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= 034314
(98 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 = 45.8 bits (107), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 36/58 (62%), Gaps = 1/58 (1%)
Query: 1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
EFR + K +P S+ V K GE W ++++++K PY+ KA K K +YEKD+ +Y
Sbjct: 21 CSEFRPKIKSTNP-GISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKYEKDVADY 77
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 3 EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
E+R + K +HP S+ K GE W S DK PY KA K K +YEKD+ Y
Sbjct: 22 EYRPKIKSEHP-GLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKYEKDIAAY 76
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 3 EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
E R + K +HP S+ K GE W S DK PY KA K K +YEKD+ Y
Sbjct: 21 EHRPKIKSEHP-GLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKYEKDIAAY 75
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 28/40 (70%)
Query: 19 AAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
A + K G+ WK+++ A+K P+V +AE+ +V++ +D NY
Sbjct: 35 AELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNY 74
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 35/57 (61%), Gaps = 1/57 (1%)
Query: 3 EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN 59
E R+ + ++P + + VGK GEKWK+++ +K PY AKA+ K YE + + YN
Sbjct: 34 ENRDIVRSENP-DITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYN 89
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 35/57 (61%), Gaps = 1/57 (1%)
Query: 3 EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYN 59
E R+ + ++P + + VGK GEKWK+++ +K PY AKA+ K YE + + YN
Sbjct: 34 ENRDIVRSENP-DITFGQVGKKLGEKWKALTPEEKQPYEAKAQADKKRYESEKELYN 89
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 28/40 (70%)
Query: 19 AAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
A + K G+ WK+++ A+K P+V +AE+ +V++ +D NY
Sbjct: 31 AELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNY 70
>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 = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
E+R + K +HP S+ V K GE W + + DK PY KA K K +YEKD+ Y
Sbjct: 16 CSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAY 72
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 36.6 bits (83), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 28/40 (70%)
Query: 19 AAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
A + K G+ WK+++ A+K P+V +AE+ +V++ +D NY
Sbjct: 36 AELSKMLGKSWKALTLAEKRPFVEEAERLRVQHMQDHPNY 75
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/54 (37%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 5 REQYKKDHPKNK-SVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKN 57
RE++KK HP + + A K E+WK+MS +K+ + A+ K Y+++MKN
Sbjct: 24 REEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSDKARYDREMKN 77
>pdb|1HME|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1
pdb|1HMF|A Chain A, Structure Of The Hmg Box Motif In The B-Domain Of Hmg1
Length = 77
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
E+R + K +HP S+ V K GE W + + DK PY KA K K +YEKD+ Y
Sbjct: 18 CSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAY 74
>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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 29/40 (72%)
Query: 19 AAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
A + K G+ W+ ++E++K P+V +AE+ +V+++KD +Y
Sbjct: 58 AELSKTLGKLWRLLNESEKRPFVEEAERLRVQHKKDHPDY 97
>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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
E+R + K +HP S+ V K GE W + + DK PY KA K K +YEKD+ Y
Sbjct: 14 CSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAY 70
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/56 (42%), Positives = 32/56 (57%), Gaps = 1/56 (1%)
Query: 3 EFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
E+R + K +HP S+ V K GE W + + DK PY KA K K +YEKD+ Y
Sbjct: 102 EYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAY 156
Score = 31.6 bits (70), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 27/47 (57%)
Query: 21 VGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTK 67
+ K G +WK ++EA+K P+ +A+K + + + NY R+ E K
Sbjct: 35 ISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRKGETKK 81
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 5 REQYKKDHPK-NKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
RE++KK HP + + + K E+WK+MS +K + A+ K YE++MK Y
Sbjct: 17 REEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 71
>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 = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/47 (36%), Positives = 30/47 (63%)
Query: 16 KSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQ 62
K VAA+GK G W ++S+ +K PY +++ +V YE++ Y +R+
Sbjct: 50 KDVAAIGKMIGAAWNALSDEEKKPYERMSDEDRVRYEREKAEYAQRK 96
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 24/58 (41%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
E+R + K +HP S+ V K GE W + + DK PY KA K K +YEKD+ Y
Sbjct: 113 CSEYRPKIKGEHP-GLSIGDVAKKLGEMWNNTAADDKQPYEKKAAKLKEKYEKDIAAY 169
Score = 35.0 bits (79), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 1 MEEFREQYKKDHPK-NKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
++ RE++KK HP + + + K E+WK+MS +K + A+ K YE++MK Y
Sbjct: 27 VQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 85
>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 = 0.010, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 1 MEEFREQYKKDHPK-NKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
++ RE++KK HP + + + K E+WK+MS +K + A+ K YE++MK Y
Sbjct: 19 VQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 77
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 28/43 (65%)
Query: 19 AAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR 61
A + K G++WK + ++DK P++ +AE+ ++++ D +Y R
Sbjct: 31 AEISKRLGKRWKLLKDSDKIPFIQEAERLRLKHMADYPDYKYR 73
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 1/55 (1%)
Query: 5 REQYKKDHPK-NKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
RE++KK HP + + + K E+WK+MS +K + A+ K YE++MK Y
Sbjct: 23 REEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREMKTY 77
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNR 60
+ E REQ + HP + + K G +W + A+K Y+ +AEK K +Y K++ Y +
Sbjct: 19 LNERREQIRTRHP-DLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQYLKELWAYQQ 77
