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= psy16978
(154 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 120 bits (302), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 59/69 (85%), Positives = 64/69 (92%), Gaps = 1/69 (1%)
Query: 31 SGPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRR 90
+G NG RRRGRQTYTR+QTLELEKEFH NHYLTRRRRIE+AHAL LTERQIKIWFQNRR
Sbjct: 14 AGTNGL-RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRR 72
Query: 91 MKLKKELRA 99
MKLKKE++A
Sbjct: 73 MKLKKEIQA 81
>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 = 114 bits (286), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 55/59 (93%), Positives = 57/59 (96%)
Query: 38 RRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
R+RGRQTYTR+QTLELEKEFHFN YLTRRRRIEIAHALCLTERQIKIWFQNRRMK KKE
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 60
>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 = 112 bits (280), Expect = 8e-26, Method: Compositional matrix adjust.
Identities = 54/59 (91%), Positives = 56/59 (94%)
Query: 38 RRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
R+RGRQTYTR+QTLELEKEFHFN YLTRRRRIEIAHAL LTERQIKIWFQNRRMK KKE
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 60
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 112 bits (280), Expect = 8e-26, Method: Compositional matrix adjust.
Identities = 54/60 (90%), Positives = 56/60 (93%)
Query: 37 PRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
R+RGRQTYTR+QTLELEKEFHFN YLTRRRRIEIAHAL LTERQIKIWFQNRRMK KKE
Sbjct: 2 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
>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 = 104 bits (260), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 50/58 (86%), Positives = 53/58 (91%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
+R R +YTR+QTLELEKEFHFN YLTRRRRIEIAHAL LTERQIKIWFQNRRMK KKE
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 86
>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 = 102 bits (254), Expect = 8e-23, Method: Compositional matrix adjust.
Identities = 49/53 (92%), Positives = 50/53 (94%)
Query: 44 TYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
TYTR+QTLELEKEFHFN YLTRRRRIEIAHAL LTERQIKIWFQNRRMK KKE
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 54
>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 = 102 bits (254), Expect = 9e-23, Method: Compositional matrix adjust.
Identities = 47/58 (81%), Positives = 54/58 (93%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
+R RQTYTR+QTLELEKEFHFN Y+TRRRRI+IA+AL L+ERQIKIWFQNRRMK KK+
Sbjct: 4 KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKD 61
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 84.7 bits (208), Expect = 2e-17, Method: Compositional matrix adjust.
Identities = 41/57 (71%), Positives = 47/57 (82%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
R+ R YT++QTLELEKEF FN YLTR RR E+A L LTERQ+KIWFQNRRMK+KK
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 81.6 bits (200), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 41/57 (71%), Positives = 46/57 (80%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
R+ R YT+ QTLELEKEF FN YLTR RR E+A L LTERQ+KIWFQNRRMK+KK
Sbjct: 14 RKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70
>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 = 79.7 bits (195), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 40/58 (68%), Positives = 45/58 (77%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
+R R YTR Q LELEKEF FN Y++R RR+E+A L LTER IKIWFQNRRMK KKE
Sbjct: 4 KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 75.1 bits (183), Expect = 2e-14, Method: Compositional matrix adjust.
