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= 023291
(284 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 52.0 bits (123), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/51 (49%), Positives = 32/51 (62%)
Query: 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
R + +Q LEK FE + L P + +LAK L L RQV WFQNRRA+W+
Sbjct: 13 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 47.8 bits (112), Expect = 6e-06, Method: Composition-based stats.
Identities = 25/56 (44%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 65 KKRR--LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
++RR T+EQ+ LEK F + L + Q+A L L QV +WFQNRRA+WK
Sbjct: 8 RRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
>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 = 44.3 bits (103), Expect = 8e-05, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 40/64 (62%), Gaps = 5/64 (7%)
Query: 63 PEKKRR-----LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARW 117
P++K+R T+ Q+ LEK+F + + + +LA K+GL ++ VWFQNRRA+W
Sbjct: 2 PKRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKW 61
Query: 118 KTKQ 121
+ ++
Sbjct: 62 RKQE 65
>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 = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/61 (39%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 64 EKKRRLTAE---QVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTK 120
E KR+ T+ Q LEK F L R+ ++A L L RQ+ +WFQNRR +WK +
Sbjct: 27 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 86
Query: 121 Q 121
Sbjct: 87 H 87
>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 = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 58 YDEQLPEKKRR----LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNR 113
Y + P K+++ T QV LEK F + L + LA+ L + QV WFQNR
Sbjct: 9 YQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNR 68
Query: 114 RARWKTKQLE 123
R +W+ + E
Sbjct: 69 RTKWRRQTAE 78
>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 = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/67 (37%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 62 LPEKKRR----LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARW 117
LP KKR+ T Q + LE+ F + L + LA + L P QV +WFQN R +
Sbjct: 5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKT 64
Query: 118 KTKQLER 124
K Q E+
Sbjct: 65 KRAQNEK 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 = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 23/50 (46%), Positives = 28/50 (56%)
Query: 73 QVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQL 122
QV LE+ F + L + LAK L L QV +WFQNRR + K KQL
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL 64
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 43.1 bits (100), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/53 (37%), Positives = 34/53 (64%)
Query: 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121
T+ Q+ LEK+F + + + +LA K+GL ++ VWFQNRRA+W+ ++
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 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 = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/51 (41%), Positives = 28/51 (54%)
Query: 70 TAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTK 120
T Q LEK F L R+ ++A L L RQ+ +WFQNRR +WK +
Sbjct: 4 TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 54
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 34/53 (64%)
Query: 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121
T+ Q+ LEK+F + + + +LA K+GL ++ VWFQNRRA+W+ ++
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 30/55 (54%)
Query: 66 KRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTK 120
++ T Q LEK F L R+ ++A L L RQ+ +WFQNRR +WK +
Sbjct: 7 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 61
>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 = 42.4 bits (98), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 30/55 (54%)
Query: 66 KRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTK 120
++ T Q LEK F L R+ ++A L L RQ+ +WFQNRR +WK +
Sbjct: 6 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE 60
>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 = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 30/55 (54%)
Query: 66 KRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTK 120
++ T Q LEK F L R+ ++A L L RQ+ +WFQNRR +WK +
Sbjct: 6 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 60
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 28/50 (56%)
Query: 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
T Q+ LEK FE + L + LA+ LGL QV W+QNRR +WK
Sbjct: 24 FTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 21/52 (40%), Positives = 33/52 (63%)
Query: 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTK 120
TAEQ+ LE++FE + + + +LA++ L +V VWF NRRARW+ +
Sbjct: 9 FTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 30/50 (60%)
Query: 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
T EQ+ LEK FE + + + +LA K+ L ++ VWF NRRA+W+
Sbjct: 14 FTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWR 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 = 41.2 bits (95), Expect = 6e-04, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 30/54 (55%)
Query: 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQL 122
L +Q+H L + A + + K QL + GL PR + VWFQN+R + K + +
Sbjct: 10 LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 31/50 (62%)
Query: 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
T EQ+ LE F+ + + QLA+K+ L+ +V VWF+NRRA+W+
Sbjct: 14 FTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWR 63
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 41.2 bits (95), Expect = 7e-04, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 30/55 (54%)
Query: 66 KRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTK 120
++ T Q LEK F + L R+ ++A L L RQ+ +WFQNRR + K +
Sbjct: 24 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKE 78
>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 = 41.2 bits (95), Expect = 7e-04, Method: Composition-based stats.
