RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy14249
(60 letters)
>1wz6_A HMG-box transcription factor BBX; bobby SOX homolog, HMG_BOX
domain, structural genomics, NPPSFA, riken structural
genomics/proteomics initiative; NMR {Mus musculus}
Length = 82
Score = 71.9 bits (177), Expect = 4e-19
Identities = 16/43 (37%), Positives = 25/43 (58%)
Query: 9 TAKEQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
++ RRPMNAF+++ K R + E+P L N +K+LA
Sbjct: 2 SSGSSGARRPMNAFLLFCKRHRSLVRQEHPRLDNRGATKILAD 44
>2e6o_A HMG box-containing protein 1; HMG-box domain, HMG-box
transcription factor 1, high mobility group box
transcription factor 1, structural genomics; NMR {Homo
sapiens}
Length = 87
Score = 71.7 bits (176), Expect = 6e-19
Identities = 15/50 (30%), Positives = 23/50 (46%)
Query: 2 SAHQQQKTAKEQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
S+ + +RPMNAFM++AK R + P N +S +L
Sbjct: 5 SSGGTVSATSPNKCKRPMNAFMLFAKKYRVEYTQMYPGKDNRAISVILGD 54
>3f27_D Transcription factor SOX-17; protein-DNA complex, HMG domain,
endodermal, activator, DNA- nucleus, transcription
regulation, transcrip complex; HET: DNA; 2.75A {Mus
musculus} PDB: 2yul_A
Length = 83
Score = 68.0 bits (167), Expect = 1e-17
Identities = 31/42 (73%), Positives = 36/42 (85%)
Query: 10 AKEQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
+ RIRRPMNAFMVWAK ERK+LA +NPDLHNA+LSKML +
Sbjct: 2 SFTSRIRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGK 43
>4euw_A Transcription factor SOX-9; protein-DNA complex, HMG domain,
activator, DNA-binding, NUC transcription; HET: DNA;
2.77A {Homo sapiens}
Length = 106
Score = 68.2 bits (167), Expect = 2e-17
Identities = 25/47 (53%), Positives = 34/47 (72%)
Query: 5 QQQKTAKEQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
Q + + ++RPMNAFMVWA+ R+KLAD+ P LHNA+LSK L +
Sbjct: 20 YFQSSKNKPHVKRPMNAFMVWAQAARRKLADQYPHLHNAELSKTLGK 66
>1hry_A Human SRY; DNA, DNA-binding protein, DNA binding protein/DNA
complex; HET: DNA; NMR {Homo sapiens} SCOP: a.21.1.1
PDB: 1hrz_A*
Length = 76
Score = 67.2 bits (165), Expect = 2e-17
Identities = 19/40 (47%), Positives = 32/40 (80%)
Query: 12 EQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
+ R++RPMNAF+VW++ +R+K+A ENP + N+++SK L
Sbjct: 2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGY 41
>4a3n_A Transcription factor SOX-17; 2.40A {Homo sapiens}
Length = 71
Score = 66.1 bits (162), Expect = 7e-17
Identities = 30/37 (81%), Positives = 34/37 (91%)
Query: 15 IRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
IRRPMNAFMVWAK ERK+LA +NPDLHNA+LSKML +
Sbjct: 3 IRRPMNAFMVWAKDERKRLAQQNPDLHNAELSKMLGK 39
>1i11_A Transcription factor SOX-5; HMG BOX, DNA bending, DNA
recognition, chromatin, DNA binding protein, DNA
sequence specific, testis determining.; NMR {Mus
musculus} SCOP: a.21.1.1
Length = 81
Score = 65.3 bits (160), Expect = 1e-16
Identities = 22/40 (55%), Positives = 30/40 (75%)
Query: 12 EQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
I+RPMNAFMVWAK ER+K+ PD+HN+++SK+L
Sbjct: 2 SPHIKRPMNAFMVWAKDERRKILQAFPDMHNSNISKILGS 41
>1j46_A SRY, sex-determining region Y protein; MALE sex determining
factor, SRY, sex-reversal mutation; NMR {Homo sapiens}
SCOP: a.21.1.1 PDB: 1j47_A
Length = 85
Score = 64.5 bits (158), Expect = 3e-16
Identities = 19/40 (47%), Positives = 32/40 (80%)
Query: 12 EQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
+ R++RPMNAF+VW++ +R+K+A ENP + N+++SK L
Sbjct: 2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGY 41
