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= 040769
(257 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 26/63 (41%), Positives = 41/63 (65%)
Query: 79 GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
GSS +S + + T +QLE+LE FQE D + +LAR++ L+ ++ VWF+NRRA
Sbjct: 1 GSSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRA 60
Query: 139 RWK 141
+W+
Sbjct: 61 KWR 63
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 22/51 (43%), Positives = 33/51 (64%)
Query: 91 RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
R ++DQ LE+ F+ + L P + +LA+ L L RQ+ WFQNRRA+W+
Sbjct: 13 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWR 63
>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 = 1e-05, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 38/63 (60%)
Query: 79 GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
GSS +S Q + T +Q+E+LE+ F+ D + +LA ++ L +I VWF NRRA
Sbjct: 1 GSSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRA 60
Query: 139 RWK 141
+W+
Sbjct: 61 KWR 63
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 34/53 (64%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
TS QLE LE++F D + +LA ++GL +I VWFQNRRA+W+ ++
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 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 = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 77 HYGSSSTSSQERKKR----LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVW 132
H G+S+ ++ KR T Q LE+ F L R++++A L L RQI +W
Sbjct: 16 HLGTSTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIW 75
Query: 133 FQNRRARWK 141
FQNRR +WK
Sbjct: 76 FQNRRMKWK 84
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 34/57 (59%)
Query: 85 SQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
S+ R+ TS+QL LE+ F + L + ++A L L Q+ +WFQNRRA+WK
Sbjct: 7 SRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 32/50 (64%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
+S+QL L+R F E L R+ +L+ ELGL QI +WFQN+RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 34/53 (64%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
TS QLE LE++F D + +LA ++GL +I VWFQNRRA+W+ ++
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 58
>pdb|1HDD|C Chain C, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|1HDD|D Chain D, Crystal Structure Of An Engrailed Homeodomain-Dna Complex
At 2.8 Angstroms Resolution: A Framework For
Understanding Homeodomain-Dna Interactions
pdb|2JWT|A Chain A, Solution Structure Of Engrailed Homeodomain Wt
Length = 61
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 32/50 (64%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
+S+QL L+R F E L R+ +L+ ELGL QI +WFQN+RA+ K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/48 (45%), Positives = 31/48 (64%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139
+S+QL L+R F E L R+ +L+ ELGL QI +WFQN+RA+
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
pdb|3A01|F Chain F, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
Length = 67
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 34/53 (64%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
TS QLE LE++F D + +LA ++GL +I VWFQNRRA+W+ ++
Sbjct: 13 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE 65
>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 = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 31/50 (62%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
+S+QL L+R F E L R+ +L+ ELGL QI +WFQN RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 39/63 (61%)
Query: 79 GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
GSS +S ++ + +S QL +L+R FQ+ L + +LA LGL Q+ +WFQN+R+
Sbjct: 1 GSSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRS 60
Query: 139 RWK 141
+ K
Sbjct: 61 KIK 63
>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 = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/50 (46%), Positives = 31/50 (62%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
+S+QL L+R F E L R+ +L+ ELGL QI +WFQN RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAKIK 57
>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 = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 32/50 (64%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
+S+QL L+R F E L R+ +L+ ELGL QI +WF+N+RA+ K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 43.9 bits (102), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/62 (38%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 82 STSSQERKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139
S+ S RKKR+ + QL LER + + D++ K++ L RQI +WFQNRR +
Sbjct: 2 SSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVK 61
Query: 140 WK 141
K
Sbjct: 62 EK 63
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 31/50 (62%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
+S+QL L+R F E L R+ +L+ ELGL QI +WF N+RA+ K
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 25/57 (43%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 88 RKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142
