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= psy16797
(99 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 72.0 bits (175), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 39/57 (68%), Positives = 41/57 (71%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
KR RTAYT QLL LEKEF YI R +R +LA LNL ER IKIWFQNRRMK KK
Sbjct: 4 KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
>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 = 70.9 bits (172), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 37/67 (55%), Positives = 45/67 (67%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80
KR R YT Q L LEKEF+ YI R +R +A L+L ERQIKIWFQNRRMK KK +T
Sbjct: 4 KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKDRT 63
Query: 81 PEDNLEY 87
+ + E+
Sbjct: 64 LDSSPEH 70
>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 = 68.9 bits (167), Expect = 6e-13, Method: Compositional matrix adjust.
Identities = 33/57 (57%), Positives = 44/57 (77%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
+R RTA+T +QL LEKEF ++NY+ R +R +LA +LNL E IK+WFQNRRMK K+
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 67.8 bits (164), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 35/65 (53%), Positives = 44/65 (67%)
Query: 13 IADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR 72
IA ++R R YT Q L LEKEF+ +Y+ R +R ++A L+L ERQIKIWFQNRR
Sbjct: 13 IAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRR 72
Query: 73 MKKKK 77
MK KK
Sbjct: 73 MKLKK 77
>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 = 67.8 bits (164), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 35/57 (61%), Positives = 42/57 (73%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
KR RT+YT Q L LEKEF+ Y+ R +R ++A L+L ERQIKIWFQNRRMK KK
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 85
>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 = 65.5 bits (158), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 34/58 (58%), Positives = 41/58 (70%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
+KR R YT Q L LEKEF+ Y+ R +R ++A L+L ERQIKIWFQNRRMK KK
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 59
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 65.1 bits (157), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 34/58 (58%), Positives = 41/58 (70%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
+KR R YT Q L LEKEF+ Y+ R +R ++A L+L ERQIKIWFQNRRMK KK
Sbjct: 3 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 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 = 65.1 bits (157), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 32/58 (55%), Positives = 41/58 (70%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
KR RTA++S QL L++EFN+ Y+ +R QL+ EL L E QIKIWFQN+R K KK
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 61
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 64.7 bits (156), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 32/58 (55%), Positives = 41/58 (70%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
KR RTA++S QL L++EFN+ Y+ +R QL+ EL L E QIKIWFQN+R K KK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 59
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 64.7 bits (156), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 32/60 (53%), Positives = 43/60 (71%)
Query: 18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
+ ++ R YT +Q L LEKEF Y+ R +R+++A+ LNL ERQ+KIWFQNRRMK KK
Sbjct: 11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 64.3 bits (155), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 32/57 (56%), Positives = 41/57 (71%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
++ R YT Q L LEKEF Y+ R +R+++A+ LNL ERQ+KIWFQNRRMK KK
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 64.3 bits (155), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 31/54 (57%), Positives = 40/54 (74%)
Query: 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
RT +T+ QL LEKEF+ Y+ RA+R ++A L L E Q+KIWFQNRRMK+KK
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91
>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 = 63.9 bits (154), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 32/58 (55%), Positives = 40/58 (68%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
KR RTA++S QL L++EFN+ Y+ +R QL+ EL L E QIKIWFQN R K KK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKKS 59
>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 = 63.9 bits (154), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 34/58 (58%), Positives = 40/58 (68%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
+KR R YT Q L LEKEF+ Y+ R +R ++A L L ERQIKIWFQNRRMK KK
