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= 033573
(116 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 = 54.3 bits (129), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 25/46 (54%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKW 95
KKDPN PKRPPSAFF+F E+R K EHP + ++ K GE W
Sbjct: 3 KKDPNAPKRPPSAFFLFCSEYRPKIKSEHPGL-SIGDTAKKLGEMW 47
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 53.5 bits (127), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 25/45 (55%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKW 95
KDPN PKRPPSAFF+F E+R K EHP + ++ V K GE W
Sbjct: 97 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMW 140
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA-VSAVGKAGGEKWKSLT 99
DP KP+ S++ F++ R+ +K++HP+ S K E+WK+++
Sbjct: 12 DPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS 60
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 25/45 (55%), Positives = 30/45 (66%), Gaps = 1/45 (2%)
Query: 51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKW 95
KDPN PKRPPSAFF+F E+R K EHP + ++ V K GE W
Sbjct: 84 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMW 127
Score = 29.6 bits (65), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
KRP +AF V+ + R+ E+P ++ S + K G +WK LT+A K
Sbjct: 6 KRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEK 51
>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 = 53.1 bits (126), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 25/47 (53%), Positives = 31/47 (65%), Gaps = 1/47 (2%)
Query: 51 KDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKS 97
KDPN PKRPPSAFF+F E+R K EHP + ++ V K GE W +
Sbjct: 2 KDPNAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNN 47
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 52.4 bits (124), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 25/46 (54%), Positives = 29/46 (63%), Gaps = 1/46 (2%)
Query: 50 KKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKW 95
KKDPN PKRPPSAFF+F E R K EHP + ++ K GE W
Sbjct: 2 KKDPNAPKRPPSAFFLFCSEHRPKIKSEHPGL-SIGDTAKKLGEMW 46
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 49.7 bits (117), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 23/53 (43%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEH 106
N PKRPPS FF+F EFR K +P + ++ V K GE W +L D+ K+ +
Sbjct: 8 NAPKRPPSGFFLFCSEFRPKIKSTNPGI-SIGDVAKKLGEMWNNLNDSEKQPY 59
>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 = 47.0 bits (110), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 22/44 (50%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKS 97
N PKRPPSAFF+F E+R K EHP + ++ V K GE W +
Sbjct: 3 NAPKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNN 45
>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 = 4e-06, Method: Compositional matrix adjust.
Identities = 24/55 (43%), Positives = 33/55 (60%), Gaps = 1/55 (1%)
Query: 52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEH 106
DPN PKR SA+ F E R + + E+P++ VGK GEKWK+LT K+ +
Sbjct: 17 DPNAPKRALSAYMFFANENRDIVRSENPDI-TFGQVGKKLGEKWKALTPEEKQPY 70
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 46.6 bits (109), Expect = 4e-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 = 4e-06, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 36/57 (63%), Gaps = 4/57 (7%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVK 110
+KPKRP SA+ ++L R+ K+E+P +K V+ V K GGE W+++ D K W K
Sbjct: 3 DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD---KSEWEAK 55
>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 = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/61 (42%), Positives = 37/61 (60%), Gaps = 1/61 (1%)
Query: 47 KSAKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNV-KAVSAVGKAGGEKWKSLTDAIKKE 105
+ AKKDPN PKR S++ F +E R E+P + K V+A+GK G W +L+D KK
Sbjct: 14 RKAKKDPNAPKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKP 73
Query: 106 H 106
+
Sbjct: 74 Y 74
>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 = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 36/57 (63%), Gaps = 4/57 (7%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVK 110
+KPKRP SA+ ++L R+ K+E+P +K V+ V K GGE W+++ D K W K
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD---KSEWEAK 54
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 46.2 bits (108), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 36/57 (63%), Gaps = 4/57 (7%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVK 110
+KPKRP SA+ ++L R+ K+E+P +K V+ V K GGE W+++ D K W K
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD---KSEWEAK 54
>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 = 45.1 bits (105), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 36/57 (63%), Gaps = 4/57 (7%)
Query: 54 NKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHWMVK 110
+KPKRP SA+ ++L R+ K+E+P +K V+ V K GGE W+++ D K W K
Sbjct: 2 DKPKRPLSAYALWLNSARESIKRENPGIK-VTEVAKRGGELWRAMKD---KSEWEAK 54
>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 = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/42 (50%), Positives = 27/42 (64%), Gaps = 1/42 (2%)
Query: 56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKS 97
PKRPPSAFF+F E+R K EHP + ++ V K GE W +
Sbjct: 3 PKRPPSAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNN 43
>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 = 2e-05, Method: Compositional matrix adjust.
