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= psy13591
(339 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 = 115 bits (288), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 53/79 (67%), Positives = 62/79 (78%)
Query: 257 LYPWMKSNQDASYSCKTGGGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQL 316
+YPWMK + + G KR R +Y+RYQTLELEKEFH+N+YL+R+RRIEIAH L L
Sbjct: 8 IYPWMKRVHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSL 67
Query: 317 TERQIKIWFQNRRMKLKKE 335
TERQIKIWFQNRRMK KKE
Sbjct: 68 TERQIKIWFQNRRMKWKKE 86
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 111 bits (277), Expect = 6e-25, Method: Compositional matrix adjust.
Identities = 55/80 (68%), Positives = 60/80 (75%), Gaps = 7/80 (8%)
Query: 256 TLYPWMKSNQDASYSCKTGGGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQ 315
T YPWM T G +R RQTY+RYQTLELEKEFH N YL+R+RRIE+AH L
Sbjct: 6 TFYPWMAI-------AGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALS 58
Query: 316 LTERQIKIWFQNRRMKLKKE 335
LTERQIKIWFQNRRMKLKKE
Sbjct: 59 LTERQIKIWFQNRRMKLKKE 78
>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 = 104 bits (260), Expect = 6e-23, Method: Compositional matrix adjust.
Identities = 49/59 (83%), Positives = 54/59 (91%)
Query: 277 NKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKKE 335
KR RQTY+RYQTLELEKEFH+N+YL+R+RRIEIAH L LTERQIKIWFQNRRMK KKE
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 60
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 104 bits (260), Expect = 6e-23, Method: Compositional matrix adjust.
Identities = 49/59 (83%), Positives = 54/59 (91%)
Query: 277 NKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKKE 335
KR RQTY+RYQTLELEKEFH+N+YL+R+RRIEIAH L LTERQIKIWFQNRRMK KKE
Sbjct: 3 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
>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 = 104 bits (259), Expect = 9e-23, Method: Compositional matrix adjust.
Identities = 49/59 (83%), Positives = 54/59 (91%)
Query: 277 NKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKKE 335
KR RQTY+RYQTLELEKEFH+N+YL+R+RRIEIAH L LTERQIKIWFQNRRMK KKE
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 60
>pdb|1FTZ|A Chain A, Nuclear Magnetic Resonance Solution Structure Of The Fushi
Tarazu Homeodomain From Drosophila And Comparison With
The Antennapedia Homeodomain
Length = 70
Score = 99.4 bits (246), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 44/62 (70%), Positives = 58/62 (93%)
Query: 277 NKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKKEK 336
+KR+RQTY+RYQTLELEKEFH+N+Y++R+RRI+IA+ L L+ERQIKIWFQNRRMK KK++
Sbjct: 3 SKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKDR 62
Query: 337 IV 338
+
Sbjct: 63 TL 64
>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 = 98.2 bits (243), Expect = 7e-21, Method: Compositional matrix adjust.
Identities = 45/53 (84%), Positives = 50/53 (94%)
Query: 283 TYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKKE 335
TY+RYQTLELEKEFH+N+YL+R+RRIEIAH L LTERQIKIWFQNRRMK KKE
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 54
>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 = 88.6 bits (218), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 43/61 (70%), Positives = 49/61 (80%)
Query: 275 GGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
G NKR+R Y+R Q LELEKEF +NKY+SR RR+E+A L LTER IKIWFQNRRMK KK
Sbjct: 1 GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
Query: 335 E 335
E
Sbjct: 61 E 61
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 81.3 bits (199), Expect = 8e-16, Method: Compositional matrix adjust.
Identities = 42/84 (50%), Positives = 52/84 (61%), Gaps = 4/84 (4%)
Query: 255 ATLYPWMKSNQDASYSCKTG----GGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEI 310
A + WMK ++ + K G R ++ Q ELEKEFH+NKYLSR RR+EI
Sbjct: 8 ARTFDWMKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEI 67
Query: 311 AHELQLTERQIKIWFQNRRMKLKK 334
A L+L E Q+KIWFQNRRMK KK
Sbjct: 68 AATLELNETQVKIWFQNRRMKQKK 91
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 80.9 bits (198), Expect = 9e-16, Method: Compositional matrix adjust.
