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= psy3264
(156 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 139 bits (350), Expect = 6e-34, Method: Compositional matrix adjust.
Identities = 76/159 (47%), Positives = 101/159 (63%), Gaps = 24/159 (15%)
Query: 8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
KPRG+M++YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F +MA D
Sbjct: 15 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 74
Query: 68 KKRYDTEMQSYTPPAGEK------------------------RGKIKQDNPEYGVGDIAK 103
K RY+ EM++Y PP GE R KIK ++P +GD+AK
Sbjct: 75 KARYEREMKTYIPPKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAK 134
Query: 104 ELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS 142
+LG+ W + K YE+ A K K +YEK++ AY+ +
Sbjct: 135 KLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKG 173
>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 = 117 bits (294), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 53/77 (68%), Positives = 65/77 (84%)
Query: 8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
KPRG+M++YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F +MA D
Sbjct: 7 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 66
Query: 68 KKRYDTEMQSYTPPAGE 84
K RY+ EM++Y PP GE
Sbjct: 67 KARYEREMKTYIPPKGE 83
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 67 DKKRYDTEMQSYTPPAGEKRGKIKQDNPEYGV--GDIAKELGKKWADVDPSVKTKYEQMA 124
D K+ +M SY R + K+ +P+ V + +K+ ++W + K K+E MA
Sbjct: 4 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 63
Query: 125 EKDKARYEKEMTAY 138
+ DKARYE+EM Y
Sbjct: 64 KADKARYEREMKTY 77
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 114 bits (284), Expect = 3e-26, Method: Compositional matrix adjust.
Identities = 52/77 (67%), Positives = 64/77 (83%)
Query: 8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
KPRG+M++YAFFVQ REEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F +MA D
Sbjct: 7 KPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 66
Query: 68 KKRYDTEMQSYTPPAGE 84
K RY+ EM++Y PP GE
Sbjct: 67 KARYEREMKTYIPPKGE 83
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 67 DKKRYDTEMQSYTPPAGEKRGKIKQDNPEYGV--GDIAKELGKKWADVDPSVKTKYEQMA 124
D K+ +M SY R + K+ +P+ V + +K+ ++W + K K+E MA
Sbjct: 4 DPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 63
Query: 125 EKDKARYEKEMTAY 138
+ DKARYE+EM Y
Sbjct: 64 KADKARYEREMKTY 77
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 108 bits (269), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 49/71 (69%), Positives = 61/71 (85%)
Query: 8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
KPRG+M++YAFFVQ CREEHKKKHP+ +V F+EFSKKC+ERWKTMS KEK +F +MA D
Sbjct: 1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60
Query: 68 KKRYDTEMQSY 78
K RY+ EM++Y
Sbjct: 61 KARYEREMKTY 71
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 75 MQSYTPPAGEKRGKIKQDNPEYGV--GDIAKELGKKWADVDPSVKTKYEQMAEKDKARYE 132
M SY R + K+ +P+ V + +K+ ++W + K K+E MA+ DKARYE
Sbjct: 6 MSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYE 65
Query: 133 KEMTAY 138
+EM Y
Sbjct: 66 REMKTY 71
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 106 bits (264), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 49/70 (70%), Positives = 59/70 (84%)
Query: 8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
KPRG+M++YAFFVQ REEHKKKHP+ +V FAEFSKKC+ERWKTMS KEK +F +MA D
Sbjct: 8 KPRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSD 67
Query: 68 KKRYDTEMQS 77
K RYD EM++
Sbjct: 68 KARYDREMKN 77
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 75 MQSYTPPAGEKRGKIKQDNPEYGV--GDIAKELGKKWADVDPSVKTKYEQMAEKDKARYE 132
M SY R + K+ +P+ V + +K+ ++W + K+K+E MA+ DKARY+
