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= psy16514
(155 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 79.7 bits (195), Expect = 6e-16, Method: Compositional matrix adjust.
Identities = 38/63 (60%), Positives = 46/63 (73%)
Query: 10 KPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKW 69
K ++G R VF++LQ GLEKRF+ QKY+S PDR LAE LGL QVK W+QNRRMKW
Sbjct: 13 KAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKW 72
Query: 70 RNS 72
+ S
Sbjct: 73 KKS 75
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain
From Human Cdna
Length = 70
Score = 63.5 bits (153), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 31/52 (59%), Positives = 39/52 (75%)
Query: 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
FS+ Q LEK+F+ QKY+S P+RK+LA+ L L + QVK WFQNRR KWR S
Sbjct: 14 FSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRS 65
>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 = 62.4 bits (150), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 32/69 (46%), Positives = 42/69 (60%), Gaps = 2/69 (2%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR--NSKER 75
R F+ +Q LEKRF QKY++ +R LA L + D+QVK WFQNRR KWR ++ER
Sbjct: 21 RTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEER 80
Query: 76 ELLANGGSR 84
E +R
Sbjct: 81 EAERQAANR 89
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 61.2 bits (147), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 26/55 (47%), Positives = 38/55 (69%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
R ++S Q L++RFQ +Y++ P+R +LA LGL +QVKIWFQN+R K + S
Sbjct: 11 RTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKS 65
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 61.2 bits (147), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 32/65 (49%), Positives = 40/65 (61%), Gaps = 3/65 (4%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
GK RR RR F+ Q LEK F +KY+S +R ++A L L + QVKIWFQNRR K
Sbjct: 5 GKSRR---RRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAK 61
Query: 69 WRNSK 73
W+ K
Sbjct: 62 WKRIK 66
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 59.3 bits (142), Expect = 9e-10, Method: Compositional matrix adjust.
Identities = 28/52 (53%), Positives = 36/52 (69%)
Query: 17 RRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
RR +FS Q LE+RF+ QKY+S P+R+ LA + L +QVKIWFQN R K
Sbjct: 5 RRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYK 56
>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 = 58.5 bits (140), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 28/60 (46%), Positives = 39/60 (65%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G P + RR +F+ Q LE+RF+ Q+Y+S P+R+ LA + L +QVKIWFQN R K
Sbjct: 4 GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYK 63
>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 = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/51 (54%), Positives = 36/51 (70%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
R +FS Q LE+RF+ Q+Y+S P+R +LA L L +QVKIWFQNRR K
Sbjct: 6 RVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYK 56
>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 = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 27/53 (50%), Positives = 34/53 (64%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
R ++ Q LEK F KYIS+P R +LA L L + +KIWFQNRRMKW+
Sbjct: 7 RTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWK 59
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 56.6 bits (135), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 27/60 (45%), Positives = 38/60 (63%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G P + RR +F+ Q LE+RF+ Q+Y+S P+R+ L + L +QVKIWFQN R K
Sbjct: 7 GLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYK 66
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 56.6 bits (135), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 27/50 (54%), Positives = 34/50 (68%)
Query: 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
FS Q LE+RF QKY++ +R LA+ L + D+QVK WFQNRR KWR
Sbjct: 4 FSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWR 53
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 38/59 (64%)
Query: 14 GMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
G R +F+D Q + LE FQ KY R++LA K+ L++ +V++WF+NRR KWR S
Sbjct: 7 GRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRS 65
>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 = 54.7 bits (130), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 24/40 (60%), Positives = 31/40 (77%)
Query: 29 LEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
LE++F QKY+S P+R LA+ L L ++QVKIWFQNRR K
Sbjct: 19 LERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYK 58
>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 = 54.3 bits (129), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 43/69 (62%), Gaps = 3/69 (4%)
Query: 2 STTIFDRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIW 61
++T+ G+ +R +R ++ Q LEK F +Y+++ R ++A L L + Q+KIW
Sbjct: 19 TSTVNANGETKR---QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIW 75
Query: 62 FQNRRMKWR 70
FQNRRMKW+
Sbjct: 76 FQNRRMKWK 84
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 53.9 bits (128), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 29/59 (49%), Positives = 38/59 (64%), Gaps = 1/59 (1%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKERE 76
R F+ Q LEK F KY+S+ R ++A L L ++QVKIWFQNRRMK + +ERE
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMK-QKKRERE 95
