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= psy15887
         (104 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>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 = 86.3 bits (212), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 41/43 (95%), Positives = 42/43 (97%)

Query: 49 QRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          QRRQRTHFTSQQLQELEATF RNRYPDMSTREEIA+WTNLTEA
Sbjct: 3  QRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEA 45


>pdb|2L7M|P Chain P, Solution Structure Of The Pitx2 Homeodomain R24h Mutant
          Length = 68

 Score = 84.0 bits (206), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 40/43 (93%), Positives = 41/43 (95%)

Query: 49 QRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          QRRQRTHFTSQQLQELEATF RN YPDMSTREEIA+WTNLTEA
Sbjct: 3  QRRQRTHFTSQQLQELEATFQRNHYPDMSTREEIAVWTNLTEA 45


>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 = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 27/44 (61%), Positives = 33/44 (75%)

Query: 48 RQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          +QRR RT F++ QL ELE  F R +YPD+ TREE+A  TNLTEA
Sbjct: 17 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEA 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 = 54.7 bits (130), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 28/44 (63%), Positives = 33/44 (75%)

Query: 48 RQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          +QRR RT FTS QL+ELE  F+R  YPD+ TREE+AM   LTEA
Sbjct: 5  KQRRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEA 48


>pdb|2M0C|A Chain A, Solution Nmr Structure Of Homeobox Domain Of Human Alx4,
          Northeast Structural Genomics Consortium (Nesg) Target
          Hr4490c
          Length = 75

 Score = 51.6 bits (122), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 25/44 (56%), Positives = 33/44 (75%)

Query: 48 RQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          ++RR RT FTS QL+ELE  F +  YPD+  RE++AM T+LTEA
Sbjct: 8  KKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEA 51


>pdb|3CMY|A Chain A, Structure Of A Homeodomain In Complex With Dna
          Length = 61

 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 26/43 (60%), Positives = 31/43 (72%)

Query: 49 QRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          QRR RT FT++QL+ELE  F R  YPD+ TREE+A    LTEA
Sbjct: 2  QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEA 44


>pdb|3LNQ|A Chain A, Structure Of Aristaless Homeodomain In Complex With Dna
          Length = 58

 Score = 50.4 bits (119), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 26/41 (63%), Positives = 30/41 (73%)

Query: 51 RQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          R RT FTS QL+ELE  F+R  YPD+ TREE+AM   LTEA
Sbjct: 1  RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEA 41


>pdb|2DMS|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
          Protein Otx2
          Length = 80

 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 24/42 (57%), Positives = 30/42 (71%)

Query: 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          RR+RT FT  QL  LEA FA+ RYPD+  REE+A+  NL E+
Sbjct: 8  RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPES 49


>pdb|3A02|A Chain A, Crystal Structure Of Aristaless Homeodomain
          Length = 60

 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/36 (63%), Positives = 27/36 (75%)

Query: 56 FTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          FTS QL+ELE  F+R  YPD+ TREE+AM   LTEA
Sbjct: 6  FTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEA 41


>pdb|2DMU|A Chain A, Solution Structure Of The Homeobox Domain Of Homeobox
          Protein Goosecoid
          Length = 70

 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 27/41 (65%)

Query: 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTE 90
          RR RT FT +QL+ LE  F   +YPD+ TRE++A   +L E
Sbjct: 8  RRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLRE 48


>pdb|2CUE|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
          Paired Box Protein Pax-6
          Length = 80

 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 19/41 (46%), Positives = 25/41 (60%)

Query: 51 RQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          R RT FT +Q++ LE  F R  YPD+  RE +A   +L EA
Sbjct: 9  RNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEA 49


>pdb|2M34|A Chain A, Nmr Structure Of The Homeodomain Transcription Factor
          Gbx1 From Homo Sapiens
          Length = 71

 Score = 36.2 bits (82), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 19/43 (44%), Positives = 27/43 (62%)

Query: 48 RQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTE 90
          + RR+RT FTS+QL ELE  F   +Y  ++ R +IA    L+E
Sbjct: 6  KSRRRRTAFTSEQLLELEKEFHCKKYLSLTERSQIAHALKLSE 48


>pdb|2K40|A Chain A, Nmr Structure Of Hesx-1 Homeodomain Double Mutant
          R31lE42L
          Length = 67

 Score = 33.5 bits (75), Expect = 0.034,   Method: Compositional matrix adjust.
 Identities = 17/39 (43%), Positives = 22/39 (56%)

