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= psy11996
(222 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 138 bits (347), Expect = 3e-33, Method: Compositional matrix adjust.
Identities = 68/69 (98%), Positives = 68/69 (98%)
Query: 2 STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 61
STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNR
Sbjct: 20 STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNR 79
Query: 62 RMKWKKEHK 70
RMKWKKEHK
Sbjct: 80 RMKWKKEHK 88
Score = 137 bits (345), Expect = 5e-33, Method: Compositional matrix adjust.
Identities = 70/83 (84%), Positives = 72/83 (86%), Gaps = 3/83 (3%)
Query: 112 YHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 171
Y W R ++ TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL
Sbjct: 9 YPWMKRV---HLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL 65
Query: 172 CLTERQIKIWFQNRRMKWKKEHK 194
LTERQIKIWFQNRRMKWKKEHK
Sbjct: 66 SLTERQIKIWFQNRRMKWKKEHK 88
>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 (285), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 56/60 (93%), Positives = 58/60 (96%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE+K
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 62
Score = 114 bits (285), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 56/60 (93%), Positives = 58/60 (96%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE+K
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 62
>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 = 111 bits (277), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 55/60 (91%), Positives = 57/60 (95%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE+K
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62
Score = 111 bits (277), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 55/60 (91%), Positives = 57/60 (95%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE+K
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 110 bits (276), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 55/61 (90%), Positives = 57/61 (93%)
Query: 9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
E KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE
Sbjct: 2 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
Query: 69 H 69
+
Sbjct: 62 N 62
Score = 110 bits (276), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 55/61 (90%), Positives = 57/61 (93%)
Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
E KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE
Sbjct: 2 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
Query: 193 H 193
+
Sbjct: 62 N 62
>pdb|1SAN|A Chain A, The Des(1-6)antennapedia Homeodomain: Comparison Of The
Nmr Solution Structure And The Dna Binding Affinity
With The Intact Antennapedia Homeodomain
Length = 62
Score = 107 bits (267), Expect = 5e-24, Method: Compositional matrix adjust.
Identities = 52/55 (94%), Positives = 54/55 (98%)
Query: 16 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
+YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE+K
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 56
Score = 107 bits (267), Expect = 5e-24, Method: Compositional matrix adjust.
Identities = 52/55 (94%), Positives = 54/55 (98%)
Query: 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
+YTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE+K
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 56
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 103 bits (258), Expect = 6e-23, Method: Compositional matrix adjust.
Identities = 52/68 (76%), Positives = 56/68 (82%)
Query: 1 MSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN 60
M+ NG +R R +YTRYQTLELEKEFH N YLTRRRRIE+AHAL LTERQIKIWFQN
Sbjct: 11 MAIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQN 70
Query: 61 RRMKWKKE 68
RRMK KKE
Sbjct: 71 RRMKLKKE 78
Score = 101 bits (251), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 51/67 (76%), Positives = 54/67 (80%)
Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
NG +R R +YTRYQTLELEKEFH N YLTRRRRIE+AHAL LTERQIKIWFQNR
Sbjct: 12 AIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNR 71
Query: 186 RMKWKKE 192
RMK KKE
Sbjct: 72 RMKLKKE 78
>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 = 103 bits (258), Expect = 6e-23, Method: Compositional matrix adjust.
Identities = 49/65 (75%), Positives = 58/65 (89%)
Query: 9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
++KR R +YTRYQTLELEKEFHFNRY+TRRRRI+IA+AL L+ERQIKIWFQNRRMK KK+
Sbjct: 2 DSKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKD 61
Query: 69 HKMAS 73
+ S
Sbjct: 62 RTLDS 66
Score = 103 bits (258), Expect = 6e-23, Method: Compositional matrix adjust.
Identities = 49/65 (75%), Positives = 58/65 (89%)
Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
++KR R +YTRYQTLELEKEFHFNRY+TRRRRI+IA+AL L+ERQIKIWFQNRRMK KK+
Sbjct: 2 DSKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKD 61
Query: 193 HKMAS 197
+ S
Sbjct: 62 RTLDS 66
>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 = 90.5 bits (223), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 44/62 (70%), Positives = 50/62 (80%)
Query: 8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
G KR RT+YTR Q LELEKEF FN+Y++R RR+E+A L LTER IKIWFQNRRMKWKK
Sbjct: 1 GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
Query: 68 EH 69
E
Sbjct: 61 EE 62
Score = 90.5 bits (223), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 44/62 (70%), Positives = 50/62 (80%)
Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
G KR RT+YTR Q LELEKEF FN+Y++R RR+E+A L LTER IKIWFQNRRMKWKK
Sbjct: 1 GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
Query: 192 EH 193
E
Sbjct: 61 EE 62
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 85.1 bits (209), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 42/58 (72%), Positives = 48/58 (82%)
Query: 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
T+++R YT+YQTLELEKEF FN YLTR RR E+A L LTERQ+KIWFQNRRMK KK
Sbjct: 1 TRKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58
Score = 85.1 bits (209), Expect = 3e-17, Method: Compositional matrix adjust.
