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= psy14571
(123 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 79.7 bits (195), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 42/75 (56%), Positives = 53/75 (70%), Gaps = 4/75 (5%)
Query: 46 PTSPSTDYTTPLTALKYPPSAALSQHQSLLNNSG-RTNFTNKQLTELEKEFHFNKYLTRA 104
PT+ + D+ + + PP A L + SG RTNFT +QLTELEKEFHFNKYL+RA
Sbjct: 6 PTARTFDW---MKVKRNPPKTAKVSEPGLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRA 62
Query: 105 RRIEIASVLQLNETQ 119
RR+EIA+ L+LNETQ
Sbjct: 63 RRVEIAATLELNETQ 77
>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 = 57.0 bits (136), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 32/63 (50%), Positives = 38/63 (60%), Gaps = 5/63 (7%)
Query: 62 YPPSAALSQHQSLLNNSG-----RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLN 116
YP + S +N +G RT++T Q ELEKEFHFN+YLTR RRIEIA L L
Sbjct: 9 YPWMKRVHLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLT 68
Query: 117 ETQ 119
E Q
Sbjct: 69 ERQ 71
>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 = 56.6 bits (135), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 27/45 (60%), Positives = 30/45 (66%)
Query: 75 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
+ GR +T Q ELEKEFHFN+YLTR RRIEIA L L E Q
Sbjct: 1 MRKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQ 45
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 55.8 bits (133), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 27/42 (64%), Positives = 29/42 (69%)
Query: 78 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
GR +T Q ELEKEFHFN+YLTR RRIEIA L L E Q
Sbjct: 5 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQ 46
>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 = 55.8 bits (133), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 27/42 (64%), Positives = 29/42 (69%)
Query: 78 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
GR +T Q ELEKEFHFN+YLTR RRIEIA L L E Q
Sbjct: 4 RGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQ 45
>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 = 52.8 bits (125), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 24/40 (60%), Positives = 30/40 (75%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
R +T Q ELEKEFHFN+Y+TR RRI+IA+ L L+E Q
Sbjct: 7 RQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQ 46
>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 = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 25/37 (67%), Positives = 27/37 (72%)
Query: 83 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
+T Q ELEKEFHFN+YLTR RRIEIA L L E Q
Sbjct: 3 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQ 39
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 51.2 bits (121), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/45 (57%), Positives = 28/45 (62%)
Query: 75 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
L GR +T Q ELEKEFH N YLTR RRIE+A L L E Q
Sbjct: 19 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQ 63
>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 = 49.7 bits (117), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 24/42 (57%), Positives = 30/42 (71%)
Query: 76 NNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNE 117
N RT +T QL ELEKEF FNKY++R RR+E+A +L L E
Sbjct: 3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTE 44
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 47.0 bits (110), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 23/41 (56%), Positives = 29/41 (70%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQT 120
RT FT++QL ELEKEFH KYL+ R +IA L+L+E Q
Sbjct: 11 RTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQV 51
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 45.8 bits (107), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/44 (54%), Positives = 26/44 (59%)
Query: 78 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTS 121
R +T Q ELEKEF FN YLTR RR E+A VL L E Q
Sbjct: 3 KKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVK 46
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/44 (52%), Positives = 26/44 (59%)
Query: 78 SGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTS 121
R +T Q ELEKEF FN YLTR RR E+A +L L E Q
Sbjct: 15 KKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVK 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 = 42.4 bits (98), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 20/41 (48%), Positives = 30/41 (73%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQT 120
RT F+++QL L++EF+ N+YLT RR +++S L LNE Q
Sbjct: 8 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQV 48
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/40 (50%), Positives = 30/40 (75%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT F+++QL L++EF+ N+YLT RR +++S L LNE Q
Sbjct: 7 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQ 46
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/40 (50%), Positives = 30/40 (75%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT F+++QL L++EF+ N+YLT RR +++S L LNE Q
Sbjct: 5 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQ 44
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/40 (50%), Positives = 30/40 (75%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT F+++QL L++EF+ N+YLT RR +++S L LNE Q
Sbjct: 7 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQ 46
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/40 (50%), Positives = 30/40 (75%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT F+++QL L++EF+ N+YLT RR +++S L LNE Q
Sbjct: 3 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQ 42
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/40 (50%), Positives = 30/40 (75%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT F+++QL L++EF+ N+YLT RR +++S L LNE Q
Sbjct: 5 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQ 44
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/40 (50%), Positives = 30/40 (75%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT F+++QL L++EF+ N+YLT RR +++S L LNE Q
Sbjct: 5 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQ 44
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/40 (50%), Positives = 30/40 (75%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT F+++QL L++EF+ N+YLT RR +++S L LNE Q
Sbjct: 3 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQ 42
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 29/40 (72%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT F+++QL ++EF+ N+YLT RR +++S L LNE Q
Sbjct: 7 RTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQ 46
>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 = 39.3 bits (90), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 25/40 (62%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT+FT Q+ ELEK FH KYL A R +A L++ + Q
Sbjct: 21 RTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQ 60
>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna
pdb|1JGG|B Chain B, Even-Skipped Homeodomain Complexed To At-Rich Dna
Length = 60
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/39 (51%), Positives = 26/39 (66%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNET 118
RT FT QL LEKEF+ Y++R RR E+A+ L L E+
Sbjct: 5 RTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPES 43