Identities = 38/58 (65%), Positives = 47/58 (81%)
Query: 277 NKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
++ R Y++YQTLELEKEF +N YL+R 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 = 79.7 bits (195), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 37/61 (60%), Positives = 47/61 (77%)
Query: 274 GGGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLK 333
++ R Y+++QTLELEKEF +N YL+R RR E+A L LTERQ+KIWFQNRRMK+K
Sbjct: 10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMK 69
Query: 334 K 334
K
Sbjct: 70 K 70
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 75.9 bits (185), Expect = 3e-14, Method: Composition-based stats.
Identities = 36/63 (57%), Positives = 45/63 (71%)
Query: 274 GGGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLK 333
GG ++R R ++ Q LELEKEFH KYLS R +IAH L+L+E Q+KIWFQNRR K K
Sbjct: 4 GGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
Query: 334 KEK 336
+ K
Sbjct: 64 RIK 66
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 60.5 bits (145), Expect = 1e-09, Method: Composition-based stats.
Identities = 26/62 (41%), Positives = 39/62 (62%)
Query: 273 TGGGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKL 332
+G ++ R YS +Q L++ F +YL+ R E+A L LT+ Q+KIWFQN+R K+
Sbjct: 3 SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKI 62
Query: 333 KK 334
KK
Sbjct: 63 KK 64
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 60.5 bits (145), Expect = 1e-09, Method: Composition-based stats.
Identities = 28/57 (49%), Positives = 38/57 (66%)
Query: 278 KRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
+RSR ++ Q + LEK F KYLS RI++A L L++ Q+K W+QNRRMK KK
Sbjct: 18 RRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 60.1 bits (144), Expect = 2e-09, Method: Composition-based stats.
Identities = 28/62 (45%), Positives = 43/62 (69%)
Query: 273 TGGGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKL 332
+G ++ R YS+ Q ELE+E+ NK++++ +R +I+ L+ERQI IWFQNRR+K
Sbjct: 3 SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKE 62
Query: 333 KK 334
KK
Sbjct: 63 KK 64
>pdb|3A01|A Chain A, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
pdb|3A01|E Chain E, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
Length = 93
Score = 59.3 bits (142), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 28/67 (41%), Positives = 42/67 (62%)
Query: 269 YSCKTGGGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNR 328
Y +T K+ R +++R Q ELEK FH KYL+ R +A L++T+ Q+K WFQNR
Sbjct: 9 YQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNR 68
Query: 329 RMKLKKE 335
R K +++
Sbjct: 69 RTKWRRQ 75
>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 = 58.5 bits (140), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 30/59 (50%), Positives = 41/59 (69%)
Query: 278 KRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKKEK 336
+R R ++R Q LEKEF+ Y+SR RR E+A +L L E IK+WFQNRRMK K+++
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR 60
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|1HDD|D Chain D, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|2JWT|A Chain A, Solution Structure Of Engrailed Homeodomain Wt
Length = 61
Score = 58.5 bits (140), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 29/57 (50%), Positives = 41/57 (71%)
Query: 278 KRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
KR R +S Q L++EF+ N+YL+ +RR +++ EL L E QIKIWFQN+R K+KK
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 57.8 bits (138), Expect = 9e-09, Method: Composition-based stats.
Identities = 29/57 (50%), Positives = 41/57 (71%)
Query: 278 KRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
KR R +S Q L++EF+ N+YL+ +RR +++ EL 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 = 57.4 bits (137), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/59 (47%), Positives = 41/59 (69%)
Query: 276 GNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
KR R +S Q L++EF+ N+YL+ +RR +++ EL L E QIKIWF+N+R K+KK
Sbjct: 2 AEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>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 = 57.0 bits (136), Expect = 1e-08, Method: Composition-based stats.
Identities = 29/57 (50%), Positives = 40/57 (70%)
Query: 278 KRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
KR R +S Q L++EF+ N+YL+ +RR +++ EL L E QIKIWFQN R K+KK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>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 = 57.0 bits (136), Expect = 2e-08, Method: Composition-based stats.