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 53.9 bits (128), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 34/53 (64%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
R ++ Q LEK F +Y+++ R ++A L L + Q+KIWFQNRRMKW+
Sbjct: 7 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 59
>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 = 53.5 bits (127), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 34/53 (64%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
R ++ Q LEK F +Y+++ R ++A L L + Q+KIWFQNRRMKW+
Sbjct: 6 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58
>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 = 53.1 bits (126), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 34/53 (64%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
R ++ Q LEK F +Y+++ R ++A L L + Q+KIWFQNRRMKW+
Sbjct: 6 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 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 = 52.8 bits (125), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 33/51 (64%)
Query: 20 VFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
++ Q LEK F +Y+++ R ++A L L + Q+KIWFQNRRMKW+
Sbjct: 2 TYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 52
>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 = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 25/51 (49%), Positives = 34/51 (66%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
R F+ Q LEK F + Y+S+P R +LA +L L +S +K+WFQNRRMK
Sbjct: 5 RTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMK 55
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/60 (43%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G RRG R ++ Q LEK F Y+++ R ++A L L + Q+KIWFQNRRMK
Sbjct: 18 GLRRRG---RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMK 74
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 34/53 (64%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
R F+ Q + LEK F Y R++LA K+GL ++++++WFQNRR KWR
Sbjct: 3 RTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 55
>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 = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 38/61 (62%), Gaps = 1/61 (1%)
Query: 11 PRRGMMR-RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKW 69
P+R R R F+ Q + LEK F Y R++LA K+GL ++++++WFQNRR KW
Sbjct: 2 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKW 61
Query: 70 R 70
R
Sbjct: 62 R 62
>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 = 50.1 bits (118), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 23/51 (45%), Positives = 31/51 (60%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
R ++ Q LEK F +YI++ R +A L L + Q+KIWFQNRRMK
Sbjct: 7 RQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMK 57
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 49.7 bits (117), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 27/64 (42%), Positives = 39/64 (60%), Gaps = 3/64 (4%)
Query: 7 DRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRR 66
++GK RR R F+ Q + LEK FQ Y R++LA + L +++V++WFQNRR
Sbjct: 5 NKGKKRRN---RTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRR 61
Query: 67 MKWR 70
KWR
Sbjct: 62 AKWR 65
>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 = 49.7 bits (117), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 26/51 (50%), Positives = 32/51 (62%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
R VFS Q L+ RFQ QKY+S ++L+ L L QVK WFQN+RMK
Sbjct: 7 RTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMK 57
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 49.3 bits (116), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 33/50 (66%)
Query: 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
F+ Q + LEK F Y R++LA K+GL ++++++WFQNRR KWR
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWR 55
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 49.3 bits (116), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 34/51 (66%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
R F+ Q LE++F+ ++Y+S +R + + L L ++QVKIWFQNRR K
Sbjct: 4 RTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAK 54
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/58 (46%), Positives = 33/58 (56%)
Query: 11 PRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
P + R VFS Q L RFQ QKY+S ++L+ L L QVK WFQN+RMK
Sbjct: 19 PVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMK 76
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 47.4 bits (111), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 37/55 (67%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
R FS Q L++ F +Y+++ R++L+ +LGL ++Q+KIWFQN+R K + S
Sbjct: 5 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 59
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 47.4 bits (111), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 35/55 (63%)
Query: 14 GMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G +R ++ +Q K LE+ + K+I+K R++++ L + QV IWFQNRR+K
Sbjct: 1 GRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVK 55
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna
Complex At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|1HDD|D Chain D, Crystal Structure Of An Engrailed Homeodomain-Dna
Complex At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|2JWT|A Chain A, Solution Structure Of Engrailed Homeodomain Wt
Length = 61
Score = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 37/55 (67%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
R FS Q L++ F +Y+++ R++L+ +LGL ++Q+KIWFQN+R K + S
Sbjct: 7 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 61
