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= psy526
(274 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 88.6 bits (218), Expect = 4e-18, Method: Compositional matrix adjust.
Identities = 41/51 (80%), Positives = 46/51 (90%)
Query: 70 AQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120
QV ELE++F+ QKYLS PERA +AK+LKLTETQVKIWFQNRRYKTKRKQL
Sbjct: 14 TQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL 64
>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 = 83.6 bits (205), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 41/59 (69%), Positives = 46/59 (77%), Gaps = 1/59 (1%)
Query: 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
GR+K R FS AQVYELE+RF Q+YLS PER +A LKLT TQVKIWFQNRRYK+K
Sbjct: 1 GRRK-PRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>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 = 80.5 bits (197), Expect = 9e-16, Method: Compositional matrix adjust.
Identities = 37/61 (60%), Positives = 46/61 (75%)
Query: 59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
+K++ R F+ AQ YELE+RF Q+YLS PER +A ++LT TQVKIWFQN RYKTKR
Sbjct: 8 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA 67
Query: 119 Q 119
Q
Sbjct: 68 Q 68
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 80.1 bits (196), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 40/60 (66%), Positives = 45/60 (75%), Gaps = 1/60 (1%)
Query: 59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
R+KR R FS AQVYELE+RF QKYLS PER +A + LT TQVKIWFQN RYK KR+
Sbjct: 2 RRKR-RVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 79.3 bits (194), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 36/61 (59%), Positives = 45/61 (73%)
Query: 59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
+K++ R F+ AQ YELE+RF Q+YLS PER + ++LT TQVKIWFQN RYKTKR
Sbjct: 11 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRA 70
Query: 119 Q 119
Q
Sbjct: 71 Q 71
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 77.8 bits (190), Expect = 7e-15, Method: Composition-based stats.
Identities = 36/62 (58%), Positives = 46/62 (74%)
Query: 56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
P G+ +R R AF+ Q+ ELEK F+ +KYLS ER+ +A +LKL+E QVKIWFQNRR K
Sbjct: 3 PGGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKW 62
Query: 116 KR 117
KR
Sbjct: 63 KR 64
>pdb|3A01|A Chain A, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
pdb|3A01|E Chain E, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
Length = 93
Score = 73.2 bits (178), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 38/74 (51%), Positives = 51/74 (68%), Gaps = 1/74 (1%)
Query: 52 QSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNR 111
Q++ P RKK R +F+ QV ELEKRF+ QKYL+ ERA +A+ LK+T+ QVK WFQNR
Sbjct: 10 QNRTPPKRKK-PRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNR 68
Query: 112 RYKTKRKQLQLLEG 125
R K +R+ + E
Sbjct: 69 RTKWRRQTAEEREA 82
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 69.7 bits (169), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 36/66 (54%), Positives = 46/66 (69%), Gaps = 2/66 (3%)
Query: 54 QPPTGRKK--RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNR 111
+P T KK RSR F+ Q+ LEKRF QKYLS P+R D+A+SL L++ QVK W+QNR
Sbjct: 9 EPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNR 68
Query: 112 RYKTKR 117
R K K+
Sbjct: 69 RMKWKK 74
>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 = 69.7 bits (169), Expect = 2e-12, Method: Composition-based stats.
Identities = 32/62 (51%), Positives = 43/62 (69%)
Query: 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
G KR+R A++ AQ+ ELEK F KY+S P R ++A L LTE +KIWFQNRR K K+
Sbjct: 1 GSNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
Query: 118 KQ 119
++
Sbjct: 61 EE 62
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 68.9 bits (167), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 40/84 (47%), Positives = 53/84 (63%), Gaps = 8/84 (9%)
Query: 36 RDLPKPAALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAK 95
R+ PK A +S PGL P+G R F+ Q+ ELEK F+ KYLS R ++A
Sbjct: 18 RNPPKTAKVSE-PGLGS---PSG----LRTNFTTRQLTELEKEFHFNKYLSRARRVEIAA 69
Query: 96 SLKLTETQVKIWFQNRRYKTKRKQ 119
+L+L ETQVKIWFQNRR K K+++
Sbjct: 70 TLELNETQVKIWFQNRRMKQKKRE 93
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 67.8 bits (164), Expect = 6e-12, Method: Composition-based stats.