Identities = 22/50 (44%), Positives = 32/50 (64%), Gaps = 1/50 (2%)
Query: 56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKE 105
PKR +AF ++L + R+ K+E+P +K V+ + K GGE WK L D K E
Sbjct: 4 PKRATTAFMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKELKDKSKWE 52
>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 = 0.003, 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|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 34.7 bits (78), Expect = 0.015, 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|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 34.3 bits (77), Expect = 0.020, 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|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 = 32.7 bits (73), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA-VSAVGKAGGEKWKSLT 99
K DP KP+ S++ F++ R+ +K++HP+ S K E+WK+++
Sbjct: 1 GKGDPKKPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS 52
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 32.0 bits (71), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 49 AKKDPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKA-VSAVGKAGGEKWKSLT 99
K DP KP+ S++ F++ R+ +K++HP+ S K E+WK+++
Sbjct: 1 GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMS 52
>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 = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 52 DPNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEH 106
DPN+P++P SA+ +F + + K ++PN V K W L + K+ +
Sbjct: 14 DPNEPQKPVSAYALFFRDTQAAIKGQNPNA-TFGEVSKIVASMWDGLGEEQKQVY 67
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
+RP +AF V+ ++ RK Q++P++ + + K G+ WK+LT A K+
Sbjct: 4 RRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKR 50
>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 = 31.2 bits (69), Expect = 0.14, 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|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 31/48 (64%), Gaps = 1/48 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
+RP +AF V+ ++ RK Q++P++ + + K G+ WK+LT A K+
Sbjct: 8 RRPMNAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKR 54
>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 = 0.16, 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|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 = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
PK+P S++ F +E ++K ++P+ K + + ++W+ L D+ KK
Sbjct: 10 PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRI-AQRWRELPDSKKK 57
Score = 27.7 bits (60), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 5/50 (10%)
Query: 55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
KPKRP SA+ V++ E + K + P K K E WK+L+D+ K+
Sbjct: 114 KPKRPRSAYNVYVAERFQEAKGDSPQEKL-----KTVKENWKNLSDSEKE 158
>pdb|1O4X|B Chain B, Ternary Complex Of The Dna Binding Domains Of The Oct1 And
Sox2 Transcription Factors With A 19mer Oligonucleotide
From The Hoxb1 Regulatory Element
Length = 88
Score = 30.8 bits (68), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 53 PNKPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
P++ KRP +AF V+ R+ QE+P + S + K G +WK L++ K+
Sbjct: 5 PDRVKRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKR 55
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 30.8 bits (68), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
+RP +AF V+ ++ RK Q++P++ + K G+ WK+LT A K+
Sbjct: 9 RRPMNAFMVWAKDERKRLAQQNPDLHNAE-LSKMLGKSWKALTLAEKR 55
>pdb|1J46|A Chain A, 3d Solution Nmr Structure Of The Wild Type Hmg-Box Domain
Of The Human Male Sex Determining Factor Sry Complexed
To Dna
Length = 85
Score = 30.8 bits (68), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
KRP +AF V+ + R+ E+P ++ S + K G +WK LT+A K
Sbjct: 6 KRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEK 51
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
Length = 238
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
PK+P S++ F +E ++K ++P+ K + + ++W+ L D+ KK
Sbjct: 42 PKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRI-AQRWRELPDSKKK 89
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 5/50 (10%)
