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= psy13343
(396 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2LE4|A Chain A, Solution Structure Of The Hmg Box Dna-Binding Domain Of
Human Stem Cell Transcription Factor Sox2
Length = 81
Score = 134 bits (337), Expect = 9e-32, Method: Compositional matrix adjust.
Identities = 62/67 (92%), Positives = 65/67 (97%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
DRVKRPMNAFMVWSRGQRRKMAQ+NPKMHNSEISKRLGAEWKLL+E KRPFIDEAKRLR
Sbjct: 2 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 61
Query: 141 AVHMKEH 147
A+HMKEH
Sbjct: 62 ALHMKEH 68
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 134 bits (336), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 62/67 (92%), Positives = 65/67 (97%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
DRVKRPMNAFMVWSRGQRRKMAQ+NPKMHNSEISKRLGAEWKLL+E KRPFIDEAKRLR
Sbjct: 1 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 60
Query: 141 AVHMKEH 147
A+HMKEH
Sbjct: 61 ALHMKEH 67
>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 = 134 bits (336), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 62/67 (92%), Positives = 65/67 (97%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
DRVKRPMNAFMVWSRGQRRKMAQ+NPKMHNSEISKRLGAEWKLL+E KRPFIDEAKRLR
Sbjct: 6 DRVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 65
Query: 141 AVHMKEH 147
A+HMKEH
Sbjct: 66 ALHMKEH 72
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 96.3 bits (238), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 43/67 (64%), Positives = 56/67 (83%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
DRVKRPMNAF+VWSR QRRKMA +NP+M NSEISK+LG +WK+L E K PF EA++L+
Sbjct: 3 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQ 62
Query: 141 AVHMKEH 147
A+H +++
Sbjct: 63 AMHREKY 69
>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 = 96.3 bits (238), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 43/67 (64%), Positives = 56/67 (83%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
DRVKRPMNAF+VWSR QRRKMA +NP+M NSEISK+LG +WK+L E K PF EA++L+
Sbjct: 3 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQ 62
Query: 141 AVHMKEH 147
A+H +++
Sbjct: 63 AMHREKY 69
>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 = 95.5 bits (236), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 43/67 (64%), Positives = 56/67 (83%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
DRVKRPMNAF+VWSR QRRKMA +NP+M NSEISK+LG +WK+L E K PF EA++L+
Sbjct: 3 DRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQ 62
Query: 141 AVHMKEH 147
A+H +++
Sbjct: 63 AMHREKY 69
>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 = 94.0 bits (232), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 42/67 (62%), Positives = 56/67 (83%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLR 140
DRVKRP+NAF+VWSR QRRKMA +NP+M NSEISK+LG +WK+L E K PF EA++L+
Sbjct: 3 DRVKRPINAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQ 62
Query: 141 AVHMKEH 147
A+H +++
Sbjct: 63 AMHREKY 69
>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 = 91.7 bits (226), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 40/65 (61%), Positives = 51/65 (78%)
Query: 83 VKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAV 142
VKRPMNAFMVW++ RRK+A P +HN+E+SK LG W+LLNE KRPF++EA+RLR
Sbjct: 30 VKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLRVQ 89
Query: 143 HMKEH 147
H K+H
Sbjct: 90 HKKDH 94
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 90.5 bits (223), Expect = 1e-18, Method: Compositional matrix adjust.
Identities = 37/66 (56%), Positives = 53/66 (80%)
Query: 82 RVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRA 141
R++RPMNAFMVW++ +R+++AQ NP +HN+E+SK LG WK L KRPF++EA+RLR
Sbjct: 6 RIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRV 65
Query: 142 VHMKEH 147
HM++H
Sbjct: 66 QHMQDH 71
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 90.5 bits (223), Expect = 2e-18, Method: Compositional matrix adjust.
Identities = 36/65 (55%), Positives = 52/65 (80%)
Query: 83 VKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAV 142
++RPMNAFMVW++ +R+++AQ NP +HN+E+SK LG WK L KRPF++EA+RLR
Sbjct: 8 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 67
Query: 143 HMKEH 147
HM++H
Sbjct: 68 HMQDH 72
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 89.4 bits (220), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 36/65 (55%), Positives = 52/65 (80%)
Query: 83 VKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAV 142
++RPMNAFMVW++ +R+++AQ NP +HN+E+SK LG WK L KRPF++EA+RLR
Sbjct: 3 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLRVQ 62
Query: 143 HMKEH 147
HM++H
Sbjct: 63 HMQDH 67
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 88.6 bits (218), Expect = 5e-18, Method: Compositional matrix adjust.
