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= psy14249
         (60 letters)

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

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



>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
          Length = 83

 Score = 69.7 bits (169), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 31/38 (81%), Positives = 35/38 (92%)

Query: 14 RIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
          RIRRPMNAFMVWAK ERK+LA +NPDLHNA+LSKML +
Sbjct: 6  RIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGK 43


>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
          Factor Sox-17
          Length = 82

 Score = 68.6 bits (166), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 30/43 (69%), Positives = 36/43 (83%)

Query: 9  TAKEQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
          ++    IRRPMNAFMVWAK ERK+LA +NPDLHNA+LSKML +
Sbjct: 2  SSGSSGIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGK 44


>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
          Length = 71

 Score = 67.4 bits (163), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 30/37 (81%), Positives = 34/37 (91%)

Query: 15 IRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
          IRRPMNAFMVWAK ERK+LA +NPDLHNA+LSKML +
Sbjct: 3  IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGK 39


>pdb|4EUW|A Chain A, Crystal Structure Of A Hmg Domain Of Transcription
          Factor Sox-9 Bound To Dna (Sox-9DNA) FROM HOMO SAPIENS
          AT 2.77 A RESOLUTION
          Length = 106

 Score = 58.9 bits (141), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 25/46 (54%), Positives = 35/46 (76%)

Query: 7  QKTAKEQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLARI 52
          Q +  +  ++RPMNAFMVWA+  R+KLAD+ P LHNA+LSK L ++
Sbjct: 22 QSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKL 67


>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
          Length = 79

 Score = 57.4 bits (137), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 34/37 (91%)

Query: 15 IRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
          I+RPMNAFMVW+++ER+K+ +++PD+HNA++SK L +
Sbjct: 3  IKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGK 39


>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
          Human Stem Cell Transcription Factor Sox2
          Length = 81

 Score = 56.6 bits (135), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 32/37 (86%)

Query: 14 RIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
          R++RPMNAFMVW++ +R+K+A ENP +HN+++SK L 
Sbjct: 3  RVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLG 39


>pdb|1O4X|B Chain B, Ternary Complex Of The Dna Binding Domains Of The Oct1
          And Sox2 Transcription Factors With A 19mer
          Oligonucleotide From The Hoxb1 Regulatory Element
          Length = 88

 Score = 56.6 bits (135), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 32/37 (86%)

Query: 14 RIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
          R++RPMNAFMVW++ +R+K+A ENP +HN+++SK L 
Sbjct: 7  RVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLG 43


>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
          Length = 80

 Score = 56.6 bits (135), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 21/37 (56%), Positives = 32/37 (86%)

Query: 14 RIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
          R++RPMNAFMVW++ +R+K+A ENP +HN+++SK L 
Sbjct: 2  RVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLG 38


>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
          Box From Mouse
          Length = 81

 Score = 54.3 bits (129), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 22/36 (61%), Positives = 30/36 (83%)

Query: 15 IRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
          I+RPMNAFMVWAK ER+K+    PD+HN+++SK+L 
Sbjct: 5  IKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILG 40


>pdb|1HRZ|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By
          Multi-Dimensional Heteronuclear-Edited And-Filtered Nmr
 pdb|1HRY|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By
          Multid-Dimensional Heteronuclear-Edited And-Filtered
          Nmr
          Length = 76

 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 19/37 (51%), Positives = 31/37 (83%)

Query: 14 RIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
          R++RPMNAF+VW++ +R+K+A ENP + N+++SK L 
Sbjct: 4  RVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 40


>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
          Length = 159

 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 32/39 (82%)

Query: 12 EQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
          + R++RPMNAF+VW++ +R+K+A ENP + N+++SK L 
Sbjct: 2  QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 40



 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 13/42 (30%), Positives = 22/42 (52%)

Query: 16  RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLARILLTCA 57
           +RP +AF ++    R K+  E+P L   D++K L  +    A
Sbjct: 90  KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA 131


>pdb|1J46|A Chain A, 3d Solution Nmr Structure Of The Wild Type Hmg-Box
          Domain Of The Human Male Sex Determining Factor Sry
          Complexed To Dna
          Length = 85

 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 19/39 (48%), Positives = 32/39 (82%)

Query: 12 EQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
          + R++RPMNAF+VW++ +R+K+A ENP + N+++SK L 
Sbjct: 2  QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLG 40


>pdb|1J47|A Chain A, 3d Solution Nmr Structure Of The M9i Mutant Of The
          Hmg-Box Domain Of The Human Male Sex Determining Factor
          Sry Complexed To Dna
          Length = 85

 Score = 48.5 bits (114), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 32/39 (82%)

Query: 12 EQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
          + R++RP+NAF+VW++ +R+K+A ENP + N+++SK L 
Sbjct: 2  QDRVKRPINAFIVWSRDQRRKMALENPRMRNSEISKQLG 40


