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= 032199
(145 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 67.4 bits (163), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 36/73 (49%), Positives = 43/73 (58%), Gaps = 1/73 (1%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
DPN PKRP SAFF+F E+R + K +HP S+ K GE W S DK PY KA
Sbjct: 5 DPNAPKRPPSAFFLFCSEYRPKIKSEHP-GLSIGDTAKKLGEMWSEQSAKDKQPYEQKAA 63
Query: 94 KRKVEYEKDMKNY 106
K K +YEKD+ Y
Sbjct: 64 KLKEKYEKDIAAY 76
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 65.9 bits (159), Expect = 8e-12, Method: Compositional matrix adjust.
Identities = 36/73 (49%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
DPN PKRP SAFF+F E R + K +HP S+ K GE W S DK PY KA
Sbjct: 4 DPNAPKRPPSAFFLFCSEHRPKIKSEHP-GLSIGDTAKKLGEMWSEQSAKDKQPYEQKAA 62
Query: 94 KRKVEYEKDMKNY 106
K K +YEKD+ Y
Sbjct: 63 KLKEKYEKDIAAY 75
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 65.9 bits (159), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 32/71 (45%), Positives = 46/71 (64%), Gaps = 1/71 (1%)
Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
N PKRP S FF+F EFR + K +P S+ V K GE W ++++++K PY+ KA K
Sbjct: 8 NAPKRPPSGFFLFCSEFRPKIKSTNP-GISIGDVAKKLGEMWNNLNDSEKQPYITKAAKL 66
Query: 96 KVEYEKDMKNY 106
K +YEKD+ +Y
Sbjct: 67 KEKYEKDVADY 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 = 62.4 bits (150), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 36/73 (49%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
DPN PKRP SAFF+F E+R + K +HP S+ V K GE W + + DK PY KA
Sbjct: 3 DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAA 61
Query: 94 KRKVEYEKDMKNY 106
K K +YEKD+ Y
Sbjct: 62 KLKEKYEKDIAAY 74
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 62.0 bits (149), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 36/73 (49%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
DPN PKRP SAFF+F E+R + K +HP S+ V K GE W + + DK PY KA
Sbjct: 85 DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAA 143
Query: 94 KRKVEYEKDMKNY 106
K K +YEKD+ Y
Sbjct: 144 KLKEKYEKDIAAY 156
Score = 39.3 bits (90), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 43/72 (59%), Gaps = 1/72 (1%)
Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
KRP +AF V+ + R + ++P+ ++ + + K G +WK ++EA+K P+ +A+K +
Sbjct: 6 KRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAM 64
Query: 99 YEKDMKNYNRRQ 110
+ + NY R+
Sbjct: 65 HREKYPNYKYRK 76
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 61.6 bits (148), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 36/73 (49%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
DPN PKRP SAFF+F E+R + K +HP S+ V K GE W + + DK PY KA
Sbjct: 98 DPNAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAA 156
Query: 94 KRKVEYEKDMKNY 106
K K +YEKD+ Y
Sbjct: 157 KLKEKYEKDIAAY 169
Score = 46.2 bits (108), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPK-NKSVAAVGKAGGEKWKSMSEADKAPYVAKA 92
DP KP+ S++ F++ RE++KK HP + + + K E+WK+MS +K + A
Sbjct: 12 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 71
Query: 93 EKRKVEYEKDMKNY 106
+ K YE++MK Y
Sbjct: 72 KADKARYEREMKTY 85
>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 = 58.2 bits (139), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 34/71 (47%), Positives = 43/71 (60%), Gaps = 1/71 (1%)
Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
N PKRP SAFF+F E+R + K +HP S+ V K GE W + + DK PY KA K
Sbjct: 3 NAPKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKL 61
Query: 96 KVEYEKDMKNY 106
K +YEKD+ Y
Sbjct: 62 KEKYEKDIAAY 72
>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 = 55.8 bits (133), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 31/74 (41%), Positives = 45/74 (60%), Gaps = 1/74 (1%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
DPN PKR SA+ F E R+ + ++P + + VGK GEKWK+++ +K PY AKA+
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENP-DITFGQVGKKLGEKWKALTPEEKQPYEAKAQ 75
Query: 94 KRKVEYEKDMKNYN 107
K YE + + YN
Sbjct: 76 ADKKRYESEKELYN 89
>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 = 55.8 bits (133), Expect = 7e-09, Method: Compositional matrix adjust.
