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= 034589
         (90 letters)

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

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



>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 = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 23/48 (47%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
          DPN PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +
Sbjct: 3  DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTA 49


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

 Score = 47.8 bits (112), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/48 (47%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
          DPN PKRP SAFF+F  E+R + K +HP   S+    K  GE W   S
Sbjct: 5  DPNAPKRPPSAFFLFCSEYRPKIKSEHP-GLSIGDTAKKLGEMWSEQS 51


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

 Score = 47.4 bits (111), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/44 (52%), Positives = 28/44 (63%), Gaps = 1/44 (2%)

Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKW 77
           DPN PKRP SAFF+F  E+R + K +HP   S+  V K  GE W
Sbjct: 85  DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMW 127



 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 14/45 (31%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          KRP +AF V+  + R +   ++P+ ++ + + K  G +WK ++EA
Sbjct: 6  KRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEA 49


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

 Score = 47.0 bits (110), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 23/44 (52%), Positives = 28/44 (63%), Gaps = 1/44 (2%)

Query: 34  DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKW 77
           DPN PKRP SAFF+F  E+R + K +HP   S+  V K  GE W
Sbjct: 98  DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMW 140



 Score = 35.8 bits (81), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPK-NKSVAAVGKAGGEKWKSMSEAVSG 86
          DP KP+   S++  F++  RE++KK HP  + + +   K   E+WK+MS    G
Sbjct: 12 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 65


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

 Score = 45.8 bits (107), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 23/48 (47%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
          DPN PKRP SAFF+F  E R + K +HP   S+    K  GE W   S
Sbjct: 4  DPNAPKRPPSAFFLFCSEHRPKIKSEHP-GLSIGDTAKKLGEMWSEQS 50


>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 = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 28/46 (60%), Gaps = 1/46 (2%)

Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
          N PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +
Sbjct: 3  NAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTA 47


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

 Score = 42.4 bits (98), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 31/47 (65%), Gaps = 1/47 (2%)

Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          +KPKRP SA+ +++   RE  K+++P  K V  V K GGE W++M +
Sbjct: 3  DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 48


>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 = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 31/47 (65%), Gaps = 1/47 (2%)

Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          +KPKRP SA+ +++   RE  K+++P  K V  V K GGE W++M +
Sbjct: 2  DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 47


>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From
          High Mobility Group Protein B3
          Length = 81

 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 20/48 (41%), Positives = 29/48 (60%), Gaps = 1/48 (2%)

Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          N PKRP S FF+F  EFR + K  +P   S+  V K  GE W +++++
Sbjct: 8  NAPKRPPSGFFLFCSEFRPKIKSTNP-GISIGDVAKKLGEMWNNLNDS 54


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

 Score = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 31/47 (65%), Gaps = 1/47 (2%)

Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          +KPKRP SA+ +++   RE  K+++P  K V  V K GGE W++M +
Sbjct: 2  DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 47


>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 = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 20/44 (45%), Positives = 27/44 (61%), Gaps = 1/44 (2%)

Query: 38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
          PKRP SAFF+F  E+R + K +HP   S+  V K  GE W + +
Sbjct: 3  PKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTA 45


>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 = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/47 (42%), Positives = 31/47 (65%), Gaps = 1/47 (2%)

Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          +KPKRP SA+ +++   RE  K+++P  K V  V K GGE W++M +
Sbjct: 2  DKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 47


>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
          Length = 77

 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 31/49 (63%), Gaps = 1/49 (2%)

Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMS 81
          DPNKP+   S++  F++  RE++KK HP +  + A   K   E+WK+MS
Sbjct: 5  DPNKPRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMS 53


>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 = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/48 (41%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
          DPN PKR  SA+  F  E R+  + ++P + +   VGK  GEKWK+++
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENP-DITFGQVGKKLGEKWKALT 63


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

 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 20/48 (41%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
          DPN PKR  SA+  F  E R+  + ++P + +   VGK  GEKWK+++
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENP-DITFGQVGKKLGEKWKALT 63


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

 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 29/46 (63%), Gaps = 1/46 (2%)

Query: 35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSM 80
          PNK KRP +AF +F +++R +Y + +P  K   A+    G++WK M
Sbjct: 15 PNKCKRPMNAFMLFAKKYRVEYTQMYP-GKDNRAISVILGDRWKKM 59


>pdb|2LHJ|A Chain A, Nmr Structure Of The High Mobility Group Protein-Like
          Protein Nhp1 From Babesia Bovis T2bo (Baboa.00841.A)
          Length = 97

 Score = 38.5 bits (88), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 20/50 (40%), Positives = 31/50 (62%), Gaps = 1/50 (2%)

Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPK-NKSVAAVGKAGGEKWKSMSE 82
          DPN PKR  S++  F +E R +   ++P+  K VAA+GK  G  W ++S+
Sbjct: 19 DPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSD 68


>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
          Subunit Of Fact
          Length = 73

 Score = 37.4 bits (85), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          PKR  +AF +++ + RE  K+++P  K V  + K GGE WK + +
Sbjct: 4  PKRATTAFMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKELKD 47


