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= 031573
(157 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 50.8 bits (120), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRA 126
PK+PP+ FF F +FR + NP I S+ + K GE W + EK Y A + +
Sbjct: 10 PKRPPSGFFLFCSEFRPKIKSTNPGI-SIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKE 68
Query: 127 EFDRAMADY 135
++++ +ADY
Sbjct: 69 KYEKDVADY 77
>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 = 46.6 bits (109), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 45/74 (60%), Gaps = 4/74 (5%)
Query: 67 PKKPP---TAFFYFLEDFRKGFQEQNPDIK-SMRAIGKACGEKWKTMTYEEKVKYYDIAT 122
PKKP +++ +F++ R+ ++++PD + K C E+WKTM+ +EK K+ D+A
Sbjct: 5 PKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK 64
Query: 123 EKRAEFDRAMADYI 136
+A ++R M YI
Sbjct: 65 ADKARYEREMKTYI 78
>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 = 46.6 bits (109), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDI-KSMRAIGKACGEKWKTMTYEEKVKYYDIATEKR 125
PK+ +++ +F ++ R +NP+I K + AIGK G W ++ EEK Y ++ E R
Sbjct: 23 PKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDR 82
Query: 126 AEFDRAMADYIKRK 139
++R A+Y +RK
Sbjct: 83 VRYEREKAEYAQRK 96
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 46.6 bits (109), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 45/74 (60%), Gaps = 4/74 (5%)
Query: 67 PKKPP---TAFFYFLEDFRKGFQEQNPDIK-SMRAIGKACGEKWKTMTYEEKVKYYDIAT 122
PKKP +++ +F++ R+ ++++PD + K C E+WKTM+ +EK K+ D+A
Sbjct: 5 PKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK 64
Query: 123 EKRAEFDRAMADYI 136
+A ++R M YI
Sbjct: 65 ADKARYEREMKTYI 78
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 45/74 (60%), Gaps = 4/74 (5%)
Query: 67 PKKPP---TAFFYFLEDFRKGFQEQNPDIK-SMRAIGKACGEKWKTMTYEEKVKYYDIAT 122
PKKP +++ +F++ R+ ++++PD + K C E+WKTM+ +EK K+ D+A
Sbjct: 13 PKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK 72
Query: 123 EKRAEFDRAMADYI 136
+A ++R M YI
Sbjct: 73 ADKARYEREMKTYI 86
Score = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRA 126
PK+PP+AFF F ++R + ++P + S+ + K GE W ++K Y A + +
Sbjct: 102 PKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKE 160
Query: 127 EFDRAMADY 135
++++ +A Y
Sbjct: 161 KYEKDIAAY 169
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
Mobility Group Protein B3
Length = 86
Score = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 72 TAFFYFLEDFRKGFQEQNPDIKSMRA-IGKACGEKWKTMTYEEKVKYYDIATEKRAEFDR 130
+A+ +F++ R+ +++NP++ A K C E+WKTM+ +EK K+ ++A + +DR
Sbjct: 21 SAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDR 80
Query: 131 AMADY 135
M DY
Sbjct: 81 EMKDY 85
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 39/70 (55%), Gaps = 3/70 (4%)
Query: 66 MPKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKR 125
MPK+ TAF +L D R+ + +NP IK + I K GE WK + ++K K+ D A + +
Sbjct: 3 MPKRATTAFMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKEL--KDKSKWEDAAAKDK 59
Query: 126 AEFDRAMADY 135
+ M +Y
Sbjct: 60 QRYHDEMRNY 69
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIK-SMRAIGKACGEKWKTMTYEEKVKYYDIATEKR 125
P+ +++ +F++ R+ ++++PD + K C E+WKTM+ +EK K+ D+A +
Sbjct: 9 PRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSDK 68
Query: 126 AEFDRAM 132
A +DR M
Sbjct: 69 ARYDREM 75
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 43.5 bits (101), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 42/70 (60%), Gaps = 1/70 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIK-SMRAIGKACGEKWKTMTYEEKVKYYDIATEKR 125
P+ +++ +F++ R+ ++++PD + K C E+WKTM+ +EK K+ D+A +