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 35.8 bits (81), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 30/47 (63%), Gaps = 3/47 (6%)
Query: 76 NNSGRTN---FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
+SGR ++ QL ELE+E+ NK++T+ +R +I++ L+E Q
Sbjct: 4 GSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQ 50
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/41 (48%), Positives = 25/41 (60%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQT 120
RT FT QL LE++F +YL+ A R E +S L L ETQ
Sbjct: 4 RTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQV 44
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 24/40 (60%)
Query: 81 TNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQT 120
F+N Q ELEK+F KYL+ R +A +LQL+E Q
Sbjct: 12 VRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQV 51
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 19/40 (47%), Positives = 24/40 (60%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT FT QL LEK F KYL+ RI++A L L++ Q
Sbjct: 21 RTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQ 60
>pdb|3RKQ|A Chain A, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
pdb|3RKQ|B Chain B, Nkx2.5 Homeodomain Dimer Bound To Anf-242 Dna
Length = 58
Score = 33.5 bits (75), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 25/41 (60%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQT 120
R F+ Q+ ELE+ F +YL+ R ++ASVL+L TQ
Sbjct: 6 RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQV 46
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 33.1 bits (74), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 26/40 (65%)
Query: 83 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122
+T QL ELE+E+ NK++T+ +R I++ L+E Q +
Sbjct: 14 YTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTI 53
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 33.1 bits (74), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 26/40 (65%)
Query: 83 FTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122
+T QL ELE+E+ NK++T+ +R I++ L+E Q +
Sbjct: 8 YTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTI 47
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 32.3 bits (72), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 23/39 (58%)
Query: 81 TNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
T+F+ Q+ ELE+ F KYL A R +A L++ + Q
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQ 40
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 24/40 (60%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT FT+ Q+ ELE+ F +YLT R ++++ L L Q
Sbjct: 6 RTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQ 45
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 24/41 (58%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQT 120
RT +++ QL L++ F +YL R E+A+ L L +TQ
Sbjct: 11 RTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQV 51
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 21/28 (75%)
Query: 92 EKEFHFNKYLTRARRIEIASVLQLNETQ 119
++EF+ N+YLT RR +++S L LNE Q
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQ 29
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 30.0 bits (66), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 24/47 (51%)
Query: 75 LNNSGRTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTS 121
+ R F+ Q+ ELE+ F KYL+ R +AS++ L TQ
Sbjct: 1 MRRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVK 47
>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 = 29.6 bits (65), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 24/40 (60%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT+FT++QL ELE F N+Y + R EIA L E +
Sbjct: 7 RTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEAR 46
>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 = 29.3 bits (64), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 21/36 (58%)
Query: 87 QLTELEKEFHFNKYLTRARRIEIASVLQLNETQTSF 122
Q+ ELE++F KYL+ R +A L+L ETQ
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKI 50
>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 = 28.9 bits (63), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 23/42 (54%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTS 121
R FT Q ELE+ F +YL+ R +AS+++L TQ
Sbjct: 13 RVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVK 54
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 23/40 (57%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQ 119
RT+FT++QL ELE F N Y + R EIA L E +
Sbjct: 7 RTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEAR 46
>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 = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLN--ETQTSFE 123
RT F+ QL L+ F KYL+ + E++S+L L+ + +T F+
Sbjct: 7 RTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQ 52
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 26.9 bits (58), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%)
Query: 80 RTNFTNKQLTELEKEFHFNKYLTRARRIEIASVLQLNETQTS 121
R FT Q ELE+ F +YL+ R + S+++L TQ
Sbjct: 16 RVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVK 57
>pdb|1GTM|A Chain A, Structure Of Glutamate Dehydrogenase
pdb|1GTM|B Chain B, Structure Of Glutamate Dehydrogenase
pdb|1GTM|C Chain C, Structure Of Glutamate Dehydrogenase
Length = 419
Score = 26.2 bits (56), Expect = 5.0, Method: Composition-based stats.
Identities = 11/24 (45%), Positives = 17/24 (70%)
Query: 69 SQHQSLLNNSGRTNFTNKQLTELE 92
++H S+ + G TN TN++L ELE
Sbjct: 265 NEHGSVKDFPGATNITNEELLELE 288
>pdb|1EUZ|A Chain A, Glutamate Dehydrogenase From Thermococcus Profundus In The
Unligated State
pdb|1EUZ|B Chain B, Glutamate Dehydrogenase From Thermococcus Profundus In The
Unligated State
pdb|1EUZ|C Chain C, Glutamate Dehydrogenase From Thermococcus Profundus In The
Unligated State
pdb|1EUZ|D Chain D, Glutamate Dehydrogenase From Thermococcus Profundus In The
Unligated State
pdb|1EUZ|E Chain E, Glutamate Dehydrogenase From Thermococcus Profundus In The
Unligated State
pdb|1EUZ|F Chain F, Glutamate Dehydrogenase From Thermococcus Profundus In The
Unligated State
Length = 419
Score = 25.8 bits (55), Expect = 6.0, Method: Composition-based stats.
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 70 QHQSLLNNSGRTNFTNKQLTELE 92
+H S+ + G TN TN++L ELE
Sbjct: 266 EHGSVKDFPGATNITNEELLELE 288
>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 = 25.4 bits (54), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 4/45 (8%)
Query: 56 PLTALKYPPSAALSQHQSLLNNSGRTNFTNKQLTELEKEFHFNKY 100
++ + P AL + Q RT F+ QL ELE+ F +Y
Sbjct: 2 DISDCESEPGIALKRKQ----RRSRTTFSASQLDELERAFERTQY 42
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 0.126 0.351
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,822,017
Number of Sequences: 62578
Number of extensions: 98553
Number of successful extensions: 218
Number of sequences better than 100.0: 55
Number of HSP's better than 100.0 without gapping: 55
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 163
Number of HSP's gapped (non-prelim): 55
length of query: 123
length of database: 14,973,337
effective HSP length: 85
effective length of query: 38
effective length of database: 9,654,207
effective search space: 366859866
effective search space used: 366859866
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: 45 (21.9 bits)