RKKR T Q LE+ F + L DR+ ++AR L L RQ+ +WFQNRR + K
Sbjct: 2 RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKK 58
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 25/56 (44%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 88 RKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
RKKR T Q LE+ F + L DR+ ++AR L L RQ+ +WFQNRR + K
Sbjct: 14 RKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMK 69
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 30/48 (62%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139
+S+QL +R F E L R+ +L+ ELGL QI +WFQN+RA+
Sbjct: 10 FSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 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 = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 40/68 (58%), Gaps = 4/68 (5%)
Query: 81 SSTSSQERKKR----LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNR 136
S S++ +K+R TS QLE LE+ FQ+ D + +LA L ++ VWFQNR
Sbjct: 1 SHMSNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNR 60
Query: 137 RARWKSKQ 144
RA+W+ ++
Sbjct: 61 RAKWRKRE 68
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 28/49 (57%)
Query: 93 TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
T Q LE+ F L R++++A L L RQI +WFQNRR +WK
Sbjct: 4 TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 52
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%)
Query: 79 GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
G+ + + + T QL LE+ F+++ L ++ LA LGL Q+ W+QNRR
Sbjct: 11 GTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRM 70
Query: 139 RWK 141
+WK
Sbjct: 71 KWK 73
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 32/52 (61%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK 143
T++QLE LER+F+ D + +LA+ L ++ VWF NRRARW+ +
Sbjct: 9 FTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 60
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 28/49 (57%)
Query: 93 TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
T Q LE+ F L R++++A L L RQI +WFQNRR +WK
Sbjct: 11 TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 59
>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 = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 28/50 (56%)
Query: 93 TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142
T Q LE+ F L R++++A L L RQI +WFQNRR +WK
Sbjct: 10 TRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 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 = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 28/49 (57%)
Query: 93 TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
T Q LE+ F L R++++A L L RQI +WFQNRR +WK
Sbjct: 10 TRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 58
>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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 71 MEKNIHHYGSSSTSSQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQ 128
M + I H + T + +K R T Q+ LE+ F ++ L + LAR L + Q
Sbjct: 1 MARRIGHPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQ 60
Query: 129 IAVWFQNRRARWKSKQLE 146
+ WFQNRR +W+ + E
Sbjct: 61 VKTWFQNRRTKWRRQTAE 78
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 88 RKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
RKKR+ T QL+ LER + + D++ +++ L RQ+ +WFQNRR + K
Sbjct: 8 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 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 = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/52 (40%), Positives = 30/52 (57%)
Query: 93 TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144
T QL LE+ F + R+++LA L L R I +WFQNRR +WK ++
Sbjct: 11 TRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE 62
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 88 RKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
RKKR+ T QL+ LER + + D++ +++ L RQ+ +WFQNRR + K
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>pdb|2L9R|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Homeobox
Protein Nkx-3.1 From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6470a
Length = 69
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 28/50 (56%)
Query: 96 QLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL 145
Q+ LER F + L + LA+ L L Q+ +WFQNRR + K KQL
Sbjct: 15 QVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL 64
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 30/50 (60%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
+S+QL L+R F E L R+ +L+ ELGL Q+ WF+N RA+ K
Sbjct: 11 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 1/68 (1%)
Query: 84 SSQERKK-RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142
SQ R++ TS QL+ LE +FQ D + ++A L ++ VWF+NRRA+W+
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 143 KQLELLYD 150
++ ++ D
Sbjct: 61 REEFIVTD 68
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 44/84 (52%), Gaps = 11/84 (13%)
Query: 79 GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRK--MKLARELGLQPRQIAVWFQNR 136
GSS +S + + QL +++ F I +PD K +LA++ GL R + VWFQN
Sbjct: 1 GSSGSSGKRMRTSFKHHQLRTMKSYF--AINHNPDAKDLKQLAQKTGLTKRVLQVWFQNA 58
Query: 137 RARWKSKQLELLYDSLKQEYDAVS 160
RA+++ + L+QE VS