Identities = 42/58 (72%), Positives = 48/58 (82%)
Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
T+++R YT+YQTLELEKEF FN YLTR RR E+A L LTERQ+KIWFQNRRMK KK
Sbjct: 1 TRKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 82.8 bits (203), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 42/61 (68%), Positives = 50/61 (81%)
Query: 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
T+++R YT++QTLELEKEF FN YLTR RR E+A L LTERQ+KIWFQNRRMK KK +
Sbjct: 13 TRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN 72
Query: 70 K 70
K
Sbjct: 73 K 73
Score = 82.8 bits (203), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 42/61 (68%), Positives = 50/61 (81%)
Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
T+++R YT++QTLELEKEF FN YLTR RR E+A L LTERQ+KIWFQNRRMK KK +
Sbjct: 13 TRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKIN 72
Query: 194 K 194
K
Sbjct: 73 K 73
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 78.6 bits (192), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 36/61 (59%), Positives = 48/61 (78%)
Query: 7 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
G+++R+RT++T Q LELEKEFH +YL+ R +IAHAL L+E Q+KIWFQNRR KWK
Sbjct: 4 GGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
Query: 67 K 67
+
Sbjct: 64 R 64
Score = 78.6 bits (192), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 36/61 (59%), Positives = 48/61 (78%)
Query: 131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
G+++R+RT++T Q LELEKEFH +YL+ R +IAHAL L+E Q+KIWFQNRR KWK
Sbjct: 4 GGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
Query: 191 K 191
+
Sbjct: 64 R 64
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 77.4 bits (189), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 38/60 (63%), Positives = 44/60 (73%)
Query: 8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
G RT++T Q ELEKEFHFN+YL+R RR+EIA L L E Q+KIWFQNRRMK KK
Sbjct: 32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91
Score = 77.4 bits (189), Expect = 5e-15, Method: Compositional matrix adjust.
Identities = 38/60 (63%), Positives = 44/60 (73%)
Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
G RT++T Q ELEKEFHFN+YL+R RR+EIA L L E Q+KIWFQNRRMK KK
Sbjct: 32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK 91
>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 = 63.9 bits (154), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 29/58 (50%), Positives = 39/58 (67%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
K+ RTS+TR Q ELEK FH +YL R +A L +T+ Q+K WFQNRR KW+++
Sbjct: 18 KKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75
Score = 63.9 bits (154), Expect = 7e-11, Method: Compositional matrix adjust.
Identities = 29/58 (50%), Positives = 39/58 (67%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
K+ RTS+TR Q ELEK FH +YL R +A L +T+ Q+K WFQNRR KW+++
Sbjct: 18 KKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 63.5 bits (153), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 31/66 (46%), Positives = 43/66 (65%), Gaps = 2/66 (3%)
Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
GT G +R RT +T Q + LEK F +YL+ RI++A +L L++ Q+K W+QNR
Sbjct: 11 GTKAKKG--RRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNR 68
Query: 186 RMKWKK 191
RMKWKK
Sbjct: 69 RMKWKK 74
Score = 63.5 bits (153), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 28/57 (49%), Positives = 40/57 (70%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
+R RT +T Q + LEK F +YL+ RI++A +L L++ Q+K W+QNRRMKWKK
Sbjct: 18 RRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 62.0 bits (149), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 29/66 (43%), Positives = 48/66 (72%), Gaps = 2/66 (3%)
Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
G+ ++G +++R Y++ Q ELE+E+ N+++T+ +R +I+ A L+ERQI IWFQNR
Sbjct: 1 GSSGSSG--RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNR 58
Query: 186 RMKWKK 191
R+K KK
Sbjct: 59 RVKEKK 64
Score = 60.8 bits (146), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 27/63 (42%), Positives = 45/63 (71%)
Query: 5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64
++ +++R Y++ Q ELE+E+ N+++T+ +R +I+ A L+ERQI IWFQNRR+K
Sbjct: 2 SSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK 61
Query: 65 WKK 67
KK
Sbjct: 62 EKK 64
>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 = 62.0 bits (149), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 31/59 (52%), Positives = 42/59 (71%)
Query: 9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
+ KR RT+++ Q L++EF+ NRYLT RRR +++ L L E QIKIWFQN+R K KK
Sbjct: 2 DEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
Score = 62.0 bits (149), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 31/59 (52%), Positives = 42/59 (71%)
Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
+ KR RT+++ Q L++EF+ NRYLT RRR +++ L L E QIKIWFQN+R K KK
Sbjct: 2 DEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 61.2 bits (147), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 31/57 (54%), Positives = 41/57 (71%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
KR RT+++ Q L++EF+ NRYLT RRR +++ L L E QIKIWFQN+R K KK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
Score = 61.2 bits (147), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 31/57 (54%), Positives = 41/57 (71%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
KR RT+++ Q L++EF+ NRYLT RRR +++ L L E QIKIWFQN+R K KK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 60.1 bits (144), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 29/60 (48%), Positives = 42/60 (70%)
Query: 8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
G+ KR RT+++ Q ++EF+ NRYLT RRR +++ L L E QIKIWFQN+R K ++
Sbjct: 1 GDEKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
Score = 60.1 bits (144), Expect = 8e-10, Method: Compositional matrix adjust.
