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= 026974
(230 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 43.5 bits (101), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/62 (37%), Positives = 31/62 (50%)
Query: 59 GNGGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRAR 118
G G R ++ T Q LE F H L R+ ++A L L RQ+ +WFQNRR +
Sbjct: 15 GTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMK 74
Query: 119 DK 120
K
Sbjct: 75 LK 76
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 31/50 (62%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
++EQ L+ F L R+ +L++ELGL+ Q+ +WFQN+RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 57
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 31/50 (62%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
++EQ L+ F L R+ +L++ELGL+ Q+ +WFQN+RA+ K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 59
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 30/48 (62%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRAR 118
++EQ L+ F L R+ +L++ELGL+ Q+ +WFQN+RA+
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 53
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 30/50 (60%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
++EQ L+ F L R+ +L++ELGL+ Q+ +WFQN RA+ K
Sbjct: 8 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNERAKIK 57
>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 = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 31/53 (58%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKK 123
T +Q LE F E+ + R+ +LAA+L L + VWFQNRR +DK ++
Sbjct: 8 FTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQR 60
>pdb|3A01|B Chain B, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
pdb|3A01|F Chain F, Crystal Structure Of Aristaless And Clawless Homeodomains
Bo
Length = 67
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 37/71 (52%), Gaps = 12/71 (16%)
Query: 48 PKRRQRKRNTNGNGGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQ 107
PKR+QR+ T T+ Q E LE F H + +++LA ++GL +
Sbjct: 2 PKRKQRRYRTT------------FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEAR 49
Query: 108 VAVWFQNRRAR 118
+ VWFQNRRA+
Sbjct: 50 IQVWFQNRRAK 60
>pdb|1P7I|A Chain A, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|B Chain B, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|C Chain C, Crystal Structure Of Engrailed Homeodomain Mutant K52a
pdb|1P7I|D Chain D, Crystal Structure Of Engrailed Homeodomain Mutant K52a
Length = 59
Score = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 30/50 (60%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
++EQ L+ F L R+ +L++ELGL+ Q+ +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 = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 31/50 (62%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
++EQ L+ F L R+ +L++ELGL+ Q+ +WF+N+RA+ K
Sbjct: 10 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIK 59
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 41.2 bits (95), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 28/49 (57%)
Query: 72 TAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
T Q + LE + + D++ +++A L RQV +WFQNRR ++K
Sbjct: 9 TKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 57
>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 = 17/49 (34%), Positives = 28/49 (57%)
Query: 72 TAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
T Q + LE + + D++ +++A L RQV +WFQNRR ++K
Sbjct: 15 TKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEK 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 = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 30/50 (60%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
++EQ L+ F L R+ +L++ELGL+ Q+ +WF N+RA+ K
Sbjct: 6 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFANKRAKIK 55
>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
Box B13
Length = 70
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 59 GNGGFRALKKR-KLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRA 117
G+ G KKR + Q LE + + D++ K++A L RQ+ +WFQNRR
Sbjct: 1 GSSGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRV 60
Query: 118 RDK 120
++K
Sbjct: 61 KEK 63
>pdb|1AU7|A Chain A, Pit-1 MutantDNA COMPLEX
pdb|1AU7|B Chain B, Pit-1 MutantDNA COMPLEX
Length = 146
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 67 KKRKLTAEQA--ELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
+KR+ T A + LE HFG K S ++A EL L+ V VWF NRR R+K
Sbjct: 88 RKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREK 143
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 29/48 (60%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRAR 118
++EQ + F L R+ +L++ELGL+ Q+ +WFQN+RA+
Sbjct: 10 FSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAK 57
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound To
The Consensus Dna Binding Site Taatcc
Length = 68
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/50 (42%), Positives = 27/50 (54%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
T+ Q LE HF L + R L+A+L L QV +WF+NRR R K
Sbjct: 9 FTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHK 58
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 29/54 (53%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKI 124
L +Q L + + ++ K++L GL PR + VWFQN+R +DK + I
Sbjct: 10 LNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRSI 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 = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 67 KKRKLTAEQAEL--LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
+K ++ QA++ LE F + L + +D+LA+ L L QV +WFQNRR + K