Identities = 29/57 (50%), Positives = 40/57 (70%)
Query: 278 KRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
KR R +S Q L++EF+ N+YL+ +RR +++ EL L E QIKIWFQN R K+KK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
>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 = 56.6 bits (135), Expect = 2e-08, Method: Composition-based stats.
Identities = 26/50 (52%), Positives = 37/50 (74%)
Query: 288 QTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKKEKI 337
Q +ELE++F + KYLS R +A L+LTE Q+KIWFQNRR K K++++
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL 64
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 56.6 bits (135), Expect = 2e-08, Method: Composition-based stats.
Identities = 26/57 (45%), Positives = 36/57 (63%)
Query: 278 KRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
++ R ++ Q L LE++F +YLS R E + L LTE Q+KIWFQNRR K K+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 55.8 bits (133), Expect = 3e-08, Method: Composition-based stats.
Identities = 27/60 (45%), Positives = 41/60 (68%)
Query: 275 GGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
G KR R +S Q ++EF+ N+YL+ +RR +++ EL L E QIKIWFQN+R K+++
Sbjct: 1 GDEKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
>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 = 28/51 (54%), Positives = 36/51 (70%)
Query: 284 YSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
+S QT+ELEK+F KYLS R +A LQL+ERQ+K WFQNRR K ++
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 55.8 bits (133), Expect = 4e-08, Method: Composition-based stats.
Identities = 24/53 (45%), Positives = 36/53 (67%)
Query: 283 TYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKKE 335
++SR Q LELE+ F KYL+ R +A L++T+ Q+K WFQNRR K +++
Sbjct: 3 SFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>pdb|3RKQ|A Chain A, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
pdb|3RKQ|B Chain B, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
Length = 58
Score = 55.5 bits (132), Expect = 5e-08, Method: Composition-based stats.
Identities = 27/58 (46%), Positives = 37/58 (63%)
Query: 276 GNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLK 333
G ++ R +S+ Q ELE+ F +YLS R ++A L+LT Q+KIWFQNRR K K
Sbjct: 1 GRRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|1DU0|A Chain A, Engrailed Homeodomain Q50a Variant Dna Complex
pdb|1DU0|B Chain B, Engrailed Homeodomain Q50a Variant Dna Complex
Length = 57
Score = 55.1 bits (131), Expect = 6e-08, Method: Composition-based stats.
Identities = 27/56 (48%), Positives = 39/56 (69%)
Query: 279 RSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
R R +S Q L++EF+ N+YL+ +RR +++ EL L E QIKIWF N+R K+KK
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 54.7 bits (130), Expect = 7e-08, Method: Composition-based stats.
Identities = 25/57 (43%), Positives = 40/57 (70%)
Query: 278 KRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
++ R Y++ Q ELE+E+ NK++++ +R I+ L+ERQ+ IWFQNRR+K KK
Sbjct: 8 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 54.7 bits (130), Expect = 8e-08, Method: Composition-based stats.
Identities = 25/57 (43%), Positives = 40/57 (70%)
Query: 278 KRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
++ R Y++ Q ELE+E+ NK++++ +R I+ L+ERQ+ IWFQNRR+K KK
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58
>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 = 54.3 bits (129), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 27/61 (44%), Positives = 40/61 (65%)
Query: 274 GGGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLK 333
G KR R +S Q L++EF+ N+YL+ +RR +++ EL L E Q+K WF+N R K+K
Sbjct: 1 GSDEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
Query: 334 K 334
K
Sbjct: 61 K 61
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 53.9 bits (128), Expect = 1e-07, Method: Composition-based stats.
Identities = 26/54 (48%), Positives = 38/54 (70%)
Query: 279 RSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKL 332
R R +S Q L++EF+ N+YL+ +RR +++ EL L E QIKIWFQN+R K+
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54
>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
pdb|1FJL|B Chain B, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
pdb|1FJL|C Chain C, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
Length = 81
Score = 53.1 bits (126), Expect = 2e-07, Method: Composition-based stats.