Identities = 29/60 (48%), Positives = 42/60 (70%)
Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
G+ KR RT+++ Q ++EF+ NRYLT RRR +++ L L E QIKIWFQN+R K ++
Sbjct: 1 GDEKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52e
Length = 59
Score = 60.1 bits (144), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 31/57 (54%), Positives = 40/57 (70%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
KR RT+++ Q L++EF+ NRYLT RRR +++ L L E QIKIWFQN R K KK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
Score = 60.1 bits (144), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 31/57 (54%), Positives = 40/57 (70%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
KR RT+++ Q L++EF+ NRYLT 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 = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 31/57 (54%), Positives = 40/57 (70%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
KR RT+++ Q L++EF+ NRYLT RRR +++ L L E QIKIWFQN R K KK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
Score = 60.1 bits (144), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 31/57 (54%), Positives = 40/57 (70%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
KR RT+++ Q L++EF+ NRYLT 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 = 59.7 bits (143), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/57 (52%), Positives = 41/57 (71%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
KR RT+++ Q L++EF+ NRYLT RRR +++ L L E QIKIWF+N+R K KK
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
Score = 59.7 bits (143), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/57 (52%), Positives = 41/57 (71%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
KR RT+++ Q L++EF+ NRYLT RRR +++ L L E QIKIWF+N+R K KK
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>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 = 58.9 bits (141), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 31/59 (52%), Positives = 41/59 (69%)
Query: 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
+R RT++TR Q LEKEF+ Y++R RR E+A L L E IK+WFQNRRMK K++
Sbjct: 1 VRRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
Score = 58.9 bits (141), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 31/59 (52%), Positives = 41/59 (69%)
Query: 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
+R RT++TR Q LEKEF+ Y++R RR E+A L L E IK+WFQNRRMK K++
Sbjct: 1 VRRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 57.4 bits (137), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 26/54 (48%), Positives = 37/54 (68%)
Query: 15 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
TS++R Q LELE+ F +YL R +A AL +T+ Q+K WFQNRR KW+++
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
Score = 57.4 bits (137), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 26/54 (48%), Positives = 37/54 (68%)
Query: 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
TS++R Q LELE+ F +YL R +A AL +T+ Q+K WFQNRR KW+++
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 57.4 bits (137), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 27/59 (45%), Positives = 42/59 (71%)
Query: 9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
E +++R YT+ Q ELE+E+ N+++T+ +R I+ L+ERQ+ IWFQNRR+K KK
Sbjct: 6 EGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
Score = 57.4 bits (137), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 27/59 (45%), Positives = 42/59 (71%)
Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
E +++R YT+ Q ELE+E+ N+++T+ +R I+ L+ERQ+ IWFQNRR+K KK
Sbjct: 6 EGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
>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 = 57.4 bits (137), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 29/56 (51%), Positives = 39/56 (69%)
Query: 12 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
R RT+++ Q L++EF+ NRYLT RRR +++ L L E QIKIWF N+R K KK
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
Score = 57.4 bits (137), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 29/56 (51%), Positives = 39/56 (69%)
Query: 136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
R RT+++ Q L++EF+ NRYLT RRR +++ L L E QIKIWF N+R K KK
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 57.0 bits (136), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 28/53 (52%), Positives = 38/53 (71%)
Query: 12 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64
R RT+++ Q L++EF+ NRYLT RRR +++ L L E QIKIWFQN+R K
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
Score = 57.0 bits (136), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 28/53 (52%), Positives = 38/53 (71%)
Query: 136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 188
R RT+++ Q L++EF+ NRYLT RRR +++ L L E QIKIWFQN+R K
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>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 = 1e-08, Method: Compositional matrix adjust.
Identities = 26/57 (45%), Positives = 41/57 (71%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
+++R YT+ Q ELE+E+ N+++T+ +R I+ L+ERQ+ IWFQNRR+K KK
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58
Score = 56.2 bits (134), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 26/57 (45%), Positives = 41/57 (71%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
+++R YT+ Q ELE+E+ N+++T+ +R I+ L+ERQ+ IWFQNRR+K KK
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 56.2 bits (134), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/67 (40%), Positives = 42/67 (62%), Gaps = 2/67 (2%)
Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
G+ ++G ++ RT Y+ +Q L++ F +YL R E+A +L LT+ Q+KIWFQN+
Sbjct: 1 GSSGSSG--RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNK 58
Query: 186 RMKWKKE 192
R K KK
Sbjct: 59 RSKIKKS 65
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 27/65 (41%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 5 NANGETKRQ-RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 63
++G + R+ RT Y+ +Q L++ F +YL R E+A +L LT+ Q+KIWFQN+R
Sbjct: 1 GSSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRS 60
Query: 64 KWKKE 68
K KK
Sbjct: 61 KIKKS 65
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/51 (49%), Positives = 36/51 (70%)
Query: 17 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
++ QT+ELEK+F +YL+ R +A L L+ERQ+K WFQNRR KW++
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/51 (49%), Positives = 36/51 (70%)
Query: 141 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
++ QT+ELEK+F +YL+ R +A L L+ERQ+K WFQNRR KW++
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
>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 = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/59 (47%), Positives = 40/59 (67%)
Query: 9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
+ KR RT+++ Q L++EF+ NRYLT RRR +++ L L E Q+K WF+N R K KK
Sbjct: 3 DEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 28/59 (47%), Positives = 40/59 (67%)
Query: 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
+ KR RT+++ Q L++EF+ NRYLT RRR +++ L L E Q+K WF+N R K KK
Sbjct: 3 DEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 55.1 bits (131), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 29/73 (39%), Positives = 43/73 (58%)
Query: 2 STVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 61
S ++ G+ +R RT++T YQ ELEK F Y R ++A LTE ++++WFQNR
Sbjct: 1 SHMSNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNR 60
Query: 62 RMKWKKEHKMASM 74
R KW+K + M
Sbjct: 61 RAKWRKRERFGQM 73
Score = 54.7 bits (130), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 28/67 (41%), Positives = 40/67 (59%)
Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
G+ +R RT++T YQ ELEK F Y R ++A LTE ++++WFQNRR KW+K
Sbjct: 7 GKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRK 66
Query: 192 EHKMASM 198
+ M
Sbjct: 67 RERFGQM 73
>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 = 6e-08, Method: Compositional matrix adjust.
