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= psy14923
(180 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
Length = 238
Score = 55.8 bits (133), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/117 (23%), Positives = 62/117 (52%)
Query: 49 PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
PKKP++ Y +F + +NP+ K E+ + +++ W+++ +++KK ++ Y E ++
Sbjct: 42 PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQV 101
Query: 109 YAQNVKKYHDELTPEAIEFLRXXXXXXXXXXXXXXXXXLFRETGKPKKPGNSFYLFI 165
Y + + ++ ++LTP I L GKPK+P +++ +++
Sbjct: 102 YKEEISRFKEQLTPSQIXSLEKEIXDKHLKRKAXTKKKELTLLGKPKRPRSAYNVYV 158
Score = 26.2 bits (56), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 11/77 (14%)
Query: 43 LSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEY 102
L++ KPK+P + Y + + + +P K+ K V E WK + ++EK+ L ++
Sbjct: 141 LTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKL----KTVKENWKNLSDSEKE-LYIQH 195
Query: 103 AKEKEIYAQNVKKYHDE 119
AKE E +YH+E
Sbjct: 196 AKEDET------RYHNE 206
>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 = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/117 (22%), Positives = 60/117 (51%)
Query: 49 PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
PKKP++ Y +F + +NP+ K E+ + +++ W+++ +++KK ++ Y E ++
Sbjct: 10 PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQDAYRAEWQV 69
Query: 109 YAQNVKKYHDELTPEAIEFLRXXXXXXXXXXXXXXXXXLFRETGKPKKPGNSFYLFI 165
Y + + ++ ++LTP I L GKPK+P +++ +++
Sbjct: 70 YKEEISRFKEQLTPSQIMSLEKEIMDKHLKRKAMTKKKELTLLGKPKRPRSAYNVYV 126
Score = 27.3 bits (59), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 11/78 (14%)
Query: 43 LSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEY 102
L++ KPK+P + Y + + + +P K+ K V E WK + ++EK+ L ++
Sbjct: 109 LTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKL----KTVKENWKNLSDSEKE-LYIQH 163
Query: 103 AKEKEIYAQNVKKYHDEL 120
AKE E +YH+E+
Sbjct: 164 AKEDET------RYHNEM 175
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 54.3 bits (129), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 42/69 (60%)
Query: 49 PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
PK P+T Y +F + R +I R+P++ E+TK++ EW K+ AEK+R +E KEK+
Sbjct: 8 PKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQ 67
Query: 109 YAQNVKKYH 117
Y + + Y
Sbjct: 68 YLKELWAYQ 76
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human Upstream
Binding Factor
Length = 99
Score = 51.2 bits (121), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 56/81 (69%), Gaps = 1/81 (1%)
Query: 46 PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
P+ PKKPLTPYF+F + R K + +P + +++TK++S+++K++ E +K + ++ +E
Sbjct: 8 PDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQRE 67
Query: 106 KEIYAQNVKKYHDELTPEAIE 126
K+ + +N+ ++ ++ P+ I+
Sbjct: 68 KQEFERNLARFRED-HPDLIQ 87
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 47.4 bits (111), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/68 (36%), Positives = 38/68 (55%)
Query: 49 PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
PK+P + +F F + R KI NP I I +V K + E W + ++EK+ + AK KE
Sbjct: 10 PKRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEK 69
Query: 109 YAQNVKKY 116
Y ++V Y
Sbjct: 70 YEKDVADY 77
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 39/73 (53%), Gaps = 2/73 (2%)
Query: 45 IPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAK 104
+ +KPK+PL+ Y + R I NP IK+ EV K E W+ + +K E + AK
Sbjct: 1 MSDKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAK 58
Query: 105 EKEIYAQNVKKYH 117
K+ Y + VK++
Sbjct: 59 AKDDYDRAVKEFE 71
>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 = 45.4 bits (106), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEK 106
+KPK+PL+ Y + R I NP IK+ EV K E W+ + +K E + AK K
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAK 59
Query: 107 EIYAQNVKKYH 117
+ Y + VK++
Sbjct: 60 DDYDRAVKEFE 70
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEK 106
+KPK+PL+ Y + R I NP IK+ EV K E W+ + +K E + AK K
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAK 59
Query: 107 EIYAQNVKKYH 117
+ Y + VK++
Sbjct: 60 DDYDRAVKEFE 70
>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 = 44.7 bits (104), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 2/71 (2%)
Query: 47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEK 106
+KPK+PL+ Y + R I NP IK+ EV K E W+ + +K E + AK K
Sbjct: 2 DKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAM--KDKSEWEAKAAKAK 59
Query: 107 EIYAQNVKKYH 117
+ Y + VK++
Sbjct: 60 DDYDRAVKEFE 70
>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 = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 39/76 (51%)
