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= psy7107
(76 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 81.3 bits (199), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 38/49 (77%), Positives = 44/49 (89%)
Query: 27 KRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
KRKQRR RTTFTS QL+ELE+AF THYPD++TREE+AMKI LTEAR+Q
Sbjct: 3 KRKQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 51
>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
Northeast Structural Genomics Consortium (Nesg) Target
Hr4490c
Length = 75
Score = 77.8 bits (190), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 35/52 (67%), Positives = 45/52 (86%)
Query: 24 LTEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
++ K K+RR RTTFTS QL+ELE+ FQ+THYPD+Y RE++AM+ DLTEARVQ
Sbjct: 3 MSNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQ 54
>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 = 77.0 bits (188), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 35/49 (71%), Positives = 43/49 (87%)
Query: 27 KRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
KRKQRR RTTF+++QL ELERAF+ T YPDIYTREE+A + +LTEAR+Q
Sbjct: 15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQ 63
>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
Length = 61
Score = 74.7 bits (182), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 35/46 (76%), Positives = 40/46 (86%)
Query: 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
QRR RTTFT+ QL+ELERAF+ THYPDIYTREE+A + LTEARVQ
Sbjct: 2 QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQ 47
>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
Length = 58
Score = 72.8 bits (177), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 33/44 (75%), Positives = 39/44 (88%)
Query: 32 RIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
R RTTFTS QL+ELE+AF THYPD++TREE+AMKI LTEAR+Q
Sbjct: 1 RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 44
>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
Length = 60
Score = 68.2 bits (165), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 30/40 (75%), Positives = 36/40 (90%)
Query: 36 TFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
TFTS QL+ELE+AF THYPD++TREE+AMKI LTEAR+Q
Sbjct: 5 TFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQ 44
>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
Length = 68
Score = 63.5 bits (153), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 31/45 (68%), Positives = 35/45 (77%)
Query: 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 74
QRR RT FTS QL+ELE FQ HYPD+ TREEIA+ +LTEARV
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEARV 47
>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Otx2
Length = 80
Score = 61.2 bits (147), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 29/45 (64%), Positives = 35/45 (77%)
Query: 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
RR RTTFT AQL LE F +T YPDI+ REE+A+KI+L E+RVQ
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQ 52
>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Paired Box Protein Pax-6
Length = 80
Score = 60.5 bits (145), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 25/44 (56%), Positives = 34/44 (77%)
Query: 32 RIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
R RT+FT Q++ LE+ F+ THYPD++ RE +A KIDL EAR+Q
Sbjct: 9 RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQ 52
>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 = 60.5 bits (145), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 30/46 (65%), Positives = 35/46 (76%)
Query: 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
QRR RT FTS QL+ELE FQ YPD+ TREEIA+ +LTEARV+
Sbjct: 3 QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVR 48
>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Goosecoid
Length = 70
Score = 52.4 bits (124), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 25/45 (55%), Positives = 32/45 (71%)
Query: 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
RR RT FT QL+ LE FQET YPD+ TRE++A K+ L E +V+
Sbjct: 8 RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVE 52
>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
Length = 58
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/45 (44%), Positives = 28/45 (62%)
Query: 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
R+ RT FT+AQL LER F++ Y I R E + + LTE +V+
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVK 45
>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
Gbx1 From Homo Sapiens
Length = 71
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 28/47 (59%)
Query: 29 KQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
K RR RT FTS QL ELE+ F Y + R +IA + L+E +V+
Sbjct: 6 KSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSEVQVK 52
>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
Homeobox Protein Dlx-5
Length = 70
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 29/45 (64%)
Query: 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
R+ RT ++S QL L+R FQ+T Y + R E+A + LT+ +V+
Sbjct: 8 RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVK 52
>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
R31lE42L
Length = 67
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/45 (42%), Positives = 27/45 (60%)
Query: 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
RR RT FT Q++ LE F+ YP I E++A K++L R+Q
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQ 46
>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 = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 29/46 (63%)
Query: 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
++R RT F+S QL L+R F E Y R++++ ++ L EA+V+
Sbjct: 4 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVK 49
>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 = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 29/46 (63%)
Query: 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
++R RT F+S QL L+R F E Y R++++ ++ L EA+++
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIK 48
>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 = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 29/46 (63%)
Query: 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
++R RT F+S QL L+R F E Y R++++ ++ L EA+++
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIK 46
>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 = 34.7 bits (78), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 29/46 (63%)
Query: 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
++R RT F+S QL L+R F E Y R++++ ++ L EA+++
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIK 48
>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 = 34.3 bits (77), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 29/46 (63%)
Query: 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
++R RT F+S QL L+R F E Y R++++ ++ L EA+++
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIK 46
>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
Length = 60
Score = 34.3 bits (77), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 29/46 (63%)
Query: 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
++R RT F+S QL L+R F E Y R++++ ++ L EA+++
Sbjct: 1 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIK 46
>pdb|1DU0|A Chain A, Engrailed Homeodomain Q50a Variant Dna Complex
pdb|1DU0|B Chain B, Engrailed Homeodomain Q50a Variant Dna Complex
Length = 57
Score = 33.9 bits (76), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 27/44 (61%)
Query: 32 RIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
R RT F+S QL L+R F E Y R++++ ++ L EA+++
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIK 44
>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
Length = 54
Score = 33.9 bits (76), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 27/44 (61%)