Identities = 26/58 (44%), Positives = 37/58 (63%)
Query: 278 KRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKKE 335
+RSR T+S Q ELE+ F +Y R E+A LTE +I++WFQNRR +L+K+
Sbjct: 19 RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 76
>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
pdb|3A01|F Chain F, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
Length = 67
Score = 51.2 bits (121), Expect = 7e-07, Method: Composition-based stats.
Identities = 26/61 (42%), Positives = 39/61 (63%)
Query: 278 KRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKKEKI 337
+R R T++ +Q ELEK F Y R E+A ++ LTE +I++WFQNRR K +K++
Sbjct: 7 RRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 66
Query: 338 V 338
V
Sbjct: 67 V 67
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 50.4 bits (119), Expect = 1e-06, Method: Composition-based stats.
Identities = 25/58 (43%), Positives = 37/58 (63%)
Query: 279 RSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKKEK 336
R R T++ +Q ELEK F Y R E+A ++ LTE +I++WFQNRR K +K++
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 49.7 bits (117), Expect = 2e-06, Method: Composition-based stats.
Identities = 25/59 (42%), Positives = 37/59 (62%)
Query: 280 SRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKKEKIV 338
S T++ +Q ELEK F Y R E+A ++ LTE +I++WFQNRR K +K++ V
Sbjct: 2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 60
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 49.7 bits (117), Expect = 3e-06, Method: Composition-based stats.
Identities = 23/58 (39%), Positives = 37/58 (63%)
Query: 276 GNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLK 333
G +R+R T++ Q ELE+ F +YL+ R +++ +L L Q+KIWF+NRR + K
Sbjct: 1 GPRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 49.3 bits (116), Expect = 3e-06, Method: Composition-based stats.
Identities = 23/60 (38%), Positives = 36/60 (60%)
Query: 276 GNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKKE 335
G +RSR T++ Q ELE+ F Y R E+A +LTE ++++WF NRR + +K+
Sbjct: 1 GQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|1NK2|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES
pdb|1NK3|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, MINIMIZED AVERAGE
Structure
pdb|1VND|A Chain A, VndNK-2 Protein (Homeodomain), Nmr
Length = 77
Score = 48.5 bits (114), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 36/58 (62%)
Query: 277 NKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
++ R +++ QT ELE+ F +YLS R +A ++LT Q+KIWFQN R K K+
Sbjct: 9 KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKR 66
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 47.8 bits (112), Expect = 8e-06, Method: Composition-based stats.
Identities = 23/42 (54%), Positives = 34/42 (80%)
Query: 293 EKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
++EF+ N+YL+ +RR +++ EL L E QIKIWFQN+R K+KK
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43
>pdb|2L7F|P Chain P, Solution Structure Of The Pitx2 Homeodomain
pdb|2LKX|A Chain A, Nmr Structure Of The Homeodomain Of Pitx2 In Complex With
A Taatcc Dna Binding Site
Length = 68
Score = 47.8 bits (112), Expect = 8e-06, Method: Composition-based stats.
Identities = 24/62 (38%), Positives = 35/62 (56%)
Query: 275 GGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
G +R R ++ Q ELE F N+Y R EIA LTE ++++WF+NRR K +K
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 335 EK 336
+
Sbjct: 61 RE 62
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 47.8 bits (112), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 25/59 (42%), Positives = 36/59 (61%)
Query: 277 NKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKKE 335
++ R +S+ Q ELE+ F KYLS R +A + LT Q+KIWFQN R K+K++
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 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 = 47.8 bits (112), Expect = 9e-06, Method: Composition-based stats.
Identities = 23/60 (38%), Positives = 37/60 (61%)
Query: 275 GGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
G ++ R +S+ Q L+ F KYLS ++ E++ L L+ +Q+K WFQN+RMK K+
Sbjct: 1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 47.0 bits (110), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/60 (41%), Positives = 36/60 (60%)
Query: 275 GGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
G +R+R T++ YQ ELEK F Y R ++A LTE ++++WFQNRR K +K
Sbjct: 7 GKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRK 66
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 277 NKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
++ R +++ QT ELE+ F +YLS R + ++LT Q+KIWFQN R K K+
Sbjct: 12 KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKR 69
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 24/62 (38%), Positives = 34/62 (54%)
Query: 275 GGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
G +R R ++ Q ELE F N Y R EIA LTE ++++WF+NRR K +K
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 335 EK 336
+
Sbjct: 61 RE 62
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 45.4 bits (106), Expect = 4e-05, Method: Composition-based stats.
