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= 004026
(778 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 49.7 bits (117), Expect = 6e-06, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 34/59 (57%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
RK+ +T Q ELE F + ++R+E++ LCL RQ+K WFQNRR + K +
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 60
>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 = 49.7 bits (117), Expect = 6e-06, Method: Composition-based stats.
Identities = 24/63 (38%), Positives = 37/63 (58%), Gaps = 2/63 (3%)
Query: 74 PPRKKRYHR--HTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQM 131
P RK+R +R T Q++ELE F +PD R EL+ ++ L +++ WFQNRR +
Sbjct: 2 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKW 61
Query: 132 KTQ 134
+ Q
Sbjct: 62 RKQ 64
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 48.9 bits (115), Expect = 1e-05, Method: Composition-based stats.
Identities = 22/64 (34%), Positives = 37/64 (57%)
Query: 73 NPPRKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
N R++ +T Q ELE F + ++R+E++ L L RQ+K WFQNRR ++K
Sbjct: 17 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLK 76
Query: 133 TQLE 136
+++
Sbjct: 77 KEIQ 80
>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 = 47.8 bits (112), Expect = 3e-05, Method: Composition-based stats.
Identities = 24/61 (39%), Positives = 36/61 (59%), Gaps = 2/61 (3%)
Query: 76 RKKRYHRHT--PQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKT 133
RK+R R T Q+ ELE F+ +PD R EL++R L +++ WFQNRR +++
Sbjct: 16 RKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRK 75
Query: 134 Q 134
Q
Sbjct: 76 Q 76
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 47.4 bits (111), Expect = 4e-05, Method: Composition-based stats.
Identities = 26/66 (39%), Positives = 38/66 (57%), Gaps = 1/66 (1%)
Query: 75 PRKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
PR+ R T QI ELE F + + + +LS +L L T QVK WF+NRR + K Q
Sbjct: 2 PRRTRT-TFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ 60
Query: 135 LERHEN 140
++H++
Sbjct: 61 SDQHKD 66
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 47.0 bits (110), Expect = 4e-05, Method: Composition-based stats.
Identities = 21/56 (37%), Positives = 37/56 (66%), Gaps = 2/56 (3%)
Query: 79 RYHR--HTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
R HR T +Q++ LE+LF+E +PD R +L++++ L +V+ WF+NRR + +
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 46.2 bits (108), Expect = 7e-05, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQL 135
R++R H T QQ+QELE+ F+ +PD R E++ L +V+ WF+NRR + + +
Sbjct: 4 RRQRTH-FTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
Query: 136 E 136
E
Sbjct: 63 E 63
>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 = 45.8 bits (107), Expect = 8e-05, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQL 135
R++R H T QQ+QELE+ F+ +PD R E++ L +V+ WF+NRR + + +
Sbjct: 4 RRQRTH-FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
Query: 136 E 136
E
Sbjct: 63 E 63
>pdb|1AHD|P Chain P, Determination Of The Nmr Solution Structure Of An
Antennapedia Homeodomain-Dna Complex
pdb|2HOA|A Chain A, Structure Determination Of The Antp(C39->s) Homeodomain
From Nuclear Magnetic Resonance Data In Solution Using A
Novel Strategy For The Structure Calculation With The
Programs Diana, Caliba, Habas And Glomsa
Length = 68
Score = 45.8 bits (107), Expect = 9e-05, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 33/59 (55%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
RK+ +T Q ELE F + ++R+E++ L L RQ+K WFQNRR + K +
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 60
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 45.8 bits (107), Expect = 9e-05, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 33/59 (55%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
RK+ +T Q ELE F + ++R+E++ L L RQ+K WFQNRR + K +
Sbjct: 3 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 45.8 bits (107), Expect = 1e-04, Method: Composition-based stats.
Identities = 23/60 (38%), Positives = 37/60 (61%), Gaps = 2/60 (3%)
Query: 77 KKRYHR--HTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
KKR +R T Q++ELE +F++ +PD R +L+ R L +V+ WFQNRR + + +
Sbjct: 8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR 67
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 45.4 bits (106), Expect = 1e-04, Method: Composition-based stats.
Identities = 26/57 (45%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
RKKR +T Q ELE F + +R E+++ L L RQVK WFQNRR +MK
Sbjct: 14 RKKRC-PYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMK 69
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 45.1 bits (105), Expect = 2e-04, Method: Composition-based stats.