Identities = 33/69 (47%), Positives = 42/69 (60%), Gaps = 1/69 (1%)
Query: 38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKV 97
PKRP SAFF+F E+R + K +HP S+ V K GE W + + DK PY KA K K
Sbjct: 3 PKRPPSAFFLFCSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKE 61
Query: 98 EYEKDMKNY 106
+YEKD+ Y
Sbjct: 62 KYEKDIAAY 70
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 55.8 bits (133), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 31/74 (41%), Positives = 45/74 (60%), Gaps = 1/74 (1%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
DPN PKR SA+ F E R+ + ++P + + VGK GEKWK+++ +K PY AKA+
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENP-DITFGQVGKKLGEKWKALTPEEKQPYEAKAQ 75
Query: 94 KRKVEYEKDMKNYN 107
K YE + + YN
Sbjct: 76 ADKKRYESEKELYN 89
>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 = 52.8 bits (125), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 28/78 (35%), Positives = 48/78 (61%), Gaps = 1/78 (1%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPK-NKSVAAVGKAGGEKWKSMSEADKAPYVAKA 92
DPN PKR S++ F +E R + ++P+ K VAA+GK G W ++S+ +K PY +
Sbjct: 19 DPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMS 78
Query: 93 EKRKVEYEKDMKNYNRRQ 110
++ +V YE++ Y +R+
Sbjct: 79 DEDRVRYEREKAEYAQRK 96
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/71 (40%), Positives = 46/71 (64%), Gaps = 3/71 (4%)
Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
+KPKRP SA+ +++ RE K+++P K V V K GGE W++M DK+ + AKA K
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKA 58
Query: 96 KVEYEKDMKNY 106
K +Y++ +K +
Sbjct: 59 KDDYDRAVKEF 69
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/71 (40%), Positives = 46/71 (64%), Gaps = 3/71 (4%)
Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
+KPKRP SA+ +++ RE K+++P K V V K GGE W++M DK+ + AKA K
Sbjct: 3 DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKA 59
Query: 96 KVEYEKDMKNY 106
K +Y++ +K +
Sbjct: 60 KDDYDRAVKEF 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 = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 29/71 (40%), Positives = 46/71 (64%), Gaps = 3/71 (4%)
Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
+KPKRP SA+ +++ RE K+++P K V V K GGE W++M DK+ + AKA K
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKA 58
Query: 96 KVEYEKDMKNY 106
K +Y++ +K +
Sbjct: 59 KDDYDRAVKEF 69
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 50.1 bits (118), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 45/73 (61%), Gaps = 1/73 (1%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNK-SVAAVGKAGGEKWKSMSEADKAPYVAKA 92
DPNKP+ S++ F++ RE++KK HP + + A K E+WK+MS +K+ + A
Sbjct: 5 DPNKPRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMA 64
Query: 93 EKRKVEYEKDMKN 105
+ K Y+++MKN
Sbjct: 65 KSDKARYDREMKN 77
>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 = 50.1 bits (118), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 29/71 (40%), Positives = 46/71 (64%), Gaps = 3/71 (4%)
Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
+KPKRP SA+ +++ RE K+++P K V V K GGE W++M DK+ + AKA K
Sbjct: 2 DKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKA 58
Query: 96 KVEYEKDMKNY 106
K +Y++ +K +
Sbjct: 59 KDDYDRAVKEF 69
>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 = 47.0 bits (110), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 44/75 (58%), Gaps = 3/75 (4%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSV--AAVGKAGGEKWKSMSEADKAPYVAK 91
DP KP+ S++ F++ RE++KK HP + SV + K E+WK+MS +K +
Sbjct: 4 DPKKPRGKMSSYAFFVQTCREEHKKKHP-DASVNFSEFSKKCSERWKTMSAKEKGKFEDM 62
Query: 92 AEKRKVEYEKDMKNY 106
A+ K YE++MK Y
Sbjct: 63 AKADKARYEREMKTY 77
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 40/69 (57%), Gaps = 3/69 (4%)
Query: 38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKV 97
PKR +AF +++ + RE K+++P K V + K GGE WK + DK+ + A K K
Sbjct: 4 PKRATTAFMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKELK--DKSKWEDAAAKDKQ 60
Query: 98 EYEKDMKNY 106
Y +M+NY
Sbjct: 61 RYHDEMRNY 69
>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 = 46.2 bits (108), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 46/73 (63%), Gaps = 3/73 (4%)