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 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 = 63.5 bits (153), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 32/58 (55%), Positives = 40/58 (68%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
KR RTA++S QL L++EFN+ Y+ +R QL+ EL L E QIKIWFQN R K KK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKKS 59
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 63.2 bits (152), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 33/60 (55%), Positives = 42/60 (70%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80
+R RTA+TS QLL LEKEF+ + Y+ +R Q+A L L E Q+KIWFQNRR K K+ K
Sbjct: 8 RRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKRIKA 67
>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 = 63.2 bits (152), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 31/60 (51%), Positives = 42/60 (70%)
Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
+KR RTA++S QL L++EFN+ Y+ +R QL+ EL L E QIKIWF+N+R K KK
Sbjct: 2 AEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 63.2 bits (152), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 42/57 (73%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
++ RT +T+ QLLALE++F Q+ Y+ A+R + + L+L E Q+KIWFQNRR K K+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 61.2 bits (147), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 29/55 (52%), Positives = 39/55 (70%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
+KR RTA++S QL ++EFN+ Y+ +R QL+ EL L E QIKIWFQN+R K
Sbjct: 3 EKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57
>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 = 60.8 bits (146), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 30/57 (52%), Positives = 39/57 (68%)
Query: 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
R RTA++S QL L++EFN+ Y+ +R QL+ EL L E QIKIWF N+R K KK
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKKS 57
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 60.8 bits (146), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 29/53 (54%), Positives = 38/53 (71%)
Query: 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
R RTA++S QL L++EFN+ Y+ +R QL+ EL L E QIKIWFQN+R K
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 60.8 bits (146), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 31/61 (50%), Positives = 41/61 (67%), Gaps = 1/61 (1%)
Query: 17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
KKG+ R+RT +T QL+ LEK F +Q Y+ R LA+ L L + Q+K W+QNRRMK K
Sbjct: 15 KKGR-RSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
Query: 77 K 77
K
Sbjct: 74 K 74
>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 = 60.5 bits (145), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 31/52 (59%), Positives = 37/52 (71%)
Query: 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
YT Q L LEKEF+ Y+ R +R ++A L+L ERQIKIWFQNRRMK KK
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 53
>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 = 58.9 bits (141), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 29/57 (50%), Positives = 39/57 (68%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
KR RTA++S QL L++EFN+ Y+ +R QL+ EL L E Q+K WF+N R K KK
Sbjct: 5 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 57.0 bits (136), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 26/57 (45%), Positives = 38/57 (66%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
++ RT Y+S QL AL++ F + Y+ +R +LA L L + Q+KIWFQN+R K KK
Sbjct: 8 RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 56.2 bits (134), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 28/59 (47%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
G+K+ R YT QL LE+E+ +I + KR +++ NL ERQ+ IWFQNRR+K+KK
Sbjct: 1 GRKK-RVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 56.2 bits (134), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 28/59 (47%), Positives = 40/59 (67%), Gaps = 1/59 (1%)
Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
G+K+ R YT QL LE+E+ +I + KR +++ NL ERQ+ IWFQNRR+K+KK
Sbjct: 7 GRKK-RVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
>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 = 55.8 bits (133), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 26/58 (44%), Positives = 36/58 (62%)
Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
G+++ R ++ Q+ LE+ F QQ Y+ +R QLA L L Q+KIWFQNRR K K
Sbjct: 1 GRRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 55.8 bits (133), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 25/54 (46%), Positives = 36/54 (66%)
Query: 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
R Y+ QL LE+E+ +I + KR +++ +L ERQI IWFQNRR+K+KK
Sbjct: 11 RIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK 64
>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 = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 42/67 (62%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79