Sbjct: 2 PRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADK 61
Query: 126 AEFDRAMADY 135
A ++R M Y
Sbjct: 62 ARYEREMKTY 71
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 42.7 bits (99), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKY 117
PK+ +A+ +F + R + +NPDI + +GK GEKWK +T EEK Y
Sbjct: 21 PKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALTPEEKQPY 70
>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 = 42.7 bits (99), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 21/51 (41%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKY 117
PK+ +A+ +F + R + +NPDI + +GK GEKWK +T EEK Y
Sbjct: 21 PKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALTPEEKQPY 70
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRA 126
PK+PP+AFF F ++R + ++P + S+ K GE W + ++K Y A + +
Sbjct: 9 PKRPPSAFFLFCSEYRPKIKSEHPGL-SIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKE 67
Query: 127 EFDRAMADY 135
++++ +A Y
Sbjct: 68 KYEKDIAAY 76
>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 = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRA 126
PK+PP+AFF F ++R + ++P + S+ + K GE W ++K Y A + +
Sbjct: 5 PKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKE 63
Query: 127 EFDRAMADY 135
++++ +A Y
Sbjct: 64 KYEKDIAAY 72
>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 = 5e-04, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRA 126
PK+PP+AFF F ++R + ++P + S+ + K GE W ++K Y A + +
Sbjct: 3 PKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKE 61
Query: 127 EFDRAMADY 135
++++ +A Y
Sbjct: 62 KYEKDIAAY 70
>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 = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRA 126
PK+PP+AFF F ++R + ++P + S+ + K GE W ++K Y A + +
Sbjct: 7 PKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKE 65
Query: 127 EFDRAMADY 135
++++ +A Y
Sbjct: 66 KYEKDIAAY 74
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 39/69 (56%), Gaps = 1/69 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRA 126
PK+PP+AFF F ++R + ++P + S+ + K GE W ++K Y A + +
Sbjct: 89 PKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKE 147
Query: 127 EFDRAMADY 135
++++ +A Y
Sbjct: 148 KYEKDIAAY 156
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRA 126
PK+PP+AFF F + R + ++P + S+ K GE W + ++K Y A + +
Sbjct: 8 PKRPPSAFFLFCSEHRPKIKSEHPGL-SIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKE 66
Query: 127 EFDRAMADY 135
++++ +A Y
Sbjct: 67 KYEKDIAAY 75
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 68 KKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRAE 127
++P AF + +D RK +QNPD+ + + K G+ WK +T EK + + A R +
Sbjct: 9 RRPMNAFMVWAKDERKRLAQQNPDLHNAE-LSKMLGKSWKALTLAEKRPFVEEAERLRVQ 67
Query: 128 FDRAMADY 135
+ +Y
Sbjct: 68 HMQDHPNY 75
>pdb|2LEF|A Chain A, Lef1 Hmg Domain (From Mouse), Complexed With Dna (15bp),
Nmr, 12 Structures
Length = 86
Score = 39.7 bits (91), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 68 KKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKR 125
KKP AF ++++ R ++ +K AI + G +W ++ EE+ KYY++A ++R
Sbjct: 4 KKPLNAFMLYMKEMRANVVAES-TLKESAAINQILGRRWHALSREEQAKYYELARKER 60
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 68 KKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRAE 127
++P AF + +D RK +QNPD+ + + K G+ WK +T EK + + A R +
Sbjct: 4 RRPMNAFMVWAKDERKRLAQQNPDLHNAE-LSKMLGKSWKALTLAEKRPFVEEAERLRVQ 62
Query: 128 FDRAMADY 135
+ +Y
Sbjct: 63 HMQDHPNY 70
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 68 KKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRAE 127
++P AF + +D RK +QNPD+ + + K G+ WK +T EK + + A R +