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 35/55 (63%)
Query: 14 GMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G +R ++ +Q K LE+ + K+I+K R++++ L + QV IWFQNRR+K
Sbjct: 7 GRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVK 61
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 35/51 (68%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
R FS Q L++ F +Y+++ R++L+ +LGL ++Q+KIWFQN+R K
Sbjct: 3 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 32/52 (61%)
Query: 17 RRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
+R ++ Q LEK F Y+++ R ++A L L + QVKIWFQNRRMK
Sbjct: 4 KRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMK 55
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 46.6 bits (109), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 36/55 (65%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
R FS Q ++ F +Y+++ R++L+ +LGL ++Q+KIWFQN+R K R S
Sbjct: 7 RTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIRRS 61
>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 = 46.6 bits (109), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 36/55 (65%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
R FS Q L++ F +Y+++ R++L+ +LGL ++Q+KIWFQN R K + S
Sbjct: 5 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIKKS 59
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 46.6 bits (109), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 34/57 (59%)
Query: 14 GMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
G R F+ Q + LEK F+ Y R++LA K+ L ++++++WF NRR KWR
Sbjct: 7 GQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWR 63
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 77
Score = 46.2 bits (108), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/52 (44%), Positives = 32/52 (61%)
Query: 17 RRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
+R ++ Q LEK F Y+++ R ++A L L + QVKIWFQNRRMK
Sbjct: 16 KRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMK 67
>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 = 46.2 bits (108), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 36/55 (65%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
R FS Q L++ F +Y+++ R++L+ +LGL ++Q+KIWFQN R K + S
Sbjct: 5 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIKKS 59
>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 = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 37/55 (67%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
R FS Q L++ F +Y+++ R++L+ +LGL ++Q+KIWF+N+R K + S
Sbjct: 7 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKKS 61
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/59 (37%), Positives = 36/59 (61%)
Query: 14 GMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
G +R +S Q + LE+ + K+I+K R+K++ L + Q+ IWFQNRR+K + S
Sbjct: 7 GRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKS 65
>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 = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 36/55 (65%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
R FS Q L++ F +Y+++ R++L+ +LGL ++Q+KIWF N+R K + S
Sbjct: 3 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIKKS 57
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 11 PRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRR 66
PRR R F+ Q LE+ F +Y++ P L+ KL L +QVKIWF+NRR
Sbjct: 2 PRRT---RTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRR 54
>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 = 43.1 bits (100), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G RR +R F+ Q + LE FQ +Y R+++A L +++V++WF+NRR K
Sbjct: 1 GSQRR---QRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAK 57
Query: 69 WRNSKE 74
WR +E
Sbjct: 58 WRKREE 63
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 42.7 bits (99), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 37/66 (56%), Gaps = 3/66 (4%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G RR +R F+ Q + LE FQ Y R+++A L +++V++WF+NRR K
Sbjct: 1 GSQRR---QRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAK 57
Query: 69 WRNSKE 74
WR +E
Sbjct: 58 WRKREE 63
>pdb|2HOS|A Chain A, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOS|B Chain B, Phage-selected Homeodomain Bound To Unmodified Dna
pdb|2HOT|A Chain A, Phage Selected Homeodomain Bound To Modified Dna
pdb|2HOT|B Chain B, Phage Selected Homeodomain Bound To Modified Dna
Length = 63
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 35/55 (63%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
R FS Q L++ F +Y+++ R++L+ +LGL ++QVK WF+N R K + S
Sbjct: 8 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKKS 62
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 42.0 bits (97), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 33/53 (62%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
R F+ Q + LE+ F+ Y R++LA++ L +++V++WF NRR +WR
Sbjct: 6 RTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWR 58
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 33/53 (62%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
R FS Q LE+ F+ +Y R++LA++ L ++++++WFQNRR + R
Sbjct: 22 RTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR 74
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/40 (42%), Positives = 30/40 (75%)
Query: 33 FQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
F +Y+++ R++L+ +LGL ++Q+KIWFQN+R K + S
Sbjct: 5 FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 44
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 39.3 bits (90), Expect = 0.001, Method: Composition-based stats.
Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR--NSKERE 76
F + R L + + Y S ++++LAE GL +QV WF+NRR + R +KERE
Sbjct: 501 FKEKSRGVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEAKERE 558
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 36/62 (58%), Gaps = 1/62 (1%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKW-RNSKERE 76
R F+ Q + LE F++ Y + LA+KL L+ +++IWFQNRR K R+ +E +
Sbjct: 5 RTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQ 64
Query: 77 LL 78
L
Sbjct: 65 FL 66
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 2/65 (3%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSKEREL 77
R F Q + ++ F I D K+LA+K GL +++WFQN R K+R + R+
Sbjct: 11 RTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQ- 69
Query: 78 LANGG 82
NGG
Sbjct: 70 -ENGG 73
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 37.4 bits (85), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 32/57 (56%)
Query: 14 GMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
G R F+ Q LE F +Y R+++A K+ L +S+V++WF+NRR K R
Sbjct: 7 GRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCR 63
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 34.7 bits (78), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 20/42 (47%), Positives = 26/42 (61%), Gaps = 5/42 (11%)
Query: 36 QKYI--SKPDRKKL---AEKLGLKDSQVKIWFQNRRMKWRNS 72
QKY+ S P RK L A ++GLK V++WFQN R + R S
Sbjct: 34 QKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKS 75
>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 = 34.3 bits (77), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 31/43 (72%)
Query: 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
R LE+ F+ ++ ++ +++++A+K G+ QV++WF N+RM+
Sbjct: 377 RAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 419
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 33.5 bits (75), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 31/43 (72%)
Query: 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
R LE+ F+ ++ ++ +++++A+K G+ QV++WF N+RM+
Sbjct: 9 RAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 51
>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 = 33.1 bits (74), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 34/51 (66%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
++ S R LE+ F+ ++ ++ +++++A+K G+ QV++WF N+RM+
Sbjct: 9 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 32.7 bits (73), Expect = 0.076, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 34/51 (66%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
++ S R LE+ F+ ++ ++ +++++A+K G+ QV++WF N+RM+
Sbjct: 9 KSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 59
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 32.7 bits (73), Expect = 0.078, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 24/33 (72%)
Query: 38 YISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
Y S+ +++LA+K G+ SQV WF N+R++++
Sbjct: 28 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 32.7 bits (73), Expect = 0.085, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 24/33 (72%)
Query: 38 YISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
Y S+ +++LA+K G+ SQV WF N+R++++
Sbjct: 30 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 62
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 32.7 bits (73), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 29/60 (48%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G R RR S + LE+ F S + ++AE+L L+ V++WF NRR +
Sbjct: 82 GANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQR 141
>pdb|1S7E|A Chain A, Solution Structure Of Hnf-6
Length = 147
Score = 32.3 bits (72), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 30/49 (61%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRR 66
R VF+D+QR+ L F+ K SK + ++++LGL+ S V +F N R
Sbjct: 99 RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 147
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 32.3 bits (72), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G RR R ++ +++ R LEK F + + D +AE+L ++ +++WF NRR K
Sbjct: 97 GLSRRRKKRTSIETNI-RVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQK 155
>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 = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 12/14 (85%), Positives = 14/14 (100%)