>pdb|2LY4|A Chain A, Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-BoxP53
          Transactivation Domain Interaction And Is Regulated By
          The Acidic Tail
          Length = 83

 Score = 36.2 bits (82), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPK-NKSVAAVGKAGGEKWKSMSEAVSG 86
          DP KP+   S++  F++  RE++KK HP  + + +   K   E+WK+MS    G
Sbjct: 4  DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 57


>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
          Length = 83

 Score = 35.4 bits (80), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 1/54 (1%)

Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPK-NKSVAAVGKAGGEKWKSMSEAVSG 86
          DP KP+   S++  F++  RE++KK HP  + + +   K   E+WK+MS    G
Sbjct: 4  DPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKG 57


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

 Score = 35.4 bits (80), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 1/47 (2%)

Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
           KPKRP SA F+F EE R Q +++ P+  S + + +     W  +SE
Sbjct: 19 EKPKRPVSAMFIFSEEKRRQLQEERPEL-SESELTRLLARMWNDLSE 64


>pdb|2CO9|A Chain A, Solution Structure Of The Hmg_box Domain Of Thymus High
          Mobility Group Box Protein Tox From Mouse
          Length = 102

 Score = 32.3 bits (72), Expect = 0.066,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)

Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          DPN+P++P SA+ +F  + +   K  +P N +   V K     W  + E
Sbjct: 14 DPNEPQKPVSAYALFFRDTQAAIKGQNP-NATFGEVSKIVASMWDGLGE 61


>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
          Cisplatin-modified Dna Duplex
          Length = 71

 Score = 31.6 bits (70), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 3/47 (6%)

Query: 37 KPKRPASAFFVFMEEFREQYKKDHPKNKSV--AAVGKAGGEKWKSMS 81
          KP+   S++  F++  RE++KK HP + SV  +   K   E+WK+MS
Sbjct: 1  KPRGKMSSYAFFVQTCREEHKKKHP-DASVNFSEFSKKCSERWKTMS 46


>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
          Length = 238

 Score = 31.6 bits (70), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 5/53 (9%)

Query: 37  KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL 89
           KPKRP SA+ V++ E  ++ K D P+ K      K   E WK++S++   L +
Sbjct: 146 KPKRPRSAYNVYVAERFQEAKGDSPQEKL-----KTVKENWKNLSDSEKELYI 193


>pdb|3TQ6|A Chain A, Crystal Structure Of Human Mitochondrial Transcription
           Factor A, Tfam Or Mttfa, Bound To The Light Strand
           Promoter Lsp
 pdb|3TQ6|B Chain B, Crystal Structure Of Human Mitochondrial Transcription
           Factor A, Tfam Or Mttfa, Bound To The Light Strand
           Promoter Lsp
          Length = 214

 Score = 31.6 bits (70), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 5/53 (9%)

Query: 37  KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL 89
           KPKRP SA+ V++ E  ++ K D P+ K      K   E WK++S++   L +
Sbjct: 114 KPKRPRSAYNVYVAERFQEAKGDSPQEK-----LKTVKENWKNLSDSEKELYI 161


>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B
          Length = 67

 Score = 31.6 bits (70), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 19/53 (35%), Positives = 30/53 (56%), Gaps = 5/53 (9%)

Query: 37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEAVSGLVL 89
          KPKRP SA+ V++ E  ++ K D P+ K      K   E WK++S++   L +
Sbjct: 2  KPKRPRSAYNVYVAERFQEAKGDSPQEKL-----KTVKENWKNLSDSEKELYI 49


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

 Score = 30.0 bits (66), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 1/48 (2%)

Query: 35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSE 82
          P+ PK+P + +F F  E R +Y K HP+  S   + K   +K+K + E
Sbjct: 8  PDFPKKPLTPYFRFFMEKRAKYAKLHPEM-SNLDLTKILSKKYKELPE 54


>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 = 29.6 bits (65), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          P++ KRP +AF V+    R +  +++PK  + + + K  G +WK +SE 
Sbjct: 5  PDRVKRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSET 52


>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 = 28.9 bits (63), Expect = 0.87,   Method: Compositional matrix adjust.
 Identities = 14/45 (31%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          KRP +AF V+  + R +   ++P+ ++ + + K  G +WK ++EA
Sbjct: 6  KRPINAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEA 49


>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 = 28.5 bits (62), Expect = 0.91,   Method: Compositional matrix adjust.
 Identities = 14/45 (31%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          KRP +AF V+  + R +   ++P+ ++ + + K  G +WK ++EA
Sbjct: 6  KRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEA 49


>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 = 28.5 bits (62), Expect = 0.93,   Method: Compositional matrix adjust.
 Identities = 14/45 (31%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          KRP +AF V+  + R +   ++P+ ++ + + K  G +WK ++EA
Sbjct: 6  KRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEA 49


>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
          Protein Hmgx2
          Length = 92

 Score = 28.5 bits (62), Expect = 0.99,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          PK P + +  F+ E REQ +  HP +     + K  G +W  +  A
Sbjct: 8  PKAPVTGYVRFLNERREQIRTRHP-DLPFPEITKMLGAEWSKLQPA 52