Sbjct: 59 RAKFRR-------NLLRQENGGVS 75
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 81 SSTSSQERKKRLTSDQLESLE--RSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
+ T+ R+ R T + ++LE + F L R++++A L L RQI +WFQNRR
Sbjct: 14 AGTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRM 73
Query: 139 RWK 141
+ K
Sbjct: 74 KLK 76
>pdb|1NK2|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, 20 STRUCTURES
pdb|1NK3|P Chain P, VndNK-2 HomeodomainDNA COMPLEX, NMR, MINIMIZED AVERAGE
Structure
pdb|1VND|A Chain A, VndNK-2 Protein (Homeodomain), Nmr
Length = 77
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 79 GSSSTSSQERKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNR 136
S +++RK+R+ T Q LER F+++ L + LA + L P Q+ +WFQN
Sbjct: 1 ASDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNH 60
Query: 137 RARWKSKQLELLYDS 151
R + K Q E Y+
Sbjct: 61 RYKTKRAQNEKGYEG 75
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 1/68 (1%)
Query: 84 SSQERKK-RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142
SQ R++ TS QL+ LE +FQ D + ++A L ++ VWF+NRRA+W+
Sbjct: 1 GSQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRK 60
Query: 143 KQLELLYD 150
++ ++ D
Sbjct: 61 REEFIVTD 68
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 36/67 (53%), Gaps = 3/67 (4%)
Query: 78 YGSSSTSSQERKKRLTSDQL---ESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQ 134
Y +++ ++KR T+ + ++LER F E K M++A EL L+ + VWF
Sbjct: 77 YNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFC 136
Query: 135 NRRARWK 141
NRR R K
Sbjct: 137 NRRQREK 143
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/59 (44%), Positives = 36/59 (61%), Gaps = 8/59 (13%)
Query: 87 ERKKRL----TSDQLESLERSFQEEIKLDPDRKM--KLARELGLQPRQIAVWFQNRRAR 139
+R KRL T +QLE L + + + +P RKM +A E+GL+ R + VWFQN RAR
Sbjct: 15 QRDKRLRTTITPEQLEILYQKYL--LDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRAR 71
>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 = 0.003, Method: Compositional matrix adjust.
Identities = 21/46 (45%), Positives = 27/46 (58%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137
T DQL LE+ F +E + R+ +LA +L L I VWFQNRR
Sbjct: 8 FTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRR 53
>pdb|2P81|A Chain A, Engrailed Homeodomain Helix-Turn-Helix Motif
Length = 44
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/41 (46%), Positives = 26/41 (63%)
Query: 101 ERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
+R F E L R+ +L+ ELGL QI +WFQN+RA+ K
Sbjct: 2 KREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 31/55 (56%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146
T+ QL LE+ F L R++++A L L Q+ +WFQNRR + K ++ E
Sbjct: 41 FTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 95
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 30/50 (60%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
T+ QL +LER F+++ L + + + L L Q+ +WFQNRRA+ K
Sbjct: 7 FTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 38/74 (51%), Gaps = 2/74 (2%)
Query: 80 SSSTSSQERKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137
S +++RK+R+ T Q LER F+++ L + L + L P Q+ +WFQN R
Sbjct: 5 SDGLPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHR 64
Query: 138 ARWKSKQLELLYDS 151
+ K Q E Y+
Sbjct: 65 YKTKRAQNEKGYEG 78
>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 = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 35/58 (60%), Gaps = 2/58 (3%)
Query: 86 QERKKRLT--SDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
++R+ R T + QL+ LER+F+ D + +LA+ L +I VWFQNRRAR +
Sbjct: 17 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLR 74
>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 = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 28/57 (49%)
Query: 93 TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLY 149
T +QL L+ +F P+ KLA+E GL I WF + R WK+ L+ Y
Sbjct: 33 TPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLKWYY 89
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 30/55 (54%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146
T +Q+E LE F+ D LA++L L+ +I +WFQNRRA+ K E
Sbjct: 8 FTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRE 62
>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 = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 27/54 (50%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL 145
L QL +L + + D K +L GL PR I VWFQN+R + K + +
Sbjct: 10 LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 63
>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 = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 26/40 (65%)
Query: 100 LERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139
LE+ F+ + L+ K ++A++ G+ P Q+ VWF N+R R
Sbjct: 380 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMR 419
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 35.4 bits (80), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 26/50 (52%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
+ Q+ LER F + L + LA+ L + Q+ WFQNRR +W+
Sbjct: 4 FSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWR 53
