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= psy4868
(169 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 126 bits (317), Expect = 5e-30, Method: Compositional matrix adjust.
Identities = 60/66 (90%), Positives = 63/66 (95%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118
QRNRTSFT +QI+ LEKEFERTHYPDVFARERLAAKI LPEARIQVWFSNRRAKWRREEK
Sbjct: 8 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 67
Query: 119 LRNQRQ 124
LRNQR+
Sbjct: 68 LRNQRR 73
>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
pdb|3A01|F Chain F, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
Length = 67
Score = 96.3 bits (238), Expect = 8e-21, Method: Compositional matrix adjust.
Identities = 43/61 (70%), Positives = 51/61 (83%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118
+R RT+FT+ Q++ LEK F RTHYPDVF RE LA KIGL EARIQVWF NRRAKWR++EK
Sbjct: 7 RRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 66
Query: 119 L 119
+
Sbjct: 67 V 67
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 94.0 bits (232), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 42/58 (72%), Positives = 48/58 (82%)
Query: 60 RNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117
R RT+FT+ Q++ LEK F RTHYPDVF RE LA KIGL EARIQVWF NRRAKWR++E
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 92.0 bits (227), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 40/59 (67%), Positives = 48/59 (81%)
Query: 61 NRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKL 119
+ +FT+ Q++ LEK F RTHYPDVF RE LA KIGL EARIQVWF NRRAKWR++EK+
Sbjct: 2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 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 = 90.5 bits (223), Expect = 4e-19, Method: Compositional matrix adjust.
Identities = 38/60 (63%), Positives = 50/60 (83%)
Query: 60 RNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKL 119
RNRT+FT+ Q++ LEK F++THYPDV+ARE+LA + L EAR+QVWF NRRAKWR+ E+
Sbjct: 11 RNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERF 70
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 85.5 bits (210), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 35/58 (60%), Positives = 49/58 (84%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116
+R+RT+FT +Q++ LE+ FERTHYPD++ RE LA + L EAR+QVWFSNRRA+WR++
Sbjct: 3 RRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
pdb|1FJL|B Chain B, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
pdb|1FJL|C Chain C, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
Length = 81
Score = 77.4 bits (189), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 33/58 (56%), Positives = 45/58 (77%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116
+R+RT+F+ Q+D LE+ FERT YPD++ RE LA + L EARIQVWF NRRA+ R++
Sbjct: 19 RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQ 76
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 76.6 bits (187), Expect = 6e-15, Method: Compositional matrix adjust.
Identities = 34/56 (60%), Positives = 42/56 (75%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114
+R RT+FT Q+D LE F +T YPD+F RE +A KI LPE+R+QVWF NRRAK R
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 72.8 bits (177), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 32/60 (53%), Positives = 41/60 (68%)
Query: 60 RNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKL 119
R RT FT+ Q+ LE F+R HYPD+ RE +A L EAR++VWF NRRAKWR+ E+
Sbjct: 5 RQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEF 64
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 72.4 bits (176), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 32/57 (56%), Positives = 44/57 (77%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
+R+RT FT++Q++ LE F+ T YPDV RE+LA K+ L E +++VWF NRRAKWRR
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64
>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 = 68.9 bits (167), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 31/61 (50%), Positives = 41/61 (67%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118
+R RT FT+ Q+ LE F+R YPD+ RE +A L EAR++VWF NRRAKWR+ E+
Sbjct: 4 RRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE 63
Query: 119 L 119
Sbjct: 64 F 64
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 59.7 bits (143), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 39/57 (68%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
+R RT+FT++Q+ LEKEF Y + R ++A + L E ++++WF NRRAKW+R
Sbjct: 8 RRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWKR 64
>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 = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/54 (51%), Positives = 37/54 (68%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
+R RT+FT DQ+ LEKEF + +Y R LAA++ LPE+ I+VWF NRR K
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMK 55
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 28/60 (46%), Positives = 37/60 (61%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118
+R RT+FT +QI+ LE F YP + E LA K+ L RIQ+WF NRRAK +R +
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 53.9 bits (128), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/51 (50%), Positives = 33/51 (64%)
Query: 65 FTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
F+NDQ LEK+FE Y R+RLA + L E +++ WF NRRAKWRR
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
>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 = 52.8 bits (125), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 35/59 (59%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117
+R RT++T Q+ LEKEF Y R LA + L E I++WF NRR KW++EE
Sbjct: 4 KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 52.4 bits (124), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 29/73 (39%), Positives = 41/73 (56%), Gaps = 2/73 (2%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118
+R RTSF + Q+ ++ F H PD ++LA K GL + +QVWF N RAK+RR
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRN-- 65
Query: 119 LRNQRQRGSADPT 131
L Q G + P+
Sbjct: 66 LLRQENGGVSGPS 78