Query: 46 PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
P +P+KP++ Y F + I +NPN EV+K+V+ W +GE +K+ + +
Sbjct: 15 PNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAA 74
Query: 106 KEIYAQNVKKYHDELT 121
K+ Y + + Y L
Sbjct: 75 KKEYLKQLAAYRASLV 90
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 41.2 bits (95), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 37/72 (51%)
Query: 46 PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
P PK+P + +F F + R KI +P + I + K + E W + +K+ E + AK
Sbjct: 6 PNAPKRPPSAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKL 65
Query: 106 KEIYAQNVKKYH 117
KE Y +++ Y
Sbjct: 66 KEKYEKDIAAYR 77
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 37/71 (52%)
Query: 46 PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
P PK+P + +F F + R KI +P + I + K + E W + +K+ E + AK
Sbjct: 5 PNAPKRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKL 64
Query: 106 KEIYAQNVKKY 116
KE Y +++ Y
Sbjct: 65 KEKYEKDIAAY 75
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 40.8 bits (94), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 12/79 (15%)
Query: 49 PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
PK+ T + + R I NP IK+ E+ K E WK++ +K + E+ AK+K+
Sbjct: 4 PKRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKEL--KDKSKWEDAAAKDKQ- 60
Query: 109 YAQNVKKYHDELT---PEA 124
+YHDE+ PEA
Sbjct: 61 ------RYHDEMRNYKPEA 73
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 40/69 (57%), Gaps = 3/69 (4%)
Query: 47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEK 106
EKPK+P++ F F + R ++ E P + E+T+L++ W + E +K + + A+E
Sbjct: 19 EKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKYK---AREA 75
Query: 107 EIYAQNVKK 115
+ AQ+ +K
Sbjct: 76 ALKAQSERK 84
>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 = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 46 PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLE------ 99
P PK+ L+ Y F + R+ + NP+I +V K + E+WK + EK+ E
Sbjct: 18 PNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQAD 77
Query: 100 -NEYAKEKEIY 109
Y EKE+Y
Sbjct: 78 KKRYESEKELY 88
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 46 PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLE------ 99
P PK+ L+ Y F + R+ + NP+I +V K + E+WK + EK+ E
Sbjct: 18 PNAPKRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQAD 77
Query: 100 -NEYAKEKEIY 109
Y EKE+Y
Sbjct: 78 KKRYESEKELY 88
>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 = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 40/76 (52%)
Query: 49 PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
PK+P + +F F + R KI +P + I +V K + E W +K+ E + AK KE
Sbjct: 5 PKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEK 64
Query: 109 YAQNVKKYHDELTPEA 124
Y +++ Y + P+A
Sbjct: 65 YEKDIAAYRAKGKPDA 80
>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 = 37.4 bits (85), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 40/76 (52%)
Query: 49 PKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEI 108
PK+P + +F F + R KI +P + I +V K + E W +K+ E + AK KE
Sbjct: 3 PKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEK 62
Query: 109 YAQNVKKYHDELTPEA 124
Y +++ Y + P+A
Sbjct: 63 YEKDIAAYRAKGKPDA 78
>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 = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 41/74 (55%), Gaps = 3/74 (4%)
Query: 45 IPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAK 104
+P++ K+P+ + + R K+ + NP + E++K + EWK + E EK+ +E
Sbjct: 4 MPDRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDE--- 60
Query: 105 EKEIYAQNVKKYHD 118
K + A ++K++ D
Sbjct: 61 AKRLRALHMKEHPD 74
>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 = 37.0 bits (84), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 9/75 (12%)
Query: 46 PEKPKKPLTPYFKFQGQIRNKIMERNPNI--KIIEVTKLVSEEWKKIGEAEKK---RLEN 100
P PK+ L+ Y F + R +I+ NP I + + K++ W + + EKK R+ +
Sbjct: 20 PNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSD 79
Query: 101 E----YAKEKEIYAQ 111
E Y +EK YAQ
Sbjct: 80 EDRVRYEREKAEYAQ 94
>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 = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 37/71 (52%)
Query: 46 PEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
P PK+P + +F F + R KI +P + I +V K + E W +K+ E + AK
Sbjct: 4 PNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKL 63
Query: 106 KEIYAQNVKKY 116
KE Y +++ Y
Sbjct: 64 KEKYEKDIAAY 74
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 36.2 bits (82), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 41/81 (50%)