Sbjct: 13 MSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSDKARYD 72
Query: 133 KEM 135
+EM
Sbjct: 73 REM 75
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
Mobility Group Protein B3
Length = 86
Score = 100 bits (249), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 49/66 (74%), Positives = 54/66 (81%)
Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYD 72
M+AYAFFVQ CREEHKKK+PE V FAEFSKKC+ERWKTMS KEK +F EMA DK RYD
Sbjct: 20 MSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYD 79
Query: 73 TEMQSY 78
EM+ Y
Sbjct: 80 REMKDY 85
Score = 35.0 bits (79), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 63 MADKDKKRYDTEMQSYTPPAGEKRGKIKQDNPEYGV--GDIAKELGKKWADVDPSVKTKY 120
MA D K+ +M +Y R + K+ NPE V + +K+ ++W + K+K+
Sbjct: 8 MAKGDPKKPKGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKF 67
Query: 121 EQMAEKDKARYEKEMTAY 138
++MA+ DK RY++EM Y
Sbjct: 68 DEMAKADKVRYDREMKDY 85
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 2/71 (2%)
Query: 9 PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
P+ ++AY FF R+ + ++P+ + F + KK E+WK ++ +EK+ + A DK
Sbjct: 21 PKRALSAYMFFANENRDIVRSENPD--ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADK 78
Query: 69 KRYDTEMQSYT 79
KRY++E + Y
Sbjct: 79 KRYESEKELYN 89
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 75 MQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE 134
+ +Y A E R ++ +NP+ G + K+LG+KW + P K YE A+ DK RYE E
Sbjct: 25 LSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESE 84
Query: 135 MTAYKNRSVA 144
Y N ++A
Sbjct: 85 KELY-NATLA 93
>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 = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 42/71 (59%), Gaps = 2/71 (2%)
Query: 9 PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
P+ ++AY FF R+ + ++P+ + F + KK E+WK ++ +EK+ + A DK
Sbjct: 21 PKRALSAYMFFANENRDIVRSENPD--ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADK 78
Query: 69 KRYDTEMQSYT 79
KRY++E + Y
Sbjct: 79 KRYESEKELYN 89
Score = 47.8 bits (112), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 1/70 (1%)
Query: 75 MQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE 134
+ +Y A E R ++ +NP+ G + K+LG+KW + P K YE A+ DK RYE E
Sbjct: 25 LSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESE 84
Query: 135 MTAYKNRSVA 144
Y N ++A
Sbjct: 85 KELY-NATLA 93
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/69 (40%), Positives = 41/69 (59%), Gaps = 6/69 (8%)
Query: 80 PPAG------EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEK 133
PP+G E R KIK NP +GD+AK+LG+ W +++ S K Y A K K +YEK
Sbjct: 13 PPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEK 72
Query: 134 EMTAYKNRS 142
++ YK++
Sbjct: 73 DVADYKSKG 81
Score = 30.8 bits (68), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 29/62 (46%)
Query: 17 AFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQ 76
FF+ K K + + +KK E W +++ EK+ + A K K++Y+ ++
Sbjct: 16 GFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEKDVA 75
Query: 77 SY 78
Y
Sbjct: 76 DY 77
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 48.9 bits (115), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 25/60 (41%), Positives = 37/60 (61%)
Query: 82 AGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
E R KIK ++P +GD AK+LG+ W++ K YEQ A K K +YEK++ AY+ +
Sbjct: 19 CSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKYEKDIAAYRAK 78
Score = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 9 PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
P+ +A+ F R + K +HP + + +KK E W S K+K+ + + A K K
Sbjct: 8 PKRPPSAFFLFCSEHRPKIKSEHP--GLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLK 65
Query: 69 KRYDTEMQSY 78
++Y+ ++ +Y
Sbjct: 66 EKYEKDIAAY 75