Query: 36 NKP--KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
NKP KRP +AF V+ + R + +P + A + K G+ W+ ++E++K P+V +AE
Sbjct: 26 NKPHVKRPMNAFMVWAQAARRKLADQYPHLHN-AELSKTLGKLWRLLNESEKRPFVEEAE 84
Query: 94 KRKVEYEKDMKNY 106
+ +V+++KD +Y
Sbjct: 85 RLRVQHKKDHPDY 97
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 46.2 bits (108), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 44/75 (58%), Gaps = 3/75 (4%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSV--AAVGKAGGEKWKSMSEADKAPYVAK 91
DP KP+ S++ F++ RE++KK HP + SV + K E+WK+MS +K +
Sbjct: 4 DPKKPRGKMSSYAFFVQTSREEHKKKHP-DASVNFSEFSKKCSERWKTMSAKEKGKFEDM 62
Query: 92 AEKRKVEYEKDMKNY 106
A+ K YE++MK Y
Sbjct: 63 AKADKARYEREMKTY 77
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 46.2 bits (108), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 45/68 (66%), Gaps = 1/68 (1%)
Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
+RP +AF V+ ++ R++ + +P + A + K G+ WK+++ A+K P+V +AE+ +V+
Sbjct: 4 RRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 62
Query: 99 YEKDMKNY 106
+ +D NY
Sbjct: 63 HMQDHPNY 70
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 46.2 bits (108), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 46/71 (64%), Gaps = 1/71 (1%)
Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
+RP +AF V+ ++ R++ + +P + A + K G+ WK+++ A+K P+V +AE+ +V+
Sbjct: 8 RRPMNAFMVWAKDERKRLAQQNP-DLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 66
Query: 99 YEKDMKNYNRR 109
+ +D NY R
Sbjct: 67 HMQDHPNYKYR 77
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 45.8 bits (107), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 22/68 (32%), Positives = 45/68 (66%), Gaps = 1/68 (1%)
Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
+RP +AF V+ ++ R++ + +P + A + K G+ WK+++ A+K P+V +AE+ +V+
Sbjct: 9 RRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 67
Query: 99 YEKDMKNY 106
+ +D NY
Sbjct: 68 HMQDHPNY 75
>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 = 23/71 (32%), Positives = 38/71 (53%), Gaps = 1/71 (1%)
Query: 38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKV 97
PK P + + F+ E REQ + HP + + K G +W + A+K Y+ +AEK K
Sbjct: 8 PKAPVTGYVRFLNERREQIRTRHP-DLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQ 66
Query: 98 EYEKDMKNYNR 108
+Y K++ Y +
Sbjct: 67 QYLKELWAYQQ 77
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 42.7 bits (99), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 42/72 (58%), Gaps = 3/72 (4%)
Query: 37 KPKRPASAFFVFMEEFREQYKKDHPKNKSV--AAVGKAGGEKWKSMSEADKAPYVAKAEK 94
KP+ S++ F++ RE++KK HP + SV + K E+WK+MS +K + A+
Sbjct: 1 KPRGKMSSYAFFVQTCREEHKKKHP-DASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKA 59
Query: 95 RKVEYEKDMKNY 106
K YE++MK Y
Sbjct: 60 DKARYEREMKTY 71
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
KRP +AF V+ + R + + P + A + K G++WK + ++DK P++ +AE+ +++
Sbjct: 4 KRPMNAFMVWSQIERRKIMEQSPDMHN-AEISKRLGKRWKLLKDSDKIPFIQEAERLRLK 62
Query: 99 YEKDMKNYNRR 109
+ D +Y R
Sbjct: 63 HMADYPDYKYR 73
>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B
Length = 67
Score = 42.0 bits (97), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 42/70 (60%), Gaps = 5/70 (7%)
Query: 37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRK 96
KPKRP SA+ V++ E ++ K D P+ K K E WK++S+++K Y+ A++ +
Sbjct: 2 KPKRPRSAYNVYVAERFQEAKGDSPQEKL-----KTVKENWKNLSDSEKELYIQHAKEDE 56
Query: 97 VEYEKDMKNY 106
Y +MK++
Sbjct: 57 TRYHNEMKSW 66
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 42/70 (60%), Gaps = 5/70 (7%)
Query: 37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRK 96
KPKRP SA+ V++ E ++ K D P+ K K E WK++S+++K Y+ A++ +
Sbjct: 114 KPKRPRSAYNVYVAERFQEAKGDSPQEKL-----KTVKENWKNLSDSEKELYIQHAKEDE 168
Query: 97 VEYEKDMKNY 106
Y +MK++
Sbjct: 169 TRYHNEMKSW 178
Score = 25.8 bits (55), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 12/51 (23%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPY 88
PK+P S++ F +E +K +P K+ + + ++W+ + ++ K Y
Sbjct: 10 PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRI-AQRWRELPDSKKKIY 59