Identities = 26/57 (45%), Positives = 33/57 (57%), Gaps = 1/57 (1%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
RKKR +T Q ELE F + +R E+++ L L RQVK WFQNRR +MK
Sbjct: 2 RKKRC-PYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
>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 = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 34/62 (54%)
Query: 73 NPPRKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
N K++ +T Q ELE F + ++R+E++ L L RQ+K WFQNRR + K
Sbjct: 25 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 84
Query: 133 TQ 134
+
Sbjct: 85 KE 86
>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 = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 28/77 (36%), Positives = 39/77 (50%), Gaps = 1/77 (1%)
Query: 74 PPRKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKT 133
P RKK T Q+ ELE F + + +R L++ L + QVK WFQNRRT+ +
Sbjct: 15 PKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRR 74
Query: 134 QLERHENSLLRQENDKL 150
Q E RQ ++L
Sbjct: 75 QTA-EEREAERQAANRL 90
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 32/59 (54%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
R+KR + Q+ ELE FK+ + +R L+ + L QVK WFQN R +MK Q
Sbjct: 2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQ 60
>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 = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/60 (38%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 75 PRKKRYHR--HTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
P KKR R TPQ I+ L + F++ P P ++ E +K L + V+ WF NRR +K
Sbjct: 90 PSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNRRQTLK 149
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 43.9 bits (102), Expect = 4e-04, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 31/51 (60%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
T +Q++ELE F+ +PD R EL++R L +V+ WF NRR + + Q
Sbjct: 10 TAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 43.9 bits (102), Expect = 4e-04, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 30/51 (58%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
T Q++ELE F +PD R EL+ ++ L +++ WFQNRR + + Q
Sbjct: 7 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 43.9 bits (102), Expect = 4e-04, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 30/51 (58%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
T Q++ELE F +PD R EL+ ++ L +++ WFQNRR + + Q
Sbjct: 7 TSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQ 57
>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 = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 2/65 (3%)
Query: 77 KKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQLE 136
K+ +T Q ELE F + ++R++++ L L RQ+K WFQNRR MK++ +
Sbjct: 4 KRTRQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRR--MKSKKD 61
Query: 137 RHENS 141
R +S
Sbjct: 62 RTLDS 66
>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 = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 20/52 (38%), Positives = 30/52 (57%)
Query: 83 HTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
+T Q ELE F + ++R+E++ L L RQ+K WFQNRR + K +
Sbjct: 3 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 54
>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 = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 32/57 (56%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
R+K + Q+ ELE FK+ + +R +L+ L L + QVK WFQNRR + K
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>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 = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 30/49 (61%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
+ +Q+ L+ F E + E++R +LS L L Q+K WFQN+R ++K
Sbjct: 11 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 30/49 (61%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
+ +Q+ L+ F E + E++R +LS L L Q+K WFQN+R ++K
Sbjct: 9 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>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 = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 31/58 (53%)
Query: 77 KKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
K+ +T Q+ ELE F + +R+EL+ L L R +K WFQNRR + K +
Sbjct: 4 KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKE 61
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 20/51 (39%), Positives = 29/51 (56%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
T +Q+ ELE F + +R+E++ L L QVK WFQNRR + K +
Sbjct: 42 TTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKR 92
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 31/55 (56%)
Query: 86 QQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQLERHEN 140
Q++ ++S F +PD K +L+++ L R ++ WFQN R + + L R EN
Sbjct: 17 HQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQEN 71
>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 = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 26/48 (54%)
Query: 87 QIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
Q+ ELE F + +R L+K L L QVK WFQNRR + K +
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRK 62
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 32/49 (65%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
T QI+ LE++F+ +P +L+++L LE +++ WFQNRR ++K
Sbjct: 9 TQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLK 57
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 21/51 (41%), Positives = 28/51 (54%)
Query: 82 RHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
R + Q ELE F+ + +R L+K L L RQVK WFQNRR + +
Sbjct: 13 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 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 = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 29/49 (59%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
+ +Q+ L+ F E + E++R +LS L L Q+K WFQN R ++K
Sbjct: 9 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 20/49 (40%), Positives = 26/49 (53%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
T Q+ LE F++ + +R E S L L QVK WFQNRR + K
Sbjct: 8 TTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 39.7 bits (91), Expect = 0.007, Method: Composition-based stats.