Identities = 22/64 (34%), Positives = 38/64 (59%)
Query: 273 TGGGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKL 332
+G +R+R ++++ Q LEKEF Y R +A ++ L E +I++WF NRR K
Sbjct: 3 SGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKW 62
Query: 333 KKEK 336
++E+
Sbjct: 63 RREE 66
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 45.4 bits (106), Expect = 5e-05, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 35/61 (57%)
Query: 273 TGGGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKL 332
+G +R R T++R Q LE F +Y R E+A ++ L E ++++WF+NRR K
Sbjct: 3 SGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKC 62
Query: 333 K 333
+
Sbjct: 63 R 63
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 43.5 bits (101), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 37/63 (58%)
Query: 272 KTGGGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMK 331
K +++R +S Q L F KYLS ++ E+++ L L+ +Q+K WFQN+RMK
Sbjct: 17 KVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMK 76
Query: 332 LKK 334
K+
Sbjct: 77 SKR 79
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 34/62 (54%)
Query: 273 TGGGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKL 332
+G +R R ++ Q LE F KY R ++A ++ L E ++++WF+NRR K
Sbjct: 3 SGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKW 62
Query: 333 KK 334
++
Sbjct: 63 RR 64
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 32/57 (56%)
Query: 278 KRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
+R R +++ Q LE F N Y ++A +L L +I+IWFQNRR KLK+
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKR 58
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 37.4 bits (85), Expect = 0.012, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 34/58 (58%)
Query: 277 NKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
+KR R T + Q L +++ + +RK IAHE+ L +R +++WFQN R + +K
Sbjct: 17 DKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74
>pdb|1MH3|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form I
pdb|1MH4|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form Ii
Length = 421
Score = 37.4 bits (85), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 27/42 (64%)
Query: 292 LEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLK 333
LE+ F + L+ K + 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 = 35.4 bits (80), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 33/62 (53%)
Query: 273 TGGGNKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKL 332
+G KR R ++ +Q ++ F N K ++A + LT+R +++WFQN R K
Sbjct: 3 SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKF 62
Query: 333 KK 334
++
Sbjct: 63 RR 64
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 35.4 bits (80), Expect = 0.042, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 27/42 (64%)
Query: 292 LEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLK 333
LE+ F + L+ K + E+A + +T Q+++WF N+RM+ K
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|1DTZ|A Chain A, Structure Of Camel Apo-Lactoferrin Demonstrates Its Dual
Role In Sequestering And Transporting Ferric Ions
Simultaneously:crystal Structure Of Camel
Apo-Lactoferrin At 2.6a Resolution.
pdb|1I6Q|A Chain A, Formation Of A Protein Intermediate And Its Trapping By
The Simultaneous Crystallization Process: Crystal
Structure Of An Iron-Saturated Intermediate In The Fe3+
Binding Pathway Of Camel Lactoferrin At 2.7 Resolution
Length = 689
Score = 35.0 bits (79), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 41/95 (43%), Gaps = 11/95 (11%)
Query: 134 SFDKDAKYFDKDPAKY----YDNFLNHNAMNYNQMNAFNQFHMKLNPNHTDYLRTNSDKE 189
+F KD+ F+ PAK Y+ +N ++AF + H+ P+H R+ + KE
Sbjct: 207 AFVKDSTVFESLPAKADRDQYELLCPNN--TRKPVDAFQECHLARVPSHAVVARSVNGKE 264
Query: 190 TLNATNFVPKDEAISEMVDGKPPGFNMDRNGNPVG 224
L V E GKP F + G+P G
Sbjct: 265 DLIWKLLVKAQEKFGR---GKPSAFQL--FGSPAG 294
>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 = 35.0 bits (79), Expect = 0.068, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 27/42 (64%)
Query: 292 LEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLK 333
LE+ F + L+ K + E+A + +T Q+++WF N+RM+ K
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 34.7 bits (78), Expect = 0.072, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 27/42 (64%)
Query: 292 LEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLK 333
LE+ F + L+ K + E+A + +T Q+++WF N+RM+ K
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|2NZZ|A Chain A, Nmr Structure Analysis Of The Penetratin Conjugated Gas
(374-394) Peptide
pdb|2O00|A Chain A, Nmr Structure Analysis Of The Penetratin Conjugated Gas
(374-394) Peptide
Length = 37
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 15/16 (93%), Positives = 15/16 (93%)
Query: 319 RQIKIWFQNRRMKLKK 334
RQIKIWFQNRRMK KK
Sbjct: 1 RQIKIWFQNRRMKWKK 16
>pdb|1HDP|A Chain A, Solution Structure Of A Pou-Specific Homeodomain: 3d-Nmr
Studies Of Human B-Cell Transcription Factor Oct-2
Length = 63
Score = 33.9 bits (76), Expect = 0.13, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 30/57 (52%)
Query: 278 KRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
++ R + LEK F N+ + + + 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 = 33.5 bits (75), Expect = 0.17, Method: Composition-based stats.