Query: 36 KQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEK 95
K +T + P PK+P + +F F + R KI +P + I +V K + E W +K
Sbjct: 89 KGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDK 148
Query: 96 KRLENEYAKEKEIYAQNVKKY 116
+ E + AK KE Y +++ Y
Sbjct: 149 QPYEKKAAKLKEKYEKDIAAY 169
Score = 36.2 bits (82), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 28/122 (22%), Positives = 53/122 (43%), Gaps = 23/122 (18%)
Query: 46 PEKPKKPLTPYFKFQGQIRNKIMERNPN--IKIIEVTKLVSEEWKKIGEAEKKRLENEYA 103
P+KP+ ++ Y F R + +++P+ + E +K SE WK + EK + E+
Sbjct: 13 PKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK 72
Query: 104 KEKEIYAQNVKKYHDELTPEAIEFLRXXXXXXXXXXXXXXXXXLFRETGKPKKPGNSFYL 163
+K Y + +K Y + P+ F++ PK+P ++F+L
Sbjct: 73 ADKARYEREMKTY---IPPKG------------------ETKKKFKDPNAPKRPPSAFFL 111
Query: 164 FI 165
F
Sbjct: 112 FC 113
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 35.4 bits (80), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 27/123 (21%), Positives = 51/123 (41%), Gaps = 21/123 (17%)
Query: 45 IPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAK 104
+ ++ K+P+ + + R K+ NP ++ E++K + +WK + EAEK E
Sbjct: 1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQE--- 57
Query: 105 EKEIYAQNVKKYHDELTPEAIEFLRXXXXXXXXXXXXXXXXXLFRETGKPKKPGNSFYLF 164
AQ ++ H E P F++ PK+P ++F+LF
Sbjct: 58 -----AQKLQAMHREKYPN-------------YKYRKGETKKKFKDPNAPKRPPSAFFLF 99
Query: 165 IKD 167
+
Sbjct: 100 CSE 102
Score = 34.7 bits (78), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 41/82 (50%)
Query: 36 KQQTSQPLSIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEK 95
K +T + P PK+P + +F F + R KI +P + I +V K + E W +K
Sbjct: 76 KGETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDK 135
Query: 96 KRLENEYAKEKEIYAQNVKKYH 117
+ E + AK KE Y +++ Y
Sbjct: 136 QPYEKKAAKLKEKYEKDIAAYR 157
>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 = 34.3 bits (77), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 46 PEKPKKPLTPYFKFQGQIRNKIMERNPNIKI--IEVTKLVSEEWKKIGEAEKKRLENEYA 103
P+KP+ ++ Y F R + +++P+ + E +K SE WK + EK + E+
Sbjct: 5 PKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK 64
Query: 104 KEKEIYAQNVKKY 116
+K Y + +K Y
Sbjct: 65 ADKARYEREMKTY 77
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 33.5 bits (75), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 14/67 (20%), Positives = 36/67 (53%)
Query: 50 KKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIY 109
++P+ + + R ++ ++NP++ E++K++ + WK + AEK+ E + + +
Sbjct: 9 RRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQH 68
Query: 110 AQNVKKY 116
Q+ Y
Sbjct: 69 MQDHPNY 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 = 33.1 bits (74), Expect = 0.084, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEK 106
++ K+P+ + + R K+ + NP + E++K + EWK + E EK+ +E K
Sbjct: 2 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDE---AK 58
Query: 107 EIYAQNVKKYHD 118
+ A ++K++ D
Sbjct: 59 RLRALHMKEHPD 70
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 33.1 bits (74), Expect = 0.089, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEK 106
++ K+P+ + + R K+ + NP + E++K + EWK + E EK+ +E K
Sbjct: 1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDE---AK 57
Query: 107 EIYAQNVKKYHD 118
+ A ++K++ D
Sbjct: 58 RLRALHMKEHPD 69
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 33.1 bits (74), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 2/73 (2%)
Query: 46 PEKPKKPLTPYFKFQGQIRNKIMERNPNIKI--IEVTKLVSEEWKKIGEAEKKRLENEYA 103
P+KP+ ++ Y F R + +++P+ + E +K SE WK + EK + E+
Sbjct: 5 PKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK 64
Query: 104 KEKEIYAQNVKKY 116
+K Y + +K Y
Sbjct: 65 ADKARYEREMKTY 77
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 12/53 (22%), Positives = 31/53 (58%)
Query: 44 SIPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKK 96
S + ++P+ + + R ++ ++NP++ E++K++ + WK + AEK+
Sbjct: 2 SFTSRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKR 54
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 32.7 bits (73), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 11/47 (23%), Positives = 29/47 (61%)
Query: 50 KKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKK 96
++P+ + + R ++ ++NP++ E++K++ + WK + AEK+
Sbjct: 4 RRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKR 50
>pdb|1ZIV|A Chain A, Catalytic Domain Of Human Calpain-9
Length = 339
Score = 32.3 bits (72), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 9/78 (11%)
Query: 58 KFQGQIRNKIMERNP--NIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYA--QNV 113
F+GQ I RNP ++ S EW+ +G AE+KRL + + E + ++