>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
          Length = 90

 Score = 37.4 bits (85), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 13/48 (27%), Positives = 34/48 (70%)

Query: 5  QQQKTAKEQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLARI 52
          Q+      ++ +RP++A  ++++ +R++L +E P+L  ++L+++LAR+
Sbjct: 11 QEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARM 58


>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby
          Sox Homolog
          Length = 82

 Score = 33.5 bits (75), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 16/42 (38%), Positives = 25/42 (59%)

Query: 9  TAKEQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
          ++     RRPMNAF+++ K  R  +  E+P L N   +K+LA
Sbjct: 2  SSGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILA 43


>pdb|1HSM|A Chain A, The Structure Of The Hmg Box And Its Interaction With
          Dna
 pdb|1HSN|A Chain A, The Structure Of The Hmg Box And Its Interaction With
          Dna
          Length = 79

 Score = 28.9 bits (63), Expect = 0.88,   Method: Compositional matrix adjust.
 Identities = 12/37 (32%), Positives = 21/37 (56%)

Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLARI 52
          +RP +AF ++    R K+  E+P L   D++K L  +
Sbjct: 4  KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEM 40


>pdb|1NHM|A Chain A, The Structure Of The Hmg Box And Its Interaction With
          Dna
 pdb|1NHN|A Chain A, The Structure Of The Hmg Box And Its Interaction With
          Dna
          Length = 81

 Score = 28.5 bits (62), Expect = 0.91,   Method: Compositional matrix adjust.
 Identities = 12/37 (32%), Positives = 21/37 (56%)

Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLARI 52
          +RP +AF ++    R K+  E+P L   D++K L  +
Sbjct: 6  KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEM 42


>pdb|1HME|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1
 pdb|1HMF|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1
          Length = 77

 Score = 28.5 bits (62), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 12/37 (32%), Positives = 21/37 (56%)

Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLARI 52
          +RP +AF ++    R K+  E+P L   D++K L  +
Sbjct: 8  KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEM 44


>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
           High Mobility Group Protein B1
          Length = 173

 Score = 28.5 bits (62), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 12/37 (32%), Positives = 21/37 (56%)

Query: 16  RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLARI 52
           +RP +AF ++    R K+  E+P L   D++K L  +
Sbjct: 103 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEM 139


>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
          Length = 78

 Score = 28.5 bits (62), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 12/37 (32%), Positives = 20/37 (54%)

Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLARI 52
          +RP +AF ++    R K+  E+P L   D +K L  +
Sbjct: 9  KRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEM 45


>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
          Hmg-Box Transcription Factor 1
          Length = 87

 Score = 28.5 bits (62), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 21/37 (56%)

Query: 14 RIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
          + +RPMNAFM++AK  R +     P   N  +S +L 
Sbjct: 17 KCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILG 53


>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
          Length = 74

 Score = 28.1 bits (61), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 10/32 (31%), Positives = 21/32 (65%)

Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSK 47
          +RP++A+M+W    R+ +  ENP +   +++K
Sbjct: 6  KRPLSAYMLWLNSARESIKRENPGIKVTEVAK 37


>pdb|1QRV|A Chain A, Crystal Structure Of The Complex Of Hmg-D And Dna
 pdb|1QRV|B Chain B, Crystal Structure Of The Complex Of Hmg-D And Dna
          Length = 73

 Score = 28.1 bits (61), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 10/32 (31%), Positives = 21/32 (65%)

Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSK 47
          +RP++A+M+W    R+ +  ENP +   +++K
Sbjct: 5  KRPLSAYMLWLNSARESIKRENPGIKVTEVAK 36


>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
          Domain Of Hmg-D From Drosophila Melanogaster
          Length = 73

 Score = 28.1 bits (61), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 10/32 (31%), Positives = 21/32 (65%)

Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSK 47
          +RP++A+M+W    R+ +  ENP +   +++K
Sbjct: 5  KRPLSAYMLWLNSARESIKRENPGIKVTEVAK 36


>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
          Length = 79

 Score = 27.7 bits (60), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 12/37 (32%), Positives = 20/37 (54%)

Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLARI 52
          +RP +AF ++    R K+  E+P L   D +K L  +
Sbjct: 10 KRPPSAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEM 46


>pdb|2LEF|A Chain A, Lef1 Hmg Domain (From Mouse), Complexed With Dna (15bp),
          Nmr, 12 Structures
          Length = 86

 Score = 27.3 bits (59), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 12/37 (32%), Positives = 24/37 (64%)

Query: 15 IRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
          I++P+NAFM++ K  R  +  E+    +A ++++L R
Sbjct: 3  IKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGR 39


>pdb|3SHW|A Chain A, Crystal Structure Of Zo-1 Pdz3-Sh3-Guk Supramodule Complex
           With Connexin-45 Peptide
          Length = 468

 Score = 26.9 bits (58), Expect = 2.6,   Method: Composition-based stats.
 Identities = 13/31 (41%), Positives = 18/31 (58%)