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 35.4 bits (80), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 32/56 (57%), Gaps = 2/56 (3%)
Query: 88 RKKRL--TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
RK+R+ + Q+ LER F+++ L + LA + L P Q+ +WFQN R + K
Sbjct: 3 RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMK 58
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 35.4 bits (80), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 27/50 (54%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
TS Q+ LE+ F + L R L+ +L L Q+ +WF+NRR R K
Sbjct: 9 FTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
>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 = 35.0 bits (79), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 24/42 (57%)
Query: 100 LERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
LE+ F + R++ +A L L RQI +WFQNRR + K
Sbjct: 18 LEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSK 59
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 35.0 bits (79), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 87 ERKKRLTSDQLESLERSFQEEIKL-DPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
E +T DQ+E LE +F + K DP +A E GL Q WF+ R A W+
Sbjct: 3 EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 58
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 34.7 bits (78), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%)
Query: 79 GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
GSS +S + + T QL+ LE F + D + ++A ++ L ++ VWF+NRRA
Sbjct: 1 GSSGSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRA 60
Query: 139 RWK 141
+ +
Sbjct: 61 KCR 63
>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 = 34.7 bits (78), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 9/63 (14%)
Query: 79 GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
G SS S Q R LE+ F+ + L+ K ++A++ G+ P Q+ VWF N+R
Sbjct: 8 GKSSISPQAR---------AFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRM 58
Query: 139 RWK 141
R K
Sbjct: 59 RSK 61
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 34.7 bits (78), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 27/42 (64%)
Query: 100 LERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
LE+ F+ + L+ K ++A++ G+ P Q+ VWF N+R R K
Sbjct: 12 LEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 34.3 bits (77), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 9/63 (14%)
Query: 79 GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138
G SS S Q R LE F+ + L+ K ++A++ G+ P Q+ VWF N+R
Sbjct: 8 GKSSISPQAR---------AFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRM 58
Query: 139 RWK 141
R K
Sbjct: 59 RSK 61
>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 = 33.9 bits (76), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 30/52 (57%), Gaps = 2/52 (3%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK 143
+ Q+ LER F+++ L + +LA L L Q+ +WFQNR R+KSK
Sbjct: 9 FSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNR--RYKSK 58
>pdb|2HI3|A Chain A, Solution Structure Of The Homeodomain-Only Protein Hop
Length = 73
Score = 33.9 bits (76), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 93 TSDQLESLERSFQEEIKL-DPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
T DQ+E LE +F + K DP +A E GL Q WF+ R A W+
Sbjct: 10 TEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWR 59
>pdb|3L1P|A Chain A, Pou Protein:dna Complex
pdb|3L1P|B Chain B, Pou Protein:dna Complex
Length = 155
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 74 NIHHYGSSSTSSQERKKRLTSDQLE---SLERSFQEEIKLDPDRKMKLARELGLQPRQIA 130
N+ S T Q RK++ TS + SLE F + K + +A +LGL+ +
Sbjct: 82 NLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVR 141
Query: 131 VWFQNRRARWK 141
VWF NRR + K
Sbjct: 142 VWFSNRRQKGK 152
>pdb|1O4X|A Chain A, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 167
Score = 31.6 bits (70), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 85 SQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
S+ RKKR + ++ +LE+SF E K + +A +L ++ I VWF NRR + K
Sbjct: 102 SERRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 160
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 31.6 bits (70), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 85 SQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
S+ RKKR + ++ +LE+SF E K + +A +L ++ I VWF NRR + K
Sbjct: 99 SRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 157
>pdb|1HF0|A Chain A, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1HF0|B Chain B, Crystal Structure Of The Dna-Binding Domain Of Oct-1 Bound
To Dna As A Dimer
pdb|1GT0|C Chain C, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 159
Score = 31.2 bits (69), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 85 SQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
S+ RKKR + ++ +LE+SF E K + +A +L ++ I VWF NRR + K
Sbjct: 98 SRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEK 156
>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 = 30.8 bits (68), Expect = 0.68, Method: Composition-based stats.