Query: 55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
KPKRP SA+ V++ E + K + P K K E WK+L+D+ K+
Sbjct: 146 KPKRPRSAYNVYVAERFQEAKGDSPQEKL-----KTVKENWKNLSDSEKE 190
>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 = 0.21, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 27/45 (60%), Gaps = 1/45 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDA 101
KRP +AF V+ + R+ E+P ++ S + K G +WK LT+A
Sbjct: 6 KRPINAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEA 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 = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIK 103
KRP +AF V+ + R+ E+P ++ S + K G +WK LT+A K
Sbjct: 6 KRPMNAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEK 51
>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby
Sox Homolog
Length = 82
Score = 29.6 bits (65), Expect = 0.39, 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|2D9X|A Chain A, Solution Structure Of The Ph Domain Of Oxysterol Binding
Protein-Related Protein 11 From Human
Length = 120
Score = 29.6 bits (65), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 87 VGKAGGEKWK-SLTDAIKKEHWMVKFVICT 115
V A GE++K TDA +++HW+ + ICT
Sbjct: 74 VNAASGEQYKLRATDAKERQHWVSRLQICT 103
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 29.6 bits (65), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 31/51 (60%), Gaps = 1/51 (1%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEHW 107
KRP +AF V+ ++ R+ Q P++ S + K G +WK++T+ K+ ++
Sbjct: 6 KRPMNAFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMTNLEKQPYY 55
>pdb|2A4E|A Chain A, Crystal Structure Of Mouse Cadherin-11 Ec1-2
Length = 215
Score = 28.5 bits (62), Expect = 0.98, 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|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 28.5 bits (62), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
KRP +AF V+ R+ QE+P + S + K G +WK L++ K+
Sbjct: 5 KRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKR 51
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 57 KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
KRP +AF V+ R+ QE+P + S + K G +WK L++ K+
Sbjct: 4 KRPMNAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKR 50
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 27/46 (58%), Gaps = 1/46 (2%)
Query: 55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKA-VSAVGKAGGEKWKSLT 99
KP+ S++ F++ R+ +K++HP+ S K E+WK+++
Sbjct: 1 KPRGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMS 46
>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B
Length = 67
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 28/50 (56%), Gaps = 5/50 (10%)
Query: 55 KPKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
KPKRP SA+ V++ E + K + P K K E WK+L+D+ K+
Sbjct: 2 KPKRPRSAYNVYVAERFQEAKGDSPQEKL-----KTVKENWKNLSDSEKE 46
>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 = 27.7 bits (60), Expect = 1.8, 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|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 = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 31/53 (58%), Gaps = 3/53 (5%)
Query: 54 NKP--KRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKK 104
NKP KRP +AF V+ + R+ ++P++ + + K G+ W+ L ++ K+
Sbjct: 26 NKPHVKRPMNAFMVWAQAARRKLADQYPHLHN-AELSKTLGKLWRLLNESEKR 77
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 56 PKRPPSAFFVFLEEFRKVYKQEHPNVKAVSAVGKAGGEKWKSLTDAIKKEH 106
PK P + + FL E R+ + HP++ + K G +W L A K+ +
Sbjct: 8 PKAPVTGYVRFLNERREQIRTRHPDL-PFPEITKMLGAEWSKLQPAEKQRY 57
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
0.312 0.127 0.363
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,287,628
Number of Sequences: 62578
Number of extensions: 110554
Number of successful extensions: 443
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: 388
Number of HSP's gapped (non-prelim): 59
length of query: 116
length of database: 14,973,337
effective HSP length: 79
effective length of query: 37
effective length of database: 10,029,675
effective search space: 371097975
effective search space used: 371097975
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: 45 (21.9 bits)