Sbjct: 3 RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 28/50 (56%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
++ + LE F + L S K+++A + G+ P QV VWF N+R R K
Sbjct: 372 ISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 421
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 4/66 (6%)
Query: 67 KKRK----LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTK 122
KKRK T Q LE F + L + ++ LA+ + L P QV +WFQN R + K
Sbjct: 8 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRA 67
Query: 123 KIEETY 128
+ E+ Y
Sbjct: 68 QNEKGY 73
>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 = 16/38 (42%), Positives = 25/38 (65%)
Query: 83 FGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
F L R+ +L++ELGL+ Q+ +WFQN+RA+ K
Sbjct: 5 FNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIK 42
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 29/48 (60%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRAR 118
T+ Q E LE F H + +++LA ++GL ++ VWFQNRRA+
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAK 53
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 29/48 (60%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRAR 118
T+ Q E LE F H + +++LA ++GL ++ VWFQNRRA+
Sbjct: 6 FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAK 53
>pdb|1LE8|A Chain A, Crystal Structure Of The Mata1MATALPHA2-3a Heterodimer
Bound To Dna Complex
Length = 53
Score = 38.1 bits (87), Expect = 0.004, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 29/53 (54%)
Query: 68 KRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
K ++ + LE F + L S K+++A + G+ P QV VWF N+R R K
Sbjct: 1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 53
>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 = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 29/50 (58%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
++EQ L+ F L R+ +L++ELGL+ QV WF+N RA+ K
Sbjct: 11 FSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIK 60
>pdb|2DA3|A Chain A, Solution Structure Of The Third Homeobox Domain Of At-
Binding Transcription Factor 1 (Atbf1)
Length = 80
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/50 (40%), Positives = 28/50 (56%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
+T EQ E+L + + D +A E+GL R V VWFQN RAR++
Sbjct: 24 ITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARER 73
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 29/55 (52%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIE 125
T Q LE F L R+ ++AA L L+ QV +WFQNRR + K ++ E
Sbjct: 41 FTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE 95
>pdb|1FTT|A Chain A, Thyroid Transcription Factor 1 Homeodomain (Rattus
Norvegicus)
Length = 68
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 33/56 (58%), Gaps = 2/56 (3%)
Query: 67 KKRKLTAEQAEL--LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
+KR++ QA++ LE F + L + ++ LA+ + L P QV +WFQN R + K
Sbjct: 3 RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMK 58
>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
Length = 60
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/49 (42%), Positives = 26/49 (53%)
Query: 72 TAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
T Q LE F L DR+ ++A L L RQV +WFQNRR + K
Sbjct: 9 TKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMK 57
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 56 NTNGNGGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNR 115
++G+ G R + T EQ E LE F H + +++LAA++ L ++ VWF NR
Sbjct: 1 GSSGSSGQR--NRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNR 58
Query: 116 RAR 118
RA+
Sbjct: 59 RAK 61
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 67 KKRK----LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTK 122
KKRK T Q LE F + L + ++ L + + L P QV +WFQN R + K
Sbjct: 11 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVKIWFQNHRYKTKRA 70
Query: 123 KIEETY 128
+ E+ Y
Sbjct: 71 QNEKGY 76
>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 = 37.4 bits (85), Expect = 0.007, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 29/53 (54%)
Query: 68 KRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
K ++ + LE F + L S K+++A + G+ P QV VWF N+R R K
Sbjct: 9 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 26/46 (56%)
Query: 79 LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKI 124
LE F ++ L + + LA L L QV +WFQNRR + K K++
Sbjct: 19 LERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQL 64
>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 77
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/58 (43%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 72 TAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIEETYA 129
T Q LE F L DR+ ++A L L RQV +WFQNRR K KKI + A
Sbjct: 21 TKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRM--KMKKINKDRA 76
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor Gbx1
From Homo Sapiens
Length = 71
Score = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 31/60 (51%)
Query: 61 GGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
GG ++ T+EQ LE F + L + ++A L L QV +WFQNRRA+ K
Sbjct: 4 GGKSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVKIWFQNRRAKWK 63
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 36.6 bits (83), Expect = 0.010, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 59 GNGGFRALKKRKLTAE-QAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRA 117
G+ G K R + + Q L+ F L + +LAA LGL QV +WFQN+R+
Sbjct: 1 GSSGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRS 60
Query: 118 RDK 120
+ K
Sbjct: 61 KIK 63
>pdb|1AKH|A Chain A, Mat A1ALPHA2DNA TERNARY COMPLEX
Length = 61
Score = 36.6 bits (83), Expect = 0.012, Method: Composition-based stats.
