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= 031104
(165 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 = 56.2 bits (134), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 37/75 (49%), Gaps = 1/75 (1%)
Query: 50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDXXXXXXXXX 109
KKDPN PKRPPSAFF+F E+R K EHP + ++ K GE W +
Sbjct: 3 KKDPNAPKRPPSAFFLFCSEYRPKIKSEHPGL-SIGDTAKKLGEMWSEQSAKDKQPYEQK 61
Query: 110 XXXXXLDYEKLMTAY 124
YEK + AY
Sbjct: 62 AAKLKEKYEKDIAAY 76
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 55.5 bits (132), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDXXXXXXXXXX 110
KDPN PKRPPSAFF+F E+R K EHP + ++ V K GE W +
Sbjct: 97 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKA 155
Query: 111 XXXXLDYEKLMTAY 124
YEK + AY
Sbjct: 156 AKLKEKYEKDIAAY 169
Score = 33.1 bits (74), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA-VSAVGKAGGEKWKSLTDXXXXXXXXXX 110
DP KP+ S++ F++ R+ +K++HP+ S K E+WK+++
Sbjct: 12 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMA 71
Query: 111 XXXXLDYEKLMTAY 124
YE+ M Y
Sbjct: 72 KADKARYEREMKTY 85
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDXXXXXXXXXX 110
KDPN PKRPPSAFF+F E+R K EHP + ++ V K GE W +
Sbjct: 84 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKA 142
Query: 111 XXXXLDYEKLMTAY 124
YEK + AY
Sbjct: 143 AKLKEKYEKDIAAY 156
Score = 28.1 bits (61), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
KRP +AF V+ + R+ E+P ++ S + K G +WK LT+
Sbjct: 6 KRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTE 48
>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 = 55.1 bits (131), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 30/74 (40%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDXXXXXXXXXX 110
KDPN PKRPPSAFF+F E+R K EHP + ++ V K GE W +
Sbjct: 2 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKA 60
Query: 111 XXXXLDYEKLMTAY 124
YEK + AY
Sbjct: 61 AKLKEKYEKDIAAY 74
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 54.7 bits (130), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDXXXXXXXXX 109
KKDPN PKRPPSAFF+F E R K EHP + ++ K GE W +
Sbjct: 2 KKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGL-SIGDTAKKLGEMWSEQSAKDKQPYEQK 60
Query: 110 XXXXXLDYEKLMTAY 124
YEK + AY
Sbjct: 61 AAKLKEKYEKDIAAY 75
>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 = 49.3 bits (116), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 34/71 (47%), Gaps = 1/71 (1%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDXXXXXXXXXXXXX 113
N PKRPPSAFF+F E+R K EHP + ++ V K GE W +
Sbjct: 3 NAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKL 61
Query: 114 XLDYEKLMTAY 124
YEK + AY
Sbjct: 62 KEKYEKDIAAY 72
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 48.5 bits (114), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 33/71 (46%), Gaps = 1/71 (1%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDXXXXXXXXXXXXX 113
N PKRPPS FF+F EFR K +P + ++ V K GE W +L D
Sbjct: 8 NAPKRPPSGFFLFCSEFRPKIKSTNPGI-SIGDVAKKLGEMWNNLNDSEKQPYITKAAKL 66
Query: 114 XLDYEKLMTAY 124
YEK + Y
Sbjct: 67 KEKYEKDVADY 77
>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 = 47.4 bits (111), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/69 (37%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDXXXXXXXXXXXXXXL 115
PKRPPSAFF+F E+R K EHP + ++ V K GE W +
Sbjct: 3 PKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKE 61
Query: 116 DYEKLMTAY 124
YEK + AY
Sbjct: 62 KYEKDIAAY 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 = 46.6 bits (109), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/48 (47%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLT 99
DPN PKR SA+ F E R + + E+P++ VGK GEKWK+LT
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALT 63
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 46.6 bits (109), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/48 (47%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLT 99
DPN PKR SA+ F E R + + E+P++ VGK GEKWK+LT
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALT 63
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 46.2 bits (108), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
+KPKRP SA+ ++L R+ K+E+P +K V+ V K GGE W+++ D
Sbjct: 3 DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 48
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
+KPKRP SA+ ++L R+ K+E+P +K V+ V K GGE W+++ D
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 47
>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 = 45.8 bits (107), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
+KPKRP SA+ ++L R+ K+E+P +K V+ V K GGE W+++ D
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 47
>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 = 45.4 bits (106), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 1/79 (1%)
Query: 47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNV-KAVSAVGKAGGEKWKSLTDXXXXX 105
+ AKKDPN PKR S++ F +E R E+P + K V+A+GK G W +L+D
Sbjct: 14 RKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKP 73
Query: 106 XXXXXXXXXLDYEKLMTAY 124
+ YE+ Y
Sbjct: 74 YERMSDEDRVRYEREKAEY 92
>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 = 2e-05, Method: Compositional matrix adjust.