Identities = 21/66 (31%), Positives = 35/66 (53%), Gaps = 3/66 (4%)
Query: 275 GGNKRSRQTYSRYQT---LELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMK 331
G + R R+ + +T + LEK F N+ + + IA +L + + I++WF NRR K
Sbjct: 2 GSHMRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 61
Query: 332 LKKEKI 337
K+ I
Sbjct: 62 EKRIDI 67
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 32.7 bits (73), Expect = 0.29, Method: Composition-based stats.
Identities = 15/16 (93%), Positives = 15/16 (93%)
Query: 319 RQIKIWFQNRRMKLKK 334
RQIKIWFQNRRMK KK
Sbjct: 1 RQIKIWFQNRRMKWKK 16
>pdb|1BW5|A Chain A, The Nmr Solution Structure Of The Homeodomain Of The Rat
Insulin Gene Enhancer Protein Isl-1, 50 Structures
Length = 66
Score = 32.3 bits (72), Expect = 0.37, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 7/62 (11%)
Query: 285 SRYQTLELEKEFHYNK--YLSRKR-----RIEIAHELQLTERQIKIWFQNRRMKLKKEKI 337
+R +T+ EK+ H + Y + R + ++ L+ R I++WFQN+R K KK I
Sbjct: 4 TRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63
Query: 338 VM 339
+M
Sbjct: 64 MM 65
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 32.3 bits (72), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 42/86 (48%), Gaps = 4/86 (4%)
Query: 255 ATLYPWMKSNQD--ASYSCKTGGG--NKRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEI 310
A L W++ + A Y+ K G ++ R T S LE+ F + S + + +
Sbjct: 61 AILSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRM 120
Query: 311 AHELQLTERQIKIWFQNRRMKLKKEK 336
A EL L + +++WF NRR + K+ K
Sbjct: 121 AEELNLEKEVVRVWFCNRRQREKRVK 146
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 31.6 bits (70), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 276 GNKRSRQTYSRYQT---LELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKL 332
G R R+ + +T + LEK F N+ + + IA +L + + I++WF NRR K
Sbjct: 97 GLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKE 156
Query: 333 KK 334
K+
Sbjct: 157 KR 158
>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 = 31.6 bits (70), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 276 GNKRSRQTYSRYQT---LELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKL 332
G R R+ + +T + LEK F N+ + + IA +L + + I++WF NRR K
Sbjct: 96 GLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKE 155
Query: 333 KK 334
K+
Sbjct: 156 KR 157
>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 = 31.6 bits (70), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 276 GNKRSRQTYSRYQT---LELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKL 332
G R R+ + +T + LEK F N+ + + IA +L + + I++WF NRR K
Sbjct: 99 GLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKE 158
Query: 333 KK 334
K+
Sbjct: 159 KR 160
>pdb|1OCT|C Chain C, Crystal Structure Of The Oct-1 Pou Domain Bound To An
Octamer Site: Dna Recognition With Tethered Dna-Binding
Modules
Length = 156
Score = 31.2 bits (69), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 276 GNKRSRQTYSRYQT---LELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKL 332
G R R+ + +T + LEK F N+ + + IA +L + + I++WF NRR K
Sbjct: 92 GLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKE 151
Query: 333 KK 334
K+
Sbjct: 152 KR 153
>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 = 0.97, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 35/61 (57%), Gaps = 5/61 (8%)
Query: 278 KRSRQTYSRYQTLELEKEFHY----NKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLK 333
+R R+ +S+ Q E+ E+ Y N Y S + + E+A + +T Q+ WF N+R++ K
Sbjct: 2 RRKRRNFSK-QASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
Query: 334 K 334
K
Sbjct: 61 K 61
>pdb|1KZ2|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain Derivative [w6f,W14f]