Identities = 19/53 (35%), Positives = 29/53 (54%)
Query: 68 KRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
K ++ + LE F + L S K+++A + G+ P QV VWF N+R R K
Sbjct: 9 KSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>pdb|2E1O|A Chain A, Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From
Human Cdna
Length = 70
Score = 36.6 bits (83), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/49 (38%), Positives = 26/49 (53%)
Query: 70 KLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRAR 118
+ + +Q LE F + L + +LA L L RQV WFQNRRA+
Sbjct: 13 RFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAK 61
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 35.8 bits (81), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 26/48 (54%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRAR 118
TAEQ E LE F H + +++LA L +V VWF NRRAR
Sbjct: 9 FTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRAR 56
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 35.8 bits (81), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 25/50 (50%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
T Q LE F + L + + ++ L L QV +WFQNRRA+ K
Sbjct: 7 FTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAK 56
>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 = 34.7 bits (78), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 23/42 (54%)
Query: 79 LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
LE F L R+ ++A L L RQ+ +WFQNRR + K
Sbjct: 11 LEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 52
>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 = 34.7 bits (78), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 80 EMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
E HF L R+ ++A L L RQ+ +WFQNRR + K
Sbjct: 46 EFHFNRY--LTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 84
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 34.3 bits (77), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 80 EMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
E HF L R+ ++A L L RQ+ +WFQNRR + K
Sbjct: 21 EFHFNRY--LTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 59
>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 = 34.3 bits (77), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 22/42 (52%)
Query: 79 LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
LE F + R+ +A L L RQ+ +WFQNRR + K
Sbjct: 18 LEKEFHFNRYITRRRRIDIANALSLSERQIKIWFQNRRMKSK 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 = 33.9 bits (76), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 23/42 (54%)
Query: 79 LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
LE F L R+ ++A L L RQ+ +WFQNRR + K
Sbjct: 17 LEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWK 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 = 33.9 bits (76), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 23/42 (54%)
Query: 79 LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
LE F L R+ ++A L L RQ+ +WFQNRR + K
Sbjct: 17 LEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 58
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 33.9 bits (76), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 30/60 (50%)
Query: 59 GNGGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRAR 118
N G + + T+ Q E LE F H + +++LA L +V VWFQNRRA+
Sbjct: 4 SNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAK 63
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 33.5 bits (75), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIEETYAT 130
T++Q + LE F H + ++++A L +V VWF+NRRA K +K EE T
Sbjct: 10 FTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARVRVWFKNRRA--KWRKREEFIVT 67
>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 = 32.7 bits (73), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 3/56 (5%)
Query: 68 KRKLTA-EQAELLEMH--FGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
KR TA +A+LLE+ F + R+ +LA L L R + +WFQNRR + K
Sbjct: 4 KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWK 59
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant R31lE42L
Length = 67
Score = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 29/58 (50%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIEETY 128
T Q E+LE F D + LA +L L+ ++ +WFQNRRA+ K E +
Sbjct: 8 FTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRESQF 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 = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 27/56 (48%)
Query: 79 LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIEETYATLKTA 134
LE F + L S + LA L + QV WFQNRR + + + EE A + A
Sbjct: 32 LEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEEREAERQAA 87
>pdb|4EGC|A Chain A, Crystal Structure Of Mbp-fused Human Six1 Bound To Human
Eya2 Eya Domain
Length = 559
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 15/33 (45%), Positives = 21/33 (63%)
Query: 94 KDKLAAELGLDPRQVAVWFQNRRARDKTKKIEE 126
K +LA GL QV+ WF+NRR RD+ + +E
Sbjct: 524 KRELAEATGLTTTQVSNWFKNRRQRDRAAEAKE 556
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 22/42 (52%)
Query: 79 LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
LE F + L + + LA LGL QV W+QNRR + K
Sbjct: 32 LEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWK 73
>pdb|1B72|B Chain B, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 87
Score = 31.6 bits (70), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 65 ALKKRKLTAEQA-----ELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARD 119
A +KR+ +QA E H N + E + K++LA + G+ QV+ WF N+R R
