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= 023725
(278 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 51.2 bits (121), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 26/51 (50%), Positives = 32/51 (62%)
Query: 44 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
R + DQ LEK FE + L P + +LAK L L RQV WFQNRRA+W+
Sbjct: 13 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
>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 = 47.8 bits (112), Expect = 6e-06, Method: Composition-based stats.
Identities = 24/59 (40%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 41 KKRRLTVDQVQFLE--KSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97
K++R + + Q LE K F L R+I++A L L RQ+ IWFQNRR +WK +
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH 87
>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 = 47.8 bits (112), Expect = 7e-06, Method: Composition-based stats.
Identities = 26/62 (41%), Positives = 34/62 (54%), Gaps = 2/62 (3%)
Query: 41 KKRRLTVDQVQFLE--KSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQL 98
K+ R T + Q LE K F L R+I++A L L RQ+ IWFQNRR +WK +
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 62
Query: 99 EK 100
K
Sbjct: 63 TK 64
>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 = 47.8 bits (112), Expect = 7e-06, Method: Composition-based stats.
Identities = 22/48 (45%), Positives = 28/48 (58%)
Query: 53 LEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEK 100
LEK F L R+I++A L L RQ+ IWFQNRR +WK + K
Sbjct: 17 LEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK 64
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 47.4 bits (111), Expect = 8e-06, Method: Composition-based stats.
Identities = 27/60 (45%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 40 EKKR-RLTVDQVQFLE--KSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 96
E+KR R T + Q LE K F L R+I++A L L RQ+ IWFQNRR +WK +
Sbjct: 2 ERKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
>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 = 47.4 bits (111), Expect = 8e-06, Method: Composition-based stats.
Identities = 22/48 (45%), Positives = 28/48 (58%)
Query: 53 LEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEK 100
LEK F L R+I++A L L RQ+ IWFQNRR +WK + K
Sbjct: 11 LEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK 58
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 47.0 bits (110), Expect = 1e-05, Method: Composition-based stats.
Identities = 25/56 (44%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 41 KKRR--LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
++RR T +Q+ LEK F + L + Q+A L L QV IWFQNRRA+WK
Sbjct: 8 RRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 45.8 bits (107), Expect = 3e-05, Method: Composition-based stats.
Identities = 20/44 (45%), Positives = 27/44 (61%)
Query: 53 LEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 96
LEK F + L R+I++A L L RQ+ IWFQNRR + K +
Sbjct: 35 LEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 45.4 bits (106), Expect = 3e-05, Method: Composition-based stats.
Identities = 22/46 (47%), Positives = 28/46 (60%)
Query: 49 QVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
Q+ LEK FE + L +I LA+ LGL QV W+QNRR +WK
Sbjct: 28 QLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
>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 = 44.3 bits (103), Expect = 7e-05, Method: Composition-based stats.
Identities = 24/53 (45%), Positives = 30/53 (56%)
Query: 49 QVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKD 101
QV LE+ F + L + LAK+L L QV IWFQNRR + K KQL +
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLSSE 67
>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 = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/52 (40%), Positives = 30/52 (57%)
Query: 46 TVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97
T Q+ LEK F + R+++LA L L R + IWFQNRR +WK ++
Sbjct: 11 TRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 30/55 (54%)
Query: 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 99
T Q+ LEK F L R++++A L L QV IWFQNRR + K ++ E
Sbjct: 41 FTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 95
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 26/69 (37%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 39 PEKKRR----LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
P KKR+ T Q LE+ F + L + L + L P QV IWFQN R + K
Sbjct: 9 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTK 68
Query: 95 TKQLEKDYD 103
Q EK Y+
Sbjct: 69 RAQNEKGYE 77
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 41.2 bits (95), Expect = 6e-04, Method: Composition-based stats.