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 25/60 (41%), Positives = 37/60 (61%)
Query: 82 AGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
E R KIK ++P +GD AK+LG+ W++ K YEQ A K K +YEK++ AY+ +
Sbjct: 20 CSEYRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKYEKDIAAYRAK 79
Score = 32.7 bits (73), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 19/70 (27%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 9 PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
P+ +A+ F R + K +HP + + +KK E W S K+K+ + + A K K
Sbjct: 9 PKRPPSAFFLFCSEYRPKIKSEHP--GLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLK 66
Query: 69 KRYDTEMQSY 78
++Y+ ++ +Y
Sbjct: 67 EKYEKDIAAY 76
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 47.0 bits (110), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 43/146 (29%), Positives = 69/146 (47%), Gaps = 25/146 (17%)
Query: 19 FVQVCREEHKKKHPEE-NVVFAEFSKKCAERWKTMSEKEKKRFHEMADK----------- 66
F+ R++ +K E + +E SK+ +WK ++E EK F + A K
Sbjct: 12 FIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPN 71
Query: 67 -------DKKRYDTEMQSYTPPAG------EKRGKIKQDNPEYGVGDIAKELGKKWADVD 113
KK++ PP+ E R KIK ++P +GD+AK+LG+ W +
Sbjct: 72 YKYRKGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTA 131
Query: 114 PSVKTKYEQMAEKDKARYEKEMTAYK 139
K YE+ A K K +YEK++ AY+
Sbjct: 132 ADDKQPYEKKAAKLKEKYEKDIAAYR 157
Score = 29.6 bits (65), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 37/67 (55%)
Query: 75 MQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE 134
M ++ + ++R K+ +NP +I+K+LG +W + + K + Q A+K +A + ++
Sbjct: 9 MNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
Query: 135 MTAYKNR 141
YK R
Sbjct: 69 YPNYKYR 75
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 4/74 (5%)
Query: 9 PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
P+ TA+ ++ RE K+++P + E +KK E WK + K+K ++ + A KDK
Sbjct: 4 PKRATTAFMLWLNDTRESIKRENP--GIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDK 59
Query: 69 KRYDTEMQSYTPPA 82
+RY EM++Y P A
Sbjct: 60 QRYHDEMRNYKPEA 73
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/54 (44%), Positives = 33/54 (61%), Gaps = 2/54 (3%)
Query: 86 RGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
R IK++NP V +IAK+ G+ W ++ K+K+E A KDK RY EM YK
Sbjct: 19 RESIKRENPGIKVTEIAKKGGEMWKELKD--KSKWEDAAAKDKQRYHDEMRNYK 70
>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 = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 75 MQSYTPPAGEKRGKIKQDNPEYG--VGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYE 132
+ SY A EKR +I +NPE V I K +G W + K YE+M+++D+ RYE
Sbjct: 27 LSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYE 86
Query: 133 KEMTAYKNRSV 143
+E Y R V
Sbjct: 87 REKAEYAQRKV 97
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 37/71 (52%)
Query: 9 PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
P+ +++Y FF + R E ++PE A K W +S++EKK + M+D+D+
Sbjct: 23 PKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDR 82
Query: 69 KRYDTEMQSYT 79
RY+ E Y
Sbjct: 83 VRYEREKAEYA 93
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 43.5 bits (101), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 40/70 (57%), Gaps = 2/70 (2%)
Query: 9 PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
P+ +T Y F+ RE+ + +HP ++ F E +K W + EK+R+ + A+K+K
Sbjct: 8 PKAPVTGYVRFLNERREQIRTRHP--DLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEK 65
Query: 69 KRYDTEMQSY 78
++Y E+ +Y
Sbjct: 66 QQYLKELWAY 75
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 36/57 (63%)
Query: 84 EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKN 140
E+R +I+ +P+ +I K LG +W+ + P+ K +Y AEK+K +Y KE+ AY+
Sbjct: 21 ERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQ 77