>1gt0_D Transcription factor SOX-2; POU factors, SOX proteins; 2.6A {Mus
musculus} SCOP: a.21.1.1 PDB: 2le4_A 1o4x_B
Length = 80
Score = 64.5 bits (158), Expect = 3e-16
Identities = 21/38 (55%), Positives = 32/38 (84%)
Query: 14 RIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
R++RPMNAFMVW++ +R+K+A ENP +HN+++SK L
Sbjct: 2 RVKRPMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGA 39
>3u2b_C Transcription factor SOX-4; HMG domain, transcriptional
regulation, transcription-DNA CO; HET: DNA; 2.40A {Mus
musculus}
Length = 79
Score = 63.0 bits (154), Expect = 1e-15
Identities = 21/37 (56%), Positives = 34/37 (91%)
Query: 15 IRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
I+RPMNAFMVW+++ER+K+ +++PD+HNA++SK L +
Sbjct: 3 IKRPMNAFMVWSQIERRKIMEQSPDMHNAEISKRLGK 39
>1wgf_A Upstream binding factor 1; transcription factor, DNA binding,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Mus
musculus} SCOP: a.21.1.1
Length = 90
Score = 62.4 bits (152), Expect = 2e-15
Identities = 13/47 (27%), Positives = 33/47 (70%)
Query: 5 QQQKTAKEQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
Q+ ++ +RP++A ++++ +R++L +E P+L ++L+++LAR
Sbjct: 11 QEGGKGGSEKPKRPVSAMFIFSEEKRRQLQEERPELSESELTRLLAR 57
>2lef_A LEF-1 HMG, protein (lymphoid enhancer-binding factor); LEF1, HMG,
TCR-A, transcription factor; HET: DNA; NMR {Mus
musculus} SCOP: a.21.1.1
Length = 86
Score = 61.9 bits (151), Expect = 4e-15
Identities = 12/37 (32%), Positives = 24/37 (64%)
Query: 15 IRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
I++P+NAFM++ K R + E+ +A ++++L R
Sbjct: 3 IKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGR 39
>2gzk_A Sex-determining region on Y / HMGB1; protein-DNA complex, HMG
BOX, amphoterin, DNA/structural protein complex; NMR
{Homo sapiens} SCOP: a.21.1.1 a.21.1.1
Length = 159
Score = 59.1 bits (143), Expect = 3e-13
Identities = 19/40 (47%), Positives = 32/40 (80%)
Query: 12 EQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
+ R++RPMNAF+VW++ +R+K+A ENP + N+++SK L
Sbjct: 2 QDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGY 41
Score = 45.2 bits (107), Expect = 5e-08
Identities = 13/48 (27%), Positives = 23/48 (47%)
Query: 4 HQQQKTAKEQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
++K +RP +AF ++ R K+ E+P L D++K L
Sbjct: 78 ETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGE 125
>2cs1_A PMS1 protein homolog 1; DNA mismatch repair protein PMS1,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 92
Score = 50.9 bits (122), Expect = 9e-11
Identities = 9/43 (20%), Positives = 20/43 (46%)
Query: 9 TAKEQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
++ I++PM+A ++ + R + ENP D + +
Sbjct: 2 SSGSSGIKKPMSASALFVQDHRPQFLIENPKTSLEDATLQIEE 44
>2crj_A SWI/SNF-related matrix-associated actin- dependent regulator of
chromatin subfamily...; structural DNA-binding protein
BRAF35, DNA-bending; NMR {Mus musculus}
Length = 92
Score = 48.1 bits (115), Expect = 1e-09
Identities = 8/37 (21%), Positives = 20/37 (54%)
Query: 14 RIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
+ P+ ++ + R+++ +PDL +++KML
Sbjct: 7 GPKAPVTGYVRFLNERREQIRTRHPDLPFPEITKMLG 43
>1hme_A High mobility group protein fragment-B; DNA-binding; NMR {Rattus
norvegicus} SCOP: a.21.1.1 PDB: 1hmf_A 1nhm_A 1nhn_A
1hsm_A 1hsn_A 1j3c_A 1j3d_A 2yqi_A
Length = 77
Score = 47.2 bits (113), Expect = 2e-09
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
+RP +AF ++ R K+ E+P L D++K L
Sbjct: 8 KRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLG 42