Identities = 26/62 (41%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 40 EKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 99
+K+ T Q LEK F L +R+ ++A+ L L RQV IWFQNRR K K++
Sbjct: 15 KKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM--KMKKIN 72
Query: 100 KD 101
KD
Sbjct: 73 KD 74
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/66 (37%), Positives = 35/66 (53%), Gaps = 2/66 (3%)
Query: 40 EKKRRLTVDQVQF--LEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97
++KRR+ + Q LE+ F + L + LA + L P QV IWFQN R + K Q
Sbjct: 9 KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68
Query: 98 LEKDYD 103
EK Y+
Sbjct: 69 NEKGYE 74
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 1/67 (1%)
Query: 46 TVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVL 105
T QV LEK F + L + LA+ L + QV WFQNRR +W+ +Q ++ +
Sbjct: 25 TRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWR-RQTAEEREAE 83
Query: 106 QNSYNSL 112
+ + N L
Sbjct: 84 RQAANRL 90
>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 = 40.0 bits (92), Expect = 0.001, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 39/64 (60%), Gaps = 5/64 (7%)
Query: 39 PEKKRR-----LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARW 93
P++K+R T Q++ LEK+F + + + +LA +GL ++ +WFQNRRA+W
Sbjct: 2 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKW 61
Query: 94 KTKQ 97
+ ++
Sbjct: 62 RKQE 65
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 20/42 (47%), Positives = 26/42 (61%)
Query: 53 LEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
LEK F L +R+ ++A+ L L RQV IWFQNRR + K
Sbjct: 16 LEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 32/49 (65%)
Query: 49 QVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97
Q++ LEK+F + + + +LA +GL ++ +WFQNRRA+W+ ++
Sbjct: 10 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 39.3 bits (90), Expect = 0.002, Method: Composition-based stats.
Identities = 23/62 (37%), Positives = 33/62 (53%), Gaps = 2/62 (3%)
Query: 41 KKRRLTVDQVQF--LEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQL 98
+KRR+ Q Q LE+ F+ + L + LA + L P QV IWFQN R + K +
Sbjct: 3 RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62
Query: 99 EK 100
+K
Sbjct: 63 DK 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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 29/47 (61%)
Query: 48 DQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
+Q+ L++ F L R+ QL+ +LGL Q+ IWFQN+RA+ K
Sbjct: 13 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 29/47 (61%)
Query: 48 DQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
+Q+ L++ F L R+ QL+ +LGL Q+ IWFQN+RA+ K
Sbjct: 11 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 39.3 bits (90), Expect = 0.002, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 34/59 (57%)
Query: 38 QPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 96
Q + T +Q++ LE++FE + + + +LA+ L +V +WF NRRARW+ +
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 32/49 (65%)
Query: 49 QVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97
Q++ LEK+F + + + +LA +GL ++ +WFQNRRA+W+ ++
Sbjct: 10 QLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 19/48 (39%), Positives = 26/48 (54%)
Query: 49 QVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 96
QV LE+ F + L + LAK L + QV WFQNRR +W+ +
Sbjct: 8 QVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>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 = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 23/56 (41%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 41 KKRRLTVDQVQFLE--KSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
K+ R T + Q LE K F + R+I +A L L RQ+ IWFQNRR + K
Sbjct: 4 KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSK 59
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 29/48 (60%)
Query: 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 92
+ +Q+ L++ F L R+ QL+ +LGL Q+ IWFQN+RA+
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 35/61 (57%), Gaps = 4/61 (6%)
Query: 41 KKRR----LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 96
KKRR T Q++ LEK F+ + + + QLA L +V +WFQNRRA+W+ +
Sbjct: 8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR 67
Query: 97 Q 97
+
Sbjct: 68 E 68
>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 = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 25/41 (60%)
Query: 52 FLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 92
FLE+ F + L + K ++AK G+ P QV +WF N+R R
Sbjct: 379 FLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 419
>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 = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 27/48 (56%)
Query: 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 92
T DQ+ LEK F EN + R+ +LA L L + +WFQNRR +
Sbjct: 8 FTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMK 55
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 38.1 bits (87), Expect = 0.005, Method: Composition-based stats.
Identities = 18/46 (39%), Positives = 27/46 (58%)
Query: 49 QVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
Q+ L++ F+ L + +LA LGL QV IWFQN+R++ K
Sbjct: 18 QLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 63
>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 = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 28/47 (59%)
Query: 48 DQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
+Q+ L++ F L R+ QL+ +LGL Q+ IWFQN RA+ K
Sbjct: 11 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 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 = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 40 EKKRR--LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
EK+ R + +Q+ L++ F L R+ QL+ +LGL Q+ IWF+N+RA+ K
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>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 = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/47 (40%), Positives = 28/47 (59%)
Query: 48 DQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
+Q+ L++ F L R+ QL+ +LGL Q+ IWFQN RA+ K
Sbjct: 11 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 57
>pdb|1DU0|A Chain A, Engrailed Homeodomain Q50a Variant Dna Complex
pdb|1DU0|B Chain B, Engrailed Homeodomain Q50a Variant Dna Complex
Length = 57
Score = 37.0 bits (84), Expect = 0.011, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 29/50 (58%)
Query: 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
+ +Q+ L++ F L R+ QL+ +LGL Q+ IWF N+RA+ K
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>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 = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 31/56 (55%)
Query: 39 PEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
P+ K ++ FLE+ F + L + K ++AK G+ P QV +WF N+R R K
Sbjct: 6 PKGKSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 26/43 (60%)
Query: 52 FLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
FLE+ F + L + K ++AK G+ P QV +WF N+R R K
Sbjct: 11 FLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 31/56 (55%)
Query: 39 PEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
P+ K ++ FLE+ F + L + K ++AK G+ P QV +WF N+R R K
Sbjct: 6 PKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 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 = 37.0 bits (84), Expect = 0.012, Method: Composition-based stats.
