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= psy3281
(317 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 132 bits (333), Expect = 2e-31, Method: Composition-based stats.
Identities = 62/63 (98%), Positives = 63/63 (100%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 61
Query: 298 KSK 300
K+K
Sbjct: 62 KTK 64
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 128 bits (321), Expect = 5e-30, Method: Composition-based stats.
Identities = 60/61 (98%), Positives = 60/61 (98%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKE
Sbjct: 2 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
Query: 297 N 297
N
Sbjct: 62 N 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 = 127 bits (318), Expect = 1e-29, Method: Composition-based stats.
Identities = 61/63 (96%), Positives = 62/63 (98%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKEN
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61
Query: 298 KSK 300
K+K
Sbjct: 62 KTK 64
>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 = 121 bits (303), Expect = 5e-28, Method: Compositional matrix adjust.
Identities = 61/84 (72%), Positives = 66/84 (78%), Gaps = 10/84 (11%)
Query: 225 PSPLYPWMR----------SQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHA 274
P +YPWM+ + E KR R +YTRYQTLELEKEFHFNRYLTRRRRIEIAHA
Sbjct: 5 PPQIYPWMKRVHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHA 64
Query: 275 LCLTERQIKIWFQNRRMKWKKENK 298
L LTERQIKIWFQNRRMKWKKE+K
Sbjct: 65 LSLTERQIKIWFQNRRMKWKKEHK 88
>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 = 117 bits (292), Expect = 1e-26, Method: Composition-based stats.
Identities = 55/57 (96%), Positives = 56/57 (98%)
Query: 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSK 300
TYTRYQTLELEKEFHFNRYLTRRRRIEIAHAL LTERQIKIWFQNRRMKWKKENK+K
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK 58
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 114 bits (284), Expect = 1e-25, Method: Composition-based stats.
Identities = 57/72 (79%), Positives = 60/72 (83%), Gaps = 3/72 (4%)
Query: 228 LYPWMR---SQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKI 284
YPWM + R+RGRQTYTRYQTLELEKEFH N YLTRRRRIE+AHAL LTERQIKI
Sbjct: 7 FYPWMAIAGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKI 66
Query: 285 WFQNRRMKWKKE 296
WFQNRRMK KKE
Sbjct: 67 WFQNRRMKLKKE 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 = 105 bits (261), Expect = 5e-23, Method: Composition-based stats.
Identities = 50/60 (83%), Positives = 56/60 (93%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
+ KR RQTYTRYQTLELEKEFHFNRY+TRRRRI+IA+AL L+ERQIKIWFQNRRMK KK+
Sbjct: 2 DSKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKD 61
>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 = 92.0 bits (227), Expect = 3e-19, Method: Composition-based stats.
Identities = 42/58 (72%), Positives = 47/58 (81%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
KR R YTR Q LELEKEF FN+Y++R RR+E+A L LTER IKIWFQNRRMKWKKE
Sbjct: 4 KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 91.3 bits (225), Expect = 7e-19, Method: Composition-based stats.
Identities = 46/75 (61%), Positives = 56/75 (74%), Gaps = 1/75 (1%)
Query: 226 SPLYPWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIW 285
+P W+ ++ RK+ R YT++QTLELEKEF FN YLTR RR E+A L LTERQ+KIW
Sbjct: 2 NPAANWLHARSTRKK-RCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIW 60
Query: 286 FQNRRMKWKKENKSK 300
FQNRRMK KK NK +
Sbjct: 61 FQNRRMKMKKINKDR 75
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 89.4 bits (220), Expect = 2e-18, Method: Composition-based stats.
Identities = 42/59 (71%), Positives = 47/59 (79%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
++ R YT+YQTLELEKEF FN YLTR RR E+A L LTERQ+KIWFQNRRMK KK N
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN 60
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 76.6 bits (187), Expect = 2e-14, Method: Composition-based stats.
Identities = 34/57 (59%), Positives = 42/57 (73%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
+R R +T Q LELEKEFH +YL+ R +IAHAL L+E Q+KIWFQNRR KWK+
Sbjct: 8 RRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKR 64
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 74.3 bits (181), Expect = 7e-14, Method: Composition-based stats.
Identities = 38/62 (61%), Positives = 46/62 (74%), Gaps = 2/62 (3%)
Query: 242 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKD 301
R +T Q ELEKEFHFN+YL+R RR+EIA L L E Q+KIWFQNRRMK KK + ++
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKK--RERE 95
Query: 302 GG 303
GG
Sbjct: 96 GG 97
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 62.8 bits (151), Expect = 2e-10, Method: Composition-based stats.
