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= 015772
(400 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 38.9 bits (89), Expect = 0.005, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 28/57 (49%)
Query: 231 STRKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
S + K +S Q AFLEE F+ +L + P QV VWF N+R R+K
Sbjct: 5 SPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 3/72 (4%)
Query: 228 NGCSTRKKLR---LSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRA 284
+G +K+ R +K Q+ LE F++ L+ L P QV++WFQN R
Sbjct: 3 DGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRY 62
Query: 285 RTKLKQTEVDCE 296
+TK Q E E
Sbjct: 63 KTKRAQNEKGYE 74
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 38.1 bits (87), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%)
Query: 233 RKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTKLKQTE 292
++++ +K Q+ LE F++ L+ L P QV++WFQN R +TK Q E
Sbjct: 14 KRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRAQNE 73
Query: 293 VDCE 296
E
Sbjct: 74 KGYE 77
>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 = 37.7 bits (86), Expect = 0.011, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 28/57 (49%)
Query: 231 STRKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
S + K +S Q AFLE+ F+ +L + P QV VWF N+R R+K
Sbjct: 5 SPKGKSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 37.7 bits (86), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%)
Query: 238 LSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
+S Q AFLE+ F+ +L + P QV VWF N+R R+K
Sbjct: 372 ISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>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 = 37.4 bits (85), Expect = 0.016, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 33/62 (53%)
Query: 226 DENGCSTRKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRAR 285
+ NG + R++ ++ Q+ LE+ F + LT +L RQ+++WFQNRR +
Sbjct: 23 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK 82
Query: 286 TK 287
K
Sbjct: 83 WK 84
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 37.4 bits (85), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 28/53 (52%)
Query: 235 KLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
++R S Q+ LE+ F+ L+P L RQV+ WFQNRRA+ +
Sbjct: 11 QVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 37.4 bits (85), Expect = 0.017, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 30/60 (50%)
Query: 228 NGCSTRKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
NG R + ++ Q+ LE+ F + LT +L RQ+++WFQNRR + K
Sbjct: 17 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLK 76
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 36.6 bits (83), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%)
Query: 238 LSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
+S Q AFLE+ F+ +L + P QV VWF N+R R+K
Sbjct: 4 ISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 36.2 bits (82), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 31/58 (53%), Gaps = 1/58 (1%)
Query: 231 STRKKL-RLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
STRKK +K Q+ LE+ F + LT NL RQV++WFQNRR + K
Sbjct: 12 STRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMK 69
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 35.8 bits (81), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 26/49 (53%)
Query: 239 SKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
+K Q+ LE+ F + LT NL RQV++WFQNRR + K
Sbjct: 9 TKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 35.0 bits (79), Expect = 0.070, Method: Composition-based stats.
Identities = 21/61 (34%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 228 NGCSTRKK-LRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRART 286
+G S RKK + SK Q LE + + +T +L RQ+ +WFQNRR +
Sbjct: 3 SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKE 62
Query: 287 K 287
K
Sbjct: 63 K 63
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 34.7 bits (78), Expect = 0.11, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 27/55 (49%)
Query: 233 RKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
+K++ +K Q LE + + +T NL RQV +WFQNRR + K
Sbjct: 3 KKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>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 = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 25/50 (50%)
Query: 238 LSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
S +Q A L+ F E+ LT L Q+++WFQN+RA+ K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>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 = 33.9 bits (76), Expect = 0.18, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 21/45 (46%)
Query: 246 LEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTKLKQ 290
LE F L+ L QV++WFQNRR +TK KQ
Sbjct: 19 LERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 33.9 bits (76), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 25/50 (50%)
Query: 238 LSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
S +Q A L+ F E+ LT L Q+++WFQN+RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 33.9 bits (76), Expect = 0.19, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 28/59 (47%)
Query: 229 GCSTRKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
G S R++ + +Q LE+ F L+ L QV++WFQNRRA+ K
Sbjct: 5 GKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 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 = 33.1 bits (74), Expect = 0.27, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 27/55 (49%)
Query: 233 RKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
+ ++ S+ Q LE FK+ L+ L QV++WFQNRR ++K
Sbjct: 4 KPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 33.1 bits (74), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 27/55 (49%)