Identities = 13/27 (48%), Positives = 18/27 (66%)
Query: 80 RQVAIWFQNRRARWKTKQLEKDYDVLQ 106
RQ+ IWFQNRR +WK + D++Q
Sbjct: 1 RQIKIWFQNRRMKWKKRVFNDARDIIQ 27
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 37.0 bits (84), Expect = 0.013, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 41 KKRRLTVDQVQF--LEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
+K+R+ +VQ LE+ + + +++ +++ L RQV IWFQNRR + K
Sbjct: 8 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 36.6 bits (83), Expect = 0.017, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 34/60 (56%)
Query: 38 QPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97
Q ++ T Q+Q LE +F+ + + + ++A L +V +WF+NRRA+W+ ++
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 92
+ +Q+ ++ F L R+ QL+ +LGL Q+ IWFQN+RA+
Sbjct: 10 FSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 36.2 bits (82), Expect = 0.018, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 30/58 (51%)
Query: 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDY 102
T +Q++ LE F V + LA+ L L+ ++ IWFQNRRA+ K E +
Sbjct: 8 FTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQF 65
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 39/61 (63%), Gaps = 8/61 (13%)
Query: 38 QPEKKRRL----TVDQVQFLEKSFEVENKLEPERKI--QLAKDLGLQPRQVAIWFQNRRA 91
+P++ +RL T +Q++ L + + +++ P RK+ +A ++GL+ R V +WFQN RA
Sbjct: 13 EPQRDKRLRTTITPEQLEILYQKYLLDS--NPTRKMLDHIAHEVGLKKRVVQVWFQNTRA 70
Query: 92 R 92
R
Sbjct: 71 R 71
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 36.2 bits (82), Expect = 0.020, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 41 KKRRLTVDQVQF--LEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
+K+R+ +VQ LE+ + + +++ +++ L RQV IWFQNRR + K
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>pdb|2L7F|P Chain P, Solution Structure Of The Pitx2 Homeodomain
pdb|2LKX|A Chain A, Nmr Structure Of The Homeodomain Of Pitx2 In Complex
With A Taatcc Dna Binding Site
Length = 68
Score = 35.8 bits (81), Expect = 0.024, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 33/60 (55%)
Query: 38 QPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97
Q ++ T Q+Q LE +F+ + + ++A L +V +WF+NRRA+W+ ++
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 35.8 bits (81), Expect = 0.024, Method: Composition-based stats.
Identities = 17/41 (41%), Positives = 25/41 (60%)
Query: 54 EKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
++ F L R+ QL+ +LGL Q+ IWFQN+RA+ K
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 35.8 bits (81), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 26/49 (53%)
Query: 46 TVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
T Q+ LE+ F + L + + + L L QV IWFQNRRA+ K
Sbjct: 8 TTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 35.8 bits (81), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 31/50 (62%)
Query: 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
T +Q++ LE F+ + + QLA+ + L+ +V +WF+NRRA+W+
Sbjct: 14 FTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 35.4 bits (80), Expect = 0.039, Method: Composition-based stats.