Length = 16
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/16 (87%), Positives = 15/16 (93%)
Query: 319 RQIKIWFQNRRMKLKK 334
RQIKI+FQNRRMK KK
Sbjct: 1 RQIKIFFQNRRMKFKK 16
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 30.8 bits (68), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 5/61 (8%)
Query: 278 KRSRQTYSRYQTLELEKEFHY----NKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLK 333
+R R+ +++ Q E+ E+ Y N Y S + + E+A + +T Q+ WF N+R++ K
Sbjct: 2 RRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 334 K 334
K
Sbjct: 61 K 61
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 30.8 bits (68), Expect = 1.0, Method: Composition-based stats.
Identities = 14/15 (93%), Positives = 14/15 (93%)
Query: 320 QIKIWFQNRRMKLKK 334
QIKIWFQNRRMK KK
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 30.8 bits (68), Expect = 1.2, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 26/51 (50%)
Query: 284 YSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
++ YQ L+ F N Y ++++ L L R I +WFQN R K +K
Sbjct: 14 FTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 4/51 (7%)
Query: 288 QTLELEKEFHY----NKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
Q E+ E+ Y N Y S + + E+A + +T Q+ WF N+R++ KK
Sbjct: 13 QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>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 = 30.4 bits (67), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 26/45 (57%)
Query: 290 LELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
+ LEK F N+ + + IA +L + + I++WF NRR K K+
Sbjct: 117 VALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 161
>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 = 14/40 (35%), Positives = 23/40 (57%)
Query: 292 LEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMK 331
L + + +N Y S + + E+A LT Q+ WF+NRR +
Sbjct: 509 LREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQR 548
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 5/61 (8%)
Query: 278 KRSRQTYSRYQTLELEKEFHY----NKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLK 333
+R R+ +++ Q E+ E+ Y N Y S + + E+A + +T Q+ WF N+R++ K
Sbjct: 2 RRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 334 K 334
K
Sbjct: 61 K 61
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 30.0 bits (66), Expect = 2.0, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 278 KRSRQTYSRYQTLELEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLKK 334
KR R + LE F S ++ IA++L L + +++WF NRR K K+
Sbjct: 9 KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 65
>pdb|1C02|A Chain A, Crystal Structure Of Yeast Ypd1p
pdb|1C02|B Chain B, Crystal Structure Of Yeast Ypd1p
Length = 166
Score = 30.0 bits (66), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 18/35 (51%)
Query: 176 PNHTDYLRTNSDKETLNATNFVPKDEAISEMVDGK 210
PN T+ + T SDK +N N DE I VD K
Sbjct: 96 PNKTELVNTLSDKSIINGINIDEDDEEIKIQVDDK 130
>pdb|1C03|A Chain A, Crystal Structure Of Ypd1p (Triclinic Form)
pdb|1C03|B Chain B, Crystal Structure Of Ypd1p (Triclinic Form)
pdb|1C03|C Chain C, Crystal Structure Of Ypd1p (Triclinic Form)
pdb|1C03|D Chain D, Crystal Structure Of Ypd1p (Triclinic Form)
Length = 168
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 18/35 (51%)
Query: 176 PNHTDYLRTNSDKETLNATNFVPKDEAISEMVDGK 210
PN T+ + T SDK +N N DE I VD K
Sbjct: 97 PNKTELVNTLSDKSIINGINIDEDDEEIKIQVDDK 131
>pdb|1OXB|A Chain A, Complex Between Ypd1 And Sln1 Response Regulator Domain In
Space Group P2(1)2(1)2(1)
pdb|1OXK|A Chain A, Complex Between Ypd1 And Sln1 Response Regulator Domain In
Space Group P3(2)
