ R +LA+ L L Q+KIWFQN+R K K
Sbjct: 3 RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>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 = 51.2 bits (121), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 38/58 (65%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
++R RT F+ +QL L+ F NRY R+E+A L EA++++WF+N+RAK +K
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 49.7 bits (117), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 37/58 (63%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
++R RT F+ +QL L+ F N Y R+E+A L EA++++WF+N+RAK +K
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 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 = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 39/65 (60%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+K+++ R F+ Q L+ F + RYL+ R+ LA+ + L Q+KIWFQN R K K+
Sbjct: 7 NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66
Query: 74 ASGQK 78
A +K
Sbjct: 67 AQNEK 71
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 35/59 (59%)
Query: 20 RTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQK 78
R FS Q+ L+ F + +YL+ R+ LA+ + L Q+KIWFQN R K+K+ + K
Sbjct: 6 RVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK 64
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 34/52 (65%)
Query: 22 AFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
F+ QL L+ F+ Y R+ELA ++GL EA+I++WFQN+RAK +K
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 38/58 (65%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
+RPRTAF+ Q+ L+ F N Y ++LA +L L +I+IWFQN+RAK+K++
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRS 59
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 39/66 (59%)
Query: 8 SGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNK 67
S + K++R RT F+ QL L+ F + Y R++LA L EA++++WFQN+
Sbjct: 1 SHMSNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNR 60
Query: 68 RAKIKK 73
RAK +K
Sbjct: 61 RAKWRK 66
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 16 EKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
++R RT F+ EQL L+ F Y R+ELA L EA++++WF N+RA+ +K
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRK 59
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 47.4 bits (111), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 40/61 (65%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
S ++ R +S QL L+ E+ N+++T+ +R++++ L+E QI IWFQN+R K KK
Sbjct: 5 SSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
Query: 74 A 74
+
Sbjct: 65 S 65
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 38/65 (58%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+K+++ R F+ Q L+ F + RYL+ R+ L + + L Q+KIWFQN R K K+
Sbjct: 10 NKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKR 69
Query: 74 ASGQK 78
A +K
Sbjct: 70 AQNEK 74
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 40/61 (65%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
S +R RT F+ EQL L+ F E +Y R++LA ++ L E ++++WF+N+RAK ++
Sbjct: 5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64
Query: 74 A 74
+
Sbjct: 65 S 65
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 38/60 (63%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
S +R RT+F+ EQ+ L+ EF Y R+ LA ++ L EA+I++WF N+RAK ++
Sbjct: 5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRR 64
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 42/73 (57%), Gaps = 6/73 (8%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
S +R RT F+ QL L+ F + RY R+E+A ++ L E+++++WF+N+RAK ++
Sbjct: 5 SSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQ 64
Query: 74 A------SGQKNP 80
GQ P
Sbjct: 65 QQQQQQNGGQSGP 77
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 37/58 (63%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
++ R ++ QL L+ E+ N+++T+ +R+ ++ L+E Q+ IWFQN+R K KK
Sbjct: 8 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV 65
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 37/58 (63%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
++ R ++ QL L+ E+ N+++T+ +R+ ++ L+E Q+ IWFQN+R K KK
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKV 59
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/52 (42%), Positives = 34/52 (65%)
Query: 23 FSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
FS +Q L+ +F +YL+ R+ LA L L+E Q+K WFQN+RAK +++
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRS 65
>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 = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 30/47 (63%)
Query: 27 QLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
Q+ L+ +F+ +YL+ R LA L L E Q+KIWFQN+R K K+
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 31/53 (58%)
Query: 21 TAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
T+FS Q+ L+ F +YL R LA L + +AQ+K WFQN+R K ++
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 34/60 (56%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
S KR RT+F QL +K F N + ++LA + GL + +++WFQN RAK ++
Sbjct: 5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRR 64
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 37/60 (61%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
++KR RT + EQL L ++ + T + +A+E+GL + +++WFQN RA+ +K+
Sbjct: 16 RDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKS 75
>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 = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 32/61 (52%)
Query: 15 KEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
K R RT + +QL L+ + N +++L GL+ I++WFQNKR K KK
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61
Query: 75 S 75
S
Sbjct: 62 S 62
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 32/53 (60%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQN 66