>1wxl_A Single-strand recognition protein; FACT, SSRP1, HMG, DNA binding
protein; NMR {Drosophila melanogaster}
Length = 73
Score = 46.5 bits (111), Expect = 3e-09
Identities = 10/36 (27%), Positives = 18/36 (50%)
Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
+R AFM+W R+ + ENP + +++K
Sbjct: 5 KRATTAFMLWLNDTRESIKRENPGIKVTEIAKKGGE 40
>3nm9_A HMG-D, high mobility group protein D; DNA bending,
non-sequence-specific, HMG chromosomal protein; HET:
DNA; 2.85A {Drosophila melanogaster} PDB: 1e7j_A*
1hma_A 1qrv_A*
Length = 73
Score = 45.4 bits (108), Expect = 1e-08
Identities = 9/36 (25%), Positives = 20/36 (55%)
Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
+RP++A+ +W R+ + ENP + +++K
Sbjct: 5 KRPLSAYALWLNSARESIKRENPGIKVTEVAKRGGE 40
>2co9_A Thymus high mobility group box protein TOX; TOX protein, HMG box
domain, structural genomics, NPPSFA; NMR {Mus musculus}
Length = 102
Score = 43.2 bits (102), Expect = 1e-07
Identities = 7/36 (19%), Positives = 23/36 (63%)
Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
++P++A+ ++ + + + +NP+ ++SK++A
Sbjct: 19 QKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVAS 54
>1cg7_A Protein (NON histone protein 6 A); HMG BOX, DNA bending, DNA
recognition, chromatin, DNA binding protein; NMR
{Saccharomyces cerevisiae} SCOP: a.21.1.1 PDB: 1j5n_A
1lwm_A
Length = 93
Score = 41.9 bits (99), Expect = 3e-07
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
+R ++A+M +A R + ENPD+ + K L
Sbjct: 22 KRALSAYMFFANENRDIVRSENPDITFGQVGKKLGE 57
>1k99_A Upstream binding factor 1; alpha-helix, L-shape, DNA binding
protein; NMR {Homo sapiens} SCOP: a.21.1.1
Length = 99
Score = 41.6 bits (98), Expect = 4e-07
Identities = 10/36 (27%), Positives = 23/36 (63%)
Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
++P+ + + +R K A +P++ N DL+K+L++
Sbjct: 12 KKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSK 47
>2d7l_A WD repeat and HMG-box DNA binding protein 1; high mobility group
box domain, helix-turn-helix, structural genomics,
NPPSFA; NMR {Homo sapiens}
Length = 81
Score = 40.2 bits (93), Expect = 1e-06
Identities = 11/37 (29%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 16 RRPMNAFMVWAKVERKKLADENPDLHN-ADLSKMLAR 51
RP F +W + R + +NPD + AD+ K
Sbjct: 7 GRPKTGFQMWLEENRSNILSDNPDFSDEADIIKEGMI 43
>2lhj_A High mobility group protein homolog NHP1; structural genomics,
seattle structural genomics center for infectious
disease, ssgcid; NMR {Babesia bovis}
Length = 97
Score = 39.7 bits (93), Expect = 2e-06
Identities = 11/40 (27%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 14 RIRRPMNAFMVWAKVERKKLADENPDLHN--ADLSKMLAR 51
+R ++++M +AK +R ++ ENP++ A + KM+
Sbjct: 22 APKRALSSYMFFAKEKRVEIIAENPEIAKDVAAIGKMIGA 61
>2yrq_A High mobility group protein B1; HMG box domain, DNA binding,
helix-turn-helix motif, structural genomics, NPPSFA; NMR
{Homo sapiens}
Length = 173
Score = 40.4 bits (94), Expect = 4e-06
Identities = 13/48 (27%), Positives = 23/48 (47%)
Query: 4 HQQQKTAKEQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
++K +RP +AF ++ R K+ E+P L D++K L
Sbjct: 91 ETKKKFKDPNAPKRPPSAFFLFCSEYRPKIKGEHPGLSIGDVAKKLGE 138
Score = 31.9 bits (72), Expect = 0.005
Identities = 7/37 (18%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 16 RRPMNAFMVWAKVERKKLADENPD--LHNADLSKMLA 50
R M+++ + + R++ ++PD ++ ++ SK +
Sbjct: 17 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCS 53
>1ckt_A High mobility group 1 protein; high-mobility group domain, BENT
DNA, protein-drug-DNA compl regulation-DNA complex;