Identities = 31/53 (58%), Positives = 42/53 (79%)
Query: 66 AFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
+FS +QV ELE+RF QKYL+ ERA +AK+L++T+ QVK WFQNRR K +R+
Sbjct: 3 SFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 66.6 bits (161), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 32/51 (62%), Positives = 38/51 (74%)
Query: 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
FS+ Q ELEK+F QKYLS PER +AK L+L+E QVK WFQNRR K +R
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR 64
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 65.9 bits (159), Expect = 2e-11, Method: Composition-based stats.
Identities = 32/57 (56%), Positives = 42/57 (73%)
Query: 61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
++ R F+ AQ+ LE++F ++YLS ERA+ + SL LTETQVKIWFQNRR K KR
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKR 57
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 64.7 bits (156), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 32/61 (52%), Positives = 45/61 (73%), Gaps = 2/61 (3%)
Query: 57 TGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
+GRK R+ +S Q+ L++RF +YL+ PERA++A SL LT+TQVKIWFQN+R K K
Sbjct: 6 SGRKPRT--IYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 63
Query: 117 R 117
+
Sbjct: 64 K 64
>pdb|2R5Y|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A CONSENSUS HOX-Exd
Site
pdb|2R5Z|A Chain A, Structure Of ScrEXD COMPLEX BOUND TO A DNA SEQUENCE
Derived From The Fkh Gene
Length = 88
Score = 62.8 bits (151), Expect = 2e-10, Method: Composition-based stats.
Identities = 29/62 (46%), Positives = 41/62 (66%)
Query: 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
G KR R +++ Q ELEK F+ +YL+ R ++A +L LTE Q+KIWFQNRR K K+
Sbjct: 26 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKK 85
Query: 118 KQ 119
+
Sbjct: 86 EH 87
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 62.4 bits (150), Expect = 2e-10, Method: Composition-based stats.
Identities = 28/59 (47%), Positives = 40/59 (67%)
Query: 60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
+KR R ++ Q ELEK F+ +YL+ R ++A +L LTE Q+KIWFQNRR K K++
Sbjct: 3 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 62.0 bits (149), Expect = 3e-10, Method: Composition-based stats.
Identities = 28/61 (45%), Positives = 40/61 (65%)
Query: 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
G ++R R ++ Q ELEK F+ YL+ R ++A +L LTE Q+KIWFQNRR K K+
Sbjct: 18 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKK 77
Query: 118 K 118
+
Sbjct: 78 E 78
>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 = 61.6 bits (148), Expect = 4e-10, Method: Composition-based stats.
Identities = 28/59 (47%), Positives = 40/59 (67%)
Query: 60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
+KR R ++ Q ELEK F+ +YL+ R ++A +L LTE Q+KIWFQNRR K K++
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 60
>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 = 61.6 bits (148), Expect = 4e-10, Method: Composition-based stats.
Identities = 28/59 (47%), Positives = 40/59 (67%)
Query: 60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
+KR R ++ Q ELEK F+ +YL+ R ++A +L LTE Q+KIWFQNRR K K++
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 60
>pdb|1FTZ|A Chain A, Nuclear Magnetic Resonance Solution Structure Of The Fushi
Tarazu Homeodomain From Drosophila And Comparison With
The Antennapedia Homeodomain
Length = 70
Score = 61.2 bits (147), Expect = 6e-10, Method: Composition-based stats.
Identities = 27/59 (45%), Positives = 41/59 (69%)
Query: 61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
KR+R ++ Q ELEK F+ +Y++ R D+A +L L+E Q+KIWFQNRR K+K+ +
Sbjct: 4 KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSKKDR 62
>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna
pdb|1JGG|B Chain B, Even-Skipped Homeodomain Complexed To At-Rich Dna
Length = 60
Score = 59.3 bits (142), Expect = 3e-09, Method: Composition-based stats.
Identities = 27/59 (45%), Positives = 39/59 (66%)
Query: 61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
+R R AF+ Q+ LEK F + Y+S P R ++A L L E+ +K+WFQNRR K KR++
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR 60
>pdb|2VI6|A Chain A, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|B Chain B, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|C Chain C, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|D Chain D, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|E Chain E, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|F Chain F, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|G Chain G, Crystal Structure Of The Nanog Homeodomain
pdb|2VI6|H Chain H, Crystal Structure Of The Nanog Homeodomain
Length = 62
Score = 56.6 bits (135), Expect = 1e-08, Method: Composition-based stats.