Identities = 11/17 (64%), Positives = 14/17 (82%)
Query: 127 RQIAVWFQNRRARWKSK 143
RQI +WFQNRR +WK +
Sbjct: 1 RQIKIWFQNRRMKWKKR 17
>pdb|1OCT|C Chain C, Crystal Structure Of The Oct-1 Pou Domain Bound To An
Octamer Site: Dna Recognition With Tethered Dna-Binding
Modules
Length = 156
Score = 30.8 bits (68), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 85 SQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
S+ RKKR + ++ +LE+SF E K + +A +L ++ I VWF NRR + K
Sbjct: 94 SRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 152
>pdb|1CQT|A Chain A, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
pdb|1CQT|B Chain B, Crystal Structure Of A Ternary Complex Containing An Oca-B
Peptide, The Oct-1 Pou Domain, And An Octamer Element
Length = 163
Score = 30.8 bits (68), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 2/59 (3%)
Query: 85 SQERKKR--LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
S+ RKKR + ++ +LE+SF E K + +A +L ++ I VWF NRR + K
Sbjct: 101 SRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 159
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 30.8 bits (68), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 20/29 (68%)
Query: 113 DRKMKLARELGLQPRQIAVWFQNRRARWK 141
+ K +LA++ G+ Q++ WF N+R R+K
Sbjct: 34 EAKEELAKKCGITVSQVSNWFGNKRIRYK 62
>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 = 30.4 bits (67), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 19/27 (70%)
Query: 115 KMKLARELGLQPRQIAVWFQNRRARWK 141
K +LAR+ G+ Q++ WF N+R R+K
Sbjct: 34 KEELARKCGITVSQVSNWFGNKRIRYK 60
>pdb|2DA1|A Chain A, Solution Structure Of The First Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 30/57 (52%)
Query: 79 GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQN 135
GSS +S + + R+T DQL L + F ++ ++A + GL + I WF+N
Sbjct: 1 GSSGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRN 57
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 20/29 (68%)
Query: 113 DRKMKLARELGLQPRQIAVWFQNRRARWK 141
+ K +LA++ G+ Q++ WF N+R R+K
Sbjct: 32 EAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 112 PDRKMKLARELGLQPRQIAVWFQNRRAR 139
P K +LA GL Q++ WF+NRR R
Sbjct: 521 PREKRELAEATGLTTTQVSNWFKNRRQR 548
>pdb|1KZ0|A Chain A, Solution Structure Of The Third Helix Of Antennapedia
Homeodomain
Length = 16
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 127 RQIAVWFQNRRARWKS 142
RQI +WFQNRR +WK
Sbjct: 1 RQIKIWFQNRRMKWKK 16
>pdb|3QGH|A Chain A, Crystal Structure Of The Hepatitis C Virus Ns5b
Rna-Dependent Rna Polymerase Genotype 1a Complex With
N-Cyclopropyl-6-[(3r)-3-{[4-
(Trifluoromethoxy)benzyl]carbamoyl}-4-{[4-
(Trifluoromethoxy)
Phenyl]sulfonyl}piperazin-1-Yl]pyridazine-3-Carboxamide
pdb|3QGI|A Chain A, Crystal Structure Of The Hepatitis C Virus Ns5b
Rna-Dependent Rna Polymerase Genotype 1a Complex With
N-[(2s)-Butan-2-Yl]-6-[(3r)-3-
{[4-(Trifluoromethoxy)benzyl]carbamoyl}-4-{[4-
(Trifluoromethoxy)
Phenyl]sulfonyl}piperazin-1-Yl]pyridazine-3-Carboxamide
Length = 571
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 26/37 (70%), Gaps = 3/37 (8%)
Query: 76 HH---YGSSSTSSQERKKRLTSDQLESLERSFQEEIK 109
HH Y ++S S+ +R+K++T D+L+ L+ +Q+ +K
Sbjct: 34 HHNLVYSTTSRSACQRQKKVTFDRLQVLDSHYQDVLK 70
>pdb|3HKW|A Chain A, Hcv Ns5b Genotype 1a In Complex With 1,5 Benzodiazepine
Inhi
pdb|3HKW|B Chain B, Hcv Ns5b Genotype 1a In Complex With 1,5 Benzodiazepine
Inhi
pdb|3HKW|C Chain C, Hcv Ns5b Genotype 1a In Complex With 1,5 Benzodiazepine
