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= 032085
(147 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 55.8 bits (133), Expect = 9e-09, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
S FF+F EFR + K +P S+ V K GE W ++++ EK P++ +A K K Y K+
Sbjct: 15 SGFFLFCSEFRPKIKSTNPG-ISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEKD 73
Query: 105 MQDY 108
+ DY
Sbjct: 74 VADY 77
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 47.4 bits (111), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 1/64 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
SAFF+F E+R + K HP S+ K GE W S +K P+ ++A K K Y K+
Sbjct: 14 SAFFLFCSEYRPKIKSEHPGL-SIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKYEKD 72
Query: 105 MQDY 108
+ Y
Sbjct: 73 IAAY 76
>pdb|1NHM|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna
pdb|1NHN|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna
Length = 81
Score = 46.2 bits (108), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
SAFF+F E+R + K HP S+ V K GE W + + D+K P+ ++A K K Y K+
Sbjct: 10 SAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKD 68
Query: 105 MQDY 108
+ Y
Sbjct: 69 IAAY 72
>pdb|1HSM|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna
pdb|1HSN|A Chain A, The Structure Of The Hmg Box And Its Interaction With Dna
Length = 79
Score = 45.8 bits (107), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
SAFF+F E+R + K HP S+ V K GE W + + D+K P+ ++A K K Y K+
Sbjct: 8 SAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKD 66
Query: 105 MQDY 108
+ Y
Sbjct: 67 IAAY 70
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 45.8 bits (107), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
SAFF+F E R + K HP S+ K GE W S +K P+ ++A K K Y K+
Sbjct: 13 SAFFLFCSEHRPKIKSEHPGL-SIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKYEKD 71
Query: 105 MQDY 108
+ Y
Sbjct: 72 IAAY 75
>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 = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
SAFF+F E+R + K HP S+ V K GE W + + D+K P+ ++A K K Y K+
Sbjct: 12 SAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKD 70
Query: 105 MQDY 108
+ Y
Sbjct: 71 IAAY 74
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
SAFF+F E+R + K HP S+ V K GE W + + D+K P+ ++A K K Y K+
Sbjct: 107 SAFFLFCSEYRPKIKGEHPGL-SIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKD 165
Query: 105 MQDY 108
+ Y
Sbjct: 166 IAAY 169
Score = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPN-NKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNK 103
S++ F++ R++ K+ HP+ + + + K E+WK+MS EK F + A+ K+ Y +
Sbjct: 21 SSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYER 80
Query: 104 NMQDY 108
M+ Y
Sbjct: 81 EMKTY 85
>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 = 44.3 bits (103), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 39/66 (59%), Gaps = 1/66 (1%)
Query: 46 AFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNM 105
AF V+ + R++ + +P+ + A + K G+ W+ ++E EK PFVE AE+ + + K+
Sbjct: 36 AFMVWAQAARRKLADQYPHLHN-AELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDH 94
Query: 106 QDYNKQ 111
DY Q
Sbjct: 95 PDYKYQ 100
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 43.9 bits (102), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
SAFF+F E+R + K HP S+ V K GE W + + D+K P+ ++A K K Y K+
Sbjct: 94 SAFFLFCSEYRPKIKGEHPG-LSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKD 152
Query: 105 MQDY 108
+ Y
Sbjct: 153 IAAY 156
Score = 32.3 bits (72), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
+AF V+ + R++ +P ++ + + K G +WK ++E EK PF + A+K ++ + +
Sbjct: 10 NAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
Query: 105 MQDY 108
+Y
Sbjct: 69 YPNY 72
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
SA+ F E R + +P+ + VGK GEKWK+++ +EK P+ +A+ K Y
Sbjct: 26 SAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESE 84
Query: 105 MQDYNKQLA 113
+ YN LA
Sbjct: 85 KELYNATLA 93
>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 = 41.6 bits (96), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 37/69 (53%), Gaps = 1/69 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
SA+ F E R + +P+ + VGK GEKWK+++ +EK P+ +A+ K Y
Sbjct: 26 SAYMFFANENRDIVRSENPD-ITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESE 84
Query: 105 MQDYNKQLA 113
+ YN LA
Sbjct: 85 KELYNATLA 93