+K+ RT++T Q+ LEK F++Q Y+ A+R LA+ L + + Q+K WFQNRR K ++
Sbjct: 17 RKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQT 76
Query: 80 TPEDNLE 86
E E
Sbjct: 77 AEEREAE 83
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 24/48 (50%), Positives = 34/48 (70%)
Query: 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
++++Q + LEK+F Q Y+ +R +LAK L L ERQ+K WFQNRR K
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 61
>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 = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/61 (44%), Positives = 41/61 (67%)
Query: 17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
K+ ++R RT +TS QL LEK F++ +Y R +LA ++ L E +I++WFQNRR K +
Sbjct: 3 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 62
Query: 77 K 77
K
Sbjct: 63 K 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 = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 42/64 (65%)
Query: 17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
K+ ++R+RT ++++QL LE+ F + Y R +LA+ NL E +I++WFQNRR + +
Sbjct: 15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR 74
Query: 77 KGKT 80
K T
Sbjct: 75 KQHT 78
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 37/53 (69%)
Query: 25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
T+++ +Q+L LE+ F +Q Y+ A+R LAK L + + Q+K WFQNRR K ++
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54
>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 = 51.6 bits (122), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/48 (50%), Positives = 33/48 (68%)
Query: 30 NQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
Q++ LE++F+ Q Y+ +R LAK L L E Q+KIWFQNRR K K+
Sbjct: 14 TQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKR 61
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 51.2 bits (121), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 36/58 (62%)
Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
G +R RT +TS+Q+ LE+ F Q Y+ + L+ +L L Q+KIWF+NRR + K
Sbjct: 1 GPRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 51.2 bits (121), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 37/58 (63%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
K++ RT ++S QL L F +Q Y+ + +L+ LNL +Q+K WFQN+RMK K+
Sbjct: 22 KQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR 79
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 50.8 bits (120), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/61 (49%), Positives = 39/61 (63%), Gaps = 1/61 (1%)
Query: 18 KGKKRA-RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
KGKKR RT +TS QL LEK F + +Y R QLA +L E ++++WFQNRR K +
Sbjct: 6 KGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWR 65
Query: 77 K 77
K
Sbjct: 66 K 66
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 37/56 (66%)
Query: 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
R RT +TS QL LEK F++ +Y R +LA ++ L E +I++WFQNRR K +K
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 50.1 bits (118), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 39/57 (68%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
+R RT++T Q+ ALEKEF + +Y R +LA +++L E +I++WF NRR K ++
Sbjct: 8 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRR 64
>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 = 48.9 bits (115), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 38/58 (65%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
K++ RT ++ QL AL+ F +Q Y+ + +L+ LNL +Q+K WFQN+RMK K+
Sbjct: 3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 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 = 48.9 bits (115), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 34/60 (56%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79
K++ R +T Q LE+ F QQ Y+ +R LA + L Q+KIWFQN R K K+ +
Sbjct: 9 KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 37/57 (64%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
+R RT +T QL ALE F + Y R QLA++++L E ++++WF+NRR K ++
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 47.8 bits (112), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 38/59 (64%)
Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
G++R+RT +T+ QL LE+ F + +Y R +LA+ L E ++++WF NRR + +K
Sbjct: 1 GQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRK 59
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 47.8 bits (112), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/42 (54%), Positives = 29/42 (69%)
Query: 37 KEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
+EFN+ Y+ +R QL+ EL L E QIKIWFQN+R K KK
Sbjct: 3 REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 44
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 37/59 (62%)
Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