Identities = 20/52 (38%), Positives = 29/52 (55%)
Query: 70 TAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121
T Q+ LEK F + R+ +LA L L R + +WFQNRR +WK ++
Sbjct: 11 TRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62
>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 = 41.2 bits (95), Expect = 7e-04, Method: Composition-based stats.
Identities = 22/60 (36%), Positives = 36/60 (60%), Gaps = 2/60 (3%)
Query: 59 DEQLPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
DE+ P + ++EQ+ L++ F L R+ QL+ +LGL Q+ +WFQN+RA+ K
Sbjct: 2 DEKRP--RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 36/61 (59%), Gaps = 4/61 (6%)
Query: 65 KKRR----LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTK 120
KKRR T+ Q+ LEK F+ + + + QLA + L +V VWFQNRRA+W+ +
Sbjct: 8 KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKR 67
Query: 121 Q 121
+
Sbjct: 68 E 68
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 35/57 (61%), Gaps = 2/57 (3%)
Query: 64 EKKRR--LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
EK+ R ++EQ+ L++ F L R+ QL+ +LGL Q+ +WFQN+RA+ K
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 23/61 (37%), Positives = 33/61 (54%)
Query: 64 EKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLE 123
+K+ T Q LEK F L +R+ ++A+ L L RQV +WFQNRR + K +
Sbjct: 15 KKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKD 74
Query: 124 R 124
R
Sbjct: 75 R 75
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 62 LPEKKRR----LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARW 117
LP KKR+ T Q + LE+ F + L + L + L P QV +WFQN R +
Sbjct: 8 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKT 67
Query: 118 KTKQLER 124
K Q E+
Sbjct: 68 KRAQNEK 74
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 40.0 bits (92), Expect = 0.001, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 30/48 (62%)
Query: 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRAR 116
++EQ+ L++ F L R+ QL+ +LGL Q+ +WFQN+RA+
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 34/60 (56%)
Query: 59 DEQLPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
E+ P+ K ++ + LE+ F + L + K ++AKK G+ P QV VWF N+R R K
Sbjct: 2 KEKSPKGKSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 34/60 (56%)
Query: 59 DEQLPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
E+ P+ K ++ + LE+ F + L + K ++AKK G+ P QV VWF N+R R K
Sbjct: 2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 21/59 (35%), Positives = 36/59 (61%), Gaps = 2/59 (3%)
Query: 62 LPEKKRR--LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
+ EK+ R ++EQ+ L++ F L R+ QL+ +LGL Q+ +WF+N+RA+ K
Sbjct: 1 MAEKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 22/55 (40%), Positives = 31/55 (56%)
Query: 64 EKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
+K+ T Q LEK F L +R+ ++A+ L L RQV +WFQNRR + K
Sbjct: 3 KKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
>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 = 0.002, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 64 EKKRR--LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
EK+ R ++EQ+ L++ F L R+ QL+ +LGL Q+ +WFQN RA+ K
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 57
>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 = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 64 EKKRR--LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
EK+ R ++EQ+ L++ F L R+ QL+ +LGL Q+ +WFQN RA+ K
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 21/62 (33%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 65 KKRRL--TAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQL 122
+KRR+ + QV+ LE+ F+ + L + LA + L P QV +WFQN R + K +
Sbjct: 3 RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62
Query: 123 ER 124
++
Sbjct: 63 DK 64
>pdb|1JGG|A Chain A, Even-Skipped Homeodomain Complexed To At-Rich Dna
pdb|1JGG|B Chain B, Even-Skipped Homeodomain Complexed To At-Rich Dna
Length = 60
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/46 (43%), Positives = 27/46 (58%)
Query: 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRR 114
T +Q+ LEK F EN + R+ +LA +L L + VWFQNRR
Sbjct: 8 FTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRR 53
>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 = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
++EQ+ L++ F L R+ QL+ +LGL Q+ +WF N+RA+ K
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>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 = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 28/54 (51%)
Query: 70 TAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLE 123
T EQ+H+L+ +F PE +LAK+ GL + WF + R WK L+
Sbjct: 33 TPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLK 86
>pdb|1MH3|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form I
pdb|1MH4|A Chain A, Maltose Binding-A1 Homeodomain Protein Chimera, Crystal
Form Ii
Length = 421
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 26/43 (60%)