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 40.8 bits (94), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 39/63 (61%), Gaps = 4/63 (6%)
Query: 46 AFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNM 105
AF V+ ++ RK+ + +P+ + A + K G+ WK+++ EK PFVE AE+ + + M
Sbjct: 14 AFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKRPFVEEAERLRVQH---M 69
Query: 106 QDY 108
QD+
Sbjct: 70 QDH 72
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 40/64 (62%), Gaps = 4/64 (6%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
+AF V+ ++ RK+ + +P+ + A + K G+ WK+++ EK PFVE AE+ + +
Sbjct: 8 NAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKRPFVEEAERLRVQH--- 63
Query: 105 MQDY 108
MQD+
Sbjct: 64 MQDH 67
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 39.3 bits (90), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 40/64 (62%), Gaps = 4/64 (6%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
+AF V+ ++ RK+ + +P+ + A + K G+ WK+++ EK PFVE AE+ + +
Sbjct: 12 NAFMVWAKDERKRLAQQNPDLHN-AELSKMLGKSWKALTLAEKRPFVEEAERLRVQH--- 67
Query: 105 MQDY 108
MQD+
Sbjct: 68 MQDH 71
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
Mobility Group Protein B3
Length = 86
Score = 38.5 bits (88), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNK-SVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNK 103
SA+ F++ R++ K+ +P + A K E+WK+MS EK+ F E A+ K Y++
Sbjct: 21 SAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDR 80
Query: 104 NMQDY 108
M+DY
Sbjct: 81 EMKDY 85
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
+AF V+ + R++ E P+ + A + K G++WK + + +K PF++ AE+ + + +
Sbjct: 8 NAFMVWSQIERRKIMEQSPDMHN-AEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMAD 66
Query: 105 MQDY 108
DY
Sbjct: 67 YPDY 70
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 37.0 bits (84), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 40/64 (62%), Gaps = 1/64 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNK-SVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNK 103
S++ F++ R++ K+ HP++ + A K E+WK+MS EK+ F + A+ K+ Y++
Sbjct: 14 SSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSDKARYDR 73
Query: 104 NMQD 107
M++
Sbjct: 74 EMKN 77
>pdb|2LY4|A Chain A, Hmgb1-Facilitated P53 Dna Binding Occurs Via Hmg-BoxP53
Transactivation Domain Interaction And Is Regulated By
The Acidic Tail
Length = 83
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPN-NKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNK 103
S++ F++ R++ K+ HP+ + + + K E+WK+MS EK F + A+ K+ Y +
Sbjct: 13 SSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYER 72
Query: 104 NMQDY 108
M+ Y
Sbjct: 73 EMKTY 77
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPN-NKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNK 103
S++ F++ R++ K+ HP+ + + + K E+WK+MS EK F + A+ K+ Y +
Sbjct: 7 SSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYER 66
Query: 104 NMQDY 108
M+ Y
Sbjct: 67 EMKTY 71
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 36.2 bits (82), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
+ + F+ E R+Q + HP+ + K G +W + EK +++ AEK K Y K
Sbjct: 13 TGYVRFLNERREQIRTRHPD-LPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKE 71
Query: 105 MQDYNK 110
+ Y +
Sbjct: 72 LWAYQQ 77
>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 = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 46 AFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNM 105
AF V+ R++ + +P + + + K G +WK +SE EK PF++ A++ ++ + K
Sbjct: 14 AFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEH 72
Query: 106 QDY 108
DY
Sbjct: 73 PDY 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 = 36.2 bits (82), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 46 AFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNM 105
AF V+ R++ + +P + + + K G +WK +SE EK PF++ A++ ++ + K
Sbjct: 10 AFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEH 68
Query: 106 QDY 108
DY
Sbjct: 69 PDY 71
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
+AF V+ R++ + +P + + + K G +WK +SE EK PF++ A++ ++ + K
Sbjct: 8 NAFMVWSRGQRRKMAQENPKMHN-SEISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKE 66
Query: 105 MQDY 108
DY
Sbjct: 67 HPDY 70
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 35.8 bits (81), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 1/65 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPN-NKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNK 103