Sbjct: 1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSE-EAKEELAKKCGITVSQVSNWFGNKRIRY 59
Query: 120 K 120
K
Sbjct: 60 K 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 = 31.2 bits (69), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 12/70 (17%)
Query: 49 KRRQRKRNTNGNGGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQV 108
KR+QR+ T +A Q + LE F + +++LA L ++
Sbjct: 15 KRKQRRSRTT------------FSASQLDELERAFERTQYPDIYTREELAQRTNLTEARI 62
Query: 109 AVWFQNRRAR 118
VWFQNRRAR
Sbjct: 63 QVWFQNRRAR 72
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 31.2 bits (69), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 59 GNGGFRALKKRKL-TAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRA 117
G+ G + R + T EQ E LE F + +++LA ++ L +V VWF+NRRA
Sbjct: 1 GSSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRA 60
Query: 118 R 118
+
Sbjct: 61 K 61
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 30.8 bits (68), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 19/38 (50%)
Query: 79 LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRR 116
LE F + L S + LA L + QV WFQNRR
Sbjct: 12 LERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRR 49
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 30.8 bits (68), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 24/45 (53%)
Query: 74 EQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRAR 118
Q ++ +F H ++ +LA + GL R + VWFQN RA+
Sbjct: 17 HQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAK 61
>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 = 0.79, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 57 TNGNGG--FRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQN 114
++G+ G F K ++ TAEQ +L+ F N L + ++L A+ L R++ WF
Sbjct: 2 SSGSSGPDFTPQKFKEKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTE 61
Query: 115 RRARDKTKKIEE 126
++ K+K ++E
Sbjct: 62 KK---KSKALKE 70
>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 = 0.84, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 5/58 (8%)
Query: 67 KKRKLTAEQAELLE----MHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
K+R + + +E+L H N + E + K++LA + G+ QV+ WF N+R R K
Sbjct: 4 KRRNFSKQASEILNEYFYSHLSNPYPSE-EAKEELARKCGITVSQVSNWFGNKRIRYK 60
>pdb|1LFU|P Chain P, Nmr Solution Stucture Of The Extended Pbx Homeodomain
Bound To Dna
Length = 82
Score = 30.4 bits (67), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 65 ALKKRKLTAEQA-----ELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARD 119
A +KR+ +QA E H N + E + K++LA + G+ QV+ WF N+R R
Sbjct: 2 ARRKRRNFNKQATEILNEYFYSHLSNPYPSE-EAKEELAKKSGITVSQVSNWFGNKRIRY 60
Query: 120 K 120
K
Sbjct: 61 K 61
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 30.0 bits (66), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 2/65 (3%)
Query: 56 NTNGNGGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNR 115
++G+ G R ++ T Q ++LE F + ++++A ++ L +V VWF+NR
Sbjct: 1 GSSGSSGRR--ERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNR 58
Query: 116 RARDK 120
RA+ +
Sbjct: 59 RAKCR 63
>pdb|2L7F|P Chain P, Solution Structure Of The Pitx2 Homeodomain
pdb|2LKX|A Chain A, Nmr Structure Of The Homeodomain Of Pitx2 In Complex With
A Taatcc Dna Binding Site
Length = 68
Score = 30.0 bits (66), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIEETYAT 130
T++Q + LE F + ++++A L +V VWF+NRRA K +K EE T
Sbjct: 10 FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRA--KWRKREEFIVT 67
>pdb|1PUF|B Chain B, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound To
Dna
Length = 73
Score = 29.6 bits (65), Expect = 1.6, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 5/58 (8%)
Query: 67 KKRKLTAEQAELLE----MHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
K+R + E+L H N + E + K++LA + G+ QV+ WF N+R R K
Sbjct: 4 KRRNFNKQATEILNEYFYSHLSNPYPSE-EAKEELAKKCGITVSQVSNWFGNKRIRYK 60
>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 = 1.6, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 70 KLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKK 123
+ T Q +L+ F + D ++L+ L L R + VWFQN AR K +K
Sbjct: 13 RFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQN--ARQKARK 64
>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 = 15/50 (30%), Positives = 25/50 (50%)
Query: 71 LTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
++ Q +L F + L + +L+ L L +QV WFQN+R + K
Sbjct: 29 FSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSK 78
>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 = 2.5, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 97 LAAELGLDPRQVAVWFQNRRARDK 120
+A +LGL+ V VWF NRR + K
Sbjct: 129 IANQLGLEKDVVRVWFSNRRQKGK 152
>pdb|2XSD|C Chain C, Crystal Structure Of The Dimeric Oct-6 (Pou3f1) Pou Domain
Bound To Palindromic More Dna
Length = 164
Score = 28.5 bits (62), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 17/42 (40%), Positives = 21/42 (50%)
Query: 79 LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
LE HF K + LA L L+ V VWF NRR ++K
Sbjct: 114 LESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEK 155
>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 = 28.5 bits (62), Expect = 3.2, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 2/56 (3%)
Query: 67 KKRKLTAEQAEL--LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
+K + QA+L L+ F + L + +L++ L L +QV WFQN+R + K
Sbjct: 4 QKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCK 59
>pdb|1DU6|A Chain A, Solution Structure Of The Truncated Pbx Homeodomain
Length = 64
Score = 28.5 bits (62), Expect = 3.3, Method: Composition-based stats.