Identities = 21/47 (44%), Positives = 33/47 (70%), Gaps = 1/47 (2%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
+KPKRP SA+ ++L R+ K+E+P +K V+ V K GGE W+++ D
Sbjct: 2 DKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD 47
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 20/45 (44%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
PKR +AF ++L + R+ K+E+P +K V+ + K GGE WK L D
Sbjct: 4 PKRATTAFMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKELKD 47
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
Hmg-Box Transcription Factor 1
Length = 87
Score = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 28/46 (60%), Gaps = 1/46 (2%)
Query: 53 PNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSL 98
PNK KRP +AF +F +++R Y Q +P K A+ G++WK +
Sbjct: 15 PNKCKRPMNAFMLFAKKYRVEYTQMYPG-KDNRAISVILGDRWKKM 59
>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 = 35.0 bits (79), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 1/77 (1%)
Query: 49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA-VSAVGKAGGEKWKSLTDXXXXXXX 107
K DP KP+ S++ F++ R+ +K++HP+ S K E+WK+++
Sbjct: 1 GKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFE 60
Query: 108 XXXXXXXLDYEKLMTAY 124
YE+ M Y
Sbjct: 61 DMAKADKARYEREMKTY 77
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 34.7 bits (78), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 31/52 (59%), Gaps = 1/52 (1%)
Query: 49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA-VSAVGKAGGEKWKSLT 99
K DPNKP+ S++ F++ R+ +K++HP+ + K E+WK+++
Sbjct: 2 GKGDPNKPRGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMS 53
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 34.7 bits (78), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 1/47 (2%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
KPKRP SA F+F EE R+ ++E P + + S + + W L++
Sbjct: 19 EKPKRPVSAMFIFSEEKRRQLQEERPEL-SESELTRLLARMWNDLSE 64
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 34.3 bits (77), Expect = 0.033, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 1/77 (1%)
Query: 49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA-VSAVGKAGGEKWKSLTDXXXXXXX 107
K DP KP+ S++ F++ R+ +K++HP+ S K E+WK+++
Sbjct: 1 GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFE 60
Query: 108 XXXXXXXLDYEKLMTAY 124
YE+ M Y
Sbjct: 61 DMAKADKARYEREMKTY 77
>pdb|2CO9|A Chain A, Solution Structure Of The Hmg_box Domain Of Thymus High
Mobility Group Box Protein Tox From Mouse
Length = 102
Score = 32.3 bits (72), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 1/73 (1%)
Query: 52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDXXXXXXXXXXX 111
DPN+P++P SA+ +F + + K ++PN V K W L +
Sbjct: 14 DPNEPQKPVSAYALFFRDTQAAIKGQNPNA-TFGEVSKIVASMWDGLGEEQKQVYKKKTE 72
Query: 112 XXXLDYEKLMTAY 124
+Y K + AY
Sbjct: 73 AAKKEYLKQLAAY 85
>pdb|2V2Q|A Chain A, Ispe In Complex With Ligand
pdb|2V2Q|B Chain B, Ispe In Complex With Ligand
pdb|2V2V|A Chain A, Ispe In Complex With Ligand
pdb|2V2V|B Chain B, Ispe In Complex With Ligand
pdb|2V2Z|A Chain A, Ispe In Complex With Adp And Cdpme
pdb|2V2Z|B Chain B, Ispe In Complex With Adp And Cdpme
pdb|2V34|A Chain A, Ispe In Complex With Cytidine And Ligand
pdb|2V34|B Chain B, Ispe In Complex With Cytidine And Ligand
pdb|2V8P|A Chain A, Ispe In Complex With Adp And Cdp
pdb|2V8P|B Chain B, Ispe In Complex With Adp And Cdp
pdb|2VF3|A Chain A, Aquifex Aeolicus Ispe In Complex With Ligand
pdb|2VF3|B Chain B, Aquifex Aeolicus Ispe In Complex With Ligand
Length = 271
Score = 31.6 bits (70), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 15/38 (39%), Positives = 21/38 (55%)
Query: 6 GKGAVKKDKNEVVKPVEDRAAGKRKAVLKASRSSNKRT 43
GK A+ + K EV++PVE +GK V+ SS R
Sbjct: 140 GKSAIGRGKGEVLEPVETEISGKITLVIPQVSSSTGRV 177