++R RT +TS QL LE F + +Y + R ++A NL E ++++WF+NRR K +K
Sbjct: 2 SQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 37/71 (52%), Gaps = 1/71 (1%)
Query: 10 DSLIADEKKGKKRARTA-YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWF 68
S ++D KKR R +T Q LE+ F QQ Y+ +R L + L Q+KIWF
Sbjct: 1 GSHMSDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWF 60
Query: 69 QNRRMKKKKGK 79
QN R K K+ +
Sbjct: 61 QNHRYKTKRAQ 71
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 35/58 (60%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
+++ R ++ Q+ LE+ F QQ Y+ +R LA ++L Q+KIWFQN R K K+
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKR 59
>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 = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 36/59 (61%)
Query: 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
++R RT +TS QL LE F + Y + R ++A NL E ++++WF+NRR K +K
Sbjct: 2 SQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 45.8 bits (107), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 34/52 (65%)
Query: 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
+TS QL LEK F++ +Y R +LA ++ L E +I++WFQNRR K +K
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 56
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/58 (44%), Positives = 34/58 (58%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
+R RTA+T NQ+ LE F Y LA++LNL +I+IWFQNRR K K+
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRS 59
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 33/54 (61%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
+R RT +T QL LE F + Y R ++A ++NL E ++++WF+NRR K
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 36/62 (58%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79
+++ RT+ +N +ALEK F + + +A +LN+ + I++WF NRR K+K+
Sbjct: 104 RRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRIN 163
Query: 80 TP 81
P
Sbjct: 164 PP 165
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 28/53 (52%)
Query: 25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
T +T QL L+ F+ Y + QL+ LNL R I +WFQN R K +K
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
>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 = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
+++ RT+ +N +ALEK F + + +A +LN+ + I++WF NRR K+K+
Sbjct: 100 RRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEKR 157
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
+++ RT+ +N +ALEK F + +A++LN+ + I++WF NRR K+K+
Sbjct: 101 RRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 46/78 (58%), Gaps = 2/78 (2%)
Query: 2 DRVQKYLDDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCE 61
++V ++ + A+E+K K+R + + ALE+ F + + + ++A+ELNL +
Sbjct: 71 EQVGALYNEKVGANERKRKRRTTISIAAKD--ALERHFGEHSKPSSQEIMRMAEELNLEK 128
Query: 62 RQIKIWFQNRRMKKKKGK 79
+++WF NRR ++K+ K
Sbjct: 129 EVVRVWFCNRRQREKRVK 146
>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 = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
+++ RT+ +N +ALEK F + + +A +LN+ + I++WF NRR K+K+
Sbjct: 103 RRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
+++ RT+ +N +ALEK F + + +A +LN+ + I++WF NRR K+K+
Sbjct: 96 RRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 153
>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 = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 30/61 (49%)
Query: 12 LIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNR 71
+ E K++ RT++T + AL F + + + AKELN +++WF NR
Sbjct: 85 FVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNR 144
Query: 72 R 72
R
Sbjct: 145 R 145
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
+++ RT+ +N +ALEK F + + +A +LN+ + I++WF NRR K+K+
Sbjct: 7 RRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 64
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 35.8 bits (81), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%)
Query: 15 DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
+E + KR RT T QL L +++ + R +A E+ L +R +++WFQN R +
Sbjct: 12 EEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRAR 71
Query: 75 KKK 77
++K
Sbjct: 72 ERK 74
>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 = 33.5 bits (75), Expect = 0.030, Method: Composition-based stats.
Identities = 12/42 (28%), Positives = 27/42 (64%)
Query: 35 LEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
LE+ F ++ + ++ ++AK+ + Q+++WF N+RM+ K
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>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 = 32.7 bits (73), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 15/16 (93%), Positives = 15/16 (93%)
Query: 62 RQIKIWFQNRRMKKKK 77
RQIKIWFQNRRMK KK
Sbjct: 1 RQIKIWFQNRRMKWKK 16
>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 = 32.3 bits (72), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 21/44 (47%)