Identities = 18/59 (30%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 66 LKKRKLTAEQAELLE----MHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
++ R + + E+L H N + E + K++LA + G+ QV+ WF N+R R K
Sbjct: 5 IEGRHMNKQATEILNEYFYSHLSNPYPSE-EAKEELAKKCGITVSQVSNWFGNKRIRYK 62
>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 = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 25/59 (42%)
Query: 70 KLTAEQAELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDKTKKIEETY 128
K T EQ +L+ F + DKLA E GL + WF + R K ++ Y
Sbjct: 31 KKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGNLKWYY 89
>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 = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 79 LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
LE F K S+ +A +L ++ + VWF NRR ++K
Sbjct: 115 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFSNRRQKEK 156
>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 = 28.1 bits (61), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 79 LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
LE F K S+ +A +L ++ + VWF NRR ++K
Sbjct: 119 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 160
>pdb|1E3O|C Chain C, Crystal Structure Of Oct-1 Pou Dimer Bound To More
Length = 160
Score = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 79 LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
LE F K S+ +A +L ++ + VWF NRR ++K
Sbjct: 116 LEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEK 157
>pdb|1OCP|A Chain A, Solution Structure Of Oct3 Pou-Homeodomain
Length = 67
Score = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 97 LAAELGLDPRQVAVWFQNRRARDK 120
+A +LGL+ V VWF NRR + K
Sbjct: 41 IANQLGLEKDVVRVWFCNRRQKGK 64
>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 = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 29/74 (39%), Gaps = 16/74 (21%)
Query: 43 GEPSKPKRRQRKRNTNGNGGFRALKKRKLTAEQAELLEMHFGNEHKLESDRKDKLAAELG 102
GEPSK +RKR T+ T + E L +F + A EL
Sbjct: 88 GEPSK----KRKRRTS------------FTPQAIEALNAYFEKNPLPTGQEITEXAKELN 131
Query: 103 LDPRQVAVWFQNRR 116
D V VWF NRR
Sbjct: 132 YDREVVRVWFSNRR 145
>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 = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 79 LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
LE F K S+ +A +L ++ + VWF NRR ++K
Sbjct: 111 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 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 = 27.7 bits (60), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 79 LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
LE F K S+ +A +L ++ + VWF NRR ++K
Sbjct: 118 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 159
>pdb|3IYN|A Chain A, 3.6-Angstrom Cryoem Structure Of Human Adenovirus Type 5
pdb|3IYN|B Chain B, 3.6-Angstrom Cryoem Structure Of Human Adenovirus Type 5
pdb|3IYN|C Chain C, 3.6-Angstrom Cryoem Structure Of Human Adenovirus Type 5
pdb|3IYN|D Chain D, 3.6-Angstrom Cryoem Structure Of Human Adenovirus Type 5
pdb|3IYN|E Chain E, 3.6-Angstrom Cryoem Structure Of Human Adenovirus Type 5