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human Upstream
Binding Factor
Length = 99
Score = 31.2 bits (69), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 1/55 (1%)
Query: 46 VKSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
+K KK P+ PK+P + +F F E R Y + HP + + + K +K+K L +
Sbjct: 1 MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLD-LTKILSKKYKELPE 54
>pdb|1O4X|B Chain B, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 88
Score = 30.4 bits (67), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 1/48 (2%)
Query: 53 PNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
P++ KRP +AF V+ R+ QE+P + S + K G +WK L++
Sbjct: 5 PDRVKRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSE 51
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 30.4 bits (67), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLT 99
+RP +AF V+ ++ RK Q++P++ + + K G+ WK+LT
Sbjct: 4 RRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALT 45
>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby
Sox Homolog
Length = 82
Score = 30.4 bits (67), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNV 81
+RP +AF +F + R + +QEHP +
Sbjct: 9 RRPMNAFLLFCKRHRSLVRQEHPRL 33
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 30.0 bits (66), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLT 99
+RP +AF V+ ++ RK Q++P++ + + K G+ WK+LT
Sbjct: 8 RRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALT 49
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 30.0 bits (66), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 27/43 (62%), Gaps = 1/43 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLT 99
+RP +AF V+ ++ RK Q++P++ + K G+ WK+LT
Sbjct: 9 RRPMNAFMVWAKDERKRLAQQNPDLHNAE-LSKMLGKSWKALT 50
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 29.6 bits (65), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 1/71 (1%)
Query: 55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKA-VSAVGKAGGEKWKSLTDXXXXXXXXXXXXX 113
KP+ S++ F++ R+ +K++HP+ S K E+WK+++
Sbjct: 1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKAD 60
Query: 114 XLDYEKLMTAY 124
YE+ M 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 = 29.3 bits (64), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
KRP +AF V+ + R+ E+P ++ S + K G +WK LT+
Sbjct: 6 KRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTE 48
>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 = 29.3 bits (64), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
PK+P S++ F +E ++K ++P+ K + + ++W+ L D
Sbjct: 10 PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRI-AQRWRELPD 53
Score = 26.6 bits (57), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 5/46 (10%)
Query: 55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
KPKRP SA+ V++ E + K + P K K E WK+L+D
Sbjct: 114 KPKRPRSAYNVYVAERFQEAKGDSPQEKL-----KTVKENWKNLSD 154
>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 = 16/44 (36%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
KRP +AF V+ + R+ E+P ++ S + K G +WK LT+
Sbjct: 6 KRPINAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTE 48
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
Length = 238
Score = 29.3 bits (64), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 26/45 (57%), Gaps = 1/45 (2%)
Query: 56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
PK+P S++ F +E ++K ++P+ K + + ++W+ L D
Sbjct: 42 PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRI-AQRWRELPD 85
Score = 26.6 bits (57), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 5/46 (10%)
Query: 55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
KPKRP SA+ V++ E + K + P K K E WK+L+D
Sbjct: 146 KPKRPRSAYNVYVAERFQEAKGDSPQEKL-----KTVKENWKNLSD 186