Identities = 28/64 (43%), Positives = 42/64 (65%)
Query: 232 MRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 291
M E ++ R YT+ Q ELE+E+ N+++T+ +R I+ L+ERQ+ IWFQNRR+
Sbjct: 1 MSHMLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRV 60
Query: 292 KWKK 295
K KK
Sbjct: 61 KEKK 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 = 62.4 bits (150), Expect = 3e-10, Method: Composition-based stats.
Identities = 30/59 (50%), Positives = 40/59 (67%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
+ KR R ++ Q L++EF+ NRYLT RRR +++ L L E QIKIWFQN+R K KK
Sbjct: 2 DEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>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 = 62.4 bits (150), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 28/61 (45%), Positives = 40/61 (65%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
+RK+ R ++TR Q ELEK FH +YL R +A L +T+ Q+K WFQNRR KW+++
Sbjct: 16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75
Query: 297 N 297
Sbjct: 76 T 76
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 62.0 bits (149), Expect = 4e-10, Method: Composition-based stats.
Identities = 28/61 (45%), Positives = 40/61 (65%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
+R R +T Q + LEK F +YL+ RI++A +L L++ Q+K W+QNRRMKWKK
Sbjct: 18 RRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP 77
Query: 299 S 299
S
Sbjct: 78 S 78
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 61.6 bits (148), Expect = 5e-10, Method: Composition-based stats.
Identities = 30/57 (52%), Positives = 39/57 (68%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
KR R ++ Q L++EF+ NRYLT RRR +++ L L E QIKIWFQN+R K KK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 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 = 60.8 bits (146), Expect = 1e-09, Method: Composition-based stats.
Identities = 29/57 (50%), Positives = 39/57 (68%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
KR R ++ Q L++EF+ NRYLT RRR +++ L L E QIKIWF+N+R K KK
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 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 = 60.5 bits (145), Expect = 1e-09, Method: Composition-based stats.
Identities = 30/57 (52%), Positives = 38/57 (66%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
KR R ++ Q L++EF+ NRYLT RRR +++ L L E QIKIWFQN R K KK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 60.5 bits (145), Expect = 1e-09, Method: Composition-based stats.
Identities = 26/57 (45%), Positives = 40/57 (70%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
++ R YT+ Q ELE+E+ N+++T+ +R I+ L+ERQ+ IWFQNRR+K KK
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 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 = 60.5 bits (145), Expect = 1e-09, Method: Composition-based stats.
Identities = 30/57 (52%), Positives = 38/57 (66%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
KR R ++ Q L++EF+ NRYLT RRR +++ L L E QIKIWFQN R K KK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 60.1 bits (144), Expect = 1e-09, Method: Composition-based stats.
Identities = 24/53 (45%), Positives = 36/53 (67%)
Query: 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
+++R Q LELE+ F +YL R +A AL +T+ Q+K WFQNRR KW+++
Sbjct: 3 SFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>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 = 3e-09, Method: Composition-based stats.
Identities = 30/58 (51%), Positives = 39/58 (67%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
+R R +TR Q LEKEF+ Y++R RR E+A L L E IK+WFQNRRMK K++
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 58.5 bits (140), Expect = 4e-09, Method: Composition-based stats.
Identities = 28/61 (45%), Positives = 43/61 (70%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
++ R Y++ Q ELE+E+ N+++T+ +R +I+ A L+ERQI IWFQNRR+K KK
Sbjct: 8 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP 67
Query: 299 S 299
S
Sbjct: 68 S 68
>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 = 58.2 bits (139), Expect = 6e-09, Method: Composition-based stats.
Identities = 28/62 (45%), Positives = 40/62 (64%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
+++R R T+T +Q ELEK F Y R E+A + LTE +I++WFQNRR KW+K+
Sbjct: 5 KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 64
Query: 297 NK 298
K
Sbjct: 65 EK 66
>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 = 58.2 bits (139), Expect = 6e-09, Method: Composition-based stats.
Identities = 28/56 (50%), Positives = 37/56 (66%)
Query: 240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
R R ++ 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 = 57.4 bits (137), Expect = 1e-08, Method: Composition-based stats.
Identities = 27/53 (50%), Positives = 36/53 (67%)
Query: 240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 292
R R ++ Q L++EF+ NRYLT RRR +++ L L E QIKIWFQN+R K
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 57.4 bits (137), Expect = 1e-08, Method: Composition-based stats.