Identities = 23/60 (38%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 75 PRKKRYHR--HTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
P KKR R T Q ELE F++ + +R L+ + L QVK WFQN R + K
Sbjct: 9 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTK 68
>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 = 39.7 bits (91), Expect = 0.007, Method: Composition-based stats.
Identities = 23/60 (38%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 75 PRKKRYHR--HTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
P KKR R T Q ELE F++ + +R L+ + L QVK WFQN R + K
Sbjct: 6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTK 65
>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 = 39.3 bits (90), Expect = 0.008, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 30/49 (61%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
+ +Q+ L+ F E + E++R +LS L L Q+K WF+N+R ++K
Sbjct: 11 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 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 = 39.3 bits (90), Expect = 0.008, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 29/49 (59%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
+ +Q+ L+ F E + E++R +LS L L Q+K WFQN R ++K
Sbjct: 9 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 57
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 29/48 (60%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQM 131
+ +Q+ L+ F E + E++R +LS L L Q+K WFQN+R ++
Sbjct: 7 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKI 54
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 38.9 bits (89), Expect = 0.012, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQL 135
RKKR +T Q++ELE + + +R +S L RQV WFQNRR + K +
Sbjct: 2 RKKRV-PYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI 60
Query: 136 ER 137
+
Sbjct: 61 NK 62
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 38.5 bits (88), Expect = 0.013, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQL 135
RKKR +T Q++ELE + + +R +S L RQV WFQNRR + K +
Sbjct: 8 RKKRV-PYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI 66
Query: 136 ER 137
+
Sbjct: 67 NK 68
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 38.5 bits (88), Expect = 0.013, Method: Composition-based stats.
Identities = 20/48 (41%), Positives = 27/48 (56%)
Query: 87 QIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
Q+ ELE F + +R L+K L + QVK WFQNRRT+ + Q
Sbjct: 8 QVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ 55
>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 = 38.5 bits (88), Expect = 0.014, Method: Composition-based stats.
Identities = 17/49 (34%), Positives = 29/49 (59%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
+ +Q+ L+ F E + E++R +LS L L Q+K WF N+R ++K
Sbjct: 7 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 38.1 bits (87), Expect = 0.018, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 30/56 (53%)
Query: 77 KKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
++R T +Q+ ELE F + +R +++ L L QVK WFQNRR + K
Sbjct: 8 RRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
>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 = 38.1 bits (87), Expect = 0.021, Method: Composition-based stats.
Identities = 23/58 (39%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 79 RYHRHTPQQIQELESLFK---ECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKT 133
R HR T + ++ LES F E P+ D K L K L Q+K W NRR + KT
Sbjct: 30 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 87
>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 = 37.7 bits (86), Expect = 0.023, Method: Composition-based stats.
Identities = 23/58 (39%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 79 RYHRHTPQQIQELESLFK---ECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKT 133
R HR T + ++ LES F E P+ D K L K L Q+K W NRR + KT
Sbjct: 1 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 58
>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 = 37.7 bits (86), Expect = 0.025, Method: Composition-based stats.
Identities = 23/58 (39%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 79 RYHRHTPQQIQELESLFK---ECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKT 133
R HR T + ++ LES F E P+ D K L K L Q+K W NRR + KT
Sbjct: 5 RGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT 62
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 37.7 bits (86), Expect = 0.026, Method: Composition-based stats.
Identities = 16/38 (42%), Positives = 24/38 (63%)
Query: 95 FKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
F E + E++R +LS L L Q+K WFQN+R ++K
Sbjct: 5 FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 37.4 bits (85), Expect = 0.029, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 29/49 (59%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
+ +Q+ + F E + E++R +LS L L Q+K WFQN+R +++
Sbjct: 11 SSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIR 59
>pdb|1X2M|A Chain A, Solution Structure Of The Homeobox Domain Of Mouse Lag1
Longevity Assurance Homolog 6
Length = 64
Score = 37.4 bits (85), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 91 LESLFKE-CPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
LE +F HPDEK+ LSK+L + R ++ WF+ RR Q K
Sbjct: 15 LEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57
>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 = 37.0 bits (84), Expect = 0.037, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 29/49 (59%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
+ +Q+ L+ F E + E++R +LS L L QVK WF+N R ++K
Sbjct: 12 SSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 37.0 bits (84), Expect = 0.038, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 28/46 (60%)
Query: 87 QIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
Q+ L+ F++ + +R EL+ L L QVK WFQN+R+++K
Sbjct: 18 QLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 63
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 37.0 bits (84), Expect = 0.041, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
RKKR ++ Q++ELE + + +R ++S L RQ+ WFQNRR + K
Sbjct: 8 RKKRI-PYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 63
>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 = 0.061, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 25/42 (59%)
Query: 91 LESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
LE++F + P P +Q ++ +L LE V+ WF NRR + K
Sbjct: 111 LETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGK 152
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 36.2 bits (82), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 30/49 (61%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
T Q+ LE+LF + +PD R E++ ++ L +V+ WF+NRR + +
Sbjct: 15 TRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>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 = 36.2 bits (82), Expect = 0.064, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 78 KRYHR-HTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
+RY T Q+ LE F + + +R EL+ +L L +K WFQNRR + K Q
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ 59
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 36.2 bits (82), Expect = 0.070, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
T Q+ LE F++ + R++L++ L L QVK W+QNRR + K
Sbjct: 25 TELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 35.8 bits (81), Expect = 0.086, Method: Composition-based stats.
Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 76 RKKR-YHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
RK+R +++ + + E P+P E+ + EL+K+ + QV WF N+R + K
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN 62
Query: 135 LER-HENSLLRQENDKLRAENMS 156
+ + E + + + A N+S
Sbjct: 63 IGKFQEEANIYAAKTAVTATNVS 85
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 35.8 bits (81), Expect = 0.096, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 76 RKKR-YHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
RK+R +++ + + E P+P E+ + EL+K+ + QV WF N+R + K
Sbjct: 3 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKN 62
Query: 135 LERHE 139
+ + +
Sbjct: 63 IGKFQ 67
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 35.4 bits (80), Expect = 0.13, Method: Composition-based stats.
Identities = 17/65 (26%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 76 RKKR-YHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
RK+R +++ + + E P+P E+ + EL+K+ + QV WF N+R + K
Sbjct: 4 RKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKSGITVSQVSNWFGNKRIRYKKN 63
Query: 135 LERHE 139
+ + +
Sbjct: 64 IGKFQ 68
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 35.4 bits (80), Expect = 0.14, Method: Composition-based stats.
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 82 RHTPQQIQEL--ESLFKEC--PHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
RH +Q E+ E + P+P E+ + EL+K+ + QV WF N+R + K
Sbjct: 8 RHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 62
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 35.0 bits (79), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 23/42 (54%)
Query: 91 LESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
LES F +CP P + L+ L LE V+ WF NRR + K
Sbjct: 114 LESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEK 155
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 35.0 bits (79), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 26/42 (61%)
Query: 91 LESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
LE++F +CP P +Q ++ +L LE V+ WF NRR + K
Sbjct: 23 LETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGK 64
>pdb|2CQX|A Chain A, Solution Structure Of Rsgi Ruh-034, A Homeodomain From
Mouse Cdna
Length = 72
Score = 35.0 bits (79), Expect = 0.18, Method: Composition-based stats.
Identities = 15/33 (45%), Positives = 23/33 (69%)
Query: 100 HPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
+PDEK+ LSK+L R+++ WF++RR Q K
Sbjct: 33 YPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK 65
>pdb|2DA5|A Chain A, Solution Structure Of The Second Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 3 (Triple Homeobox 1
Protein)
Length = 75
Score = 34.7 bits (78), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 29/56 (51%)
Query: 79 RYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
+Y P+Q++ LES F + P P +++ L + R++ WF RR ++ +
Sbjct: 10 KYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAE 65
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 34.3 bits (77), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 91 LESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRR 128
L + P+P +++ EL++ L T QV WF+NRR
Sbjct: 509 LREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRR 546
>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 = 34.3 bits (77), Expect = 0.30, Method: Composition-based stats.