Query: 76 LLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
LE+ F + L + K ++AKK G+ P QV VWF N+R R K
Sbjct: 379 FLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 25/46 (54%)
Query: 73 QVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
QV LE+ F + L + LAK L + QV WFQNRR +W+
Sbjct: 8 QVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWR 53
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 29/55 (52%)
Query: 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLE 123
T Q+ LEK F L R+ ++A L L QV +WFQNRR + K ++ E
Sbjct: 41 FTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 95
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 2/58 (3%)
Query: 59 DEQLPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRAR 116
DE+ P + ++EQ+ ++ F L R+ QL+ +LGL Q+ +WFQN+RA+
Sbjct: 2 DEKRP--RTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/43 (44%), Positives = 26/43 (60%)
Query: 76 LLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
LE+ F + L + K ++AKK G+ P QV VWF N+R R K
Sbjct: 11 FLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 26/50 (52%)
Query: 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
T Q+ LE+ F + L + + + L L QV +WFQNRRA+ K
Sbjct: 7 FTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>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 = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 25/42 (59%)
Query: 73 QVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRR 114
QV+ LE+ F+ + L + QLA L L QV +WFQNRR
Sbjct: 13 QVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRR 54
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 37.4 bits (85), Expect = 0.009, Method: Composition-based stats.
Identities = 22/59 (37%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 63 PEKKRR-LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTK 120
P + R T+ Q+ LE+ F L R L+ KL L QV +WF+NRR R K +
Sbjct: 2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQ 60
>pdb|1FJL|A Chain A, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
pdb|1FJL|B Chain B, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
pdb|1FJL|C Chain C, Homeodomain From The Drosophila Paired Protein Bound To A
Dna Oligonucleotide
Length = 81
Score = 37.4 bits (85), Expect = 0.010, Method: Composition-based stats.
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 4/64 (6%)
Query: 62 LPEKKRR----LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARW 117
L K+RR +A Q+ LE++FE + + +LA++ L ++ VWFQNRRAR
Sbjct: 14 LKRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARL 73
Query: 118 KTKQ 121
+ +
Sbjct: 74 RKQH 77
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 37.4 bits (85), Expect = 0.010, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 27/46 (58%)
Query: 73 QVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
Q+ L++ F+ L + +LA LGL QV +WFQN+R++ K
Sbjct: 18 QLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIK 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 = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 59 DEQLPEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
DE+ P ++EQ+ L++ F L R+ QL+ +LGL QV WF+N RA+ K
Sbjct: 3 DEKRPRTA--FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 36/60 (60%), Gaps = 8/60 (13%)
Query: 63 PEKKRRL----TAEQVHLLEKSFEAENKLEPERK--GQLAKKLGLQPRQVAVWFQNRRAR 116
P++ +RL T EQ+ +L + + ++ P RK +A ++GL+ R V VWFQN RAR
Sbjct: 14 PQRDKRLRTTITPEQLEILYQKYLLDS--NPTRKMLDHIAHEVGLKKRVVQVWFQNTRAR 71
>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 = 36.2 bits (82), Expect = 0.021, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 27/53 (50%)
Query: 66 KRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
++ T Q LEK F + R+ +A L L RQ+ +WFQNRR + K
Sbjct: 7 RQTYTRYQTLELEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSK 59
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 36.2 bits (82), Expect = 0.022, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 62 LPEKKRRLTAEQVHL--LEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
L +K+R+ +V L LE+ + + +++ +++ L RQV +WFQNRR + K
Sbjct: 5 LEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 63
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 35.8 bits (81), Expect = 0.031, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 65 KKRRLTAEQVHL--LEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
+K+R+ +V L LE+ + + +++ +++ L RQV +WFQNRR + K
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 35.4 bits (80), Expect = 0.034, Method: Composition-based stats.
Identities = 19/55 (34%), Positives = 28/55 (50%)
Query: 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQLE 123
T Q+ +LE F + LA+KL L+ ++ +WFQNRRA+ K E
Sbjct: 8 FTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRE 62
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 35.4 bits (80), Expect = 0.039, Method: Composition-based stats.