HET: DNA 5IU; 2.50A {Rattus norvegicus} SCOP: a.21.1.1
PDB: 1j3x_A
Length = 71
Score = 35.1 bits (81), Expect = 1e-04
Identities = 7/37 (18%), Positives = 19/37 (51%), Gaps = 2/37 (5%)
Query: 16 RRPMNAFMVWAKVERKKLADENPDLHN--ADLSKMLA 50
R M+++ + + R++ ++PD ++ SK +
Sbjct: 3 RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCS 39
>1aab_A High mobility group protein; HMG-BOX, DNA-binding; NMR {Rattus
norvegicus} SCOP: a.21.1.1
Length = 83
Score = 35.0 bits (81), Expect = 1e-04
Identities = 7/37 (18%), Positives = 21/37 (56%), Gaps = 2/37 (5%)
Query: 16 RRPMNAFMVWAKVERKKLADENPD--LHNADLSKMLA 50
R M+++ + + R++ ++PD ++ ++ SK +
Sbjct: 9 RGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCS 45
>2eqz_A High mobility group protein B3; HMG-box domain, mobility group
protein 2A, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 86
Score = 35.0 bits (81), Expect = 2e-04
Identities = 8/37 (21%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 16 RRPMNAFMVWAKVERKKLADENPDLHN--ADLSKMLA 50
+ M+A+ + + R++ +NP++ A+ SK +
Sbjct: 17 KGKMSAYAFFVQTCREEHKKKNPEVPVNFAEFSKKCS 53
>3tmm_A Transcription factor A, mitochondrial; HMG, high mobility group,
transcription, LSP1, mitochon transcription-DNA
complex; HET: DNA; 2.50A {Homo sapiens}
Length = 238
Score = 34.4 bits (78), Expect = 7e-04
Identities = 7/46 (15%), Positives = 23/46 (50%)
Query: 5 QQQKTAKEQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
+ + ++P+++++ ++K + +NPD +L + +A
Sbjct: 32 RGSSSVLASCPKKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIA 77
Score = 25.6 bits (55), Expect = 1.1
Identities = 5/48 (10%), Positives = 21/48 (43%)
Query: 1 MSAHQQQKTAKEQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKM 48
+ ++++ + +RP +A+ V+ ++ ++P + +
Sbjct: 133 KAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKEN 180
>3tq6_A Transcription factor A, mitochondrial; transcription,
transcription regulation, mitochondrion; HET: DNA BRU
1PE; 2.45A {Homo sapiens}
Length = 214
Score = 33.6 bits (76), Expect = 0.001
Identities = 7/35 (20%), Positives = 21/35 (60%)
Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLA 50
++P+++++ ++K + +NPD +L + +A
Sbjct: 11 KKPVSSYLRFSKEQLPIFKAQNPDAKTTELIRRIA 45
Score = 23.9 bits (51), Expect = 3.4
Identities = 5/48 (10%), Positives = 21/48 (43%)
Query: 1 MSAHQQQKTAKEQRIRRPMNAFMVWAKVERKKLADENPDLHNADLSKM 48
+ ++++ + +RP +A+ V+ ++ ++P + +
Sbjct: 101 KAMTKKKELTLLGKPKRPRSAYNVYVAERFQEAKGDSPQEKLKTVKEN 148
>3fgh_A Transcription factor A, mitochondrial; HMG domain, mitochondrial
transcription, activator, DNA- binding, mitochondrion,
phosphoprotein; 1.35A {Homo sapiens}
Length = 67
Score = 30.3 bits (69), Expect = 0.007
Identities = 6/36 (16%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 16 RRPMNAFMVWAKVERKKLADENPDLHNADLSKMLAR 51
+RP +A+ V+ ++ ++P + K +
Sbjct: 4 KRPRSAYNVYVAERFQEAKGDSPQ----EKLKTVKE 35
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.320 0.127 0.373
Gapped
Lambda K H
0.267 0.0696 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 869,642
Number of extensions: 35486
Number of successful extensions: 94
Number of sequences better than 10.0: 1
Number of HSP's gapped: 94
Number of HSP's successfully gapped: 37
Length of query: 60
Length of database: 6,701,793
Length adjustment: 31
Effective length of query: 29
Effective length of database: 5,836,242
Effective search space: 169251018
Effective search space used: 169251018
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (23.5 bits)