Sbjct: 257 SFRGQRIELIRIRNPWGQVEWNGSWSDSSPEWRSVGPAEQKRLCHTALDDGEFWMAFKDF 316
Query: 114 KKYHDE-----LTPEAIE 126
K + D+ LTP+A+E
Sbjct: 317 KAHFDKVEICNLTPDALE 334
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 32.0 bits (71), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 29/46 (63%)
Query: 50 KKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEK 95
K+P+ + + R KIME++P++ E++K + + WK + +++K
Sbjct: 4 KRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDK 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 = 32.0 bits (71), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 29/51 (56%)
Query: 45 IPEKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEK 95
+ ++ K+P+ + + R K+ NP ++ E++K + +WK + EAEK
Sbjct: 1 VQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEK 51
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 48 KPKKPLTPYFKFQGQIRNKIMERNPN--IKIIEVTKLVSEEWKKIGEAEKKRLENEYAKE 105
KP+ ++ Y F R + +++P+ + E +K SE WK + EK + E+ +
Sbjct: 1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60
Query: 106 KEIYAQNVKKY 116
K Y + +K Y
Sbjct: 61 KARYEREMKTY 71
>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 = 31.2 bits (69), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 28/49 (57%)
Query: 47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEK 95
++ K+P+ + + R K+ NP ++ E++K + +WK + EAEK
Sbjct: 3 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEK 51
>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 = 30.8 bits (68), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 28/49 (57%)
Query: 47 EKPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEK 95
++ K+P+ + + R K+ NP ++ E++K + +WK + EAEK
Sbjct: 3 DRVKRPINAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEK 51
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 30.0 bits (66), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 36/69 (52%), Gaps = 3/69 (4%)
Query: 50 KKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIY 109
K+P+ + + R KI++ P++ ++K++ WK + EK+ E A+ +
Sbjct: 6 KRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQAR---LS 62
Query: 110 AQNVKKYHD 118
Q+++KY D
Sbjct: 63 KQHLEKYPD 71
>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 = 0.84, Method: Compositional matrix adjust.
Identities = 11/47 (23%), Positives = 28/47 (59%)
Query: 50 KKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKK 96
K+P+ + + R K+ ++ P++ E++K + + W+ + E+EK+
Sbjct: 31 KRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKR 77
>pdb|2P0R|A Chain A, Structure Of Human Calpain 9 In Complex With Leupeptin
pdb|2P0R|B Chain B, Structure Of Human Calpain 9 In Complex With Leupeptin
Length = 333
Score = 29.6 bits (65), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 37/76 (48%), Gaps = 9/76 (11%)
Query: 58 KFQGQIRNKIMERNP--NIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYA--QNV 113
F+GQ I RNP ++ S EW+ +G AE+KRL + + E + ++
Sbjct: 258 SFRGQRIELIRIRNPWGQVEWNGSWSDSSPEWRSVGPAEQKRLCHTALDDGEFWMAFKDF 317
Query: 114 KKYHDE-----LTPEA 124
K + D+ LTP+A
Sbjct: 318 KAHFDKVEICNLTPDA 333
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
Mobility Group Protein B3
Length = 86
Score = 28.1 bits (61), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 53 LTPYFKFQGQIRNKIMERNPNIKI--IEVTKLVSEEWKKIGEAEKKRLENEYAKEKEIYA 110
++ Y F R + ++NP + + E +K SE WK + EK + + +K Y
Sbjct: 20 MSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYD 79
Query: 111 QNVKKY 116
+ +K Y
Sbjct: 80 REMKDY 85
>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B
Length = 67
Score = 26.9 bits (58), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 38/73 (52%), Gaps = 11/73 (15%)
Query: 48 KPKKPLTPYFKFQGQIRNKIMERNPNIKIIEVTKLVSEEWKKIGEAEKKRLENEYAKEKE 107
KPK+P + Y + + + +P K+ K V E WK + ++EK+ L ++AKE E
Sbjct: 2 KPKRPRSAYNVYVAERFQEAKGDSPQEKL----KTVKENWKNLSDSEKE-LYIQHAKEDE 56
Query: 108 IYAQNVKKYHDEL 120
+YH+E+
Sbjct: 57 T------RYHNEM 63
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
0.315 0.134 0.383
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,067,970
Number of Sequences: 62578
Number of extensions: 180311
Number of successful extensions: 476
Number of sequences better than 100.0: 53
Number of HSP's better than 100.0 without gapping: 42
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 420
Number of HSP's gapped (non-prelim): 63
length of query: 180
length of database: 14,973,337
effective HSP length: 93
effective length of query: 87
effective length of database: 9,153,583
effective search space: 796361721
effective search space used: 796361721
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 48 (23.1 bits)