S KRPRT + +QL L+ F N +E + +E+A++ GL + IK WF+N
Sbjct: 5 SSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN 57
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 37/75 (49%), Gaps = 9/75 (12%)
Query: 13 RSKEKRPRTAFSGEQLSR---------LKVEFTENRYLTERRRQELANELGLNEAQIKIW 63
R K PRT + GE+ S L+ + N Y + R ++ELA GL Q+ W
Sbjct: 482 RRKFPLPRTIWDGEETSYCFKEKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSNW 541
Query: 64 FQNKRAKIKKASGQK 78
F+N+R + + A ++
Sbjct: 542 FKNRRQRDRAAEAKE 556
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 29/54 (53%)
Query: 21 TAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
T F+ QL L+ F N Y + ++L+N L L I +WFQN R K +K+
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS 65
>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 = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 33/59 (55%)
Query: 14 SKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72
SK+++ RT+F+ + + L F +N T + E A EL + +++WF N+R +K
Sbjct: 91 SKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRRQTLK 149
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 25/40 (62%)
Query: 38 NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ 77
N Y +E ++ELA + G+ +Q+ WF NKR + KK G+
Sbjct: 26 NPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK 65
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 25/40 (62%)
Query: 38 NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ 77
N Y +E ++ELA + G+ +Q+ WF NKR + KK G+
Sbjct: 26 NPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK 65
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 23/36 (63%)
Query: 38 NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
N Y +E ++ELA + G+ +Q+ WF NKR + KK
Sbjct: 28 NPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 33.5 bits (75), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 29/56 (51%)
Query: 24 SGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQKN 79
S EQLS LK F N++ + + L GL+ +++ WF ++R + G ++
Sbjct: 16 SHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGSRS 71
>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 = 33.5 bits (75), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 17 KRPRTAFS---GEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKK 73
+R R FS E L+ N Y +E ++ELA + G+ +Q+ WF NKR + KK
Sbjct: 2 RRKRRNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKK 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 = 33.5 bits (75), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 15 KEKRPR--TAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72
KEK P+ ++ S + + L+ F + L + ++E+A + G+ Q+++WF NKR + K
Sbjct: 2 KEKSPKGKSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 33.5 bits (75), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 15 KEKRPR--TAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72
KEK P+ ++ S + + L+ F + L + ++E+A + G+ Q+++WF NKR + K
Sbjct: 2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 33.5 bits (75), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 25/40 (62%)
Query: 38 NRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASGQ 77
N Y +E ++ELA + G+ +Q+ WF NKR + KK G+
Sbjct: 27 NPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKKNIGK 66
>pdb|1S7E|A Chain A, Solution Structure Of Hnf-6
Length = 147
Score = 32.3 bits (72), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 32/60 (53%)
Query: 9 GKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
GKD+ + K+PR F+ Q L F EN+ ++ + ++ +LGL + + +F N R
Sbjct: 88 GKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 147
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 32.0 bits (71), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 12/28 (42%), Positives = 21/28 (75%)
Query: 48 ELANELGLNEAQIKIWFQNKRAKIKKAS 75
+AN+LGL + +++WF N+R K K++S
Sbjct: 40 HIANQLGLEKDVVRVWFCNRRQKGKRSS 67
>pdb|2D5V|A Chain A, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
pdb|2D5V|B Chain B, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
Length = 164
Score = 32.0 bits (71), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 32/60 (53%)
Query: 9 GKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
GKD+ + K+PR F+ Q L F EN+ ++ + ++ +LGL + + +F N R
Sbjct: 90 GKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 149
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 21/27 (77%)
Query: 49 LANELGLNEAQIKIWFQNKRAKIKKAS 75
+AN+LGL + +++WF N+R K K++S
Sbjct: 129 IANQLGLEKDVVRVWFSNRRQKGKRSS 155
>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 = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 28/66 (42%), Gaps = 6/66 (9%)
Query: 7 KSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQN 66
KSG + +K P EQL LK F ++ + +LA E GL I WF +
Sbjct: 22 KSGSTGKICKKTP------EQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGD 75
Query: 67 KRAKIK 72
R K
Sbjct: 76 TRYAWK 81
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 23/38 (60%)
Query: 35 FTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIK 72
F + L + ++E+A + G+ Q+++WF NKR + K
Sbjct: 16 FRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>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 = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 26 EQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
EQL+ LKV + +N++ + L GL + +IK WF + R
Sbjct: 16 EQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTR 58
>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 = 30.4 bits (67), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 11/32 (34%), Positives = 21/32 (65%)
Query: 41 LTERRRQELANELGLNEAQIKIWFQNKRAKIK 72
L + ++E+A + G+ Q+++WF NKR + K