>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 = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 24/55 (43%), Positives = 33/55 (60%)
Query: 62 RTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116
RTSFT Q+ LEK F + Y R LA + + +A+++ WF NRR KWRR+
Sbjct: 21 RTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQ 75
>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 = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/60 (43%), Positives = 35/60 (58%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118
+R RTS+T Q LEKEF Y R +A + L E +I++WF NRR KW++E K
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEHK 88
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 35/57 (61%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
+R+RT FT Q+ LEK FE+ Y R LA +GL + +++ W+ NRR KW++
Sbjct: 18 RRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKK 74
>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 = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 40/53 (75%)
Query: 60 RNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
R RT+F+++Q+ L++EF Y R++L++++GL EA+I++WF+N+RAK
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAK 53
>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 = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 40/54 (74%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
+R RT+F+++Q+ L++EF Y R++L++++GL EA+I++WF N+RAK
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAK 57
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 40/54 (74%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
+R RT+F+++Q+ L++EF Y R++L++++GL EA+I++WF N+RAK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 55
>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 = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 40/54 (74%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
+R RT+F+++Q+ L++EF Y R++L++++GL EA+I++WF N+RAK
Sbjct: 4 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 50.4 bits (119), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 41/57 (71%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
+R RT+F+++Q+ ++EF Y R++L++++GL EA+I++WF N+RAK RR
Sbjct: 4 KRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 50.1 bits (118), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 39/53 (73%)
Query: 60 RNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
R RT+F+++Q+ L++EF Y R++L++++GL EA+I++WF N+RAK
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>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 = 49.7 bits (117), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 39/54 (72%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
+R RT+F+++Q+ L++EF Y R++L++++GL EA+I++WF N RAK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAK 55
>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 = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 39/54 (72%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
+R RT+F+++Q+ L++EF Y R++L++++GL EA+I++WF N RAK
Sbjct: 2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK 55
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 32/54 (59%)
Query: 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116
TSF+ Q+ LE+ F R Y R LA + + +A+++ WF NRR KWRR+
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 37/54 (68%)
Query: 62 RTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
RT +++ Q+ L++ F++T Y + R LAA +GL + ++++WF N+R+K ++
Sbjct: 11 RTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKK 64
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 34/57 (59%)
Query: 62 RTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118
RT+FT Q+ LEKEF Y R +AA + L E ++++WF NRR K ++ E+
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER 94
>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 = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 34/60 (56%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118
+R R ++T Q LEKEF Y R +A + L E +I++WF NRR KW++E K
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 62
>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 = 47.0 bits (110), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 34/60 (56%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118
+R R ++T Q LEKEF Y R +A + L E +I++WF NRR KW++E K
Sbjct: 3 KRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK 62
>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 = 47.0 bits (110), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 38/54 (70%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
+R RT+F+++Q+ L++EF Y R++L++++GL EA+++ WF N RAK
Sbjct: 5 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAK 58
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 46.6 bits (109), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 33/54 (61%)
Query: 62 RTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
RT FT Q+ LE++F + Y + R ++ + L E ++++WF NRRAK +R
Sbjct: 4 RTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 35/61 (57%), Gaps = 6/61 (9%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARER---LAAKIGLPEARIQVWFSNRRAKWRR 115
+R R ++T Q LEKEF H+ R R +A + L E +I++WF NRR KW++
Sbjct: 4 KRGRQTYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 60
Query: 116 E 116
E
Sbjct: 61 E 61
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 33/58 (56%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRRE 116
+R R ++T Q LEKEF HY R +A + L E +I++WF NRR K ++E
Sbjct: 21 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 31/51 (60%)
Query: 60 RNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRR 110
R RT+FT+ QI LE+ F + Y L+AK+ L A++++WF NRR
Sbjct: 4 RTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRR 54
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 64 SFTNDQIDNLEKEFERTH-YPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKL 119
+ T DQ++ LE F + + +PD +AA+ GL E + Q WF R A+WRR E L
Sbjct: 7 TMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGL 63
>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 = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 31/55 (56%)