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 28.9 bits (63), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 27/44 (61%), Gaps = 1/44 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
KRP +AF V+ ++ R+ Q P++ S + K G +WK++T+
Sbjct: 6 KRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMTN 48
>pdb|1HRZ|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By
Multi-Dimensional Heteronuclear-Edited And-Filtered Nmr
pdb|1HRY|A Chain A, The 3d Structure Of The Human Sry-Dna Complex Solved By
Multid-Dimensional Heteronuclear-Edited And-Filtered Nmr
Length = 76
Score = 28.9 bits (63), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
KRP +AF V+ + R+ E+P ++ S + K G +WK LT+
Sbjct: 6 KRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTE 48
>pdb|2A4E|A Chain A, Crystal Structure Of Mouse Cadherin-11 Ec1-2
Length = 215
Score = 28.5 bits (62), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 5/55 (9%)
Query: 41 KRTKNVKSAKKDPNKPKRPPSAFFVFLEEFRK-----VYKQEHPNVKAVSAVGKA 90
+ T ++ +D N+P PPS F V +++ +++ H NV S VG +
Sbjct: 71 QYTLMAQAVDRDTNRPLEPPSEFIVKVQDINDNPPEFLHEIYHANVPERSNVGTS 125
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 28.1 bits (61), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
KRP +AF V+ R+ QE+P + S + K G +WK L++
Sbjct: 4 KRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSE 46
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 28.1 bits (61), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
KRP +AF V+ R+ QE+P + S + K G +WK L++
Sbjct: 5 KRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSE 47
>pdb|1EYY|A Chain A, Crystal Structure Of The Nadp+ Dependent Aldehyde
Dehydrogenase From Vibrio Harveyi.
pdb|1EYY|B Chain B, Crystal Structure Of The Nadp+ Dependent Aldehyde
Dehydrogenase From Vibrio Harveyi.
pdb|1EYY|C Chain C, Crystal Structure Of The Nadp+ Dependent Aldehyde
Dehydrogenase From Vibrio Harveyi.
pdb|1EYY|D Chain D, Crystal Structure Of The Nadp+ Dependent Aldehyde
Dehydrogenase From Vibrio Harveyi.
pdb|1EZ0|A Chain A, Crystal Structure Of The Nadp+ Dependent Aldehyde
Dehydrogenase From Vibrio Harveyi.
pdb|1EZ0|B Chain B, Crystal Structure Of The Nadp+ Dependent Aldehyde
Dehydrogenase From Vibrio Harveyi.
pdb|1EZ0|C Chain C, Crystal Structure Of The Nadp+ Dependent Aldehyde
Dehydrogenase From Vibrio Harveyi.
pdb|1EZ0|D Chain D, Crystal Structure Of The Nadp+ Dependent Aldehyde
Dehydrogenase From Vibrio Harveyi
Length = 510
Score = 27.3 bits (59), Expect = 3.8, Method: Composition-based stats.
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 3/41 (7%)
Query: 55 KPKRPPSAFFVFLEEFRKVYKQ---EHPNVKAVSAVGKAGG 92
K ++ P A F L+ ++ Q HP +KAV G GG
Sbjct: 193 KQEQLPQAIFTLLQGNQRALGQALVSHPEIKAVGFTGSVGG 233
>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B
Length = 67
Score = 26.6 bits (57), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 25/46 (54%), Gaps = 5/46 (10%)
Query: 55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTD 100
KPKRP SA+ V++ E + K + P K K E WK+L+D
Sbjct: 2 KPKRPRSAYNVYVAERFQEAKGDSPQEKL-----KTVKENWKNLSD 42
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.309 0.126 0.349
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,087,277
Number of Sequences: 62578
Number of extensions: 96957
Number of successful extensions: 367
Number of sequences better than 100.0: 47
Number of HSP's better than 100.0 without gapping: 33
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 321
Number of HSP's gapped (non-prelim): 52
length of query: 165
length of database: 14,973,337
effective HSP length: 91
effective length of query: 74
effective length of database: 9,278,739
effective search space: 686626686
effective search space used: 686626686
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)