Inhi
Length = 581
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 26/37 (70%), Gaps = 3/37 (8%)
Query: 76 HH---YGSSSTSSQERKKRLTSDQLESLERSFQEEIK 109
HH Y ++S S+ +R+K++T D+L+ L+ +Q+ +K
Sbjct: 36 HHNMVYSTTSRSACQRQKKVTFDRLQVLDSHYQDVLK 72
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 11/27 (40%), Positives = 19/27 (70%)
Query: 115 KMKLARELGLQPRQIAVWFQNRRARWK 141
K +LA++ G+ Q++ WF N+R R+K
Sbjct: 34 KEELAKKCGITVSQVSNWFGNKRIRYK 60
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription Factor
Nanog Homeodomain Fragment
Length = 84
Score = 29.3 bits (64), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR---ARWK 141
+S QL L FQ + L + +L+ L L +Q+ WFQN+R RW+
Sbjct: 29 FSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQ 81
>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 = 2.1, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 32/58 (55%)
Query: 84 SSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141
+ Q+ + + QL +L+ FQ++ L + +L+ L L +Q+ WFQN+R + K
Sbjct: 2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCK 59
>pdb|2DA2|A Chain A, Solution Structure Of The Second Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 70
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 22/49 (44%)
Query: 91 RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139
R T QL L+ F D +L+ L L R I VWFQN R +
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQK 61
>pdb|2DA5|A Chain A, Solution Structure Of The Second Homeobox Domain Of Zinc
Fingers And Homeoboxes Protein 3 (Triple Homeobox 1
Protein)
Length = 75
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 79 GSSSTSSQERKKRLTSDQLESLERSF-QEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137
GSS +S + K +QL +LE SF Q + LD + +L E + R+I WF RR
Sbjct: 1 GSSGSSGPTKYKERAPEQLRALESSFAQNPLPLDEELD-RLRSETKMTRREIDSWFSERR 59
Query: 138 AR 139
+
Sbjct: 60 KK 61
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 11/29 (37%), Positives = 20/29 (68%)
Query: 113 DRKMKLARELGLQPRQIAVWFQNRRARWK 141
+ K +LA++ G+ Q++ WF N+R R+K
Sbjct: 33 EAKEELAKKSGITVSQVSNWFGNKRIRYK 61
>pdb|3FRZ|A Chain A, Crystal Structure Of Hcv Ns5b Rna Polymerase In Complex
With
Length = 576
Score = 28.5 bits (62), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 26/37 (70%), Gaps = 3/37 (8%)
Query: 76 HH---YGSSSTSSQERKKRLTSDQLESLERSFQEEIK 109
HH Y ++S S+ +R+K++T D+L+ L+ +++ +K
Sbjct: 33 HHNMVYATTSRSAGQRQKKVTFDRLQDLDDHYRDVLK 69
>pdb|1POG|A Chain A, Solution Structure Of The Oct-1 Pou-Homeo Domain
Determined By Nmr And Restrained Molecular Dynamics
Length = 67
Score = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 84 SSQERKKRLTSDQLE---SLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARW 140
S R+K+ TS + +LE+SF E K + +A +L ++ I VWF NRR +
Sbjct: 3 SHMRRRKKRTSIETNIRVALEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKE 62
Query: 141 K 141
K
Sbjct: 63 K 63
>pdb|1OS5|A Chain A, Crystal Structure Of Hcv Ns5b Rna Polymerase Complexed
With A Novel Non-Competitive Inhibitor
Length = 576
Score = 28.1 bits (61), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 26/37 (70%), Gaps = 3/37 (8%)
Query: 76 HH---YGSSSTSSQERKKRLTSDQLESLERSFQEEIK 109
HH Y ++S S+ +R+K++T D+L+ L+ +++ +K
Sbjct: 33 HHNMVYATTSRSAGQRQKKVTFDRLQVLDDHYRDVLK 69
>pdb|1OMQ|A Chain A, Structure Of Penetratin In Bicellar Solution
Length = 16
Score = 28.1 bits (61), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 128 QIAVWFQNRRARWK 141