>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 = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 36/56 (64%)
Query: 84 EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
E R KIK ++P +GD+AK+LG+ W + K YE+ A K K +YEK++ AY+
Sbjct: 20 EYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYR 75
Score = 26.2 bits (56), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 9 PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
P+ +A+ F R + K +HP ++ + +KK E W + +K+ + + A K K
Sbjct: 7 PKRPPSAFFLFCSEYRPKIKGEHPGLSI--GDVAKKLGEMWNNTAADDKQPYEKKAAKLK 64
Query: 69 KRYDTEMQSY 78
++Y+ ++ +Y
Sbjct: 65 EKYEKDIAAY 74
>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 = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 37/59 (62%)
Query: 84 EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS 142
E R KIK ++P +GD+AK+LG+ W + K YE+ A K K +YEK++ AY+ +
Sbjct: 16 EYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKG 74
Score = 26.6 bits (57), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 9 PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
P+ +A+ F R + K +HP ++ + +KK E W + +K+ + + A K K
Sbjct: 3 PKRPPSAFFLFCSEYRPKIKGEHPGLSI--GDVAKKLGEMWNNTAADDKQPYEKKAAKLK 60
Query: 69 KRYDTEMQSY 78
++Y+ ++ +Y
Sbjct: 61 EKYEKDIAAY 70
>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 = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 37/59 (62%)
Query: 84 EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRS 142
E R KIK ++P +GD+AK+LG+ W + K YE+ A K K +YEK++ AY+ +
Sbjct: 18 EYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAYRAKG 76
Score = 26.6 bits (57), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 17/70 (24%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
Query: 9 PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
P+ +A+ F R + K +HP + + +KK E W + +K+ + + A K K
Sbjct: 5 PKRPPSAFFLFCSEYRPKIKGEHP--GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLK 62
Query: 69 KRYDTEMQSY 78
++Y+ ++ +Y
Sbjct: 63 EKYEKDIAAY 72
>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 = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
KP+ ++AYA ++ RE K+++P + E +K+ E W+ M K+K + A K
Sbjct: 3 KPKRPLSAYALWLNSARESIKRENP--GIKVTEVAKRGGELWRAM--KDKSEWEAKAAKA 58
Query: 68 KKRYDTEMQSY 78
K YD ++ +
Sbjct: 59 KDDYDRAVKEF 69
>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B
Length = 67
Score = 35.8 bits (81), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 38/72 (52%), Gaps = 6/72 (8%)
Query: 8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
KP+ +AY +V +E K P+E + K E WK +S+ EK+ + + A +D
Sbjct: 2 KPKRPRSAYNVYVAERFQEAKGDSPQEKL------KTVKENWKNLSDSEKELYIQHAKED 55
Query: 68 KKRYDTEMQSYT 79
+ RY EM+S+
Sbjct: 56 ETRYHNEMKSWA 67
>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 = 35.8 bits (81), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 9 PRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDK 68
P+ ++AYA F + + K ++P N F E SK A W + E++K+ + + + K
Sbjct: 18 PQKPVSAYALFFRDTQAAIKGQNP--NATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAK 75
Query: 69 KRYDTEMQSY 78
K Y ++ +Y
Sbjct: 76 KEYLKQLAAY 85
Score = 26.9 bits (58), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 29/61 (47%)
Query: 84 EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNRSV 143
+ + IK NP G+++K + W + K Y++ E K Y K++ AY+ V
Sbjct: 31 DTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEYLKQLAAYRASLV 90
Query: 144 A 144
+
Sbjct: 91 S 91
>pdb|2CS1|A Chain A, Solution Structure Of The Hmg Domain Of Human Dna
Mismatch Repair Protein
Length = 92
Score = 35.8 bits (81), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 40/63 (63%), Gaps = 2/63 (3%)
Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYD 72
M+A A FVQ R + ++P+ ++ A + E WKT+SE+EK ++ E A KD +RY+
Sbjct: 12 MSASALFVQDHRPQFLIENPKTSLEDATL--QIEELWKTLSEEEKLKYEEKATKDLERYN 69
Query: 73 TEM 75
++M
Sbjct: 70 SQM 72
>pdb|1V64|A Chain A, Solution Structure Of The 3rd Hmg Box Of Mouse Ubf1
Length = 108
Score = 35.8 bits (81), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 24/35 (68%)
Query: 45 CAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSYT 79
C+++WK +S+KEK +H+ D+ KK Y+ E+ +
Sbjct: 48 CSQQWKLLSQKEKDAYHKKCDQKKKDYEVELLRFL 82
>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 = 34.7 bits (78), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 6/71 (8%)
Query: 8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
KP+ +AY +V +E K P+E + K E WK +S+ EK+ + + A +D
Sbjct: 114 KPKRPRSAYNVYVAERFQEAKGDSPQEKL------KTVKENWKNLSDSEKELYIQHAKED 167
Query: 68 KKRYDTEMQSY 78
+ RY EM+S+
Sbjct: 168 ETRYHNEMKSW 178
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 33.9 bits (76), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
KP+ ++AY ++ RE K+++P + E +K+ E W+ M K+K + A K
Sbjct: 3 KPKRPLSAYMLWLNSARESIKRENP--GIKVTEVAKRGGELWRAM--KDKSEWEAKAAKA 58
Query: 68 KKRYDTEMQSY 78
K YD ++ +
Sbjct: 59 KDDYDRAVKEF 69
>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 = 33.9 bits (76), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
KP+ ++AY ++ RE K+++P + E +K+ E W+ M K+K + A K
Sbjct: 3 KPKRPLSAYMLWLNSARESIKRENP--GIKVTEVAKRGGELWRAM--KDKSEWEAKAAKA 58
Query: 68 KKRYDTEMQSY 78
K YD ++ +
Sbjct: 59 KDDYDRAVKEF 69
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 33.9 bits (76), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 20/71 (28%), Positives = 37/71 (52%), Gaps = 4/71 (5%)
Query: 8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
KP+ ++AY ++ RE K+++P + E +K+ E W+ M K+K + A K
Sbjct: 4 KPKRPLSAYMLWLNSARESIKRENP--GIKVTEVAKRGGELWRAM--KDKSEWEAKAAKA 59
Query: 68 KKRYDTEMQSY 78
K YD ++ +
Sbjct: 60 KDDYDRAVKEF 70
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 33.1 bits (74), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 37/67 (55%)
Query: 75 MQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE 134
M ++ A ++R ++ Q NP+ +++K LGK W + + K + + AE+ + ++ ++
Sbjct: 11 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQD 70
Query: 135 MTAYKNR 141
YK R
Sbjct: 71 HPNYKYR 77
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 36/65 (55%)
Query: 75 MQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE 134
M ++ A ++R ++ Q NP+ +++K LGK W + + K + + AE+ + ++ ++
Sbjct: 7 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQD 66
Query: 135 MTAYK 139
YK
Sbjct: 67 HPNYK 71
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
Length = 238
Score = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 37/71 (52%), Gaps = 6/71 (8%)
Query: 8 KPRGRMTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKD 67
KP+ +AY +V +E K P+E + K E WK +S+ EK+ + + A +D
Sbjct: 146 KPKRPRSAYNVYVAERFQEAKGDSPQEKL------KTVKENWKNLSDSEKELYIQHAKED 199
Query: 68 KKRYDTEMQSY 78
+ RY E +S+
Sbjct: 200 ETRYHNEXKSW 210
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 32.0 bits (71), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 36/67 (53%)
Query: 75 MQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE 134
M ++ + +R KI + +P+ +I+K LGK+W + S K + Q AE+ + ++ +
Sbjct: 7 MNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMAD 66
Query: 135 MTAYKNR 141
YK R
Sbjct: 67 YPDYKYR 73
Score = 27.3 bits (59), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 36/66 (54%), Gaps = 2/66 (3%)
Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYD 72
M A+ + Q+ R + ++ P+ + AE SK+ +RWK + + +K F + A++ + ++