Identities = 28/61 (45%), Positives = 40/61 (65%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
+R RT++T +Q ELEK F Y R E+A + LTE +I++WFQNRR KW+K+ K
Sbjct: 7 RRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 66
Query: 71 M 71
+
Sbjct: 67 V 67
Score = 54.3 bits (129), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 28/61 (45%), Positives = 40/61 (65%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
+R RT++T +Q ELEK F Y R E+A + LTE +I++WFQNRR KW+K+ K
Sbjct: 7 RRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 66
Query: 195 M 195
+
Sbjct: 67 V 67
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 53.9 bits (128), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 38/57 (66%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
++ RT +T Q L LE++F +YL+ R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
Score = 53.9 bits (128), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/57 (47%), Positives = 38/57 (66%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
++ RT +T Q L LE++F +YL+ R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>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 = 53.9 bits (128), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 29/60 (48%), Positives = 37/60 (61%)
Query: 8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
G +RQRT +T Q ELE F NRY R EIA LTE ++++WF+NRR KW+K
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Score = 53.9 bits (128), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 29/60 (48%), Positives = 37/60 (61%)
Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
G +RQRT +T Q ELE F NRY R EIA LTE ++++WF+NRR KW+K
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 2/70 (2%)
Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
G+ ++G+ R RTS+T+ Q LEKEF Y R +A + L E +I++WF NR
Sbjct: 1 GSSGSSGQ--RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNR 58
Query: 186 RMKWKKEHKM 195
R KW++E K+
Sbjct: 59 RAKWRREEKL 68
Score = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 26/67 (38%), Positives = 39/67 (58%)
Query: 5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64
++ +R RTS+T+ Q LEKEF Y R +A + L E +I++WF NRR K
Sbjct: 2 SSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAK 61
Query: 65 WKKEHKM 71
W++E K+
Sbjct: 62 WRREEKL 68
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 51.6 bits (122), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/58 (46%), Positives = 37/58 (63%)
Query: 12 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
R RT++T +Q ELEK F Y R E+A + LTE +I++WFQNRR KW+K+
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
Score = 51.6 bits (122), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 27/58 (46%), Positives = 37/58 (63%)
Query: 136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
R RT++T +Q ELEK F Y R E+A + LTE +I++WFQNRR KW+K+
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/41 (60%), Positives = 31/41 (75%)
Query: 27 KEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
+EF+ NRYLT RRR +++ L L E QIKIWFQN+R K KK
Sbjct: 3 REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43
Score = 51.6 bits (122), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/41 (60%), Positives = 31/41 (75%)
Query: 151 KEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
+EF+ NRYLT RRR +++ L L E QIKIWFQN+R K KK
Sbjct: 3 REFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 51.2 bits (121), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 28/60 (46%), Positives = 36/60 (60%)
Query: 8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
G +RQRT +T Q ELE F N Y R EIA LTE ++++WF+NRR KW+K
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Score = 51.2 bits (121), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 28/60 (46%), Positives = 36/60 (60%)
Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
G +RQRT +T Q ELE F N Y R EIA LTE ++++WF+NRR KW+K
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 50.4 bits (119), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 36/56 (64%)
Query: 16 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 71
++T +Q ELEK F Y R E+A + LTE +I++WFQNRR KW+K+ K+
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 60
Score = 50.4 bits (119), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 36/56 (64%)
Query: 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195
++T +Q ELEK F Y R E+A + LTE +I++WFQNRR KW+K+ K+
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 60
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/63 (42%), Positives = 38/63 (60%), Gaps = 4/63 (6%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
+R RT++T Q ELE+ F RYLT R +++ L L Q+KIWF+NRR + HK
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRR----RRHK 58
Query: 71 MAS 73
+ S
Sbjct: 59 IQS 61
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/63 (42%), Positives = 38/63 (60%), Gaps = 4/63 (6%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
+R RT++T Q ELE+ F RYLT R +++ L L Q+KIWF+NRR + HK
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRR----RRHK 58
Query: 195 MAS 197
+ S
Sbjct: 59 IQS 61
>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 = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/49 (48%), Positives = 33/49 (67%)
Query: 21 QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69
Q +ELE++F +YL+ R +A L LTE Q+KIWFQNRR K K++
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/49 (48%), Positives = 33/49 (67%)
Query: 145 QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193
Q +ELE++F +YL+ R +A L LTE Q+KIWFQNRR K K++
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63
>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 = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 33/53 (62%)
Query: 14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
R +++ Q ELE+ F RYL+ R ++A L LT Q+KIWFQNRR K K
Sbjct: 6 RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