Query: 61 RQA 63
+A
Sbjct: 78 SEA 80
>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 = 33.9 bits (76), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 35/58 (60%), Gaps = 3/58 (5%)
Query: 1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
+ RE K+++P K V V K GGE W++M DK+ + AKA K K +Y++ +K +
Sbjct: 15 LNSARESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEF 69
>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 = 33.9 bits (76), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 34/54 (62%), Gaps = 3/54 (5%)
Query: 5 REQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
RE K+++P K V V K GGE W++M DK+ + AKA K K +Y++ +K +
Sbjct: 19 RESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEF 69
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 33.9 bits (76), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 34/54 (62%), Gaps = 3/54 (5%)
Query: 5 REQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
RE K+++P K V V K GGE W++M DK+ + AKA K K +Y++ +K +
Sbjct: 19 RESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEF 69
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 33.9 bits (76), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 34/54 (62%), Gaps = 3/54 (5%)
Query: 5 REQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
RE K+++P K V V K GGE W++M DK+ + AKA K K +Y++ +K +
Sbjct: 20 RESIKRENPGIK-VTEVAKRGGELWRAMK--DKSEWEAKAAKAKDDYDRAVKEF 70
>pdb|2EQZ|A Chain A, Solution Structure Of The First Hmg-Box Domain From High
Mobility Group Protein B3
Length = 86
Score = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 35/55 (63%), Gaps = 1/55 (1%)
Query: 5 REQYKKDHPKNK-SVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
RE++KK +P+ + A K E+WK+MS +K+ + A+ KV Y+++MK+Y
Sbjct: 31 REEHKKKNPEVPVNFAEFSKKCSERWKTMSGKEKSKFDEMAKADKVRYDREMKDY 85
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 32.7 bits (73), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 32/58 (55%), Gaps = 3/58 (5%)
Query: 1 MEEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
+ + RE K+++P K V + K GGE WK + DK+ + A K K Y +M+NY
Sbjct: 15 LNDTRESIKRENPGIK-VTEIAKKGGEMWKELK--DKSKWEDAAAKDKQRYHDEMRNY 69
>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 = 0.29, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 27/47 (57%)
Query: 21 VGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTK 67
+ K G +WK +SE +K P++ +A++ + + K+ +Y R TK
Sbjct: 38 ISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTK 84
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 30.0 bits (66), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 27/47 (57%)
Query: 21 VGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTK 67
+ K G +WK +SE +K P++ +A++ + + K+ +Y R TK
Sbjct: 33 ISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTK 79
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 30.0 bits (66), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 27/47 (57%)
Query: 21 VGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRRQAEGTK 67
+ K G +WK +SE +K P++ +A++ + + K+ +Y R TK
Sbjct: 34 ISKRLGAEWKLLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTK 80
>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 = 30.0 bits (66), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 21 VGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR 61
+ K G +WK ++EA+K P+ +A+K + + + NY R
Sbjct: 35 ISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR 75
>pdb|1J47|A Chain A, 3d Solution Nmr Structure Of The M9i Mutant Of The
Hmg-Box Domain Of The Human Male Sex Determining Factor
Sry Complexed To Dna
Length = 85
Score = 29.6 bits (65), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 21 VGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR 61
+ K G +WK ++EA+K P+ +A+K + + + NY R
Sbjct: 35 ISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR 75
>pdb|1J46|A Chain A, 3d Solution Nmr Structure Of The Wild Type Hmg-Box
Domain Of The Human Male Sex Determining Factor Sry
Complexed To Dna
Length = 85
Score = 29.6 bits (65), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 21 VGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR 61
+ K G +WK ++EA+K P+ +A+K + + + NY R
Sbjct: 35 ISKQLGYQWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYR 75
>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 = 26.9 bits (58), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 2 EEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNYNRR 61
E F+E K D P+ K K E WK++S+++K Y+ A++ + Y +MK++ +
Sbjct: 128 ERFQEA-KGDSPQEKL-----KTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSWEEQ 181
Query: 62 QAE 64
E
Sbjct: 182 MIE 184
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human
Upstream Binding Factor
Length = 99
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 30/54 (55%), Gaps = 1/54 (1%)
Query: 5 REQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
R +Y K HP+ ++ + K +K+K + E K Y+ ++ K E+E+++ +
Sbjct: 26 RAKYAKLHPEMSNLD-LTKILSKKYKELPEKKKMKYIQDFQREKQEFERNLARF 78
>pdb|3FGH|A Chain A, Human Mitochondrial Transcription Factor A Box B
Length = 67
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 6/57 (10%)
Query: 2 EEFREQYKKDHPKNKSVAAVGKAGGEKWKSMSEADKAPYVAKAEKRKVEYEKDMKNY 58
E F+E K D P+ K K E WK++S+++K Y+ A++ + Y +MK++
Sbjct: 16 ERFQEA-KGDSPQEKL-----KTVKENWKNLSDSEKELYIQHAKEDETRYHNEMKSW 66
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 25.8 bits (55), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 21 VGKAGGEKWKSMSEADKAPYV---AKAEKRKVEYEKDMK 56
+ K G +WK+M+ +K PY A+ K+ +E D K
Sbjct: 35 ISKILGSRWKAMTNLEKQPYYEEQARLSKQHLEKYPDYK 73
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 0.121 0.338
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,106,879
Number of Sequences: 62578
Number of extensions: 62643
Number of successful extensions: 268
Number of sequences better than 100.0: 52
Number of HSP's better than 100.0 without gapping: 36
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 224
Number of HSP's gapped (non-prelim): 55
length of query: 98
length of database: 14,973,337
effective HSP length: 64
effective length of query: 34
effective length of database: 10,968,345
effective search space: 372923730
effective search space used: 372923730
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: 45 (21.9 bits)