Query: 233 RKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
+K++ +K Q LE + + +T NL RQV +WFQNRR + K
Sbjct: 9 KKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 33.1 bits (74), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 28/55 (50%)
Query: 233 RKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
++++ S+ Q LE FK+ L+ +L P QV++WFQN R + K
Sbjct: 4 KRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMK 58
>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 = 32.7 bits (73), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 36/80 (45%), Gaps = 5/80 (6%)
Query: 219 DGCSELEDENGCSTRKKLR-----LSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPR 273
+ S+ E E G + ++K R S Q LE +F+ NL
Sbjct: 1 EDISDCESEPGIALKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEA 60
Query: 274 QVEVWFQNRRARTKLKQTEV 293
+++VWFQNRRAR + + T V
Sbjct: 61 RIQVWFQNRRARLRKQHTSV 80
>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 = 32.7 bits (73), Expect = 0.38, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 232 TRKKLR--LSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTKLK 289
T++K+R S+ Q L++ F++ L+ NL +QV+ WFQN+R + K
Sbjct: 2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW 61
Query: 290 Q 290
Q
Sbjct: 62 Q 62
>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 = 32.7 bits (73), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 24/50 (48%)
Query: 238 LSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
S +Q A L+ F E+ LT L Q+++WFQN RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57
>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 = 32.3 bits (72), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 25/50 (50%)
Query: 238 LSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
S +Q A L+ F E+ LT L Q+++WF+N+RA+ K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 32.3 bits (72), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 24/48 (50%)
Query: 238 LSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRAR 285
S +Q A L+ F E+ LT L Q+++WFQN+RA+
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>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 = 32.3 bits (72), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 24/50 (48%)
Query: 238 LSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
S +Q A L+ F E+ LT L Q+++WFQN RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 57
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 32.3 bits (72), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%)
Query: 246 LEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
LE F++ L+ +L QV++WFQNRRA+ K
Sbjct: 15 LERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>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 = 32.0 bits (71), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 32/61 (52%)
Query: 231 STRKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTKLKQ 290
S R + ++ Q+ LE+ F + +T +L RQ+++WFQNRR ++K +
Sbjct: 3 SKRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKDR 62
Query: 291 T 291
T
Sbjct: 63 T 63
>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 = 32.0 bits (71), Expect = 0.64, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 28/55 (50%)
Query: 233 RKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
R + ++ Q+ LE+ F + LT +L RQ+++WFQNRR + K
Sbjct: 4 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 31.6 bits (70), Expect = 0.71, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 28/55 (50%)
Query: 233 RKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
R + ++ Q+ LE+ F + LT +L RQ+++WFQNRR + K
Sbjct: 5 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 59
>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 = 31.6 bits (70), Expect = 0.74, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 26/49 (53%)
Query: 239 SKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
++ Q+ LE+ F + LT +L RQ+++WFQNRR + K
Sbjct: 4 TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 52
>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 = 31.2 bits (69), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 24/50 (48%)
Query: 238 LSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
S +Q A L+ F E+ LT L Q+++WF N+RA+ K
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 30.8 bits (68), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 27/59 (45%)
Query: 229 GCSTRKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
G R + S +Q A + F E+ LT L Q+++WFQN+RA+ +
Sbjct: 1 GDEKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIR 59
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 30.8 bits (68), Expect = 1.4, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 25/53 (47%)
Query: 233 RKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRAR 285
R + + +Q LE F+E +LR +VEVWF+NRRA+
Sbjct: 9 RHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAK 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 = 30.8 bits (68), Expect = 1.4, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 27/55 (49%)
Query: 233 RKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
R + ++ Q+ LE+ F + LT L RQ+++WFQNRR + K
Sbjct: 4 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 58
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 30.4 bits (67), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 24/48 (50%)
Query: 242 QSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTKLK 289
Q A LE+ F + LT L QV++WF+NRR R K++
Sbjct: 13 QIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ 60