Identities = 27/59 (45%), Positives = 39/59 (66%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
+ KR R ++ Q ++EF+ NRYLT RRR +++ L L E QIKIWFQN+R K ++
Sbjct: 2 DEKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 56.6 bits (135), Expect = 2e-08, Method: Composition-based stats.
Identities = 27/57 (47%), Positives = 36/57 (63%)
Query: 240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
R R T+T +Q ELEK F Y R E+A + LTE +I++WFQNRR KW+K+
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 55.8 bits (133), Expect = 3e-08, Method: Composition-based stats.
Identities = 26/55 (47%), Positives = 35/55 (63%)
Query: 244 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
T+T +Q ELEK F Y R E+A + LTE +I++WFQNRR KW+K+ K
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 55.8 bits (133), Expect = 3e-08, Method: Composition-based stats.
Identities = 26/55 (47%), Positives = 37/55 (67%)
Query: 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299
++ QT+ELEK+F +YL+ R +A L L+ERQ+K WFQNRR KW++ S
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGPS 68
>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 = 55.5 bits (132), Expect = 4e-08, Method: Composition-based stats.
Identities = 27/59 (45%), Positives = 38/59 (64%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
+ KR R ++ Q L++EF+ NRYLT RRR +++ L L E Q+K WF+N R K KK
Sbjct: 3 DEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 55.5 bits (132), Expect = 4e-08, Method: Composition-based stats.
Identities = 26/57 (45%), Positives = 37/57 (64%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
++ R +T Q L LE++F +YL+ R E + +L LTE Q+KIWFQNRR K K+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 55.1 bits (131), Expect = 5e-08, Method: Composition-based stats.
Identities = 25/42 (59%), Positives = 32/42 (76%)
Query: 254 EKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
++EF+ NRYLT RRR +++ L L E QIKIWFQN+R K KK
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43
>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 = 54.3 bits (129), Expect = 9e-08, Method: Composition-based stats.
Identities = 26/55 (47%), Positives = 36/55 (65%)
Query: 249 QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKSKDGG 303
Q +ELE++F +YL+ R +A L LTE Q+KIWFQNRR K K++ S + G
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSELG 69
>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 = 53.5 bits (127), Expect = 2e-07, Method: Composition-based stats.
Identities = 26/61 (42%), Positives = 36/61 (59%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
++R R +T Q ELE F NRY R EIA LTE ++++WF+NRR KW+K
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
Query: 298 K 298
+
Sbjct: 63 E 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 = 52.4 bits (124), Expect = 3e-07, Method: Composition-based stats.
Identities = 26/57 (45%), Positives = 36/57 (63%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294
R++ R +++ Q ELE+ F RYL+ R ++A L LT Q+KIWFQNRR K K
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 52.0 bits (123), Expect = 5e-07, Method: Composition-based stats.
Identities = 25/61 (40%), Positives = 37/61 (60%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
++ R Y+ +Q L++ F +YL R E+A +L LT+ Q+KIWFQN+R K KK
Sbjct: 8 RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGP 67
Query: 299 S 299
S
Sbjct: 68 S 68
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 50.8 bits (120), Expect = 9e-07, Method: Composition-based stats.
Identities = 25/61 (40%), Positives = 35/61 (57%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
++R R +T Q ELE F N Y R EIA LTE ++++WF+NRR KW+K
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
Query: 298 K 298
+
Sbjct: 63 E 63
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 35/59 (59%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
++R R T+T Q ELE+ F Y R E+A LTE ++++WF NRR +W+K+
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>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 = 49.3 bits (116), Expect = 3e-06, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 42/70 (60%)
Query: 230 PWMRSQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNR 289
P + + +++R R T++ Q ELE+ F +Y R E+A LTE +I++WFQNR
Sbjct: 10 PGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNR 69
Query: 290 RMKWKKENKS 299
R + +K++ S
Sbjct: 70 RARLRKQHTS 79
>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 = 3e-06, Method: Composition-based stats.
Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK-KEN 297
+R R T+T Q ELE+ F RYLT R +++ L L Q+KIWF+NRR + K + +
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62
Query: 298 KSKD 301
+ KD
Sbjct: 63 QHKD 66
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 38/62 (61%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
+++R R T+T YQ ELEK F Y R ++A LTE ++++WFQNRR KW+K
Sbjct: 8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR 67
Query: 297 NK 298
+
Sbjct: 68 ER 69
>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 = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 26/64 (40%), Positives = 38/64 (59%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
++++ R +T+ QT ELE+ F RYL+ R +A + LT Q+KIWFQN R K K+
Sbjct: 8 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA 67
Query: 297 NKSK 300
K
Sbjct: 68 QNEK 71
>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 = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 37/58 (63%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
+++ R +++ Q L+ F +YL+ ++ E++ L L+ +Q+K WFQN+RMK K+
Sbjct: 3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/69 (36%), Positives = 39/69 (56%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
+R R ++T+ Q LEKEF Y R +A + L E +I++WF NRR KW++E K
Sbjct: 8 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 67
Query: 299 SKDGGSDAG 307
++ +G
Sbjct: 68 LRNQRRQSG 76
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 37/64 (57%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
++++ R +T+ QT ELE+ F RYL+ R + + LT Q+KIWFQN R K K+
Sbjct: 11 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRA 70
Query: 297 NKSK 300
K
Sbjct: 71 QNEK 74
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 45.4 bits (106), Expect = 4e-05, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 39/64 (60%), Gaps = 3/64 (4%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK---W 293
++++ R ++ Q L F +YL+ ++ E+++ L L+ +Q+K WFQN+RMK W
Sbjct: 21 KKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRW 80
Query: 294 KKEN 297
+K N
Sbjct: 81 QKNN 84
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 38/65 (58%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
R++ R +++ Q ELE+ F +YL+ R +A + LT Q+KIWFQN R K K++
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQA 61
Query: 298 KSKDG 302
K K
Sbjct: 62 KDKAA 66
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 39/69 (56%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
+R R T+TR Q LE F RY R E+A + L E ++++WF+NRR K +++ +
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ 67
Query: 299 SKDGGSDAG 307
+ G +G
Sbjct: 68 QQQNGGQSG 76
>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 = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 18/24 (75%), Positives = 20/24 (83%), Gaps = 2/24 (8%)
Query: 280 RQIKIWFQNRRMKWKKE--NKSKD 301
RQIKIWFQNRRMKWKK N ++D
Sbjct: 1 RQIKIWFQNRRMKWKKRVFNDARD 24
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 33/61 (54%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
+R R +T Q LE F +Y R ++A + L E ++++WF+NRR KW++
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP 67
Query: 299 S 299
S
Sbjct: 68 S 68
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 41.2 bits (95), Expect = 8e-04, Method: Composition-based stats.
Identities = 16/16 (100%), Positives = 16/16 (100%)
Query: 280 RQIKIWFQNRRMKWKK 295
RQIKIWFQNRRMKWKK
Sbjct: 1 RQIKIWFQNRRMKWKK 16
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 15/15 (100%), Positives = 15/15 (100%)
Query: 281 QIKIWFQNRRMKWKK 295
QIKIWFQNRRMKWKK
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 32/60 (53%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
+R R +T+ Q LE F N Y ++A L L +I+IWFQNRR K K+ ++
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
>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 = 36.6 bits (83), Expect = 0.020, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 30/60 (50%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
R++ R + LEK F N+ T + IA L + + I++WF NRR K K+ N
Sbjct: 1 RRKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEKRIN 60
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 35.8 bits (81), Expect = 0.031, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 30/62 (48%)
Query: 234 SQFERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 293
S R++ R + + LEK F N+ T IA L + + I++WF NRR K
Sbjct: 3 SHMRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKE 62
Query: 294 KK 295
K+
Sbjct: 63 KR 64
>pdb|1KZ2|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain Derivative [w6f,W14f]
Length = 16
Score = 34.7 bits (78), Expect = 0.075, Method: Composition-based stats.
Identities = 14/16 (87%), Positives = 16/16 (100%)
Query: 280 RQIKIWFQNRRMKWKK 295
RQIKI+FQNRRMK+KK
Sbjct: 1 RQIKIFFQNRRMKFKK 16
>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 = 34.3 bits (77), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 253 LEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294
LE+ F + L + + E+A +T Q+++WF N+RM+ K
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 36/69 (52%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 298
KR R ++ +Q ++ F N + ++A LT+R +++WFQN R K+++
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLL 67
Query: 299 SKDGGSDAG 307
++ G +G
Sbjct: 68 RQENGGVSG 76
>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 = 0.15, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 31/61 (50%)
Query: 237 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
ER++ R + + LEK F N+ T IA L + + I++WF NRR K K+
Sbjct: 103 ERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRI 162
Query: 297 N 297
N
Sbjct: 163 N 163
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%)
Query: 239 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
KR R T T Q L +++ + TR+ IAH + L +R +++WFQN R + +K
Sbjct: 18 KRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 33.5 bits (75), Expect = 0.17, Method: Composition-based stats.