Sbjct: 8 RRPMNAFMVWAKDERKRLAQQNPDLHNA-ELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 66
Query: 128 FDRAMADY 135
+ +Y
Sbjct: 67 HMQDHPNY 74
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRA 126
PK+P +A+ +L R+ + +NP IK + + K GE W+ M ++K ++ A + +
Sbjct: 5 PKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAM--KDKSEWEAKAAKAKD 61
Query: 127 EFDRAMADY 135
++DRA+ ++
Sbjct: 62 DYDRAVKEF 70
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRA 126
PK+P +A+ +L R+ + +NP IK + + K GE W+ M ++K ++ A + +
Sbjct: 4 PKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAM--KDKSEWEAKAAKAKD 60
Query: 127 EFDRAMADY 135
++DRA+ ++
Sbjct: 61 DYDRAVKEF 69
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRA 126
PK+P +A+ +L R+ + +NP IK + + K GE W+ M ++K ++ A + +
Sbjct: 4 PKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAM--KDKSEWEAKAAKAKD 60
Query: 127 EFDRAMADY 135
++DRA+ ++
Sbjct: 61 DYDRAVKEF 69
>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 = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 41/69 (59%), Gaps = 3/69 (4%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRA 126
PK+P +A+ +L R+ + +NP IK + + K GE W+ M ++K ++ A + +
Sbjct: 4 PKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAM--KDKSEWEAKAAKAKD 60
Query: 127 EFDRAMADY 135
++DRA+ ++
Sbjct: 61 DYDRAVKEF 69
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 28/52 (53%), Gaps = 1/52 (1%)
Query: 68 KKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYD 119
K+P AF + +D R+ + PD+ + I K G +WK MT EK YY+
Sbjct: 6 KRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMTNLEKQPYYE 56
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 35.0 bits (79), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRA 126
PK P T + FL + R+ + ++PD+ I K G +W + EK +Y D A +++
Sbjct: 8 PKAPVTGYVRFLNERREQIRTRHPDL-PFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQ 66
Query: 127 EFDRAMADY 135
++ + + Y
Sbjct: 67 QYLKELWAY 75
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 34.3 bits (77), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 1/51 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKY 117
PK+P +A F F E+ R+ QE+ P++ S + + W ++ ++K KY
Sbjct: 21 PKRPVSAMFIFSEEKRRQLQEERPEL-SESELTRLLARMWNDLSEKKKAKY 70
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human Upstream
Binding Factor
Length = 99
Score = 34.3 bits (77), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 40/69 (57%), Gaps = 1/69 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRA 126
PKKP T +F F + R + + +P++ ++ + K +K+K + ++K+KY ++
Sbjct: 11 PKKPLTPYFRFFMEKRAKYAKLHPEMSNL-DLTKILSKKYKELPEKKKMKYIQDFQREKQ 69
Query: 127 EFDRAMADY 135
EF+R +A +
Sbjct: 70 EFERNLARF 78
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 34.3 bits (77), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 68 KKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRAE 127
K+P AF + + R+ EQ+PD+ + I K G++WK + +K+ + A R
Sbjct: 4 KRPMNAFMVWSQIERRKIMEQSPDMHNA-EISKRLGKRWKLLKDSDKIPFIQEAERLRL- 61
Query: 128 FDRAMADY 135
+ MADY
Sbjct: 62 --KHMADY 67
>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 = 0.056, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 1/68 (1%)
Query: 68 KKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRAE 127
++P AF F + R ++++P + + R K + W + +EK KY D+A E +
Sbjct: 9 RRPMNAFLLFCKRHRSLVRQEHPRLDN-RGATKILADWWAVLDPKEKQKYTDMAKEYKDA 67
Query: 128 FDRAMADY 135
F +A Y
Sbjct: 68 FMKANPGY 75
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
Hmg-Box Transcription Factor 1
Length = 87