Identities = 29/62 (46%), Positives = 39/62 (62%)
Query: 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
G K++ R FS AQ+ L+ RF QKYLS + +++ L L+ QVK WFQN+R K KR
Sbjct: 1 GTKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKR 60
Query: 118 KQ 119
Q
Sbjct: 61 WQ 62
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 56.2 bits (134), Expect = 2e-08, Method: Composition-based stats.
Identities = 28/57 (49%), Positives = 36/57 (63%)
Query: 61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
++ R ++ Q ELEK F YL+ R +VA+ L LTE QVKIWFQNRR K K+
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 55.8 bits (133), Expect = 2e-08, Method: Composition-based stats.
Identities = 28/57 (49%), Positives = 36/57 (63%)
Query: 61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
++ R ++ Q ELEK F YL+ R +VA+ L LTE QVKIWFQNRR K K+
Sbjct: 14 RKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 55.8 bits (133), Expect = 2e-08, Method: Composition-based stats.
Identities = 25/56 (44%), Positives = 37/56 (66%)
Query: 61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
+R+R F+ +Q+ ELE+ F +YL+ P AD++ L L QVKIWF+NRR + K
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
>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 = 55.8 bits (133), Expect = 3e-08, Method: Composition-based stats.
Identities = 25/52 (48%), Positives = 36/52 (69%)
Query: 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
++ Q ELEK F+ +YL+ R ++A +L LTE Q+KIWFQNRR K K++
Sbjct: 3 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 54
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 55.8 bits (133), Expect = 3e-08, Method: Composition-based stats.
Identities = 26/60 (43%), Positives = 37/60 (61%)
Query: 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
G +KR R AFS Q+ ++ FN +YL+ R ++ L L E Q+KIWFQN+R K +R
Sbjct: 1 GDEKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRR 60
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|1HDD|D Chain D, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|2JWT|A Chain A, Solution Structure Of Engrailed Homeodomain Wt
Length = 61
Score = 55.5 bits (132), Expect = 3e-08, Method: Composition-based stats.
Identities = 26/58 (44%), Positives = 37/58 (63%)
Query: 60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
+KR R AFS Q+ L++ FN +YL+ R ++ L L E Q+KIWFQN+R K K+
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 60
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 55.5 bits (132), Expect = 3e-08, Method: Composition-based stats.
Identities = 26/58 (44%), Positives = 37/58 (63%)
Query: 60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
+KR R AFS Q+ L++ FN +YL+ R ++ L L E Q+KIWFQN+R K K+
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 58
>pdb|1P7J|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52e
pdb|1P7J|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52e
Length = 59
Score = 54.7 bits (130), Expect = 5e-08, Method: Composition-based stats.
Identities = 26/58 (44%), Positives = 36/58 (62%)
Query: 60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
+KR R AFS Q+ L++ FN +YL+ R ++ L L E Q+KIWFQN R K K+
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKK 58
>pdb|1P7I|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52a
Length = 59
Score = 54.3 bits (129), Expect = 8e-08, Method: Composition-based stats.
Identities = 26/58 (44%), Positives = 36/58 (62%)
Query: 60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
+KR R AFS Q+ L++ FN +YL+ R ++ L L E Q+KIWFQN R K K+
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKK 58
>pdb|2HDD|A Chain A, Engrailed Homeodomain Q50k Variant Dna Complex
pdb|2HDD|B Chain B, Engrailed Homeodomain Q50k Variant Dna Complex
Length = 61
Score = 53.9 bits (128), Expect = 9e-08, Method: Composition-based stats.