Identities = 16/41 (39%), Positives = 25/41 (60%)
Query: 78 EKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
++ F L R+ QL+ +LGL Q+ +WFQN+RA+ K
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 35.0 bits (79), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 32/53 (60%)
Query: 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121
T++Q+ LE +F+ + + + ++A L +V VWF+NRRA+W+ ++
Sbjct: 10 FTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 34.7 bits (78), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 26/62 (41%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 66 KRRLTAEQVHLLE--KSFEAENKLEPERK--GQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121
KR T+ + H L KS+ A N P+ K QLA+K GL R + VWFQN RA+++
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINH-NPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNL 66
Query: 122 LE 123
L
Sbjct: 67 LR 68
>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 = 34.3 bits (77), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 31/53 (58%)
Query: 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWKTKQ 121
T++Q+ LE +F+ + + ++A L +V VWF+NRRA+W+ ++
Sbjct: 10 FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 62
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 34.3 bits (77), Expect = 0.090, Method: Composition-based stats.
Identities = 16/56 (28%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 65 KKRRL--TAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
+K+R+ + Q+ LE+ + A + +++ +++ L RQ+ +WFQNRR + K
Sbjct: 8 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEK 63
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 26/49 (53%)
Query: 68 RLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRAR 116
R T Q+ +L+ F+A + + QL+ L L R + VWFQN R +
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQK 61
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 69 LTAEQVHLLEKSFEAENK-LEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
+T +QV +LE +F NK +P +A + GL Q WF+ R A W+
Sbjct: 8 MTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 58
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 33.1 bits (74), Expect = 0.17, Method: Composition-based stats.
Identities = 15/29 (51%), Positives = 20/29 (68%)
Query: 90 ERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
E K +LAKK G+ QV+ WF N+R R+K
Sbjct: 32 EAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 32.7 bits (73), Expect = 0.25, Method: Composition-based stats.
Identities = 15/29 (51%), Positives = 20/29 (68%)
Query: 90 ERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
E K +LAKK G+ QV+ WF N+R R+K
Sbjct: 34 EAKEELAKKCGITVSQVSNWFGNKRIRYK 62
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 32.3 bits (72), Expect = 0.28, Method: Composition-based stats.
Identities = 15/29 (51%), Positives = 20/29 (68%)
Query: 90 ERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
E K +LAKK G+ QV+ WF N+R R+K
Sbjct: 32 EAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 70 TAEQVHLLEKSFEAENK-LEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
T +QV +LE +F NK +P +A + GL Q WF+ R A W+
Sbjct: 10 TEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 59
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 32.3 bits (72), Expect = 0.30, Method: Composition-based stats.
Identities = 15/29 (51%), Positives = 20/29 (68%)
Query: 90 ERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
E K +LAKK G+ QV+ WF N+R R+K
Sbjct: 33 EAKEELAKKSGITVSQVSNWFGNKRIRYK 61
>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 = 32.0 bits (71), Expect = 0.41, Method: Composition-based stats.
Identities = 10/17 (58%), Positives = 14/17 (82%)
Query: 104 RQVAVWFQNRRARWKTK 120
RQ+ +WFQNRR +WK +
Sbjct: 1 RQIKIWFQNRRMKWKKR 17
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 32.0 bits (71), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 37/66 (56%), Gaps = 7/66 (10%)
Query: 59 DEQLPEKKRR----LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRR 114
++++P KK++ ++ Q+ +L F+ + L ++ +L+ L L +QV WFQN+R
Sbjct: 15 EDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQR 74
Query: 115 ---ARW 117
RW
Sbjct: 75 MKSKRW 80
>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 = 31.6 bits (70), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 60 EQLPEKKRRLTAEQVHL---LEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRAR 116
E L E++++ T+ + ++ LEKSF K E +A +L ++ + VWF NRR +
Sbjct: 99 EGLSERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 158
Query: 117 WK 118
K
Sbjct: 159 EK 160
>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 = 0.60, Method: Composition-based stats.
Identities = 14/29 (48%), Positives = 20/29 (68%)
Query: 90 ERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
E K +LA+K G+ QV+ WF N+R R+K
Sbjct: 32 EAKEELARKCGITVSQVSNWFGNKRIRYK 60
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 31.2 bits (69), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 89 PERKGQLAKKLGLQPRQVAVWFQNRRAR 116
P K +LA+ GL QV+ WF+NRR R
Sbjct: 521 PREKRELAEATGLTTTQVSNWFKNRRQR 548
>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 = 30.8 bits (68), Expect = 0.94, Method: Composition-based stats.