Query: 31 QLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
QL ALE F Q L + +L E + R+I WF RR K
Sbjct: 18 QLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKK 61
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 32.3 bits (72), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 15/16 (93%), Positives = 15/16 (93%)
Query: 62 RQIKIWFQNRRMKKKK 77
RQIKIWFQNRRMK KK
Sbjct: 1 RQIKIWFQNRRMKWKK 16
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 32.3 bits (72), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 30/54 (55%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74
KR RT++ +QL ++ F + QLA++ L +R +++WFQN R K
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAK 61
>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 = 32.0 bits (71), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 19/56 (33%), Positives = 25/56 (44%)
Query: 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
R RT QL L + + QL + L R I++WFQN+R K KK
Sbjct: 5 RVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKK 60
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 32.0 bits (71), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%)
Query: 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
KR RT T +QL L + F+ N + ++A + L ++ IK WF+N K+++
Sbjct: 8 KRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQ 64
>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 = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 37/64 (57%), Gaps = 12/64 (18%)
Query: 20 KKRARTAYTSNQLLALEKEF--NQ----QNYILRAKRHQLAKELNLCERQIKIWFQNRRM 73
+++ RT+ +N ALEK F NQ + +L A++ + KE+ I++WF NRR
Sbjct: 1 RRKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEV------IRVWFCNRRQ 54
Query: 74 KKKK 77
K+K+
Sbjct: 55 KEKR 58
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 14/15 (93%), Positives = 14/15 (93%)
Query: 63 QIKIWFQNRRMKKKK 77
QIKIWFQNRRMK KK
Sbjct: 2 QIKIWFQNRRMKWKK 16
>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 = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 12/55 (21%), Positives = 32/55 (58%)
Query: 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
+ +++ + LE+ F ++ + ++ ++AK+ + Q+++WF N+RM+ K
Sbjct: 7 KGKSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 30.4 bits (67), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 12/55 (21%), Positives = 32/55 (58%)
Query: 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
+ +++ + LE+ F ++ + ++ ++AK+ + Q+++WF N+RM+ K
Sbjct: 7 KGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 12/42 (28%), Positives = 27/42 (64%)
Query: 35 LEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76
LE+ F ++ + ++ ++AK+ + Q+++WF N+RM+ K
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|2DMP|A Chain A, Solution Structure Of The Third Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 2
Length = 89
Score = 30.0 bits (66), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 23/45 (51%)
Query: 28 TSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR 72
T Q+ LE F + ++ +A+ +L E L R+I WF RR
Sbjct: 21 TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERR 65
>pdb|3P8C|A Chain A, Structure And Control Of The Actin Regulatory Wave Complex
Length = 1253
Score = 29.6 bits (65), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 19/88 (21%), Positives = 43/88 (48%), Gaps = 2/88 (2%)
Query: 10 DSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQ 69
+SLIAD+ KK R++ +L +EK F+++++ ++ L C ++WF+
Sbjct: 567 ESLIADKSGSKKTLRSSLEGPTILDIEK-FHRESF-FYTHLINFSETLQQCCDLSQLWFR 624
Query: 70 NRRMKKKKGKTPEDNLEYKLHYTTHSHL 97
++ G+ + +E + + H+
Sbjct: 625 EFFLELTMGRRIQFPIEMSMPWILTDHI 652
>pdb|1KZ2|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain Derivative [w6f,W14f]
Length = 16
Score = 29.3 bits (64), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 14/16 (87%), Positives = 15/16 (93%)
Query: 62 RQIKIWFQNRRMKKKK 77
RQIKI+FQNRRMK KK
Sbjct: 1 RQIKIFFQNRRMKFKK 16
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 29.3 bits (64), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 31 QLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR 72
QL AL+ F + + +++ L K L R+++ WF +RR
Sbjct: 19 QLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRR 60
>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 = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 5/64 (7%)
Query: 28 TSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEY 87
T QL L+ F + + + +LAKE L I WF + R K G NL++
Sbjct: 33 TPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNG-----NLKW 87
Query: 88 KLHY 91
+Y
Sbjct: 88 YYYY 91
>pdb|2DA4|A Chain A, Solution Structure Of The Homeobox Domain Of The
Hypothetical Protein, Dkfzp686k21156
Length = 80