Identities = 25/58 (43%), Positives = 37/58 (63%)
Query: 60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
+KR R AFS Q+ L++ FN +YL+ R ++ L L E Q+KIWF+N+R K K+
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 30/80 (37%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 40 KPAALSNLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKL 99
+P + N + + P +K+++R FS Q+ L RF QKYLS + +++ L L
Sbjct: 3 QPTSAENSVAKKEDKVPV-KKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNL 61
Query: 100 TETQVKIWFQNRRYKTKRKQ 119
+ QVK WFQN+R K+KR Q
Sbjct: 62 SYKQVKTWFQNQRMKSKRWQ 81
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/65 (40%), Positives = 41/65 (63%), Gaps = 2/65 (3%)
Query: 53 SQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRR 112
S +GRKKR +S Q+ ELE+ + A K+++ +R ++ + L+E Q+ IWFQNRR
Sbjct: 2 SSGSSGRKKR--IPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRR 59
Query: 113 YKTKR 117
K K+
Sbjct: 60 VKEKK 64
>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
pdb|1FJL|B Chain B, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
pdb|1FJL|C Chain C, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
Length = 81
Score = 53.1 bits (126), Expect = 2e-07, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 45/72 (62%), Gaps = 4/72 (5%)
Query: 48 PGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIW 107
PG+A + +++RSR FS +Q+ ELE+ F +Y R ++A+ LTE ++++W
Sbjct: 10 PGIALKR----KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVW 65
Query: 108 FQNRRYKTKRKQ 119
FQNRR + +++
Sbjct: 66 FQNRRARLRKQH 77
>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 = 52.4 bits (124), Expect = 3e-07, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 37/62 (59%)
Query: 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
G ++R R F+ Q+ ELE F +Y R ++A LTE +V++WF+NRR K ++
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 118 KQ 119
++
Sbjct: 61 RE 62
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 52.0 bits (123), Expect = 3e-07, Method: Composition-based stats.
Identities = 24/53 (45%), Positives = 33/53 (62%)
Query: 62 RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYK 114
R R AFS Q+ L++ FN +YL+ R ++ L L E Q+KIWFQN+R K
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
pdb|3A01|F Chain F, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
Length = 67
Score = 51.6 bits (122), Expect = 5e-07, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 40/64 (62%)
Query: 56 PTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKT 115
P +++R R F+ Q+ ELEK F+ Y R ++A + LTE ++++WFQNRR K
Sbjct: 2 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKW 61
Query: 116 KRKQ 119
++++
Sbjct: 62 RKQE 65
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 51.6 bits (122), Expect = 5e-07, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 36/62 (58%)
Query: 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
G ++R R F+ Q+ ELE F Y R ++A LTE +V++WF+NRR K ++
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 118 KQ 119
++
Sbjct: 61 RE 62
>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 = 51.2 bits (121), Expect = 5e-07, Method: Composition-based stats.
Identities = 24/56 (42%), Positives = 34/56 (60%)
Query: 62 RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
R R AFS Q+ L++ FN +YL+ R ++ L L E Q+KIWF N+R K K+
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKK 56
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 51.2 bits (121), Expect = 6e-07, Method: Composition-based stats.
Identities = 24/60 (40%), Positives = 38/60 (63%), Gaps = 2/60 (3%)
Query: 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
GRKKR ++ Q+ ELE+ + K+++ +R ++ + L+E QV IWFQNRR K K+
Sbjct: 7 GRKKR--VPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 64
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 50.8 bits (120), Expect = 8e-07, Method: Composition-based stats.
Identities = 24/60 (40%), Positives = 38/60 (63%), Gaps = 2/60 (3%)
Query: 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
GRKKR ++ Q+ ELE+ + K+++ +R ++ + L+E QV IWFQNRR K K+
Sbjct: 1 GRKKR--VPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKK 58
>pdb|2HOS|A Chain A, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOS|B Chain B, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOT|A Chain A, Phage Selected Homeodomain Bound To Modified Dna
pdb|2HOT|B Chain B, Phage Selected Homeodomain Bound To Modified Dna
Length = 63
Score = 49.3 bits (116), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 35/58 (60%)
Query: 60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
+KR R AFS Q+ L++ FN +YL+ R ++ L L E QVK WF+N R K K+
Sbjct: 4 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKK 61
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 49.3 bits (116), Expect = 2e-06, Method: Composition-based stats.