QI +WFQNRR +WK
Sbjct: 2 QIKIWFQNRRMKWK 15
>pdb|2HAI|A Chain A, Crystal Structure Of Hcv Ns5b Rna Polymerase In Complex
With Novel Class Of Dihydropyrone-Containing Inhibitor
Length = 576
Score = 28.1 bits (61), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 26/37 (70%), Gaps = 3/37 (8%)
Query: 76 HH---YGSSSTSSQERKKRLTSDQLESLERSFQEEIK 109
HH Y ++S S+ +R+K++T D+L+ L+ +++ +K
Sbjct: 33 HHNMVYATTSRSAGQRQKKVTFDRLQVLDDHYRDVLK 69
>pdb|2XI2|A Chain A, Hcv-H77 Ns5b Apo Polymerase
pdb|2XI2|B Chain B, Hcv-H77 Ns5b Apo Polymerase
pdb|2XI2|C Chain C, Hcv-H77 Ns5b Apo Polymerase
pdb|2XI3|A Chain A, Hcv-H77 Ns5b Polymerase Complexed With Gtp
pdb|2XI3|B Chain B, Hcv-H77 Ns5b Polymerase Complexed With Gtp
Length = 576
Score = 27.7 bits (60), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 25/37 (67%), Gaps = 3/37 (8%)
Query: 76 HH---YGSSSTSSQERKKRLTSDQLESLERSFQEEIK 109
HH Y ++S S+ +R+K++T D+L+ L+ + + +K
Sbjct: 33 HHNLVYSTTSRSACQRQKKVTFDRLQVLDSHYHDVLK 69
>pdb|1QVR|A Chain A, Crystal Structure Analysis Of Clpb
pdb|1QVR|B Chain B, Crystal Structure Analysis Of Clpb
pdb|1QVR|C Chain C, Crystal Structure Analysis Of Clpb
Length = 854
Score = 27.7 bits (60), Expect = 7.0, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 30/59 (50%), Gaps = 8/59 (13%)
Query: 141 KSKQLELLYDSLKQEYDAVSREKL--------KLQEEVMKLKRMLKEQGTSTRNMMNKQ 191
K QLE+ ++LK+E D S+E+L KL EE+ KL+ + + R + Q
Sbjct: 409 KKLQLEIEREALKKEKDPDSQERLKAIEAEIAKLTEEIAKLRAEWEREREILRKLREAQ 467
>pdb|4EKW|A Chain A, Crystal Structure Of The Navab Voltage-Gated Sodium
Channel (Wild- Type, 3.2 A)
pdb|4EKW|B Chain B, Crystal Structure Of The Navab Voltage-Gated Sodium
Channel (Wild- Type, 3.2 A)
pdb|4EKW|C Chain C, Crystal Structure Of The Navab Voltage-Gated Sodium
Channel (Wild- Type, 3.2 A)
pdb|4EKW|D Chain D, Crystal Structure Of The Navab Voltage-Gated Sodium
Channel (Wild- Type, 3.2 A)
Length = 285
Score = 27.3 bits (59), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 26/39 (66%), Gaps = 3/39 (7%)
Query: 148 LYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQGTSTRN 186
+ D ++ D ++ E +KL+EE+++LK ++K TS +N
Sbjct: 250 IIDEVQSHEDNINNEIIKLREEIVELKELIK---TSLKN 285
>pdb|3RW0|A Chain A, Crystal Structure Of The Navab Voltage-Gated Sodium
Channel (Met221cys, 2.95 A)
pdb|3RW0|B Chain B, Crystal Structure Of The Navab Voltage-Gated Sodium
Channel (Met221cys, 2.95 A)
Length = 285
Score = 27.3 bits (59), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 26/39 (66%), Gaps = 3/39 (7%)
Query: 148 LYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQGTSTRN 186
+ D ++ D ++ E +KL+EE+++LK ++K TS +N
Sbjct: 250 IIDEVQSHEDNINNEIIKLREEIVELKELIK---TSLKN 285
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 0.129 0.370
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,598,333
Number of Sequences: 62578
Number of extensions: 209041
Number of successful extensions: 812
Number of sequences better than 100.0: 105
Number of HSP's better than 100.0 without gapping: 95
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 714
Number of HSP's gapped (non-prelim): 107
length of query: 257
length of database: 14,973,337
effective HSP length: 97
effective length of query: 160
effective length of database: 8,903,271
effective search space: 1424523360
effective search space used: 1424523360
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)