Score = 32.7 bits (73), Expect = 0.088, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 68 KKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKY 117
K+P AF F + +R + + P K RAI G++WK M EE+ Y
Sbjct: 19 KRPMNAFMLFAKKYRVEYTQMYPG-KDNRAISVILGDRWKKMKNEERRMY 67
>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 = 32.3 bits (72), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 68 KKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRAE 127
K+P AF + R+ ++NP + + I K G +WK ++ EK + D A RA
Sbjct: 9 KRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKRPFIDEAKRLRAL 67
Query: 128 FDRAMADY 135
+ DY
Sbjct: 68 HMKEHPDY 75
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 32.3 bits (72), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 68 KKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRAE 127
K+P AF + R+ ++NP + + I K G +WK ++ EK + D A RA
Sbjct: 5 KRPMNAFMVWSRGQRRKMAQENPKMHNS-EISKRLGAEWKLLSETEKRPFIDEAKRLRAL 63
Query: 128 FDRAMADY 135
+ DY
Sbjct: 64 HMKEHPDY 71
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 32.0 bits (71), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 68 KKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRAE 127
K+P AF + R+ ++NP + + I K G +WK ++ EK + D A RA
Sbjct: 4 KRPMNAFMVWSRGQRRKMAQENPKMHNS-EISKRLGAEWKLLSETEKRPFIDEAKRLRAL 62
Query: 128 FDRAMADY 135
+ DY
Sbjct: 63 HMKEHPDY 70
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
Length = 238
Score = 30.8 bits (68), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYD 119
PKKP +++ F ++ F+ QNPD K+ I + ++W+ + +K Y D
Sbjct: 42 PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELI-RRIAQRWRELPDSKKKIYQD 93
>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 = 30.4 bits (67), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYD 119
PKKP +++ F ++ F+ QNPD K+ I + ++W+ + +K Y D
Sbjct: 10 PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELI-RRIAQRWRELPDSKKKIYQD 61
>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 = 29.6 bits (65), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 31/68 (45%), Gaps = 1/68 (1%)
Query: 68 KKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRAE 127
K+P AF + + R+ +Q P + + + K G+ W+ + EK + + A R +
Sbjct: 31 KRPMNAFMVWAQAARRKLADQYPHLHNA-ELSKTLGKLWRLLNESEKRPFVEEAERLRVQ 89
Query: 128 FDRAMADY 135
+ DY
Sbjct: 90 HKKDHPDY 97
>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 = 29.6 bits (65), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 1/69 (1%)
Query: 67 PKKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRA 126
P+KP +A+ F D + + QNP+ + + K W + E+K Y +
Sbjct: 18 PQKPVSAYALFFRDTQAAIKGQNPN-ATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKK 76
Query: 127 EFDRAMADY 135
E+ + +A Y
Sbjct: 77 EYLKQLAAY 85
>pdb|2CS1|A Chain A, Solution Structure Of The Hmg Domain Of Human Dna Mismatch
Repair Protein
Length = 92
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 1/80 (1%)
Query: 68 KKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVKYYDIATEKRAE 127
KKP +A F++D R F +NP S+ E WKT++ EEK+KY + AT+
Sbjct: 9 KKPMSASALFVQDHRPQFLIENPKT-SLEDATLQIEELWKTLSEEEKLKYEEKATKDLER 67
Query: 128 FDRAMADYIKRKENGKVENS 147
++ M I+++ +++S
Sbjct: 68 YNSQMKRAIEQESQMSLKDS 87
>pdb|2L3F|A Chain A, Solution Nmr Structure Of A Putative Uracil Dna
Glycosylase From Methanosarcina Acetivorans, Northeast
Structural Genomics Consortium Target Mvr76
Length = 166
Score = 27.7 bits (60), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 19/38 (50%)
Query: 79 EDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKVK 116
E RK NP R +G A GE + M YE+K+K