pdb|1OXK|C Chain C, Complex Between Ypd1 And Sln1 Response Regulator Domain In
Space Group P3(2)
pdb|1OXK|E Chain E, Complex Between Ypd1 And Sln1 Response Regulator Domain In
Space Group P3(2)
pdb|1OXK|G Chain G, Complex Between Ypd1 And Sln1 Response Regulator Domain In
Space Group P3(2)
pdb|1OXK|I Chain I, Complex Between Ypd1 And Sln1 Response Regulator Domain In
Space Group P3(2)
pdb|1OXK|K Chain K, Complex Between Ypd1 And Sln1 Response Regulator Domain In
Space Group P3(2)
Length = 166
Score = 30.0 bits (66), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 18/35 (51%)
Query: 176 PNHTDYLRTNSDKETLNATNFVPKDEAISEMVDGK 210
PN T+ + T SDK +N N DE I VD K
Sbjct: 96 PNKTELVNTLSDKSIINGINIDEDDEEIKIQVDDK 130
>pdb|2R25|A Chain A, Complex Of Ypd1 And Sln1-R1 With Bound Mg2+ And Bef3-
Length = 167
Score = 29.6 bits (65), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 18/35 (51%)
Query: 176 PNHTDYLRTNSDKETLNATNFVPKDEAISEMVDGK 210
PN T+ + T SDK +N N DE I VD K
Sbjct: 97 PNKTELVNTLSDKSIINGINIDEDDEEIKIQVDDK 131
>pdb|1QSP|A Chain A, Crystal Structure Of The Yeast Phosphorelay Protein Ypd1
pdb|1QSP|B Chain B, Crystal Structure Of The Yeast Phosphorelay Protein Ypd1
Length = 165
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/35 (42%), Positives = 18/35 (51%)
Query: 176 PNHTDYLRTNSDKETLNATNFVPKDEAISEMVDGK 210
PN T+ + T SDK +N N DE I VD K
Sbjct: 95 PNKTELVNTLSDKSIINGINIDEDDEEIKIQVDDK 129
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 29.3 bits (64), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 11/25 (44%), Positives = 17/25 (68%)
Query: 310 IAHELQLTERQIKIWFQNRRMKLKK 334
+A LQL + +++WF NRR K K+
Sbjct: 132 LADSLQLEKEVVRVWFCNRRQKEKR 156
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 29.3 bits (64), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 5/61 (8%)
Query: 278 KRSRQTYSRYQTLELEKEFHY----NKYLSRKRRIEIAHELQLTERQIKIWFQNRRMKLK 333
+R R+ +++ Q E+ E+ Y N Y S + + E+A + +T Q+ WF N+R++ K
Sbjct: 3 RRKRRNFNK-QATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
Query: 334 K 334
K
Sbjct: 62 K 62
>pdb|3D1N|I Chain I, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|J Chain J, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|K Chain K, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|L Chain L, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|M Chain M, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|N Chain N, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|O Chain O, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|P Chain P, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
Length = 151
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 29/64 (45%), Gaps = 3/64 (4%)
Query: 273 TGG--GNKRSRQTYSRYQTLE-LEKEFHYNKYLSRKRRIEIAHELQLTERQIKIWFQNRR 329
GG KR R+T Q +E L F N + + E A EL +++WF NRR
Sbjct: 86 VGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRR 145
Query: 330 MKLK 333
LK
Sbjct: 146 QTLK 149
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.314 0.130 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,239,699
Number of Sequences: 62578
Number of extensions: 411524
Number of successful extensions: 873
Number of sequences better than 100.0: 103
Number of HSP's better than 100.0 without gapping: 95
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 769
Number of HSP's gapped (non-prelim): 112
length of query: 339
length of database: 14,973,337
effective HSP length: 99
effective length of query: 240
effective length of database: 8,778,115
effective search space: 2106747600
effective search space used: 2106747600
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 bits)