S++ F++ R++ K+ HP+ + + + K E+WK+MS EK F + A+ K+ Y +
Sbjct: 13 SSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYER 72
Query: 104 NMQDY 108
M+ Y
Sbjct: 73 EMKTY 77
>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 = 34.3 bits (77), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 35/65 (53%), Gaps = 1/65 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPN-NKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNK 103
S++ F +E R + +P K VA +GK G W ++S++EK P+ +++ + Y +
Sbjct: 28 SSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYER 87
Query: 104 NMQDY 108
+Y
Sbjct: 88 EKAEY 92
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 33.5 bits (75), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 46 AFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNM 105
AF V+ ++ R++ +A P+ + + + K G +WK+M+ EK P+ E + + +
Sbjct: 11 AFMVWAKDERRKILQAFPDMHN-SNISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKY 69
Query: 106 QDY 108
DY
Sbjct: 70 PDY 72
>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 = 32.3 bits (72), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
+AF V+ + R++ +P ++ + + K G +WK ++E EK PF + A+K ++ + +
Sbjct: 10 NAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
Query: 105 MQDY 108
+Y
Sbjct: 69 YPNY 72
>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 = 32.3 bits (72), Expect = 0.099, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
+AF V+ + R++ +P ++ + + K G +WK ++E EK PF + A+K ++ + +
Sbjct: 10 NAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
Query: 105 MQDY 108
+Y
Sbjct: 69 YPNY 72
>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 = 32.3 bits (72), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
+AF V+ + R++ +P ++ + + K G +WK ++E EK PF + A+K ++ + +
Sbjct: 10 NAFIVWSRDQRRKMALENPRMRN-SEISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREK 68
Query: 105 MQDY 108
+Y
Sbjct: 69 YPNY 72
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 32.0 bits (71), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 35/64 (54%), Gaps = 3/64 (4%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKN 104
+AF +++ + R+ K +P K V + K GE WK + +K+ + + A K K Y+
Sbjct: 9 TAFMLWLNDTRESIKRENPGIK-VTEIAKKGGEMWKELK--DKSKWEDAAAKDKQRYHDE 65
Query: 105 MQDY 108
M++Y
Sbjct: 66 MRNY 69
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 30.8 bits (68), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 45 SAFFVFMEEFRKQFKEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVER 93
SA F+F EE R+Q +E P S + + + W +SE +KA + R
Sbjct: 26 SAMFIFSEEKRRQLQEERPEL-SESELTRLLARMWNDLSEKKKAKYKAR 73
>pdb|3ZUQ|A Chain A, Crystal Structure Of An Engineered Botulinum Neurotoxin
Type B-Derivative, Lc-B-Gs-Hn-B
Length = 906
Score = 28.5 bits (62), Expect = 1.5, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 28/50 (56%)
Query: 73 KAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQLADGVNAAEEN 122
KA + +++ E K + +EK KS+ N + D N +L +G+N A +N
Sbjct: 756 KALNYQAQALEEIIKYRYNIYSEKEKSNINIDFNDINSKLNEGINQAIDN 805
>pdb|1EPW|A Chain A, Crystal Structure Of Clostridium Neurotoxin Type B
pdb|1F31|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With A Trisaccharide
pdb|1I1E|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With Doxorubicin
pdb|1G9A|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With An Inhibitor (Experiment 3)
pdb|1G9B|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With An Inhibitor (Experiment 1)
pdb|1G9C|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With An Inhibitor (Experiment 4)
pdb|1G9D|A Chain A, Crystal Structure Of Clostridium Botulinum Neurotoxin B
Complexed With An Inhibitor (Experiment 2)
pdb|1S0B|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 4.0
pdb|1S0C|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 5.0
pdb|1S0D|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 5.5
pdb|1S0E|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 6.0
pdb|1S0F|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B At Ph 7.0
pdb|1S0G|A Chain A, Crystal Structure Of Botulinum Neurotoxin Type B Apo Form
pdb|2NP0|A Chain A, Crystal Structure Of The Botulinum Neurotoxin Type B
Complexed With Synaptotagamin-Ii Ectodomain
Length = 1290
Score = 28.1 bits (61), Expect = 1.8, Method: Composition-based stats.
