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= psy15636
(101 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 = 112 bits (280), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 53/58 (91%), Positives = 56/58 (96%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
+KRPMNAFMVWSRGQRRKMA +NPKMHNSEISKRLGAEWKLL+E EKRPFIDEAKRLR
Sbjct: 4 VKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 61
>pdb|1GT0|D Chain D, Crystal Structure Of A PouHMGDNA TERNARY COMPLEX
Length = 80
Score = 112 bits (280), Expect = 5e-26, Method: Compositional matrix adjust.
Identities = 53/58 (91%), Positives = 56/58 (96%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
+KRPMNAFMVWSRGQRRKMA +NPKMHNSEISKRLGAEWKLL+E EKRPFIDEAKRLR
Sbjct: 3 VKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 60
>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 = 112 bits (280), Expect = 6e-26, Method: Compositional matrix adjust.
Identities = 53/58 (91%), Positives = 56/58 (96%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
+KRPMNAFMVWSRGQRRKMA +NPKMHNSEISKRLGAEWKLL+E EKRPFIDEAKRLR
Sbjct: 8 VKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWKLLSETEKRPFIDEAKRLR 65
>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 = 90.5 bits (223), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 41/58 (70%), Positives = 51/58 (87%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
+KRPMNAF+VWSR QRRKMAL+NP+M NSEISK+LG +WK+LTE EK PF EA++L+
Sbjct: 5 VKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQ 62
>pdb|2GZK|A Chain A, Structure Of A Complex Of Tandem Hmg Boxes And Dna
Length = 159
Score = 90.5 bits (223), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 41/58 (70%), Positives = 51/58 (87%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
+KRPMNAF+VWSR QRRKMAL+NP+M NSEISK+LG +WK+LTE EK PF EA++L+
Sbjct: 5 VKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQ 62
Score = 32.0 bits (71), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 28/49 (57%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPF 93
KRP +AF ++ R K+ ++P + +++K+LG W +K+P+
Sbjct: 90 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 138
>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 = 90.1 bits (222), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 41/58 (70%), Positives = 51/58 (87%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
+KRPMNAF+VWSR QRRKMAL+NP+M NSEISK+LG +WK+LTE EK PF EA++L+
Sbjct: 5 VKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQ 62
>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 = 89.0 bits (219), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 40/58 (68%), Positives = 51/58 (87%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
+KRP+NAF+VWSR QRRKMAL+NP+M NSEISK+LG +WK+LTE EK PF EA++L+
Sbjct: 5 VKRPINAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAEKWPFFQEAQKLQ 62
>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 = 82.4 bits (202), Expect = 6e-17, Method: Compositional matrix adjust.
Identities = 36/58 (62%), Positives = 47/58 (81%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
+KRPMNAFMVW++ RRK+A P +HN+E+SK LG W+LL E EKRPF++EA+RLR
Sbjct: 30 VKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGKLWRLLNESEKRPFVEEAERLR 87
>pdb|2YUL|A Chain A, Solution Structure Of The Hmg Box Of Human Transcription
Factor Sox-17
Length = 82
Score = 81.6 bits (200), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 35/58 (60%), Positives = 48/58 (82%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
I+RPMNAFMVW++ +R+++A NP +HN+E+SK LG WK LT EKRPF++EA+RLR
Sbjct: 8 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLR 65
>pdb|4A3N|A Chain A, Crystal Structure Of Hmg-Box Of Human Sox17
Length = 71
Score = 81.3 bits (199), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 35/58 (60%), Positives = 48/58 (82%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
I+RPMNAFMVW++ +R+++A NP +HN+E+SK LG WK LT EKRPF++EA+RLR
Sbjct: 3 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLR 60
>pdb|3F27|D Chain D, Structure Of Sox17 Bound To Dna
Length = 83
Score = 81.3 bits (199), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 35/58 (60%), Positives = 48/58 (82%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
I+RPMNAFMVW++ +R+++A NP +HN+E+SK LG WK LT EKRPF++EA+RLR
Sbjct: 7 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGKSWKALTLAEKRPFVEEAERLR 64
>pdb|3U2B|C Chain C, Structure Of The Sox4 Hmg Domain Bound To Dna
Length = 79
Score = 80.9 bits (198), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 39/58 (67%), Positives = 47/58 (81%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
IKRPMNAFMVWS+ +RRK+ +P MHN+EISKRLG WKLL + +K PFI EA+RLR
Sbjct: 3 IKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGKRWKLLKDSDKIPFIQEAERLR 60
>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 = 4e-14, Method: Compositional matrix adjust.