Identities = 15/53 (28%), Positives = 31/53 (58%)
Query: 49 QVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKD 101
Q++ ++ F + + + + QLA+ GL R + +WFQN RA+++ L ++
Sbjct: 18 QLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQE 70
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 35.0 bits (79), Expect = 0.044, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 39 PEKKRR-LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 96
P + R T Q+ LE+ F L R L+ L L QV IWF+NRR R K +
Sbjct: 2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ 60
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 34.7 bits (78), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 40 EKKRRLTVDQVQFLEKSFEVENKL-EPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
E +T DQV+ LE +F NK +P +A + GL Q WF+ R A W+
Sbjct: 3 EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 58
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 34.7 bits (78), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 30/50 (60%)
Query: 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
T +Q++ LEK FE + + + +LA + L ++ +WF NRRA+W+
Sbjct: 14 FTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWR 63
>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 = 34.7 bits (78), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 27/47 (57%)
Query: 48 DQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
+Q+ L++ F L R+ QL+ +LGL QV WF+N RA+ K
Sbjct: 14 EQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>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 = 34.7 bits (78), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 20/42 (47%), Positives = 24/42 (57%)
Query: 49 QVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 90
QV LE+ F+ + L + QLA L L QV IWFQNRR
Sbjct: 13 QVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR 54
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 34.3 bits (77), Expect = 0.082, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 41 KKRRL--TVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
+K+R+ + Q++ LE+ + + +++ +++ L RQ+ IWFQNRR + K
Sbjct: 8 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 63
>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 = 33.9 bits (76), Expect = 0.092, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 27/54 (50%)
Query: 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQL 98
L Q+ L + + + K QL + GL PR + +WFQN+R + K + +
Sbjct: 10 LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 49/100 (49%), Gaps = 9/100 (9%)
Query: 4 FEDVHLA--NGSNNRPFFRPFDRDENGDEDFDEY-----FHQPEKKRRLTVD-QVQF-LE 54
FE + L+ N S RP + + + +E+ E Q K++R +++ +V++ LE
Sbjct: 53 FEALQLSLKNMSKLRPLLEKWVEEADNNENLQEISKSETLVQARKRKRTSIENRVRWSLE 112
Query: 55 KSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
F K ++ +A LGL+ V +WF NRR + K
Sbjct: 113 TMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGK 152
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 46 TVDQVQFLEKSFEVENKL-EPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
T DQV+ LE +F NK +P +A + GL Q WF+ R A W+
Sbjct: 10 TEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 59
>pdb|3NAR|A Chain A, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And Homeoboxes
Protein 1, Homeodomain 4)
pdb|3NAR|B Chain B, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And Homeoboxes
Protein 1, Homeodomain 4)
Length = 96
Score = 32.7 bits (73), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 27/57 (47%)
Query: 46 TVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDY 102
T +Q+ L+ +F PE +LAK+ GL + WF + R WK L+ Y
Sbjct: 33 TPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLKWYY 89
>pdb|2J04|B Chain B, The Tau60-Tau91 Subcomplex Of Yeast Transcription Factor
Iiic
pdb|2J04|D Chain D, The Tau60-Tau91 Subcomplex Of Yeast Transcription Factor
Iiic
Length = 524
Score = 32.0 bits (71), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 36/72 (50%)
Query: 147 TELPVVNKQEPPQISEPVADSAASEGKVCKASVVACKQEDISSAKSDIFDSDSPNYTDGV 206
T++ V E P ++ +ADS + + V C ++ A+ D+ D + P++ D V
Sbjct: 247 TDVHVFKMCEKPSLTLSLADSLITTFDFLSPTTVVCGFKNGFVAEFDLTDPEVPSFYDQV 306
Query: 207 HSSLLETCDSSY 218
H S + + ++Y
Sbjct: 307 HDSYILSVSTAY 318
>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 = 32.0 bits (71), Expect = 0.43, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 41 KKRRLTVDQVQF-LEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
KKR V+F LEKSF K E + +A+ L ++ + +WF NRR + K
Sbjct: 3 KKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEK 57
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 31.6 bits (70), Expect = 0.47, Method: Composition-based stats.
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 80 RQVAIWFQNRRARWK 94
RQ+ IWFQNRR +WK
Sbjct: 1 RQIKIWFQNRRMKWK 15
>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 = 31.6 bits (70), Expect = 0.49, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 40 EKKRRLTVDQVQF--LEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 97
++K R Q Q L+ F+ + L ++ +L+ L L +QV WFQN+R + K Q
Sbjct: 3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ 62
>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To
A Dna Oligonucleotide
pdb|1FJL|B Chain B, Homeodomain From The Drosophila Paired Protein Bound To
A Dna Oligonucleotide
pdb|1FJL|C Chain C, Homeodomain From The Drosophila Paired Protein Bound To
A Dna Oligonucleotide
Length = 81
Score = 31.6 bits (70), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%)
Query: 45 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
+ Q+ LE++FE + + +LA+ L ++ +WFQNRRAR +
Sbjct: 25 FSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR 74
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 31.2 bits (69), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 34/60 (56%), Gaps = 2/60 (3%)
Query: 37 HQPEKKRRLTVDQVQ--FLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
++ ++KRR T+ LE+ F +K + +++A++L L+ V +WF NRR R K
Sbjct: 84 NERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 143
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 31.2 bits (69), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 65 PERKIQLAKDLGLQPRQVAIWFQNRRAR 92
P K +LA+ GL QV+ WF+NRR R
Sbjct: 521 PREKRELAEATGLTTTQVSNWFKNRRQR 548
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 31.2 bits (69), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 66 ERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
E K +LAK G+ QV+ WF N+R R+K
Sbjct: 32 EAKEELAKKCGITVSQVSNWFGNKRIRYK 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 = 30.0 bits (66), Expect = 1.4, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 2/60 (3%)
Query: 37 HQPEKKRRLTVDQ--VQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
H +K+R +++ LEKSF K E +A L ++ + +WF NRR + K
Sbjct: 4 HMRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 63
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 27/47 (57%)
Query: 42 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQN 88
+ R+T DQ++ L + F++ N E+ ++A GL + + WF+N
Sbjct: 11 RTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN 57
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 29.6 bits (65), Expect = 1.7, Method: Composition-based stats.