Sbjct: 7 MNAFMVWSQIERRKIMEQSPDMHN--AEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHM 64
Query: 73 TEMQSY 78
+ Y
Sbjct: 65 ADYPDY 70
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human Upstream
Binding Factor
Length = 99
Score = 31.6 bits (70), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 31/56 (55%)
Query: 84 EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYK 139
EKR K + +PE D+ K L KK+ ++ K KY Q +++K +E+ + ++
Sbjct: 24 EKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARFR 79
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 30.8 bits (68), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 36/67 (53%)
Query: 75 MQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE 134
M ++ + +R K+ Q+NP+ +I+K LG +W + + K + A++ +A + KE
Sbjct: 8 MNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKE 67
Query: 135 MTAYKNR 141
YK R
Sbjct: 68 HPDYKYR 74
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 30.8 bits (68), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 36/67 (53%)
Query: 75 MQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE 134
M ++ + +R K+ Q+NP+ +I+K LG +W + + K + A++ +A + KE
Sbjct: 7 MNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKE 66
Query: 135 MTAYKNR 141
YK R
Sbjct: 67 HPDYKYR 73
>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 = 30.8 bits (68), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 37/67 (55%)
Query: 75 MQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE 134
M ++ + ++R K+ +NP +I+K+LG +W + + K + Q A+K +A + ++
Sbjct: 9 MNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
Query: 135 MTAYKNR 141
YK R
Sbjct: 69 YPNYKYR 75
>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 = 30.8 bits (68), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 37/72 (51%)
Query: 70 RYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKA 129
R M ++ + +R K+ Q+NP+ +I+K LG +W + + K + A++ +A
Sbjct: 7 RVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLRA 66
Query: 130 RYEKEMTAYKNR 141
+ KE YK R
Sbjct: 67 LHMKEHPDYKYR 78
>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 = 30.8 bits (68), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 37/67 (55%)
Query: 75 MQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE 134
M ++ + ++R K+ +NP +I+K+LG +W + + K + Q A+K +A + ++
Sbjct: 9 MNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
Query: 135 MTAYKNR 141
YK R
Sbjct: 69 YPNYKYR 75
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 30.8 bits (68), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 16/66 (24%), Positives = 37/66 (56%)
Query: 75 MQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKE 134
M ++ A ++R ++ Q NP+ +++K LGK W + + K + + AE+ + ++ ++
Sbjct: 12 MNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQD 71
Query: 135 MTAYKN 140
YK+
Sbjct: 72 HPNYKS 77
>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 = 30.4 bits (67), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 37/76 (48%)
Query: 64 ADKDKKRYDTEMQSYTPPAGEKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQM 123
+ K+K M ++ A R K+ P +++K LGK W ++ S K + +
Sbjct: 23 SSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEE 82
Query: 124 AEKDKARYEKEMTAYK 139
AE+ + +++K+ YK
Sbjct: 83 AERLRVQHKKDHPDYK 98
Score = 29.3 bits (64), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMADK 66
M A+ + Q R + ++P ++ AE SK + W+ ++E EK+ F E A++
Sbjct: 34 MNAFMVWAQAARRKLADQYP--HLHNAELSKTLGKLWRLLNESEKRPFVEEAER 85
>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 = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 33/58 (56%)
Query: 84 EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKNR 141