Identities = 33/57 (57%), Positives = 43/57 (75%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRL 100
IKRPMNAFMVW++ +RRK+ P MHNS ISK LG+ WK +T +EK+P+ +E RL
Sbjct: 5 IKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMTNLEKQPYYEEQARL 61
>pdb|2YQI|A Chain A, Solution Structure Of The Second Hmg-Box Domain From High
Mobility Group Protein B3
Length = 81
Score = 42.7 bits (99), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 34/57 (59%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
KRP + F ++ R K+ NP + +++K+LG W L + EK+P+I +A +L+
Sbjct: 11 KRPPSGFFLFCSEFRPKIKSTNPGISIGDVAKKLGEMWNNLNDSEKQPYITKAAKLK 67
>pdb|1CG7|A Chain A, Hmg Protein Nhp6a From Saccharomyces Cerevisiae
Length = 93
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 31/49 (63%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPF 93
KR ++A+M ++ R + +NP + ++ K+LG +WK LT EK+P+
Sbjct: 22 KRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPY 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 = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 31/49 (63%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPF 93
KR ++A+M ++ R + +NP + ++ K+LG +WK LT EK+P+
Sbjct: 22 KRALSAYMFFANENRDIVRSENPDITFGQVGKKLGEKWKALTPEEKQPY 70
>pdb|2E6O|A Chain A, Solution Structure Of The Hmg Box Domain From Human
Hmg-Box Transcription Factor 1
Length = 87
Score = 39.7 bits (91), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 31/57 (54%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRL 100
KRPMNAFM++++ R + P N IS LG WK + E+R + EAK L
Sbjct: 18 CKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGDRWKKMKNEERRMYTLEAKAL 74
>pdb|1WZ6|A Chain A, Solution Structure Of The Hmg_box Domain Of Murine Bobby
Sox Homolog
Length = 82
Score = 37.0 bits (84), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 33/57 (57%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
+RPMNAF+++ + R + ++P++ N +K L W +L EK+ + D AK +
Sbjct: 9 RRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILADWWAVLDPKEKQKYTDMAKEYK 65
>pdb|2CRJ|A Chain A, Solution Structure Of The Hmg Domain Of Mouse Hmg Domain
Protein Hmgx2
Length = 92
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 33/55 (60%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKR 99
K P+ ++ + +R ++ +P + EI+K LGAEW L EK+ ++DEA++
Sbjct: 9 KAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLGAEWSKLQPAEKQRYLDEAEK 63
>pdb|1J3D|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 78
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 33/57 (57%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
KRP +AF ++ R K+ ++P + + +K+LG W + +K+P+ +A +L+
Sbjct: 9 KRPPSAFFLFCSEHRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLK 65
>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 = 0.005, Method: Compositional matrix adjust.
Identities = 15/51 (29%), Positives = 34/51 (66%), Gaps = 2/51 (3%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHN--SEISKRLGAEWKLLTEMEKRPF 93
KR ++++M +++ +R ++ +NP++ + I K +GA W L++ EK+P+
Sbjct: 24 KRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGAAWNALSDEEKKPY 74
>pdb|1HMA|A Chain A, The Solution Structure And Dynamics Of The Dna Binding
Domain Of Hmg-D From Drosophila Melanogaster
Length = 73
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 27/43 (62%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTE 87
KRP++A+M+W R + +NP + +E++KR G W+ + +
Sbjct: 5 KRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD 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 = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 27/43 (62%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTE 87
KRP++A+M+W R + +NP + +E++KR G W+ + +
Sbjct: 5 KRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD 47
>pdb|1E7J|A Chain A, Hmg-D Complexed To A Bulge Dna
Length = 74
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 27/43 (62%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTE 87
KRP++A+M+W R + +NP + +E++KR G W+ + +
Sbjct: 6 KRPLSAYMLWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD 48
>pdb|1J3C|A Chain A, Solution Structure Of The C-Terminal Domain Of The Hmgb2
Length = 79
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 33/57 (57%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
KRP +AF ++ R K+ ++P + + +K+LG W + +K+P+ +A +L+
Sbjct: 10 KRPPSAFFLFCSEYRPKIKSEHPGLSIGDTAKKLGEMWSEQSAKDKQPYEQKAAKLK 66
>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 = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 13/43 (30%), Positives = 26/43 (60%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTE 87
KRP++A+ +W R + +NP + +E++KR G W+ + +
Sbjct: 5 KRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGELWRAMKD 47
>pdb|1WXL|A Chain A, Solution Structure Of The Hmg-Box Domain In The Ssrp1
Subunit Of Fact
Length = 73
Score = 33.5 bits (75), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 25/46 (54%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEK 90
KR AFM+W R + +NP + +EI+K+ G WK L + K
Sbjct: 5 KRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGEMWKELKDKSK 50
>pdb|2LEF|A Chain A, Lef1 Hmg Domain (From Mouse), Complexed With Dna (15bp),
Nmr, 12 Structures
Length = 86
Score = 33.5 bits (75), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 34/58 (58%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRLR 101
IK+P+NAFM++ + R + ++ ++ I++ LG W L+ E+ + + A++ R
Sbjct: 3 IKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQAKYYELARKER 60
>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 = 33.5 bits (75), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 28/49 (57%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPF 93
KRP +AF ++ R K+ ++P + +++K+LG W +K+P+
Sbjct: 4 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 52
>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 = 33.5 bits (75), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 28/49 (57%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPF 93