Sbjct: 390 LNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>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 = 29.6 bits (65), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%)
Query: 9 GKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
G + S+ ++ RT+ L+ F EN+ T +A++L + + I++WF N+R
Sbjct: 93 GIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRR 152
Query: 69 AKIKK 73
K K+
Sbjct: 153 QKEKR 157
>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 = 29.6 bits (65), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 35/67 (52%)
Query: 9 GKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
G + S+ ++ RT+ L+ F EN+ T +A++L + + I++WF N+R
Sbjct: 89 GIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRR 148
Query: 69 AKIKKAS 75
K K+ +
Sbjct: 149 QKEKRIN 155
>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 = 29.3 bits (64), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 26/49 (53%)
Query: 26 EQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKA 74
EQ++ LK F ++++ + L GL ++IK WF + R + ++
Sbjct: 14 EQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG 62
>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 = 29.3 bits (64), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%)
Query: 9 GKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
G + S+ ++ RT+ L+ F EN+ T +A++L + + I++WF N+R
Sbjct: 97 GIEGLSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRR 156
Query: 69 AKIKK 73
K K+
Sbjct: 157 QKEKR 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 = 29.3 bits (64), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 35/67 (52%)
Query: 9 GKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
G + S+ ++ RT+ L+ F EN+ T +A++L + + I++WF N+R
Sbjct: 96 GIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRR 155
Query: 69 AKIKKAS 75
K K+ +
Sbjct: 156 QKEKRIN 162
>pdb|2CUF|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Hypothetical Protein Flj21616
Length = 95
Score = 28.9 bits (63), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 30/63 (47%), Gaps = 15/63 (23%)
Query: 26 EQLSRLKVEFTENRYLTERRRQELANELG---------------LNEAQIKIWFQNKRAK 70
E L+ ++ F EN+Y E +R+E+AN + ++ WF N+R +
Sbjct: 17 ECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKE 76
Query: 71 IKK 73
IK+
Sbjct: 77 IKR 79
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 33/65 (50%)
Query: 9 GKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKR 68
G + S+ ++ RT+ L+ F EN+ T +A +L + + I++WF N+R
Sbjct: 94 GIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRR 153
Query: 69 AKIKK 73
K K+
Sbjct: 154 QKEKR 158
>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 = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/15 (80%), Positives = 13/15 (86%)
Query: 59 QIKIWFQNKRAKIKK 73
QIKIWFQN+R K KK
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 30/59 (50%)
Query: 17 KRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKAS 75
++ RT+ L+ F EN+ T +A++L + + I++WF N+R K K+
Sbjct: 8 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRID 66
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 27.3 bits (59), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 12/15 (80%), Positives = 13/15 (86%)
Query: 59 QIKIWFQNKRAKIKK 73
QIKIWFQN+R K KK
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 12/15 (80%), Positives = 13/15 (86%)
Query: 59 QIKIWFQNKRAKIKK 73
QIKIWFQN+R K KK
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 25.8 bits (55), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 7 KSGKDKRSKEKRPRTAFSGEQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQN 66
K G ++R +++R + + + L+ F E+ + + +A EL L + +++WF N
Sbjct: 80 KVGANERKRKRRTTISIAAKDA--LERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCN 137
Query: 67 KRAKIKKA 74
+R + K+
Sbjct: 138 RRQREKRV 145
>pdb|2CQX|A Chain A, Solution Structure Of Rsgi Ruh-034, A Homeodomain From
Mouse Cdna
Length = 72
Score = 25.8 bits (55), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 32 KVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKIKKASG 76
KV + +Y E+R + L+ +L + +I+ WF+++R + K SG
Sbjct: 25 KVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQ-DKPSG 68
>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 = 25.4 bits (54), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 21/46 (45%)
Query: 26 EQLSRLKVEFTENRYLTERRRQELANELGLNEAQIKIWFQNKRAKI 71
EQL L+ F +N + L +E + +I WF +R K+
Sbjct: 17 EQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKV 62
>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 = 25.4 bits (54), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 3/51 (5%)
Query: 23 FSGEQLSRLKVEF---TENRYLTERRRQELANELGLNEAQIKIWFQNKRAK 70
F+ E + L+ F EN YL + + L L+ QIK W N+R K
Sbjct: 9 FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRK 59
>pdb|1KZ2|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain Derivative [w6f,W14f]
Length = 16
Score = 25.4 bits (54), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 59 QIKIWFQNKRAKIKK 73
QIKI+FQN+R K KK
Sbjct: 2 QIKIFFQNRRMKFKK 16
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
0.314 0.128 0.353
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,468,374
Number of Sequences: 62578
Number of extensions: 75944
Number of successful extensions: 242
Number of sequences better than 100.0: 104
Number of HSP's better than 100.0 without gapping: 101
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 140
Number of HSP's gapped (non-prelim): 105
length of query: 120
length of database: 14,973,337
effective HSP length: 82
effective length of query: 38
effective length of database: 9,841,941
effective search space: 373993758
effective search space used: 373993758
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 45 (21.9 bits)