pdb|3IYN|F Chain F, 3.6-Angstrom Cryoem Structure Of Human Adenovirus Type 5
pdb|3IYN|G Chain G, 3.6-Angstrom Cryoem Structure Of Human Adenovirus Type 5
pdb|3IYN|H Chain H, 3.6-Angstrom Cryoem Structure Of Human Adenovirus Type 5
pdb|3IYN|I Chain I, 3.6-Angstrom Cryoem Structure Of Human Adenovirus Type 5
pdb|3IYN|J Chain J, 3.6-Angstrom Cryoem Structure Of Human Adenovirus Type 5
pdb|3IYN|K Chain K, 3.6-Angstrom Cryoem Structure Of Human Adenovirus Type 5
pdb|3IYN|L Chain L, 3.6-Angstrom Cryoem Structure Of Human Adenovirus Type 5
pdb|1VSZ|A Chain A, Crystal Structure Of Human Adenovirus At 3.5a
pdb|1VSZ|B Chain B, Crystal Structure Of Human Adenovirus At 3.5a
pdb|1VSZ|C Chain C, Crystal Structure Of Human Adenovirus At 3.5a
pdb|1VSZ|D Chain D, Crystal Structure Of Human Adenovirus At 3.5a
pdb|1VSZ|E Chain E, Crystal Structure Of Human Adenovirus At 3.5a
pdb|1VSZ|F Chain F, Crystal Structure Of Human Adenovirus At 3.5a
pdb|1VSZ|G Chain G, Crystal Structure Of Human Adenovirus At 3.5a
pdb|1VSZ|H Chain H, Crystal Structure Of Human Adenovirus At 3.5a
pdb|1VSZ|I Chain I, Crystal Structure Of Human Adenovirus At 3.5a
pdb|1VSZ|J Chain J, Crystal Structure Of Human Adenovirus At 3.5a
pdb|1VSZ|K Chain K, Crystal Structure Of Human Adenovirus At 3.5a
pdb|1VSZ|L Chain L, Crystal Structure Of Human Adenovirus At 3.5a
Length = 952
Score = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 1/86 (1%)
Query: 25 SQFYPSDVLTPTGIVPQQGEPSKPKRRQRKRNTNGNGGFRALKKRKLTAEQAELLEMHFG 84
SQ+Y +++ G V ++ P KP + TN NGG L K++ +++ +EM F
Sbjct: 209 SQWYETEINHAAGRVLKKTTPMKPCYGSYAKPTNENGGQGILVKQQNGKLESQ-VEMQFF 267
Query: 85 NEHKLESDRKDKLAAELGLDPRQVAV 110
+ + + D L ++ L V +
Sbjct: 268 STTEATAGNGDNLTPKVVLYSEDVDI 293
>pdb|2BVI|F Chain F, The Quasi-Atomic Model Of Human Adenovirus Type 5 Capsid
(Part 2)
pdb|2BVI|G Chain G, The Quasi-Atomic Model Of Human Adenovirus Type 5 Capsid
(Part 2)
pdb|2BVI|H Chain H, The Quasi-Atomic Model Of Human Adenovirus Type 5 Capsid
(Part 2)
pdb|2BVI|I Chain I, The Quasi-Atomic Model Of Human Adenovirus Type 5 Capsid
(Part 2)
pdb|2BVI|J Chain J, The Quasi-Atomic Model Of Human Adenovirus Type 5 Capsid
(Part 2)
pdb|2BVI|K Chain K, The Quasi-Atomic Model Of Human Adenovirus Type 5 Capsid
(Part 2)
pdb|2BVI|L Chain L, The Quasi-Atomic Model Of Human Adenovirus Type 5 Capsid
(Part 2)
pdb|2BVI|M Chain M, The Quasi-Atomic Model Of Human Adenovirus Type 5 Capsid
(Part 2)
pdb|2BVI|N Chain N, The Quasi-Atomic Model Of Human Adenovirus Type 5 Capsid
(Part 2)
pdb|2BVI|O Chain O, The Quasi-Atomic Model Of Human Adenovirus Type 5 Capsid
(Part 2)
pdb|2BVI|P Chain P, The Quasi-Atomic Model Of Human Adenovirus Type 5 Capsid
(Part 2)
pdb|2BVI|Q Chain Q, The Quasi-Atomic Model Of Human Adenovirus Type 5 Capsid
(Part 2)
pdb|1P30|A Chain A, Refinement Of Adenovirus Type 5 Hexon With Cns
pdb|3TG7|A Chain A, Crystal Structure Of Adenovirus Serotype 5 Hexon At 1.6a
Resolution
Length = 951
Score = 27.7 bits (60), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 1/86 (1%)