Query: 64 SFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118
++T Q LEKEF Y R +A + L E +I++WF NRR KW++E K
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENK 56
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 66 TNDQIDNLEKEFERTH-YPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKL 119
T DQ++ LE F + + +PD +AA+ GL E + Q WF R A+WRR E L
Sbjct: 10 TEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGL 64
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 43.1 bits (100), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 33/59 (55%)
Query: 60 RNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118
+ R F+ Q+ LE+ F++ Y RE LA+ I L ++++WF N R K +R+ K
Sbjct: 4 KRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62
>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 = 40.0 bits (92), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 30/51 (58%)
Query: 62 RTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
R F+ Q+ LE+ F++ Y R++LA+ + L ++++WF NRR K
Sbjct: 6 RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYK 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 = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 6/64 (9%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARER---LAAKIGLPEARIQVWFSNRRAKWRR 115
+R R ++T Q LEKEF H+ R R +A + L E +I++WF NRR K ++
Sbjct: 4 KRTRQTYTRYQTLELEKEF---HFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKK 60
Query: 116 EEKL 119
+ L
Sbjct: 61 DRTL 64
>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 = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 31/59 (52%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117
++ R FT Q LE+ F + Y RE LA+ I L ++++WF N R K +R +
Sbjct: 10 RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68
>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 = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 28/49 (57%)
Query: 69 QIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117
Q+ LE++F Y R LA + L E ++++WF NRR K +R++
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 28/39 (71%)
Query: 74 EKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
++EF Y R++L++++GL EA+I++WF N+RAK
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 40
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 29/54 (53%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
++ R +T Q+ LE+E+ + R R++A L E ++ +WF NRR K
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVK 55
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 29/54 (53%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
++ R +T Q+ LE+E+ + R R++A L E ++ +WF NRR K
Sbjct: 8 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVK 61
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 30/59 (50%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117
++ R FT Q LE+ F + Y RE L + I L ++++WF N R K +R +
Sbjct: 13 RKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRAQ 71
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 33/60 (55%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEK 118
Q+ RT F++ Q+ L F+R Y + + L+ + L +++ WF N+R K +R +K
Sbjct: 23 QKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQK 82
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 29/54 (53%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
++ R ++ Q+ LE+E+ + R +++A L E +I +WF NRR K
Sbjct: 8 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK 61
>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 = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 32/57 (56%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
Q+ RT F+ Q+ L+ F++ Y + + L++ + L +++ WF N+R K +R
Sbjct: 4 QKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 33/57 (57%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
+R RTS N +LE F ++ P + +A ++GL + ++VWFSNRR K +R
Sbjct: 97 KRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKR 153
>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 = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 24/53 (45%)
Query: 60 RNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
R RT Q+ L + PD +E+L GL I+VWF N+R K
Sbjct: 5 RVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCK 57
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 36.6 bits (83), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 34/57 (59%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
+R RT+ T +Q++ L +++ P + +A ++GL + +QVWF N RA+ R+
Sbjct: 18 KRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERK 74
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 35.4 bits (80), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 28/54 (51%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
++ R +T Q LEKEF Y R +A + L E ++++WF NRR K
Sbjct: 14 RKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMK 67
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 35.0 bits (79), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTH----YPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114
+R R +F N Q + E+ +H YP A+E LA K G+ +++ WF N+R +++
Sbjct: 2 RRKRRNF-NKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 115 R 115
+
Sbjct: 61 K 61
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 4/53 (7%)
Query: 67 NDQIDNLEKEFERTH----YPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
N Q + E+ +H YP A+E LA K G+ +++ WF N+R ++++
Sbjct: 11 NKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 35.0 bits (79), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 28/54 (51%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
++ R +T Q LEKEF Y R +A + L E ++++WF NRR K
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMK 55
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 34.7 bits (78), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTH----YPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114
+R R +F N Q + E+ +H YP A+E LA K G+ +++ WF N+R +++
Sbjct: 2 RRKRRNF-NKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
Query: 115 R 115
+
Sbjct: 61 K 61