Query: 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNL 88
          RR RT FT  Q++ LE  F  N YP +   E++A   NL
Sbjct: 2  RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNL 40


>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 = 33.1 bits (74), Expect = 0.041,   Method: Compositional matrix adjust.
 Identities = 19/41 (46%), Positives = 24/41 (58%)

Query: 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTE 90
          +R RT +T  QL ELE  F  N+Y     R E+A+  NLTE
Sbjct: 4  KRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTE 44


>pdb|2LD5|A Chain A, Solution Nmr-Derived Complex Structure Of Hoxa13 Dna
          Binding Domain Bound To Dna
          Length = 67

 Score = 32.7 bits (73), Expect = 0.050,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 25/41 (60%)

Query: 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTE 90
          R++R  +T  QL+ELE  +A N++     R  I+  TNL+E
Sbjct: 2  RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSE 42


>pdb|2L7Z|A Chain A, Nmr Structure Of A13 Homedomain
          Length = 73

 Score = 32.7 bits (73), Expect = 0.052,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 25/41 (60%)

Query: 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTE 90
          R++R  +T  QL+ELE  +A N++     R  I+  TNL+E
Sbjct: 8  RKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSE 48


>pdb|2CRA|A Chain A, Solution Structure Of The Homeobox Domain Of Human Homeo
          Box B13
          Length = 70

 Score = 30.4 bits (67), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 14/41 (34%), Positives = 26/41 (63%)

Query: 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTE 90
          R++R  ++  QL+ELE  +A N++     R +I+  T+L+E
Sbjct: 8  RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSE 48


>pdb|1B72|A Chain A, Pbx1, Homeobox Protein Hox-B1DNA TERNARY COMPLEX
          Length = 97

 Score = 30.4 bits (67), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 18/38 (47%), Positives = 23/38 (60%)

Query: 53 RTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTE 90
          RT+FT++QL ELE  F  N+Y   + R EIA    L E
Sbjct: 38 RTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNE 75


>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 = 30.0 bits (66), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 23/41 (56%)

Query: 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTE 90
          +RQRT +T  Q  ELE  F  NRY     R EIA   +LTE
Sbjct: 29 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTE 69


>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 = 28.9 bits (63), Expect = 0.70,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 25/43 (58%)

Query: 49 QRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          ++R RT F+S+QL  L+  F  NRY     R++++    L EA
Sbjct: 4  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEA 46


>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 = 28.9 bits (63), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 25/43 (58%)

Query: 49 QRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          ++R RT F+S+QL  L+  F  NRY     R++++    L EA
Sbjct: 3  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEA 45


>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 = 28.9 bits (63), Expect = 0.80,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 25/43 (58%)

Query: 49 QRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          ++R RT F+S+QL  L+  F  NRY     R++++    L EA
Sbjct: 3  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEA 45


>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 = 28.9 bits (63), Expect = 0.80,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 25/43 (58%)

Query: 49 QRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          ++R RT F+S+QL  L+  F  NRY     R++++    L EA
Sbjct: 1  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEA 43


>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 = 28.9 bits (63), Expect = 0.84,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 25/43 (58%)

Query: 49 QRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          ++R RT F+S+QL  L+  F  NRY     R++++    L EA
Sbjct: 1  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEA 43


>pdb|3HDD|A Chain A, Engrailed Homeodomain Dna Complex
 pdb|3HDD|B Chain B, Engrailed Homeodomain Dna Complex
          Length = 60

 Score = 28.5 bits (62), Expect = 0.89,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 25/43 (58%)

Query: 49 QRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          ++R RT F+S+QL  L+  F  NRY     R++++    L EA
Sbjct: 1  EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEA 43


>pdb|1PUF|A Chain A, Crystal Structure Of Hoxa9 And Pbx1 Homeodomains Bound
          To Dna
          Length = 77

 Score = 28.1 bits (61), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 17/41 (41%), Positives = 21/41 (51%)

Query: 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTE 90
          R++R  +T  Q  ELE  F  N Y     R E+A   NLTE
Sbjct: 14 RKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTE 54


>pdb|1ZQ3|P Chain P, Nmr Solution Structure Of The Bicoid Homeodomain Bound
          To The Consensus Dna Binding Site Taatcc
          Length = 68

 Score = 28.1 bits (61), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 14/24 (58%), Positives = 16/24 (66%)

Query: 50 RRQRTHFTSQQLQELEATFARNRY 73
          RR RT FTS Q+ ELE  F + RY
Sbjct: 3  RRTRTTFTSSQIAELEQHFLQGRY 26


>pdb|1IG7|A Chain A, Msx-1 HomeodomainDNA COMPLEX STRUCTURE
          Length = 58