Score = 48.5 bits (114), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/53 (47%), Positives = 33/53 (62%)
Query: 138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
R +++ Q ELE+ F RYL+ R ++A L LT Q+KIWFQNRR K K
Sbjct: 6 RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|1NK2|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES
pdb|1NK3|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, MINIMIZED AVERAGE
Structure
pdb|1VND|A Chain A, VndNK-2 Protein (Homeodomain), Nmr
Length = 77
Score = 47.0 bits (110), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 36/57 (63%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
+++R +T+ QT ELE+ F RYL+ R +A + LT Q+KIWFQN R K K+
Sbjct: 10 RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66
Score = 47.0 bits (110), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 36/57 (63%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
+++R +T+ QT ELE+ F RYL+ R +A + LT Q+KIWFQN R K K+
Sbjct: 10 RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66
>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 = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 38/63 (60%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
+R RT+++ Q ELE+ F +Y R E+A LTE +I++WFQNRR + +K+H
Sbjct: 19 RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT 78
Query: 71 MAS 73
S
Sbjct: 79 SVS 81
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 38/63 (60%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
+R RT+++ Q ELE+ F +Y R E+A LTE +I++WFQNRR + +K+H
Sbjct: 19 RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT 78
Query: 195 MAS 197
S
Sbjct: 79 SVS 81
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 46.2 bits (108), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 29/67 (43%), Positives = 38/67 (56%), Gaps = 1/67 (1%)
Query: 1 MSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN 60
MS N + KR R +T+ QT ELE+ F RYL+ R + + LT Q+KIWFQN
Sbjct: 4 MSDGLPNKKRKR-RVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQN 62
Query: 61 RRMKWKK 67
R K K+
Sbjct: 63 HRYKTKR 69
Score = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 35/57 (61%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
+++R +T+ QT ELE+ F RYL+ R + + LT Q+KIWFQN R K K+
Sbjct: 13 RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKR 69
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68
+R RT++T Q ELE+ F Y R E+A LTE ++++WF NRR +W+K+
Sbjct: 3 RRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192
+R RT++T Q ELE+ F Y R E+A LTE ++++WF NRR +W+K+
Sbjct: 3 RRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>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 = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 38/60 (63%)
Query: 8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
G ++ RT +++ Q L+ F +YL+ ++ E++ L L+ +Q+K WFQN+RMK K+
Sbjct: 1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
Score = 43.9 bits (102), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 38/60 (63%)
Query: 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
G ++ RT +++ Q L+ F +YL+ ++ E++ L L+ +Q+K WFQN+RMK K+
Sbjct: 1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 43.5 bits (101), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 37/60 (61%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
+++R +++ Q ELE+ F +YL+ R +A + LT Q+KIWFQN R K K++ K
Sbjct: 3 RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62
Score = 43.5 bits (101), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 37/60 (61%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
+++R +++ Q ELE+ F +YL+ R +A + LT Q+KIWFQN R K K++ K
Sbjct: 3 RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 43.5 bits (101), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 39/65 (60%), Gaps = 2/65 (3%)
Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
G+ ++G +R+RT++TR Q LE F RY R E+A + L E ++++WF+NR
Sbjct: 1 GSSGSSG--RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNR 58
Query: 186 RMKWK 190
R K +
Sbjct: 59 RAKCR 63
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 36/62 (58%)
Query: 5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64
++ +R+RT++TR Q LE F RY R E+A + L E ++++WF+NRR K
Sbjct: 2 SSGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61
Query: 65 WK 66
+
Sbjct: 62 CR 63
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 38/66 (57%), Gaps = 2/66 (3%)
Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
G+ ++G +R RT +T Q LE F +Y R ++A + L E ++++WF+NR
Sbjct: 1 GSSGSSG--RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNR 58
Query: 186 RMKWKK 191
R KW++
Sbjct: 59 RAKWRR 64
Score = 40.8 bits (94), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%)
Query: 5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64
++ +R RT +T Q LE F +Y R ++A + L E ++++WF+NRR K
Sbjct: 2 SSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAK 61
Query: 65 WKK 67
W++
Sbjct: 62 WRR 64
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 34/60 (56%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
+R RT++T+ Q LE F N Y ++A L L +I+IWFQNRR K K+ H+
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 34/60 (56%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
+R RT++T+ Q LE F N Y ++A L L +I+IWFQNRR K K+ H+
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 35/57 (61%)
Query: 14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70
RT ++ Q L F +YL+ ++ E+++ L L+ +Q+K WFQN+RMK K+ K
Sbjct: 26 RTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK 82
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 35/57 (61%)
Query: 138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194
RT ++ Q L F +YL+ ++ E+++ L L+ +Q+K WFQN+RMK K+ K
Sbjct: 26 RTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK 82
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 37/66 (56%), Gaps = 2/66 (3%)
Query: 126 GTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 185