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 30/63 (47%), Gaps = 6/63 (9%)
Query: 17 KKGKKRARTAYTSNQLLALEKEFNQQ----NYILRAKRHQLAKELNL-CERQIKIWFQNR 71
G + RT ++ L L+K ++ + R K +A ELN+ CE ++ W NR
Sbjct: 5 SSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCE-IVRTWIGNR 63
Query: 72 RMK 74
R K
Sbjct: 64 RRK 66
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%)
Query: 18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
+ +KR RT+ + +LE F + + +A +L L + +++WF NRR K K+
Sbjct: 94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79
K++ RT+ ALE F + + LA L L + +++WF NRR K+K+
Sbjct: 99 KRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKR-M 157
Query: 80 TP 81
TP
Sbjct: 158 TP 159
>pdb|1EUC|B Chain B, Crystal Structure Of Dephosphorylated Pig Heart, Gtp-
Specific Succinyl-Coa Synthetase
Length = 396
Score = 26.6 bits (57), Expect = 3.3, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 25/49 (51%)
Query: 1 MDRVQKYLDDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAK 49
M +Q+Y L++D +R A T+N+ L K N + +L+A+
Sbjct: 1 MVNLQEYQSKKLMSDNGVKVQRFFVADTANEALEAAKRLNAKEIVLKAQ 49
>pdb|1EUD|B Chain B, Crystal Structure Of Phosphorylated Pig Heart,
Gtp-Specific Succinyl-Coa Synthetase
Length = 396
Score = 26.6 bits (57), Expect = 3.3, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 25/49 (51%)
Query: 1 MDRVQKYLDDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAK 49
M +Q+Y L++D +R A T+N+ L K N + +L+A+
Sbjct: 1 MVNLQEYQSKKLMSDNGVKVQRFFVADTANEALEAAKRLNAKEIVLKAQ 49
>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 = 26.6 bits (57), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 26/51 (50%)
Query: 28 TSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78
T Q+ L+ F Q + A+ ++L + L +IK WF + R + ++G
Sbjct: 12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG 62
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 50 RHQLAKELNLCERQIKIWFQNRRMKKKK--GKTPED 83
+ +LAK+ + Q+ WF N+R++ KK GK E+
Sbjct: 34 KEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEE 69
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 44 YILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
Y + +LAK+ + Q+ WF N+R++ KK
Sbjct: 30 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 26.2 bits (56), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 50 RHQLAKELNLCERQIKIWFQNRRMKKKK--GKTPED 83
+ +LAK+ + Q+ WF N+R++ KK GK E+
Sbjct: 35 KEELAKKSGITVSQVSNWFGNKRIRYKKNIGKFQEE 70
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 26.2 bits (56), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 50 RHQLAKELNLCERQIKIWFQNRRMKKKK--GKTPED 83
+ +LAK+ + Q+ WF N+R++ KK GK E+
Sbjct: 34 KEELAKKCGITVSQVSNWFGNKRIRYKKNIGKFQEE 69
>pdb|2FP4|B Chain B, Crystal Structure Of Pig Gtp-Specific Succinyl-Coa
Synthetase In Complex With Gtp
pdb|2FPG|B Chain B, Crystal Structure Of Pig Gtp-Specific Succinyl-Coa
Synthetase In Complex With Gdp
pdb|2FPI|B Chain B, Crystal Structure Of Pig Gtp-Specific Succinyl-Coa
Synthetase From Polyethylene Glycol
pdb|2FPP|B Chain B, Crystal Structure Of Pig Gtp-Specific Succinyl-Coa
Synthetase From Polyethylene Glycol With Chloride Ions
Length = 395
Score = 26.2 bits (56), Expect = 5.5, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 4 VQKYLDDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAK 49
+Q+Y L++D +R A T+N+ L K N + +L+A+
Sbjct: 3 LQEYQSKKLMSDNGVKVQRFFVADTANEALEAAKRLNAKEIVLKAQ 48
>pdb|2JT9|B Chain B, Nmr Structure Of Immunosuppressory Peptide Containing
Cyclolinopeptide X And Antennapedia(43-58) Sequences
Length = 17
Score = 25.8 bits (55), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 13/16 (81%), Positives = 13/16 (81%)
Query: 62 RQIKIWFQNRRMKKKK 77
RQIKI FQNRR K KK
Sbjct: 1 RQIKIXFQNRRXKXKK 16
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 25.4 bits (54), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 31/61 (50%)
Query: 18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77
+ +KR RT+ + +LE F + + +A +L L + +++WF NRR K K+
Sbjct: 6 QARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 65
Query: 78 G 78
Sbjct: 66 S 66
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
0.317 0.130 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,886,868
Number of Sequences: 62578
Number of extensions: 96457
Number of successful extensions: 321
Number of sequences better than 100.0: 106
Number of HSP's better than 100.0 without gapping: 103
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 215
Number of HSP's gapped (non-prelim): 106
length of query: 99
length of database: 14,973,337
effective HSP length: 65
effective length of query: 34
effective length of database: 10,905,767
effective search space: 370796078
effective search space used: 370796078
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)