Query: 32 RIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
R RT F+S QL L+R F E Y R++++ ++ L EA+++
Sbjct: 1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIK 44
>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 = 33.5 bits (75), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 21 EGVLTEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
+G+ +KRK+R FT AQ ELER F++ Y RE +A I LT +V+
Sbjct: 3 DGLPNKKRKRR---VLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVK 54
>pdb|1B8I|A Chain A, Structure Of The Homeotic UbxEXDDNA TERNARY COMPLEX
Length = 81
Score = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 6/63 (9%)
Query: 13 PYKVYSGHEGVLTEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEA 72
P+ +G G+ +RR R T+T Q ELE+ F HY R E+A + LTE
Sbjct: 9 PWMAIAGTNGL------RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTER 62
Query: 73 RVQ 75
+++
Sbjct: 63 QIK 65
>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
Length = 97
Score = 33.5 bits (75), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 18/43 (41%), Positives = 25/43 (58%)
Query: 33 IRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
+RT FT+ QL ELE+ F Y R EIA ++L E +V+
Sbjct: 37 LRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVK 79
>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
To The Consensus Dna Binding Site Taatcc
Length = 68
Score = 32.7 bits (73), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
RR RTTFTS+Q+ ELE+ F + Y +++ K+ L A+V+
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVK 47
>pdb|2DMQ|A Chain A, Solution Structure Of The Homeobox Domain Of LimHOMEOBOX
Protein Lhx9
Length = 80
Score = 32.7 bits (73), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTE 71
+R+RT+F QL+ ++ F H PD +++A K LT+
Sbjct: 8 KRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTK 48
>pdb|2DMT|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
Protein Barh-Like 1
Length = 80
Score = 32.3 bits (72), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 18/51 (35%), Positives = 30/51 (58%)
Query: 25 TEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
T+ +K RR RT FT QL LE+ F++ Y R ++A + L++ +V+
Sbjct: 12 TKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVK 62
>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 = 32.3 bits (72), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 27/46 (58%)
Query: 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
+R RT +T AQL ELE+ F Y R E+A+ ++LTE ++
Sbjct: 3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIK 48
>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
Length = 61
Score = 32.3 bits (72), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 28/46 (60%)
Query: 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
++R RT F+S QL +R F E Y R++++ ++ L EA+++
Sbjct: 3 EKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEAQIK 48
>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
Protein)
Length = 80
Score = 32.0 bits (71), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 21 EGVLTEKRKQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
+G+ +KRK+R + FT AQ ELER F++ Y RE + I LT +V+
Sbjct: 6 DGLPNKKRKRRVL---FTKAQTYELERRFRQQRYLSAPEREHLTSLIRLTPTQVK 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 = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 27/45 (60%)
Query: 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
RR RT FT QL LE+ F + +Y R E+A +++L E+ ++
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIK 46
>pdb|3A01|A Chain A, Crystal Structure Of Aristaless And Clawless
Homeodomains Bo
pdb|3A01|E Chain E, Crystal Structure Of Aristaless And Clawless
Homeodomains Bo
Length = 93
Score = 30.0 bits (66), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 29/47 (61%)
Query: 29 KQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
K+++ RT+FT Q+ ELE+ F + Y R +A + +T+A+V+
Sbjct: 16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVK 62
>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 = 1.00, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 27/44 (61%)
Query: 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 74
+++RT F+ AQL L+ FQ+ Y + +E++ ++L+ +V
Sbjct: 4 QKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQV 47
>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 = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 25/45 (55%)
Query: 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
+R RT++T Q ELE+ F Y R EIA + LTE +++
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK 73
>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
Length = 73
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 23/44 (52%)
Query: 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 74
R+ R +T QLKELER + + R I+ +L+E +V
Sbjct: 8 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQV 51
>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
Binding Domain Bound To Dna
Length = 67
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 23/44 (52%)
Query: 31 RRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 74
R+ R +T QLKELER + + R I+ +L+E +V
Sbjct: 2 RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQV 45
>pdb|2CUF|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
Hypothetical Protein Flj21616
Length = 95
Score = 26.9 bits (58), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 36 TFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQK 76
T+ L +E F E YPD REEIA + A +QK
Sbjct: 13 TWRKECLAVMESYFNENQYPDEAKREEIA---NACNAVIQK 50
>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 = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 25/46 (54%)
Query: 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
++R R T+T Q ELE+ F Y R EIA + LTE +++
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK 47
>pdb|3A03|A Chain A, Crystal Structure Of Hox11l1 Homeodomain
Length = 56
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 24/41 (58%)
Query: 35 TTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
T+F+ +Q+ ELER F Y R +A + +T+A+V+
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVK 42
>pdb|9ANT|A Chain A, Antennapedia Homeodomain-Dna Complex
pdb|9ANT|B Chain B, Antennapedia Homeodomain-Dna Complex
Length = 62
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 25/46 (54%)
Query: 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
++R R T+T Q ELE+ F Y R EIA + LTE +++
Sbjct: 3 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIK 48
>pdb|2KT0|A Chain A, Solution Structure Of Human Stem Cell Transcription
Factor Nanog Homeodomain Fragment
Length = 84
Score = 26.2 bits (56), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 26/46 (56%)
Query: 29 KQRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARV 74
K+++ RT F+S QL L FQ Y + +E++ ++L+ +V
Sbjct: 21 KKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQV 66
>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 = 25.8 bits (55), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 25/46 (54%)
Query: 30 QRRIRTTFTSAQLKELERAFQETHYPDIYTREEIAMKIDLTEARVQ 75
++R R T+T Q ELE+ F Y R EIA + LTE +++
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIK 47
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
0.321 0.135 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,985,727
Number of Sequences: 62578
Number of extensions: 57347
Number of successful extensions: 242
Number of sequences better than 100.0: 51
Number of HSP's better than 100.0 without gapping: 49
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 193
Number of HSP's gapped (non-prelim): 51
length of query: 76
length of database: 14,973,337
effective HSP length: 45
effective length of query: 31
effective length of database: 12,157,327
effective search space: 376877137
effective search space used: 376877137
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)