KRP +AF ++ R K+ ++P + +++K+LG W +K+P+
Sbjct: 8 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 56
>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 = 33.5 bits (75), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 28/49 (57%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPF 93
KRP +AF ++ R K+ ++P + +++K+LG W +K+P+
Sbjct: 6 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 54
>pdb|1WGF|A Chain A, Solution Structure Of The 4th Hmg-Box Of Mouse Ubf1
Length = 90
Score = 33.1 bits (74), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 31/49 (63%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPF 93
KRP++A ++S +RR++ + P++ SE+++ L W L+E +K +
Sbjct: 22 KRPVSAMFIFSEEKRRQLQEERPELSESELTRLLARMWNDLSEKKKAKY 70
>pdb|2YRQ|A Chain A, Solution Structure Of The Tandem Hmg Box Domain From Human
High Mobility Group Protein B1
Length = 173
Score = 32.3 bits (72), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 28/49 (57%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPF 93
KRP +AF ++ R K+ ++P + +++K+LG W +K+P+
Sbjct: 103 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGEMWNNTAADDKQPY 151
Score = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 24/49 (48%)
Query: 50 AFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAK 98
AF V + + K + ++ SE SK+ WK ++ EK F D AK
Sbjct: 24 AFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK 72
>pdb|1K99|A Chain A, Solution Structure Of The First Hmg Box In Human
Upstream Binding Factor
Length = 99
Score = 29.3 bits (64), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 32/55 (58%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKR 99
K+P+ + + +R K A +P+M N +++K L ++K L E +K +I + +R
Sbjct: 12 KKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYKELPEKKKMKYIQDFQR 66
>pdb|3TMM|A Chain A, Tfam Imposes A U-Turn On Mitochondrial Dna
Length = 238
Score = 28.9 bits (63), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 12/51 (23%), Positives = 29/51 (56%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFID 95
K+P+++++ +S+ Q NP +E+ +R+ W+ L + +K+ + D
Sbjct: 43 KKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQD 93
>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 = 28.5 bits (62), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 12/51 (23%), Positives = 29/51 (56%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFID 95
K+P+++++ +S+ Q NP +E+ +R+ W+ L + +K+ + D
Sbjct: 11 KKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIAQRWRELPDSKKKIYQD 61
>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 = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 12/49 (24%), Positives = 27/49 (55%)
Query: 45 KRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPF 93
++P++A+ ++ R + + NP E+SK + + W L E +K+ +
Sbjct: 19 QKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDGLGEEQKQVY 67
>pdb|1AAB|A Chain A, Nmr Structure Of Rat Hmg1 Hmga Fragment
Length = 83
Score = 27.3 bits (59), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 24/49 (48%)
Query: 50 AFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAK 98
AF V + + K + ++ SE SK+ WK ++ EK F D AK
Sbjct: 16 AFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK 64
>pdb|4GKL|A Chain A, Crystal Structure Of A Noncanonic Maltogenic Alpha-amylase
Amyb From Thermotoga Neapolitana
pdb|4GKL|B Chain B, Crystal Structure Of A Noncanonic Maltogenic Alpha-amylase
Amyb From Thermotoga Neapolitana
Length = 422
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 11/48 (22%), Positives = 22/48 (45%)
Query: 53 VWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAKRL 100
+W G R + + NP + N+ ++ W+ + K F D+ R+
Sbjct: 352 LWRHGNRFILCVLNPLLENTSVTLDFSGIWENICIHSKNVFNDDIVRV 399
>pdb|1CKT|A Chain A, Crystal Structure Of Hmg1 Domain A Bound To A
Cisplatin-modified Dna Duplex
Length = 71
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 24/49 (48%)
Query: 50 AFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAK 98
AF V + + K + ++ SE SK+ WK ++ EK F D AK
Sbjct: 10 AFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK 58
>pdb|1J3X|A Chain A, Solution Structure Of The N-Terminal Domain Of The Hmgb2
Length = 77
Score = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 24/49 (48%)
Query: 50 AFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAK 98
AF V + + K + ++ +E SK+ WK ++ EK F D AK
Sbjct: 17 AFFVQTSREEHKKKHPDSSVNFAEFSKKCSERWKTMSAKEKSKFEDMAK 65
>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 = 26.9 bits (58), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 24/49 (48%)
Query: 50 AFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTEMEKRPFIDEAK 98
AF V + + K + ++ SE SK+ WK ++ EK F D AK
Sbjct: 16 AFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAK 64
>pdb|2CS1|A Chain A, Solution Structure Of The Hmg Domain Of Human Dna
Mismatch Repair Protein
Length = 92
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 26/44 (59%)
Query: 44 IKRPMNAFMVWSRGQRRKMALDNPKMHNSEISKRLGAEWKLLTE 87
IK+PM+A ++ + R + ++NPK + + ++ WK L+E
Sbjct: 8 IKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEELWKTLSE 51
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
0.322 0.132 0.398
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,754,928
Number of Sequences: 62578
Number of extensions: 44127
Number of successful extensions: 140
Number of sequences better than 100.0: 45
Number of HSP's better than 100.0 without gapping: 44
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 94
Number of HSP's gapped (non-prelim): 47
length of query: 101
length of database: 14,973,337
effective HSP length: 67
effective length of query: 34
effective length of database: 10,780,611
effective search space: 366540774
effective search space used: 366540774
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)