Identities = 18/46 (39%), Positives = 27/46 (58%)
Query: 87 QIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
Q+ L+ F++ + +Q ELS L L +QVK WFQN+R + K
Sbjct: 14 QLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCK 59
>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 = 34.3 bits (77), Expect = 0.31, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 6/64 (9%)
Query: 76 RKKRYHRHTPQQIQEL--ESLFKEC--PHPDEKQRLELSKRLCLETRQVKFWFQNRRTQM 131
R+KR R+ +Q E+ E + P+P E+ + EL+++ + QV WF N+R +
Sbjct: 2 RRKR--RNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRY 59
Query: 132 KTQL 135
K +
Sbjct: 60 KKNI 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 = 0.37, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 26/49 (53%)
Query: 86 QQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
+Q+ L + + P PD + +L + L R ++ WFQN+R + K +
Sbjct: 13 KQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKR 61
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 33.9 bits (76), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 29/51 (56%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMKTQ 134
T +QI+ LE F+ +PD R L+ ++ L +++ WF NRR + + +
Sbjct: 15 TQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRRE 65
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 33.5 bits (75), Expect = 0.44, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 75 PRKKRYHR--HTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
P KK+ R + Q+ L F+ + +Q ELS L L +QVK WFQN+R + K
Sbjct: 19 PVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSK 78
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 33.1 bits (74), Expect = 0.56, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 29/60 (48%)
Query: 73 NPPRKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
N ++KR + LE F E P ++ + +++ L LE V+ WF NRR + K
Sbjct: 84 NERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 143
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 33.1 bits (74), Expect = 0.68, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 28/49 (57%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
+PQ LE +F+ + K++ E++K+ + QV+ WF N+R + K
Sbjct: 13 SPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 33.1 bits (74), Expect = 0.69, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 28/49 (57%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
+PQ LE +F+ + K++ E++K+ + QV+ WF N+R + K
Sbjct: 5 SPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>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 = 32.7 bits (73), Expect = 0.70, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 28/49 (57%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
+PQ LE +F+ + K++ E++K+ + QV+ WF N+R + K
Sbjct: 13 SPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1MH3|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form I
pdb|1MH4|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form Ii
Length = 421
Score = 32.7 bits (73), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 28/49 (57%)
Query: 84 TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
+PQ LE +F+ + K++ E++K+ + QV+ WF N+R + K
Sbjct: 373 SPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|1HF0|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1HF0|B Chain B, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1GT0|C Chain C, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 159
Score = 31.6 bits (70), Expect = 1.9, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
RKKR T ++ LE F E P ++ ++ +L +E ++ WF NRR + K
Sbjct: 101 RKKRTSIETNIRVA-LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEK 156
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 31.2 bits (69), Expect = 2.1, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 1/60 (1%)
Query: 74 PPRKKRYHRH-TPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
P R KR TP+Q++ L + +P K ++ + L+ R V+ WFQN R + +
Sbjct: 14 PQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARER 73
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 31.2 bits (69), Expect = 2.1, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
RKKR T ++ LE F E P + ++++L +E ++ WF NRR + K
Sbjct: 102 RKKRTSIETNIRVA-LEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 157
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of Human
Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 30.4 bits (67), Expect = 3.6, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 26/48 (54%)
Query: 81 HRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRR 128
++ + +Q+ L+ F P + + L+K L TR+V+ WF +RR
Sbjct: 13 NKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRR 60
>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 = 30.4 bits (67), Expect = 3.7, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
RKKR T ++ LE F E P ++ ++ +L +E ++ WF NRR + K
Sbjct: 97 RKKRTSIETNIRVA-LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 152
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 167
Score = 30.4 bits (67), Expect = 4.3, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
RKKR T ++ LE F E P ++ ++ +L +E ++ WF NRR + K
Sbjct: 105 RKKRTSIETNIRVA-LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 160
>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 = 30.4 bits (67), Expect = 4.3, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
RKKR T ++ LE F E P ++ ++ +L +E ++ WF NRR + K
Sbjct: 104 RKKRTSIETNIRVA-LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 159
>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 = 5.6, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 76 RKKRYHRHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRRTQMK 132
RKKR T ++ LE F E P ++ ++ +L +E ++ WF NRR + K
Sbjct: 8 RKKRTSIETNIRVA-LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 63
>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 = 29.3 bits (64), Expect = 8.9, Method: Composition-based stats.
Identities = 13/47 (27%), Positives = 24/47 (51%)
Query: 82 RHTPQQIQELESLFKECPHPDEKQRLELSKRLCLETRQVKFWFQNRR 128
+ T +QI L++ F + PD+ + L + L ++K WF + R
Sbjct: 10 KKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHR 56
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
0.319 0.134 0.401
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,514,365
Number of Sequences: 62578
Number of extensions: 845748
Number of successful extensions: 1900
Number of sequences better than 100.0: 87
Number of HSP's better than 100.0 without gapping: 76
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1822
Number of HSP's gapped (non-prelim): 89
length of query: 778
length of database: 14,973,337
effective HSP length: 106
effective length of query: 672
effective length of database: 8,340,069
effective search space: 5604526368
effective search space used: 5604526368
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.8 bits)