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEK 94
P++ KRP +AF V+ R + +++PK + + + K G +WK +SE +K P++ +A++
Sbjct: 5 PDRVKRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKRPFIDEAKR 63
Query: 95 RKVEYEKDMKNYNRR 109
+ + K+ +Y R
Sbjct: 64 LRALHMKEHPDYKYR 78
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
Hmg-Box Transcription Factor 1
Length = 87
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 34/58 (58%), Gaps = 1/58 (1%)
Query: 35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKA 92
PNK KRP +AF +F +++R +Y + +P K A+ G++WK M ++ Y +A
Sbjct: 15 PNKCKRPMNAFMLFAKKYRVEYTQMYP-GKDNRAISVILGDRWKKMKNEERRMYTLEA 71
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/65 (36%), Positives = 36/65 (55%), Gaps = 1/65 (1%)
Query: 37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRK 96
KPKRP SA F+F EE R Q +++ P+ S + + + W +SE KA Y A+ K
Sbjct: 20 KPKRPVSAMFIFSEEKRRQLQEERPEL-SESELTRLLARMWNDLSEKKKAKYKAREAALK 78
Query: 97 VEYEK 101
+ E+
Sbjct: 79 AQSER 83
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human Upstream
Binding Factor
Length = 99
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 1/77 (1%)
Query: 35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEK 94
P+ PK+P + +F F E R +Y K HP+ ++ + K +K+K + E K Y+ ++
Sbjct: 8 PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNL-DLTKILSKKYKELPEKKKMKYIQDFQR 66
Query: 95 RKVEYEKDMKNYNRRQP 111
K E+E+++ + P
Sbjct: 67 EKQEFERNLARFREDHP 83
>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 = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
++ KRP +AF V+ + R + ++P+ ++ + + K G +WK ++EA+K P+ +A+K
Sbjct: 3 DRVKRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKL 61
Query: 96 KVEYEKDMKNYNRR 109
+ + + NY R
Sbjct: 62 QAMHREKYPNYKYR 75
>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 = 39.7 bits (91), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
KRP +AF V+ + R + ++P+ ++ + + K G +WK ++EA+K P+ +A+K +
Sbjct: 6 KRPINAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAM 64
Query: 99 YEKDMKNYNRR 109
+ + NY R
Sbjct: 65 HREKYPNYKYR 75
>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 = 39.7 bits (91), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 42/71 (59%), Gaps = 1/71 (1%)
Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
KRP +AF V+ + R + ++P+ ++ + + K G +WK ++EA+K P+ +A+K +
Sbjct: 6 KRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAM 64
Query: 99 YEKDMKNYNRR 109
+ + NY R
Sbjct: 65 HREKYPNYKYR 75
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
Mobility Group Protein B3
Length = 86
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 41/65 (63%), Gaps = 1/65 (1%)
Query: 43 SAFFVFMEEFREQYKKDHPKN-KSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEK 101
SA+ F++ RE++KK +P+ + A K E+WK+MS +K+ + A+ KV Y++
Sbjct: 21 SAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDR 80
Query: 102 DMKNY 106
+MK+Y
Sbjct: 81 EMKDY 85
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
Length = 238
Score = 38.9 bits (89), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 41/70 (58%), Gaps = 5/70 (7%)
Query: 37 KPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRK 96
KPKRP SA+ V++ E ++ K D P+ K K E WK++S+++K Y+ A++ +
Sbjct: 146 KPKRPRSAYNVYVAERFQEAKGDSPQEKL-----KTVKENWKNLSDSEKELYIQHAKEDE 200
Query: 97 VEYEKDMKNY 106
Y + K++
Sbjct: 201 TRYHNEXKSW 210
Score = 25.8 bits (55), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 12/51 (23%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 38 PKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPY 88
PK+P S++ F +E +K +P K+ + + ++W+ + ++ K Y
Sbjct: 42 PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRI-AQRWRELPDSKKKIY 91
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
++ KRP +AF V+ R + +++PK + + + K G +WK +SE +K P++ +A++
Sbjct: 2 DRVKRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKRPFIDEAKRL 60
Query: 96 KVEYEKDMKNYNRR 109
+ + K+ +Y R
Sbjct: 61 RALHMKEHPDYKYR 74
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 44/74 (59%), Gaps = 1/74 (1%)