Query: 25 SQFYPSDVLTPTGIVPQQGEPSKPKRRQRKRNTNGNGGFRALKKRKLTAEQAELLEMHFG 84
SQ+Y +++ G V ++ P KP + TN NGG L K++ +++ +EM F
Sbjct: 208 SQWYETEINHAAGRVLKKTTPMKPCYGSYAKPTNENGGQGILVKQQNGKLESQ-VEMQFF 266
Query: 85 NEHKLESDRKDKLAAELGLDPRQVAV 110
+ + + D L ++ L V +
Sbjct: 267 STTEATAGNGDNLTPKVVLYSEDVDI 292
>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 = 6.7, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 22/42 (52%)
Query: 79 LEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQNRRARDK 120
LE F K S+ +A +L ++ + VWF NRR ++K
Sbjct: 22 LEKSFLENQKPTSEEITMIADQLNMEKEVIRVWFCNRRQKEK 63
>pdb|1X2N|A Chain A, Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Pknox1
Length = 73
Score = 27.3 bits (59), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 6/65 (9%)
Query: 59 GNGGFRALKKRKLTAEQA-----ELLEMHFGNEHKLESDRKDKLAAELGLDPRQVAVWFQ 113
G+ G KR + + A L H G+ + E D K ++AA+ L QV WF
Sbjct: 1 GSSGSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTE-DEKKQIAAQTNLTLLQVNNWFI 59
Query: 114 NRRAR 118
N R R
Sbjct: 60 NARRR 64
>pdb|2GQS|A Chain A, Saicar Synthetase Complexed With Cair-Mg2+ And Adp
pdb|2GQS|B Chain B, Saicar Synthetase Complexed With Cair-Mg2+ And Adp
Length = 237
Score = 27.3 bits (59), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 23/98 (23%), Positives = 39/98 (39%), Gaps = 12/98 (12%)
Query: 132 KTAHENVVVEKTRLESEVATLKEKLSVAEKE-----------IKKMSELIEGISLNNPSA 180
K A + + RL S+ L +KL + E +K++ + EGI LN P
Sbjct: 60 KLAEAGIPTQMERLLSDTECLVKKLDMVPVECVVRNRAAGSLVKRLG-IEEGIELNPPLF 118
Query: 181 TIPTDMDTVDSPFTLDPFAGNLGWFDYEDLLYLLQQNY 218
+ D + P + + GW E+L + + Y
Sbjct: 119 DLFLKNDAMHDPMVNESYCETFGWVSKENLARMKELTY 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 = 26.9 bits (58), Expect = 8.5, Method: Composition-based stats.
Identities = 10/30 (33%), Positives = 17/30 (56%)
Query: 106 RQVAVWFQNRRARDKTKKIEETYATLKTAH 135
RQ+ +WFQNRR + K + + ++ H
Sbjct: 1 RQIKIWFQNRRMKWKKRVFNDARDIIQRMH 30
>pdb|1UHS|A Chain A, Solution Structure Of Mouse Homeodomain-Only Protein Hop
Length = 72
Score = 26.9 bits (58), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 3/49 (6%)
Query: 71 LTAEQAELLEMHFG--NEHKLESDRKDKLAAELGLDPRQVAVWFQNRRA 117
+T +Q E+LE +F N+H + +AAE GL Q WF+ R A
Sbjct: 8 MTEDQVEILEYNFNKVNKHP-DPTTLCLIAAEAGLTEEQTQKWFKQRLA 55
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
0.313 0.130 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,657,337
Number of Sequences: 62578
Number of extensions: 263507
Number of successful extensions: 771
Number of sequences better than 100.0: 122
Number of HSP's better than 100.0 without gapping: 99
Number of HSP's successfully gapped in prelim test: 23
Number of HSP's that attempted gapping in prelim test: 664
Number of HSP's gapped (non-prelim): 126
length of query: 230
length of database: 14,973,337
effective HSP length: 96
effective length of query: 134
effective length of database: 8,965,849
effective search space: 1201423766
effective search space used: 1201423766
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)