Identities = 27/73 (36%), Positives = 43/73 (58%)
Query: 61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120
+R R F+ AQ+ LE F +Y R +VA + L E++V++WF+NRR K +++Q
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ 67
Query: 121 QLLEGSLNTPSAG 133
Q G + PS+G
Sbjct: 68 QQQNGGQSGPSSG 80
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 49.3 bits (116), Expect = 3e-06, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 37/59 (62%)
Query: 60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
++RSR F+ Q+ ELE+ F Y R ++A+ KLTE +V++WF NRR + +++
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 48.9 bits (115), Expect = 3e-06, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 36/58 (62%)
Query: 62 RSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
R R F+ Q+ ELEK F+ Y R ++A + LTE ++++WFQNRR K ++++
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 38/62 (61%)
Query: 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
G+K+R+R F+ Q+ ELEK F Y R +A LTE +V++WFQNRR K ++
Sbjct: 7 GKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRK 66
Query: 118 KQ 119
++
Sbjct: 67 RE 68
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 47.4 bits (111), Expect = 9e-06, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 35/57 (61%)
Query: 63 SRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
S F+ Q+ ELEK F+ Y R ++A + LTE ++++WFQNRR K ++++
Sbjct: 2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 45.8 bits (107), Expect = 3e-05, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 31/59 (52%)
Query: 61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQ 119
+R R AF+ Q+ LE F Y D+A+ L L +++IWFQNRR K KR
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSH 60
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 45.8 bits (107), Expect = 3e-05, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 40/73 (54%)
Query: 61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120
+R+R +F+ Q+ LEK F Y R +A + L E ++++WF NRR K +R++
Sbjct: 8 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEK 67
Query: 121 QLLEGSLNTPSAG 133
+ + PS+G
Sbjct: 68 LRNQRRQSGPSSG 80
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 44.7 bits (104), Expect = 6e-05, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 32/57 (56%)
Query: 61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
+R R F+ Q+ LE F KY R +A+ + L E +V++WF+NRR K +R
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRR 64
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 18/42 (42%), Positives = 27/42 (64%)
Query: 76 EKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
++ FN +YL+ R ++ L L E Q+KIWFQN+R K K+
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKK 43
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 38/73 (52%)
Query: 61 KRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQL 120
KR R +F H Q+ ++ F + +A+ LT+ +++WFQN R K +R L
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLL 67
Query: 121 QLLEGSLNTPSAG 133
+ G ++ PS+G
Sbjct: 68 RQENGGVSGPSSG 80
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/78 (34%), Positives = 36/78 (46%), Gaps = 10/78 (12%)
Query: 58 GRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
GRK++ R + LE F S E +A SL+L + V++WF NRR K KR
Sbjct: 97 GRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKR 156
Query: 118 KQLQLLEGSLNTPSAGNG 135
TP+AG G
Sbjct: 157 M----------TPAAGAG 164
>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 = 16/42 (38%), Positives = 28/42 (66%)
Query: 75 LEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
LE+ F ++ L+ E+ +VAK +T QV++WF N+R ++K
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 37.4 bits (85), Expect = 0.008, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 28/42 (66%)
Query: 75 LEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
LE+ F ++ L+ E+ +VAK +T QV++WF N+R ++K
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>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 = 37.0 bits (84), Expect = 0.012, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 31/58 (53%)
Query: 60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
+++ R + + LEK F A + + E +A+ L + + +++WF NRR K KR
Sbjct: 1 RRKKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEKR 58
>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 = 36.2 bits (82), Expect = 0.019, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 28/42 (66%)
Query: 75 LEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
LE+ F ++ L+ E+ +VAK +T QV++WF N+R ++K
Sbjct: 20 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 36.2 bits (82), Expect = 0.019, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 28/42 (66%)
Query: 75 LEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
LE+ F ++ L+ E+ +VAK +T QV++WF N+R ++K
Sbjct: 20 LEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 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 = 35.8 bits (81), Expect = 0.026, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 29/59 (49%)
Query: 59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
R+++ R + LEK F + + E +A L + + +++WF NRR K KR
Sbjct: 6 RRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 64
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 30/59 (50%)
Query: 59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
RK++ R S A LE+ F S E +A+ L L + V++WF NRR + KR
Sbjct: 86 RKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKR 144
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 35.8 bits (81), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 35/72 (48%)
Query: 46 NLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVK 105
NL +++S+ +KR R + + + LE F S + +A L L + V+
Sbjct: 82 NLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVR 141
Query: 106 IWFQNRRYKTKR 117
+WF NRR K KR
Sbjct: 142 VWFSNRRQKGKR 153
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 33.9 bits (76), Expect = 0.11, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 28/58 (48%)
Query: 60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
+KR R + + + LE F S + +A L L + V++WF NRR K KR
Sbjct: 8 RKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKR 65
>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 = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 29/59 (49%)
Query: 59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
R+++ R + LEK F + + E +A L + + +++WF NRR K KR
Sbjct: 99 RRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEKR 157
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of Human
Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 33.5 bits (75), Expect = 0.13, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 68 SHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRKQLQLLEGSL 127
SH Q+ L+ F ++ E + K L+ +V+ WF +RRY + L+GS
Sbjct: 16 SHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRN-----LKGSR 70
Query: 128 NTPSAG 133
+ PS+G
Sbjct: 71 SGPSSG 76
>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 = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 29/59 (49%)
Query: 59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
R+++ R + LEK F + + E +A L + + +++WF NRR K KR
Sbjct: 102 RRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 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 = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 29/59 (49%)
Query: 59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
R+++ R + LEK F + + E +A L + + +++WF NRR K KR
Sbjct: 95 RRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 153
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 30/59 (50%)
Query: 59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
R+++ R + LEK F + + + +A+ L + + +++WF NRR K KR
Sbjct: 100 RRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKR 158
>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 = 32.0 bits (71), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
R+K+ + ++ +V LEK F + + E +A L + + +++WF NRR K KR
Sbjct: 104 RRKKRTSIETNIRVA-LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEKR 161
>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 = 32.0 bits (71), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 2/71 (2%)
Query: 46 NLPGLAQSQPPTGRKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVK 105
NL +P RK+R+ +F+ + L F +G E + AK L V+
Sbjct: 81 NLXEFVGGEPSKKRKRRT--SFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVR 138
Query: 106 IWFQNRRYKTK 116
+WF NRR K
Sbjct: 139 VWFSNRRQTLK 149
>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 = 31.6 bits (70), Expect = 0.51, Method: Composition-based stats.