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

 Score = 27.7 bits (60), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 13/43 (30%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
          K+P +AF ++M+E R     +    +S AA+ +  G +W ++S
Sbjct: 4  KKPLNAFMLYMKEMRANVVAESTLKES-AAINQILGRRWHALS 45


>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
          Mobility Group Protein B3
          Length = 86

 Score = 27.7 bits (60), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 15/40 (37%), Positives = 25/40 (62%), Gaps = 1/40 (2%)

Query: 43 SAFFVFMEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMS 81
          SA+  F++  RE++KK +P+   + A   K   E+WK+MS
Sbjct: 21 SAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMS 60


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

 Score = 26.6 bits (57), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 8/24 (33%), Positives = 16/24 (66%)

Query: 39 KRPASAFFVFMEEFREQYKKDHPK 62
          +RP +AF +F +  R   +++HP+
Sbjct: 9  RRPMNAFLLFCKRHRSLVRQEHPR 32


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

 Score = 26.6 bits (57), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 1/45 (2%)

Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          KRP +AF V+    R +  +++PK  + + + K  G +WK +SE 
Sbjct: 4  KRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSET 47


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

 Score = 26.6 bits (57), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 1/45 (2%)

Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          KRP +AF V+    R +  +++PK  + + + K  G +WK +SE 
Sbjct: 5  KRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSET 48


>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 = 26.2 bits (56), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 3/50 (6%)

Query: 36 NKP--KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          NKP  KRP +AF V+ +  R +    +P   + A + K  G+ W+ ++E+
Sbjct: 26 NKPHVKRPMNAFMVWAQAARRKLADQYPHLHN-AELSKTLGKLWRLLNES 74


>pdb|2CS1|A Chain A, Solution Structure Of The Hmg Domain Of Human Dna
          Mismatch Repair Protein
          Length = 92

 Score = 26.2 bits (56), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 25/43 (58%), Gaps = 1/43 (2%)

Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMS 81
          K+P SA  +F+++ R Q+  ++PK  S+        E WK++S
Sbjct: 9  KKPMSASALFVQDHRPQFLIENPKT-SLEDATLQIEELWKTLS 50


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

 Score = 25.8 bits (55), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 13/45 (28%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          +RP +AF V+ ++ R++  + +P +   A + K  G+ WK+++ A
Sbjct: 4  RRPMNAFMVWAKDERKRLAQQNP-DLHNAELSKMLGKSWKALTLA 47


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

 Score = 25.8 bits (55), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 13/45 (28%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          +RP +AF V+ ++ R++  + +P +   A + K  G+ WK+++ A
Sbjct: 9  RRPMNAFMVWAKDERKRLAQQNP-DLHNAELSKMLGKSWKALTLA 52


>pdb|3IFS|A Chain A, 2.0 Angstrom Resolution Crystal Structure Of
           Glucose-6-Phosphate Isomerase (Pgi) From Bacillus
           Anthracis.
 pdb|3IFS|B Chain B, 2.0 Angstrom Resolution Crystal Structure Of
           Glucose-6-Phosphate Isomerase (Pgi) From Bacillus
           Anthracis.
 pdb|3IFS|C Chain C, 2.0 Angstrom Resolution Crystal Structure Of
           Glucose-6-Phosphate Isomerase (Pgi) From Bacillus
           Anthracis.
 pdb|3IFS|D Chain D, 2.0 Angstrom Resolution Crystal Structure Of
           Glucose-6-Phosphate Isomerase (Pgi) From Bacillus
           Anthracis.
 pdb|3IFS|E Chain E, 2.0 Angstrom Resolution Crystal Structure Of
           Glucose-6-Phosphate Isomerase (Pgi) From Bacillus
           Anthracis.
 pdb|3IFS|F Chain F, 2.0 Angstrom Resolution Crystal Structure Of
           Glucose-6-Phosphate Isomerase (Pgi) From Bacillus
           Anthracis
          Length = 453

 Score = 25.4 bits (54), Expect = 7.9,   Method: Composition-based stats.
 Identities = 12/34 (35%), Positives = 18/34 (52%)

Query: 41  PASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGG 74
           PA AF +F +   E+Y K+  + +  A   KA G
Sbjct: 155 PALAFRIFRKLLEEKYGKEEARKRIYATTDKARG 188


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

 Score = 25.4 bits (54), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 13/45 (28%), Positives = 28/45 (62%), Gaps = 1/45 (2%)

Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEA 83
          +RP +AF V+ ++ R++  + +P +   A + K  G+ WK+++ A
Sbjct: 8  RRPMNAFMVWAKDERKRLAQQNP-DLHNAELSKMLGKSWKALTLA 51


  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
   0.309    0.126    0.354 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,202,640
Number of Sequences: 62578
Number of extensions: 59109
Number of successful extensions: 228
Number of sequences better than 100.0: 45
Number of HSP's better than 100.0 without gapping: 32
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 179
Number of HSP's gapped (non-prelim): 50
length of query: 90
length of database: 14,973,337
effective HSP length: 57
effective length of query: 33
effective length of database: 11,406,391
effective search space: 376410903
effective search space used: 376410903
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 45 (21.9 bits)