++R K+ +NP +I+K+LG +W + + K + Q A+K +A + ++ YK R
Sbjct: 18 DQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR 75
>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby
Sox Homolog
Length = 82
Score = 28.5 bits (62), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 27/55 (49%)
Query: 86 RGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEKEMTAYKN 140
R ++Q++P K L WA +DP K KY MA++ K + K Y++
Sbjct: 23 RSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDAFMKANPGYRS 77
Score = 27.3 bits (59), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 13 MTAYAFFVQVCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMA 64
M A+ F + R +++HP + A +K A+ W + KEK+++ +MA
Sbjct: 12 MNAFLLFCKRHRSLVRQEHPRLDNRGA--TKILADWWAVLDPKEKQKYTDMA 61
>pdb|2CTO|A Chain A, Solution Structure Of The Hmg Box Like Domain From Human
Hypothetical Protein Flj14904
Length = 93
Score = 28.1 bits (61), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 3/52 (5%)
Query: 14 TAYAFFVQ-VCREEHKKKHPEENVVFAEFSKKCAERWKTMSEKEKKRFHEMA 64
AY FFVQ E ++ P V A+ C+ W + E+EK+++ EMA
Sbjct: 16 NAYYFFVQEKIPELRRRGLPVARV--ADAIPYCSSDWALLREEEKEKYAEMA 65
>pdb|1GHI|A Chain A, Structure Of Beta-Lactamase Glu166asp:asn170gln Mutant
pdb|1GHM|A Chain A, Structures Of The Acyl-Enzyme Complex Of The
Staphylococcus Aureus Beta-Lactamase Mutant
Glu166asp:asn170gln With Degraded Cephaloridine
pdb|1GHP|A Chain A, Structures Of The Acyl-Enzyme Complex Of The
Staphylococcus Aureus Beta-Lactamase Mutant
Glu166asp:asn170gln With Degraded Benzylpenicillin
Length = 258
Score = 27.7 bits (60), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/28 (46%), Positives = 18/28 (64%), Gaps = 2/28 (7%)
Query: 55 KEKKRFHEMADK--DKKRYDTEMQSYTP 80
K K+R E+ DK + RYD E+Q Y+P
Sbjct: 115 KVKQRLKELGDKVTNPVRYDIELQYYSP 142
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 26.9 bits (58), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 27/50 (54%)
Query: 84 EKRGKIKQDNPEYGVGDIAKELGKKWADVDPSVKTKYEQMAEKDKARYEK 133
EKR +++++ PE ++ + L + W D+ K KY+ KA+ E+
Sbjct: 34 EKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYKAREAALKAQSER 83
>pdb|1L8Y|A Chain A, Solution Structure Of Hmg Box 5 In Human Upstream
Binding Factor
pdb|1L8Z|A Chain A, Solution Structure Of Hmg Box 5 In Human Upstream
Binding Factor
pdb|2HDZ|A Chain A, Crystal Structure Analysis Of The Ubf Hmg Box5
Length = 91
Score = 26.2 bits (56), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 49 WKTMSEKEKKRFHEMADKDKKRYDTEMQSY-TPPAGEKRGK 88
W M +KEK + + A +D+KRY+ E+ PPA K
Sbjct: 42 WNNMEKKEKLMWIKKAAEDQKRYERELSEMRAPPAATNSSK 82
>pdb|2LEF|A Chain A, Lef1 Hmg Domain (From Mouse), Complexed With Dna (15bp),
Nmr, 12 Structures
Length = 86
Score = 26.2 bits (56), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 11/40 (27%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 39 AEFSKKCAERWKTMSEKEKKRFHEMADKDKKRYDTEMQSY 78
A ++ RW +S +E+ +++E+A K+++ MQ Y
Sbjct: 31 AAINQILGRRWHALSREEQAKYYELARKERQ---LHMQLY 67
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
0.308 0.126 0.363
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,070,596
Number of Sequences: 62578
Number of extensions: 210315
Number of successful extensions: 711
Number of sequences better than 100.0: 64
Number of HSP's better than 100.0 without gapping: 47
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 611
Number of HSP's gapped (non-prelim): 108
length of query: 156
length of database: 14,973,337
effective HSP length: 91
effective length of query: 65
effective length of database: 9,278,739
effective search space: 603118035
effective search space used: 603118035
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: 47 (22.7 bits)