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 30.0 bits (66), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 229 GCSTRKKLRLSKQQS--AFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRART 286
G S R+K R S + + LE+SF E+ T N+ + VWF NRR +
Sbjct: 97 GLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKE 156
Query: 287 K 287
K
Sbjct: 157 K 157
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 29.6 bits (65), Expect = 2.9, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 228 NGCSTRKKLRL-SKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRART 286
+G S RK + S Q A L+ F++ L L QV++WFQN+R++
Sbjct: 3 SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKI 62
Query: 287 K 287
K
Sbjct: 63 K 63
>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 = 29.6 bits (65), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 229 GCSTRKKLRLSKQQS--AFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRART 286
G S R+K R S + + LE+SF E+ T N+ + VWF NRR +
Sbjct: 96 GLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKE 155
Query: 287 K 287
K
Sbjct: 156 K 156
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 29.6 bits (65), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 22/30 (73%), Gaps = 2/30 (6%)
Query: 269 NLRPRQVEVWFQNRRARTKLKQTEVDCEYL 298
NL ++++WFQNRRA KLK++ + ++L
Sbjct: 39 NLELDRIQIWFQNRRA--KLKRSHRESQFL 66
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 29.6 bits (65), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 18/42 (42%)
Query: 246 LEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
LE F EH+ + NL V VWF NRR R K
Sbjct: 102 LERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 143
>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 = 29.3 bits (64), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 28/59 (47%)
Query: 229 GCSTRKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
G + R + ++ Q LE+ F + ++ NL R +++WFQNRR + K
Sbjct: 1 GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWK 59
>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 = 29.3 bits (64), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 23/50 (46%)
Query: 238 LSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
S +Q A L+ F E+ LT L QV+ WF+N RA+ K
Sbjct: 11 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 28.9 bits (63), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 21/42 (50%)
Query: 246 LEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
L + F+ L+ NL +QV+ WFQN+R ++K
Sbjct: 37 LNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSK 78
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 28.9 bits (63), Expect = 6.0, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 247 EESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTK 287
+ F E+ LT L Q+++WFQN+RA+ K
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>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 = 28.5 bits (62), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 229 GCSTRKKLRLSKQQS--AFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRART 286
G S R+K R S + + LE+SF E+ T N+ + VWF NRR +
Sbjct: 100 GLSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKE 159
Query: 287 K 287
K
Sbjct: 160 K 160
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 28.5 bits (62), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 29/62 (46%)
Query: 229 GCSTRKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTKL 288
G R++ + QQ LE +F+ + NL +V VWF+NRRA+ +
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 289 KQ 290
++
Sbjct: 61 RE 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 = 28.1 bits (61), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 229 GCSTRKKLRLSKQQS--AFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRART 286
G S R+K R S + + LE+SF E+ T N+ + VWF NRR +
Sbjct: 99 GLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKE 158
Query: 287 K 287
K
Sbjct: 159 K 159
>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 = 28.1 bits (61), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 29/62 (46%)
Query: 229 GCSTRKKLRLSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRARTKL 288
G R++ + QQ LE +F+ + NL +V VWF+NRRA+ +
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 289 KQ 290
++
Sbjct: 61 RE 62
>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 = 28.1 bits (61), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 229 GCSTRKKLRLSKQQS--AFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRRART 286
G S R+K R S + + LE+SF E+ T N+ + VWF NRR +
Sbjct: 92 GLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKE 151
Query: 287 K 287
K
Sbjct: 152 K 152
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 28.1 bits (61), Expect = 9.9, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 31/69 (44%), Gaps = 2/69 (2%)
Query: 226 DENGCSTRKKLR--LSKQQSAFLEESFKEHTTLTPXXXXXXXXXXNLRPRQVEVWFQNRR 283
E G + LR + +Q LE+ F + L+ L QV++WFQNRR
Sbjct: 27 SEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRR 86
Query: 284 ARTKLKQTE 292
+ K ++ E
Sbjct: 87 MKQKKRERE 95
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 0.129 0.382
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,175,310
Number of Sequences: 62578
Number of extensions: 168413
Number of successful extensions: 445
Number of sequences better than 100.0: 62
Number of HSP's better than 100.0 without gapping: 54
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 391
Number of HSP's gapped (non-prelim): 62
length of query: 400
length of database: 14,973,337
effective HSP length: 101
effective length of query: 299
effective length of database: 8,652,959
effective search space: 2587234741
effective search space used: 2587234741
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)