G+ ++G KR RTS+ +Q ++ F N + ++A LT+R +++WFQN
Sbjct: 1 GSSGSSG--KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNA 58
Query: 186 RMKWKK 191
R K+++
Sbjct: 59 RAKFRR 64
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%)
Query: 5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64
++ KR RTS+ +Q ++ F N + ++A LT+R +++WFQN R K
Sbjct: 2 SSGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAK 61
Query: 65 WKK 67
+++
Sbjct: 62 FRR 64
>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 = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/16 (100%), Positives = 16/16 (100%)
Query: 52 RQIKIWFQNRRMKWKK 67
RQIKIWFQNRRMKWKK
Sbjct: 1 RQIKIWFQNRRMKWKK 16
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/16 (100%), Positives = 16/16 (100%)
Query: 176 RQIKIWFQNRRMKWKK 191
RQIKIWFQNRRMKWKK
Sbjct: 1 RQIKIWFQNRRMKWKK 16
>pdb|3NB3|A Chain A, The Host Outer Membrane Proteins Ompa And Ompc Are Packed
At Specific Sites In The Shigella Phage Sf6 Virion As
Structural Components
pdb|3NB3|B Chain B, The Host Outer Membrane Proteins Ompa And Ompc Are Packed
At Specific Sites In The Shigella Phage Sf6 Virion As
Structural Components
pdb|3NB3|C Chain C, The Host Outer Membrane Proteins Ompa And Ompc Are Packed
At Specific Sites In The Shigella Phage Sf6 Virion As
Structural Components
Length = 346
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 33/121 (27%), Positives = 46/121 (38%), Gaps = 16/121 (13%)
Query: 37 RRRRIEIAHALC--LTERQIK----IWFQNRRMKWKKEHKMASMNNPNLYTQYQTQGKSC 90
++ I IA AL T Q W+ ++ W + H +NN N T G
Sbjct: 2 KKTAIAIAVALAGFATVAQAAPKDNTWYTGAKLGWSQYHDTGFINN-NGPTHENKLGAGA 60
Query: 91 TGRYQVRPITSPHGAYHG-DLRYHWTNRAPLK-YVKRGTVNANGETKRQRTSYTRYQTLE 148
G YQV P Y G ++ Y W R P K V+ G A G + Y L+
Sbjct: 61 FGGYQVNP-------YVGFEMGYDWLGRMPYKGSVENGAYKAQGVQLTAKLGYPITDDLD 113
Query: 149 L 149
+
Sbjct: 114 I 114
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 16/16 (100%), Positives = 16/16 (100%)
Query: 52 RQIKIWFQNRRMKWKK 67
RQIKIWFQNRRMKWKK
Sbjct: 1 RQIKIWFQNRRMKWKK 16
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 16/16 (100%), Positives = 16/16 (100%)
Query: 176 RQIKIWFQNRRMKWKK 191
RQIKIWFQNRRMKWKK
Sbjct: 1 RQIKIWFQNRRMKWKK 16
>pdb|1BXW|A Chain A, Outer Membrane Protein A (Ompa) Transmembrane Domain
Length = 172
Score = 35.4 bits (80), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 37/95 (38%), Gaps = 10/95 (10%)
Query: 57 WFQNRRMKWKKEHKMASMNNPNLYTQYQTQGKSCTGRYQVRPITSPHGAYHG-DLRYHWT 115
W+ ++ W + H +NN N T G G YQV P Y G ++ Y W
Sbjct: 8 WYTGAKLGWSQYHDTGLINN-NGPTHENKLGAGAFGGYQVNP-------YVGFEMGYDWL 59
Query: 116 NRAPLK-YVKRGTVNANGETKRQRTSYTRYQTLEL 149
R P K V+ G A G + Y L++
Sbjct: 60 GRMPYKGSVENGAYKAQGVQLTAKLGYPITDDLDI 94
>pdb|1QJP|A Chain A, High Resolution Structure Of The Outer Membrane Protein A
(ompa) Transmembrane Domain
Length = 171
Score = 35.4 bits (80), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 37/95 (38%), Gaps = 10/95 (10%)
Query: 57 WFQNRRMKWKKEHKMASMNNPNLYTQYQTQGKSCTGRYQVRPITSPHGAYHG-DLRYHWT 115
W+ ++ W + H +NN N T G G YQV P Y G ++ Y W
Sbjct: 7 WYTGAKLGWSQYHDTGFINN-NGPTHENKLGAGAFGGYQVNP-------YVGFEMGYDWL 58
Query: 116 NRAPLK-YVKRGTVNANGETKRQRTSYTRYQTLEL 149
R P K V+ G A G + Y L++
Sbjct: 59 GRMPYKGSVENGAYKAQGVQLTAKLGYPITDDLDI 93
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 35.4 bits (80), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 33/57 (57%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
KR RT+ T Q L +++ + TR+ IAH + L +R +++WFQN R + +K
Sbjct: 18 KRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74
Score = 35.4 bits (80), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 33/57 (57%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
KR RT+ T Q L +++ + TR+ IAH + L +R +++WFQN R + +K
Sbjct: 18 KRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 34.3 bits (77), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 15/15 (100%), Positives = 15/15 (100%)
Query: 53 QIKIWFQNRRMKWKK 67
QIKIWFQNRRMKWKK
Sbjct: 2 QIKIWFQNRRMKWKK 16
Score = 34.3 bits (77), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 15/15 (100%), Positives = 15/15 (100%)
Query: 177 QIKIWFQNRRMKWKK 191
QIKIWFQNRRMKWKK
Sbjct: 2 QIKIWFQNRRMKWKK 16
>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 = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%)
Query: 4 VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 63
+ E +++RTS + LEK F N+ T IA L + + I++WF NRR
Sbjct: 98 IEGLSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQ 157
Query: 64 KWKK 67
K K+
Sbjct: 158 KEKR 161
Score = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%)
Query: 128 VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 187
+ E +++RTS + LEK F N+ T IA L + + I++WF NRR
Sbjct: 98 IEGLSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQ 157
Query: 188 KWKK 191
K K+
Sbjct: 158 KEKR 161
>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 = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
+++RTS + LEK F N+ T IA L + + I++WF NRR K K+
Sbjct: 101 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEKR 157
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
+++RTS + LEK F N+ T IA L + + I++WF NRR K K+
Sbjct: 101 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEKR 157
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
+++RTS + LEK F N+ T IA L + + I++WF NRR K K+
Sbjct: 102 RKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
+++RTS + LEK F N+ T IA L + + I++WF NRR K K+
Sbjct: 102 RKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158
>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 = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 25 LEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
LE+ F + L + + E+A +T Q+++WF N+RM+ K
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 149 LEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
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 = 32.7 bits (73), Expect = 0.18, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 27/53 (50%)