Identities = 11/16 (68%), Positives = 14/16 (87%)
Query: 103 QVKIWFQNRRYKTKRK 118
Q+KIWFQNRR K K++
Sbjct: 2 QIKIWFQNRRMKWKKR 17
>pdb|1BW5|A Chain A, The Nmr Solution Structure Of The Homeodomain Of The Rat
Insulin Gene Enhancer Protein Isl-1, 50 Structures
Length = 66
Score = 30.8 bits (68), Expect = 0.79, Method: Composition-based stats.
Identities = 13/64 (20%), Positives = 30/64 (46%)
Query: 59 RKKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKRK 118
+ R R + Q++ L + A + + + L+ +++WFQN+R K K++
Sbjct: 2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61
Query: 119 QLQL 122
+ +
Sbjct: 62 SIMM 65
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 30.8 bits (68), Expect = 0.82, Method: Composition-based stats.
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 103 QVKIWFQNRRYKTKR 117
Q+KIWFQNRR K K+
Sbjct: 2 QIKIWFQNRRMKWKK 16
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 30.8 bits (68), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 22/33 (66%)
Query: 84 YLSGPERADVAKSLKLTETQVKIWFQNRRYKTK 116
Y S E+ ++A++ LT TQV WF+NRR + +
Sbjct: 518 YPSPREKRELAEATGLTTTQVSNWFKNRRQRDR 550
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 30.8 bits (68), Expect = 0.95, Method: Composition-based stats.
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 103 QVKIWFQNRRYKTKR 117
Q+KIWFQNRR K K+
Sbjct: 2 QIKIWFQNRRMKWKK 16
>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 = 30.4 bits (67), Expect = 1.2, Method: Composition-based stats.
Identities = 14/61 (22%), Positives = 34/61 (55%), Gaps = 11/61 (18%)
Query: 60 KKRSRAAFSHAQVYELEKRFNAQKYLSGPERADVAKSLKLT---ETQVKIWFQNRRYKTK 116
+K+++ +H + L+ +F P+ A+V + +++T +++K WF + RY+ +
Sbjct: 9 RKKTKEQIAHLKASFLQSQF--------PDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQ 60
Query: 117 R 117
R
Sbjct: 61 R 61
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 25/51 (49%)
Query: 67 FSHAQVYELEKRFNAQKYLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
F+ Q+ L+ F+A Y E ++ L L + +WFQN R K ++
Sbjct: 14 FTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARK 64
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 27.3 bits (59), Expect = 9.5, Method: Compositional matrix adjust.
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 84 YLSGPERADVAKSLKLTETQVKIWFQNRRYKTKR 117
Y S + ++AK +T +QV WF N+R + K+
Sbjct: 30 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK 63
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.313 0.130 0.380
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,855,889
Number of Sequences: 62578
Number of extensions: 246280
Number of successful extensions: 398
Number of sequences better than 100.0: 85
Number of HSP's better than 100.0 without gapping: 82
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 316
Number of HSP's gapped (non-prelim): 85
length of query: 274
length of database: 14,973,337
effective HSP length: 97
effective length of query: 177
effective length of database: 8,903,271
effective search space: 1575878967
effective search space used: 1575878967
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)