Identities = 37/57 (64%), Positives = 41/57 (71%)
Query: 42 RQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELR 98
R +T Q ELEKEFHFN YL+R RR+EIA L L E Q+KIWFQNRRMK KK R
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER 94
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 71.6 bits (174), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 38/65 (58%), Positives = 44/65 (67%), Gaps = 1/65 (1%)
Query: 31 SGPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRR 90
S P G RRR R +T Q LELEKEFH YL+ R +IAHAL L+E Q+KIWFQNRR
Sbjct: 1 SAPGGKSRRR-RTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRR 59
Query: 91 MKLKK 95
K K+
Sbjct: 60 AKWKR 64
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 64.7 bits (156), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 30/64 (46%), Positives = 44/64 (68%)
Query: 32 GPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRM 91
G +G R+ R Y++ Q ELE+E+ N ++T+ +R +I+ A L+ERQI IWFQNRR+
Sbjct: 1 GSSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRV 60
Query: 92 KLKK 95
K KK
Sbjct: 61 KEKK 64
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 62.0 bits (149), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 28/65 (43%), Positives = 39/65 (60%)
Query: 32 GPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRM 91
G +G R+ R Y+ FQ L++ F YL R E+A +L LT+ Q+KIWFQN+R
Sbjct: 1 GSSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRS 60
Query: 92 KLKKE 96
K+KK
Sbjct: 61 KIKKS 65
>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 = 59.3 bits (142), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 31/58 (53%), Positives = 40/58 (68%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
RR R +TR Q LEKEF+ +Y++R RR E+A L L E IK+WFQNRRMK K++
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 37/57 (64%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
RR R +T Q + LEK F YL+ RI++A +L L++ Q+K W+QNRRMK KK
Sbjct: 18 RRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74
>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 = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 39/57 (68%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
+R R ++ Q L++EF+ N YLT RRR +++ L L E QIKIWFQN+R K+KK
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 57.4 bits (137), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 28/63 (44%), Positives = 42/63 (66%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELR 98
R+ R YT+ Q ELE+E+ N ++T+ +R I+ L+ERQ+ IWFQNRR+K KK +
Sbjct: 8 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVIN 67
Query: 99 AVK 101
+K
Sbjct: 68 KLK 70
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 57.4 bits (137), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 39/57 (68%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
+R R ++ Q L++EF+ N YLT RRR +++ L L E QIKIWFQN+R K+KK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 57.4 bits (137), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 28/63 (44%), Positives = 42/63 (66%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKELR 98
R+ R YT+ Q ELE+E+ N ++T+ +R I+ L+ERQ+ IWFQNRR+K KK +
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVIN 61
Query: 99 AVK 101
+K
Sbjct: 62 KLK 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 = 57.4 bits (137), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 28/65 (43%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 34 NGCP--RRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRM 91
N P R++ R ++TR Q ELEK FH YL R +A L +T+ Q+K WFQNRR
Sbjct: 11 NRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRT 70
Query: 92 KLKKE 96
K +++
Sbjct: 71 KWRRQ 75
>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 = 56.6 bits (135), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 38/57 (66%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
+R R ++ Q L++EF+ N YLT RRR +++ L L E QIKIWFQN R K+KK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
>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 = 56.2 bits (134), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 38/57 (66%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
+R R ++ Q L++EF+ N YLT RRR +++ L L E QIKIWFQN R K+KK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex
pdb|2HDD|B Chain B, Engrailed Homeodomain Q50k Variant Dna Complex
Length = 61
Score = 55.8 bits (133), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 39/57 (68%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
+R R ++ Q L++EF+ N YLT RRR +++ L L E QIKIWF+N+R K+KK
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 36/57 (63%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
R+ R +T Q L LE++F YL+ R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 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 = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/56 (48%), Positives = 37/56 (66%)
Query: 40 RGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
R R ++ Q L++EF+ N YLT RRR +++ L L E QIKIWF N+R K+KK
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>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 = 53.9 bits (128), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 38/61 (62%)
Query: 35 GCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLK 94
G +R R ++ Q L++EF+ N YLT RRR +++ L L E Q+K WF+N R K+K