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 34.3 bits (77), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 31/57 (54%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
+R RTS N +LE F + P + +A ++GL + ++VWF NRR K +R
Sbjct: 9 KRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 65
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 34.3 bits (77), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 28/53 (52%)
Query: 63 TSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
T FT+ Q+ L+ F+ YP E+L+ + LP I VWF N R K R+
Sbjct: 12 TRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 33.9 bits (76), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTH----YPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114
+R R +F N Q + E+ +H YP A+E LA K G+ +++ WF N+R +++
Sbjct: 3 RRKRRNF-NKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
Query: 115 R 115
+
Sbjct: 62 K 62
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 33.9 bits (76), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 28/50 (56%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSN 108
+R RT T+DQ+ L + F+ + P + +A K GLP+ I+ WF N
Sbjct: 8 KRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN 57
>pdb|3NAU|A Chain A, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And Homeoboxes
Protein 2, Homeodomain 2)
pdb|3NAU|B Chain B, Crystal Structure Of Zhx2 Hd2 (Zinc-Fingers And Homeoboxes
Protein 2, Homeodomain 2)
Length = 66
Score = 33.5 bits (75), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 28/50 (56%)
Query: 66 TNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
T +QI +L+ F ++ +PD RL GL + I+ WFS+ R + +R
Sbjct: 12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61
>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 = 33.5 bits (75), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 25/49 (51%)
Query: 66 TNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114
T +Q+ L+ F RT +P ++LA + GL I WF + R W+
Sbjct: 33 TPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWK 81
>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 = 32.7 bits (73), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 5/61 (8%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTH----YPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114
+R R +F+ Q + E+ +H YP A+E LA K G+ +++ WF N+R +++
Sbjct: 2 RRKRRNFS-KQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
Query: 115 R 115
+
Sbjct: 61 K 61
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of Human
Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 31.6 bits (70), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 24/49 (48%)
Query: 66 TNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWR 114
+++Q+ L+ F R +P E L GL ++ WFS+RR R
Sbjct: 16 SHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCR 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 = 31.6 bits (70), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 25/51 (49%)
Query: 60 RNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRR 110
+ RTSFT I+ L FE+ P A ++ ++VWFSNRR
Sbjct: 95 KRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRR 145
>pdb|1HF0|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1HF0|B Chain B, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1GT0|C Chain C, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 159
Score = 31.2 bits (69), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 29/57 (50%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
++ RTS + LEK F P +A ++ + + I+VWFSNRR K +R
Sbjct: 101 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEKR 157
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 31.2 bits (69), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 29/57 (50%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
++ RTS + LEK F P +A ++ + + I+VWFSNRR K +R
Sbjct: 102 RKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 31.2 bits (69), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 26/57 (45%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
++ RTS LE F + P LA + L + ++VWF NRR K +R
Sbjct: 100 RKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKR 156
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 30.4 bits (67), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 30/57 (52%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
++ RT+ + D LE+ F P R+A ++ L + ++VWF NRR + +R
Sbjct: 88 RKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 144
>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 = 30.0 bits (66), Expect = 0.64, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
++ RTS + LEK F P +A ++ + + I+VWF NRR K +R
Sbjct: 105 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 161
>pdb|1CQT|A Chain A, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
pdb|1CQT|B Chain B, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
Length = 163
Score = 30.0 bits (66), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
++ RTS + LEK F P +A ++ + + I+VWF NRR K +R
Sbjct: 104 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 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 = 29.6 bits (65), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
++ RTS + LEK F P +A ++ + + I+VWF NRR K +R
Sbjct: 97 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 153
>pdb|2DMP|A Chain A, Solution Structure Of The Third Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 2
Length = 89
Score = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 7/64 (10%)
Query: 66 TNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREEKLRNQRQR 125
T Q+ LE F ++ +P +RL + L I WFS RR KLR+ ++
Sbjct: 21 TQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERR-------KLRDSMEQ 73
Query: 126 GSAD 129
D
Sbjct: 74 AVLD 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 = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 23/40 (57%)
Query: 73 LEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
LE+ F R + +E +A K G+ +++VWF N+R +
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 29.3 bits (64), Expect = 1.2, Method: Composition-based stats.