Identities = 14/42 (33%), Positives = 25/42 (59%)
Query: 253 LEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294
LE+ F + L + + E+A +T Q+++WF N+RM+ K
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>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 = 32.7 bits (73), Expect = 0.25, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 30/55 (54%)
Query: 240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294
+G+ + + LE+ F + L + + E+A +T Q+++WF N+RM+ K
Sbjct: 7 KGKSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 32.7 bits (73), Expect = 0.26, Method: Composition-based stats.
Identities = 15/55 (27%), Positives = 30/55 (54%)
Query: 240 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294
+G+ + + LE+ F + L + + E+A +T Q+++WF N+RM+ K
Sbjct: 7 KGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 0.32, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 27/55 (49%)
Query: 245 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENKS 299
+T YQ L+ F N Y ++++ L L R I +WFQN R K +K S
Sbjct: 14 FTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPS 68
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 31.6 bits (70), Expect = 0.54, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 239 KRGRQTYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294
+R R+ + + Q E+ E+ + N Y + + E+A +T Q+ WF N+R+++K
Sbjct: 2 RRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 295 K 295
K
Sbjct: 61 K 61
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 31.2 bits (69), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 240 RGRQTYTRYQT---LELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
R R+ T +T + LEK F N+ T IA L + + I++WF NRR K K+
Sbjct: 100 RRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI 159
Query: 297 N 297
N
Sbjct: 160 N 160
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 31.2 bits (69), Expect = 0.85, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 239 KRGRQTYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294
+R R+ + + Q E+ E+ + N Y + + E+A +T Q+ WF N+R+++K
Sbjct: 2 RRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 295 K 295
K
Sbjct: 61 K 61
>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 = 31.2 bits (69), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 240 RGRQTYTRYQT---LELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 296
R R+ T +T + LEK F N+ T IA L + + I++WF NRR K K+
Sbjct: 99 RRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEKRI 158
Query: 297 N 297
N
Sbjct: 159 N 159
>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 = 31.2 bits (69), Expect = 0.88, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 239 KRGRQTYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294
+R R+ +++ Q E+ E+ + N Y + + E+A +T Q+ WF N+R+++K
Sbjct: 2 RRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
Query: 295 K 295
K
Sbjct: 61 K 61
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 30.8 bits (68), Expect = 0.92, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 239 KRGRQTYTRYQTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 294
+R R+ + + Q E+ E+ + N Y + + E+A +T Q+ WF N+R+++K
Sbjct: 3 RRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
Query: 295 K 295
K
Sbjct: 62 K 62
>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 = 30.8 bits (68), Expect = 0.99, Method: Composition-based stats.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 7/59 (11%)
Query: 246 TRYQTLELEKEFHFNR--YLTRRR-----RIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
TR +T+ EK+ H R Y R + ++ L+ R I++WFQN+R K KK +
Sbjct: 4 TRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62
>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 = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 30/60 (50%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
R++ R + + LEK F N+ T IA L + + I++WF NRR K K+ N
Sbjct: 103 RRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRIN 162
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 253 LEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 292
L + + N Y + R + E+A A LT Q+ WF+NRR +
Sbjct: 509 LREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 548
>pdb|1OCT|C Chain C, Crystal Structure Of The Oct-1 Pou Domain Bound To An
Octamer Site: Dna Recognition With Tethered Dna-Binding
Modules
Length = 156
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 30/60 (50%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
R++ R + + LEK F N+ T IA L + + I++WF NRR K K+ N
Sbjct: 96 RRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKRIN 155
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 29.3 bits (64), Expect = 3.2, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 29/60 (48%)
Query: 238 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEN 297
RKR R + LE F + ++ IA+ L L + +++WF NRR K K+ +
Sbjct: 8 RKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRSS 67
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 28.5 bits (62), Expect = 5.5, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 4/51 (7%)
Query: 249 QTLELEKEFHF----NRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 295
Q E+ E+ + N Y + + E+A +T Q+ WF N+R+++KK
Sbjct: 13 QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
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
0.316 0.134 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,291,610
Number of Sequences: 62578
Number of extensions: 395675
Number of successful extensions: 1104
Number of sequences better than 100.0: 88
Number of HSP's better than 100.0 without gapping: 81
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1022
Number of HSP's gapped (non-prelim): 89
length of query: 317
length of database: 14,973,337
effective HSP length: 99
effective length of query: 218
effective length of database: 8,778,115
effective search space: 1913629070
effective search space used: 1913629070
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)