Sbjct: 1 GSDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
Query: 95 K 95
K
Sbjct: 61 K 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 = 53.5 bits (127), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 29/58 (50%), Positives = 37/58 (63%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
RR R T+T FQ ELEK F HY R E+A + LTE +I++WFQNRR K +K+
Sbjct: 7 RRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 64
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 53.5 bits (127), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 26/54 (48%), Positives = 36/54 (66%)
Query: 40 RGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKL 93
R R ++ Q L++EF+ N YLT RRR +++ L L E QIKIWFQN+R K+
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 53.1 bits (126), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 38/57 (66%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
+R R ++ Q ++EF+ N YLT RRR +++ L L E QIKIWFQN+R K+++
Sbjct: 4 KRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 52.8 bits (125), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 24/41 (58%), Positives = 31/41 (75%)
Query: 55 KEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
+EF+ N YLT RRR +++ L L E QIKIWFQN+R K+KK
Sbjct: 3 REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/51 (47%), Positives = 34/51 (66%)
Query: 45 YTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
++ QT+ELEK+F YL+ R +A L L+ERQ+K WFQNRR K ++
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 36/57 (63%)
Query: 40 RGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
R R T+T FQ ELEK F HY R E+A + LTE +I++WFQNRR K +K+
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/66 (42%), Positives = 38/66 (57%)
Query: 33 PNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 92
N +RR R T+T +Q ELEK F HY R ++A LTE ++++WFQNRR K
Sbjct: 4 SNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAK 63
Query: 93 LKKELR 98
+K R
Sbjct: 64 WRKRER 69
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/53 (49%), Positives = 34/53 (64%)
Query: 44 TYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
T+T FQ ELEK F HY R E+A + LTE +I++WFQNRR K +K+
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>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 = 50.1 bits (118), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 26/57 (45%), Positives = 35/57 (61%)
Query: 38 RRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLK 94
RR+ R +++ Q ELE+ F YL+ R ++A L LT Q+KIWFQNRR K K
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 50.1 bits (118), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 34/53 (64%)
Query: 44 TYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
+++R Q LELE+ F YL R +A AL +T+ Q+K WFQNRR K +++
Sbjct: 3 SFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>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 = 49.3 bits (116), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 24/48 (50%), Positives = 32/48 (66%)
Query: 49 QTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
Q +ELE++F YL+ R +A L LTE Q+KIWFQNRR K K++
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK 62
>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 = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 35/58 (60%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
RR R T++ Q ELE+ F Y R E+A LTE +I++WFQNRR +L+K+
Sbjct: 19 RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 76
>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 = 47.8 bits (112), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/64 (42%), Positives = 38/64 (59%), Gaps = 2/64 (3%)
Query: 34 NGCP--RRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRM 91
+G P +R+ R +T+ QT ELE+ F YL+ R +A + LT Q+KIWFQN R
Sbjct: 3 DGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRY 62
Query: 92 KLKK 95
K K+
Sbjct: 63 KTKR 66
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 37/65 (56%)
Query: 32 GPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRM 91
G +G +R R ++T+ Q LEKEF HY R +A + L E +I++WF NRR
Sbjct: 1 GSSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRA 60
Query: 92 KLKKE 96
K ++E
Sbjct: 61 KWRRE 65
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 33/56 (58%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLK 94
RR R T+T Q ELE+ F YLT R +++ L L Q+KIWF+NRR + K
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 46.2 bits (108), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 37/64 (57%), Gaps = 2/64 (3%)
Query: 34 NGCP--RRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRM 91
+G P +R+ R +T+ QT ELE+ F YL+ R + + LT Q+KIWFQN R
Sbjct: 6 DGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRY 65
Query: 92 KLKK 95
K K+
Sbjct: 66 KTKR 69
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 37/61 (60%)
Query: 38 RRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKEL 97
RR+ R +++ Q ELE+ F YL+ R +A + LT Q+KIWFQN R K+K++
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61
Query: 98 R 98
+
Sbjct: 62 K 62
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/57 (45%), Positives = 33/57 (57%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
RR R +T Q ELE F NHY R EIA LTE ++++WF+NRR K +K
Sbjct: 4 RRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 34/58 (58%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