Query: 15 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
T +T YQ L+ F N Y ++++ L L R I +WFQN R K +K
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
Score = 32.7 bits (73), Expect = 0.18, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 27/53 (50%)
Query: 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
T +T YQ L+ F N Y ++++ L L R I +WFQN R K +K
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
>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 = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
+++RTS + LEK F N+ T IA L + + I++WF NRR K K+
Sbjct: 104 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 160
Score = 32.0 bits (71), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
+++RTS + LEK F N+ T IA L + + I++WF NRR K K+
Sbjct: 104 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 160
>pdb|1KZ2|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain Derivative [w6f,W14f]
Length = 16
Score = 31.6 bits (70), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 14/16 (87%), Positives = 16/16 (100%)
Query: 52 RQIKIWFQNRRMKWKK 67
RQIKI+FQNRRMK+KK
Sbjct: 1 RQIKIFFQNRRMKFKK 16
Score = 31.6 bits (70), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 14/16 (87%), Positives = 16/16 (100%)
Query: 176 RQIKIWFQNRRMKWKK 191
RQIKI+FQNRRMK+KK
Sbjct: 1 RQIKIFFQNRRMKFKK 16
>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 = 31.6 bits (70), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
+++RTS + LEK F N+ T IA L + + I++WF NRR K K+
Sbjct: 97 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 153
Score = 31.6 bits (70), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
+++RTS + LEK F N+ T IA L + + I++WF NRR K K+
Sbjct: 97 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 153
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 31.2 bits (69), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 32 NRYLTRRRRIEIAHALCLTERQIKIWFQNRR 62
N Y + R + E+A A LT Q+ WF+NRR
Sbjct: 516 NPYPSPREKRELAEATGLTTTQVSNWFKNRR 546
Score = 31.2 bits (69), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 14/31 (45%), Positives = 19/31 (61%)
Query: 156 NRYLTRRRRIEIAHALCLTERQIKIWFQNRR 186
N Y + R + E+A A LT Q+ WF+NRR
Sbjct: 516 NPYPSPREKRELAEATGLTTTQVSNWFKNRR 546
>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 = 0.51, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
+++RTS LEK F N+ T + IA L + + I++WF NRR K K+
Sbjct: 2 RKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEKR 58
Score = 31.2 bits (69), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
+++RTS LEK F N+ T + IA L + + I++WF NRR K K+
Sbjct: 2 RKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEKR 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 = 30.4 bits (67), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
+++RTS + LEK F N+ T IA L + + I++WF NRR K K+
Sbjct: 8 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 64
Score = 30.4 bits (67), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 30/57 (52%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
+++RTS + LEK F N+ T IA L + + I++WF NRR K K+
Sbjct: 8 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 64
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 10 TKRQRTSYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 65
+R+R ++ + Q E+ E+ + N Y + + E+A +T Q+ WF N+R+++
Sbjct: 1 ARRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRY 59
Query: 66 KK 67
KK
Sbjct: 60 KK 61
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 134 TKRQRTSYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 189
+R+R ++ + Q E+ E+ + N Y + + E+A +T Q+ WF N+R+++
Sbjct: 1 ARRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRY 59
Query: 190 KK 191
KK
Sbjct: 60 KK 61
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 21 QTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
Q E+ E+ + N Y + + E+A +T Q+ WF N+R+++KK
Sbjct: 13 QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
Score = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 145 QTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
Q E+ E+ + N Y + + E+A +T Q+ WF N+R+++KK
Sbjct: 13 QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>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 = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 29/110 (26%), Positives = 43/110 (39%), Gaps = 8/110 (7%)
Query: 88 KSCTGRYQVRPITSPHGAYHGDLRYHWTNRAPLKYVKRGTVN----ANGET---KRQRTS 140
+S R++ IT + W N A L+ + G N GE +++RTS
Sbjct: 41 QSAISRFEKLDITPKSAQKLKPVLEKWLNEAELRN-QEGQQNLXEFVGGEPSKKRKRRTS 99
Query: 141 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
+T L F N T + E A L +++WF NRR K
Sbjct: 100 FTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRRQTLK 149
Score = 27.3 bits (59), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 25/56 (44%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
+++RTS+T L F N T + E A L +++WF NRR K
Sbjct: 94 RKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRRQTLK 149
>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 = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 10 TKRQRTSYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 65
+R+R ++++ Q E+ E+ + N Y + + E+A +T Q+ WF N+R+++
Sbjct: 1 ARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRY 59
Query: 66 KK 67
KK
Sbjct: 60 KK 61
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 134 TKRQRTSYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 189
+R+R ++++ Q E+ E+ + N Y + + E+A +T Q+ WF N+R+++
Sbjct: 1 ARRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRY 59
Query: 190 KK 191
KK
Sbjct: 60 KK 61
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 10 TKRQRTSYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 65
+R+R ++ + Q E+ E+ + N Y + + E+A +T Q+ WF N+R+++
Sbjct: 1 ARRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRY 59
Query: 66 KK 67
KK
Sbjct: 60 KK 61