Sbjct: 26 ESIRKQQYYGNPGNDFWRLVGHAIGENLQDMAYEKKLK 63
>pdb|4FBW|A Chain A, Crystal Structure Of An Unfused Mre11-Nbs1 Complex With
Two Manganese Ions Per Active Site
pdb|4FBW|B Chain B, Crystal Structure Of An Unfused Mre11-Nbs1 Complex With
Two Manganese Ions Per Active Site
Length = 417
Score = 27.7 bits (60), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 21/48 (43%)
Query: 68 KKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKV 115
+KPP D+ G+Q +NP S R +G+ Y +KV
Sbjct: 363 EKPPLPLIRLRVDYTGGYQTENPQRFSNRFVGRVANATDVVQFYLKKV 410
>pdb|3TEQ|A Chain A, Crystal Structure Of Soar Domain
pdb|3TEQ|B Chain B, Crystal Structure Of Soar Domain
pdb|3TEQ|C Chain C, Crystal Structure Of Soar Domain
pdb|3TEQ|D Chain D, Crystal Structure Of Soar Domain
Length = 101
Score = 27.7 bits (60), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 3/41 (7%)
Query: 104 EKWKTMTYEEKVKYYDI---ATEKRAEFDRAMADYIKRKEN 141
+KW +T+E +V+YY+I EK+ + A+ IK+K N
Sbjct: 5 QKWLQLTHEVEVQYYNIKKQNAEKQLMVAKEGAEKIKKKRN 45
>pdb|2VLD|A Chain A, Crystal Structure Of A Repair Endonuclease From Pyrococcus
Abyssi
pdb|2VLD|B Chain B, Crystal Structure Of A Repair Endonuclease From Pyrococcus
Abyssi
Length = 251
Score = 27.3 bits (59), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 9/28 (32%), Positives = 17/28 (60%)
Query: 19 NLKMVLRKRPTRHSVVAAVGIEKEGKSI 46
K + R++P RH +V G++K+G +
Sbjct: 144 GFKPIYREKPIRHGIVDVXGVDKDGNIV 171
>pdb|4FCX|B Chain B, S.Pombe Mre11 Apoenzym
pdb|4FCX|A Chain A, S.Pombe Mre11 Apoenzym
Length = 404
Score = 26.9 bits (58), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 17/34 (50%)
Query: 68 KKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGKA 101
+KPP D+ G+Q +NP S R +G+
Sbjct: 358 EKPPLPLIRLRVDYTGGYQTENPQRFSNRFVGRV 391
>pdb|4FBK|A Chain A, Crystal Structure Of A Covalently Fused Nbs1-Mre11 Complex
With One Manganese Ion Per Active Site
pdb|4FBK|B Chain B, Crystal Structure Of A Covalently Fused Nbs1-Mre11 Complex
With One Manganese Ion Per Active Site
pdb|4FBQ|A Chain A, Crystal Structure Of A Covalently Fused Nbs1-Mre11 Complex
With Two Manganese Ions Per Active Site
pdb|4FBQ|B Chain B, Crystal Structure Of A Covalently Fused Nbs1-Mre11 Complex
With Two Manganese Ions Per Active Site
Length = 472
Score = 26.6 bits (57), Expect = 6.2, Method: Composition-based stats.
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 68 KKPPTAFFYFLEDFRKGFQEQNPDIKSMRAIGK 100
+KPP D+ G+Q +NP S R +G+
Sbjct: 426 EKPPLPLIRLRVDYTGGYQTENPQRFSNRFVGR 458
>pdb|4B4T|L Chain L, Near-Atomic Resolution Structural Model Of The Yeast 26s
Proteasome
Length = 437
Score = 26.6 bits (57), Expect = 6.8, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 23/38 (60%)
Query: 78 LEDFRKGFQEQNPDIKSMRAIGKACGEKWKTMTYEEKV 115
+ D K + + DIK++++IG+ GE K ++ E+ +
Sbjct: 81 IRDLEKLYDKTENDIKALQSIGQLIGEVMKELSEEKYI 118
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
0.310 0.126 0.347
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,107,867
Number of Sequences: 62578
Number of extensions: 142779
Number of successful extensions: 469
Number of sequences better than 100.0: 54
Number of HSP's better than 100.0 without gapping: 38
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 423
Number of HSP's gapped (non-prelim): 55
length of query: 157
length of database: 14,973,337
effective HSP length: 91
effective length of query: 66
effective length of database: 9,278,739
effective search space: 612396774
effective search space used: 612396774
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 47 (22.7 bits)