RR R T+T Q ELE+ F HY R E+A LTE ++++WF NRR + +K+
Sbjct: 3 RRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>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 = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 32/57 (56%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
RR R +T Q ELE F N Y R EIA LTE ++++WF+NRR K +K
Sbjct: 4 RRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 33/61 (54%)
Query: 32 GPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRM 91
G +G RR R T+TR Q LE F Y R E+A + L E ++++WF+NRR
Sbjct: 1 GSSGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRA 60
Query: 92 K 92
K
Sbjct: 61 K 61
>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 = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 36/59 (61%)
Query: 37 PRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
+++ R +++ Q L+ F YL+ ++ E++ L L+ +Q+K WFQN+RMK K+
Sbjct: 2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 39.3 bits (90), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 38 RRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
+++ R ++ Q L F YL+ ++ E+++ L L+ +Q+K WFQN+RMK K+
Sbjct: 22 KQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKR 79
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 34/66 (51%)
Query: 32 GPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRM 91
G +G +R R ++ Q ++ F NH + ++A LT+R +++WFQN R
Sbjct: 1 GSSGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARA 60
Query: 92 KLKKEL 97
K ++ L
Sbjct: 61 KFRRNL 66
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 31/57 (54%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
RR R +T+ Q LE F N Y ++A L L +I+IWFQNRR KLK+
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKR 58
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%)
Query: 32 GPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRM 91
G +G RR R +T Q LE F Y R ++A + L E ++++WF+NRR
Sbjct: 1 GSSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRA 60
Query: 92 KLKK 95
K ++
Sbjct: 61 KWRR 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 = 35.0 bits (79), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 32 GPNGCPRRRGRQTYTRFQT-LELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRR 90
G G RRR ++T + LEK F N T IA L + + I++WF NRR
Sbjct: 93 GIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRR 152
Query: 91 MKLKK 95
K K+
Sbjct: 153 QKEKR 157
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 35.0 bits (79), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 32 GPNGCPRRRGRQTYTRFQT-LELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRR 90
G G RRR ++T + LEK F N T IA L + + I++WF NRR
Sbjct: 94 GIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRR 153
Query: 91 MKLKK 95
K K+
Sbjct: 154 QKEKR 158
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 34.3 bits (77), Expect = 0.033, Method: Composition-based stats.
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 53 LEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 92
L + + N Y + R + E+A A LT Q+ WF+NRR +
Sbjct: 509 LREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 548
>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 = 33.9 bits (76), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 15/18 (83%), Positives = 16/18 (88%)
Query: 80 RQIKIWFQNRRMKLKKEL 97
RQIKIWFQNRRMK KK +
Sbjct: 1 RQIKIWFQNRRMKWKKRV 18
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 33.9 bits (76), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNH----YLTRRRRIEIAHALCLTERQIKIWFQNRRMKLK 94
RR R+ + + Q E+ E+ ++H Y + + E+A +T Q+ WF N+R++ K
Sbjct: 2 RRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 95 KELRAVKE 102
K + +E
Sbjct: 61 KNIGKFQE 68
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 33.5 bits (75), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNH----YLTRRRRIEIAHALCLTERQIKIWFQNRRMKLK 94
RR R+ + + Q E+ E+ ++H Y + + E+A +T Q+ WF N+R++ K
Sbjct: 3 RRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
Query: 95 KELRAVKE 102
K + +E
Sbjct: 62 KNIGKFQE 69
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 33.5 bits (75), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNH----YLTRRRRIEIAHALCLTERQIKIWFQNRRMKLK 94
RR R+ + + Q E+ E+ ++H Y + + E+A +T Q+ WF N+R++ K
Sbjct: 2 RRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 95 KELRAVKE 102
K + +E
Sbjct: 61 KNIGKFQE 68
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 33.1 bits (74), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 15/16 (93%), Positives = 15/16 (93%)
Query: 80 RQIKIWFQNRRMKLKK 95
RQIKIWFQNRRMK KK
Sbjct: 1 RQIKIWFQNRRMKWKK 16
>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 = 33.1 bits (74), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNH----YLTRRRRIEIAHALCLTERQIKIWFQNRRMKLK 94
RR R+ +++ Q E+ E+ ++H Y + + E+A +T Q+ WF N+R++ K
Sbjct: 2 RRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
Query: 95 KEL 97
K +
Sbjct: 61 KNI 63
>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 = 33.1 bits (74), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 32 GPNGCPRRRGRQTYTRFQT-LELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRR 90
G G RRR ++T + LEK F N T IA L + + I++WF NRR
Sbjct: 89 GIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRR 148
Query: 91 MKLKK 95
K K+
Sbjct: 149 QKEKR 153