Identities = 40/65 (61%), Positives = 51/65 (78%)
Query: 83 VKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAV 142
+KRPMNAFMVWS+ +RRK+ + +P MHN+EISKRLG WKLL + K PFI EA+RLR
Sbjct: 3 IKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLRLK 62
Query: 143 HMKEH 147
HM ++
Sbjct: 63 HMADY 67
>pdb|1I11|A Chain A, Solution Structure Of The Dna Binding Domain, Sox-5 Hmg
Box From Mouse
Length = 81
Score = 72.8 bits (177), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 32/65 (49%), Positives = 46/65 (70%)
Query: 83 VKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAV 142
+KRPMNAFMVW++ +RRK+ Q P MHNS ISK LG+ WK + K+P+ +E RL
Sbjct: 5 IKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARLSKQ 64
Query: 143 HMKEH 147
H++++
Sbjct: 65 HLEKY 69
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
Hmg-Box Transcription Factor 1
Length = 87
Score = 45.4 bits (106), Expect = 6e-05, Method: Composition-based stats.
Identities = 23/59 (38%), Positives = 34/59 (57%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRL 139
++ KRPMNAFM++++ R + Q P N IS LG WK + + +R + EAK L
Sbjct: 16 NKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKAL 74
>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby
Sox Homolog
Length = 82
Score = 44.7 bits (104), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 37/63 (58%)
Query: 83 VKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAV 142
+RPMNAF+++ + R + Q++P++ N +K L W +L+ + K+ + D AK +
Sbjct: 8 ARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYKDA 67
Query: 143 HMK 145
MK
Sbjct: 68 FMK 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 = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 33/49 (67%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAK 129
D+ KRP++A+M+W R + ++NP + +E++KR G W+ + ++++
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSE 50
>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 = 44.3 bits (103), Expect = 1e-04, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 33/49 (67%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAK 129
D+ KRP++A+M+W R + ++NP + +E++KR G W+ + ++++
Sbjct: 2 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSE 50
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 33/49 (67%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAK 129
D+ KRP++A+M+W R + ++NP + +E++KR G W+ + ++++
Sbjct: 3 DKPKRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSE 51
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 37/63 (58%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVH 143
KRP + F ++ R K+ NP + +++K+LG W LN+ K+P+I +A +L+ +
Sbjct: 11 KRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLKEKY 70
Query: 144 MKE 146
K+
Sbjct: 71 EKD 73
>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 = 42.0 bits (97), Expect = 6e-04, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 32/49 (65%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAK 129
D+ KRP++A+ +W R + ++NP + +E++KR G W+ + ++++
Sbjct: 2 DKPKRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKDKSE 50
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 38.9 bits (89), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 37/63 (58%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVH 143
K P+ ++ + +R ++ +P + EI+K LGAEW L K+ ++DEA++ + +
Sbjct: 9 KAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEKEKQQY 68
Query: 144 MKE 146
+KE
Sbjct: 69 LKE 71
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 37.7 bits (86), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 28/46 (60%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAK 129
KR AFM+W R + ++NP + +EI+K+ G WK L +++K
Sbjct: 5 KRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSK 50
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 37.4 bits (85), Expect = 0.014, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 33/54 (61%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAK 137
KR ++A+M ++ R + +NP + ++ K+LG +WK L + K+P+ +A+
Sbjct: 22 KRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQ 75
>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 = 37.4 bits (85), Expect = 0.014, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 33/54 (61%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAK 137
KR ++A+M ++ R + +NP + ++ K+LG +WK L + K+P+ +A+
Sbjct: 22 KRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPYEAKAQ 75
>pdb|2LEF|A Chain A, Lef1 Hmg Domain (From Mouse), Complexed With Dna (15bp),
Nmr, 12 Structures
Length = 86
Score = 37.4 bits (85), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 38/63 (60%)
Query: 83 VKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAV 142
+K+P+NAFM++ + R + ++ ++ I++ LG W L+ + + + + A++ R +
Sbjct: 3 IKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKERQL 62
Query: 143 HMK 145
HM+
Sbjct: 63 HMQ 65
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 37.4 bits (85), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 33/49 (67%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAK 129
++ KRP++A ++S +RR++ ++ P++ SE+++ L W L+E+ K
Sbjct: 19 EKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKK 67
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 35.4 bits (80), Expect = 0.058, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 36/63 (57%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVH 143
KRP +AF ++ R K+ ++P + + +K+LG W + + K+P+ +A +L+ +
Sbjct: 9 KRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKY 68
Query: 144 MKE 146
K+