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 66 ERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
E K +LAK G+ QV+ WF N+R R+K
Sbjct: 34 EAKEELAKKCGITVSQVSNWFGNKRIRYK 62
>pdb|1B8I|B Chain B, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
pdb|2R5Y|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|B Chain B, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 63
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/29 (44%), Positives = 19/29 (65%)
Query: 66 ERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
E K +LA+ G+ QV+ WF N+R R+K
Sbjct: 32 EAKEELARKCGITVSQVSNWFGNKRIRYK 60
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 29.6 bits (65), Expect = 1.8, Method: Composition-based stats.
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 66 ERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
E K +LAK G+ QV+ WF N+R R+K
Sbjct: 32 EAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 81 QVAIWFQNRRARWK 94
Q+ IWFQNRR +WK
Sbjct: 2 QIKIWFQNRRMKWK 15
>pdb|3K2A|A Chain A, Crystal Structure Of The Homeobox Domain Of Human
Homeobox Protein Meis2
pdb|3K2A|B Chain B, Crystal Structure Of The Homeobox Domain Of Human
Homeobox Protein Meis2
Length = 67
Score = 29.3 bits (64), Expect = 2.6, Method: Composition-based stats.
Identities = 15/27 (55%), Positives = 17/27 (62%)
Query: 66 ERKIQLAKDLGLQPRQVAIWFQNRRAR 92
E+K QLA+D GL QV WF N R R
Sbjct: 29 EQKKQLAQDTGLTILQVNNWFINARRR 55
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 28.9 bits (63), Expect = 2.9, Method: Composition-based stats.
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 66 ERKIQLAKDLGLQPRQVAIWFQNRRARWK 94
E K +LAK G+ QV+ WF N+R R+K
Sbjct: 33 EAKEELAKKSGITVSQVSNWFGNKRIRYK 61
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 28.9 bits (63), Expect = 3.2, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 34 EYFHQPEKKRRLTVD-QVQF-LEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRA 91
E Q K++R +++ +V++ LE F K ++ +A LGL+ V +WF NRR
Sbjct: 2 ETLVQARKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQ 61
Query: 92 RWK 94
+ K
Sbjct: 62 KGK 64
>pdb|3D1N|I Chain I, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|J Chain J, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|K Chain K, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|L Chain L, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|M Chain M, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|N Chain N, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|O Chain O, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
pdb|3D1N|P Chain P, Structure Of Human Brn-5 Transcription Factor In Complex
With Corticotrophin-Releasing Hormone Gene Promoter
Length = 151
Score = 28.1 bits (61), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 7/73 (9%)
Query: 24 RDENGDEDFDEYFH-QPEKKRR----LTVDQVQFLEKSFEVENKLEPERKI-QLAKDLGL 77
R++ G ++ E+ +P KKR+ T ++ L FE +N L ++I + AK+L
Sbjct: 74 RNQEGQQNLXEFVGGEPSKKRKRRTSFTPQAIEALNAYFE-KNPLPTGQEITEXAKELNY 132
Query: 78 QPRQVAIWFQNRR 90
V +WF NRR
Sbjct: 133 DREVVRVWFSNRR 145
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
0.313 0.132 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,146,467
Number of Sequences: 62578
Number of extensions: 300233
Number of successful extensions: 801
Number of sequences better than 100.0: 92
Number of HSP's better than 100.0 without gapping: 85
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 716
Number of HSP's gapped (non-prelim): 92
length of query: 278
length of database: 14,973,337
effective HSP length: 98
effective length of query: 180
effective length of database: 8,840,693
effective search space: 1591324740
effective search space used: 1591324740
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 bits)