>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 = 32.7 bits (73), Expect = 0.077, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 32 GPNGCPRRRGRQTYTRFQT-LELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRR 90
G G RRR ++T + LEK F N T IA L + + I++WF NRR
Sbjct: 96 GIEGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRR 155
Query: 91 MKLKK 95
K K+
Sbjct: 156 QKEKR 160
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%)
Query: 39 RRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
+R R T T Q L +++ + TR+ IAH + L +R +++WFQN R + +K
Sbjct: 18 KRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 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 = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 53 LEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLK 94
LE+ F L + + E+A +T Q+++WF N+RM+ K
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 26/52 (50%)
Query: 45 YTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKKE 96
+T +Q L+ F N Y ++++ L L R I +WFQN R K +K
Sbjct: 14 FTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS 65
>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 = 32.0 bits (71), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 53 LEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLK 94
LE+ F L + + E+A +T Q+++WF N+RM+ K
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 32.0 bits (71), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 53 LEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLK 94
LE+ F L + + E+A +T Q+++WF N+RM+ K
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 31.6 bits (70), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 14/15 (93%), Positives = 14/15 (93%)
Query: 81 QIKIWFQNRRMKLKK 95
QIKIWFQNRRMK KK
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 31.6 bits (70), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 49 QTLELEKEFHFNH----YLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
Q E+ E+ ++H Y + + E+A +T Q+ WF N+R++ KK
Sbjct: 13 QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 31.6 bits (70), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 53 LEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLK 94
LE+ F L + + E+A +T Q+++WF N+RM+ K
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 167
Score = 31.2 bits (69), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 32 GPNGCPRRRGRQTYTRFQT-LELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRR 90
G G RR ++T + LEK F N T IA L + + I++WF NRR
Sbjct: 97 GIEGLSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRR 156
Query: 91 MKLKK 95
K K+
Sbjct: 157 QKEKR 161
>pdb|1KZ2|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain Derivative [w6f,W14f]
Length = 16
Score = 30.4 bits (67), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 14/16 (87%), Positives = 15/16 (93%)
Query: 80 RQIKIWFQNRRMKLKK 95
RQIKI+FQNRRMK KK
Sbjct: 1 RQIKIFFQNRRMKFKK 16
>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 = 29.6 bits (65), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 28/58 (48%)
Query: 38 RRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
RR+ R + LEK F N T + IA L + + I++WF NRR K K+
Sbjct: 1 RRKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEKR 58
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 28/58 (48%)
Query: 38 RRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMKLKK 95
RR+ R + + LEK F N T IA L + + I++WF NRR K K+
Sbjct: 7 RRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 64
>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 = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 29/62 (46%), Gaps = 2/62 (3%)
Query: 35 GCP-RRRGRQTYTRFQTLE-LEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 92
G P ++R R+T Q +E L F N T + E A L +++WF NRR
Sbjct: 88 GEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRRQT 147
Query: 93 LK 94
LK
Sbjct: 148 LK 149
>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 = 27.3 bits (59), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 11/19 (57%), Positives = 15/19 (78%)
Query: 77 LTERQIKIWFQNRRMKLKK 95
L+ R I++WFQN+R K KK
Sbjct: 42 LSPRVIRVWFQNKRCKDKK 60
>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 = 4.0, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 71 IAHALCLTERQIKIWFQNRRMKLKK 95
IA+ L L + +++WF NRR K K+
Sbjct: 129 IANQLGLEKDVVRVWFSNRRQKGKR 153
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 26.9 bits (58), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 27/57 (47%)
Query: 32 GPNGCPRRRGRQTYTRFQTLELEKEFHFNHYLTRRRRIEIAHALCLTERQIKIWFQN 88
G +G +R R T Q L + F N+ + + E+A L ++ IK WF+N
Sbjct: 1 GSSGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN 57
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
0.327 0.136 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,117,489
Number of Sequences: 62578
Number of extensions: 147777
Number of successful extensions: 1513
Number of sequences better than 100.0: 87
Number of HSP's better than 100.0 without gapping: 86
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1425
Number of HSP's gapped (non-prelim): 88
length of query: 154
length of database: 14,973,337
effective HSP length: 90
effective length of query: 64
effective length of database: 9,341,317
effective search space: 597844288
effective search space used: 597844288
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 47 (22.7 bits)