Query: 57 QVKIWFQNRRMKWR 70
Q+KIWFQNRRMKW+
Sbjct: 2 QIKIWFQNRRMKWK 15
>pdb|2D5V|A Chain A, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
pdb|2D5V|B Chain B, Crystal Structure Of Hnf-6alpha Dna-Binding Domain In
Complex With The Ttr Promoter
Length = 164
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 30/49 (61%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRR 66
R VF+D+QR+ L F+ K SK + ++++LGL+ S V +F N R
Sbjct: 101 RLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR 149
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
To Dna
Length = 73
Score = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 24/33 (72%)
Query: 38 YISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
Y S+ +++LA+K G+ SQV WF N+R++++
Sbjct: 28 YPSEEAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 32.0 bits (71), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 12/14 (85%), Positives = 14/14 (100%)
Query: 57 QVKIWFQNRRMKWR 70
Q+KIWFQNRRMKW+
Sbjct: 2 QIKIWFQNRRMKWK 15
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 31.6 bits (70), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 26/52 (50%)
Query: 21 FSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
F+D Q + L+ F Y + ++L+ L L + +WFQN R K R S
Sbjct: 14 FTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKS 65
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 31.6 bits (70), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 12/14 (85%), Positives = 14/14 (100%)
Query: 57 QVKIWFQNRRMKWR 70
Q+KIWFQNRRMKW+
Sbjct: 2 QIKIWFQNRRMKWK 15
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 31.6 bits (70), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 24/33 (72%)
Query: 38 YISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
Y S+ +++LA+K G+ SQV WF N+R++++
Sbjct: 29 YPSEEAKEELAKKSGITVSQVSNWFGNKRIRYK 61
>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 = 31.2 bits (69), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 23/33 (69%)
Query: 38 YISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWR 70
Y S+ +++LA K G+ SQV WF N+R++++
Sbjct: 28 YPSEEAKEELARKCGITVSQVSNWFGNKRIRYK 60
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 29.3 bits (64), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 28/55 (50%)
Query: 18 RAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
R +D Q + L + F I S+ K++A+K GL +K WF+N K R S
Sbjct: 11 RTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQS 65
>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 = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 31/67 (46%)
Query: 6 FDRGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNR 65
F G+P + RR F+ + L F+ + + + A++L V++WF NR
Sbjct: 85 FVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEXAKELNYDREVVRVWFSNR 144
Query: 66 RMKWRNS 72
R +N+
Sbjct: 145 RQTLKNT 151
>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 = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G RR R ++ +++ R LEK F + + + +A++L ++ +++WF NRR K
Sbjct: 96 GLSRRRKKRTSIETNI-RVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQK 154
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 28.9 bits (63), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 47 LAEKLGLKDSQVKIWFQNRRMKWRNS 72
+A +LGL+ V++WF NRR K + S
Sbjct: 129 IANQLGLEKDVVRVWFSNRRQKGKRS 154
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 28.5 bits (62), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 1/61 (1%)
Query: 14 GMMRRAVFSDLQRKGLEKRF-QIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNS 72
G A ++ Q + LE F ++ K+ +A + GL + Q + WF+ R +WR S
Sbjct: 1 GSEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 60
Query: 73 K 73
+
Sbjct: 61 E 61
>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 = 28.5 bits (62), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 24/43 (55%)
Query: 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
R LEK F + + + +AE+L ++ +++WF NRR K
Sbjct: 13 RFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQK 55
>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 = 28.5 bits (62), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 20/31 (64%), Gaps = 3/31 (9%)
Query: 41 KPD---RKKLAEKLGLKDSQVKIWFQNRRMK 68
+PD +++L E GL +++WFQN+R K