Sbjct: 69 EKD 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 = 35.0 bits (79), Expect = 0.064, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 34/51 (66%), Gaps = 2/51 (3%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHN--SEISKRLGAEWKLLNEQAKRPF 132
KR ++++M +++ +R ++ +NP++ + I K +GA W L+++ K+P+
Sbjct: 24 KRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPY 74
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 35.0 bits (79), Expect = 0.077, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 36/63 (57%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVH 143
KRP +AF ++ R K+ ++P + + +K+LG W + + K+P+ +A +L+ +
Sbjct: 10 KRPPSAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLKEKY 69
Query: 144 MKE 146
K+
Sbjct: 70 EKD 72
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human Upstream
Binding Factor
Length = 99
Score = 32.3 bits (72), Expect = 0.53, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 34/58 (58%)
Query: 81 DRVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKR 138
D K+P+ + + +R K A+ +P+M N +++K L ++K L E+ K +I + +R
Sbjct: 9 DFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQR 66
>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 = 31.2 bits (69), Expect = 1.1, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 27/49 (55%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPF 132
KRP +AF ++ R K+ ++P + +++K+LG W K+P+
Sbjct: 8 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 56
>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 = 30.8 bits (68), Expect = 1.3, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 27/49 (55%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPF 132
KRP +AF ++ R K+ ++P + +++K+LG W K+P+
Sbjct: 4 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 52
>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 = 30.8 bits (68), Expect = 1.4, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 27/49 (55%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPF 132
KRP +AF ++ R K+ ++P + +++K+LG W K+P+
Sbjct: 6 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 54
>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 = 29.6 bits (65), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/63 (20%), Positives = 34/63 (53%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVH 143
++P++A+ ++ R + + NP E+SK + + W L E+ K+ + + + + +
Sbjct: 19 QKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVYKKKTEAAKKEY 78
Query: 144 MKE 146
+K+
Sbjct: 79 LKQ 81
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 29.3 bits (64), Expect = 3.5, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 31/65 (47%)
Query: 82 RVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRA 141
R K AF V + + K + ++ SE SK+ WK ++ + K F D AK +A
Sbjct: 3 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA 62
Query: 142 VHMKE 146
+ +E
Sbjct: 63 RYERE 67
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 29.3 bits (64), Expect = 3.9, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 31/65 (47%)
Query: 82 RVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRA 141
R K AF V + + K + ++ SE SK+ WK ++ + K F D AK +A
Sbjct: 9 RGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA 68
Query: 142 VHMKE 146
+ +E
Sbjct: 69 RYERE 73
>pdb|1BEE|A Chain A, Haloalkane Dehalogenase Mutant With Trp 175 Replaced By
Tyr
pdb|1BEZ|A Chain A, Haloalkane Dehalogenase Mutant With Trp 175 Replaced By
Tyr At Ph 5
Length = 310
Score = 28.9 bits (63), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 218 MMDPATYQQHSAYTTHMSSGYPRYDMTGMHPSSTSLNSYMN 258
M DP T SA+ T + G+ Y + PS L+ +M
Sbjct: 152 MTDPVTQPAFSAFVTQPADGFTAYKYDLVTPSDLRLDQFMK 192
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 28.9 bits (63), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 29/58 (50%)
Query: 89 AFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRAVHMKE 146
AF V + + K + ++ SE SK+ WK ++ + K F D AK +A + +E
Sbjct: 24 AFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYERE 81
Score = 28.5 bits (62), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 27/49 (55%)
Query: 84 KRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPF 132
KRP +AF ++ R K+ ++P + +++K+LG W K+P+
Sbjct: 103 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 151
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 28.9 bits (63), Expect = 5.6, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 31/65 (47%)
Query: 82 RVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRA 141
R K AF V + + K + ++ +E SK+ WK ++ + K F D AK +A
Sbjct: 10 RGKMSSYAFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAKSDKA 69
Query: 142 VHMKE 146
+ +E
Sbjct: 70 RYDRE 74
>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 = 28.9 bits (63), Expect = 5.7, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 31/65 (47%)
Query: 82 RVKRPMNAFMVWSRGQRRKMAQDNPKMHNSEISKRLGAEWKLLNEQAKRPFIDEAKRLRA 141
R K AF V + + K + ++ SE SK+ WK ++ + K F D AK +A
Sbjct: 9 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKA 68
Query: 142 VHMKE 146
+ +E
Sbjct: 69 RYERE 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
0.315 0.129 0.392
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,987,935
Number of Sequences: 62578
Number of extensions: 278848
Number of successful extensions: 678
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 42
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 634
Number of HSP's gapped (non-prelim): 45
length of query: 396
length of database: 14,973,337
effective HSP length: 101
effective length of query: 295
effective length of database: 8,652,959
effective search space: 2552622905
effective search space used: 2552622905
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)