Query: 11  KEQRIRRPMNAFMVWAKVERKKLADENPDLH 41
           +E    RP+  F   A V R+KLA E PD++
Sbjct: 219 REAGFLRPVTIFGPIADVAREKLAREEPDIY 249


>pdb|3TSW|A Chain A, Crystal Structure Of The Pdz3-Sh3-Guk Core Module Of Human
           Zo-1
 pdb|3TSW|C Chain C, Crystal Structure Of The Pdz3-Sh3-Guk Core Module Of Human
           Zo-1
 pdb|3TSW|D Chain D, Crystal Structure Of The Pdz3-Sh3-Guk Core Module Of Human
           Zo-1
 pdb|3TSZ|A Chain A, Crystal Structure Of Pdz3-Sh3-Guk Core Module From Human
           Zo-1 In Complex With 12mer Peptide From Human Jam-A
           Cytoplasmic Tail
          Length = 391

 Score = 26.9 bits (58), Expect = 2.8,   Method: Composition-based stats.
 Identities = 13/31 (41%), Positives = 18/31 (58%)

Query: 11  KEQRIRRPMNAFMVWAKVERKKLADENPDLH 41
           +E    RP+  F   A V R+KLA E PD++
Sbjct: 227 REAGFLRPVTIFGPIADVAREKLAREEPDIY 257


>pdb|3LH5|A Chain A, Crystal Structure Of The Sh3-Guanylate Kinase Core Domain
           Of Zo-1
          Length = 251

 Score = 26.6 bits (57), Expect = 3.5,   Method: Composition-based stats.
 Identities = 13/31 (41%), Positives = 18/31 (58%)

Query: 11  KEQRIRRPMNAFMVWAKVERKKLADENPDLH 41
           +E    RP+  F   A V R+KLA E PD++
Sbjct: 87  REAGFLRPVTIFGPIADVAREKLAREEPDIY 117


>pdb|2D7L|A Chain A, Solution Structure Of The Hmg Box Domain From Human Wd
          Repeat And Hmg-Box Dna Binding Protein 1
          Length = 81

 Score = 26.2 bits (56), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 4/43 (9%)

Query: 17 RPMNAFMVWAKVERKKLADENPDLHN-ADLSK---MLARILLT 55
          RP   F +W +  R  +  +NPD  + AD+ K   +  R+L T
Sbjct: 8  RPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMIRFRVLST 50


>pdb|1J5N|A Chain A, Solution Structure Of The Non-Sequence-Specific Hmgb
          Protein Nhp6a In Complex With Sry Dna
 pdb|1LWM|A Chain A, Solution Structure Of The Sequence-Non-Specific Hmgb
          Protein Nhp6a
          Length = 93

 Score = 25.8 bits (55), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 11/35 (31%), Positives = 19/35 (54%)

Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
          +R ++A+M +A   R  +  ENPD+    + K L 
Sbjct: 22 KRALSAYMFFANENRDIVRSENPDITFGQVGKKLG 56


>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
          Length = 93

 Score = 25.8 bits (55), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 11/35 (31%), Positives = 19/35 (54%)

Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
          +R ++A+M +A   R  +  ENPD+    + K L 
Sbjct: 22 KRALSAYMFFANENRDIVRSENPDITFGQVGKKLG 56


>pdb|3NM9|A Chain A, Hmgd(M13a)-Dna Complex
 pdb|3NM9|D Chain D, Hmgd(M13a)-Dna Complex
 pdb|3NM9|G Chain G, Hmgd(M13a)-Dna Complex
 pdb|3NM9|J Chain J, Hmgd(M13a)-Dna Complex
 pdb|3NM9|M Chain M, Hmgd(M13a)-Dna Complex
 pdb|3NM9|P Chain P, Hmgd(M13a)-Dna Complex
          Length = 73

 Score = 25.8 bits (55), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 9/32 (28%), Positives = 20/32 (62%)

Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSK 47
          +RP++A+ +W    R+ +  ENP +   +++K
Sbjct: 5  KRPLSAYALWLNSARESIKRENPGIKVTEVAK 36


>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human
          Upstream Binding Factor
          Length = 99

 Score = 25.4 bits (54), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 10/36 (27%), Positives = 23/36 (63%)

Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
          ++P+  +  +   +R K A  +P++ N DL+K+L++
Sbjct: 12 KKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSK 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
   0.320    0.127    0.373 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,512,411
Number of Sequences: 62578
Number of extensions: 37737
Number of successful extensions: 118
Number of sequences better than 100.0: 35
Number of HSP's better than 100.0 without gapping: 35
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 82
Number of HSP's gapped (non-prelim): 36
length of query: 60
length of database: 14,973,337
effective HSP length: 31
effective length of query: 29
effective length of database: 13,033,419
effective search space: 377969151
effective search space used: 377969151
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)