 Score = 28.1 bits (61), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 24/41 (58%)

Query: 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTE 90
          R+ RT FT+ QL  LE  F + +Y  ++ R E +   +LTE
Sbjct: 1  RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTE 41


>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 = 28.1 bits (61), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 23/41 (56%)

Query: 51 RQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          R RT F+S+QL  L+  F  NRY     R++++    L EA
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEA 41


>pdb|2DN0|A Chain A, Solution Structure Of The Second Homeobox Domain Of
          Human Zinc Fingers And Homeoboxes Protein 3
          Length = 76

 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 11/31 (35%), Positives = 18/31 (58%)

Query: 59 QQLQELEATFARNRYPDMSTREEIAMWTNLT 89
          +QL  L+ +F RN++P  S  E +   T L+
Sbjct: 18 EQLSALKGSFCRNQFPGQSEVEHLTKVTGLS 48


>pdb|1ENH|A Chain A, Structural Studies Of The Engrailed Homeodomain
          Length = 54

 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 23/41 (56%)

Query: 51 RQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          R RT F+S+QL  L+  F  NRY     R++++    L EA
Sbjct: 1  RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEA 41


>pdb|2CUF|A Chain A, Solution Structure Of The Homeobox Domain Of The Human
          Hypothetical Protein Flj21616
          Length = 95

 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 13/27 (48%), Positives = 17/27 (62%)

Query: 61 LQELEATFARNRYPDMSTREEIAMWTN 87
          L  +E+ F  N+YPD + REEIA   N
Sbjct: 19 LAVMESYFNENQYPDEAKREEIANACN 45


>pdb|2LP0|A Chain A, The Solution Structure Of Homeodomain-Protein Complex
          Length = 60

 Score = 27.7 bits (60), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 17/41 (41%), Positives = 21/41 (51%)

Query: 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTE 90
          R++R  +T  Q  ELE  F  N Y     R E+A   NLTE
Sbjct: 2  RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTE 42


>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 = 27.7 bits (60), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 16/42 (38%), Positives = 22/42 (52%)

Query: 48 RQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLT 89
          ++R++R  FT  Q  ELE  F + RY     RE +A    LT
Sbjct: 8  KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLT 49


>pdb|1ZTR|A Chain A, Solution Structure Of Engrailed Homeodomain L16a Mutant
          Length = 61

 Score = 26.6 bits (57), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 15/43 (34%), Positives = 24/43 (55%)

Query: 49 QRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          ++R RT F+S+QL   +  F  NRY     R++++    L EA
Sbjct: 3  EKRPRTAFSSEQLARAKREFNENRYLTERRRQQLSSELGLNEA 45


>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 = 25.8 bits (55), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 14/40 (35%), Positives = 21/40 (52%)

Query: 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLT 89
          R+ R  F+  Q+ ELE  F + RY     R+++A    LT
Sbjct: 3  RKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLT 42


>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 = 25.8 bits (55), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 14/44 (31%), Positives = 25/44 (56%)

Query: 48 RQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTEA 91
          ++++ RT FT  Q+ ELE  F + +Y   + R  +A    +T+A
Sbjct: 16 KRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDA 59


>pdb|2DJN|A Chain A, The Solution Structure Of The Homeobox Domain Of Human
          Homeobox Protein Dlx-5
          Length = 70

 Score = 25.8 bits (55), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 14/41 (34%), Positives = 23/41 (56%)

Query: 50 RRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLTE 90
          R+ RT ++S QL  L+  F + +Y  +  R E+A    LT+
Sbjct: 8  RKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQ 48


>pdb|1QRY|A Chain A, Homeobox Protein Vnd (Ventral Nervous System Defective
          Protein)
          Length = 80

 Score = 25.8 bits (55), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 21/42 (50%)

Query: 48 RQRRQRTHFTSQQLQELEATFARNRYPDMSTREEIAMWTNLT 89
          ++R++R  FT  Q  ELE  F + RY     RE +     LT
Sbjct: 11 KKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLTSLIRLT 52


  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
   0.320    0.131    0.378 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,125,734
Number of Sequences: 62578
Number of extensions: 44974
Number of successful extensions: 179
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 48
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 131
Number of HSP's gapped (non-prelim): 48
length of query: 104
length of database: 14,973,337
effective HSP length: 69
effective length of query: 35
effective length of database: 10,655,455
effective search space: 372940925
effective search space used: 372940925
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)