Identities = 16/50 (32%), Positives = 28/50 (56%)
Query: 73 KAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQLADGVNAAEEN 122
KA + +++ E K + +EK KS+ N + D N +L +G+N A +N
Sbjct: 720 KALNYQAQALEEIIKYRYNIYSEKEKSNINIDFNDINSKLNEGINQAIDN 769
>pdb|2XHL|B Chain B, Structure Of A Functional Derivative Of Clostridium
Botulinum Neurotoxin Type B
Length = 433
Score = 27.3 bits (59), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/50 (32%), Positives = 28/50 (56%)
Query: 73 KAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQLADGVNAAEEN 122
KA + +++ E K + +EK KS+ N + D N +L +G+N A +N
Sbjct: 283 KALNYQAQALEEIIKYRYNIYSEKEKSNINIDFNDINSKLNEGINQAIDN 332
>pdb|3I44|A Chain A, Crystal Structure Of Aldehyde Dehydrogenase From
Bartonella Henselae At 2.0a Resolution
Length = 497
Score = 26.2 bits (56), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 4/37 (10%)
Query: 73 KAAGEKWKSMSEDEKAPFVERA----EKRKSDYNKNM 105
K A + WK+ S E+ FVE+ EKR SD K +
Sbjct: 73 KKAFQTWKTTSPHERLGFVEKILEIYEKRSSDMAKTI 109
>pdb|2QVC|A Chain A, Crystal Structure Of A Periplasmic Sugar Abc Transporter
From Thermotoga Maritima
pdb|2QVC|B Chain B, Crystal Structure Of A Periplasmic Sugar Abc Transporter
From Thermotoga Maritima
pdb|2QVC|C Chain C, Crystal Structure Of A Periplasmic Sugar Abc Transporter
From Thermotoga Maritima
pdb|2QVC|D Chain D, Crystal Structure Of A Periplasmic Sugar Abc Transporter
From Thermotoga Maritima
Length = 313
Score = 25.8 bits (55), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 30/69 (43%), Gaps = 8/69 (11%)
Query: 59 KEAHPNNKSVATVGKAAGEKWKSMSEDEKAPFVERAEKRKSDYNKNMQDYNKQLADGVNA 118
K HP V KAAG K++ D K FV +K D N +Q +A+GVN
Sbjct: 10 KSVHPYWSQVEQGVKAAG---KALGVDTKF-FV----PQKEDINAQLQXLESFIAEGVNG 61
Query: 119 AEENESDKS 127
SD +
Sbjct: 62 IAIAPSDPT 70
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
0.304 0.120 0.321
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,144,056
Number of Sequences: 62578
Number of extensions: 95704
Number of successful extensions: 191
Number of sequences better than 100.0: 46
Number of HSP's better than 100.0 without gapping: 38
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 142
Number of HSP's gapped (non-prelim): 49
length of query: 147
length of database: 14,973,337
effective HSP length: 90
effective length of query: 57
effective length of database: 9,341,317
effective search space: 532455069
effective search space used: 532455069
T: 11
A: 40
X1: 16 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.9 bits)
S2: 47 (22.7 bits)