Identities = 21/55 (38%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 65 KKRRLTAEQVHL-LEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
KKR V LEKSF A K E +A++L ++ + VWF NRR + K
Sbjct: 3 KKRTSIETNVRFALEKSFLANQKPTSEEILLIAEQLHMEKEVIRVWFCNRRQKEK 57
>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 = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 60 EQLPEKKRRLTAEQVHL---LEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRAR 116
E L ++++ T+ + ++ LEKSF K E +A +L ++ + VWF NRR +
Sbjct: 95 EGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQK 154
Query: 117 WK 118
K
Sbjct: 155 EK 156
>pdb|2ECB|A Chain A, The Solution Structure Of The Third Homeobox Domain Of
Human Zinc Fingers And Homeoboxes Protein
Length = 89
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 28/52 (53%)
Query: 63 PEKKRRLTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRR 114
P+K + TAEQ+ +L+ SF + L E +L + L R++ WF ++
Sbjct: 12 PQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKK 63
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%)
Query: 69 LTAEQVHLLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRAR 116
T Q+ +LE F + + ++A K+ L +V VWF+NRRA+
Sbjct: 14 FTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAK 61
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 60 EQLPEKKRRLTAEQVHL---LEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRAR 116
E L ++++ T+ + ++ LEKSF K E +A++L ++ + VWF NRR +
Sbjct: 96 EGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQK 155
Query: 117 WK 118
K
Sbjct: 156 EK 157
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 29.6 bits (65), Expect = 1.8, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 22/42 (52%)
Query: 77 LEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRARWK 118
LEKSF K E +A +L ++ + VWF NRR + K
Sbjct: 22 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 63
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 29.6 bits (65), Expect = 1.9, Method: Composition-based stats.
Identities = 10/15 (66%), Positives = 13/15 (86%)
Query: 104 RQVAVWFQNRRARWK 118
RQ+ +WFQNRR +WK
Sbjct: 1 RQIKIWFQNRRMKWK 15
>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 = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 60 EQLPEKKRRLTAEQVHL---LEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRAR 116
E L ++++ T+ + ++ LEKSF K E +A +L ++ + VWF NRR +
Sbjct: 98 EGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 157
Query: 117 WK 118
K
Sbjct: 158 EK 159
>pdb|1OCT|C Chain C, Crystal Structure Of The Oct-1 Pou Domain Bound To An
Octamer Site: Dna Recognition With Tethered Dna-Binding
Modules
Length = 156
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 60 EQLPEKKRRLTAEQVHL---LEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRAR 116
E L ++++ T+ + ++ LEKSF K E +A +L ++ + VWF NRR +
Sbjct: 91 EGLSRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQK 150
Query: 117 WK 118
K
Sbjct: 151 EK 152
>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 = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 63 PEKKRRLTAEQVHL--LEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQNRRA---RW 117
++K R Q L L+ F+ + L ++ +L+ L L +QV WFQN+R RW
Sbjct: 2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW 61
Query: 118 K 118
+
Sbjct: 62 Q 62
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 28.1 bits (61), Expect = 6.0, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 105 QVAVWFQNRRARWK 118
Q+ +WFQNRR +WK
Sbjct: 2 QIKIWFQNRRMKWK 15
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 27.7 bits (60), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 22/67 (32%), Positives = 35/67 (52%), Gaps = 6/67 (8%)
Query: 58 YDEQL----PEKKRRLTAEQVH--LLEKSFEAENKLEPERKGQLAKKLGLQPRQVAVWFQ 111
Y+E++ ++KRR T LE+ F +K + ++A++L L+ V VWF
Sbjct: 77 YNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFC 136
Query: 112 NRRARWK 118
NRR R K
Sbjct: 137 NRRQREK 143
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 0.131 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,169,761
Number of Sequences: 62578
Number of extensions: 245377
Number of successful extensions: 435
Number of sequences better than 100.0: 88
Number of HSP's better than 100.0 without gapping: 84
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 351
Number of HSP's gapped (non-prelim): 88
length of query: 284
length of database: 14,973,337
effective HSP length: 98
effective length of query: 186
effective length of database: 8,840,693
effective search space: 1644368898
effective search space used: 1644368898
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)