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 134 TKRQRTSYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 189
+R+R ++ + Q E+ E+ + N Y + + E+A +T Q+ WF N+R+++
Sbjct: 1 ARRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRY 59
Query: 190 KK 191
KK
Sbjct: 60 KK 61
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 29.6 bits (65), Expect = 1.5, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 25 LEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
LE+ F + L + + E+A +T Q+++WF N+RM+ K
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
Score = 29.6 bits (65), Expect = 1.5, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 149 LEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
LE+ F + L + + E+A +T Q+++WF N+RM+ K
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 29.3 bits (64), Expect = 1.7, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 25 LEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
LE+ F + L + + E+A +T Q+++WF N+RM+ K
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
Score = 29.3 bits (64), Expect = 1.7, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 149 LEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
LE+ F + L + + E+A +T Q+++WF N+RM+ K
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 10 TKRQRTSYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 65
+R+R ++ + Q E+ E+ + N Y + + E+A +T Q+ WF N+R+++
Sbjct: 2 ARRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRY 60
Query: 66 KK 67
KK
Sbjct: 61 KK 62
Score = 29.3 bits (64), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 134 TKRQRTSYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 189
+R+R ++ + Q E+ E+ + N Y + + E+A +T Q+ WF N+R+++
Sbjct: 2 ARRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRY 60
Query: 190 KK 191
KK
Sbjct: 61 KK 62
>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 = 29.3 bits (64), Expect = 1.8, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 25 LEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66
LE+ F + L + + E+A +T Q+++WF N+RM+ K
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
Score = 29.3 bits (64), Expect = 1.8, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 149 LEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190
LE+ F + L + + E+A +T Q+++WF N+RM+ K
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 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 = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 13/64 (20%)
Query: 18 TRYQTLELEKEFHFNR----------YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
TR +T+ EK+ H R L + + +E+ L+ R I++WFQN+R K KK
Sbjct: 4 TRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTG---LSPRVIRVWFQNKRCKDKK 60
Query: 68 EHKM 71
M
Sbjct: 61 RSIM 64
Score = 28.9 bits (63), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 13/64 (20%)
Query: 142 TRYQTLELEKEFHFNR----------YLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
TR +T+ EK+ H R L + + +E+ L+ R I++WFQN+R K KK
Sbjct: 4 TRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTG---LSPRVIRVWFQNKRCKDKK 60
Query: 192 EHKM 195
M
Sbjct: 61 RSIM 64
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 31/67 (46%)
Query: 1 MSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN 60
+ + A G +++RTS LE F + +A +L L + +++WF N
Sbjct: 90 LDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCN 149
Query: 61 RRMKWKK 67
RR K K+
Sbjct: 150 RRQKEKR 156
Score = 27.7 bits (60), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 30/64 (46%)
Query: 128 VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 187
+ A G +++RTS LE F + +A +L L + +++WF NRR
Sbjct: 93 IAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQ 152
Query: 188 KWKK 191
K K+
Sbjct: 153 KEKR 156
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67
KR+RTS LE F + + ++ IA+ L L + +++WF NRR K K+
Sbjct: 97 KRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 30/57 (52%)
Query: 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191
KR+RTS LE F + + ++ IA+ L L + +++WF NRR K K+
Sbjct: 97 KRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 27.3 bits (59), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 34/64 (53%)
Query: 4 VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 63
V AN +++RT+ + LE+ F + + + + +A L L + +++WF NRR
Sbjct: 81 VGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQ 140
Query: 64 KWKK 67
+ K+
Sbjct: 141 REKR 144
Score = 27.3 bits (59), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 34/64 (53%)
Query: 128 VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 187
V AN +++RT+ + LE+ F + + + + +A L L + +++WF NRR
Sbjct: 81 VGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQ 140
Query: 188 KWKK 191
+ K+
Sbjct: 141 REKR 144
>pdb|1QDB|A Chain A, Cytochrome C Nitrite Reductase
pdb|1QDB|B Chain B, Cytochrome C Nitrite Reductase
pdb|1QDB|C Chain C, Cytochrome C Nitrite Reductase
Length = 473
Score = 26.9 bits (58), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 6/67 (8%)
Query: 25 LEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNPNLYTQYQ 84
+ +F + +++IA AL + + K Q +WKKE K NP LY
Sbjct: 406 IAPDFDTKDKAQKLAKVDIA-ALAAEKMKFK---QTLEQEWKKEAKAKGRANPELYKDVD 461
Query: 85 T--QGKS 89
T GKS
Sbjct: 462 TINDGKS 468
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
0.322 0.132 0.415
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,138,008
Number of Sequences: 62578
Number of extensions: 284663
Number of successful extensions: 632
Number of sequences better than 100.0: 88
Number of HSP's better than 100.0 without gapping: 82
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 466
Number of HSP's gapped (non-prelim): 172
length of query: 222
length of database: 14,973,337
effective HSP length: 95
effective length of query: 127
effective length of database: 9,028,427
effective search space: 1146610229
effective search space used: 1146610229
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (23.5 bits)