Query: 36 NKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKR 95
++ KRP +AF V+ R + +++PK + + + K G +WK +SE +K P++ +A++
Sbjct: 1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKRPFIDEAKRL 59
Query: 96 KVEYEKDMKNYNRR 109
+ + K+ +Y R
Sbjct: 60 RALHMKEHPDYKYR 73
>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 = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 34 DPNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAE 93
DPN+P++P SA+ +F + + K +P N + V K W + E K Y K E
Sbjct: 14 DPNEPQKPVSAYALFFRDTQAAIKGQNP-NATFGEVSKIVASMWDGLGEEQKQVYKKKTE 72
Query: 94 KRKVEYEKDMKNY 106
K EY K + Y
Sbjct: 73 AAKKEYLKQLAAY 85
>pdb|2LEF|A Chain A, Lef1 Hmg Domain (From Mouse), Complexed With Dna (15bp),
Nmr, 12 Structures
Length = 86
Score = 33.9 bits (76), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRK 96
K+P +AF ++M+E R + +S AA+ + G +W ++S ++A Y A K +
Sbjct: 4 KKPLNAFMLYMKEMRANVVAESTLKES-AAINQILGRRWHALSREEQAKYYELARKER 60
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 32.3 bits (72), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 37/69 (53%), Gaps = 4/69 (5%)
Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYV---AKAEKR 95
KRP +AF V+ ++ R + + P + + + K G +WK+M+ +K PY A+ K+
Sbjct: 6 KRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMTNLEKQPYYEEQARLSKQ 64
Query: 96 KVEYEKDMK 104
+E D K
Sbjct: 65 HLEKYPDYK 73
>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby
Sox Homolog
Length = 82
Score = 28.1 bits (61), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 1/68 (1%)
Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
+RP +AF +F + R +++HP+ + A K + W + +K Y A++ K
Sbjct: 9 RRPMNAFLLFCKRHRSLVRQEHPRLDNRGAT-KILADWWAVLDPKEKQKYTDMAKEYKDA 67
Query: 99 YEKDMKNY 106
+ K Y
Sbjct: 68 FMKANPGY 75
>pdb|2CS1|A Chain A, Solution Structure Of The Hmg Domain Of Human Dna Mismatch
Repair Protein
Length = 92
Score = 27.7 bits (60), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 35/66 (53%), Gaps = 1/66 (1%)
Query: 39 KRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVE 98
K+P SA +F+++ R Q+ ++PK S+ E WK++SE +K Y KA K
Sbjct: 9 KKPMSASALFVQDHRPQFLIENPKT-SLEDATLQIEELWKTLSEEEKLKYEEKATKDLER 67
Query: 99 YEKDMK 104
Y MK
Sbjct: 68 YNSQMK 73
>pdb|1V64|A Chain A, Solution Structure Of The 3rd Hmg Box Of Mouse Ubf1
Length = 108
Score = 27.3 bits (59), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 37/77 (48%), Gaps = 7/77 (9%)
Query: 35 PNKPKRPASAFFVFMEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEK 94
P KP P +++ ++ E K D P + + ++WK +S+ +K Y K ++
Sbjct: 17 PTKP--PPNSYSLYCAELMANMK-DVPSTERMVLCS----QQWKLLSQKEKDAYHKKCDQ 69
Query: 95 RKVEYEKDMKNYNRRQP 111
+K +YE ++ + P
Sbjct: 70 KKKDYEVELLRFLESLP 86
>pdb|3NYN|A Chain A, Crystal Structure Of G Protein-Coupled Receptor Kinase 6
In Complex With Sangivamycin
pdb|3NYN|B Chain B, Crystal Structure Of G Protein-Coupled Receptor Kinase 6
In Complex With Sangivamycin
pdb|3NYO|A Chain A, Crystal Structure Of G Protein-Coupled Receptor Kinase 6
In Complex With Amp
pdb|3NYO|B Chain B, Crystal Structure Of G Protein-Coupled Receptor Kinase 6
In Complex With Amp
Length = 576
Score = 26.2 bits (56), Expect = 7.2, Method: Composition-based stats.
Identities = 11/41 (26%), Positives = 23/41 (56%), Gaps = 3/41 (7%)
Query: 71 KAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQP 111
K +KW+ M + P++++ E+ ++ E+D + RQP
Sbjct: 24 KGKSKKWRQMLQF---PHISQCEELRLSLERDYHSLCERQP 61
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
0.313 0.129 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,111,210
Number of Sequences: 62578
Number of extensions: 90934
Number of successful extensions: 419
Number of sequences better than 100.0: 54
Number of HSP's better than 100.0 without gapping: 46
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 323
Number of HSP's gapped (non-prelim): 59
length of query: 145
length of database: 14,973,337
effective HSP length: 89
effective length of query: 56
effective length of database: 9,403,895
effective search space: 526618120
effective search space used: 526618120
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 bits)