Identities = 14/45 (31%), Positives = 20/45 (44%)
Query: 73 LEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRREE 117
L + + YP + LA GL ++ WF NRR + R E
Sbjct: 509 LREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAE 553
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 23/40 (57%)
Query: 73 LEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
LE+ F R + +E +A K G+ +++VWF N+R +
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>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 = 28.9 bits (63), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 23/40 (57%)
Query: 73 LEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
LE+ F R + +E +A K G+ +++VWF N+R +
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 419
>pdb|2CQX|A Chain A, Solution Structure Of Rsgi Ruh-034, A Homeodomain From
Mouse Cdna
Length = 72
Score = 28.5 bits (62), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 71 DNLEKEF-ERTHYPDVFARERLAAKIGLPEARIQVWFSNRR 110
D LEK F T YPD + L+ ++ +IQ WF +RR
Sbjct: 21 DTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRR 61
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
++ RTS + LEK F P +A ++ + + I+VWF NRR K +R
Sbjct: 8 RKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 64
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 28.1 bits (61), Expect = 2.5, Method: Composition-based stats.
Identities = 13/40 (32%), Positives = 23/40 (57%)
Query: 73 LEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
LE+ F R + +E +A K G+ +++VWF N+R +
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 51
>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 = 27.7 bits (60), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 28/57 (49%)
Query: 59 QRNRTSFTNDQIDNLEKEFERTHYPDVFARERLAAKIGLPEARIQVWFSNRRAKWRR 115
++ RTS + LEK F P +A ++ + + I+VWF NRR K +R
Sbjct: 2 RKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEKR 58
>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 = 27.3 bits (59), Expect = 3.7, Method: Composition-based stats.
Identities = 8/15 (53%), Positives = 13/15 (86%)
Query: 101 RIQVWFSNRRAKWRR 115
+I++WF NRR KW++
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 27.3 bits (59), Expect = 3.8, Method: Composition-based stats.
Identities = 8/15 (53%), Positives = 13/15 (86%)
Query: 101 RIQVWFSNRRAKWRR 115
+I++WF NRR KW++
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 26.6 bits (57), Expect = 6.6, Method: Composition-based stats.
Identities = 8/15 (53%), Positives = 13/15 (86%)
Query: 101 RIQVWFSNRRAKWRR 115
+I++WF NRR KW++
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|1MNM|C Chain C, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
pdb|1MNM|D Chain D, Yeast Matalpha2MCM1DNA TERNARY TRANSCRIPTION COMPLEX
Crystal Structure
Length = 87
Score = 26.6 bits (57), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 3/51 (5%)
Query: 65 FTNDQIDNLEKEFERTH---YPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
FT + + LE F + Y D E L L +I+ W SNRR K
Sbjct: 34 FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRK 84
>pdb|1APL|C Chain C, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1APL|D Chain D, Crystal Structure Of A Mat-Alpha2 Homeodomain-Operator
Complex Suggests A General Model For Homeodomain-Dna
Interactions
pdb|1YRN|B Chain B, Crystal Structure Of The Mata1MATALPHA2 HOMEODOMAIN
Heterodimer Bound To Dna
pdb|1AKH|B Chain B, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 83
Score = 26.2 bits (56), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 3/51 (5%)
Query: 65 FTNDQIDNLEKEFERTH---YPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
FT + + LE F + Y D E L L +I+ W SNRR K
Sbjct: 9 FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRK 59
>pdb|1K61|A Chain A, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|B Chain B, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|C Chain C, Matalpha2 Homeodomain Bound To Dna
pdb|1K61|D Chain D, Matalpha2 Homeodomain Bound To Dna
Length = 60
Score = 26.2 bits (56), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 17/51 (33%), Positives = 22/51 (43%), Gaps = 3/51 (5%)
Query: 65 FTNDQIDNLEKEFERTH---YPDVFARERLAAKIGLPEARIQVWFSNRRAK 112
FT + + LE F + Y D E L L +I+ W SNRR K
Sbjct: 5 FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRK 55
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
0.312 0.130 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,797,113
Number of Sequences: 62578
Number of extensions: 163419
Number of successful extensions: 340
Number of sequences better than 100.0: 93
Number of HSP's better than 100.0 without gapping: 89
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 251
Number of HSP's gapped (non-prelim): 93
length of query: 169
length of database: 14,973,337
effective HSP length: 92
effective length of query: 77
effective length of database: 9,216,161
effective search space: 709644397
effective search space used: 709644397
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 48 (23.1 bits)