Sbjct: 27 RPDALMKEQLVEMTGLSPRVIRVWFQNKRCK 57
>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 = 28.1 bits (61), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G RR R ++ +++ R LEK F + + + +A++L ++ +++WF NRR K
Sbjct: 99 GLSRRRKKRTSIETNI-RVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 157
>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 = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 33/60 (55%), Gaps = 1/60 (1%)
Query: 9 GKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
G RR R ++ +++ R LEK F + + + +A++L ++ +++WF NRR K
Sbjct: 92 GLSRRRKKRTSIETNI-RVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 150
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 47 LAEKLGLKDSQVKIWFQNRRMK 68
+A +LGL+ V++WF NRR K
Sbjct: 41 IANQLGLEKDVVRVWFCNRRQK 62
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 27.7 bits (60), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 10/27 (37%), Positives = 17/27 (62%)
Query: 47 LAEKLGLKDSQVKIWFQNRRMKWRNSK 73
+A + GL + Q + WF+ R +WR S+
Sbjct: 36 IAAEAGLTEEQTQKWFKQRLAEWRRSE 62
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 27.3 bits (59), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%)
Query: 8 RGKPRRGMMRRAVFSDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRM 67
RG R +R R LEK F + + + +A++L ++ +++WF NRR
Sbjct: 1 RGSHMRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQ 60
Query: 68 K 68
K
Sbjct: 61 K 61
>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 = 27.3 bits (59), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 24/43 (55%)
Query: 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
R LEK F + + + +A++L ++ +++WF NRR K
Sbjct: 116 RVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 158
>pdb|1KZ2|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain Derivative [w6f,W14f]
Length = 16
Score = 26.9 bits (58), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 10/14 (71%), Positives = 14/14 (100%)
Query: 57 QVKIWFQNRRMKWR 70
Q+KI+FQNRRMK++
Sbjct: 2 QIKIFFQNRRMKFK 15
>pdb|3NAR|A Chain A, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And
Homeoboxes Protein 1, Homeodomain 4)
pdb|3NAR|B Chain B, Crystal Structure Of Zhx1 Hd4 (Zinc-Fingers And
Homeoboxes Protein 1, Homeodomain 4)
Length = 96
Score = 26.9 bits (58), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 23/43 (53%)
Query: 29 LEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRN 71
L+ F ++ S + KLA++ GL + + WF + R W+N
Sbjct: 40 LKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKN 82
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 26.6 bits (57), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 21/43 (48%)
Query: 26 RKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMK 68
+ LE F S + LA+ L L+ V++WF NRR K
Sbjct: 111 KGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQK 153
>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein 3
Length = 76
Score = 26.6 bits (57), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 25/52 (48%)
Query: 22 SDLQRKGLEKRFQIQKYISKPDRKKLAEKLGLKDSQVKIWFQNRRMKWRNSK 73
S Q L+ F ++ + + + L + GL +V+ WF +RR RN K
Sbjct: 16 SHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLK 67
>pdb|2LY9|A Chain A, Solution Nmr Structure Of Homeobox 2 Domain From Human
Zhx1 Repressor, Northeast Structural Genomics
Consortium (Nesg) Target Hr7907f
Length = 74
Score = 26.2 bits (56), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 46 KLAEKLGLKDSQVKIWFQNRRMKWRNSKERELL 78
+L + GL ++K WF + R RNSK + L
Sbjct: 38 RLMKITGLTKGEIKKWFSDTRYNQRNSKSNQCL 70
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
0.314 0.133 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,338,803
Number of Sequences: 62578
Number of extensions: 174523
Number of successful extensions: 394
Number of sequences better than 100.0: 95
Number of HSP's better than 100.0 without gapping: 92
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 299
Number of HSP's gapped (non-prelim): 95
length of query: 155
length of database: 14,973,337
effective HSP length: 91
effective length of query: 64
effective length of database: 9,278,739
effective search space: 593839296
effective search space used: 593839296
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 47 (22.7 bits)